Amino Acids and Proteins

Proteins have many structures, resulting in a wide

range of functions
Proteins account for more than 50% of the dry mass
of most cells.
Functions include:
Structural support - collagen (strength to skin and
bone)
Storage caesin (amino acids in milk)
Transport hemoglobin (transport O2)
Hormonal regulation - insulin (sugar control)
Movement- Actin/myosin (muscle contraction)
Defence Immunoglobulin (recognize viral and
bacterial infections as foreign)
Enzymes to accelerate chemical reactions
 Enzymes
Enzymes assist to
carry out a broad
range of biological
activities
Digestion of food
Making DNA
Protein processing (e.g.
activation of proinsulin,
procollagen)
Protein functions (e.g. enzymes as catalysts)

Enzymes are a type of

protein that act as
catalysts to speed up
chemical reactions.

Enzymes can perform

their functions repeatedly,
operating as workhorses
that carry out the
processes of life.
 Sucrase breaks sucrose into
glucose and fructose.

Hydrolysis of
sucrose by
sucrase is an
example of an
enzyme-catalysed
reaction.
 Turnover number
kcat (s-1)

Kcat indicates how fast enzymes can convert substrate to product.

The larger the number the be:er.
 Enzymes are highly ecient
catalysts of biological reac=ons

Rate enhancement due to lowering the energy hurdle

between substrate and product.
 Proteins (e.g. enzymes)
are made from amino acids
Amino acids are organic
molecules with carboxyl
and amino groups.
Amino acids differ in their
properties due to differing
pKa 4
side chains, called R
groups.
Polypeptides are
polymers built from a set pKa 9
of 20 amino acids.
A protein consists of
one or more
polypeptides.
You should know this picture for
the exam
 Campbell (text) simplification
The general structure of an amino acid given in, Biology Campbell does
not represent a correct ionization state for amino acids.

X
 Charge state of amino acids
In solu=on, the ioniza=on state of the amino and
carboxyl groups change with pH.

R R R

HOOC C NH3+ -OOC C NH3+ -OOC C NH2

H H H

pH 2 pH 7 pH 12

Solution is high Solution is low

in hydrogen ion in hydrogen ion
concentration Zwitter ion concentration
 Most -amino acids are chiral
kai-ral

The central -carbon

has four substituents and
is tetrahedral.

To be chiral all four

substituents must be
different.

Each amino acid has an

unique fourth substituent
R. Here, R= CH3 (alanine)
Non-polar amino acid side chains

Side-chains (pink) of non-polar molecules.

These contain carbon and hydrogen
Uncharged polar side chains

Polar side-chains contain carbon and hydrogen and

oxygen and/or nitrogen
Negatively charged side-chains

These side chains have pKa values of ~4.

pKa is a measure of acid strength. It depends on the identity and chemical properties of
the acid. pH is a measure of [H+] in a solution. For acids, the smaller the pKa, the
more acidic the substance is (the more easily a proton is lost, thus the lower the pH).
Positively charged side-chains

H+
ring structure reduces pka substantially

pKa 10 12 6.5
Aromatic side-chains
pka higher towards the right
 Amino acid polymers- Proteins
Amino acids are linked by
peptide bonds.
A polypeptide is a polymer
of amino acids.
Polypeptides range in
length from a few to more
than a thousand
monomers.
Each polypeptide has a
unique linear sequence of
amino acids.
 Drawing a tri-peptide
3 amino acids linked together

Given a table of structures for the side chains of amino

acids (e.g. earlier slides), draw the structure of the tripep=de
glutamate-valine-alanine as it exists at pH 7. Show the
correct ioniza=on state for the side-chains and the amino
and carboxy terminal ends.









 Protein structure and function
A protein consists of one or more polypeptides
twisted, folded, and coiled into a unique shape.
Protein structures are difficult to visualize.
Ribbon drawings show fold, space filling shows shape

substrate can bind

Four Levels of Protein Structure

PRIMARY
SECONDARY
TERTIARY
QUATERNARY
Primary Structure
The primary structure of a
protein is its amino acid
sequence.
Proteins are drawn from
the amino end to the
carboxy terminal end.
Amino acids are
numbered starting from
the amino end.
Proteins are polymers of
L-amino acids held
together by peptide
bonds.
 Secondary Structures
Secondary structure is the local spatial
arrangement of the polypeptide chain
Two regular arrangements are
common:
The helix
stabilized by hydrogen bonds
between nearby residues
The sheet
stabilized by hydrogen bonds
between adjacent segments that
may not be nearby
Irregular arrangement of the
polypeptide chain is called the random
coil
 Secondary Structure

Regular repea=ng
structures that are
held together by
hydrogen bonds.

-helix and -sheet

are the secondary
structures that exist
in proteins.
 Tertiary Structure
Is the overall three-dimensional shape of a
polypeptide.
It results from non-covalent interactions between
amino acids and R groups (side-chains).

Hydrophobic/
van der Waals
CH2
CH2
H3C
CH interactions
O CH3
H CH3
Hydrogen H3C
CH Polypeptide
O
bond backbone
HO C
CH2 CH2
CH2 S S
Disulde bridge
O
CH2 NH3+ -O C CH2
Ionic bond
 Quaternary Structure
The assembly of the
polypeptide chains.
The chains can be
identical or different
in sequence.
Here alpha and beta
represent the fact
that the polypeptide
chains have different
primary structures.
Hemoglobin is a
tetramer.
haemoglobin has four polypeptide chains, made of two types of polypeptides, one the alpha chain, the other the beta chain
key factor for it to be able to deliver oxygen is because of the Heme group