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

Proteins are unbranched, not like carbohydrates

Branched molecule

Unbranched moleculeProtein

Polypeptide chains can be folded in various ways

Over 170 of amino acids are knownBut 20 are commonly found in

proteins

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

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

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 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

Amino acids differ in their chemical and physical properties (size, water

solubility, electrical charge):

Because of their different R groups

Therefore, the exact sequence of amino acids

dictates

the function of each protein, whether it is: water-soluble an enzyme a hormone a structural protein

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.

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

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.

1. Peptide bonds2. Disulfide bridges3. Ionic bonds4. Hydrogen bonds5. Hydrophobic interactions

Linkages and hydrophobic interactions in proteins

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

Note R groups alternate in the Polypeptide chain

Many amino acids joined together = Polypeptide chain

N-terminus C-terminus

Show the position of a peptide bond

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.

From amino acids to proteins

two 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

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

1. Peptide bonds2. Ionic bonds3. Disulfide bridges4. Hydrophobic interactions5. Hydrogen bonds

Linkages and hydrophobic interactions in proteins

2) Ionic bond

occurs at a suitable pH between ionised -NH2 and -COOH groups

is broken by changing the pH

in aqueous solution is weaker than a covalent bond

3) Disulfide bridge (bond) when two molecules of cysteine combine,

neighbouring -SH groups are oxidised to form a disulfide bridge

Disulfide bridges are broken by

mercuric chloride

Disulfide bridges can link:

Different polypeptide chains together

Connect different parts of the same polypeptide

chain, causing the protein to bend or fold

4) Hydrogen bond in the peptide linkage the:

C-O oxygen carries a slight negative charge N-H hydrogen carries a slight positive charge

this asymmetry of charge favours H-bonding

5) Hydrophobic interactions some R groups are:

non-polar and so are hydrophobic

if a polypeptide chain contains a number of these groups and is in an aqueous environment, the chain will fold to exclude water

1. Structural2. Enzyme catalysis3. Hormones4. Transport5. Defence6. Motion7. Storage8. Regulation9. Antifreeze10. Receptors

FUNCTIONS OF PROTEINS

Functions of Proteins

Type Example Occurrence / functionStructural Collagen Component of bone,

tendons, cartilage

cartilage

tendon

bone

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

nails, horns

Functions of Proteins

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

Enzyme catalysis

Polymerases

Proteases

Synthesise nucleic acidsBreak 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

Haemoglobin

Myoglobin

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 / functionDefence Antibodies Mark foreign proteins

for elimination

Functions of ProteinsType Example Occurrence / functionDefence Fibrinogen

Thrombin

Snake venom

Precursor of fibrin in blood clottingInvolved in clotting mechanismBlocks nerve function

Functions of ProteinsType Example Occurrence / functionMotion Myosin

Actin

Contraction of muscle fibresContraction of muscle fibres

Functions of ProteinsType Example Occurrence / function

Storage Caesin Stores ions in milk

Functions of Proteins

Type Example Occurrence / function

Storage Ferretin Stores iron, especially in spleen

Ferretin

Functions of Proteins

Type Example Occurrence / function

Antifreeze Glycoproteins In arctic flea

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

4 levels of organisation

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 b Pleated

sheet

Secondary structure of many different proteins may be the same

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

secondary structure

helix is 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

pleated sheet: formed from two or more adjacent polypeptide chains

that are almost completely extended and aligned

pleated sheet may form between:

Separate polypeptide chains as in spider silk

Between different regions of a single polypeptide chain,

that is bent back on itself

pleated sheet may be present in both :

Fibrous proteinse.g. silk

Globular proteins

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

zig-zag pattern

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 the final folded shape of a globular protein

Three stages in protein folding

1. A protein is initially driven into its tertiary structure by hydrophobic exclusion from water

3. disulfide bridges (covalent links between two cysteine R groups): lock particular regions together

2. ionic bonds between oppositely charged R groups: bring regions into

close proximity

The final folding of a protein is determined by its primary structure – the chemical nature of its side groups

Myoglobin: as an example of a tertiary protein structure

153 amino acids in a single polypeptide chain

no disulfide bridges

molecule is unusual as it consists almost entirely of helices

Haem is an iron-containing compound, acting as a

prosthetic group of several pigments

The eight helical segments bend relative to each other

and form a pocket that encloses a haem group

Quaternary structure:• the precise arrangement of the aggregation

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

Haemoglobin: haem + globin• has a quaternary structure characteristic of

many multi-subunit globular proteins

• consists of four subunits:two -chain two -chain

Has a primary structure consisting of a specific sequence of amino acids

Each chain:

This then assumes a characteristic secondary structure consisting of helices and sheets that are arranged into a specific tertiary structure for each - and -globin subunit

Lastly, these subunits are then arranged into their final quaternary structure

Foetal haemoglobin is structurally different from that of an adult :

This difference in structure is important

Foetal haemoglobinhas gamma chains

instead of beta

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)

Quaternary structure occurs in many highly complex proteins

A huge variety of quaternary structures exist

Collagen is: a triple helix

a fibrous protein found in e.g. cartilage

Quaternary structure of various proteins

ATP synthase – 22 chains forming a rotating motor.

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

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 Protein

CONJUGATED : 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

Lipoprotein

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

Denaturation

Renaturation

The amino acid sequence:Remains unaffected.

The change may be:Temporary or permanent.

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.

Blood pH: 7.3-7.4

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

Hydrogen carbonate

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