The Molecules of Life

• Within cells, small organic molecules are joined

together to form larger molecules
• Macromolecules are large molecules composed
of thousands of covalently connected atoms
Most macromolecules are polymers, built from
monomers

• A polymer is a long molecule consisting of many

similar building blocks called monomers
• Three of the four classes of life’s organic
molecules are polymers:
– Carbohydrates
– Proteins
– Nucleic acids
The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation

reactions called dehydration reactions
• Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the
reverse of the dehydration reaction
 Short polymer Unlinked monomer

Dehydration removes a water

molecule, forming a new bond

Longer polymer
Dehydration reaction in the synthesis of a polymer

Hydrolysis adds a water

molecule, breaking a bond

Hydrolysis of a polymer
The Diversity of Polymers

• Each cell has thousands of different kinds of

macromolecules 1 2 3 H HO

• Macromolecules vary among cells of an organism,

vary more within a species, and vary even more
between species
• An immense variety of polymers can be built from
a small set of monomers
Carbohydrates serve as fuel and building material

• Carbohydrates include sugars and the polymers

of sugars
• The simplest carbohydrates are
monosaccharides, or single sugars
• Carbohydrate macromolecules are
polysaccharides, polymers composed of many
sugar building blocks
Sugars

• Monosaccharides have molecular formulas that

are usually multiples of CH2O

• Glucose is the most common monosaccharide

• Monosaccharides are classified by location of the

carbonyl group and by number of carbons in the
carbon skeleton
 Triose sugars Pentose sugars Hexose sugars
(C3H6O3) (C5H10O5) (C6H12O6)

Aldoses

Glyceraldehyde

Ribose
Glucose Galactose
Ketoses

Dihydroxyacetone

Ribulose
Fructose
• Monosaccharides serve as a major fuel for cells
and as raw material for building molecules

• Though often drawn as a linear skeleton, in

aqueous solutions they form rings
Linear and Abbreviated ring
ring forms structure
• A disaccharide is formed when a dehydration
reaction joins two monosaccharides
• This covalent bond is called a glycosidic bond

• Lactose = Glu + Gal

• Maltose = Glu + Glu

• Sucrose = Glu + Fru

Dehydration
1–4
reaction in the glycosidic
synthesis of maltose linkage

Glucose Glucose Maltose

Dehydration
1–2
reaction in the glycosidic
synthesis of sucrose linkage

Glucose Fructose Sucrose

Polysaccharides

• Polysaccharides, the polymers of sugars, have

storage and structural roles
• The structure and function of a polysaccharide are
determined by its sugar monomers and the
positions of glycosidic linkages
 Starch granules
in a potato tuber cell Starch (amylose)

Glucose
monomer
Glycogen granules
in muscle
tissue Glycogen

Cellulose microfibrils
in a plant cell wall Cellulose

Cellulose
Hydrogen bonds
molecules
between —OH groups
(not shown) attached to
carbons 3 and 6
Storage Polysaccharides

• Starch, a storage polysaccharide of plants,

consists entirely of glucose monomers
• Plants store surplus starch as granules within
chloroplasts and other plastids
 Chloroplast Starch

1 µm

Amylose Amylopectin

Starch: a plant polysaccharide

• Glycogen is a storage polysaccharide in animals

• Humans and other vertebrates store glycogen

mainly in liver and muscle cells
 Mitochondria Glycogen granules

0.5 µm

Glycogen

Glycogen: an animal polysaccharide

Structural Polysaccharides

• Cellulose is a major component of the tough wall

of plant cells
• Like starch, cellulose is a polymer of glucose, but
the glycosidic linkages differ
• The difference is based on two ring forms for
glucose: alpha () and beta ()
a Glucose b Glucose

a and b glucose ring structures

Starch: 1–4 linkage of a glucose monomers.

Cellulose: 1–4 linkage of b glucose monomers.

• Polymers with alpha glucose are helical
• Polymers with beta glucose are straight
• In straight structures, H atoms on one strand
can bond with OH groups on other strands
• Parallel cellulose molecules held together
this way are grouped into microfibrils, which
form strong building materials for plants
 Cellulose microfibrils
in a plant cell wall
Cell walls Microfibril

0.5 µm

Plant cells

Cellulose
molecules

 Glucose
monomer
• Enzymes that digest starch by hydrolyzing alpha
linkages can’t hydrolyze beta linkages in cellulose
• Cellulose in human food passes through the
digestive tract as insoluble fiber
• Some microbes use enzymes to digest cellulose
• Many herbivores, from cows to termites, have
symbiotic relationships with these microbes
• Chitin, another structural polysaccharide, is found
in the exoskeleton of arthropods
• Chitin also provides structural support for the cell
walls of many fungi
• Chitin can be used as surgical thread
Lipids are a diverse group of hydrophobic
molecules
• Lipids are the one class of large biological
molecules that do not form polymers
• The unifying feature of lipids is having little or no
affinity for water
• Lipids are hydrophobic becausethey consist
mostly of hydrocarbons, which form nonpolar
covalent bonds
• The most biologically important lipids are fats,
phospholipids and steroids
Fats

• Fats are constructed from two types of smaller

molecules: glycerol and fatty acids
• Glycerol is a three-carbon alcohol with a hydroxyl
group attached to each carbon
• A fatty acid consists of a carboxyl group
attached to a long carbon skeleton
 Fatty acid
(palmitic acid)

Glycerol
Dehydration reaction in the synthesis of a fat
• Fats separate from water because water
molecules form hydrogen bonds with each
other and exclude the fats
• In a fat, three fatty acids are joined to
glycerol by an ester linkage, creating a
triacylglycerol, or triglyceride
 Ester linkage

Fat molecule (triacylglycerol)

• Fatty acids vary in length (number of carbons) and
in the number and locations of double bonds
• Saturated fatty acids have the maximum number
of hydrogen atoms possible and no double bonds
• Unsaturated fatty acids have one or more double
bonds
• The major function of fats is energy storage
(a) Saturated fat (b) Unsaturated fat

Structural
formula of a
saturated fat
molecule
Structural
formula
of an
unsaturated
Space-filling fat molecule
model of
stearic acid,
a saturated
fatty acid
Space-filling
model of oleic
acid, an
unsaturated
fatty acid Double bond
causes bending.
• Fats made from saturated fatty acids are called
saturated fats
• Most animal fats are saturated
• Saturated fats are solid at room temperature
• A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits
 Stearic acid

Saturated fat and fatty acid.

• Fats made from unsaturated fatty acids are called
unsaturated fats
• Plant fats and fish fats are usually unsaturated

• Plant fats and fish fats are liquid at room

temperature and are called oils
 Oleic acid

cis double bond

causes bending
Unsaturated fat and fatty acid.
Phospholipids

• In a phospholipid, two fatty acids and a

phosphate group are attached to glycerol
• The two fatty acid tails are hydrophobic, but the
phosphate group and its attachments form a
hydrophilic head
 Hydrophilic head

Choline

Phosphate

Glycerol
Hydrophobic tails

Fatty acids

Hydrophilic
head

Hydrophobic
tails

(a) Structural formula (b) Space-filling model (c) Phospholipid (d) Phospholipid
symbol bilayer
• When phospholipids are added to water, they self-
assemble into a bilayer, with the hydrophobic tails
pointing toward the interior
• The structure of phospholipids results in a bilayer
arrangement found in cell membranes
• Phospholipids are the major component of all cell
membranes
 WATER
Hydrophilic
head

Hydrophobic
WATER
tails
Steroids

• Steroids are lipids characterized by a carbon

skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component
in animal cell membranes
• Although cholesterol is essential in animals, high
levels in the blood may contribute to
cardiovascular disease
Proteins have many structures, resulting in a wide
range of functions

• Proteins account for more than 50% of the dry

mass of most cells
• Protein functions include structural support,
storage, transport, cellular communications,
movement, and defense against foreign
substances
Enzymatic proteins Defensive proteins
Function: Selective acceleration of Function: Protection against disease
chemical reactions Example: Antibodies inactivate and help
Example: Digestive enzymes catalyze the destroy viruses and bacteria.
hydrolysis of bonds in food molecules.
Antibodies

Enzyme Virus Bacterium

Storage proteins Transport proteins

Function: Storage of amino acids Function: Transport of substances
Examples: Casein, the protein of milk, is Examples: Hemoglobin, the iron-containing
the major source of amino acids for baby protein of vertebrate blood, transports
mammals. Plants have storage proteins oxygen from the lungs to other parts of the
in their seeds. Ovalbumin is the protein body. Other proteins transport molecules
of egg white, used as an amino acid across cell membranes.
source for the developing embryo.
Transport
protein

Ovalbumin Amino acids

for embryo Cell membrane
Hormonal proteins Receptor proteins
Function: Coordination of an organism’s Function: Response of cell to chemical
activities stimuli
Example: Insulin, a hormone secreted by Example: Receptors built into the
the pancreas, causes other tissues to membrane of a nerve cell detect signaling
take up glucose, thus regulating blood molecules released by other nerve cells.
sugar concentration.
Receptor
protein

Insulin Signaling molecules

High secreted Normal
blood sugar blood sugar
Structural proteins
Contractile and motor proteins Function: Support
Function: Movement Examples: Keratin is the protein of hair,
Examples: Motor proteins are responsible horns, feathers, and other skin appendages.
for the undulations of cilia and flagella. Insects and spiders use silk fibers to make
Actin and myosin proteins are their cocoons and webs, respectively.
responsible for the contraction of Collagen and elastin proteins provide a
muscles. fibrous framework in animal connective
tissues.
Actin Myosin
Collagen

Muscle tissue 30 m Connective tissue 60 m

• Enzymes are a type of protein that acts as a
catalyst, speeding up chemical reactions

• Enzymes can perform their functions repeatedly,

functioning as workhorses that carry out the
processes of life
 Substrate
(sucrose)

Glucose

Enzyme
(sucrose)

Fructose
Polypeptides

• Polypeptides are polymers of amino acids

• A protein consists of one or more polypeptides

 Amino Acid Monomers

• Amino acids are organic molecules with carboxyl

and amino groups
• Amino acids differ in their properties due to
differing side chains, called R groups
• Cells use 20 amino acids to make thousands of
proteins
  carbon

Amino Carboxyl
group group
Nonpolar side chains; hydrophobic
Side chain
(R group)

Glycine Alanine Valine Leucine Isoleucine

(Gly or G) (Ala or A) (Val or V) (Leu or L) (le or )

Methionine Phenylalanine Tryptophan Proline

(Met or M) (Phe or F) (Trp or W) (Pro or P)
Polar side chains; hydrophilic

Serine Threonine Cysteine

(Ser or S) (Thr or T) (Cys or C)

Tyrosine Asparagine Glutamine

(Tyr or Y) (Asn or N) (Gln or Q)
Electrically charged side chains; hydrophilic

Basic (positively charged)

Acidic (negatively charged)

Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)
Learn the 20 amino acids, by R group
three letter and one letter codes for naming
them
Amino Acid Polymers
• Amino acids are linked by peptide bonds

• A polypeptide is a polymer of amino acids

• Polypeptides range in length from a few

monomers to more than a thousand
• Each polypeptide has a unique linear sequence of
amino acids
• Each polypeptide has a unique linear sequence of
amino acids, with a carboxyl end (C-terminus)
and an amino end (N-terminus)
• NCC-NCC-NCC-NCC
 Peptide bond

New peptide
bond forming

Side
chains

Back-
bone

Amino end Peptide Carboxyl end

(N-terminus) bond (C-terminus)
Protein Conformation and Function

• A functional protein consists of one or more

polypeptides twisted, folded, and coiled into a
unique shape
• The sequence of amino acids determines a
protein’s three-dimensional conformation
• A protein’s conformation determines its function

• Ribbon models and space-filling models can

depict a protein’s conformation
Antibody protein Protein from flu virus
SARS-CoV-2 Spike Protein (gene S)

Schematic 3D structure Mutations

 Four Levels of Protein Structure

• The primary structure of a protein is its unique

sequence of amino acids
• Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide chain
• Tertiary structure is determined by interactions
among various side chains (R groups)
• Quaternary structure results when a protein
consists of multiple polypeptide chains
Diagrammatically…..
Secondary Tertiary Quaternary
structure structure structure

 helix

 pleated sheet
Transthyretin Transthyretin
polypeptide protein
• Primary structure, the sequence of amino acids
in a protein, is like the order of letters in a long
word
• Primary structure is determined by inherited
genetic information
• Protein sequence can be found on Genbank.org
or at UniProtk.db
 Primary structure
Amino
acids

1 5 10

Amino end
30 25 20 15

35 40 45 50

Primary structure of transthyretin

55
70 65 60

75
80 85 90

95

115 110 105 100

120 125
Carboxyl end
 Secondary structure

• secondary structure
– Arrangement of hydrogen bonds

– between repeating constituents of the

polypeptide backbone

• Typical secondary structures :

– coil alpha helix
– folded beta pleated sheet
 Secondary structure

 helix

Hydrogen bond
 pleated sheet
 strand

Hydrogen
bond
Tertiary structure

Transthyretin
polypeptide
 Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Hydrogen
bond

Disulfide bridge

Ionic bond
Quaternary structure

Transthyretin
protein
• Quaternary structure results when two or more
polypeptide chains form one macromolecule

• Collagen is a fibrous protein consisting of three

polypeptides coiled like a rope

• Hemoglobin is a globular protein consisting of

four polypeptides: two alpha and two beta chains
 Polypeptide
chain  Chains

Iron
Heme

 Chains
Polypeptide chain Collagen Hemoglobin
Sickle-Cell Disease: A Simple Change in
Primary Structure

• A slight change in primary structure can affect a

protein’s conformation and ability to function

• Sickle-cell disease, an inherited blood disorder,

results from a single amino acid substitution in the
protein hemoglobin
 10 µm 10 µm

Red blood Normal cells are Red blood Fibers of abnormal

cell shape full of individual cell shape hemoglobin deform
hemoglobin cell into sickle
molecules, each shape.
carrying oxygen.
Figure 3.22

Secondary
Primary Quaternary Red Blood Cell
and Tertiary Function
Structure Structure Shape
Structures
Normal Molecules do not
1 hemoglobin associate with one
2 another; each carries
3 oxygen.
Normal

4

5  subunit 
6
7 
5 m


Exposed hydro- Sickle-cell Molecules crystallized

1 phobic region hemoglobin into a fiber; capacity to
carry oxygen is reduced.
2
3
Sickle-cell

4

5 
6  subunit
7 
 5 m
 What Determines Protein Conformation?

• In addition to primary structure, physical and

chemical conditions can affect conformation
• Alternations in pH, salt concentration,
temperature, or other environmental factors can
cause a protein to unravel
• This loss of a protein’s native conformation is
called denaturation
• A denatured protein is biologically inactive
 Denaturation

Normal protein Denatured protein

Renaturation
 The Protein-Folding Problem

• It is hard to predict a protein’s conformation from

its primary structure
• Most proteins probably go through several states
on their way to a stable conformation
• Chaperonins are protein molecules that assist the
proper folding of other proteins
 Cap

Hollow
cylinder

Chaperonin
(fully assembled)
 Correctly
Polypeptide folded
protein

Steps of Chaperonin The cap attaches, causing The cap comes

Action: the cylinder to change off, and the
An unfolded poly- shape in such a way that properly folded
peptide enters the it creates a hydrophilic protein is released.
cylinder from one environment for the
end. folding of the polypeptide.
• Scientists use X-ray crystallography to
determine a protein’s conformation

• Nuclear magnetic resonance (NMR) spectroscopy,

which does not require protein crystallization
 X-ray
diffraction pattern
Photographic film

Diffracted X-rays
X-ray
X-ray
source
beam

Crystal
 Nucleic acid Protein

X-ray diffraction pattern 3D computer model

Experiment
Diffracted
X-rays

X-ray
source X-ray
beam

Crystal Digital detector X-ray diffraction

pattern

Results

RNA DNA

RNA
polymerase 
 Molecular vsualisation of proteins

• https://proteopedia.org/wiki/

• Search for a protein

• View the structure, play with it, identify its parts

• Go and look up the protein on UniProtK.db

• Explore it
Nucleic acids store and transmit hereditary
information

• The amino acid sequence of a polypeptide is

programmed by a unit of inheritance called a gene
• Genes are made of DNA, a nucleic acid

• RNA controls protein synthesis

– tRNA, mRNA, rRNA, non-coding RNAs

The Roles of Nucleic Acids

• There are two types of nucleic acids:

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)

• DNA provides directions for its own replication

• DNA directs synthesis of messenger RNA (mRNA)

and, through mRNA, controls protein synthesis
• Protein synthesis occurs in ribosomes
 DNA

Synthesis of
mRNA in the nucleus
mRNA

NUCLEUS
CYTOPLASM

mRNA
Movement of
mRNA into cytoplasm
Ribosome
via nuclear pore

Synthesis
of protein

Amino
Polypeptide acids
The Structure of Nucleic Acids

• Nucleic acids are polymers called polynucleotides

• Each polynucleotide is made of monomers called

nucleotides
• Each nucleotide consists of a nitrogenous base,
a pentose sugar and a phosphate group
• The portion of a nucleotide without the phosphate
group is called a nucleoside

What is the name of the bond with which 2

nucleotides are joined together?
 Sugar-phosphate backbone
5 end (on blue background) Nitrogenous bases
Pyrimidines
5C

3C

Nucleoside

Nitrogenous
Cytosine (C) Thymine Uracil
base
(T, in DNA) (U, in RNA)
Purines

Phosphate
5C group Sugar
(pentose) Adenine (A) Guanine (G)
3C
(b) Nucleotide
Sugars
3 end
(a) Polynucleotide, or nucleic acid

Deoxyribose (in DNA) Ribose (in RNA)

(c) Nucleoside components

 5 end

Nucleoside
Nitrogenous
base

Phosphate
group Pentose
sugar
Nucleotide

3 end
Polynucleotide, or
nucleic acid
5 3 Sugar-phosphate
backbones
Hydrogen bonds

3 5 Base pair joined

by hydrogen bonding
Nucleotide Monomers

• Nucleotide monomers are made up of

nucleosides and phosphate groups
• Nucleoside = nitrogenous base + sugar
• There are two families of nitrogenous bases:
– Pyrimidines have a single six-membered ring
– Purines have a six-membered ring fused to a
five-membered ring
• In DNA, the sugar is deoxyribose
• In RNA, the sugar is ribose
 Nitrogenous bases
Pyrimidines

Cytosine Thymine (in DNA) Uracil (in RNA)

C T U

Purines

Adenine Guanine
A G

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)

Nucleoside components
 Nucleotide Polymers

• Nucleotide polymers are linked together, building a

polynucleotide
• Adjacent nucleotides are joined by covalent bonds
that form between the –OH group on the 3´ carbon of
one nucleotide and the phosphate on the 5´ carbon
on the next
• These links create a backbone of sugar-phosphate
units with nitrogenous bases as appendages
• The sequence of bases along a DNA or mRNA
polymer is unique for each gene
 The DNA Double Helix
• A DNA molecule has two polynucleotides spiraling
around an imaginary axis, forming a double helix
• In the DNA double helix, the two backbones run in
opposite 5´ to 3´ directions from each other, an
arrangement referred to as antiparallel
• One DNA molecule includes many genes

• The nitrogenous bases in DNA form hydrogen

bonds in a complementary fashion: A always
with T, and G always with C
 5 end 3 end

Sugar-phosphate
backbone

Base pair (joined by

What is the hydrogen bonding)

implication of the Old strands

antiparallel strands
Nucleotide
for the replication about to be
added to a
of DNA? new strand

5 end

New
strands

3 end 5 end

5 end 3 end
DNA and Proteins as Tape Measures of Evolution

• The linear sequences of nucleotides in DNA

molecules are passed from parents to offspring
• Two closely related species are more similar in
DNA than are more distantly related species
• Molecular biology can be used to assess
evolutionary kinship

• DNA day, Malaria day

RNA vs DNA
 Assignment
1. Go to www.dnaftb.org
Using the media files of topics 19-23
- Investigate all the backstory to the
discovery of DNA as the genetic material;
the people, the context, the sub-plot, the
deductions

2. Go to learn.genetics.utah.edu
- do the More about RNA
- More about DNA and genes: Build a DNA
molecule

All due Friday before 5pm. The first correct 5 win a

prize from me.
Animations and Videos

• Macromolecules – 1

• Macromolecules – 2

• Polymers

• Biomolecules – Carbohydrates

• Carbohydrates

• Glucose in Water

• Dehydration and Hydrolysis

Animations and Videos

• Disaccharides

• Polysaccharides

• Bozeman – Carbohydrates

• Fats

• Lipids

• Biomolecules – Lipids

• Bozeman - Lipids
Animations and Videos

• Proteins

• Protein Structure – 1

• Protein Structure – 2

• Life Cycle of a Protein

• Peptide Bond Formation

• Dehydration Synthesis of Amino Acids

• Protein Folding - 1
Animations and Videos

• Protein Folding – 2

• Protein Organization

• Protein Denaturation

• Bozeman – Proteins

• How Enzymes Work

• Enzyme Action and the Hydrolysis of Sucrose

• Enzyme Catalysis - 1
Animations and Videos
• Enzyme Catalysis – 2

• Allosteric Regulation of Enzymes

• Allosteric Enzyme

• Enzyme Changing Shape

• Bozeman – Enzymes

• Bozeman - Nucleic Acids

• Testing Organic Substances

• Chapter Quiz Questions – 1

Animations and Videos
• Chapter Quiz Questions – 2