Nucleic Acids and DNA

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 From DNA to protein- The flow of
genetic information
DNA is double
stranded providing
directions for its own
replication.

DNA directs synthesis

of messenger RNA
(mRNA) and, this,
controls protein
synthesis.

Protein synthesis
occurs in ribosomes
(molecular machine).
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
Nucleic acids (DNA, RNA) store and
transmit hereditary information
The amino acid sequence of a polypeptide
(i.e. a protein) is programmed by a unit of
inheritance called a gene.
Genes are found within DNA.
One DNA molecule includes many genes

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

Components of DNA and RNA

Fig. 5-27

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 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.
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.
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Nitrogeneous bases and sugars
There are two families of
nitrogenous bases:
pyrimidines (cytosine,
thymine, and uracil)
have a single six-
membered ring,
and purines (adenine
and guanine) which
have a six-membered
ring fused to a five-
membered ring.
In DNA, the sugar is
deoxyribose; in RNA, the
sugar is ribose. Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Assembly of DNA
A DNA molecule has two
polynucleotides, which spiral
to form a double helix.
In the DNA double helix, the
two backbones run in
opposite 5 3 directions
from each other, referred to
as antiparallel.
The nitrogenous bases in
DNA pair up and form
hydrogen bonds:
adenine (A) always with
thymine (T), Which would have the greater
and guanine (G) always with stability, a sequence of double
cytosine (C). stranded DNA rich in G+C or A+T?
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 From Gene to Protein
The flow of information is
based on a triplet code
(codon): a series of non-
overlapping, three-
nucleotide words
These triplets are the
smallest units of uniform
length that can code for all
the amino acids
Example: AGT (on the DNA
template) codes for the
amino acid serine.
Note the functions of the
template strand and the
mRNA Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Myoglobin stores and
delivers O2 in muscle
cells. This is particularly
important in deep diving
aquatic animals allowing
them to store their
oxygen while underwater.
Hemoglobin transports
and delivers O2 through
the veins and arteries.

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

Hemoglobin: The major protein of red blood cells.

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 Hemoglobin
The heme group (a
co-factor) is attached
to the polypeptide by
non-covalent bonds.

The Fe2+ ion is

coordinated to the
heme and to a
histidine side chain.

One site around the

Fe2+ is available for
O2 binding Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Hemoglobin A closer look

Heme group

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 Myoglobin and hemoglobin
Myoglobin is a single
polypeptide monomer.
Hemoglobin is a
tetramer with four
subunits.
They are homologous
proteins (i.e. have
similar primary,
secondary and tertiary
structures). Comparsion of single polypeptide chains of
myoglobin and hemoglobin.
Because they are
homologous proteins
they have similar
functions. Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
Myoglobin and hemoglobin function by
reversibly binding O2.

Myoglobin + O2 Myoglobin-O2

Hemoglobin + 4O2 Hemoglobin-4O2

Myoglobin is a single polypeptide monomer.

Hemoglobin is a tetramer allowing

communication between polypeptides
(subunits).
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
Comparison between saturation curves of
myoglobin and hemoglobin
At high pO2 values of the lungs
myoglobin and hemoglobin are
both fully loaded.
Active tissues have an pO2 of
20 torrs.
Myoglobin cannot release its
O2 at this pressure, whereas
hemoglobin can release about
75% of its oxygen here.
Myoglobin only releases its
oxygen when pO2 is 5 torrs.
This is as the last stores of O2
have been depleted. Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Sickle-cell disease
A condition where there are not enough healthy red
blood cells to carry oxygen throughout the body.
Symptoms: Fatigue, pain (veins/arteries are blocked)

In sickle-cell
Normal red anemia, red
blood cells are blood cells have
uniform and shape and
cup-shaped abnormal
shapes and
textures.

Accumulation can damage spleen making patients

vulnerable to infections. Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Sickle-Cell Hemoglobin
Sickle cell hemoglobin (HbS) has a single amino acid
difference compared with normal hemoglobin (HbA). It
occurs in the -subunit.

HbA Val-His-Leu-Thr-Pro-Glu-Glu-Lys-

HbS Val-His-Leu-Thr-Pro-Val-Glu-Lys-

Residue 1 2 3 4 5 6 7 8

This is a non-conservative amino acid substitution.

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 Where is the mutation ?
Glu is a negatively
charged side chain on the
surface of normal
hemoglobin.
Val is non-polar: The
substitution places a
hydrophobic residue on
the surface of the protein.
This greatly reduces the
solubility of the
deoxygenated form of
hemoglobin.
Val 6 forms a
hydrophobic patch on the
surface of the mutant
protein. Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Aggregation of deoxy-hemoglobin

Tetramer
Tetramer Tetramer Tetramer

Val 6 forms a hydrophobic patch on the surface of the

mutant protein.
The -chain of deoxyhemoglobin has another
hydrophobic patch formed by Phe 85 and Leu 88.
The mutant haemoglobin molecules aggregate to hide
the sticky patches. Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
Aggregation of deoxy-hemoglobin

Interaction between Val 6 and

Phe 85 and Leu 88 from an
adjacent molecule. (see next slide)

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 Sickle-cell disease is due to the
association of multiple hemoglobin
molecules

Fig. 5-22

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 Insulin
Insulin is the polypeptide
hormone that controls blood
glucose levels.

Diabetes is a disease where

Inactive
insulin molecules no longer carry
precursor
out regulation of glucose levels.
hormone

Proinsulin is the inactive precursor form of insulin. It

has a connecting piece of peptide which must be
cleaved before it can become active.
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Active Insulin
After proteolytic (enzyme)
cleavage insulin becomes
active.

Active
However, the disulfide bonds hormone
hold the two separated
chains together.

Insulin can now bind with its

receptor on the surface of
the cell, regulating glucose/
sugar levels.
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 What else determines
protein structure?
In addition to primary structure, physical and
chemical conditions can affect structure.
Alterations in pH, salt concentration,
temperature, or detergents can cause a
protein to unravel.
This loss of the native protein structure is
called denaturation.
A denatured protein is biologically inactive.

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

What else determines
protein structure?

Fig. 5-23

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 Shapes of fibrous proteins
Fibrous: are water-
insoluble proteins with
elongated shapes. They
aggregate tightly together
into fibers or sheets with
extensive intermolecular
interactions to build up
macroscopic structures.
They have repeated primary
and secondary structure.
Fibrous proteins provide the
structure and strength of
bone, skin and muscle.
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Collagen
most important of fibrous proteins

Collagen is the most abundant

protein in vertebrates.
It makes up about 30% of the
total body protein. strength and flexibility seen here
Collagen in skin
Collagen provides mechanical Strength in 2-D
strength to connective tissues
including:
skin
bone
tendon
cartlidge
blood vessels
Collagen in bone
Collagen is fibrous and not soluble in Strength in 3-D
mesh-net structure, 3D strength
water Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 There are five types of collagen
come in homologous forms similar secondary and tertiary structure but differ in final composition so have different properties

There are 28 different collagens (i.e. their amino

acid sequences are similar but distinctly different
from each other).
90% of the collagen in the body is collagen I.
collagen I: skin, tendon, vascular ligature, organs,
bone
collagen II: cartilage (main component of
cartilage)
collagen III: connective tissue around the liver
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
Synthesis of tropocollagen
from procollagen
ragged ends-unstructured part of
procollagen molecule, no immediate
purpose once collagen is assembled so

Procollagen - inactive
procollagen peptidase cleaves it

~1,000 amino acids long

procollagen has 3 polypeptide strands in the middle

Procollagen peptidase

Tropocollagen - active
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Collagen fibrils
Collagen (Mr 300,000) is a
rod-shaped molecule, 300
nM long and 1.5 nM thick.
Each chain has ~1,000
amino acids.
Collagen fibrils are made
from collagen units aligned
in a staggered fashion.
The units are cross-linked
(covalent bonds) for
strength.
3 polypeptides linking
together, wound in a helical
like structure but not exactly a
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
helix
 Three-dimensional structure
of collagen
Single chain of collagen
has a helical structure. a
Single chain of
collagen- atoms drawn
as spheres. b
A collagen molecule has
a three stranded triple-
helix of collagen- each
polypeptide chain is
coloured differently. c
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Three-dimensional structure of
collagen
from the top
understand why it is a strong structure, red
stuff filling space, no wiggle room

Looking down the long axis of collagen the inside is

very crowded with atoms. Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Inside the collagen triple helix
Glycine side-chains (only a hydrogen atom) point inside
the triple-helix. All other side-chains are too big.
small space, hard to fit anything but a single H atom

H H
H

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

Amino acid sequence of collagen
The collagen polypeptide has repeated amino acids
(typical of fibrous proteins).

Part of the sequence (54/1000 amino acids) is drawn

below.

GLYCINE

One of the amino acids (Hyp = hydroxyproline) is not

one of the twenty standard amino acids.
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
Chemically modified amino acids

Hydroxyproline is formed by a
chemical modification to the
existing structure of an amino acid.
to make collagen
molecules stronger
proline

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 4-Hydroxyproline in collagen
Forces the proline ring into a
more favorable conformation
for stabilizing the triple helix.

Offers more hydrogen

bonding potential between
the three strands of collagen.

This process is catalyzed by

prolyl hydroxylase in the
presence of ascorbate
(vitamin C).
thats why vit c is so important Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Vitamins
A vitamin is an organic compound required as
a vital nutrient by an organism.
It cannot be synthesized by the organism (e.g.
humans) and must therefore be obtained in the
diet.

Vitamin C to strengthen collagen

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
Vitamin C activates prolyl 4-hydroxylase

Prolyl hydroxylase

Fe3+

P4H

Prolyl-4-hydroxylase is a metalloenzyme (red) and

needs Fe2+ to be fully active.
Vitamin C
Vitamin C adds an electron to Fe3+ making it Fe2+,
reducing agent
activating prolylthe4-hydroxylase.
enzyme
Fe2+
Without vitamin C proline in collagen will have less
P4H of a tendency to become hydroxylated. The collagen
will be weaker. Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Scurvy
weakening of skin and tissue around vital organs

Ansons (1748) circumnavigation

resulted in 1400/1900 men dying of
scurvy.

James Lind (~1750) was the first to

undertake clinical experiments to
prove the importance of vitamin C.

Captain Cook (~1770) fed his crew

sauerkraut, oranges and lemons,
thereby eliminating the threat of the
disease.

Scurvy is a disease now known to

be caused by a lack of vitamin C
(thereby weakening collagen).
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Cross linking of
collagen triple-helices

kjkj
In this example, two lysine side chains (-NH3+)
are replaced by a CH=N covalent bond.
loses solubility when remove amino group

Thus, cross linking makes collagen stronger

(new covalent bonds) and less soluble
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
Steps in collagen biosynthesis
made on ribosome, traces back to DNA

1. Single strands of polypeptide

are made.
2. Hydroxylation of lysine and
proline side chains.
3. The triple helix is formed.
4. Procollagen is converted to
collagen by procollagen
peptidase. cleave off ragged ends
if theyre association with lysine side chains for example are close
enough to each other, they can start to form covalent links to provide
5. Bundles form. strength and direction towards long length of collagen triple helix itself

6. Cross links form. eg if vit c lacking, wont get hydroxylation

occurring, and wont get strong collagen, lead to
illness
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 You should now be able to:
Identify the functions of some proteins.
Draw the general chemical structure of an amino
acid.
Explain what it is meant by the term L-amino acid.
Look at the side-chains of amino acids and
comment on their properties.
Explain the term dehydration reaction as applied to
making peptide bonds.
Draw the structure of a tripeptide given the side-
chain structures of the amino acids.
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia
 Define the four levels of protein structure.
Explain what is meant by a disulfide bond and
their roles in protein structure.
Compare the properties and features of
globular and fibrous proteins.
Explain what is meant by the pro form of
insulin.
Explain what is meant by the native structure of
a protein and what are the factors that lead to
denaturation.

Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia

 Explain the different functions of myoglobin and
hemoglobin
Explain the molecular basis for sickle cell
anemia.
Explain how enzymes work to lower the
activation energy of chemical reactions.

Show the steps that occur in the catalytic cycle

of an enzyme.
Explain the steps involved in the production of
collagen (especially why vitamin C is required
for strong collagen)
Campbell, Reece, Meyers Biology 8e 2009 Pearson Education Australia