BIOMOLECULES

Central Dogma
Watson and Crick discovered: DNA transcription> RNA translation> proteins.
But that isnt always how it works here are some other ideas genes and DNA:
reverse transcription: RNA>cDNA
RNA makes complementary DNA, catalyzed by reverse transcriptase
this is used by retroviruses to integrate their RNA into host cells genome DNA for replication
RNA viruses: store genetic material as RNA instead of DNA
This RNA can be replicated like DNA for transcription to mRNA to make proteins
ex: Corona virus )SARS); influenza; paramixo (measles)
non-coding RNA: functional RNA that skips the step of translation and carries out functions in its own
ex: ribosomal RNA, transfer RNA (both used for translation of mRNA to proteins)
Epigenetics: study of heritable changes in DNA activity that are not caused by changes in DNA
sequence
unlike traditional genetics, where DNA sequences determines phenotype, epigenetics describes
how phenotypes can be modified without actual changes in nucleotide sequence
Main mechanisms of epigenetics: DNA methylation and histone modification
Epigenetics also explains how DNA in muscle cells is identical to DNA in skin cells, but the cells
are very different because of different expressions. Epigenetics explains how different parts of the
sequence are expressed.

Amino Acids & Proteins

Proteins are linear heteropolymers of -amino acids

Amino acids share many features, differing only at the R substituent
The -carbon is chiral when the R group is anything other
than hydrogen (so anything other than glycine, which has
an H as its R group). All chiral amino acids are optically active.
Because of tetrahedral arrangement of bonding orbitals around
the -carbon, the 4 different groups can occupy two unique spatial
arrangements (except glycine, whose R group is just a H) and
thus have two possible stereoisomers: L and D
L and D versions of an amino acid are enantiomers
- nonsuperimposable mirror images
only L-amino acids are found in proteins.
Amino Acids are classified based on their R group (charge, H-bonding ability, and acidic/basic):
Two main categories: Hydrophobic and Hydrophilic.
Hydrophobic amino acids are non-polar. Includes AA with alkyl/aliphatic & with aromatic R groups.
Hydrophilic amino acids are polar. Includes neutral, acidic, and basic R-groups.
Hydrophobic, non-polar, aliphatic/alkyl R groups:
Glycine (-H), Alanine(-CH3), Proline (R-group is ring, bonds with amino group twice), Valine(CH(CH3)2), Leucine(-CH2CH(CH3)2), Isoleucine(-CH(CH3)CH2CH3), Methionine(-CH2CH2SCH3)
non-polar side chains consist mostly of hydrocarbons
any functional groups are uncharged at biological pH (pH = 7.0)
Hydrophobic, non-polar, aromatic R groups:
Phenylalanine (-CH2-benzene), Tryptophan (two rings). Tyrosine is also an aromatic, but -OH
group makes it polar so we classify it as hydrophilic neutral.
Aromatic R-groups can absorb UV light. The higher the concentration of protein in a substance,
the more UV light is absorbed.
Hydrophilic Neutral R groups
Serine, Threonine, Cysteine, Asparagine, Glutamine, Tyrosine
Every AA in this category has an -OH or -SH in the side chain (electronegative). Thus, the T
groups can form hydrogen bonds (specifically, hydroxyl groups of Serine and Threonine, amide
groups of Asparagine & Glutamine, and to a lesser extent the sulfhydryl group of Cysteine

BIOMOLECULES

side chains are hydrophilic, thus on surface of proteins and subject to chem. modifications. can be
oxidized or reduced, affecting conformation of protein.
Hydrophilic Basic (positively charged) R groups
Lysine, Argenine, Histidine
Have N in the side chain
Hydrophilic Acidic (negatively charged) R groups
Aspartate, Glutamate
Have a second carboxyl (-COOH) group in side chain
Amino acids can act as an acid or base.
at acidic pH, the carboxyl group is protonated and the amino acid is in cationic form
at neutral pH, the carboxyl group is deprotonated but amino group is still protonated. The net
charge is zero. Such ions are called Zwitterions, and are ampholytes
at alkaline pH, amino group is neutral -NH2 and the amino acid is in the anionic form
cation

zwitterion

anion

Titration of diprotic form of glycine

amino acids with uncharged side chains (such as glycine) have two
pKa values
note: pKa is a measure of the tendency of a group to give up a
proton; tendency decreases tenfold for 1 unit pKa increase
shaded areas indicate pH regions amino acid acts as buffer
In these regions, Henderson-Hasselbalch equation can be used
to calculate proportions of proton donor and proton acceptor
species of glycine.
zwitterions predominate at pH values between the pKa values of the
amino and carboxyl groups
pI is the isoelectric point the point along the pH scale where the
amino acid has a net 0 charge.
This also means the AA is least soluble, and does not migrate in an electric field.
For amino acids without ionizable side chains (such as glycine), this is equivalent to the average of
the 2 pKa values
At the isoelectric point, removal of first H+ is essentially complete and removal of second H+ begins.
The further the pH is from pI, the greater the net electric charge of the population of glycine molecules
note: amino acids with ionizable R-groups have more complex titration curves, with three stages
corresponding to 3 possible ionization steps (and thus pI is not a simple average of pKas)

Peptide Bonds - how amino acids join together

formed by the nucleophilic addition-elimination reaction between carboxylic
group of one AA and amino group of another AA, releasing H2O molecule as
by-product. Peptide bonds are essentially amide bonds.
Mechanism: Nucleophilic amino group of second amino acid attacks
electrophilic carbonyl group of first amino acid (leaves unstable single
bonded O-). Carbonyl group reforms, with elimination of a hydroxide ion. This hydroxide ion abstracts

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a protein and is eliminate as water, while the positive charge on N is neutralized and new peptide
bond is formed.
The peptide bond experiences resonance between the CN bond because of the carbonyl group.
This means it has double bond characteristics.
Resonance structures exist when there is a possibility of
electron movement between neighboring functional groups.
Occurs because the carbonyl oxygen has a partial negative
charge and the amide nitrogen a partial positive charge, setting up a small electric dipole.
The resonance causes the peptide bonds:
to be quite rigid and nearly planar; C-N bond cannot rotate freely
to exhibit a large dipole moment in the favored trans configuration
The N-C and C-C bonds can rotate, but not the C-N bond
Backbone of a polypeptide chain can thus be pictured as a series of rigid planes, with consecutive
planes sharing a common point of rotation at C
Peptide bond cleavage happens with hydrolysis, which can occur by two means:
strong acid: acid hydrolysis + head = non-specific cleavage
proteolysis: cleavage of specific peptide bond (often between specific amino acids) by protease

Levels of Protein Structure

The primary structure of a protein consists of a sequence of amino acids linked together by covalent
bonds (peptide and disulfide). These AA can take on a variety of orientations because of the rotation
of the N-C and C-C bonds.
Secondary structure form primarily because of attractive and repulsive forces generated by
interactions between main chains of neighboring amino acid. Secondinary structure is when especially
stable arrangements of amino acids residues giving rise to recurring structural patterns (e.g. -helix
and -sheets). Depends primarily on H-bonds.
-helix : Helical backbone is held together by hydrogen bonds between the carbonyl group of
the nth amino acid and the amino (N-H) group of the (n+4)th amino acid
optimal HO bond distance of 2.8
Right handed helix is the much more common form, with 3.6 residues per turn
Side chains point our and are roughly perpendicular with the helical axis
Small hydrophobic residues such as Ala and Leu are strong helix formers
Attractive or repulsive interactions between side chains 3-4 amino acids apart
will affect formation.
-helix has a large macroscopic dipole moment, which increases w/ helix length
-sheet : occurs when there is hydrogen bonding between neighboring polypeptide chains rather
than within the same polypeptide. Sheets exist in two forms: parallel and anti-parallel
In parallel -sheets, the hydrogen-bonded strands run in the same direction; resulting in bent
H-bonds (weaker)
In antiparallel -sheets, the hydrogen-bonded strands run in opposite directions, resulting in
linear H-bonds (stronger)
A -turn occurs whenever strands in -sheets change the direction. They link successive runs
of -helix or -conformations and/or connect ends of two segments of an antiparallel -sheet.
Tertiary structure form primarily because of interactions between side chain atoms of AA and H2O
from surrounding environment. Tertiary structure is when several secondary structures come together.
It involves not just the peptide bonds of AA sequence and H-bonds of secondary structure, but
also ionic & hydrophobic interactions as well as disulfide bonds.
When a protein has two or more polypeptide subunits, their arrangement in space is referred to as
quaternary structure. This involves the same forces as tertiary structures.
For both tertiary and quaternary structures, non-polar groups are on the inside of the protein and
polar groups are on the outside.

The Special Cases of amino acids His, Pro, Gly, Cys:

Histidines side chain has a pKa of about 6.5, which is about physiological pH.

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This means it is present in both protonated and unprotonated forms through the body, which
makes His useful around active sites of enzymes because it can both stability and/or
destabilize interactions.
Recall: when pH < pKa, amino acid is protonated. When pH > pKa, its deprotonated.
Proline has a 2nd -amino group because side chain wraps around to form 2nd bond with N.
Glycine: side chain is just an H, so its -carbon is not chiral and thus not optically active. Its
small size also makes Gly very flexible.
Proline (cyclic AA) is a helix breaker because rotation around the N-C bond is impossible.
Glycine also acts as helix breaker because the tiny R-group (H) supports other conformations
Cysteine forms (reversible) disulfide bond upon
oxidation and becomes cystine.
Oxidized form is SS
Note that the disulfide residues are strongly hydrophobic.
Where do these bonds form? In oxidizing environments, like
extracellular space. (Intracellular space is a reducing environment)

Conformational Stability:
solvation shell = layer of water / solvent surround protein structure.
ex: electronegative oxygen atoms stabilize positive residues on outer shell of molecule.
native conformation: a proteins folded 3D structure, its active form
denatured form: unfolded, inactive form of protein.
Denaturation can occur by:
change in temperature: destroys 2, 3, 4 structure by breaking bonds
change in pH: destroys 3, 4 structure by breaking ionic bonds (which are dependent on + and
charge)
chemical denaturants: disrupt H-bonds, thus disrupting 2, 3, 4 structure
enzymes: break bonds between individual amino acids. This alters 1 structure, which in turn
affects/alters 2, 3, 4 structure

Many diseases are caused by errors in protein structure

If proteins lose an aspect of their native conformation, the loss of structure causes loss of function.
ex: sickle cell anemia Hemoglobin is responsible for transporting O2 through your blood. Sickle cell
anemia occurs when a genetic mutation alters the shape of O2 molecules and causes them to clump
together uselessly.
ex: fatal familial sleeping sickness genetic mutation leads to malformation of a major prion protein
Gene Therapy seeks to fix errors in protein at the source, by changing DNA (aka the instructions that
specify AA sequence of the protein)
gene editing techniques should eventually allow scientists to identify and replace mutated
portions of a gene coding for a misshapen protein.
could have unintended consequences like accidentally introducing changes in other parts of
the genome.

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Gene Control
Transcriptional Regulation
operator - sequence of DNA to which a transcription factor protein binds
promotor - sequence of DNA to which RNA polymerase binds
General Transcription Factors (GTFs) - class of proteins that bind to specific DNA sites to activate
transcription
basic transcription apparatus = GTFs + RNA Polymerase + mediator multiple protein complex
this positions RNA pol. right at start of protein coding sequence (gene) and then releases RNA
polymerase to transcribe mRNA from the DNA template.
activators (another type of DNA binding protein)
- enhance interaction b/n RNA pol. and a particular
promotor, encouraging transcription of the gene.
They do this by increasing the attraction of RNA
pol. for the promoter through interactions w/
subunits of RNA pol., or indirectly by changing
structure of DNA
ex: catabolite activator protein (CAP) - activates transcription of lac operon in E. Coli.
cyclic adenosime monophosphate (CAmp) is produced during glucose starvation, binds to
CAP and causes conformational change which allows the CAP to bind to DNA site adjacent to
promotor and the CAP then makes direct protein-protein interaction that recruits RNA pol. to
the promotor
enhancers - sites on DNA bound to by activators in order to loop the DNA in a certain way that brings
a specific promotor to initiation complex. Enhances transcription of genes in a particular gene cluster.
enhancers are usually cis-acting (acting on the same chromosome), but they dont need to be
particularly close to the gene theyre acting on.
enhancers dont act on promotor region themselves, but are bound by activator proteins which can
interact with mediator multiple protein complex. (Complex recruits RNA pol. and GTFs, leading to
transcription of the gene.)
repressors - proteins that bind to operator, impeding RNA pol. movement along the strand and thus
impeding transcription/expression of the gene.
If an inducer (molecule that initiates gene expression, like lactose with the lac operon) is present,
it can interact with repressor in a way that causes it to detach from the operator so RNA pol. is
free to further transcribe gene.
silencers - regions of DNA bound by repressor proteins in order to silence gene expression
mechanism is similar to that of enhancer sequences - silencers can be located several bases
upstream or downstream from the actual protein
when a repressor protein binds to silencer region, RNA pol. is prevented from binding to promotor
Differences between prokaryotes and eukaryotes in transcriptional regulation:
In prokaryotes, transcription regulation is needed for the cell to quickly adapt to the ever changing
environment the cell is sitting in. Presence, quantity, and type of nutrients available determines
what genes are expressed (Prok. regulation is mostly activators & repressors, rarely enhancers).
In eukaryotes, transcriptional regulation tends to involve a combination of interactions between
several transcription factors, allows for more sophisticated response to the environment.
Eukaryotes also have a nuclear envelope, which prevents simultaneous transcription and
translation, allowing an extra spatial and temporal control of gene expression.

Post- Transcriptional Regulation (regulation after DNA becomes RNA; occurs in eukaryotes)
DNA gets transcribed base-for-base into pre-mRNA. Then this pre-mRNA strand needs to be modified
before it leaves the nucleus as fully processed mRNA. Processing helps stabilize / protect the mRNA.
Only Exons make it into finished mRNA. They code for the ultimate protein product.
Introns are short non-coding segments of RNA that get cut or spliced out.

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RNA splicing is done by a spliceosome, a large molecular entity (a snRNP) that binds on either
side of the intron, loops it into a circle, and then cleaves it off and ligates the two ends of exposed
strands together.
After splicing, the RNA receives a 5 cap and a 3 poly-A tail. which help stabilize mRNA for
translation.
5 cap is on the phosphate end (five = fosphate). The cap (basically a guanine nucleotide)
converts that end of the mRNA to a 3 end by a 5-5 linkage.
The 5 cap protects the mRNA strand from exonucleases, promotes ribosome binding, and
regulates nuclear export of the mRNA.
The poly-A tail goes on the 3 end. Multiple adenosine monophosphates (basically adenine bases)
are added to act as a buffer for exonucleases. This increases half life of mRNA and again protects
from degradation, promotes translation by ribosomes, and regulates nuclear export.
The poly-A tail also helps with transcription termination for RNA polymerase
Poly-adenylation is catalyzed by the enzyme polyadenylate polymerase, which adds adenine
molecules using ATP as substrate. The poly-A tail is built until its about 250 nucleotides long.
RNA Editing - results in sequence variation in mRNA molecule. Is relatively rare. Has many catalysts.
May include insertion, deletion, and/or substitution of nucleotide bases on mRNA molecule.
Adenosine Deaminase Acting on RNA, aka ADAR, is one type of RNA editing which converts
specific adenosine residues to inosine in an mRNA molecule by hydrolytic deamination.
CDAR - involves deamination of cytosine to uridine by cytosine deaminase.
RNA editing is studied for infectious diseases because editing process alters viral enzymes
Non-Coding RNA (cRNA)
ncRNA is a functional RNA molecule that is not translated into a protein. It performs vital functions in
the cell still as RNA. (Most participate in transcription and translation in one capacity or another).
MicroRNA (miRNA) - functions in transcriptional and post-transcriptional regulation of gene
expression by base pairing with complementary sequences within mRNA molecules.
This usually results in gene silencing. The mRNAs to which miRNAs bind are prevented from
translation or sent through a pathway for degradation.
Ribosomal RNA (rRNA) - helps make up ribosomes, used in translation.
Transfer RNAs (tRNAs) - links codons in mRNA strand to corresponding amino acid for polypeptides
Small nucleolar RNA (snoRNA) - class of small RNA molecules that guide covalent modifications of
rRNA, tRNA, and snRNA through methylation or pseudouridylation (addition of an isomer of
nucleotide uridine). Also relevant during translation.
Small nuclear RNA (snRNA) - avg. length is ~150 nucleotides. Primary function is in processing of
pre-mRNA in the nucleus. They also aid in regulation of transcription factors or RNA polymerase II,
and maintaining telomeres.
can be associated with a specific set of proteins that form complexes called snRNPs
Theres a special snRNP complex called spliceosome (snRNA + snRNP = spliceosome), which
removes introns during processing of pre-mRNA. Spliceosomes work by binding to ends of an
intron and performing two sequential trans-esterification reactions that splice out introns and ligate
exons to form mature mRNA.

Oncogenes
Proto-oncogenes code for proteins that normally direct cell growth and differentiation. Then something
happens to make them oncogenes.
Products of these proto-oncogenes are involved in signal transduction and execution of mitogenic
signals (a mitogen = a chemical substance that encourages a cell to start division (mitosis))
What happens to make proto-oncogenes into oncogenes? 3 possibilities:
(1) Deletion or point-mutation (in coding sequence of gene itself or of regulatory region) - Leads to a
protein thats produced in normal amounts but is hyperactive, or to an overexpressed (unregulated)
normal gene.

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(2) Gene amplification / increase in mRNA stability - prolongs existence of mRNA (and thus its
activity), which can lead to normal protein thats overexpressed
(3) Chromosomal Rearrangement involves translocation of a gene to a nearby regulatory sequence
that causes normal protein to be overexpressed. Or you could have fusion to an actively transcribed
gene which over-expresses the fusion protein or leads to hyperactive fusion protein
Overall : Either you have a normal protein that is overexpressed (too much of it), or normal expression
of hyperactive protein.
Examples of oncogenes:
Src - non-receptor tyrosine kinase. Src stands for sarcoma, cancer of connective tissue cells.
phosphorylates specific Tyr residues
Ras - codes for small GTPase, activated by growth factor signaling, like an on-off switch. Can see
examples of these in thyroid tumors, some leukemias, etc.
Myc - codes for transcription factor that induces cell proliferation.
RTK - receptor tyrosine kinase. Adds phosphate groups to other proteins to turn them on or off.
Can cause cancer by turning receptor permanently on (ex: VEGF, epidermal growth factor, PDGF)
CTK - mediate responses to activation to receptors of cell division, differentiation.

Tumor Suppressors
Tumor suppressors genes are those whose protein products either have a halting effect on the
regulation of the cell cycle, or they can promote apoptosis. (sometimes both).
these proteins are basically big stop signs that act as safety checks to stop mistakes in cell
division that can lead to uncontrolled cell growth and cancer.
Two types of tumor suppressor proteins:
DNA Repair proteins: recognize DNA damage and either repair it or initiate apoptosis
Cell Cycle Repressor proteins: repress genes that are essential for continuation of the cell cycle.
Two-hit hypothesis with tumor suppressors - says both alleles (allele = copy for a certain gene; you
have two for any given gene) must be mutated before the effect manifests.
So if only one allele is affected, you have back-up copy that can still produce protective protein.
Another way to think about it: In mutated oncogenes, these alleles are typically dominant; In
mutation only one of the alleles yields cancerous phenotype. In mutated tumor suppressor alleles,
these mutations are recessive; both alleles must be mutated to lead to cancerous phenotype.
Examples of Tumor Suppressor proteins:
pRb (retinoblastoma protein) - prevents cell from replicating when its DNA is damaged by
preventing progression of the cell cycle from G1 phase to S (synthesis) phase. It binds and inhibits
the transcription factors that normally push cell into S phase.
This complex acts as growth suppressor and so cell remains in G1 phase.
This complex also attracts a histone deacetylase (HDAC) protein to the chromatin, which
reduces transcription of S phase promoting factors. (Recall: histone deacetylase leads to
repression of transcription)
p53 protein is found in a lot of colon, lung, and breast cancer. It activates DNA repair protein
when DNA has sustained damage. It can also arrest growth by holding cell cycle hostage at
G1> S regulation point, giving time for DNA to be repaired before cell cycle continues.
Specifically, p53 binds DNA and activates several genes, including ones that codes for a
protein called p21, which binds cyclin-CDK complex. Cyclin-CDK complex is responsible for
pushing cell from G1 to S phase.
p53 also is active in the initiation of apoptosis if damage to DNA is irreparable.
exception to the two-hit hypothesis occurs with certain mutations of p53, which can then result in a
dominant negative, meaning a mutated p53 protein prevents the protein product of the normal allele
from functioning.

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Genetic Mutations
Introduction:
Recall central dogma of molecular biology. DNA transcription> RNA translation> protein
Mutations have the effect of making the synthesized protein not right.
ex: Sickle cell disease
Hemoglobin (Hb) is a protein that coordinates to iron ions to hold onto oxygen and transport it
throughout the body. In sickle cell disease, the protein formed is HbS because one Glu residue is
replaced with Val residue. This results in HbS cells clustering together in the cell, and then they
cannot transport oxygen effectively.
Recall: red blood cells are initially generated from haematopoietic stem cells through a process
called haematopoiesis
Mutations originate at the DNA level, but effects of mutation are usually found at the protein level.
Lets look at why
Mistake during translation: correct DNA makes correct RNA, but a mistake during translation
means the wrong AA residue (such as Val instead of Glu) is put into the polypeptide.
If this happens, the cell produces only one HbS for each mistake. Cells are making tons of
proteins, so this mistake wouldnt be that big of a deal. Mutations do not arise at the protein
(translation) level.
Mistake during transcription: correct DNA makes incorrect RNA, codes for wrong protein.
If this occurs, only a few HbS will be made for each mistake, because an mRNA only goes
through translation a few times before being degraded. Thus, mutations do not arise in
transcription.
Mistakes during DNA: incorrect DNA makes incorrect RNA, codes for wrong protein.
Since DNA stores all genetic information, this mutation would result in all proteins produced
being incorrect. So we can say that mutations like the one that cause sickle cell result from
mistakes in DNA rather than RNA or protein level.
Where do these mutations come from?
Inherited: DNA is passed down from parents to offspring. mutated parent > mutated child
Spontaneous: person suddenly gets a mutation in their DNA without their parents having it.
can come from DNA replication errors, environmental factors, or be completely random

Different Types of Genetic Mutations

Mutations are mistakes in a cells DNA that lead to abnormal protein production
Point mutations: one of the DNA bases is replaced with another. Leads to a change in one RNA
nucleotide, and thus a change in one amino acid.
Frame-shift mutation: one DNA base is added to the gene sequence. This leads to an additional
base in the mRNA sequence, which changes the reading frame (codons) of the mRNA during
translation. All codons (and corresponding AA) that come after the extra base will be slightly different.
Frame-shift mutations have a more significant effect on final protein than point mutations
note: point mutation and frame shift mutations are classified by their effects on DNA.
Non-sense mutation: any genetic mutation that leads to RNA sequence codon being a stop codon
This affects resulting protein more than missense mutations, may cut off a lot of AA residues
Missense mutation: any genetic mutation that changes an amino acid from one to another.
Conservative mutation: new AA is the same type as the original (ex: Glu > Asp, both are
acidic)
Non-conservative mutation: new AA is different type than the original (ex: Ser (polar)> Phe
(non-polar, aromatic))
Silent mutations: mutation that doesnt affect the protein at all (happens bc genetic code is degerate)
Ex: In Sickle Cell, Hb is mutated to a less active form, HbS. This results from a single Glu residue >
Val. This is classified as a point-mutation, because only one DNA base is affected; and as
non-conservative, because Glu (acidic) and Val (non-polar) are very different types amino acids

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Causes of Genetic Mutations

Point Mutations are caused by base substitution: one DNA base is substituted for another
Transition: substitution of A <> G (purine for purine), or C <> T (pyramidine for pyramidine)
Transversion: substitution of A/G <> C/T (purine replaced with pyrimidine or vice versa)
Mispairing / Mismatching: when a DNA strand has a non Watson-Crick base pairing. ex: A pairs
with C, or G pairs with T. (rather than Watson-Crick A-T and G-C)
Its much more common for mispairings to occur between a pyrimidine and a purine, rather
than two pyrimidines like C and T pairing up, or two purines like A and G pairing up.
Frame-Shift mutations are caused by:
Insertion: extra DNA base finds its way into our sequence, leads to an extra mRNA base, which
shifts codon reading frame and throws off following amino acids
Base deletion: one DNA base is dropped from original sequence. Also results in a shift of mRNA
reading frame.
Large-Scale mutations - exist at chromosomal level & affect many genes instead of a few base pairs
Translocation: a gene from one chromosome is swapped for a gene on a different chromosome.
This happens on non-homologous chromosomes (e.g. one gene is from chrom. 10, swapped
for another gene from not-10). This differentiates translocation from the process of crossingover that occurs during myosis between homologous chromosomes
Chromosomal inversion: two genes on same chromosome switch places
These large scale mutations dont always affect individual nucleotides, but many of these types of
mutations affect how a genes expression is regulated, in addition to changing what the genes
actually code for.
Remember that the position of the gene on the chromosome partly determines how its regulated
(b/c of histone modification, promotor sequences, etc.)

DNA Damage from Mutagens and Carcinogens

mutagen - any chemical substance (e.g. poison) or physical event (e.g. UV radiation) that can cause
a genetic mutation. Two types of mutagens: endogenous and exogenous
endogenous mutagens - come from inside body, and are something already found in the organism
ex: Reactive Oxygen Species (ROS) - naturally occurring metabolites produced by mitochondria
during oxidative phosphorylation. (ex: O2- (superoxide) and H2O2 (hydrogen peroxide))
ROS contain oxygen and are highly reactive with different cell units. Can cause damage to
DNA by:
double-strand break : breaking DNA in two pieces
base-modification: when nucleotide bases are changed or swapped around, readily
causing point mutations
Why are ROS made at all? They do have beneficial effects, and cells have ways to make sure
they dont do damage (such as antioxidants). When ROS levels get too high, though, cell is
under oxidative stress and cant deal with ROS anymore. Thats when they cause damage
exogenous mutagens - come from outside, affecting organism from external environment.
Intercalators, ex: Ethidium Bromide (EtBr) - it jumps into a DNA helix and sticks itself between the
two strands. When these intercalators intercalate into DNA, they can deform structure of DNA
and cause serious problems.
Base Analogs: pretend to be certain bases but acts differently.
ex: 5-Bromouracil (5-BU) looks like uracil but once its incorporated into DNA it can shift into
two different forms (via a tautomerization reaction). In its keto form, it pairs best with adenine.
In enol form, it pairs best with guanine.
Carcinogens - anything that can lead to cancer (when cells divide uncontrollably and can form bi g
masses of cells called tumors). May be mutagenic, but not all are.
Some work by making mutations of DNA that can lead to cancer.
Some work by increasing the rate at which a bunch of cells divide, without actually changing DNA
ex: tobacco, asbestos, UV radiation

The effects of mutations

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10

There are many different types of mutations, resulting in huge or subtle changes; are good or bad
These mutation usually appear at the protein level. (but are usually caused at DNA level)
Genetic mutations can have advantageous, deleterious, or neutral effects
Example of a good mutation: antibiotic resistance (note - good for bacteria, not human)
Streptococcus pneumoniae is the bacteria that typically causes pneumonia. A popular treatment is
to give the infected person an antibiotic, such as penicillin, that kills bacteria & cures the infection.
Sometimes, however, the bacteria has a mutation that makes it penicillin resistant and the
antibiotic wont kill the bacteria with that mutation. This is a good because the bacteria are living
in a human host where they are likely to encounter penicillin, and this resistance means survival.
Example of a bad mutation: Cystic Fibrosis
Cystic Fibrosis is usually caused by a mutation in the CFTR gene. Makes the lungs mucus really,
really thick which makes it hard to breathe. This is bad.
Some mutations can be both good and bad
ex: sickle cell disease turns Hb into less functional HbS, which is less efficient at moving oxygen
around the body. But also makes person less susceptible to the malaria parasite (which normally
grows in blood.. cant grow as well in sickle cell blood)

Mendelian Genetics
Introduction to Mendelian Genetics
Recall: human cells contain 46 chromosomes, which contain the DNA that make each cell unique.
23 inherited from father, 23 inherited from mother.
For each chromosome, we have maternal and paternal copy.
An allele is a small section on a chromosome that codes for a specific gene. Since humans have at
least two copies of each chromosome, we can say that humans usually have 2 alleles per gene, one
from mother an one from father.
Ex: blood type is coded by a specific allele.
Lets say a guy has alleles of A A, so we say hes homozygous (two alleles are the same). He has
blood type A.
And say a girl has alleles coding for A and O; she is heterozygous. She still has blood type A,
because A is dominant and O is recessive.
We can describe a persons genes in two ways:
genotype - looks at alleles (so AA for boy and AO for girl)
phenotype - looks at physical traits (so both goy and girl have phenotype A)
Its possible for two different genotypes to make same phenotype, because of dominance.
Gene Inheritance
Lets say guy and girl have offspring. We can use a Punnett Square to determine possible
combinations of genotypes for their offspring. (1/2 will be AA, and 1/2 will be AO in this
example). Since both these genotypes code for same phenotype, offspring will be A.
If father and mother were heterozygous, 1/4 will be AA, 1/2 will be AO, and 1/4 will be OO.
So 75% of children will have blood type A and 25% will have blood type O.

Types of Dominance
Complete dominance: only the dominant allele is expressed in phenotype
ex: Blood type. In genotype AO, A is completely dominant over the O, so phenotype is simply A.
Co-dominance: Two alleles are dominant together, so in
traits of both alleles show up in the phenotype (red & blue petals)
Incomplete dominance: Neither allele is dominant over the other, so
mixture of two alleles shows up in phenotype (purple petals)

Punnett Squares and Hardy Weinberg equation

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Hardy Weignberg populations have three assumptions: no selection, no mutation, large population
HW equation = p2 +2pq + q2
ex: Suppose the brown allele for eye color (B) is completely dominant over the blue allele for eye color
(b). If two brown-eyed parents produce a child that is blue-eyed, what is the probability that at least
one out of the next two children they produce will also have blue eyes?
well the probability of having zero children with blue eyes is .75*.75 = 9/16 = 56% (bc we know
parents are Bb if theyre already had a blue eyed child)
100-56 = 44% chance they will have at least one child with blue eyes
see notebook for more details and examples of both punnett squares and the HW equation!

DNA Technology
Restriction Enzymes
Restriction Enzyme definition: an enzyme produced chiefly by certain bacteria, having the property of
cleaving DNA molecules at or near a specific sequence of bases. (ex: EcoR1)
example of purpose of REs: Lets say a virus tries to infect bacteria. It attaches to it and injects viral
DNA into the bacteria. The bacteria has to figure out a way to destroy viral DNA without destroying its
own bacterial DNA. It does this by methylating its own DNA (by the enzyme methylase) as it is
synthesized, so the bacteria recognizes non-methylated DNA as foreign. Restriction enzymes are
floating around in the cell, and if unmethylated / viral DNA enters, the REs will go destroy viral DNA.
Restriction Enzymes work by recognizing palindromic DNA sequences. If such a sequence is
methylated, it will leave it alone. If its not, it will cleave the strand in two, leaving two sticky ends:
Ex: strand GAATTC
is cleaved to G
AATTC
CTTAAG
CTTAA
G
and it now has two sticky ends. If the sticky ends contact one another (since theyre
complementary, they will just re-anneal.
We can make the restriction enzymes and re-annealing process work to our advantage by inserting a
gene of interest into the bacterial plasmid so the bacteria synthesizes that genes product.
Ex: Synthesizing insulin. Start with a bacterial plasmid DNA, and cut with EcoR1. Cut an insulin
gene with EcoR1, as well. This leaves 2 sticky ends on both the plasmid and the insulin gene that
are complementary. Then, put the insulin gene and the plasmid together to re-anneal (plus ligase,
to bind it all together. The bacteria then synthesizes human insulin!
If given the segment lengths of a plasmid after multiple REs, figure out which plasmid is correct by
looking to see what fragments are preserved as REs are used in combination. A preserved fragment
size tells you there are no RE sites on one side of the plasmid previously cut by a different RE alone.

DNA libraries and generating cDNA:

DNA library: online database where you can type in the name of protein and see its DNA sequence.
How is this DNA library made?
Step 1- generate DNA from mRNA:
The process of cDNA generation begins with the purification of the mRNA strand. Adding the
enzyme reverse transcriptase makes a complementary DNA (cDNA) sequence from given
mRNA. cDNA is single stranded, so we need to add DNA polymerase to make it double stranded.
Step 2- sequence the double stranded DNA
Amplification: inject DNA into a cloning vector (such as a plasmid or a virus), which can then be
added to bacteria and the bacteria will produce (clone) lots of the DNA segment.
Once we have lots of DNA, we can sequence it (through PCR, fluorescent labeling, and gel
electrophoresis see section on DNA sequencing).

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DNA Hybridization
DNA-Hybridization is the process of combining two complementary single-stranded DNA molecules
and allowing them to form a single double stranded molecule through base pairing.
Ex: Compare cancer cell to normal cell. Cancers have unregulated cell growth because of various
mutations in their genes. There are 3 options for what happens to genes in cancer cells:
upregulated - makes more gene products (i.e. mRNA and protein) than normal. So if this protein
is something that helps the cell proliferate, having lots more of it would lead to a cancerous cell.
downregluated: the gene makes less mRNA (and thus less protein) than normal. If the gene
product is a protein that inhibits proliferation of the cell, having less of this would lead to cancer.
no change.
We can use DNA hybridization technology to assay the gene transcription profiles of a cancer cell vs
a normal cell; this tells us whats going on with cancer genes.To do this we need to use a microarray.
A microarray, also known as a biochip, is a collection of microscopic mRNA spots attached to a
solid surface. Theyre attached because the chip has a bunch of really tiny wells on it, and in the wells
are complementary strands (complementary to a genes mRNA).
When we break a cell apart to get a the mRNA for the assay, we label it with markers. Then we
put the labeled mRNA on the chip & it binds (hybridizes) to the wells with complementary
nucleotides.
Say we have a cancer cell, whose mRNA we label blue, and a normal cell, whose mRNA we label
yellow. Once we put together a microarray, a computer can analyze it to tell us which genes of the
cancer cell are upregulated or downregulated, based on how much of the yellow or blue marker is
present for a particular gene well. If theres no change in a cancers gene from a normal one, youll
see something in the middle, like a green dot for our example.
This can help scientists tailor treatment to the individual. For example, if you know that a particular
gene in the cancer cell is upregulated, and you have a drug that can target that, you can treat the
patient with that drug (rather than just guessing on treatment plans or giving a cocktail of drugs.)

Expressing Cloned Genes

A gene is cloned by first isolating the mRNA from the gene of interest, and then converting it into DNA
via reverse transcriptase enzyme. This yields cDNA for the gene of interest (only contains exons).
Next, we take the cDNA and amplify it by inserting it into a plasmid that contains antibiotic resistant
genes. Then, we transform it, i.e. transfer the altered plasmid into a bacterium.
Once the plasmid is in the bacteria, we add antibiotics to the culture. All the genes that dont have our
inserted cDNA + antibiotic resistance plasmid will die, and our desired cDNA will be cloned many
times by the bacteria

Polymerase chain reaction (PCR):

overview: PCR, a process used to copy DNA, requires denaturing (separating) the double strands by
applying heat. Unfortunately, this heat also denatures a lot of the enzymes used to copy the strands
and make two double stranded DNA. So scientists isolated a thermos aquaticus bacteria species
that grows in yellowstone hot springs and has high heat resistance. The Taq polymerase can thus
withstand the high heat need to denature the DNA strands, and make copies of the given DNA.
Details: Start off with DNA sequence of interest, apply heat, and denature it into two strands. Then
anneal a primer for the Taq polymerase to come in and elongate the complementary strand, making
two DNA strands. Nucleotides also need to be added to the solution for the Taq polymerase to work.
Heat basically acts like helicase to separate strands & Taq polymerase acts like our own DNA
polymerase.
Repeating these steps of PCR yields an exponential increase in a particular DNA sequence.
After we do PCR one time, we get two pieces of double stranded DNA. In the second round, we
have 4 strands. After round 3, we have 8 strands. After round 4, we have 16. etc. etc.

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PCR can be useful in detecting if a target sequence was in a given sample because it uses specially
constructed primers to amplify the specific DNA sequence. If the PCR reaction produces more nucleic
acid, then the target sequence was in the sample.
Gel Electrophoresis:
Gel electrophoresis allows the separation of different sized fragments of DNA by their size by applying
an electrical charge to the gel. Remember DNA is negatively charged.
Start with a gel that has wells at the top, in which we add different sized DNA fragments. If we add
negative charge at the top (where the wells are) and a positive charge at the bottom, when we turn on
the electricity the DNA fragments will migrate towards the bottoms, towards
positive charge.
Smaller DNA fragments migrate further because they can pass through pores of
the gel more easily.
Its important to add a DNA ladder in the last well, as well. The DNA ladder is a
predetermined set of DNA fragments; they have known sizes. So when we run
the gel, we can compare how far our DNA fragments migrated with the migration
distance of the known fragment sizes, and thus estimate the approximate size of
our fragments.

Southern Blot
Southern blot basically allows you to visualize a specific pieces of interest DNA and see if that
sequence(s) are within a much longer strand of DNA.
1: Take whole strand of DNA and cleave it into many parts by enzymes.
2: Run the DNA fragments through gel electrophoresis to separate them by size.
3: Denature the DNA (make it single-stranded) by making the pH of the gel basic.
4: Transfer the gel onto a filter. This will allow us to better visualize the fragments.
5: Expose the filter to a radio-labelled DNA sequence, a probe, that is the complement to our gene of
interest. If the gene of interest is present, then our labelled DNA piece will stick to its complementary
fragment on the filter. The radiation in the probe exposes the filter on x-ray film, resulting in a signal
where the probe has bound.

DNA sequencing:
1: Use PCR to amplify sample of DNA youre interested in. This generates many strands of our DNA.
2: Normally in PCR you must add DNA nucleotides so the Taq polymerase can synthesize new
strands. With Sanger sequencing, you also want to add a dideoxynucleotides (ddNTP, which only
has a H on C-3 instead of an OH). This will prevent elongation (because phosphate group cant attach
to the H) and your DNA sample of interest will be fragmented into different lengths.
You also can fluorescently label the different dideoxy-nucleotides, so the end of each differently
sized DNA fragment has a fluorescent label.
3: Gel electrophoresis separates these fragments by size. The gel can then by analyzed by a
computer and it will tell you what the fluorescent tags are, giving you a DNA sequence.
e.g. If 2nd mark is a G, you know the 2nd nucleotide is a G. If third mark is a T, you know third
nucleotide is a T, etc.
read the amplified DNA sequence from the bottom up. The reverse compliment of the amplified
DNA will be the template strand.

Gene Expression and Function

Gene expression is the process by which a gene synthesizes some sort of product - usually a protein
but sometimes is non-coding RNA. How do we determine what the function of a gene is?
Knock-out process: Lets imagine a cell that is normally able to digest milk and use it for energy. We
want to figure out what gene is responsible for digesting milk. If we have an idea of what gene it might

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be, we can knock the gene out of that cells DNA and see if the cell is then still able to digest milk. If
not, that gene had something to do with digestion of milk. If it can still digest, that gene was irrelevant.
Reverse Genetics: Start with a gene and then sequence it. Look for a homologous sequence, i.e.
another gene sequences elsewhere in the genome that shares a similar sequence to the gene of
interest. If you know what the homologous sequence does, then you have a pretty good idea of what
your gene of interest might do.
Applications of DNA Technologies:
Medicine:
Recombinant DNA helps create insulin and human growth hormone - allows us to basically grow
these proteins that were previously very difficult to come by.
Also helps in development of vaccines. Vaccines used to just be a denatured / weak form of the
disease, and wed all hope that the human could fight the weakened virus but patients still
sometimes got the disease. With DNA technology, scientists could recreate outer shell of the virus
and inject just that. More cost effective and has a much less chance of infecting the host.
We use recombinant DNA tech to make vaccines for hep B virus, herpes virus, & malaria
Solving Crimes / Forensics:
Non-coding regions of the genome (such as short tandem repeats, STRs) can help scientists
identify individuals, as there are differing amounts of STRs between different individuals.
Mitochondrial DNA (inherited from the mother) can also help scientists identify suspects. It is
present in large amounts in the cell, so even if theres a small sample of DNA, the mitochondrial
DNA can be analyzed to match a sample with a suspect.
Y-chromosome typing (basically Y-STR, identifies short tandem repeats on the Y-chromosome)
Agriculture:
Scientists can create plants through transgenic modification that are resistant to insects,
herbicides, and delay ripening. Helps crops and economy.
Safety and ethics of DNA technologies:
Many safety concerns with exposure to recombinant DNA. For example, if a cancer gene has been
transferred into a bacterial plasmid and then that bacteria infects someone, the individual is likely to
get cancer. very bad.
How do we protect researchers from exposure? Lots of safety regulations set up by NIH.
There are also many ethical issues related to genetic modification of individuals:
Say we have the ability to modify genomes should we scan fetus for potential defects and
modify them to remove the defect? no we could inadvertently negatively affect another part of
the genome, plus we dont know what the long term effects of that modification would be.
What if an individual has a perfectly normal genome? Can we put in genes that make them
faster or smarter?
There are also ethical issues related to privacy of ones genetic information. We are able to
genetically fingerprint individuals to, for example, figure out which person left behind DNA at a
crime scene. Is it okay to just take a piece of gum you spit out and use that to implicate you in
court? Does a suspect have to give consent to be have his genetic information taken and
compared with a sample? What if the govt. could track everyone who ever opened a certain door?
How do we prevent genetic information (like from the human genome project) from being used in a
discriminatory way? If we know an individual has the gene for a specific illness, e.g., how do we
make sure employers and health insurance companies dont discriminate against that individual.

Chromosomal Inheritance
Evidence that DNA is genetic material:

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One criterion we have for biological life is that the organism must have the ability to reproduce. and
the parent must be able to pass genetic material on to offspring. How did we learn that DNA was the
genetic material? Lets explore a few early experiments.
(1) Miescher (1844-1895) - first to isolate and identify nucleic acid, worked with cells from puss
Today we know these puss cells are lymphocytes, which have very large nuclei. Miescher isolated
the material from the nucleus of lymphocytes and determined that it was made of protein and an
acid-type molecule he called nucleic acid .
(2) Roux (1850-1924) - material in nucleus is genetic material, worked with dividing cells
At this time, the nuclei material was though to be protein and/or nucleic acid.
Roux looked at dividing cells and noticed that when they divided, the organelles were not
necessary distributed in an organized and even fashion. However, the material in the nucleus
divided perfectly.
Concluded that because the material in the nucleus was divided perfectly evenly / orderly, that
must be the genetic material.
(3) Hershey-Chase (1952) - showed that nucleic acid, rather than protein, is genetic material,
worked with bacteriophages (a type of virus)
A phage has nucleic acid (can be DNA or RNA, well call it DNA here) surrounded by protein coat.
I: Hershey & Chase allowed the phages to reproduce in a medium that contained radioactively
labeled amino acids. The AA were labeled with S-35, perfect because amino acids contain sulfur
but DNA doesnt.
The phages thus produced a generation with radioactively labeled protein coats, and Hershey
& Chase then allowed them to infect a bacterial cell to reproduce.
When they centrifuged the bacteria / protein coat mixture (to get rid of protein coats) and lysed
the bacterial cells, they found new generation of viruses that were not radioactively labeled.
Concluded that the phage protein coat must have remained outside the bacterial cell, and is
not part of genetic material.
II: Hershey & Chase allowed the phages to reproduce in a medium that contained radioactive P32, perfect because phosphorus is found in DNA but not in
. A generation of viruses were produced with radioactively labeled DNA, and allowed to infect
a bacterial cell to reproduce.
After centrifuging and lysing the cell, Hershey & Chase see that the viruses inside do have a
lot of nucleotides with P-32. Concluded that the nucleic acids must be the genetic material.
Watson & Crick (1953) - identified the structure of the nucleic acids (DNA), a double stranded
helix with a sugar phosphate backbone, and on the inside are the N-bases (A, T, C, G).

Sex-Linked Traits
How is gender determined? Different for different organisms.
In some reptiles, for example, gender is determined by the environment
In other animals, such as mammals, gender is determined genetically, by a whole chromosome
In mammals, we have 22 pairs of chromosomes in the nucleus that are autosomal, meaning theyre
the standard homologous pairs of chromosomes that contain a lot of genes. Then we have two sexdetermining chromosomes, which are not homologous.
In pictures, long one is the X chromosomes; short one is the Y chromosome
Males have XY sex chromosomes (X must come from mom), females have XX (one from mom &
one from dad). Can do a punnett square to show this!
Sex is determined by the sperm (father), because that gamete can carry either an X or a Y
chromosome. The egg (mother) can only carry an X-chromosome, so its genetic makeup doesnt
determine sex of the offspring.
Do sex chromosomes have genes that arent related to the sex of offspring? Yes, but are famously
gene-poor, the Y more so than the X. (Y chromosome has ~78 gene codes, X has ~1500)
SRY gene on the Y-chromosome plays a role in the development of testes.
Recessive mutations of the genes on X- chromosomes lead to infamous disorders.
ex: mutations that cause red/green color blindness & hemophilia (inability for blood to clot well)

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Men are more likely to get recessive X-linked traits, because they only need one of the
mutations, whereas a woman would need both X chromosomes to have the mutation.
If theres a m (1/700) chance of an X-linked mutation, men have m chance of getting the
disease, while woman have m2 chance (1/700 * 1/700 = 1/490000 chance)

Genetic Recombination
Lets look at a cell starting to undergo myosis The chromatids duplicate and we now have 23
homologous pairs of maternal chromosomes and 23 paternal homologous pairs of chromosomes.
note: one chromatid = one chromosome, and two chromatids (X shape) still = one chromosome,
because we count chromosomes by number of centromeres.
During Pro-phase 1 of myosis, homologous pairs of chromosomes pair up with each other during
synapsis to form a tetrad (4 chromatids).
At some point, the chromatids cross over
each other and overlap to form a chiasma.
A protein complex forms between the pairs
called the synaptonemal complex and,
with the help of the complex, crossing over
(aka genetic recombination) occurs - the
parts of the two chromatids that are touching
will actually switch places; DNA bonds are
broken, switched, and reformed.
This crossing over means that at the end of
myosis II, when the 4 chromatids get
separated into different gametes, well have 4 different / unique gametes, two of which we can call
gametes recombinant - They have new alleles that arent even in the parents.
If crossing over didnt happen, wed only have 2 different types of gametes.
genetic recombination increases genetic variability.
single crossover - Chromatids cross over once.
two strand double cross over - Chromatids cross
over a second time and the segments essentially
switch back so we end up with what we started with.
three strand double cross over - After the initial
cross over, a set of chromatids on the same
chromosome cross over. The segment from the other
chromosome (that was just crossed over) can either
entirely switch chromatids or just a portion of it can.
four strand double crossover - Like the 3 strand,
except both pairs of chromatids cross over each
other. The segments can switch to the outside
chromatids, or, again, just a portion of them can.
Crossover on sex chromosomes only occurs in pseudoautosomal regions, but generally not
between the male-specific region on the Y chromosome and the rest of the X chromosome.
It could be bad if they did. ex: What if the sex-determining gene SRY crossed over onto an X
chromosome That would mean that the gamete that gets the Y chromosome is supposed to
lead to a male offspring but would be missing the gene for testes development.

Gene mapping
An analysis of genetic recombination (i.e. how often crossover happens for certain genes) can be
used to figure out the distance between genes on a chromosome because we know that genes that
are further apart on the chromatids are more likely to get separated (recombine) than genes
that are close together. If we can figure this out for all the genes on a chromosome, we can map it!

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Similarly, worth noting that the closer two genes are two each other on a chromosome, the less
likely it is that they will be separated / crossed over.
A centimorgan (aka genetic map unit, m.u.) = The distance between genes for which every 1 in 100
products of myosis is recombinant. If 2 genes are 6 m.u. apart, theyll be recombinant every 6/100
times, or 6% of the time.

Extranuclear inheritance
extranuclear inheritance = genetic inheritance of DNA outside of the nucleus.
DNA isnt just in the nucleus. Certain organelles (mitochondria and chloroplasts) have their own DNA
that they can replicate (and therefore replicate themselves) independently of the nucleus.
Mitochondria are found in eukaryotes, and break down energy molecules to ATP. mtDNA has ~37
genes, mostly having to do with cellular respiration that happens in the mitochondria.
Chloroplasts are found in plant and algae cells, and are the site of photosynthesis. (more
specifically, the thylakoids, within the stacks of grana of chloroplasts, make phososynthesis
happen by harnessing sunlight to make glucose).
cpDNA has ~100 genes, mostly having to do with things involved in photosynthesis.
Recall how sexual reproduction works: An egg cell and sperm cell (gametes), have half the DNA (n)
that normal cells have. So when they fuse to make a zygote, that zygote has about the amount of
DNA that a cell normally would (2n).
A sperm cell doesnt donate anything to the zygote except n DNA; its very small.
However, an egg cell is a fully formed cell with fully developed organelles in the cytoplasm, some
of which (such as mitochondria) have their own DNA.
When zygote forms, it gets 2n DNA from sperm + egg, and some organelles + their DNA from
egg.
Maternal inheritance - the inheritance of DNA that only comes from the egg cell that eventually
becomes part of the organism. Maternal inheritance is contrary to Mendelian genetics, because
mendelian genetics assumes half the DNA comes from the egg and half from the sperm; it doesnt
take into account the DNA that comes only from one of the gametes, the egg cell.
Carl Correns did an early experiment that helped discover extranuclear inheritance in chloroplasts.
He was a contemporary of Mendel, but about 40 yrs younger. (1864-1933)
Correns did a lot of experiments with the 4 oclock plant, which is unique in that within one plant
you can different colored leaves/flowers on different branches - On one branch, they might be
white; on another, green; and on the other they could be varigated (green/white mixed).
Why does this happen? One of the genes in chloroplast DNA makes chlorophyll, which makes a
leaf green. In the cell of a white leaf, though, that cpDNA could have a mutation that doesnt allow
it to produce chlorophyll (or only a tiny amount), so the leaf is white. In variegated leaves, some
cells have regular chloroplasts and others have the mutated genes, plus the varigated branch
could have a third type of cell with both regular and mutated chloroplasts within the same cell.
Correns noticed, after crossing a bunch of plants, that the progeny had nothing to do with sperm
(pollen) cell, but only the egg cell. If he took a seed from a branch with only white leaves, the
progeny would only have white leaves, no matter where the pollen came from.
Because the gene for leaf color is in the chloroplasts, this gene exhibits maternal inheritance.
The same concept applies to the mitochondria. If a person has a disease that has to do with a
mutation in the DNA in the mitochondria, we would know that the disease came from the mother.
Endosymbiotic theory - seeks to explain why mitochondria and chloroplasts have their own DNA.
Theory says mitochondria and chloroplasts were one independent prokaryotes, but eventually
joined an ancestral eukaryotic host cell (~1.5 billion years ago) and they lived together in
symbiosis. That host cell + prokaryotic cells eventually evolved into the eukaryotic cells of today.
best evidence that DNA is the genetic material: Transformation using heat-inactivated bacteria.
Heat denatures proteins. If heat-inactivated bacteria can transform (transfer genetic
information to) other bacteria, protein cannot be the genetic material, so it must be DNA.

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Penetrance measures the fraction of people with the genotype who express the corresponding
phenotype. ex: if a mutation in the gene thats responsible for an autosomal dominant disorder has
95% penetrance, then 95% of those with the mutation will develop the disease, while 5% will not.
Expressivity measures the variation in phenotype of a certain genotype. Constant expressivity
means that the genotype is expressed into the same phenotype exactly the same way, every time.
The concept of expressivity depends on the gene having 100% penetrance. If a gene has
variable expressivity, then everyone with the TALL gene is above average height.

Evolution and Population Dynamics

Evolution and Natural Selection:
Evolution is how species experience heritable (passed from one generation to the next) changes in
their traits over time.
Evolution occurs to populations, not individuals. It takes huge amount of time for even small changes.
There are four mechanisms of evolution: natural selection, mutation, genetic drift, and gene flow
natural selection = the process whereby organisms that are better adapted to their environment tend
to survive and produce more offspring. Thus those adaptations are increasingly present the
population
Natural selection is driving force of evolution. It is context dependent.
Note: natural selection only applies to heritable traits, not acquired characteristics.
ex: If you lift weights & get really buff/muscular; you wont pass on that buff-ness to your children.

Fitness and Fecundicity:

Fitness = an organisms total ability to survive and reproduce in a particular environment.
Fecundity = how easily and how often an organism can reproduce offspring
A really strong guy might have a higher survival rate than everyone else, but reproduces the same
With asexual reproduction, fecundity is determined by how quickly the cells can divide and increase
population size.
With sexual reproduction, fecundity is measured by how well an individual can mate with another, as
well as how well that individual can carry and birth offspring (applies to both men and women).
Fecundity is selected for like a survival trait. (The more fecundity a person has, the more offspring
theyll have evolves population to more individuals with more fecundity over time.)
Physical attractiveness is also an aspect of fecundity, because it helps individuals mate
Alternative Selection
Group selection: genetic traits that benefit the population as a whole will still be selected for even if
they dont benefit the individual (altruism, martyrdom, etc).
Why does a female live after menopause, since any traits they have cant be selected for once
theyre past childbearing age? Well, grandparents play a role in taking care of their grandchildren,
and help increase the fitness of their grandchildren. It benefits the population as a whole.
Natural selection acts on traits that increases survival until reproduction
Group selection acts on traits that increase survival after reproduction is possible.
Artificial Selection: an outside individual chooses which traits get passed on, instead of that
happening naturally.
ex: A farmer breeds new type of tomato plant that produces a lot of fruit, by selecting the seeds of
plants that produced an especially large amount of fruit in previous generations.
ex: A scientist in a lab can look at a tomatos DNA and select (or modify) genes with desired
phenotypes (like increased fruit production)
Bottlenecks and the Environment
Trait desirability is not constant, it depends on the environment.
Populations with large gene pools can adapt to many environmental stresses.

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What happens when a population faces a HUGE stress? Population bottleneck: A significant stress
wipes out such a large part of the population that relatively few individuals survive. Two outcomes:
Failure to adapt; goes extinct (ex: dinosaurs, couldnt adapt to change after meteor hit)
Survives the stress and ultimately recovers, though the genetic makeup may be changed.
(ex: peppered moths. Most of the population was initially white, but as pollution changed the
environment, black moths were more camouflaged and thus most of the population became black)
Bottleneck effect: a situation where a population becomes very small due to an environmental stress
and loses much of its genetic diversity

Inbreeding
Recall: large gene pools are good for a population
Inbreeding: people in a population will have offspring with a certain smaller group within that larger
population (could be because of religion, culture, or just preference)
When inbreeding occurs with non-human organisms, its almost always bc of geographic barriers.
Inbreeding means theres common ancestry, but its not just incest. Can be distantly related.
Why is inbreeding a problem?
ex: Tay Sachs disease, autosomal recessive disorder (AA = unaffected, Aa = carrier, aa =
disease) In an inbred population (like a small, old-timey Jewish population), the chance of a carrier
choosing another carrier for a mate is a higher, and some of their offspring will be diseased.
ex: Huntingtons disease, an autosomal dominant disorder (AA = unaffected, Aa & aa = diseased)
No matter who a diseased person has children with, then, theres still a chance their children will
be affected.
Carriers of autosomal dominant disorders are generally aware theyre a carrier (because carriers
express the disease) and are thus aware of the risks of having children. Carriers of autosomal
recessive disorders may not be.

Reproductive Isolation
Recall: Asexual production leads to near perfect copies of the single parent organism. Sexual
reproduction is when two organisms combine to make genetically unique offspring.
Asexual reproduction has low genetic diversity, while sexually reproducing species have high
diversity.
What is a species?
for sexual reproducers, its clear that members of different species cant produce offspring
together
for asexual reproduction, its less clear what a species is (species problem)
Sexually reproducing organisms are reproductively isolated if they are unable to freely produce
fertile offspring together. There are two categories of reproductive isolation: pre- and post-zygotic.
pre-zygotic isolation: all the forces that prevent two organisms from having offspring that occur prior
to the formation of a zygote.
(1) Temporal / habitat isolation - not all organisms mate at the same time, some mate at night vs.
day, or spring vs. fall. Some may mate in the mountains and other on the beach.
(2) Behavioral isolation - mate selection. organisms attract mates in different ways; birds may sing
or show plumage, bunnies may do a dance.
(3) Mechanical isolation - mating is physically not possible, even if the organisms wanted to.
(elephants cannot mate with mice, for example)
(4) gametic isolation- fertilization between the two gametes to form a zygote is impossible
post-zygotic isolation:
(1) Zygote mortality - even if the gametes of two organisms come together to form a successful
zygote, that zygote cannot develop into offspring
(2) Hybrid Inviability - zygote can grow into offspring, but that offspring has a high mortality rate
and will not develop into an adult.
(3) Hybrid sterility - offspring can grow into a mature adult, but cant produce offspring of their own

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stabilizing selection: a process in which extremes of a trait (being very tall or very short, for
example) are selected against, and an intermediary trait (like being average height) is selected for.
genetic drift: changes in the frequency of alleles in a gene pool, simply due to chance
Assortive mating: mates are not chosen randomly, but instead certain individuals are selected over
others possibly because of phenotype or location.
directional (disruptive) selection: when one extreme of a trait is favored over another and the
population starts to express that extreme phenotype more often
gene flow: alterations in the composition of a gene pool due to migration of individuals between
different populations

Principles of Bioenergetics
Gibbs Free Energy Introduction:

By calculating G, change in Gibbs free energy, we can tell whether or not a reaction will occur.
Gibbs free energy is a defined quantity for a given reaction (or given set of reactions).
For a reaction A > B, G = GB - GA. Always products - reactants
G is a state function. It depends only on reactants and products, not on the pathway
(intermediates) to get there. So if the reaction was A > C > B, the G would still be that above
units of G = joules / mol of reactants
G can be calculated, but not measured (unlike, e.g., temperature). G = H - T(S)
H = enthalpy; T = temperature; S = entropy
Rxn coordinate diagram to the right
Energy releasing processes have a negative Gibbs free energy, or -G, it is exergonic and will
proceed spontaneously. When G is positive, we say the reaction is non-spontaneous, or endergonic
Change in enthalpy is really a good proxy for bond energy, or whether or not energy was released
(H) or absorbed (+H).
H is more favorable
2nd law of thermodynamics says all systems tend towards disorder. Since entropy is a change in
disorder, +S is more favorable than a negative value.
G will always be negative with H and +S, and always positive with +H and S.
The higher temperature is with +H and +S, the more likely G is to be negative
The lower temperature is with H S, the more likely G is to be negative

Heat Transfer and Enthalpy

heat = the amount of energy that is transferred due to a change in temperature
Remember that whenever you have a gradient in something (ph, charge, or in this case, temperature),
that means potential energy is being stored up. If theres no opposing force, that gradient wants to
disappear.
temperature = average kinetic energy of molecules (in whatever were measuring the temperature of)
heat should always be described as a transfer, a loss or gain of energy.
heat transfer, q, occurs between a system and its surroundings.
q represents loss of heat. If its lost from the system, temperature of the surroundings (due to
transfer of energy increases.
qsystem = qsurroundings
Enthalpy refers to heat transfer for chemical reactions (the reactions = system). Tell us whether heat
was lost or gained from the perspective of the system.
Units of enthalpy = joules / mol of reactant (having it per mol allows us to take amounts into account)
Ex: When our bodies get hot, we try to cool down by evaporating water from our skin (aka we sweat.
Turns H2O(l) > H2O (g). For this reaction, H = HH2O(g) HH2O(l) This requires heating up, so
were adding energy to the system. It (the rxn) absorbs heat and is endothermic, which means
our bodies must be losing heat.
endothermic = absorption of heat/energy, H > 0
exothermic = heat/energy is being released, H < 0.

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ex: of exothermic reaction is ATP hydrolysis, breaking the phosphoanhydride bond

linking the gamma phosphate to the phosphate
ex: The bioluminescence of fireflies releases energy as light, but it consumes more
ATP in the process to do so; thus it is endergonic with a +G
Le Chateliers Principle
Any change to a chemical reaction at equilibrium will cause the rxn to proceed in the direction that
minimizes change
Increasing concentration (or partial pressure) of a reactant will shift the rxn right, in forward direction
Increasing concentration (or partial pressure) of a product will shift the rxn left, in the reverse direction
Decreasing concentration (or partial P) of a reactant will shift the rxn left, in the reverse direction.
Decreasing concentration (or partial P) of a product will shift the rxn right, in the forward direction.
Decreasing the volume of a reaction container (/ increasing total pressure) will cause rxn to shift
towards the side with least mols of gas.
Similarly, increasing the volume of the reaction container (/ decreasing total pressure) will
cause reaction to shift towards the side with the most mols of gas
Adding inert gas causes no change to the reaction.
If temperature of an exothermic reaction is increased, reaction will shift left (b/c heat is product)
If temperature of an endothermic reaction is increased, reaction will shift right (b/c heat is reactant)
Adding catalyst increases the rate of the reaction, but no change to equilibrium concentrations.

Thermodynamics and Kinetics

G only depends on energy states of products and reactants; it is a state function.

If G is negative, the reaction is thermodynamically favorable
EA refers to the energy required to reach the intermediate state during the course of the reaction; it is
not a state function very much depends on how A reactants become products.
The lower the EA is, the more kinetically favorable (thus faster) the reaction is.
Enzymes make EA lower!

Overview of Metabolism
Anabolism and Catabolism
metabolism is the study of how we can obtain the 4 major biomolecules to sustain life: proteins, fats,
carbohydrates, and nucleic acids.
We get these biomolecules from food, but not necessarily in the configuration our bodies need
Catabolism breaks down what we eat into necessary components.. e.g. breaks down proteins into
amino acids, adipose cells into fatty acids; carbohydrates into glucose, and nucleic acids into
nucleotides (c in catabolism = cut)
Anabolism: builds these components back into customized macromolecules that we really need
The process of anabolism, building up molecules, requires energy. Where does this energy come
from? Also food.
Recall: energy currency of our bodies is ATP (adenosine triphosphate). When ATP loses a phosphate
group to become ADP, it releases energy that can be used in anabolism. Of course, then this ADP
must be regenerated to ATP.
How do we regenerate ATP from ADP? By breaking down even further the initial components of
digestion, i.e. by catabolizing amino acids, fatty acids, and glucose, energy is produced that turns
ADP to ATP. This is cellular respiration.
Catabolism fuels anabolism, and both types of processes are regulated by hormones

ATP Structure and Function

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Structure of ATP: ribose nucleotide, connected on C-5 by phosphodiester bonds (high energy!) to 3
phosphate groups. On C-1 is adenosine base (double ringed purine).
When a phosphate group is removed, such as through ATP hydrolysis (cleavage of phosphate
group of ATP by water, producing ADP), energy is released because the electrons in that bond go
to a lower energy state!
ATP is used in biosynthesis, muscle contraction, and ion movement across cell membranes
How does it fuel these reactions? Hydrolysis!
ATP Hydrolysis is an exergonic, spontaneous reaction. It has a G. (Recall, G = GP-GR)
Meanwhile, many biosynthesis reactions have a +G.
Coupled reactions - When ATP hydrolysis occurs simultaneously with another reaction, usually one
that requires energy (such as addition of a phosphate group to a molecule).
Adding positive G of synthesis to the very negative G of hydrolysis leads to overall negative G
for the reaction, which means its still favorable.
ATP provides energy to a reaction really by transferring one of its phosphate groups. (Pyrophosphate
left over is cleaved immediately to reduce product concentration so that the forward reaction, actual
ATP hydrolysis and/or transfer of P group is favored.)
Where does ATP hydrolysis occur within cellular respiration?
Glycolysis (breaking down of glucose) - occurs in cytosol.
When pyruvate (product of glycolysis) is transformed into Acetyl-CoA - occurs in mitochondria
Citric Acid Cycle, where energy precursors (electron carriers) are made - occurs in mitochondria
Oxidative phosphorylation (electron transport chain) produces bulk of ATP - occurs in
mitochondria

Oxidation and Reduction, and Electron Carrier Molecules

LEO the lion goes GER: Loss of Electrons is Oxidation; Gain of Electrons is Reduction.
Called oxidation because electrons tend to be lost to oxygen, though not always. Recall that
oxygen is much more electronegative than hydrogen.
ex: 2H2 (g) + O2 (g) > 2H2O (l) + heat
Oxidation state of neutral elements is 0.
So in this reaction, hydration is oxidized from 0 to 1 and oxygen is reduced from 0 to 2-.
Oxidation means losing hydrogen atoms; reduction is gaining hydrogen atoms.
This fits with other definition about losing/gaining electrons because in the biological world,
hydrogen is what gets swapped around & tends to bond with C, N, O, F all very electronegative.
The flow of electrons is harnessed during cellular respiration to produce chemical energy, ATP
Electron transport chain contains an array of proteins that readily accept and give away electrons.
(this is like the wire in an electrochemical cell). The multiple compartments within a cell allows the
body to efficiently isolate the flow of electrons (like the two different containers for different elements
in an electrochemical cell).
As glucose breaks down (and is oxidized, meaning it loses electrons), it forms metabolites that also
become more and more oxidized. These metabolites donate their electrons at each step to electron
carrier molecules (NADH and FADH2) which directly donate electrons into electron transport chain (via
enzymes) to make energy in the form of ATP.
Overall breakdown of glucose: C6H12O6 + 6O2 > 6H2O + 6CO2 + energy
This is a combustion process; it requires fuel (glucose) and oxygen.
Why doesnt glucose spontaneously combust to produce a large burst of energy, instead of have a
bunch of stepwise reactions to break it down into metabolites?
If glucose spontaneously combusted, resulting energy would largely be in the form of heat,
which would be unusable energy. Our bodies can only really use ATP.
Spontaneous combustion of glucose is energetically favorable (i.e. it released energy), but it is
kinetically unfavorable (it has a very high activation energy)
Our body overcomes high activation energy of glucose catabolism by using enzymes.

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Enzymes produce a large number of metabolites, so we end up with many metabolites that can be
used and reused in other processes. Also, enzymes allow a slow, controlled oxidation, so we end up
with useable energy.
Because of their use in the enzymatic processes, electron carrier molecules are called cofactors.
Electron carriers in the class of enzymes called dehydrogenases, they take away hydrogen and
electrons from metabolites, most often in the form of a hydride (H-) ion. A hydride is 1 proton + 2 e Most common electron carriers: NAD+ and FAD
NAD+ + 2H+ + 2e- > NADH
FAD + 2H+ + 2e- > FADH2
The reduced form, with the hydrogens, are what shuttle the electrons to the electron transport
chain.

Mechanism of ATP Hydrolysis

1.
The first water molecule donates one of its lone pairs of electrons
to form a bond with H from the second water molecule, stealing
that H away. This turns the two water molecules into hydronium
ion (H3O+) and an unstable hydroxyl group (OH)
2.
Because of the instability of the hydroxyl group, one of its
lone pairs forms a bond with the phosphorus of the first
phosphate group of the ATP molecule.
3.
The phosphate group that made a bond with the hydroxyl group
(which is now called a phosphoryl group) breaks off from the
ATP molecule; the new bond is just too much for ATP.
4.
The electrons that formed the bond that attached that first
phosphate group move onto the neighboring oxygen, causing it to become negatively charged and
thus producing ADP and energy (in addition to leaving phosphoryl group)
The bonds of the triphosphate contain high energy e such that when the P group is removed, the e
come down to a lower energy state. This difference in energy states = energy released by the rxn.
ATP + 2 H2O > ADP + Pi + [H3O]+ + energy
Lactic acidosis occurs when there is too much ATP hydrolysis. This is when the blood and tissues
become acidic because of a build up of hydronium ions from ATP hydrolysis.
Lactic Acidosis happens when our cells arent receiving enough oxygen, like when youre doing
anaerobic exercise (sprinting).
Recall that when oxygen is absent, fermentation replaces the citric acid cycle & oxidative
phosphorylation, but glycolysis continues to occur so that some ATP are still being made.
Fermentation also causes (in addition to increasing hydronium ions) a buildup of lactate

Carbohydrates
Naming and Classification
Most have formula Cn(H2O)n
single carbohydrate = monosaccharide
Functions include:
energy source and storage (glucose = main energy for animals)
structural component of cell walls and exoskeletons (cellulose)
informational molecules in cell-cell signaling
Suffix is ose
Prefix is determined by a couple of things..
1) Number of Carbons (start counting from aldehyde functional group)
3 carbons = triose 4 carbons = tetrose 5 carbons = pentose 6 carbons = hexose
2) Aldehyde vs. Ketone (aldehyde is H-C=O group on end, ketone is C=O in middle of molecule)
ex: fructose is considered a ketohexose.
3) Stereochemistry

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With Fischer projections, look at the carbon group furthest from carbonyl carbon. When the
highest functional group (with saccharides, thatd be the OH group) is on the right side, it is
an D- configuration. When the OH is on the left side, its an L- configuration.
ex: the glyceraldehyde above is an R-aldotriose
For a monosaccharides with n chiral centers, which means there are 2n possible configurations.
Most hexoses in living organisms are D stereoisomers
However, the D vs. L distinction doesnt necessarily dictate how its optically active.
Some D steroisomers such as tetrose still rotate (overall) plane-like counterclockwise, as
opposed to clockwise, like you would see with most R stereoisomers. When this happens, it
gets a minus - distinction. So its D- tetrose.
Enantiomers - stereoisomers that are non-superimposable mirror images, they differ in configuration
around every chiral carbon.
All of the D-isomers of aldohexoses are
diastereomers - stereoisomers that are
not mirror images; have different physical
properties. Thus is true of all similar
categories, like the L-ketohexoses
Lets think this through: Each aldohexose
has 4 chiral centers, which means there
are 24 (=16) stereoisomers. Half of those
are D and half are L. So 16/2 gives us 8
D-stereoisomers of aldohexose.
Epimers: two sugars that differ only in
the configuration around 1 C atom
ex: D-Mannose and D-Galactose are
epimers of D-glucose, differing only at
C-2 and C-4
Five most common monosaccharides:
D-Mannose
D-Glucose
D-Galactose
D-Fructose
D-Ribose
(is the ketose of glucose)

(Ribose is all-right)

Cyclic Structures and Anomers

Nucleophilic attack on an aldehyde / ketone by an alcohol will lead to a hemiacetal / hemiketal
(or acetal / ketal if theres more than one alcohol attack)
No water is lost in the first step (the formation of a hemiketal / hemiaceta);
water is lost in 2nd step (formation of the ketal / acetal)
When the alcohol and the carbonyl its attacking come from the same
monosaccharide itself, we get cyclic structures >
pyranose: six-member cyclic structure
furanose: five-membered cyclic structure (f = five)
Fructose is a furanose when in its cyclic form.
These are still hemiketals / hemiketals; no water is lost.

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The former carbonyl carbon becomes a new chiral center: anomeric carbon.
This carbon is the only one that is bonded to two oxygen atoms, one
within the ring and the hydroxide group
The former carbonyl oxygen becomes a hydroxyl group. The
position of this group determines if the anomer is (trans) or (cis)
The upper right diagram of -D-Glucose is a Haworth Diagram, different from a chair confirmation.
downright up-lefting the functional groups on the right side of the
molecule in a Fischer projection will point down in their cyclic form. Those
on the right side in a Fischer projection will point down when cyclic.
If the hydroxyl group of the anomer carbon is on the same side as C-6, it is
cis ()anomer. If its on the opposite side as C-6, it is trans ().
A chair diagram follows Haworth diagram as far as what is facing where, but
can be more useful for determining cis/trans.
What causes the cyclic structure to form in the first place is some amount of acid or base, like from
water. In water (and all aqueous solution), the cyclic structures go back and forth with their linear
form.
mutarotation occurs with these monosaccharides in the water - As the rings open up, the bond
between C-1 and C-2 can rotate; when it closes again you may form the cis () or trans () forms.
These cis and trans cyclic forms reach an equilibrium in aqueous solutions. For glucose, that
equilibrium ratio is about 64% cis () and 36% trans (), but its different for different compounds

Disaccharides and Polysaccharides

The attack on the anomeric carbons OH group of one cyclic monosaccharide (which is a hemiketal /
hemiacetal) by an alcohol from another monosaccharide will lead to a glycosidic bond and formation
of a disaccharide.
With disaccharides, the glycosidic linkage forms most commonly between C-1 of the first sugar
and C-4 of the second sugar. So we call it a 1>4 glycosidic linkage. If the R-group
(another carbohydrate) of the first carbon is oriented on the same side as C-6, it a
-1,4-glycosidic linkage.
Lactose - principal disaccharide found in milk. Unlike most disaccharides, its not very sweet.
Consists of one galactose and one glucose disaccharide, joined by
-1,4-glycoside bond.
Maltose = two glucose units, joined by a -1,4-glycoside bond
In both lactose and maltose, you have two pyranoses (6-membered rings)
Sucrose - one of the most common disaccharide in nature. Principal component of table sugar
Sucrose = glucose and fructose monomers joined by a -1,1-glycoside bond
Unlike both both lactose and maltose (which consist of two pyranoses, or
6-membered rings), sucrose consists of one pyranose and one furanose.
Also unlike lactose & maltose, the two monomers in sucrose are joined at both
anomeric carbons.
With lactose and maltose (and any 1,4 glycosidic linkage), the anomeric carbon of the first monomer
becomes an acetal, while that of the second carbon is still a hemiacetal. The hemiacetal can undergo
another alcohol attack and be reduced further (more monomers can join via more glycosidic linkages).
With sucrose, however, since both anomeric carbons are joined, two acetals are formed.
Its non-reducing.
Addition of more carbohydrates onto disaccharides (via their reducing end) leads to polysaccharides.
Polysaccharides can be:
homopolysaccharides (made of one type of sugar molecule)

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heteropolysaccharides (made of multiple types of sugar molecules)

linear or branched
Cellulose is an unbranched homopolysaccharide of glucose
Glucose monomers form (1>4) linked chains
Hydrogen bonds form between adjacent monomers,
& additional H-bonds between chains >
Structure is tough and water-insoluble
Cellulose is most abundant polysaccharide in nature, found in cell walls of plants.
Cotton is nearly pure fibrous cellulose
Starch - is a mixture of two homopolysaccharides of glucose, amylose and amylopectin
amylose: unbranched polymer of (1>4) linked glucose residues
amylopectin: glucose polymer with (1>6) linkers and branch points every 24 30 residues.
functions the main storage polysaccharide in plants
Most humans lack enzymes to break down 1>4 linkages in cellulose, but can break down 1>4.
Thus we can use starch as an energy source but not really cellulose; too hard to digest.
Glycogen - is a branched homopolysaccharide of glucose
glucose monomers form (1>4) linked chains
branch points with (1>6) linkers ever 8-12 residues
functions as the main storage polysaccharide in animals, is fast source of glucose.

Keto-enol tautomerization
keto (double bonded O) and enol (double bonded carbons with an alcohol group attached to one of
them are in equilibrium with each other. There are isomers of each other (not resonance structures).
Acid-catalyzed mechanism of tautomerization:
Nucleophilic oxygen on the keto-form picks up H from
hydronium, causes the electrons of the double bond to
go to the oxygen so it now has two lone pairs of
electrons (and some resonance).
The oxygen of a water molecule then takes one of the
hydrogens from the -carbon, and the electrons from
that bond go to form the double bonded enol form.
Base-catalyzed mechanism of tautomerization:
Oxygen of hydroxide (base) ion takes one of the
protons (H) from the -carbon to make an enolate anion with two resonance structures.
In the carbanion form, the lone pair of electrons left
on the -carbon give it a negative charge. The
oxygen is still double bonded (=O)to the adjacent
carbon.
In the oxyanion form, that lone pair makes a double
bond with the adjacent carbon and pushes the
electrons from our keto group onto the oxygen atom.
So oxygen has a negative charge.
Recall, oxygen is more electronegative than carbon
so the oxyanion contributes more to the resonance
hybrid.
A lone pair from the oxyanion takes a hydrogen from
a water molecule to protonate itself, forming the final
enol isomer.
What happens if you have a chiral center at the -carbon of a keto form? Racemization
Chiral center means it has 4 different R-groups attached. Has tetrahedral geometry, sp3 hybridized
Because it has an -proton still, we can form an enol, which is achiral and thus planar/flat
When we tautomerize back to the keto form (which is non-planar), we can either form what we
started with or the other enantiomer.

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Enolization can lead to racemization (conversion of enantiomers)

Carbohydrate Metabolism
Introduction to cellular respiration
Recall, cellular respiration is the reduction of glucose to carbon dioxide to produce energy for the body
Overview: C6H12O6 + 6O2 > 6H2O + 6CO2 + energy that energy is then used to produce ATP
First stage: Glycolysis breaking down glucose (6 C) into 2 pyruvate (3 C) molecules
glycolysis requires 2 ATP, but it generates 4 ATP, yielding a net of 2 as well as reduced electron
carriers NADH and FADH2
doesnt require oxygen (is anaerobic), can occur with or without it
When you run out of oxygen, some of the byproducts of glycolysis (since they cant go into Krebs)
go into either alcoholic fermentation (yeasts) or lactic acid fermentation (humans)
Next stage: Krebs Cycle aerobic (requires oxygen). Needs 2 ATP, generates reduced e carriers
Last state: Electron transport chain aerobic. Produces 34 ATP

Glycolysis
Investment Phase: glucose is phosphorylated & converted to glyceraldehyde 3-phosphate, or GAP.
(also called phosphoglyceraldehyde, or PGAL). Requires 2 ATP.
Payoff Phase: GAP molecules are oxidized to pyruvate.
Each GAP makes 2 ATP (4 total) & an NADH
C6H12O6 + 2NAD+ + 2ATP + 4 ADP + 2 Pi
> 2 Pyruvate + 2NADH + 2ADP + 4 ATP
Step 1: Phosphorylation of Glucose (forms Glucose 6-Phosphate)
Glucose is phosphorylated by hexokinase, which requires ATP
Traps glucose inside the cell
Lowers intracellular glucose concentration to allow further uptake.
Irreversible! Regulated mainly by substrate inhibition.
Step 2: Phosphohexose Isomerization turns glucose to fructose
Catalyzed by the enzyme phosphohexose isomerase - turns
glucose-6-phosphate into fructose 6-phosphate (which is easier to
phosphorylate by PFK)
Product concentration kept low to drive rxn. forward.
First
step of glycolysis
(rather than being stored, e.g.)
Step
3:committed
Second Priming
Phosphorylation
Fructose-6-phosphate is phosphorylated by phosphofructokinase-1,
forming fructose 1,6-bisphosphate T
This step also uses ATP
Irreversible! Phosphofructokinase-1 is highly regulated by ATP and
other metabolites

Step 4: Aldol Cleavage of F-1,3-bP

Aldolase enzyme cleaves the F-1,3-bP into DHAP and GAP
Only GAP is the substrate for the next rxn though.. see step 5
GAP concentration kept low to pull rxn forward.
Step 5: Triose Phosphate Interconversion
DHAP is converted to GAP by triose phosphate isomerase,
which basically turns ketose into aldose.
GAP concentration kept low to pull rxn forward.

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Step 6: Oxidation of GAP (forms 1,3-bisphosphoglycerate)

GAP is phosphorylated by inorganic phosphate to produce1,3bisphosphoglycerate. Releases NADH in the process.
This is the first energy-yielding step in glycolysis
Catalyzed by glyceraldehyde 3-phosphate dehydrogenase
Thermodynamically unfavorable, coupled to next reaction to pull
forward

Step 7: First Production of ATP

1,3-Biphosphoglycerate donates P group to ADP to make ATP.
Were left with 3-Phosphoglycerate (the only difference between
this and GAP is that GAP has an H (aldehyde) on C-1 instead of O
Catalyzed by phosphoglycerate kinase
Thermodynamically favorable because of coupling to GAPDH rxn
Step 8: Migration of the Phosphate
Phosphate group moves from C-3 to C-2; 2-PG is more reactive.
Catalyzed by phosphoglycerate mutase
Mechanism:
1. Base catalyzed phosphoryl transfer: Phosphoryl
group is transferred from the modified phosphohistidine
of the active site onto C-2 of 3-phosphoglycerate,
forming 2,3 bisphosphoglycerate.
2. Acid Catalyzed phosphoryl transfer: That same
histidine then removes the phosphoryl group from
C-3, forming the 2-phosphoglycerate
Step 9: Dehydration of 2-PG to PEP
Alcohol group is removed, alkene formed, called
phosphoenolpyruvate
Catalyzed by enolase
Product concentration kept
low to pull rxn forward
Step 10: Second Production of ATP (and Pyruvate)
Pyruvate kinase catalyzes phosphoryl transfer from PEP onto ADP to make ATP
Loss of phosphate from PEP yields an enol that tautomerizes into ketone, forming
pyruvate

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Tautomerization: effectively lowers the concentration of the reaction product,

which drives the reaction forward toward ATP formation
Irreversible! Regulated by ATP, divalent metals, and other metabolites
Summary of Glycolysis
Used: 1 glycose; 2 ATP; 2 NAD+
Made: 2 pyruvate, 4 ATP, 2 NADH (must be reoxidized to NAD+ in order for glycolysis to continue)
Three irreversible steps:
1: Phosphorylation of glucose to form glucose-6-phosphate (catalyzed by hexokinase)
3: Phosphorylation of fructose-6-phosphate to form fructose-1,6-bisphosphate
(catalyzed by phosphofructokinase-1)
10: Phosphoryl group transferred from phosphoenolpyruvate to ADP, yielding ATP and pyruvate
(catalyzed by pyruvate kinase)

Gluconeogenesis
During the fed state, your body uses glycolysis to make energy from glucose.
During the fasting state, our body needs a way to pump glucose in the blood to keep it at a pretty
constant level. It does this in two ways.
1) Breaks down glycogen (in the liver) into glucose molecule. Unfortunately, this only lasts for
about 10-18 hours. So during an overnight fast, e.g. we need another way of making glucose..
2) Gluconeogenesis - uses precursor molecules from a non-glucose source (most commonly,
amino acids and lactate) to produce glucose.
Gluconeogenesis is almost the exact reverse of glycolysis except 3 glycolysis steps are irreversible.
The enzymes of the reaction can just change whether or not the rxn. is reversible; doesnt change G.
(1 / 10) Recall - in 10th step of glycolysis, the transfer of a phosphate from phosphoenolpyruvate,
PEP, to ADP produces pyruvate and ATP. This is irreversible. So in the corresponding first
step of gluconeogenesis, converting pyruvate to PEP requires 2 energy consuming parts:
Part 1: pyruvate carboxylase converts pyruvate to oxaloacetate (adds a carbon)
Requires ATP
Carboxylation uses a biotin cofactor (recall that biotin is a CO2 carrier)
Requires transport into the mitochrondria via malate
Part 2: phosphoenolpyruvate (PEP) carboxykinase converts oxaloacetate to PEP
Requires phosphorylation from GTP and decarboxylation
Occurs in mitochondria or cytosol depending on organism
(8 / 3) In the third step of glycolysis, fructose-6- phosphate is
phosphorylated to make fructose-1,6-bisphosphate by PFK-1. In
the corresponding step of gluconeogenesis, the enzyme fructose
1,6-bisphophotase.
Phosphotase is the opposite of a kinase; it removes P group!
(10 / 1) In the first step of glycolysis, glucose is phosphorylated
by hexokinase. In the corresponding last step of gluconeogenesis,
another phosphotase (glucose-6-phosphotase)is used to
remove the phosphate group and form glucose!
The glucose-6-phosphotase enzyme is also used in the
breakdowns of glycogen.
Some people are missing this enzyme, so they cant produce
glucose at all! Not from gluconeogenesis nor glycogen stores.
Such individuals are hypoglycemic

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Regulation of Glycolysis and Gluconeogenesis

There are both fast and slow acting forms of regulation.
Fast Acting regulations involves a couple principles:
Fast Acting - Le Chateliers Principle:
We can think about glycolysis as a series of equilibria. If we
suddenly have a big influx of glucose (say, from a piece of
cake), the rxns will shift towards breakdown of that glucose
and glycolysis is promoted.
When glucose levels have been low for a while, amino acids
start to break down into oxaloacetate, which then re-enters
the equilibria (in the 2nd step of gluconeogenesis as a
reactant!) & promotes formation of glucose via that pathway.
Fast Acting - Allosteric Regulation: activators & inhibitors bind at
not the active site on the enzyme.
Gluconeogenesis requires ATP, while glycolysis produces it.
ATP is a negative allosteric regulator of glycolysis!
So if we have tons of ATP around, it will inhibit glycolysis.
If were low on ATP, glycolysis will proceed uninhibited.
ATP thus acts on several enzymes in glycolysis.
Similarly, AMP is a negative allosteric regulator of gluconeogenesis! (acts on one enzyme)
High presence of AMP means the cell has used up, dephosphorylated most of its ATP
When this happens the cell wont want to go through energy consuming processes, so AMP
inhibits gluconeogenesis.
Hormonal Regulation - body produces specific hormones (which travel through the blood) to
regulate these metabolic pathways.
Hormones are usually released by the body when the body deviates from a set-point (in this case,
that point is the blood glucose level).
If the blood glucose level rises, insulin release is stimulated. If blood glucose levels fall, glucagon
release is stimulated. (This is sort of a macro-level of Le-Chateliers)
Insulin thus promotes glycolysis and glucagon promotes gluconeogenesis.
Cells in our body have particular receptors for hormones. When hormones bind, it causes a series
of reactions in the cell to modify enzymes involved in metabolic pathways. These modifying
reactions are often phosphorylation reactions.
Slow Acting - take advantage of transcriptional changes in the cell
changes in DNA > mRNA > proteins
This slow acting regulation allows the body to adapt to long-term changes

Pentose Phosphate Pathway

Alternative branch off glycolysis (this pathway uses glucose-6-phosphate, the product of step 1 in
glycolysis) as the starting point. It turns that G-6-P into the ribose-5-phosphate (a precursor for
DNA/RNA nucleotides) and produces NADPH, an electron carrier.
Theres lots of NAD+ in the body, and a lot of NADPH,
relative to other forms.
NADPH also gives electrons to anti-oxidants, which in turn donate
them to reactive oxygen species (ROS, are dangerous), to reduce
No ATP is consumed or produced!
There are two phases: oxidative and non-oxidative
Oxidative Phase - irreversible reactions
(1) Glucose 6 phosphate is oxidized to form lactone and NADPH
is byproduct. After this oxidation, another reaction with a different
enzyme uses water for form linear product, 6-phosphogluconate.

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(2) Next, a carbon is removed and CO2 is released, forming

ribulose-5-phosphate. NADPH is again a byproduct.
Non-oxidative Phase - these reactions are reversible!
Products and reactants can interconvert!
This allows different molecules to enter this pathway in different areas of the non-oxidative phase
and, if needed, they can be converted into more ribose-5-phosphate. (Although they cant go any
further back than that because oxidative phase reactions are irreversible.)
(3) Ribulose-5-phosphate is cleaved / converted into two different 5-carbon molecules, one of
which is ribose-5-phosphate, the precursor for DNA and RNA.
(4) The rest of the cycle is now made up of different options that depend on the cells needs. The
ribose-5-phosphate from step 3 is combined with another molecule of ribose-5-phosphate to make
one, 10-carbon atom.
Excess ribose-5-phosphate not needed for nucleotide biosynthesis is converted into other
sugars that can be used by the cell for metabolism.
The 10-carbon atom made from two ribose-5-phosphate is interconverted to create a 3-carbon
molecule and a 7-carbon molecule. The 3-carbon product can be shipped over to glycolysis if
it needs. That being said, recall that we can also work our way back up to another molecule in
this phase. So that 3-carbon molecule could also be shipped over from glycolysis and
transformed into ribose-5-phosphate for DNA and RNA production.
(5) The 3-carbon molecule and the 7-carbon molecule, from the interconversion above in step 4,
interconvert again to make a new 4-carbon molecule and 6-carbon molecule. The 4-carbon
molecule is a precursor for amino acids, while the 6-carbon molecule can be used in glycolysis.
The same reversal of steps in option 4 can happen here as well.
Summary: two most important products are NADPH and the ribose-5-phosphate sugar for nucleotides
oxidative phase uses 1 H2O, produces 2 NADPH and 1 CO2
non-oxidative phase produces ribose-5-phosphate
High levels of NADPH inhibit pentose phosphate pathway

Krebs Cycle and Oxidative Phosphorylation

Krebs Cycle
Recall: Glycolysis turns 6-C glucose into 2 3-C pyruvate
nets 2 ATP and 2 NADPH
occurs in cytosol, while Krebs occurs in mitochondrial matrix
In order to be ready for Krebs Cycle, pyruvate needs to be oxidized; CO2 is released and NADH is
formed from reduction of NAD+. Acetyl-CoA is end product.
catalyzed by pyruvate dehydrogenase complex
Use biochem for more notes

Regulation of pyruvate dehydrogenase complex regulates entry into citric acid cycle
Recall: pyruvate is 3-C, acetyl-CoA is 2-C
pyruvate is oxidized to acetyl CoA by pyruvate dehydrogenase complex.
Requires NAD+ and CoA as co-factors (reactants), releases CO2 and NADH (products)
This reaction is irreversible. acetyl coA cannot be turned back to pyruvate. This makes it appealing to
regulation (if you open them, the ball will keep rolling down the pathway).
Fatty acids can may Acetyl-CoA when broken down but, because of this step with PHC, they
cannot make pyruvate and thus cannot contribute to production of gluconeogenesis.

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This is why textbooks might say FAs cannot contribut to production of glucose (at least not most of
them)
Purpose of Acetyl-CoA:
entry into citric acid cycle, allows the molecule to be oxidized to CO2
and produce electron carrier molecules which go on to ETC to make
ATP
produces FA when ATP levels are high
Major form of regulation is allosteric regulation (binding of molecules not
at active site of PHC)
allows this step to assess whats going on in the body and what is
needed
accumulation of products > allosteric inhibitors
inhibitors that are products: A-CoA, NADH
non-product inhibitors, ATP and fatty acids
accumulation of reactants > allosteric activation
activators that are also substrates: CoA, NAD+, pyruvate
activators that are not substratse: AMP, Ca2+
Levels of ATP and AMP get at energy level of cell, tell cell if it needs to make more or has enough
and can slow down CAC. Having a low energy state in the cell (lots of AMP) alerts body to
produce more acetyl-CoA and activates PHC.
Exercising skeletal muscle involves the influx of lots of calcium. When youre exercising, your
energy needs go up, so this free Ca2+ in the cell is an alert that youre going to need more energy
and thus it activates PDC
Recall, Acetyl-CoA also produces fatty acids so if there are a lot of FAs in the cell, theres not as
much need to A-CoA
Regulation of Krebs Cycle
Acetyl Co-A is 2-C combines with OAA and is transformed before those two carbons are released
as CO2 in two different dehydrogenase steps isocitrate > alpha-ketoglutarate, and alphaketoglutarate > succinyl-CoA
Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2 H2O > 2CO2 + 3NADH + FADH2 + GTP + CoA + 3H+

Unlike glycolysis, which we can think of as on or off, the CAC is pretty much always on, but just to
different degrees. Its important for CAC to always run to some extent in order to deliver electron
carriers to ETC and make sure some level of energy is around
there are disease states that involve mutation states in glycolysis, but not really mutations of CAC
in any living individuals; its too important for life.
(1) Theres no hormonal control on CAC; its on regardless of whether were in fed or fasting state.
(2) Instead, its controlled by allosteric regulation. (allows CAC to adjust in a rather fast way to energy
needs of the cell.. figures out energy needs by seeing what molecules are floating around in the cell.
Three reactions in CAC have a large G and are largely irreversible:
OAA + citrate > citrate, by citrate synthase
isocitrate > alpha-ketoglutarate, by isocitrate dehydrogenase
alpha-ketoglutarate > succinyl-CoA, by alpha-ketoglutarate dehydrogenase
Allosteric inhibitors:
NADH inhibits all 3 enzymes (makes sense b/c its a product of the cycle. If theres a lot of it, it
signals that NADH production is faster than it can go through the ETC, so CAC should slow
down.)
ATP inhibits processes that produce energy, specifically it inhibits citrate synthase and
isocitrate DH
products within citric acid cycle can allosterically negatively feedback inhibit.
citrate - negative feedback inhibits citrate synthase
succinyl-CoA negatively feedback inhibits alpha-ketoglutarate DH and citrate synthase
Allosteric activators:

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ADP (signals the cell is running out of power and needs to produce more - activates same
enzyme that ATP inhibits: citrate synthase and isocitrate DH)
Ca2+ recall, our muscle cells require Ca2+ to contract. When were working out, we need
more energy for the contracting muscles. Ca2+ has been shown to activate isocitrate DH and
alpha-ketoglutarate DH
(3) Also regulated by substrate availability for example, if there isnt much Acetyl-CoA around, the
speed by which electron carriers are produced will slow.
ex: when citrate, under conditions of high ATP, shuttles a lot of its Acetyl-CoA into cytoplasm for
fatty acid synthesis. This takes A-CoA out of cycle and thus slows down CAC.
ex: if were starving, amino acids can break down into intermediates such as alpha-ketoglutarate
if you have more of that substrate around it will push the CAC to go faster

Oxidative Phosphorylation and the Electron Transport Chain:

Oxidative phosphorylation can be broken down into two phase:
(1) Oxidation of NADH and FADH2 (via complexes I - IV)
(2) Phosphorylation (via ATP synthase)
After Krebs Cycle, were left with 10 NADH and 2FADH2. Each NADH produces 2.5 (3), FADH
produces 1.5 (2). Why the difference? FADH2 electrons are at a slightly lower energy level.
Oxidation of NADH means losing electrons first step of ETC: NADH > NAD+ + H+ + 2e
Reduction of O2 to water last step of ETC: 2e + 2H+ + 1/2O2 > H2O
water is final electron acceptor
Over ETC, electrons get transported through different molecules (namely, QH2 and cyt.c) at each
transfer of electrons, they go down an energy level and release energy, which is used to pump
protons across the inner membrane of the mitochondria into the intermembrane space from the
matrix. (Recall: matrix is where CAC occurs and is really where all of our NADH is.)
By the time the electrons have gone down the ETC, a lot of H+ are in the intermembrane
space and a proton gradient is created (intermembrance space is more acidic) as well as an
electrochemical gradient (intermembrane space is more positive)
After gradient is created, those protons want to get back into the matrix they do so through ATP
synthase (because the membrane is impermeable to them). ATP synthase has two main parts,
connected by an axle.
As the H+ ions go through ATP synthase in the membrane, it causes the axle middle structure
to spin! As that inner axle spins, the outer shell is contorted (?) to squeeze the ADP and Pi
together to form ATP.
transfer of H+ protons selectively (via the ATP synthase enzyme) through the membrane is
chemiosmosis
adding of a phosphate group onto another molecule = phosphorylation
here its oxidative phosphorylation. direct phosphorylation of a substrate via an enzyme
without chemiosmosis or oxidation on = substrate phosphorylation
This happens on 3 different sites simultaneously.
Regulation of Oxidative Phosphorylation:
recall: purpose of OxiPhos is to produce lots of ATP
substrate phosphorylation can produce some ATP, but having the electrons shuttle down energy
levels allows the cell to produce lots of ATP efficiently.
Major regulation of oxidative phosphorylation is assessing energy needs of cell. If ATP levels are
high, oxidative phos is slowed down. but if lots of ADP compared to ATP, ETC picks up.
Oxidative phosphorylation is the common end pathway of aerobic respiration (no matter whether you
start with glucose, fatty acids, or amino acids)

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theres no major hormonal or allosteric regulation is oxidative phosphorylation. those forms allow
us to fine-tune regulation but oxidative phos is downstream from so many pathways that its
possibly not as important to fine tune (its more just getting the ball rolling down the hill.)
Le Chateliers is very relevant
Recall: NADH carries 2 e- and gets oxidized at ETC to become NAD+. These 2 e- end up (through a
complex process of chemiosmosis and ATP synthase) making ATP from ADP. And then the electrons
go on to reduce oxygen to water.
If NADH, ADP, or Pi are increased, the pathway of oxidative phosphorylation will go faster. ADP is
most important of these, though.
If ATP or NAD+ is at high levels, the ETC (and thus ATP production) is slowed. But like before,
ATP is more important than NAD+
Mitochondria, Apoptosis, and oxidative stress:
apoptosis: programmed cell death
necrosis is another type of cell death, we generally classify this is as an uncontrolled type of cell
death, usually in response to extreme stress like an infection or trauma
in contrast. apoptosis is considered to be more controlled, and even though the cell is dying it will
benefit the body / system in some way.
How / when is apoptosis triggered:
Development (ex of apoptosis in developent: early in our development, our hand just sort of
looks like a blob of knuckles.. through apoptosis the cells in between those knuckles die and
we get 5 distinct fingers.)
DNA damage (the cell has mechanisms in place to repair damage, but the damage might be
too damaged or repair may be impossible). good because we wouldnt want a damaged cell
passing on damaged DNA
Infection - especially by viruses (often times, our immune cells see theres specific proteins on
cells that mean theyre infected by viruses. immune cells send signal to infected cell to
program cell death
Stress - due to deprivation of oxygen, nutrients, or disruption of cell-to-cell connection
many cells are often receiving signals from growth factors. if these are taken away as
well, the cell might see it as a reason to go into programmed cell death.
Reactive oxygen species (ROS)
ROS are oxygen species that have acquired extra electrons are are unstable.
ex: superoxide O2 OH (no negative charge = only 1 lone electron)
H2O2
oxygen is important in cell because it is final electron acceptor in oxidative phosphorylation, but about
1/4 are improperly (partially) reduced leads to production of ROS
How to prevent interaction between ROS and important stuff in cell? some enzymes and antioxidants
try to turn it into other things and trap it, respectively
All ROS have an effect on mitochondria, which plays a role in initiating apoptosis. (mitochondria
membrane becomes more permeable than before).
the BCL-2 family of protein makes this happen
Proteins can be pro-apoptotic or anti-apoptotic, these activate and inhibit the process, respectively.
When things are going well in the cell and is not receiving apoptotic signal, balance is in favor of antiapoptic proteins; they prevent mitochondria from initiating apoptosis. When the mitochondria receive
signals downstream from apoptotic signals, balance shifts in favor of pro-apoptotic protein which
favors increase permeability of outer mitochondrial membrane.
Why increase permeability? Allows cytochrome c to exit intermembrane space and enter
cytoplasm. Cytochrome C also is part of oxidative phosphorylation; helps shuttle electrons
between complex III and IV. Cyt C molecules in cytoplasm acivated caspases (c-asp-ase) in
the cytoplasm.. these enzymes break down proteins after the aspartate residue with a cysteine
reside.

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Apoptosis utilizes caspase enzymes but necrosis doesnt. These caspase enzymes cascade; their
activation of one protein will cause that protein to go on and activate/degrade another, and on and on.
Will also activate other types of enzymes, like nucleases (break down DNA). The degradation of all
these polymers inside the cell can be recycled to surrounding cells. Neighboring cells will use
phagocytosis to eat up the nucleotide base and amino acids and things from degraded cell to use in
their own cell.
Calculating ATP produced in cellular respiration:
There are two main ways to produce ATP substrate level phosphorylation (such as by kinases,
where a phosphate group from an intermediate/substrate is just added to ADP) and oxidative
phosphorylation (via ETC & chemiosmosis where ATP synthase brings P and ADP group together
)
NADH produces 2.5 ATP; FADH2 produces 1.5 ATP
If we use the 3 and 2 rounding, we get 38 ATP produced total for one molecule of glucose
Otherwise we get 32.
Four main complexes in the electron transport chain.
complex 1 = 4 H+ pumped across
complex 2 = 0 H+ pumped across
complex 3 = 2 H+ pumped across
complex 4 = 4 H+ pumped across
NADH enters in complex 1; FADH2 enters in complex II
thus NADH is responsible for 10 protons being pumped across and FADH2 is responsible for 6.
How many protons are necessary to produce one molecule of ATP? ~ 4 H+
This is where we get the 1.5 and 2.5 numbers for FADH2 and NADH, respectively
Recall: Glycolysis takes place in the cytosol (unlike pyruvate ox and oxi phosphorylation). So NADH
from glycolysis must be able to transfer / shuttle into the mitrochondria for the electron transport chain.
Depending on when the NADH is shuttle into the ETC, it might arrive at complex I or complex III in
the ETC, which would produce a different amount. (so the amount of NADH made from glycolysis
is 3 - 5 (so total ATP is 30-32)

Fatty Acid and Protein Metabolism

Intro to Energy Storage:
Our body stores fuels so were not 100% reliant on when we intake food. How does it store?
Glycogen: stores carbohydrates (is just a long polymer of glucose)
mostly stored in the liver, some in muscles
in a health 70kg male, there would be about 480g of glycogen in his body
we can extract about 4 kcal of energy per gram of glycogen
recommended avg. intake of energy is ~2000 kcal per day
Proteins: polymer of amino acids
mostly in muscles
A healthy 70kg male would have ~6000g of protein in his body
we can extract about 4 kcal of energy per gram of protein
Fats = major source of storage fuel
mostly found in adipose tissues
A healthy 70kg male would have ~12000g of fat in his body
we can extract ~ 9kcal per gram of fat
Lets assume the 70kg guy required 2000 kcal per day.
How long would this man be able to survive (theoretically)
on each gram of fuel?
glycogen ~ 1 day; proteins ~ 12 days; fats ~60 days
Chemical structure of fat: triacylglyceride

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acyl side chain is C=O attached to R functional group

if there are all single bonds saturated
if any double bonds unsaturated
glyceride is the backbone: three CH2, which each have an O linked to acyl group
very reduced molecule
Why are fatty acids such good storage molecules?
(1) bulk of molecule is formed by these carbon-hydrogen chains; theyre high energy because they
are more reduced - have lots of electrons in their bonds. (We can extract this energy by oxidation,
and that energy can be harnessed through ETC)
(2) inert less likely to react with other molecules in the body (energy won't be wasted in side
reactions); theyre not soluble in water
(3) they dont have any other major functional role in the body (like how proteins make enzymes)
their main role can be just to store energy and we wont use them up for other needs.
(4) unlike carbs and proteins, triacylglycerides are more hydrophobic. This makes them inert but
also means they wont be weighed down by water
ex: How many grams of glycogen from water weight alone will we have if we want to have kcal
equal to the 12,000g of fat that the avg 70kg man can produce.
(3 g of water weight / g of glycogen)
12,000g of fat can product ~10 kcal/gram, so that fat can produce 120,000kcal
To account for glycogens water weight, divide 120,000 by 4kcal/g of energy from glycogen,
and multiple that by 3g H2O per gram of glycogen. 90,000g H2O would need to be involved in
same energy production as 12,000g fat - not practical. this is more than 100% of body weight.

How are fats digested, transported, and stored?:

Digested food goes down esophagus and enters stomach, mixes with acid, and then enters small
intestine. Small intestine has many loops repeating, giving lots of surface area for absorption of
nutrients.
Intestine is lined with epithelial cells (can absorb nutrients), and contains lipase enzymes to break
down the fats (some of these lipases are secreted by pancreas and others are just found on border of
epithelial cells).
The intestine is an aqueous environment, but triacylglycerides are hydrophobic; theyll want to just
cluster together instead of breaking up and dissolving into the aqueous environment.
to combat this, the liver secretes bile, which is basically a detergent for our food. Bile has both
hydrophobic and hydrophilic parts, so it can emulsify the fats and break them up so they can then
be digested by lipases.
Lipase enzymes cleave the fats at the ester linkage by adding an H2O molecule at each of those
bonds. We now have a triglycerol backbone with 3 hydroxyl groups, and 3 free carboxylic acid group
w/ hydrocarbon chains (called fatty acids).
Now how do we deliver these fatty acids to our body? Once they get into the epithelial cell, theyre
turned back into triacylglycerides. Then a lipoprotein packages these TAGs (and other hydrophobic
substances that the body absorbs, like cholesterol) into its body. These lipoproteins have polar heads
so can interact with aqueous environment in bloodstream, but still have hydrophobic environments to
hold fats in.
chylomicron = the lipoprotein made in epithelial cell
Recall that all epithelial cells are surrounded by capillaries, so they have a source of nutrients.. but
theyre also surrounded by lymphatic capillaries called lacteal.
Capillaries have tiny fenestrations / gaps to allow absorption of proteins and carbohydrates, but
these are too small to absorb chylomicron.
Lacteal capillaries, however, have much larger gaps and can take up the chylomicron molecules.
Where do these lacteal capillaries go? All over, but most of our body drains them into lymphatic
ducts (mostly the left one) near our neck and shoulder, which then empty into veins.

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Once these chylomicrons are formed in epithelial cells, absorbed into the lacteal capillary, travel
throughout the lymphatic system and are deposited near shoulder, they travel from the veins into the
arteries, and eventually make their way to the capillary beds, where these fats are absorbed.
We know that capillaries are situated next to many tissues, and theyre how these tissues get their
oxygen and nutrients. How are the fats in the chylomicron liberated and absorbed?
Lipoprotein lipase enzymes in the capillary bed essentially take the TAGs in the chylomicron and
break them up into individual fatty acids and free glycerol backbone. These enzymes are activated
by a specific protein on the chylomicron, and also activated by insulin (which is increased in
response to an influx of glucose in your body).
Nearly all tissues can take up fats from these capillaries and use them to extract ATP:
exception: brain (FAs dont cross blood brain barrier) and red blood cells (dont have mitochondria)
Muscle cells do take up FAs, and adipose cells especially do. Adipose cells eventually turn these
FAs back into TAGs and store them as big fatty droplets in their cells.
At the end of the the chylomicrons journey through the capillary bed, after lipoprotein lipase breaks
free the TAGs inside (most of which are absorbed by adipose cells), were left with a chylomicron
remnant. There might still be some TAGs and some cholesterol in there; it still contains useful things.
This is where our liver now plays a big role.
Recall, in the small intestine, we have not just FA breakdown, but also the breakdown of
carbohydrates and nucleic acids and proteins.. these are small enough to enter the adjacent
capillaries directly, rather than lymphatic capillaries (lacteal) and eventually all those capillaries funnel
into a vein that goes directly into the liver.
This means everything absorbed in the small intestine (except fats!) passes through the liver.
So after we eat a big meal and all these broken down products end up in the liver, the liver turns a lot
of the glucose into ATP and/or glycogen (which is stored in liver, remember). If we still have glucose
left after enough of that is made, its turned into fatty acids via fatty acid synthesis (see below).
The liver has a similar functionality to the small intestine in that it can turn these fatty acids back into
TAG molecules and package them into special protein carrier molecules (similar to chylomicrons) with
cholesterol and things called VLDLs (very low density lipoproteins).
VLDLs contain a protein shell with fat molecules inside, both those newly made by glucose and
those from the chylomicron remnants! And thus the liver connects these pathways.
Just like the chylomicron left the small intestine to travel to the capillary beds where it is acted upon by
lipoprotein lipase, when VLDLs arrive at the capillary bed from the liver, they can also be acted on by
the lipoprotein lipase to release fatty acids and cholesterol to cells.
What happens to the fat stored in the adipose cells?
Adipose cells have receptors on their outer membrane that can detect hormone receptors.
After weve just eaten a big meal, levels of insulin increase. A few hours after a meal, insulin levels
decrease and glucagon levels increases.
Decrease in insulin and increase in glucagon can stimulate adipose hormone receptors, which send
signals throughout their cell and tells it to release all the FAs from TAGs into the blood stream.
hormone sensitive lipase - enzyme that catalyzes breakdown of TAGs in adipose cells in
response to changing hormone levels
These fatty acids (hydrophobic) diffuse down their gradient from adipose cells into the blood
stream and, once in the blood, travel alongside long proteins called albumin (also made in the
liver). Albumin proteins help the FAs dissolve in the aqueous environment of the blood.
Once FAs are traveling in the blood, most cells can take those up to produce ATP (to sustain them
when they dont have immediate influx of fuel like glucose from a meal)
The liver is one of the biggest consumers of fatty acids, because the process of gluconeogenesis in
the liver helps the body maintain blood glucose levels during times of fasting, and it requires a lot of
ATP. The major fuel to make ATP for gluconeogenesis is fats.

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Note: B/c we dont want to waste any of the energy produced in gluconeogenesis, the process of fatty
acid synthesis (converting glucose to FAs) is also hormone sensitive; it stops when insulin levels fall!

FATTY ACID SYNTHESIS

Ultimate goal in fatty acid synthesis is for the body to deliver triacylglycerides (TAGs) or free fatty
acids (FFAs) into the blood stream so they can reach capillary beds and diffuse to surrounding
tissues, where they can be absorbed and oxidized to obtain ATP.
There are 3 main sources of TAGs for FFAs.
(1) Diet the small intestine digests and packages TAGs into chylomicron which travel through
lymphatic system but eventually make it into the bloodstream and into capillaries. see above.
(2) Adipose Cells specialized cells in our body that can store large amounts of fat. Several
hours after a meal, when insulin levels begin to drop and glucagon levels begin to rise, adipose
cells release FFAs into the bloodstream. These FFAs travel alongside albumin cells (special
protein) in the blood to get to capillaries.
(3) Liver Liver cells are especially equipped to convert extra glucose (not used in glycogen
synthesis nor oxidized via glycolysis to make ATP) into fatty acids. Then, like the small intestine,
the liver packages them into TAGs and puts them in VLDLs with cholesterol. Those VLDLs travel
through the blood and eventually make it to the bloodstream and capillary bed, where they are
absorbed by surrounding cells. (Including maybe by adipose cells which can release them later)
Well focus on this third point here.
Recall that glucose enters cells through the bloodstream and begins glycolysis in the cytoplasm of
cells. The end product of this is pyruvate (two 3-C molecules). Pyruvate is then actively transported
across the mitochondrial membranes and once it enters mitochondrial matrix, the enzyme pyruvate
dehydrogenase decarboxylates and oxidizes it to turn it into Acetyl-CoA.
A-CoA then goes into the Krebs cycle.. It first combines with oxaloacetate to make citrate, which
then undergoes more transformations (including being decarboxylated twice and producing 3
NADH and 1 FADH2 for each pyruvate) to eventually reforms OAA. The electron carriers produced
during this cycle go to ETC.
Acetyl-CoA that can be used in the Krebs cycle is also a precursor for FA synthesis but Acetyl-CoA
is made by Krebs in the matrix, while FA synthesis occurs in the cytoplasm
In order to to get Acetyl-CoA back into the cytoplasm, it must be first turned into citrate (by again
combining with OAA) via the citrate synthase enzyme. Citrate is transported into the cytoplasm and
citrate lyase cleaves it back into OAA and A-CoA.
The remaining OAA can then be decarboxylated and oxidized to pyruvate (via the intermediate
molecule malate), reducing and NADPH molecule in the process. The resulting pyruvate is then
transported back into mitochondria so the cycle can continue.
Recall: NADPH (2 of them) are also produced via the pentose phosphate pathway
Overview of fatty acid synthesis: Acetyl-CoA + 7 malonyl-CoA + 14 NADPH + 14H+
> Palmitate + 7 ADP + 7 CO2 + 8 CoA + 14 NADP+ + 6 H2O
NADPH is important in reducing the oxidized carbonyl group in A-CoA
First step of FA synthesis is to charge up Acetyl-CoA into Malonyl-CoA
This is thermodynamically unfavorable, and thus it requires one ATP molecule. (note: were
charging it up with a CO2 molecule, though,not a phosphate.) Malonyl-CoA is 3-C
enzyme used in this first step is Acetyl-CoA carboxylase
In the next steps, the CO2 molecule of Malonyl-CoA pops off (its real purpose was just to make the
rxn thermodynamically favorable), a water molecule is also lost, and 2 NADPH are used to reduce the
chain. These steps continue until weve built the 16-C palmitate FA chain
Detail: when the malonyl is decarboxylated, its CH2 becomes very electronegative. CH2 then acts
as a nucleophile to attack first carbon (the one attached to thiol bond) of the FAS, causing the
acetyl group to disassociate from the FAS subunit and bind to the carbon of the malonyl. This
growing chain is now on ACP subunit and new Acetyl-CoA binds.

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Enzyme complex used is fatty-acid synthase, with ACP & FAS subunits that each have a thiol
group. Acetyl-CoA attaches to FAS, but Malonyl-CoA is attached to ACP (note that these reactan t
molecules actually lose the CoA subunits with then bond with the enzyme.
The first step, conversion of Acetyl-CoA to Malonyl-CoA
is the big regulating step, largely because it is the ratelimiting step (it has the slowest kinetic energy).
allosteric regulation:
Citrate is allosteric activator. If theres more
citrate in the cytoplasm that means there is (or
will be shortly) more Acetyl-CoA, which should be
used for FA synthesis
Fatty acids (especially long chain) are allosteric inhibitors, basically a form of product inhibition
hormonal regulation:
Insulin activates FA synthesis
Glucagon inhibits FA synthesis. Recall, glucagon levels rise several hours after a meal. If
glucagon is elevated, that means we need to make more glucose. Without an excess of
glucose, we wont have excess Acetyl-CoA (product of breakdown of glucose) nor an excess
of fatty acids (made from glycerol or DHAP) to form triacylglycerides. In addition, glucagon
signals adipose cells to release TAGs into the bloodstream for degradation; we wouldnt want
to simultaneously break down and synthesize FAs.
Eventually a 16-C palmitic acid is the FA formed; when its done one of the H2O groups is used to
cleave thioester bond on ACP and the palmitic acid is released. This palmitic acid can then go on
to be added (with 2 other FA) to a glycerol backbone to form triacylglycerol
Note: the longer the hydrocarbon tail & the fewer unsaturated bonds of a FA, the more energy it has
FATTY ACID OXIDATION
Overview of ATP production
95% of the energy we can extract from triacylglycerides come from the CH bonds in the fatty acid
chains. The remaining 5% comes from the glycerol backbone.
In fatty acid oxidation, we break down the chain into 2-C Acetyl-CoA molecules, extract the energy of
oxidation through NADH and FADH2 which can be used to make ATP in ETC
Remember, Acetyl-CoA is what can enter the Krebs cycle, through which even more NADH and
FADH2 is reduced. Amount of ATP produced through fatty acid catabolism is huge!
For each run through Krebs cycle, we produce a net of about 10 ATP per Acetyl-CoA molecule; so
breaking down 16-C palmitic acid means we get ~80 ATP through the Krebs cycle alone. Add that
to the 27 ATP produced through fatty acid oxidation (breaking down the chain into A-CoA), and we
get a whopping 107 ATP from the oxidation of palmitate & subsequent Krebs cycle.
Compare this to the oxidation of one molecule of glucose, about 30-32 ATP.
Steps of Fatty Acid Oxidation
Fatty Acid synthesis takes place in the cytoplasm, because fats are absorbed from bloodstream to
there. But (like the Krebs cycle), FA oxidation occurs in the mitochondrial matrix we need a way to
transport fatty acids across mitochondrial membranes, which first requires activation.
There are three major phases to FA oxidation:
(1) Activation FA molecule is reacted with Co-A molecule to make fatty-acyl CoA (bonded at thiol)
Catalyzed by Acyl-Synthetase, an enzyme that is on the outer mitochondrial membrane (OMM)
This rxn is coupled to hydrolysis of ATP > AMP + P-P. The pyrophosphate produced
immediately reacts with water; this has high -G and is useful in reducing [product] to drive the rxn
forward.
(2) Transport - A carnitine molecule in cytoplasm has a hydroxyl group that attacks the C of fattyacyl CoA chain. The S-CoA moiety leaves. Now we have carnitine bonded via O to fatty acyl chain.
Catalyzed by carnitine acyl transferase I, which is also located on OMM
OMM is a bit more permeable to molecules than IMM; it contains porin proteins (basically pores).
The Acyl-Carnitine complex travels into the intermembrane space through such porins. To get

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from the intermembrane space to the mitochondrial matrix, the acyl-carnitine travels through a
transporter protein within the IMM called acyl carnitine translocase.
Once in the mitochondrial membrane, a CAT II enzyme on the matrix side of IMM catalyzes the
reverse rxn of CAT I it takes a CoA molecule from matrix (whose S atom serves as nucleophile
to attack C of fatty acid) and remakes fatty-acyl-CoA, releasing free carnitine to travel back across
the membranes into the cytoplasm for reuse. (Works because for every acyl-carnitine complex
that goes through the translocase enzyme into the matrix, a free carnitine is sent the other way.)
(3) Oxidation basically a cycle of four steps:
a) Dehydrogenation of fatty-acyl-CoA, forms double bond. FADH2 formed.
b) Hydration of double bond (water used), forms alcohol.
c) Dehydrogenation of alcohol forms ketone. NADH + H+ formed.
d) Cleavage by a thiolase (CoA-SH moiety used), thus producing A-CoA.
At the end of this cycle of 4 steps, we end up with an Acetyl-CoA molecule and an acyl-CoA chain
that is two C shorter than before. The FADH2 and NADH formed can go right to ETC, conveniently
located on the inner mitochondrial membrane!
note: called oxidation because its the carbon (2 C away from the C=O) thats being oxidized.
Regulation of FA oxidation
The rate limiting step is reaction with carnitine molecule to form Acyl-Carnitine complex.
Malonyl -CoA is an allosteric inhibitor of Carnitine Acyl Transferase I. Makes sense because
if we have a lot of malonyl-CoA, it means were synthesizing a lot of FAs, so we dont want to also
be breaking them down. Inhibiting CAT I ensures we have a net production of FA molecules.
Using this substrate of FA synthesis to regulate an enzyme in FA oxidation means the body has
essentially made these two pathways mutually exclusive; theres no gray zone.
Having the different compartments also regulates this oxidation by keeping the reactions separate

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HOW DOES THE BODY ADAPT TO STARVATION?

How does the body utilize the major energy storage fuels? What are ketones? Why cant fatty acids be converted to glucose?

In order to survive, the body must maintain proper blood glucose levels, even in periods of starvation.
(1) 3-4 hours after a meal, the body can simply turn to the glycogen storage in the liver and break it
down to get glucose. But humans only have enough glycogen to last about a day.
(2) After a day, the body relies on gluconeogenesis to produce glucose from non-carb molecules.
Remember, gluconeogenesis is basically the opposite of glycolysis, the end product of which is
pyruvate. If we can get pyruvate from other catabolic processes, we can turn it into OAA and then
into phospho-enol-pyruvate (PEP) and then eventually get back to glucose.
What types of molecules can contribute to this glucose production?
A) not Fatty Acids breakdown products of FAs cant contribute to gluconeogenesis!
Major product formed in FA catabolism is Acetyl-CoA, which is also entry point into Krebs
Cycle In Krebs, A-CoA combines w/ OAA to make citrate, ends up losing those two carbons
of A-CoA as 2 CO2 & it cycles back to OAA. This produces NADH and FADH2 for energy.
Although it can be used to make ATP via Krebs, Acetyl-CoA cannot be turned into pyruvate
to make glucose (the pyruvate > A-CoA rxn is very exergonic). It also can just go through
Krebs to make OAA that then enters gluconeogenesis, because the carbons of A-CoA are lost
during the cycle as 2 CO2 molecules.
note: some odd-chain fatty acids can be converted to Krebs cycle intermediates and enter
gluconeogenesis (odd-chains release one propionyl-CoA, a 3-C molecule which can then be
converted to succinyl-CoA).. But on the whole, we think of FAs as not contributing to
gluconeogenesis because A-CoA is the primary reactant of FA synthesis or of Krebs.
B) yes Amino Acids breakdown products of AAs can contribute to gluconeogenesis!
Many products of AA catabolism are intermediates of the Krebs cycle, which eventually form
OAA, which can then be formed into PEP and get into gluconeogenesis pathway.
Some AAs can also be turned into pyruvate, which also allows them to enter gluconeogenesis.
note: there are a few AAs that are exclusively turned into A-CoA when catabolized; these
would not contribute to gluconeogenesis in same way that A-CoA from FA catabolism doesnt.
Downside to breaking down AAs for energy is that AAs make up many important proteins /
enzymes, they comprise the bulk of our muscles, etc. and we need our muscle mass & enzymes!
(3) After a few days of starvation, we save our proteins! Tissues that rely exclusively on glucose for
energy (like the brain) can then use a different fuel called ketones to produce ATP for their cells.
Unlike AAs, these ketones are water soluble enough to cross the blood brain barrier.
Remember that in times of fasting, glucagon levels rise & insulin levels begin to drop. This
stimulates our body to (undergo gluconeogenesis & release FAs from adipose cells, as well as)
start breaking down FAs via -oxidation. FA catabolism occurs primarily in the liver and leads to
lots of Acetyl-CoA molecules.
In the beginning, a few hours to a day after our last meal, our body is working to store up A-CoA
molecules so they can enter the Krebs cycle and eventually produce lots of ATP.
Two-three days after fasting, A-CoA molecules rise to a level above what is needed for ATP
production. This happens because theres no type of product inhibition for FA oxidation like there
is for glycolysis or other pathways, and because ATP is a big regulator of ETC. (So the large
amounts of ATP that acetyl-CoA produces will signal the ETC to slow down, which means well
have increased levels of electron carriers like NADH that will then signal the Krebs cycle to slow
down, which means less A-CoA is consumed) ultimately, A-CoA levels will rise.
The extra Acetyl-CoA that develops 2-3 days after starvation can be turned into ketones in the
liver. These ketones will eventually leave the liver to enter the bloodstream, so other tissues like
the brain can then take them up, convert them back to acetyl-CoA, & use them for ATP
production.

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Several days after body shifts to making ketones, it puts less pressure on the body to use
gluconeogenesis, which means theres less pressure for amino acids to be broken down. Protein
degradation only really occurs in the first few days of starvation. After that, body shifts to use more
ketones as energy.

AMINO ACID METABOLISM

How the catabolism of AAs is unique from that of glucose and FAs

Amino acid metabolism only accounts for about 10-15% of our cells total energy production.
Fed state right after a meal has elevated insulin levels; decreased glucagon levels
Fasted state several hours after a meal has decreased insulin levels and elevated glucagon levels
Fed State
Recall that we ingest proteins from our food, which are broken down into amino acids in the small
intestine. (Essential amino acids = those that our body cannot produce and we must get from diet)
Once the AAs are broken down, they travel through bloodstream directly to the liver (like glucose)
Liver enzymes can then:
a) use these AAs directly for protein synthesis
b) convert excess amino acids into storage molecules of glucose (by making glycogen) and/or
fatty acids (by making triacylglycerides)
c) send the amino acids to other tissues (e.g. muscles) for their own protein synthesis
(b) The carbon backbone of AAs can be metabolized directly into precursor molecules for glucose &
FAs. You might hear an amino acid described as glucogenic or ketogenic. This refers to whether the
AA backbones feed into precursors of glucose synthesis or fatty acid synthesis, respectively.
Precursors for glucose are pyruvate and oxaloacetate (which is in equilibrium with Krebs cycle
intermediates). Glucogenic amino acids break down into pyruvate, OAA, and Krebs intermediates
Precursor for TAGs is acetyl-CoA (which is in equilibrium with acetoacetyl-CoA). Ketogenic amino
acids break down into Acetyl-CoA and aceto-acetyl CoA
Two amino acids are exclusively ketogenic: Lysine and Leucine (which, remember, means they
dont contribute to glucose production). Other AAs may contribute to just glucogenic pathways, or
to both.
Fasted State
Recall that in the fasted state, increased glucagon stimulates release of FAs from adipose tissues,
which are then sent to the liver for oxidation & and resulting ATP can be used to make glucose.
If a person is in severe starvation, they might be producing ketones from the A-CoA as well.
In starvation, amino acids are also released from our tissues and sent to the liver, where they can
enter a diverse array of metabolic pathways (see (b) above).
major products of AA catabolism are ketone bodies and glucose
glucogenic amino acids could support production of intermediates of gluconeogenesis and thus
contribute to production of glucose during times of fasting. Their carbon backbone is important for
glucose synthesis
ketogenic AAs that become intermediates of the Krebs cycle might contribute to ATP production
(like FAs), but remember only 10-15% of our total energy production is supplied by amino acids.
These ketogenic AAs could also make A-CoA & contribute to ketone synthesis, but remember
the purpose of ketones is to preserve degradation of protein in the muscles so we can switch
to more sustainable fuel. We think about A-CoA for ketones as mostly coming from FAs.
Unique to the breakdown of proteins is the presence of a nitrogen in the amine group (NH3+)
In fact, first step of AA catabolism is the transamination of this group to another molecule, freeing
up a carbon backbone (in the form of an -keto acid) to contribute to rest of metabolic pathways.
The common molecule that accepts the amine group is -ketoglutarate, which is an intermediate
of Krebs cycle. Upon accepting the amine group, it becomes the AA glutamate.

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When this glutamate reaches the liver, it can then donate the amine group in the form of ammonia
(NH3), which will enter the urea cycle. The urea cycle in the liver converts ammonia to urea, which
is then excreted in the urine. (Important to excrete this because ammonia is toxic at high levels)

The Endocrine System

ENDOCRINE GLAND HORMONE REVIEW
How do different parts of the body communicate with each other? Some communicate through
nerves, but not everything is connected by nerves. The endocrine system connects everything!
Endocrine system is a system of glands that secrete hormones (chemical messages) and release
them into the bloodstream so they can circulate to different parts of the body and initiate an effect.
Hypothalamus major endocrine gland in the forebrain, is about the size of a grape
Is a member of the forebrain, and thus receives many nerve signals from the brain.
called control center b/c it directs pituitary and plays a dual role b/n nervous & endocrine system
In addition to stimulating the pituitary gland, the hypothalamus makes hormones:
ADH - antidiuretic hormone, mainly regulates fluid volume in our body
Oxytocin stimulates uterus to contract for females during pregnancy
note: although the hypothalamus makes these, they are stored in and secreted from the
posterior pituitary gland.
Pituitary gland right below the hypothalamus, is about the size of a green pea
called master gland because it takes signal from hypothalamus and directs it to almost all the
other endocrine glands such that their function is ultimately dependent on the pituitary
Thyroid gland located in the neck, wraps around trachea (windpipe)
receives signal from pituitary and regulates metabolism through thyroid hormones T3
(triiodothyronine) and T4 (thyroxine); it uses these to stimulate the bodys metabolism
Parathyroid - four spots, right behind the thyroid
responsible for regulating our bodys blood calcium level. (recall: calcium is involved in muscle
contraction, bone growth, and other important, sensitive functions)
Adrenal glands located on top of the kidneys
cortex (outer part): makes adrenal cortical steroids, such as cortisol and aldosterone
cortisol is a stress hormone that increases blood sugar in times of stress so we have energy;
also has anti-inflammatory functions
aldosterone is major regulator of our bodys blood volume
medulla (inner part): makes catecholamines such as epinephrine and norepinephrine, which
are involved in our bodys fight or flight response.
Gonads release sex hormones, which are mainly involved in development of secondary sex
characteristics and developmental stages associated with those characteristics (puberty, menopause)
ovaries in females produce estrogen and progesterone; testes in male produce testosterone
Pancreas isnt as directly involved with the pituitary as other glands but still uses those hormones
to stimulate an effect: control of the blood sugar
exerts this control through hormones insulin and glucagon
How do hormones get to their destination organs when theres so many hormones around the body?
Hormones wont be received unless theres a specific receptor on the target cell
The receptor and its location are important in determining hormone function
Hormone classes help us identify which hormones have which functions:
autocrine hormones function at the cell that makes them
ex: T cells in the immune system secrete leukine hormones that signal the T cell itself to
increase effectiveness and immune function
paracrine hormones function regionally
ex: hormones released by hypothalamus that affect the pituitary
endocrine hormones function at a distance
ex: pituitary gland stimulating the gonads

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HYPOTHALAMUS AND THE PITUITARY GLAND (AND THEIR HORMONES)

The pituitary has 2 parts, which the hypothalamus interacts with in different ways.
Hypothalamus gets signals from the brain and sends hormones / signals to different parts of the
pituitary. Hormones it sends include:
Gonadotropin releasing hormone (GnRH)
Corticotrophin releasing hormone (CRH)
Thyrotropin-releasing hormone (TRH)
Growth hormone releasing hormone (GHRH)
Prolactin inhibitory factor (PIF) unlike other hormones, PIH is constantly being released and
when it stops being released, the pituitary gland is signaled to release prolactin
Anterior pituitary hypothalamus interacts with this primarily through the hypophyseal portal
system, which is a capillary system into which the hypothalamus secretes hormones (these
hormones are thus of the paracrine class)
GnRH received by the ant. pituitary from the hypothalamus stimulates release of follical
stimulating hormone (FSH) and luteinizing hormone (LH), which travel to the gonads and
stimulate gonads to release their hormones
CRH from the hypothalamus stimulates the release of adrenocorticotrophic hormone (ACTH),
which travels to the adrenal gland and stimulates it to release its own hormones
TRH from hypothalamus stimulates anterior pituitary to release thyroid stimulating hormone
(TSH), which travels to thyroid and stimulates it to release its own hormones (T3 & T4, namely)
GHRH from hypothalamus stimulates anterior pituitary to release growth hormone (GH), which
travels to the long bones and big muscles in our body to stimulate growth
When PIH stops being released, thats when the pituitary gland is stimulated to release prolactin,
which is involved in milk production in moms
Posterior Pituitary hypothalamus interacts with this primarily through stimulation of nerves that
run down the pituitary stalk.
Nerve stimuli from the hypothalamus causes the posterior pituitary to release hormones that are
actually made in the hypothalamus but stored in the pituitary, including:
ADH (antidiuretic hormone) stimulates collecting ducts in the kidneys to retain water
Oxytocin involved in uterine contractions in women
Note: some anterior pituitary glands go on to stimulate other endocrine glands; others have a direct
effect on parts of the body. Use pneumonic FLAT PEG.
FLAT hormones (FSH / LH, ACTH, and TSH) are tropic hormones - they stimulate other
endocrine glads
PEG hormones (Prolactin, Endorphins (which are not unique to the anterior pituitary), and GH) are
direct hormones - they directly stimulate a part of the body
How are hormone concentrations regulated:
One of the ways hormone concentration is controlled is through metabolism and excretion:
liver metabolizes extra / unneeded hormones and turns them into bile, which is ultimately
excreted in the digestive system
kidneys filter your blood all the time and remove waste products in the blood through urine
blood some hormones are just broken down in the blood (and their products go on to the liver
or kidneys
sweat some hormones can just be sweat out
Concentrations are also controlled through negative feedback loops conditions resulting from the
hormones action suppress further release of those hormones
Example of negative feedback loop with thyroid hormones:
The hypothalamus releases TRH (thyro-tropin releasing hormone) into the pituitary gland and, in
response to TRH, the pituitary then releases its hormone TSH (thyroid stimulating hormone) which
travels to the thyroid gland.
The thyroid gland then releases its hormones T3 (triiodothyronine) and T4 (thyroxine), which travel
all throughout the body in search of their receptors to, e.g., upregulate metabolism.

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Some of the receptors of T3 and T4 are located on the pituitary gland and hypothalamus. When/as
the thyroid hormones reach those receptors, it signals the hypothalamus and pituitary to stop
producing TRH and TSH, respectively; more thyroid hormones are clearly not needed.
Why does the pituitary gland need to be turned off if the hypothalamus is? Redundancy is just
indicative of how important feedback regulation is.

TYPES OF HORMONES
Hormones can be classified by where they function (autocrine, paracrine, endocrine) and, more
importantly, can also be classified by their structure.
Structure is key to how a hormone works.
There are three major types of hormones based on structure:
(1) Proteins and Polypeptides
Made of amino acids linked by peptide bonds
P & P type hormones are most of the bodys hormones
They range in size from small (3 AA) to large (many hundreds of AA). After about 50 AAs, we go from
calling them polypeptides to proteins.
These are made in the rough endoplasmic reticulum (RER) of the cell and then go to the golgi
apparatus, where theyre repackaged into vesicles that can eventually be excreted from cell.
Because proteins and polypeptides are made of AAs, theyre typically charged. This makes them
water soluble but also makes it difficult to cross cell membranes. For this reason, P & P hormone
receptors are usually located in or on a cell surface
When they bond to a receptor, P & P hormones can initiate a response inside the cell by initiating
of a cascade of secondary messengers
ex: insulin is a relatively large protein hormone
(2) Steroids
largely used for signaling
made from lipids (mostly from cholesterol), and thus have a characteristic structure that they all share:
a four-ringed carbon backbone (three cyclohexane, one cyclopentane)
Because theyre made from lipids, steroids dont usually have a hard time entering a cell. Unlike
proteins and polypeptides (whose receptors are on the cell surface), the receptors for steroid
hormones are located inside the cell.
Steroids thus act as primary messengers; theyre doing the signaling themselves. Receptors are often
in the cytoplasm or the nucleus of the cell.
Steroids can effect change at the level of DNA transcription and translation, make new proteins form.
ex: hormones from adrenal cortex (cortisol, etc) and from gonads (testosterone, estrogen, etc.)
(3) Tyrosine Derivatives
Recall: Tyrosine is an amino acid.
Why is it not of the polypeptides and proteins type, then? Well, theyre only
made of derivatives from a single amino acid. Additionally, they
sometimes act like P & P hormones, but other times act like steroids.
Theyre a class of their own.
ex: thyroid gland hormones like T3 (triiodothyronine) and T4 (thyroxine); these stimulate metabolism
act very similarly to steroids
ex: catecholamines like epinephrine and norepinephrine, which are produced in the medulla and are
involved in our fight or flight response.
act very similarly to P & P proteins in that they bind to the outside of a cell and stimulate
secondary messengers inside the cell.

CELLULAR MECHANISM OF HORMONE ACTION

After traveling through the body, a hormone eventually reaches the receptor on a target cell

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One mechanism: action by secondary messengers Hormone binds to a receptor on the outside
of a cell. Instead of stimulating an effect directly, it sets off a chain of secondary messengers within
the cell that themselves stimulate the effect.
When hormone binds with receptor, it causes the receptor to change conformation and interact
with the G-protein to form a complex. When this happens, the GDP bound to G-protein is
transformed to GTP .
This transformation to GTP allows the G-protein to move through the membrane and activate the
adenylate cyclase. The adenylate cyclase then transforms ATP > cyclicAMP (cAMP).
cAMP is then what triggers the effect inside the cell that the hormone is targeting in the first place.
Signal amplification: in theory one hormone can bind to a receptor, which sets off chain reaction
leading to a lot of cAMP being produced.
Because we are unable to communicate directly
Second mechanism: action by primary messenger Certain hormones like steroids and thyroid
hormones can cross the cell membrane and effect change themselves.
Steroid and thyroid hormones can typically cross the membrane on their own because, unlike
other polypeptide hormones, e.g., they are lipid based.
Hormone crosses cell membrane and binds to a receptor in the cytoplasm or the nucleus.
When the hormone binds to this receptor, it directly affects transcription (if receptor is in nucleus)
or translation (if in cytoplasm) of the protein thats being activated by the hormone.

TERPENES, CHOLESTEROL, AND STEROIDS

Terpenes are a class of lipid molecules made from repeating isoprene units
An Isoprene unit has 5 carbons 4 are bonded in a chain, the 5th branches off a middle carbon
monoterperne = 2 isoprene units, forming 10-C molecule (ex: menthol)
sesquiterpene = 3 isoprenes form a 15-C molecule (ex: ginger)
diterpene = 4 isoprenes (essentially 2 monoprenes) form 20 carbon molecule
sesterterpene = 5 isoprenes form a 25 carbon molecule
triterpene = 6 isoprenes form a 30 carbon molecule (ex: squalene)
Biosynthesis of steroids using isoprene pyrophosphate (recall: pyrophosphate is a weak base and
makes a good leaving group)
Dimethyl allyl pyrophosphate and isopentyl pyrophosphate combine head-to-tail (displacing a
pyrophosphate in the process to make geranyl pyrophosphate, a 10-C molecule
Geranyl pyrophosphate combine head-to-tail to make a third isoprene to make a 15-C farnesyl
pyrophosphate; another pyrophosphate is released.
Two farnesyl pyrophosphates combine head-to-head to make 30 carbon squalene. Squalene is
the precursor for all the steroid hormones. After a series of ring-closing reactions, it turns into
cholesterol, a four-ringed molecule.
In the case of endocrine organs that use steroid hormones to communicate, cholesterol can be
altered to form the characteristic steroid backbone
Two important classes of steroids for endocrine glands: sex hormones and adrenal cortex steroids:
Sex hormones: estrogens (estradiol and estrone, made in ovaries); progesterone (pregnancy
hormone); androgens (testosterone, androsterone)
Adrenal Cortex: cortison and cortisol (stress hormones, have various effects from antiinflammatory to increasing carbohydrate metabolism); aldosterone (one of the main hormones that
regulates blood pressure and fluid volume).

Hormonal Regulation
TISSUE SPECIFIC METABOLISM AND THE METABOLIC STATES
Absorptive State series of reactions the body goes through when food is in plenty; youre absorbing
food in the intestines and you dont need to use (much) energy you just want to store it.

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Absorptive State = generally building up molecules and storing energy

In the liver:
Glucose enters from food can be stored as glycogen or converted to triglycerides (fat storage).
In order to convert glucose molecules to triglycerides, it must be converted to glycerol and fatty
acids. (fatty acids are made from pyruvate and acetyl CoA). Glycerol and 3 fatty acids can be
combined to make triglycerides, but those triglycerides are not stored in the liver and cannot
dissolve in blood. The liver packages them into very low density lipoproteins (VLDL) and
exports them.
Amino acids enter from food The liver breaks them down into -keto acids, a process which
gives off ammonia when broken down. The ammonia is then converted to uric acid and excreted.
The -keto acids themselves can go one of two ways:
-keto acids can be converted to fatty acids for storage, and then convert those fatty acids to
triglycerides (which are again packaged in VLDLs and exported).. OR
-keto acids can be broken down (if energy is needed) into acetyl-CoA, which can then go
through Krebs and ETC to produce ATP.
In adipose tissue:
Glucose enters from food is ultimately converted to triglycerides (fat storage), but like in the
liver must first be broken down and converted into glycerol and fatty acids.
VLDLs enter from bloodstream from liver are turned into fatty acids that can then be combined
with glycerol to make triglycerides, which are stored in adipose tissue.
In muscle cells:
Glucose enters can be converted to glycogen for storage, or can be converted to pyruvate
(through glycolysis) and then acetyl-CoA for energy production through Krebs and ETC.
Amino acids enter are stored as protein in the muscle
In the brain: we dont store energy, even in the absorptive state
Glucose enters is converted to pyruvate (through glycolysis) and then acetyl-CoA for energy
production through cellular respiration
Post-Absorptive State series of reactions that the body goes through when we havent had food in
a while and we need energy; we utilize the various forms of energy storage in the body (glycogen,
proteins, triglycerides, etc.) but first have to break them down.
Post-Absorptive State = generally breaking down molecules and releasing energy
In the liver:
Glycogen is broken down into glucose, which can then be exported through the blood.
Amino acids are still taken up by the liver and converted to -keto acids, a process which gives off
ammonia that can then be converted to uric acid and excreted.
-keto acids are used to make glucose (gluconeogenesis)
-keto acids can also be broken down further into acetyl-CoA which can be used to make ATP
Glycerol and fatty acids that were combined to make triglycerides in the absorptive state can be
instead turned into glucose.
Or, those fatty acids can be broken down to form ketones, an important metabolic intermediate
that is important because it can be used by the brain.
In adipose cells:
Triglycerides are broken down into glycerol and fatty acids which are then exported to the blood,
where they eventually get to the liver and can make more glucose.
In muscle:
Proteins are broken down into their amino acids, which are then exported into the blood where
they eventually find their way to the liver and can be broken down to form -keto acids; these are
then turned into glucose, a more useable form of energy
Glycogen is also stored in muscles, and in the post-absorptive state it is broken down into
glucose, which can be converted to pyruvate (through glycolysis) which can eventually produce
ATP through the ETC.

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Note, though, that this process requires oxygen. If these cells are low on oxygen, glucose is
broken down into lactate (via lactic acid fermentation) to produce ATP, though not as much
ATP as can be produced by cellular respiration. (lactic acid disturbs pH of the blood).
Brain like in the absorptive state, the brain takes up glucose from the blood, which it can convert to
pyruvate (through glycolysis) and then acetyl-CoA for energy production through cellular respiration.
In the post-absorptive state, the brain also takes up ketone bodies & breaks them down for
energy.

INSULIN AND GLUCAGON

Glucose is the most basic form of carbohydrates. Insulin regulates storage of glucose, while glucagon
regulates release of glucose from storage.
very important! The brain uses about 120g glucose / day.
Looking at a graph of glucose conc. vs. time; blood glucose level is constantly fluctuating between
70120mg/dL. This up and down is controlled by insulin and glucagon.
Any more than that is hyperglycemia.. if we have this for a long period of time, we get eye, nerve,
and kidney disease aka diabetes.
Less than 70mg/dL is hypoglycemia this is characterized by lethargy, but if it persists you can
go into a coma or even death. We start to notice when were at 40mg/dL
When you have a big intake of glucose / sugar, like after a meal, insulin decreases blood glucose by
storing glucose in another form.
Increases rate of glycolysis, an irreversible process that converts glucose to ATP.
Increases rate of glycogenesis, a reversible process that forms of glycogen (for short-term
storage) in the liver and muscle.
Increases lipogenesis, an irreversible process that converts glucose to fatty acids and TAGs for
long-term storage in adipose tissue.
When you have decreasing blood sugar (also not good), your body releases glucagon that releases
glucose from storage to keep levels within the sweet spot.
Releases glucose from glycogen by glycogenolysis (a reverisble process)
Releases (/makes) glucose from amino acids via gluconeogenesis (a reversible process)
Converts fatty acids into ketone bodies via ketogenesis (an irreversible process). This happens
during starvation mode. Ketone bodies are unique in that they are forms of energy that pretty
much can only be used by the heart and brain.
When insulin is released, it inhibits the release of glucagon

GLUCOSE, INSULIN, AND DIABETES

Body needs energy. It gets energy from glucose via the bloodstream but needs help of insulin to get
into the cells.
Cell surfaces have insulin receptors. When insulin binds to these, it opens channels in the
membrane that allow the glucose to be taken up by the cell.
What happens if the pancreas is not producing insulin properly? The glucose channels wont be
opened up by insulin receptors and the glucose cannot get into the cell. This is type 1 diabetes.
To treat this, we inject insulin into the body so glucose can be processed properly.
If we have insulin in the body, but the insulin receptors have become desensitized to it, the glucose
channels still wont open up and the glucose cannot get into the cell. This is type 2 diabetes.
To treat this, you can take drugs or attempt lifestyle changes that help make insulin receptors
more sensitive, or (if things get bad enough) you can take insulin. The extra insulin will trigger your
receptors to work.

PRODUCTION OF INSULIN AND GLUCAGON

The pancreas sits to the back-left of the liver. Whats distinct about the pancreas is its blood supply.
It receives (like most organs) oxygen-rich blood through the arterial system, and gives off oxygenpoor blood through the venous system.

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Uniquely, the pancreas also receives nutrient-rich blood from the small intestine via the portal
venous system.
When this nutrient rich blood gets into the pancreas, it triggers the release of hormones insulin and
glucagon, which will travel back through the portal venous system and go into the liver.
Going to the liver first means insulin and glucagon have a 4x greater effect there than in the rest of
the body.
The islet of langerhans is basically an island of cells in the pancreas that releases these hormones.
cells are in the middle of the island; cells are on outside.
cells release insulin, cells release glucagon.
Insulin is stored in -cells. Its release is triggered by an
increase in in Ca2+. Details:
When blood glucose is increased in the blood, it will enter the
cell via the GLUT2 transporter.
In the cell, Glucose enters glycolysis (and other process), and
[ATP] increases as a result of oxidative phosphorylation.
ATP then binds to an ATP-gated K+ channels, closing it
this prevents K+ from leaving and depolarizes membrane
(i.e. The inside the cell is more positive than the outside).
In response to this membrane-depolarization, voltage-gated
Ca2+ channels open, allowing Ca2+ to flow into the cell.
In response to the elevation of [Ca2+] in the cytosol, insulin
is released from insulin granules off the ER, which bind to
the Ca2+ and exit the cell into the portal venouse system
via exocytosis.
In 1923, Banting & Best won the Nobel Prize for this discovery
All we really know about glycogen release is that its triggered by
amino acids.

HORMONE CONTROL OF HUNGER

The hypothalamus helps distinguish whether your body is rich or poor in energy, i.e., whether youre
full or hungry.
If you just ate, your glucose conc. is high, and insulin is released in the blood. Insulin binds to
hypothalamus, and it knows youre full.
If you dont have a high glucose conc, insulin is not in blood so hypothalamus is not inhibited; it
knows youre hungry.
If you eat a really fatty, rich meal, and the concentration of lipids it increased, your body releases a
hormone called leptin.
Leptin is similar to insulin in that it represents the presence of energy in the blood. It also binds to
the hypothalamus so your body knows its full.
When leptin is not sent to brain (again) hypothalamus is not inhibited; it knows youre hungry
When we have an empty stomach, it starts growling it says ghrelin
Ghrelin hormone is released into the blood when we have an empty stomach. It goes to the
hypothalamus, as well, and when it binds it tells the body were hungry!
Note: leptin levels rarely change. This is because its more based on the level of adipose in the body
than they level of lipids in the blood.

HORMONES, BODY MASS, AND OBESITY

What is it in your body that determines how much you way? Like a scale, there are different things
that balance energy in vs. energy out.
Energy comes from:
diet.

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hormones will determine what we do with this food.. whether that energy is stored or passed
through as waste
Insulin which regulates blood glucose levels
Leptin is related to blood lipid levels
Ghrelin tells our body whether our stomach is full or not
Energy is expelled through:
basal metabolic rate, or how much energy our body burns at rest. (~2000 kcal a day)
activity and exercise, use of energy to perform tasks (~500cal a day)
diet-induced thermogenesis, or the energy we use/burn to store the food that we eat (~10% of
the calories we bring in from our diet)
On average, what we eat vs. how much we burn will determine our body mass. But hormones also
play a big role.
Ex: mouse experiment
mouse #1 = normal
given plenty of food, was still normal
mouse #2 = missing the DB gene that encodes leptin
given plenty of food, it was hungrier, ate to excess, and became obese
mouse #3 = missing the DB gene, but was injected with serum from the normal mouse
given plenty of food, was about the same as the normal mouse