BIOL1020

Genes, Cells and Evolution

Complete course notes

2020
 Carbohydrates
Polymer: Chains of sequentially bonded mon- Figure 1: Glucose molecule
omers one after the other.
• The process of making a polymer is
called polymerisation (dehydration
reaction).
• Polymer breakdown -> hydrolysis
Glucose: (fig 1)
• Bond in 1-2 (alpha) to make sucrose (fig
2)
Figure 2: Sucrose
• Bond in a 1-4 (alpha) to make maltose
(fig 3)
• 1-6 bonds create branching (fig 4)
• 1-4 (beta) bonds create cellulose; cannot
be digested by humans but can by
ruminants. (fig 4)
Complex Carbohydrates:
• High-GI foods are broken down quickly
• Low-GI foods are broken down slower
• Better for gut health Figure 3: Maltose

Figure 4: Cellulose
Online Questions—Carbohydrates
1. Indicate which complex carbohydrate humans store as their primary energy source
and by what process this polysacharide (by catabolic reaction) is metabolized in
humans.
A. Glycogen, hydrolysis
2. Which polysaccharides provide energy storage for plants and animals, respectively?
A. Starch and glycogen
3. Sticky rice has a relatively larger proportion of amylopectin in its starch than does
long-grain rice. Long-grain rice has proportionally more amylose. Predict whether a
piece of sushi made with sticky rice would raise or lower your blood sugar more
quickly than an equal amount of rice pilaf made with long-grain rice.
A. Amylopectin is more branched than amylose, so amylopectin should be digested more
quickly. Thus, eating the sushi should raise your blood sugar more quickly than eating the
rice pilaf.
 Lipids, Proteins, DNA and
Organelles
Lipids: Figure 1: Triglycerol
• Primary storage of fats in the human body
is triglycerol (fig 1)
• Made from 1 x glycerol and 3 x fatty
acids
• Non-polar
• Adipocytes are responsible for fat
storage
• Saturated fats have no double or triple
bonds where as unsaturated fats do (fig
2).
• Unsaturated is better for health as
they break down easier
• Cis-double bonds have H+ on the same Figure 2: Saturated vs Unsaturated fats
side (fig 2).
• Trans-double bonds have H+ on opposite
sides
• Not easy to break down as enzymes
cannot recognise this orientation as
easy.
 Lipids, Proteins, DNA and
Organelles
Amino Acids (proteins): Figure 1: Amino Acid Structure
• 20 different amino acids
• The R-group is what determines the
amino acid (fig 1)
• Can be polar or non-polar
• Charged, acidic or negative
• Basic or positive
• There are four structures of amino acids
• Primary: A sequence chain of amino
acids
• Secondary: Occurs when the
sequence of amino acids are linked
by H+ bonds
Figure 2: Structures of Amino Acids
• Tertiary: Occurs when certain
attractions are present between
alpha helices and pleated sheets
• Quaternary: A protein consisting of
more than one amino acid chain.
 Lipids, Proteins, DNA and
Organelles
DNA Replication Fork (fig 1) Figure 1: DNA Replication Fork
1. Single-strand binding proteins stabilise
the unwound parental strands
2. Helicase unwinds and separates the
parental DNA strands
3. Topoisomerase breaks, swivels, and re-
joins the parental DNA ahead of the repli-
cation fork, relieving the strain caused by
unwinding
4. Primase synthesises RNA primers, using
Figure 2: Lagging Strand
the parental DNA as a template
DNA Replication Fork—Lagging (fig 2)
1. Primase joins RNA nucleotides into a
primer
2. DNA polymerase III adds DNA
nucleotides to the primer, forming a
Okazaki fragment
3. After reaching the next RNA primer to the
right, DNA polymerase III detaches
 Lipids, Proteins, DNA and
Organelles
DNA: Figure 1: Nucleic acids—Pentose Sugar
• 4 different nucleotides
• A + T and C + G
• U is only found in RNA
• C + G bonds are stronger than A + T
bonds
• The second OH group on the ribose
(RNA) is what differentiates RNA from
DNA (figure 1).
Figure 2: Components of DNA and RNA
• DNA is made up of a deoxyribose sugar,
a nitrogenous base and a phosphate
group (fig 2).
• RNA is made up of a ribose sugar, a
nitrogenous base, and a phosphate
group.
• The two DNA strands in a double helix
each have a 5’ and a 3’ end.
• Hydrogen bonds between nitrogenous
bases are used to link the two DNA
molecules that make up double stranded
DNA.
• The base pairs in doubles stranded DNA
each contain a purine and a pyrimidine
base
 Lipids, Proteins, DNA and
Organelles
Organelles: (fig 1) Figure 1: Comparison of Prokaryotes and
Eukaryotes
Prokaryote Eukaryote
• No nucleus • Nucleus

• Non-membrane • Membrane bound

bound organelles organelles

Mitochondria (is the powerhouse of the cell)

• Eukaryotes produce ATP via electron
transport chain (ETC)
Endoplasmic Reticulum (ER)
• Transport system for newly produced
proteins
• Rough ER are covered in ribosomes so
that proteins can be converted to the ER.
• Switching between rough and smooth
status
 Lipids, Proteins, DNA and
Organelles
1. Complete the following sentence: The head of a phospholipid is hydrophilic because
it has...
A. A phosphate group

2. What characteristic of lipids accounts for the separation of oil into droplets in salad
dressing even after vigorous shaking?
A. Lipids are hydrophobic

3. Complete the following sentence: An ester link...

A. binds a fatty acid to a glycerol molecule.

4. Which of these is an example of protein secondary structure?

A. α-helices

5. What residues are connected by a peptide bond?

A. The carboxyl group and the amino group

6. Which level(s) of protein structure are determined by the order of amino acids in the
polypeptide chain?
A. Primary, secondary, tertiary, quaternary.

7. DNA and RNA are made from building block called nucleotides. A nucleotide incorpo-
rated into RNA during synthesis consists of which of the following general compo-
nents?
A. A ribose sugar, a nitrogenous base and a phosphate group

8. Nucleic acids contain nitrogenous bases. Which one of the following statements
about these bases is NOT true?
A. The pyrimidine bases thymine and cytosine have a two ring structure and are larger mol-
ecules than adenine and guanosine

9. Where in the cell can protein synthesis occur in eukaryotes?

A. Rough Endoplasmic Reticulum

10. When a cell is producing a lot of proteins, which organelle is present in large num-
bers?
A. Ribosomes

11. Where is the DNA in bacteria found?

A. Nucleoid
 Cellular Function - Energy
Generation and Metabolism
Reaction Energy: Figure 1: Exergonic vs Endergonic reactions
• Energy is converted from one form to
another in a cycle of events
• In the human body, most energy is stored
as potential energy
• Metabolism is the totality of an organism’s
chemical reactions.
• Gibbs free energy: the amount of energy
in a system that can be used to do work
while pressure and temperature remain
Figure 2: Exergonic vs Endergonic reactions
constant (G).
+/- G = G final—G initial
Catabolic Reactions: (fig 1)
• Break down molecules
• Release energy (exergonic)
• -∆G
Anabolic Reactions: (fig 1)
• Synthesise molecules
• Consume energy (endergonic)
• +∆G
Laws of Thermodynamics:
0. Two bodies at thermal equilibrium are at
same T
1. Energy can never be created or de-
stroyed ∆E = q + w
2. Total entropy of the universe must
increase in every spontaneous process
∆s system + ∆s surroundings > 0
3. Entropy (s) of a pure crystalline
compound a T = 0k is 0 (no disorder)
 Cellular Function - Energy
Generation and Metabolism
Exergonic Reaction Figure 1: ATP Reaction
• In ATP the chemical energy is released
via hydrolysis of bonds between
phosphate groups (fig 1)
• Phosphoanhydride bonds are unstable
because of electrostatic repulsion
between the oxygen atoms on the
phospho-groups.
• The close proximity between these
groups destabilized ATP
• ADP has less electrostatic repulsion and
therefore has a lower potential energy
 Cellular Function - Energy
Generation and Metabolism
Energy Generation: Figure 1: Cellular Respiration of Glucose
• Respiration is the breakdown of glucose
C6, H12, O6. (fig 1)
Figure 2: Glycolysis
• The ∆G breaking down one molecule of
glucose is -686 kilo calories per mol.
Respiration:
Stage 1: Glycolysis (fig 2)
• One molecule of glucose can be split in
half and form two molecules of pyruvate.
• This produces two NADH and four ATP.
We consume two ATP molecules in this
phase, so it is a net gain of two ATP
molecules
Stage 2: Pyruvate Oxidation (fig 3)
• Pyruvate needs to be moved into the
mitochondria
• We break down pyruvate to Acetyl-CoA,
one pyruvate in, one Acetyl-CoA and CO2
out. Figure 3: Pyruvate Oxidation

• For every pyruvate oxidised, one NADH

is formed
• Acetyl-CoA then enters the citric acid
cycle
Stage 3: Citrus Acid Cycle (fig 4)
• Cycle runs twice for each molecule of
glucose because one glucose produces
two pyruvates, and two pyruvate
produces two Acetyl-CoA. Figure 4: Citrus Acid Cycle
 Cellular Function - Energy
Generation and Metabolism
Energy Generation: Figure 1: Electron Transport Chain

Stage 4: Oxidative phosphorylation

• Two step stage
• Most ATP produced
• NADH and FADH2 into ATP
• Occurs between the inner and outer
membranes of the mitochondria
Step 1: Electron Transport Chain (fig 1) Figure 2: Chemosis
• Complexes 1-4 accept electrons from
NADH and FADH2
• Final electron acceptor is Oxygen (makes
water)
Step 2: Chemosis (fig 2)
• Driven by the proton gradient
• Turning of the rod activates the catalytic
sites to produce ATP from ADT + P.
 Cellular Function - Energy
Generation and Metabolism
1. Represent the reaction that takes place during cellular respiration.
A. O2 + Glucose -> CO2 + ATP + Water
2. In addition to glucose, what other molecule that is not synthesized by the cell is re-
quired for respiration to proceed?
A. Oxygen
3. Adenosine triphosphate (ATP) is the molecule that cells use to store energy. Which
one of the following statements about ATP is false?
A. ATP consumes energy when it is hydrolysed to ADP and inorganic phosphate
4. What is the maximum theoretical yield of ATP molecules during cellular respiration?
A. 32
5. What is the actual yield of ATP molecules during cellular respiration?
A. 30-32
6. In addition to ATP, glycolysis, pyruvate oxidation and the Krebs cycle produce two
other, related types of energy storage compounds. These are FADH 2 and ________.
A. NADH
7. Taking into account that glycolysis produces two molecules of pyruvate that will be
oxidized to carbon dioxide by pyruvate dehydrogenase and the Krebs cycle, can you
work out the overall balance of ATP, NADH and FADH2 production for these steps?
Enter the values below.
Number of ATP molecules produced
A. 4
Number of NADH molecules produced
A. 10
Number of FADH2 molecules produced
A. 2
8. What would happen to the ATP yield of cellular respiration if the transporter that im-
ports pyruvate into the mitochondria stopped working? Explain.
A. ATP yield would be severely reduced - one would only get the 2 ATP produced during
glycolysis and possible some ATP from the NADH produced during glycolysis if that is im-
ported into the mitochondria.
 Cellular Function - Cell Division
Cell Division: Figure 1: Prokaryotic Cell Division
• Cells duplicate genetic material before
they divide, ensuring each daughter cell
gets an exact copy of DNA
• DNA in eukaryotes are packaged into
chromosomes
• Chromosomes consist of chromatin, a
complex of DNA and protein that
condenses in cell division
Somatic cells
• Two sets of chromosomes (one from each
parent)
Gametes (germ cells/ova + sperm)
• Only one set of chromosomes, produced
my meiosis

Prokaryotic Cell Division (fig 1)

• Asexual reproduction—binary fission
• DNA is free floating in the cytoplasm, no
membrane bound organisms
Eukaryotic Cell Division: (fig 2)
Figure 2: Eukaryotic Cell Division Cycle
• More complex than prokaryotic cells
• Consists of two phases Interphase (G1, S,
and G2) and Miotic Phase (M)
Gap 1 (G1)
• Normal metabolic processes
S Phase
• DNA replication
Gap 2 (G2)
• Preparation of cell to enter Mitosis
Miotic Phase:
• Consists of division of the contents of the
nucleus and cytokinesis, division of the
cytoplasm.
• Rapid, 30-60 minutes, with all other cell
activities on hold
Cellular Function - Cell Division
Miotic Phases: Figure 1: G2 Phase

G2 (fig 1)
• Cell is preparing to enter mitosis
• A nuclear envelope encloses the nucleus
• The nucleus contains one or more
nucleoli
• DNA has been duplicated in the previous
S phase and DNA is still in the form of
chromatin
• Two centrosomes appear, the starting
point for the miotic spindle
Mitosis 1: Prophase (fig 2) Figure 2: Prophase
• DNA condenses from Chromatin into
chromosomes
• The nucleoli disappear
• Centrosome divides and along with
microtubules, form the Miotic Spindle
Mitosis 2: Prometaphase (fig 3)
• Kinetochores are protein structures on
chromosomes that bind to microtubules
• Chromosomes are anchored to the Miotic
Spindle via kinetochores
• Chromosomes are even more condensed Figure 3: Prometaphase
• Non-kinetochores microtubules interact
with ones on the opposite pole of the
spindle, lengthening the cell
 Cellular Function - Cell Division
Miotic Phases cont.: Figure 1: Metaphase
Metaphase (fig 1)
• All sister chromatids are lined up in the
middle of the cell
• The centrosomes are now at opposite
poles of the cell
Anaphase (fig 2)
• Shortest stage of Mitosis (few mins)
• Microtubules pull sister chromatids apart
• The cell elongates as the non-
kinetochore microtubules lengthen
• As the microtubules contract, the
chromatids are pulled into opposite ends Figure 2: Anaphase
of the cell. Each chromatid becomes an
independent chromosome.
Telophase (fig 3)
• Two identical sets of chromosomes that
were separated in Anaphase become into
two developing cell nuclei
• Chromosomes become less condensed
• Any remaining spindle microtubules are
depolymerised
• Mitosis is now complete
• Cell splits into two via cytokinesis
Figure 3: Telophase and Cytokinesis
Cytokinesis:
• Actin filaments congregate near the
Metaphase plate to form a ring inside the
cell
• Pinching actions separates cytoplasm in-
to two separate cells
• In animal cells a Cleavage Furrow is
formed during cytokinesis, where as
plants form a cell plate.
 Cellular Function - Cell Division
Cell Cycle Regulation Figure 1: Cyclin Concentration Throughout Cell
Cycle
• The frequency of cell divisions varies be-
tween cell type
• The cell cycle needs to be regulated at a
molecular level by Cell Cycle Check-
points
• Passage of cell through a “checkpoint”
Figure 2: CDK Concentrations Throughout Cell
requires activation of a two-subunit pro-
Cycle
tein complex.
• It is made up of:
• Cyclin, a regulatory subunit. It fluc-
tuates through the cycle. (fig 1)
• Cyclin-Dependant Kinase (CDK) an
enzyme which can add phosphate
groups onto other proteins only
when bound to Cyclin. Concentra-
tion remains constant through cell
cycle. (fig 2)
G1 Checkpoint
• Assesses whether or not a cell has
enough energy or resources to reproduce
• If yes, it will go to the S phase
G2 Checkpoint
• Evaluates the quality of DNA that was
copied
• Any damage?
M Checkpoint
• Checks that chromosomes are attached
to the Miotic Spindle
Cellular Function - Cell Division
Cancer Figure 1: Proto-oncogene Activation
• 1 in 3 people will develop cancer in their
lifetime
• Cancer is uncontrolled proliferation
• There are a number of risk factors
including, smoking, alcohol consumption,
exposure to radiation, soluble chemicals,
fibres and infectious agents. Figure 2: p53 Tumour Suppressor
Oncogenes:
• Genes or gene products that if activated
can cause cancer
Proto-oncogene:
• Codes for proteins that promote cell
growth
• If not switched off at the right time, they
become oncogenes and cause cancer
• Can become oncogene by: (fig 1)
• Movement or translocation of the
gene so that it becomes under the
Figure 3: Perturbation of p53
control of another promoter region
(may induce overexpression)
• Abnormally amplified gene (too
many copies of the gene product)
Tumour Suppressor Genes
• Normally inhibit or suppress cell division
from happening all the time e.g. p53
(fig 2)
• If these genes stop working e.g. mutated
to a non-functional form it can also lead
to cancer (fig 3)
Cellular Function - Cell Division
1. What is the end product of both binary fission and mitosis?
A. Two daughter cells identical to the parent cell
2. Without the mitotic spindle, how would mitosis be different?
A. Sister chromatids would have to physically segregate by some other means
3. How many chromosomes does a regular adult human cell (not a gamete) have?
A. 46
4. Use your knowledge about the structure of microtubules to explain how these
cytoskeleton elements can be used to ‘pull’ the chromatids to the cell poles during
cell division.
A. Microtubules are filamentous structures that are part of the cytoskeleton. They are highly
dynamic, i.e. they continually assemble and disassemble in the cell to suit the current needs
of the cell. During cell division, shortening of the microtubules through disassembly at the
centromere side will move the chromatids to the cell poles.
5. The G1 phase of the cell cycle differs from the Go phase, in that:
A. The G1 phase is a cell growth phase where cells increase in size and cellular
components to prepare for cell division
6. What do you predict would happen in a cell that only underwent the M and S phases
of the cell cycle, without the G1 and G2 phases?
A. During the S phase, DNA replication occurs, while mitosis occurs during the M phase.
Cells grow and synthesize proteins during G1 and G2. Therefore, a cell that skips the two G
phases is expected to divide repeatedly into smaller and smaller cells without growing in
size.
7. How is metastasis linked to one of the characteristics of normally dividing cells?
A. Metastasis is the condition of cancer cells in which they are able to break free from the
primary tumour in the tissue in which they were formed, migrate to new tissues through the
blood, and form new tumours. Normal cells exhibit anchorage dependence, meaning that
they can only initiate cell division if they are attached to the extracellular matrix or some
other surface, such as the bottom of a tissue culture plate. Metastatic cells no longer require
adhesion for survival, which allows them to detach from the primary tumour, migrate to
distant sites in the body, and multiply into secondary tumours.
8. Which of the following statements about oncogenes and tumour suppressor genes is
correct?
A. A proto-oncogene can turn into an oncogene if there is a mutation in its promoter region
 Genes – The Central Dogma
The Central Dogma Figure 1: RNA Polymerase
The Central Dogma of Molecular Biology is a
summary of the information flow in the cell:
Information is encoded in the DNA sequence
of a gene, this information is transcribed into
an intermediary in this process called
messenger RNA (mRNA). The instruction, at
this stage, is still written in the language of
nucleotides, so it needs to be translated into Figure 2: Initiation
the language of amino acids, which are the
building blocks of proteins, the executors of
genetic information.
DNA Transcription
• The main enzyme involved in
transcription is RNA polymerase, which
uses a single-stranded DNA template to
synthesize a complementary strand of
RNA. (fig 1)
Stages of DNA Transcription
1. Initiation. RNA polymerase binds to a
sequence of DNA called the promoter, Figure 3: Elongation
found near the beginning of a gene.
Once bound, RNA polymerase separates
the DNA strands, providing the single-
stranded template needed for
transcription. (fig 2)
2. Elongation. One strand of DNA,
the template strand, acts as a template
for RNA polymerase. As it "reads" this
template one base at a time, the poly-
merase builds an RNA molecule out of
complementary nucleotides, making a
chain that grows from 5' to 3'. For RNA it Figure 4: Termination
is U not T. (fig 3)
3. Termination. Sequences called
terminators signal that the RNA transcript
is complete. Once they are transcribed,
they cause the transcript to be released
from the RNA polymerase. (fig 4)
 Genes – The Central Dogma
RNA Splicing Figure 1: RNA Splicing
We call the coding bits exons, and the non-
coding regions introns. The very first transcript
produced by RNA polymerase is called pre-
mRNA. Pre-mRNA needs to be
spliced so that the introns can be removed
from pre-mRNA before the mature mRNA can
be properly translated. (fig 1)
Figure 2: Elongation
DNA Translation
• mRNA is "decoded" to build a protein that
contains a specific series of amino acids.
• There are 61 codons for amino acids,
one of which is ‘start’ and another 3 stop
codons.
Stages of Translation
1. Initiation. Ribosome assembles around
the mRNA to be read This setup, called
the initiation complex, is needed in order
for translation to get started.
2. Elongation. The mRNA is read one
codon at a time, and the amino acid
matching each codon is added to a
growing protein chain. tRNAs move Figure 3: tRNA
through the A, P, and E sites of the
ribosome. This process repeats many
times as new codons are read. (fig 2)
3. Termination. The finished polypeptide
chain is released. It begins when a stop
codon enters the ribosome, triggering a
series of events that separate the chain
from its tRNA and allow it to drift out of
the ribosome.
tRNAs (fig 3)
tRNAs, are molecular "bridges" that connect
mRNA codons to the amino acids they
encode. One end of each tRNA has a
sequence of three nucleotides called
an anticodon, which can bind to specific
mRNA codons.
 Genes – The Central Dogma
mRNA to DNA (fig 1)
• Same as mRNA but convert U to T
DNA to mRNA (fig 1)
• Same as DNA but convert U to T

mRNA—5’-AUGAAAUCGUAG-3’
DNA—3’-TACTTTAGCATC-3’

A 6600 nucleotide transcribed mRNA

molecule may use only 900 of its
nucleotides to encode a protein of
300 amino acids. Why?
Many non-coding nucleotides are
present in mRNA

What is the amino acid sequence of the polypeptide resulting from translation of the following
mRNA sequence from the first start codon?
5′-UGAUG | ACU | CCU | GAG | GAG | AAG | UCU | GUC | CUU | AAA | UCU | GCC | GAA |
UAAACCUAGUAU-3

N terminus—Start | Thr | Pro | Glu | Glu | Lys | Ser | Val | Leu | Lys | Ser | Ala | Glu | Stop c-terminus

What would happen if the Trp-tRNA synthase contained a change (mutation) allowing a CUA
anticodon-carrying tRNA to be charged with Tryptophan?
Longer protein, stop codon is replaced by the Tyr protein
 Genes – The Central Dogma
1. What is accomplished during transcription?
A. DNA transfers information to RNA
2. Compare and contrast the similarities and differences in function of DNA polymerase and
RNA
polymerase. Describe two key differences in how RNA and DNA polymerase operate.
A. Key similarities:
Both are enzymes (proteins).
Both take free nucleotides and polymerase them into a long polymer: DNA or RNA.
Both make single strands of the appropriate polymer (DNA polymerase makes one strand of DNA
at a time, RNA Polymerase makes a single strand of RNA).
Both need a template strand to copy, but note: DNA Pol requires a DNA template (therefore the full
name is DNA-dependent DNA Polymerase) and RNA Pol requires a DNA template too (full name is
DNA-dependent RNA Polymerase).

Key differences:
DNA Pol requires a primer, RNA polymerase does not.
DNA works with free deoxyribonucleotides, RNA with ribonucleotides.
3. How many different types of RNA polymerases operate in a eukaryotic cell? What are their
specific roles?
A. There are three types of RNA Pol: RNAPol I, RNAPol II and RNAPol III.
RNAPol II produces mRNA transcripts
RNAPol I and RNAPol III are involved in transcription of genes producing so-called non-coding
RNA (transferRNA, ribosomalRNA, other small non-coding RNA involved in splicing, nucleolar
structure (small nucleolar RNA) etc).
4. When RNA is synthesized, the new nucleotides are added to which side(s) of the existing
RNA strand?
A. 3’ end
5. Which of the does NOT occur during transcription in bacteria?
A. DNA splicing
6. How many ribonucleotides are required to make a ‘codon’ that stores the information for
one amino acid?
A. 3
7. If you have an mRNA transcript 39 bases long, and assuming it ends in UAA, what is the
maximum number of amino acids that could be encoded in this molecule?
A. 12
8. Ribosomal RNA (rRNA) is a type of RNA that participates in the process of translation but
does not get translated itself. Which other type of RNA also meets this criteria?
A. tRNA
9. Why do we refer to the start codon as the AUG and not ATG codon?
A. RNA consists of the ribonucleotides A, U, C and G, whereas DNA consists of the
deoxyribonucleotides A, T, C and G. When referring to codons, we are talking about the sequence
of RNA strands. Thus, the start codon is AUG, not ATG.
 Genes – Lac operon
Lac Operon Figure 1: Lactose Process in Gut
• E. coli is a bacteria that lives in the gut
and uses lactose as food when glucose is
not present. An enzyme is required to
break down lactose. (fig 1)
• These enzymes - 1000-fold in 15 min Figure 2: Lac Operon—no lactose
after supply of lactose i.e. ‘inducible
enzymes’
• The genes for lactose metabolism are:
- clustered together on the chromosome
into an operon
– controlled by a single promoter
– transcribed as a single transcript
• If lactose is absent, a regulatory protein
(LacI repressor) blocks lac transcription
– by binding to an upstream ‘operator’ [O]
sequence LacI protein blocks RNA
polymerase
- Transcriptional control: energy not
wasted synthesising mRNA or enzymes Figure 3: Lac Operon—lactose present
for lactose metabolism in the absence of
lactose
• If lactose is present, lac Z Y A genes are
transcribed
– A lactose isomer (allolactose) binds to
the repressor protein
– The bound repressor protein changes
conformation and cannot bind to the
operator
– RNA polymerase can now bind &
transcribe all genes in the operon
 Genes – Viruses
Viruses Figure 1: Viral Shapes
• A virus is an obligatory, intracellular in-
fectious agent, whose genetic material
(DNA or RNA) is surrounded by a protein
capsid
• Intracellular and infectious: Viruses
infect host cells by breaching the
membrane of cellular life and
reproduce within it
• Obligatory: Require host machinery
to translate their proteins and Figure 2: Baltimore Classification of
replicate, and can not carry out any Viruses
metabolic pathway
• Made up of a nucleic acid and a
protein capsid at a minimum.
• Viruses were discovered in the 19th cen-
tury by Martinus W. Beijerinck through
tobacco
• Viruses have a variety of shapes (fig 1)
• Viruses are in different classes (fig 2)
• Some viruses break the central dogma of
biology.
• It is debated whether viruses are alive:
Like living:
- Replicate to produce progeny
- Evolve through mutation and natural
selection
- Contain nucleic acids (DNA or RNA) as
genetic information
Unlike living:
- Have only limited genetic material: 4 to
~300 genes
- Can only replicate in living cells
- Employ host cell’s replicative and
metabolic pathways (they borrow life!)
- Do not have their own ribosomes or the
ability to produce energy
- Outside cells they are essentially inert
macromolecules
 Genes – Viruses
Virus Life-Cycle (fig 1) Figure 1: Virus Life-Cycle
1. Attachment
Virus has to attach to the cell. Involves
specific interaction of the virus with the
surface of the cell through receptors.
2. Penetration
Movement of the virus into the cytoplasm.
E.g. through endocytosis.
3. Uncoating
The viral capsid is removed causing the
release of nucleic acid from the virus
particle.
4. Biosynthesis
Viral RNA enters the nucleus, where it is
replicated by the viral DNA Polymerase
5. Assembly
New phage particles are assembled.
6. Release
New viral particles are made and
released into the extracellular fluid. The
cell, which is not killed, continues to make
the new virus.
 Genes – Viruses
1. All viruses cause disease:
False
2. Bacteriophages are viruses that infect:
Prokaryotes
3. What part of Beijerinck’s experiment enabled him to conclude that the tobacco mosa-
ic in tobacco plants is not caused by a toxin?
A. Serially passaging the sap from diseased plants
4. A virus is…..
A. An obligatory, intracellular parasite, Infectious agent, Carries nucleic acids that is covered
by a capsid.
5. What is unlike life in regards to viruses?
A. They lack ribosomes, they rely on the host cell’s replication machinery, their genetic ca-
pacity is very small to afford to be independent
6. Which order of events are correct for a virus life cycle?
A. attachment > penetration > uncoating > replication > budding
7. Which is true about a lytic cycle?
A. A lytic cycle is a productive replication cycle that results in cell death
8. What must all viruses genomes produce to utilize the host ribosome?
A. mRNA
9. How do viruses break the Central Dogma of Biology?
A. By making DNA from RNA not RNA from DNA
 Genes – Genes, Alleles, and
Mutations
Genes, Alleles, Genotype and Phenotype Figure 1: Point Mutation
Genotype
The allelic constitution of an individual (at one or
several genes (gene loci)

Phenotype
The trait value of an individual (and is under the
control of its genotype) (what you can
actually see expressed)

The basic principles of heredity are:

• Inherited characteristics are determined by genes

• All individuals of a species have the same base set of genes (variation between individu-
als for a given trait is due to gene mutation)

• Variants of the same gene account for variant traits

Genetic Variation
Genetic variance occurs due to mutations these include:

• Point mutation—single base pair changes

• Insertions or deletions—1+ base pair

• Translocations, deletions or
duplications—large scale chromosomal changes

• Mutations can be in the coding region or not

• Mutations can occur in somatic or germ cells

• Mutations can be spontaneous. In

humans this spontaneous error rate is 1 bp in every 2x108 base pairs.

• Mutations can also be induced; for

example, UV light is mutagenic because it causes particular type of physical
damage of the DNA molecule that needs to be repaired by DNA repair machinery before
such DNA can be replicated.
 Genes – Genes, Alleles, and
Mutations
Genetic Variation in Bacteria Figure 1: Conjugation
Bacteria are the most genetically diverse
group of
organisms eg. ribosomal RNA gene varies
more between two E. coli strains than between
humans and platypus.
This is caused by:
• Higher rate of mutations and rapid repro- Figure 2: Transduction
duction
• Horizontal DNA transfer and genetic re-
combination
There are three ways DNA can be transferred
between bacteria:
• Conjugation—transfer by direct cell to
cell contact via a sex pilus and a
conjugative plasmid. (fig 1)
• Transformation - uptake and
incorporation of naked DNA
• Transduction—transfer ot chromosomal
or plasmid DNA from cell to cell by a
bacteriophage. (fig 2)
 Genes – Genes, Alleles, and
Mutations
Meiosis
• Meiosis ensures that the number of
chromosomes remain constant from one generation to the next.
• Only takes place in germ line cells
• Consists of 2 successive cell divisions Meiosis I and Meiosis II.
Meiosis I
1. Prophase I
- Chromosomes condense and thicken and the homologous chromosomes move closer to
each other.
- Homologous chromosomes are
inherited one from each parent so they contain the same genes in the same
location.
- It is very important that DNA recombination takes place.
- Microtubules that form spindle fibres attach to the kinetochore protein complex at each
centromere.
2. Metaphase I
- Paired chromosomes are pulled to the middle by the spindle.
- As homologous chromosomes align randomly, it results in a different combination of chro-
mosome pair alignments each time meiosis occurs.
3. Anaphase I
- Chromosomes are pulled away from each other by the spindle
- Homologous chromosomes are pulled apart
4. Telophase I
- Cytokinesis follows with splitting of the cytoplasm and duplication of the
centrosomes.
Meiosis II
• Similar to mitosis
 Genes – Recombinant DNA
Technology
Timeline of Technology Development
• The structure oof DNA was discovered in 1953
• First technological development was
isolating DNA
• The 1970s bought upon the second era of technologic advancements, creating genetic
engineering
• Ability to combine DNA molecules from different species
• Introduce the recombinant DNA into other species
• Development of recombinant drugs and organisms
• One approach was to attempt to amplify a transgene from the
genome of the candidate GMO
using the polymerase chain reaction (PCR)
• The third wave of technologies began in 2009
• Increase speed and decrease cost
Cutting DNA with Restriction Enzymes
• Found in E. coli
• Finds specific sequences of nucleotides called restriction sites that needs to be cut
DNA Ligase
• Re-joins broken pieces of DNA back
together
Gel Electrophoresis
• Determines length of DNA after DNA has been cut using restriction enzymes
• DNA has a negative charge
• Goes from negative side to positive, rate of movement is dependent on mass
PCR
• DNA fragments are selected, recognised, amplified and duplicated
• Requires DNA template
• Stages:
• 1st. 96 degrees—Denaturing—heating breaks hydrogen bonds
• 2nd. 55 degrees—Annealing—allowing hydrogen bonds to reform
• 3rd. 72 degrees—Synthesis—one cycle
 Linkage and
Recombination
Chromosomes and Linkage Figure 1: The results of crossing over during
meiosis
• 2-3 cross over events per pair of
chromosomes (recombination)
• To determine an unknown parent, cross
with a homozygous recessive parent—if
offsprings have all dominant phenotype
then parent is homozygous dominant, if
mixed, heterozygous.
Recombination Mapping with 2 Dominant
Loci
• Close together = may stay linked
• Far apart = may create recombinant gene
• Generally, there is not an even balance of
offsprings, the two larger groups are the
parental types and the smaller groups are
the recombinant types.
Recombinant Frequency

• Recombinant frequency is equivalent to a

genetic map distance of X cM
 Evolutionary Processes
Natural Selection
• Acts on populations, not individuals
• Only affect heritable traits
• Varies by environmental context
Sources of Genetic Variation—Mutation
• Deletion—removal of segments
• Duplication—repeating a segment
• Inversion—reverses a segment
• Translocation—relocation of a segment

• Humans have 12 million known single nucleotide polymorphisms (SNPs) that have 2 alleles
each
• Most are bi-allelic so they can form 3 genotypes each
• With recombination we can expect greater than 10^3 million unique gametes
Genetic Diversity
• Over time, genetic drift will remove alleles from a population. Over time, immigration will add
alleles in a population. Similarly, mutations will add alleles in a population.
Genetic Drift
• Random variations in which individuals survive
• Has more of an impact on smaller populations
Gene Flow
• When an individual moves and mates with another individual outside of its immediate gene
pool or population
 Hardy-Weinberg Equilibrium
Hardy-Weinberg Equilibrium
• P*P + 2PQ + Q*Q = 1
• The 1908 model predicts the relationship between alleles and genotypes in a population.
IF: No mutations, no genetic drift, no gene flow, no natural selection, and random mating (i.e. no
evolution)
• The HWE is a fantastic null model to compare real populations against the model
 Real-World Genetics
Epistasis and Biochemical Pathways
Epistasis: Interactions among genes that affect phenotypes. An example is how epistatic inter-
actions between Tyrp1 and Mc1r affect fur coloration in dogs.

Polygenetic Traits and Quantitative Variation

• Quantitative traits are typically polygenic, that is, they are affected by many loci. It turns out
that continuous variation can be created from a small number of loci.

Finding Quantitative Trait Loci

• Two methods—Traditional breeding technique and the other relies on the ability to genotype
thousands of individuals at hundreds of thousands of variable sites
• QTL (Quantitative Trait Locus)
1. Most phenotypic traits are affected by both environment and genetics and have a polygenic
basis
2. Associations between phenotypes and genetic loci can be determined using both traditional
breeding experiments and large scale genomic surveys
3. Standard QTL and GWAS studies can point to genomic regions (but not the actual mutations)
that contribute to the phenotype of interest
Phenotypic Variation
VP = VG + VE + VGXE
Where:

• VG is variation due to genetics

• VE is variation due to environment

• VGXE is variation due to the interaction between genetics and the environment
 Genomes
Genomes
The genome of an organism comprises a complete set of its DNA that includes all of its genes
and information required to build that organism for successful reproduction.

Virus genomes are comparatively small (although there is great variety in size and structure:
~2,000bp to ~2,000,000bp) and they may be made of DNA or RNA, double stranded or single
stranded and may be circular or linear. Sometimes introns are present in genes, and some virus-
es have non-coding RNAs, which are base pair sequences that do not code got genes.

Prokaryotes also have relatively small genomes that can be circular and/or linear and can be
made up of one or multiple DNA molecules (main genome) plus plasmids (smaller circular or line-
ar DNA molecules). As you have already studied earlier, their genes can be arranged in operons
(groups of co-regulated genes involved in a single biochemical pathway) and most DNA in pro-
karyotes genomes codes for genes – they have very little non-coding sequence and generally no
introns within genes.

Eukaryotes genomes can carry relatively large genomes made up of multiple linear chromo-
somes. There is substantial variation in genome size that does not necessarily correlate with the
complexity of an organism. For example, the genome for humans is a little more than 3 billion
DNA base pairs with ~23,000 genes and a fruit fly has about 18,000 genes in 0.2 billion base
pairs. See the table below for a comparison of genome sizes and number of genes.