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:

amino acids

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

EATING Protein-Rich Foods

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

Non-essential amino acids:can be synthesised by the

body (e.g. cysteine)

Essential amino acids: must be taken in with the

diet the body cannot make them

(e.g. methionine)

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

Draw a simple diagram illustrating the arrangement of atoms in a generalised amino

acid. (2)

Question: MAY, 2002

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

The various side groups of amino acids

Table 3.2 (Part 1)

NONPOLAR

Leucine

Amino acids are nonpolar.

The various side groups of amino acids

Table 3.2 (Part 1)

simplest amino acid

POLAR UNCHARGED

Glycine:

Use your knowledge of biology to explain the following. The discovery of the amino acid glycine in interstellar space has been interpreted, by some scientists, as indicating that life is commonplace in the universe. Other scientists do not share this view.

Question: [SEP, 2006]

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.

The various side groups of amino acids

Table 3.2 (Part 1)

POLAR CHARGED

Glutamic acidAmino acids are

polar.

Table 3.2 (Part 1)

The R-groups also have functional groups:

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

Glutamic acid:e.g. carboxyl

The various side groups of amino acids

Table 3.2 (Part 1)

AROMATIC [NONPOLAR]

Phenylalanine

Let us 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

A Disulfide Bridge

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

The side groups of amino acids

determine folding of polypeptide

Table 3.2 (Part 1)

Side chains of amino acids: show a wide variety of chemical

properties

are important to determine the: 3D structure function of the protein

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?

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).

hydrophilic amino acids

hydrophobic amino acids

WHY?

The ORDER of the side chains of amino acids in a protein :

determines how it folds into a three dimensional configuration

From amino acids to proteinstwo amino acids dipeptidethree amino acids tripeptidemore than 50 amino acids

polypeptide

6 000-1000 000 protein

Some:need time &a particular

medium

All proteins can be hydrolysed into amino acids

All proteins are broken when:heated in 6M HCl at 115C for several hours

Let us discover how two amino acids

link together

H2N

H

H

C C

O

OH

Carboxylgroup

N

H

CH3

C C

O

OHH2N

H

H

C

O

C N CC

HH

CH3

OH

O

Peptidebond

Aminogroup

H

H

H2O

+

Amino acids are joined together by a condensation reaction

A peptide bond is a covalent C-N bond formed by condensation between the -NH2 of one

amino acid and -COOH of another

H

H H H H H HO O O H H O H H O

N C C N NC C C C

H CH3CH2

OH

N-terminus

N C C

CH2

C

O

OH

CH2

N C C

CHCH3H3C

CH2

OH

H H O

N C C

H H O

N C C

H H O

N C C

CH2

SH

OH

C-terminus

Many amino acids joined together = Polypeptide chain

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

Question: [SEP, 2000]

The diagram below represents part of the primary structure of one of four polypeptide chains within the haemoglobin molecule.

1. What functional group is present at position X? Amino group

2. What name is given to the bond between two amino acids? Peptide.

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 moleculeProtein

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

7 amino acids

6 amino acids but in a different sequence

Test for Protein: Biuret Test

Protein present

Test for Protein: Biuret Test

Cheese is rich in protein.

Add an equal amount of NaOH to the solution

followed by 1-2 drops of CuSO4 solution

pestle

mortar

Purple / Lilac: Positive test

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

violet colored complex.

What dictates the function of each protein?The exact sequence of amino acids.

Proteins have many functions:

enzymes

hormones

structural proteins

DNA contains the information that determines the sequence of amino acids

DNA

MUTATION

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’?

1. PKU (phenylketonuria)2. Sickle cell anaemia

Is the amino acid sequence really important?

Let us illustrate by TWO examples:

a genetic disorderno enzyme [phenylalanine hydroxylase

(PAH)] is present to process phenylalanine

PKU (phenylketonuria)

phenylalanine builds up – causes mental retardation

In PKU persons:one amino acid is present instead of

another.

Enzyme that breaks phenylalanine [phenylalanine

hydroxylase (PAH)] has about 452 amino acids.

A person with PKU must avoid foods that are high in protein, such as:

MilkCheeseNuts Meats

PKU: no cure

Testing at birth

Sickle cell anaemiaGlu: Glutamic acid Val: Valine

At low oxygen levels , haemoglobin S crystallises in the red cells distorting them into a sickle shape.

Structure of a Protein• each protein has a characteristic three

dimensional shape called its conformation

• four levels of organisation exist:-1) Primary structure2) Secondary structure3) Tertiary structure4) Quaternary structure

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 a protein:

Primary structure of insulin: 51 amino acids

Secondary structure:• the way in which the polypeptide is arranged

in space

• bonds present: 1. Peptide2. Hydrogen

Two common secondary structures are the:-helix -pleated sheet

a helix is: in a right-handed coil the most common form of secondary

structure

Secondary structure of many different proteins may be the same

helix is in a right-handed coil, maintained by H-

bonds between: CO of one amino acid and NH group of the 5th amino acid

Radical groups jut out in all directions

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

-pleated sheet chains run parallel but in opposite directions

-pleated sheet

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

-pleated sheet

Side chains stick perpendicular to the plane of the chains assuming a

zig-zag pattern

Silk is an example of a -pleated sheet

Silk Protein Structure

It is common for a polypeptide to be partly:

- beta pleated sheet

-helix

Tertiary structure:• is when the polypeptide

chain bends and folds extensively to form a precise compact

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

Tertiary structure is determined by interactions of R-groups:

1. Disulfide bonds2. Aggregation of hydrophobic side chains3. Ionic bonds4. 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

Haem

molecule is unusual as it consists almost entirely of helices

Quaternary structure:• the precise arrangement of the aggregation

of polypeptide chains held together by hydrophobic interactions, H-bonds and ionic bonds

Quaternary structure occurs in many highly complex proteins

A huge variety of quaternary structures exist

Quaternary structure of various proteins

Antibodies comprise four chains arranged in a Y-shape.

Quaternary structure of various proteins

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

Quaternary structure of various proteins

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 H-bonds connecting the chains

Collagen is found in:

cartilage

tendon

cartilage tendons (attach

muscles to bones)

Collagen is found in:

cornea

the underlayers of skin cornea of the eye

Haemoglobin:- 574 amino acids - 4 polypeptide chains

-chain

-chain -chain

-chain

(one molecule of oxygen binds to one haem)

(a) Haemoglobin (b) Iron-containing haem group

- 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

Question: May, 2011 (End-of-Year Exam)Use your knowledge to discuss the biological

significance of the following:

Structure of foetal haemoglobin varies from that of maternal haemoglobin. (5 marks)

The final three-dimensional shape of a protein can be classified as:

Fibrous Tough Insoluble in water

Globular Soluble

KeratinSilkCollagen

EnzymesAntibodies

myosin

A few proteins have both structures e.g. the muscle protein :

long fibrous tail

a globular head

Question: [MAY, 2010]

Use your knowledge of biology to describe the significance of the following. (5 marks)

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.

Question: [SEP, 2009]

Why is it mainly proteins that function as enzymes? (2 marks)

Since proteins can twist and fold in many ways, forming a variety of

active site shapes.

Two Types of ProteinCONJUGATED : globular proteins + non-protein material (prosthetic group)

SIMPLE : only amino acids e.g. albumins, histones

Name Prosthetic group

Location

Haemoglobin Haem Red blood cellsGlycoprotein Carbohydrate Blood plasmaLipoprotein Lipid Cell membranes

Denaturation &

Renaturation

A protein spontaneously refolds into its original structure under suitable conditions

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

How long can the change be?Temporary or permanent.

Is the amino acid sequence affected?Remains unaffected.

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

protein coagulates

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 metalscause the protein to precipitate out of the

solution

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

disrupt hydrophobic interactions

form bonds with non-polar groups

this in turn disrupts intramolecular H-bonding

iv) Organic solvents & detergents

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.

Question: [MAY, 2004]

1. What change has a protein undergone if it has been denatured? (3)

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.

Question: [MAY, 2004]

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

Extreme changes in pHHeatHeavy metalsOrganic solventsDetergents

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

Functions of Proteins

Type Example Occurrence / functionStructural Collagen Component of bone,

tendons, cartilage

cartilage

Functions of Proteins

Type Example Occurrence / functionStructural Keratin Skin, feathers, hair,

nails, horns

Functions of Proteins

Type Example Occurrence / functionStructural Elastin Elastic connective tissue

(ligaments)

Functions of ProteinsType Example Occurrence / functionStructural Fibrin

Viral coat proteins

Forms blood clots

‘Wraps up ‘ nucleic acid of virus

Functions of ProteinsType Example Occurrence / function

Enzymes Hydrolytic enzymesProteases

Cleave polysaccharidesBreak down proteins

Hormones Insulin Regulate blood sugar level

Functions of ProteinsType Example Occurrence / functionTransport Haemoglobin

Myoglobin

Carries O2 and CO2 in bloodStores O2 in muscle

Functions of Proteins

Type Example Occurrence / functionTransport Serum albumin

Cytochrome

Transport in blood e.g. lipidsElectron transport

Lipoprotein

Electron carriers

Functions of ProteinsType Example Occurrence / functionTransport Membrane

transporters e.g. glucose transporters

Transport sugars into cells

Functions of Proteins

Type Example Occurrence / functionProtective Antibodies Mark foreign proteins

for elimination

Functions of ProteinsType Example Occurrence / functionProtective Fibrinogen

Thrombin

Precursor of fibrin in blood clottingInvolved in clotting mechanism

Functions of ProteinsType Example Occurrence / functionMotion Myosin

Actin

Contraction of muscle fibresContraction of muscle fibres

Functions of Proteins

Type Example Occurrence / function

Storage Caesin Stores ions in milk

Functions of Proteins

Type Example Occurrence / function

Storage Ferretin Stores iron, especially in spleen

Type Example Occurrence / function

Toxins Bacterial neurotoxins

Prolonged muscle contraction

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

Functions of Proteins

Type Example Occurrence / function

Antifreeze Glycoproteins In arctic flea

Functions of ProteinsType Example Occurrence / functionReceptors Rhodopsin Light receptor in retina

Proteins are perhaps the most important group of chemicals in living things. Evaluate this statement. [1995]

Proteins are the working molecules within the cell. Discuss. [MAY, 2000]

Give an overview of the different levels of structural organisation in protein molecules. [SEP, 2004]

Essay Titles

THE END