1

1.2 CARBOHYDRATES

1.4 PROTEINS

1.3 LIPIDS

1.5 NUCLEIC ACIDS

1.1 WATER

2

1.4 PROTEINS

1.4 Proteins (2 hours)Objectives :

• Describe the basic structure of amino acids.

• Describe the classes of amino acids and explain how they are grouped.

• Explain primary, secondary, tertiary & quaternary levels of protein structure and the types of bonds involved.

• Explain the effect of pH & temperature on the structure of protein.

• Classify proteins according to their structures.

PROTEINS

Classes ofamino acids

Formation & breakdown of dipeptide

Effect of pH &

temperature

Classification according to

structure

Structure of amino acid

Levels of protein

structure

polar, non-polar, acidic, basic

1o, 2o, 3o, 4o levels

fibrous, globular, conjugated

5

PROTEINS

• Polymers called polypeptides

• A protein consists of 1 or more polypeptides in specific conformations

• Always composed of C, H, O & nitrogen; & sometimes sulphur

• Monomers: amino acids

6

AMINO ACID

• Basic unit of a polypeptide/protein

• The components of amino acid:

–a basic amino group (-NH2)

–an acidic carboxyl group (-COOH)

–a variable R group (or side chain)

–a hydrogen atom

7

H

C CO

OH

CARBOXYLGroup

R

R Group

NH

H

AMINOGroup

Structure of amino acid

AMINO ACID

8

CLASSES OF AMINO ACIDS

• There are 20 common amino acids for proteins

• All have the same basic structure but differ in the side chain ( R group)

• Based on properties of the side chains, amino acids are grouped as:i. Non-polar ii. Polariii. Acidic iv. Basic

9

Classification of AMINO ACIDS

Based on Side chain (R group)

i. Non-polar

(eg: glycine)

ii. Polar (eg: serine)

iii. Acidic (eg: aspartic

acid)

iv. Basic (eg: lysine)

Non-polar amino acids have hydrophobic non-polar side chains

Polar amino acids have polar side chains (making them hydrophilic)

Acidic amino acids have –ve charged side chains Basic amino acids have +ve charged side chains

C CN

R

H

H

H

OH

O

C CN

R

H

H

H

OH

OH2O

Dipeptide:consists of 2 amino acids linked by peptide bond (a covalent bond)formed through condensation reaction

DIPEPTIDE : basic unit of proteinFORMATION & BREAKDOWN OF

DIPEPTIDE

14

C CN

R

H

H

H

O

C CN

R

H

H

OH

OH2O

Peptide bond

Formation of dipeptide

Peptide bond

Formation of dipeptide

A protein/polypeptide usually contains hundreds of amino acids linked by peptide bonds

Breakdown of dipeptide occurs due to hydrolysis (catalysed by protease)

DIPEPTIDE : basic unit of protein

FORMATION & BREAKDOWN OF DIPEPTIDE

• A functional protein consists of 1 or more polypeptide chains which may be twisted, folded & coiled

• Each protein has a specific 3-D conformation

• 4 levels of protein structure: primary (1O), secondary (2O), tertiary

(3O) & quaternary (4O)

LEVELS OF PROTEIN STRUCTURE

18

Primary structureCLASSIFICATION of PROTEIN

Describes the unique sequence of amino acids joined by peptide bonds in a linear polypeptide chain

The 20 common amino acids can be arranged in different ways (determined by genetic information)

Eg: glucagon consists of a sequence of 29 amino acids

LEVELS OF PROTEIN STRUCTURE

19

Glucagon consists of 29 amino acid units

Primary structureCLASSIFICATION of PROTEINLEVELS OF PROTEIN STRUCTURE

20

Lysozyme:causes lysis of the

bacterial cell wall

Primary structure of lysozyme

Secondary structure• Once a linear chain of amino acids is

formed, it spontaneously …– coils to form the alpha helix

– or folds to form the beta pleated sheet

CLASSIFICATION of PROTEINLEVELS OF PROTEIN STRUCTURE

22

The primary structure will spontaneously coil or fold,

forming the secondary structure

Alpha helix(coiled structure)

Beta pleated sheet(folded structure)

Secondary structure• Hydrogen bonds holds the secondary

structure togetherH bonds are formed between C=O & -NH groups from the peptide bond regions

maintain the stable structure of α-helix & β-pleated sheets

CLASSIFICATION of PROTEINLEVELS OF PROTEIN STRUCTURE

Hydrogen bondshold helixin shape

(a)

Hydrogen bondshold neighboringstrands of sheet

together

(b)

Secondary structure• Shown by fibrous proteins (structural

proteins) such as..

–keratin (α-helix) found in hair, nails, horn

–silk protein (β-pleated sheet) produced by many insects & spiders

CLASSIFICATION of PROTEINLEVELS OF PROTEIN STRUCTURE

27

• silk protein fibroin~ produced by many insects & spiders

28

Secondary structure

Tertiary structure• A polypeptide may be further coiled into a

globular shape which is maintained by bonds & interactions among side chains– Disulfide bonds: strong, covalent bonds between

Rs with sulfhydryl groups– Ionic bonds: strong bonds between +ve & -ve

charged Rs– H bonds: weak bonds between polar Rs– Hydrophobic & van der Waals interactions:

weak interactions between non-polar Rs

LEVELS OF PROTEIN STRUCTURE

Ionic bondHydrogenbond

Disulfide bondHydrophobicinteraction

Tertiary structure

31

(weak bond between +ve & -ve charged side chains)

(between polar side chains)

(between non-polar side chains)

(covalent bond between side chains with sulfhydryl groups)

32

Formation of disulphide bridge

Tertiary structure : globular proteins• Eg : myoglobin, enzymes, insulin

Quaternary structure

• consists of 2 or more polypeptide chains joined to form a single functional molecule

34

CLASSIFICATION of PROTEINLEVELS OF PROTEIN STRUCTURE

Quaternary structure

35

CLASSIFICATION of PROTEINLEVELS OF PROTEIN STRUCTURE

(a) Hemoglobin (b) CollagenHeme

Alpha chain( -globin)a

Beta chain( -globin)b

Alpha chain( -globin)a

Beta chain( -globin)b

• eg: haemoglobin–consists of

4 globular polypeptide chains ( 2 α & 2 β chains )

37

..Quaternary structure

CLASSIFICATION of PROTEINLEVELS OF PROTEIN STRUCTURE

38

…Quaternary structureCLASSIFICATION of PROTEIN

• eg: Collagen –fibrous protein–has 3 helical subunits

intertwined to become a strong fibre

LEVELS OF PROTEIN STRUCTURE

39

Primarystructure

Secondarystructure

Tertiarystructure

Quaternarystructure

Results from interactions among polypeptideseg.: Hb, collagen

Depends on interactions among side chains- Hydrogen

bond- Hydrophobi

c & van der Waals interactions

- Disulfide bridge

- Ionic bondeg.: globular proteins: enzymes, hormones

Results from hydrogen bonding from polypeptide backboneCan either form α-helix or β-pleated sheeteg.: fibrous proteins: keratin, silk protein of spider

The linear amino acids sequence

4 levels of protein structure

Level of structure

Type of bond

Primary covalent peptide bonds only between amino acids

Secondary hydrogen bonds between amino acids along the peptide chain

Tertiary hydrogen, ionic, disulphide bonds & hydrophobic interactions between R groups

Quaternary hydrogen & ionic bonds between polypeptide chains40

Levels of protein structure

LEVELS OF PROTEIN STRUCTURE

• Change in pH & temperature may cause denaturation of protein–where protein lose its natural specific

conformation–due to disruption of H, ionic, disulfide

bonds & hydrophobic interactions–causes the protein to lose its ability to

function

EFFECT OF pH & TEMPERATURE

How denaturation occurs at levels of protein structure

Quaternary structure (40) • Dissociation of protein sub-units • Disruption of the arrangement of the subunits

Tertiary structure (30) • Disruption of:

– Disulfide bridges– Hydrogen bonds– Ionic bonds – van der Waals & hydrophobic interactions

How denaturation occurs at levels of protein structure

Secondary structure (20) • proteins lose all regular patterns (alpha-helixes &

beta-pleated sheets) because of the disruption of hydrogen bonds

Primary structure (10) • not disrupted by denaturation • remain as sequence of amino acids held together

by covalent peptide bonds

• Denaturation is sometimes reversible; ~ an unfolded protein can be restored to its

correct folding & regains its biological activity RENATURATION

• If the denatured protein remains in aqueous environment & the denaturing agent is removed, it may renature when chemical & physical aspects of its environment revert back to normal

• Eg: keratin in rebonding technique

46

1. Fibrous proteins–polypeptide chains organized as

strands / sheets–stable structures; won’t dissolve in

water–role in mechanical & structural

functions–eg: collagen, keratin

CLASSIFICATION OF PROTEINS ACCORDING TO STRUCTURE

2. Globular proteins–polypeptides folded into spherical

shape–relatively unstable structure; may form

colloids in water–generally for metabolic & chemical

processes –eg: enzymes, haemoglobin, myoglobin

3.Conjugated proteins–proteins with non-protein material

(prosthetic group) within their structure–eg: - glycoprotein

- lipoprotein- haemoglobin- nucleoprotein- flavoprotein- mucin

[fibrous protein] [conjugated globular protein]

Classes of proteins (according to function)

Transport proteins channel proteins; haemoglobin

Defensive proteins immunoglobulin

Hormonal proteins insulin

Enzymatic proteins amylase

Contractile & motor proteins

actin; myosin

Structural proteins collagen; keratin

Storage proteins ovalbumin

SEMESTER 1SESSION 2009/2010

Question • Compare globular protein and fibrous protein and give an example for each.

[10 marks]

SEMESTER 1SESSION 1999/2000

Question• List down the functions of proteins.

[12 marks]

References

• Campbell, 8th edition

• Solomon, 9th edition

Next Subtopic….• 1.5 Nucleic acids

55

1.2 CARBOHYDRATES

1.4 PROTEINS

1.3 LIPIDS

1.5 NUCLEIC ACIDS

1.1 WATER