Proteins

Proteins are of primary importance
to the life of the cell
• by dry weight proteins are the major
components of an actively growing cell

Proteins are constructed
of monomers, called:

How do we get the amino acids
needed to build proteins?

EATING Protein-Rich
Foods

Proteins ingested are digested by
proteases
enzymes called……………………

Essential amino acids:
 must be taken in with the
diet
 the body cannot make them
(e.g. methionine)

Non-essential amino
acids:
 can be synthesised by the
body (e.g. cysteine)

Structure of an
amino acid
molecule

R = Side group/chain [varies]
What is an ‘amino acid’?
An organic molecule possessing both carboxyl
and amino groups

Sometimes books give this
[amino acid in solution]:

The α carbon atom is:
 the first carbon that attaches to a
functional group

asymmetrical

Amino acids exist in two isomeric forms:
• D-amino acids (dextro, “right”)
• L-amino acids (laevo, “left”)—this form is
found in organisms

How many different amino acids:
exist:

 over 170 are known
are commonly found in proteins:

 20

Amino acids can be
grouped based on
side chains

Table 3.2 (Part 1)

The various side groups of amino
acids
NONPOLAR

Leucine

Amino acids are
nonpolar.

Table 3.2 (Part 1)

acids
POLAR UNCHARGED

Glycine: simplest amino acid

Table 3.2 (Part 1)

acids
POLAR CHARGED

Glutamic acid

Amino acids are
polar.

Table 3.2 (Part 1)

The R-groups also have functional groups:
Glutamic acid:
e.g. carboxyl

Arginine
[polar, positively
charged]
e.g. amino group

Table 3.2 (Part 1)

The various side groups of
amino acids
AROMATIC
[NONPOLAR]

Phenylalanine

Let’s mention
three amino acids
of special interest:

 Proline
 Methionine
 Cysteine

Table 3.2 (Part 4)

Proline:
causes kinks in chains

Table 3.2 (Part 3)

Methionine:
- is often the first amino acid in a
polypeptide
- contains sulfur

Table 3.2 (Part 4)

Cysteine:
 contains sulfur
 can form disulfide bridges

Sulfhydrl group

When hair is permed – disulfide
bridges in keratin are broken
and reformed

Disulfide bridges
in straight hair

Disulfide bridges
broken & reformed

Same happens when hair is
straightened

Why do amino acids differ in their
chemical and physical properties
(size, water solubility, electrical
charge)?

Because of their
different R groups

Table 3.2 (Part 1)

The side groups of
amino acids
determine folding of
polypeptide

Side chains of amino acids:
 show a wide variety of chemical
properties
 are important to determine the:
 3D structure
of the protein
 function

hydrophilic
amino acids

hydrophobic
amino acids

Where do you expect these types of amino acids to
be placed in the ion channel spanning the plasma
membrane?

WHY?

hydrophilic
amino acids
hydrophobic
amino acids

Ions (black) can only pass through the pore of the ion
channel because this is the only part with hydrophilic
amino acids lining the pore (green = area of ion
channel with hydrophilic water-loving amino
acids). The rest of the ion channel mostly consists of
hydrophobic amino acids (purple).

ORDER of the side chains of
amino acids in a protein :
determines how it folds into a three
dimensional configuration

From amino acids to proteins
two amino acids
three amino acids
more than 50 amino
acids
6 000-1000 000

dipeptide
tripeptide
polypeptide
protein

All proteins can be hydrolysed into
amino acids
• Some:
need time &
a particular medium
• All proteins are broken when:
heated in 6M HCl at 115C for
several hours

Let’s discover how
two amino acids
link together

Amino acids are joined together by a
condensation reaction
H
H2N

C

Carboxyl
group
O

Amino
group
H

+

C
OH

N

C

CH3
H2O

H2N C C

C
OH

H

H

O

H

H O

H H

O

N C C

H

CH3

OH

Peptide
bond

A peptide bond is a covalent C-N bond formed
by condensation between the -NH2 of one
amino acid and -COOH of another

Many amino acids joined together =
Polypeptide chain
N-terminus

C-terminus

H H
H

O H H

O H

H

O H H

O H

N

C N

C

C

C

C

C
H

C
CH3

N

N C

CH2

CH2

OH

C OH

H

O H H

O H H

O

H H

O

N C

C N C

C N

C N C

C

CH2

CH
H3C
CH3

C
CH2

CH2
SH

O
OH

OH

Note R groups alternate in the
Polypeptide chain

Show the position of a peptide
bond

C-N atoms of the
peptide bonds:
lie in the same
plane to form the
backbone

Side chains of the individual
amino acids:
are arranged transversal
to each other across the
backbone – this confers
stability to the molecule

A protein molecule:
 contains 100’s and 1000’s of amino acids joined
together by peptide links into one or more
chains

3 chains in collagen (in mouse tail)

Polypeptide chains can be folded
in various ways

Proteins are unbranched, not like
carbohydrates
Branched
molecule

Unbranched
molecule
Protein

Many different types of proteins
exist. How can this be?

MILLIONS of
Antibodies exist

A LARGE NUMBER
OF ENYZMES

Because any of 20 different amino
acids might appear at any position
• E.g. a protein containing 100 amino acids
could form any of 20100 different amino acid
sequences

• this is 10130, i.e. 1 followed by 130
zeros

Number and Sequence of amino acids
determine the protein
6 amino acids

5 amino acids

6 amino acids but in
a different
sequence

7 amino acids

Test for Protein: Biuret Test

Protein present

Test for Protein: Biuret Test
Cheese is rich
in protein.

pestle

mortar

Add an equal amount of
NaOH to the solution
followed by 1-2 drops of
CuSO4 solution

When a protein reacts with copper(II) sulfate
(blue), the positive test is the formation of a
violet colored complex.

Purple / Lilac:
Positive test

Proteins have many functions:
hormones
enzymes
structural
proteins
What dictates the function of each protein?
The exact sequence of amino acids.

Where is the information stored in a cell
that determines the sequence of amino
acids?

Scrambled sequences of amino acids
are useless:
in some cases, just one wrong amino acid
can cause a protein to function incorrectly
What is the cause of
‘scrambled sequences
of amino acids’?

Is the amino acid sequence really important?
Let’s illustrate by an example: PKU
(phenylketonuria)
a genetic disorder
no enzyme is present to process
phenylalanine

phenylalanine
builds up – causes
mental retardation

A person with PKU must avoid foods that are
high in protein, such as milk, cheese, nuts or
meats

• Enzyme has about
452 amino acids

• One amino acid is
present instead of
another

PKU: no cure

Testing at birth

Glycine is one of the 20 amino acids that
occur in proteins.
Proteins, in turn are useful organic
components of cells.
Proteins play various roles within a cell.
On the otherhand, glycine, is the simplest
amino acid, having hydrogen as the radical
and could have formed much more easily
than the other amino acids.
Complex machinery is required to convert
amino acids to functional proteins.

Structure of a Protein
• each protein has a characteristic three
dimensional shape called its conformation
• four levels of organisation exist:1) Primary structure
2) Secondary structure
3) Tertiary structure
4) Quaternary structure

Primary structure of a
protein:
 the number and sequence of
amino acids held together
by peptide bonds in a
polypeptide chain
 the primary structure of each
type of protein is

unique

Primary structure of insulin:
51 amino acids

Secondary structure:
• the way in which the polypeptide is arranged
in space
• secondary structure of many different
proteins may be the same
• bonds present:
1. Peptide
2. Hydrogen

Hydrogen bonds between amino acids lead to the
secondary structure of a protein

Two common
secondary
structures are
the -helix and pleated sheet

 helix is in a right-handed coil

 helix
 is in a right-handed coil, maintained by H-bonds
between:
 CO of one amino acid and
 NH group of the fifth amino acid
 radical groups jut out in all directions

 helix:
the most common form of secondary
structure

Keratin:
 is entirely helical and thus fibrous
 hardness & stretchability of keratin
varies with degree of disulfide bridges

-pleated sheet
 occurs when two
adjacent peptide
chains bind to one
another

2) -pleated sheet

 chains run parallel but in opposite directions

Side chains stick perpendicular to the plane of
the chains assuming a zig-zag pattern

-pleated sheet

Silk is an example of a pleated sheet

Silk Protein Structure

Elastin in elastic connective tissue consists of
many cross-linked polypeptides

It is common for a polypeptide to be partly:

 an -helix
a - beta pleated sheet:
-helix

- beta pleated
sheet

Tertiary structure:
• is when the polypeptide
chain bends and folds
extensively to form a
precise compact

• is a complex, three-dimensional that
determines the final configuration of the
polypeptide

Tertiary structure is determined by
interactions of R-groups:
•
•
•
•

Disulfide bonds
Aggregation of hydrophobic side chains
Ionic bonds
Hydrogen bonds

Further folding of the polypeptide chain
contributes to the tertiary structure of a protein

Which amino
acid forms
disulfide bridges?

Cysteine

Hydrophobic Interactions are a major
force in the folding of globular proteins

Myoglobin:
 153 amino acids in a single polypeptide
chain
 no disulfide bridges
 molecule is unusual
as it consists almost
entirely of helices

Haem

Quaternary structure:
• the precise arrangement of the aggregation
of polypeptide chains held together by
hydrophobic interactions, H-bonds and ionic
bonds
• occurs in many highly complex proteins
• a huge variety of quaternary structures

Quaternary structure of various proteins
Antibodies comprise four
chains arranged in a Y-shape.


Actin
- hundreds of globular chains
arranged in a long double helix


ATP synthase - 22
chains forming a
rotating motor.

The joining of more than one polypeptide chain
leads to the quaternary structure of proteins

Collagen is:
 a triple helix
 a fibrous protein
 cannot be
stretched due to Hbonds connecting
the chains

Collagen is found in:
 cartilage
 tendons (attach
muscles to bones)

cartilage
tendon

Collagen is found in:

cornea

 the underlayers
of skin

 cornea of the eye

Haemoglobin:
- 574 amino acids
- 4 polypeptide chains
-chain

-chain

-chain

-chain

(a) Haemoglobin

(b) Iron-containing haem group

(one molecule of oxygen binds to one haem)

- haem is an iron-containing porphyrin, acting as
prosthetic group of several pigments
- prosthetic group is a non-protein group which
when firmly attached to a protein results in a
functional complex (a conjugated protein)
- porphyrin is a macromolecule
composed of four subunits

How is it possible for foetal
haemoglobin to obtain oxygen from
the maternal haemoglobin?

Foetal haemoglobin is structurally
different from that of an adult :
as it has gamma chains instead of beta

What does this difference in structure
result in?

Structural difference results in foetal haemoglobin
being able to obtain oxygen from the placenta as it has
a higher affinity for oxygen than the mother’s
haemoglobin

Structure of foetal haemoglobin varies
from that of maternal haemoglobin.

The final three-dimensional shape of a protein
can be classified as:
Fibrous
 Tough
 Insoluble in water

Globular
 Soluble

Keratin
Silk
Collagen

Enzymes
Antibodies

A few proteins have both
structures e.g. the muscle protein :
myosin
long fibrous
tail

a globular
head

Proteins have tertiary and quaternary
structure.

The tertiary and quaternary structures of
proteins create a variety of molecules,
each able to carry out a particular
function.

Since proteins can twist and fold in
many ways, forming a variety of
active site shapes.

Two Types of Protein
SIMPLE :
only amino acids
e.g. albumins, histones

CONJUGATED :
globular proteins +
non-protein
material
(prosthetic group)

Name

Prosthetic
group
Haemoglobin Haem
Glycoprotein Carbohydrate
Lipoprotein Lipid

Location
Red blood cells
Blood plasma
Cell membranes

The loss of the specific three-dimensional
conformation (secondary structure) of a protein

A protein spontaneously refolds into its original
structure under suitable conditions

Why is denaturation of proteins
considered as harmful to an
organism?

The molecule unfolds and cannot
perform its normal biological
functions.

Denaturation agents can be:
i) Heat
ii) Strong acids & alkalis and high
concentrations of salts
iii) Heavy metals (e.g. mercury)

iv) Organic solvents and detergents

i) Heat
- weak hydrogen bonds and non
polar hydrophobic interactions
are disrupted
- Why?

Heat increases the
kinetic energy

Causes the molecules
to vibrate so rapidly
and violently that
bonds break

ii) Strong acids & alkalis + high

concentrations of salts
ionic bonds are
disrupted
the protein is
coagulated

Coagulation of milk by adding salts

Breakage of peptide bonds may occur if the
protein remains in the reagent for a long time

iii) Heavy metals
cause the protein to precipitate out of the
solution

Cations (+) form strong bonds with carboxylate anions
(COOH-) and often disrupt ionic bonds

iv) Organic solvents & detergents
disrupt hydrophobic
interactions
form bonds with non-polar
groups
this in turn disrupts
intramolecular H-bonding

Why does the solution become purple when
beetroot discs are placed in detergent?

1. Proteins in cell membrane & tonoplast are
denatured.
2. Phospholipid bilayer is damaged.

Why is the skin wiped with alcohol before an
injection is given?

Alcohol is used as a disinfectant.
It denatures the protein of any
bacteria present on the skin.

What change has a protein undergone if it has been
denatured

When a protein is denatured it loses its three
dimensional shape in space. Its tertiary
structure is destroyed and cannot fold
properly. Hydrogen bonds, ionic bonds and
hydrophobic interactions that are useful to
determine the final shape of the molecule are
destroyed.

List TWO agents that may cause denaturation of a
protein. (2)

Extreme changes in pH
Heat
Heavy metals
Organic solvents
Detergents

Buffering capacity
of proteins

A buffer can donate or accept H+ to
stabilise the pH.

Why are buffers needed?
To keep solution at a constant pH.

The need of buffers in organisms
Reactions in
cells change pH
in blood.
Proteins change
shape if pH
changes.

Name THREE buffers in organisms:

Hydrogen
carbonate

Buffering capacity of amino acids

Zwitterion: a compound with both acidic and basic
groups
Isoelectric point is that pH at which a zwitterion
carries no net electrostatic charge

Buffering actions by phosphate and
hydrogen carbonate

Functions of Proteins

Type
Example Occurrence / function
Structural Collagen Component of bone,
tendons, cartilage

cartilage


Type
Structural Keratin Skin, feathers, hair,
nails, horns

Type
Structural Elastin
Elastic connective tissue
(ligaments)

Type
Example
Structural Fibrin

Occurrence / function
Forms blood clots

Viral coat proteins ‘Wraps up ‘ nucleic
acid of virus

Type
Enzymes

Example
Hydrolytic
enzymes
Proteases
Hormones Insulin

Cleave
polysaccharides
Break down proteins
Regulate blood sugar
level

Type
Example
Transport Haemoglobin Carries O2 and CO2 in
blood
Myoglobin
Stores O2 in muscle

Type
Example
Transport Serum albumin Transport in blood e.g.
lipids
Cytochrome
Electron transport

Lipoprotein

Electron carriers

Type
Example
Transport Membrane
transporters
e.g. glucose
transporters

Transport sugars into
cells

Type
Example
Protective Antibodies

Mark foreign proteins
for elimination

Type
Example
Protective Fibrinogen

Thrombin

Precursor of fibrin in blood
clotting
Involved in clotting
mechanism

Type
Motion

Example
Myosin
Actin

Contraction of muscle
fibres
Contraction of muscle
fibres

Type


Storage Caesin

Stores ions in milk

Type

Example

Storage Ferretin

Stores iron, especially in spleen

Type

Example

Toxins

Bacterial
neurotoxins

Occurrence /
function
Prolonged muscle
contraction

Patient Suffering From
Tetanus.
Painting by Sir Charles
Bell, 1809.

Type

Example

Antifreeze Glycoproteins

Occurrence /
function
In arctic flea

Type
Example
Receptors Rhodopsin Light receptor in retina

Proteins

More Related Content

What's hot

Viewers also liked

Similar to Proteins

More from Dr Muhammad Mustansar

Proteins