Proteins

Proteins are substances made up of

many amino acids.

Amino acids are organic molecules with

carboxyl and amino groups
AMINO ACIDS
Proteins

Amino acids differ in their properties due to

differing side chains, called R groups- gives
each their uniqueness
Amino acid
Each amino acid can be identified a 3-lettter or 1-
letter code
Eg. Alanine : Ala, A
Tryptophan: Trp, W
Glycine: Gly, G
Valine: Val, V
 Amino acids

Plants are able to make all the amino acids

they require from simpler substances

Animals are unable to synthesize all they

need and therefore must obtain ready made
amino acids from their diet

These are known as essential amino acids

 Polypeptides
Amino acids are linked by peptide bonds

Once these bonds are formed

The protein folds into a particular shape as a

result of four other types of bonds

Ionic bonds
Hydrogen bonds
Disulphide bonds
Hydrophobic interactions
 Amino acids are linked by peptide
bonds which results from a
condensation reaction.
As the peptide bond is formed, one
hydrogen atom from one amino acid
and one hydroxyl group from the
another amino acid join together to
form a water molecule.
 When two amino acids are joined
together a peptide bonds forms
linking the C of the carboxylic group of
one amino acid with the N of the
amino group of the other.
 Each polypeptide has a unique linear sequence
of amino acids, with a carboxyl end (C-
terminus) and an amino end (N-terminus)

Polypeptides are unbranched polymers built

from the same set of 20 amino acids

A protein is a biologically functional molecule

that consists of one or more polypeptides
A functional protein consists of one or more polypeptides
precisely twisted, folded, and coiled into a unique shape
The sequence of amino acids determines a proteins three-
dimensional structure A proteins structure determines its
function
Four Levels of Protein Structure
Primary structure - a unique
sequence of amino acids

Secondary structure- consists of coils

and folds in the polypeptide chain
Four Levels of Protein Structure

Tertiary structure - determined by

interactions among various side chains (R
groups) of the polypeptide chain.

Quaternary structure - results when a

protein consists of multiple polypeptide
chains
Primary structure is a
series of amino acids
in a polypeptide chain

This sequence is
determined by the
gene which
determines the
sequence of amino
acids
 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
 Secondary Structure
The coils and folds of secondary
structure result from hydrogen bonds
between the amino acids of the
polypeptide backbone.
 Secondary Structure

Hydrogen bonds usually form

between the O of CO group of one
amino acid ( small negative charge)
and the H of -NH group of the
amino acid four places ahead of it in
the chain.
 Secondary Structure

Typical secondary structures are:

- a coil called an helix and

- a folded structure called a pleated

sheet which are maintained in shaped by
Hydrogen Bonds.
Figure 5.20c
Secondary structure

helix

Hydrogen bond
pleated sheet

strand, shown as a flat

arrow pointing toward
the carboxyl end

Hydrogen bond
http://www.biog1105-1106.org/demos/105/unit1/fibrous_v_glob.html
Figure 5.20b

Secondary Tertiary Quaternary

structure structure structure

helix

Hydrogen bond
pleated sheet
strand
Transthyretin
Hydrogen Transthyretin protein
bond polypeptide
 Tertiary structure is determined by
interactions between R groups, rather
than interactions between backbone
constituents of the polypeptide chain (
secondary structure)

Usually the polypeptide chain bends

and folds extensively forming a precise
compact globular shape
 These interactions between R groups
include
hydrogen bonds
ionic bonds,
hydrophobic interactions
disulfide bonds.
 Hydrogen bonds

The Hydrogen Bond is formed between the

slightly negatively charged CO and the slightly
positively charged NH groups of the amino acids.

Hydrogen bonds are not very strong individually

and can be broken by high temperature or
change in pH.
 Ionic Bond

Forms between a R group with a full

negative charge and one with a full positive
charge.

Bond much stronger than hydrogen bond

but can be broken by changes in pH
 Disulfide Bonds

Disulfide Bonds form between the R groups

of the amino acid, Cysteine.

They are strong covalent bonds but can be

broken by reducing agents.
Hydrophobic Interactions

Formed between R groups which

contains only Hydrogen and Carbon
atoms.
This bond is quite weak.
Figure 5.20f

Hydrogen
bond
Hydrophobic
interactions and
van der Waals
interactions
Disulfide
bridge
Ionic bond

Polypeptide
backbone
 These four bonds stabilize the protein
and hold the protein in a very precise
shape and the shape of the protein
determines its function.
Figure 5.20e

Tertiary structure

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

Held in shape by the same kinds of bonds as

tertiary structures i.e hydrogen bonds, ionic
bonds, hydrophobic interactions, and
disulfide bonds.
Figure 5.20g

Quaternary structure

Transthyretin
protein
(four identical
polypeptides)
 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
Figure 5.20h

Collagen
Figure 5.20j
Proteins

Two main types:

1. Globular - typically water soluble(form colloids)

may function as enzymes, transporters,
regulator

2. Fibrous-insoluble in water (only function as

support) eg. Collagen and keratin
Fibrous vs Globular Proteins

Globular proteins have a precise shape

which is made up of non repeating
sequences of amino acids forming a
chain of same length while
Fibrous Proteins are made up of
repeating sequences of amino acids
with chains of varying lengths.
Fibrous vs Globular Proteins
Globular Proteins are usually water
soluble while
Fibrous Proteins are insoluble in water.
Fibrous vs Globular Proteins
Globular Proteins are usually
metabolically active and take part in
metabolic reactions

while Fibrous Proteins are usually

metabolically unreactive and have
structural roles.
Fibrous vs Globular Proteins
Globular Proteins eg. Haemoglobin,
enzymes. Antibodies, transporters in
membranes, some hormones ( eg
insulin
Fibrous Proteins eg. Collagen, keratin.
elastin
 Haemoglobin
Haemoglobin (Hb) is the protein molecule
responsible for transporting respiratory gases
 Quaternary structure of
Haemoglobin
In adult humans, the most common
haemoglobin type is called haemoglobin A,
consisting of two and two subunits they
made of 141 and 146 amino acid respectively.
This is denoted as 22. The subunits are
structurally similar and about the same size..
 Hemoglobin has a complex quaternary structure
which consists of four polypeptide chains bound
to each other.

Each of the 4 globulin protein subunits contains a

single nitrogenous pigmented molecule of heme
( non protein group).
 Each heme molecule contains a single iron
ion which associates with oxygen to form
oxyhaemoglobin (a bright red pigment).

The iron ion is able to bond with two oxygen

atoms.

Hence each haemoglobin molecule can carry

eight oxygen atoms.
 When the first oxygen molecule binds to one
haem group, the polypeptide structure
changes slightly, which makes it easier for an
oxygen molecule to bind to the other three.

This makes oxygen uptake in the lungs

efficiently.
Structure of hemoglobin
Collagen
 Collagen

Fibrous protein found in skin, tendons, bone,

teeth.

Consist of three polypeptide chains in the

shape of a helix that wind to form a rope
which is held by hydrogen bonds.
 Collagen

Collagen is usually very strong due to bonds

form between the R groups of lysines in the
molecules.

They can form fibrils which further joins to

form fibres
 Lipids
Made up of Carbon, Hydrogen and
Oxygen
They do not have dipoles so they are
insoluble in water.
Lipids include fats, which tends to be
solids at room temperature and oils
which tends to liquid
 Lipids
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 non-polar 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
Fats
Triglycerides

Three fatty acids are joined to glycerol by an ester

linkage, creating a triglycerol, or triglyceride
 Triglycerides

Triglycerides are insoluble in water because

none of their atoms carries an electrical
charge and so they are not attracted to water.
 Fats
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
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
Phospholipids

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
 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