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What are proteins?

Proteins are macromolecules
composed of amino acids linked
together through peptide bonds.

How are about proteins?

• the most widely distributed
biomolecules

• the most abundant biomolecules
(45% of human body)
• the most complex biomolecules
• the most diversified biological
functions

Proteins
• Most structurally & functionally diverse group
• Function: involved in almost everything



enzymes (pepsin, DNA polymerase)
structure (keratin, collagen)
carriers & transport (hemoglobin, aquaporin)
cell communication
• signals(insulin & other hormones)
• receptors
– defense (antibodies)
– movement (actin& myosin)
– storage (bean seed proteins)

§1. .1 Amino Acids • The basic building blocks of proteins • About 300 types of AAs in nature. a carboxyl group. • The C atom is an optically active center. • An amino group. but only 20 types are used for protein synthesis in biological systems. a H atom and a R group are connected to a C atom.

L-Amino acid + - H3N OOC C R H .

Amino acids • Structure – central carbon – amino group – carboxyl group (acid) – R group (side chain) H O H | || N —C— C—OH | H R • variable group There are only 20 different amino acids but they can be joined together • different for each amino acid in many different combinations to form the diverse range of proteins that • confers unique chemical exist on this planet properties to each amino acid – like 20 different letters of an alphabet – can make many words (proteins) .

and (4) acidic. also called side chains.1. (2) polar. • R groups are different in their size. • Aas are grouped as (1) non-polar.§1. hydrogen bonding capability and chemical reactivity. charge. neutral. make each AA unique and distinctive.a Classification • The R groups. (3) basic. . hydrophobic.

.Non-polar and hydrophobic AAs • R groups are non-polar. • R groups are uncharged. • AAs are insoluble in H2O. hydrophobic aliphatic or aromatic groups.

.TYPES OF AMINO ACIDS • Equal number of amino and carboxyl groups makes it neutral. more • number of amino than carboxyl groups makes it basic and more • carboxyl groups as compared to amino groups makes it acidic.

Basic AAs • R groups have one -NH2. • R groups are positively charged at neutral pH (=7.0). . • AAs are highly hydrophilic.

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4). . • AAs are soluble in H2O. • R groups are negatively charged at physiological pH (=7.Acidic AAs • R groups have –COOH.

Aspartic acid (Asp or D) glutamic acid (Glu or E) .

The amino acids.1. which can be synthesised in the body.Glutamic acid 4.2.Glutamine On the other hand. Alanine 3. those which cannot be synthesised in the body and must be obtained through diet.Aspartic acid 5. are known as essential amino acids . are known as nonessential amino acids. Valine* Leucine* Isoleucine*Arginine*Lysine* . Glycine.

amino acids show amphoteric behaviour as • they react both with acids and bases. These are water-soluble.Zwitter Ion Amino acids are usually colourless. In aqueous solution. all other naturally occurring α-amino . high melting solids and behave like salts rather than simple amines or carboxylic acids. • Except glycine. • In zwitter ionic form. the carboxyl group can lose a proton and amino group can accept a proton. crystalline solids. giving rise to a dipolar ion known as zwitter ion. This isneutral but contains both positive and negative • charges. This behaviour is due to the presence of both acidic (carboxyl group) and basic (amino group) groups in the same molecule.

This characteristic pH is called isoelectric point.Amphoteric Nature In zwitter ionic form. amino acids show amphoteric behaviour as they react both with acids and bases. . pI is determined by pK. Isoelectric point AAs in solution at certain pH are predominantly in dipolar form.and -NH3+ groups. the ionization constant of the ionizable groups. designated as pI. fully ionized but without net charge due to -COO.

R CH COOH NH2 R CH COOH NH3+ - +OH +H+ R CH COONH3 + - +OH +H+ R CH COONH2 pH<pI pH=pI pH>pI cation amphoteric anion .

Peptides A Peptide and peptide bond A peptide bond is a covalent bond formed between the carboxyl group of one AA and the amino group of its next AA with the elimination of one H2O molecule. .

Peptides can be extended by adding multiple AAs through multiple peptide bonds in a sequential order. polypeptide AAs in peptides are called as residues. tripeptide. oligopeptide. . dipeptide.

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1 Primary Structure The primary structure of proteins is defined as a linear connection of AAs along the protein chain. Peptide bonds are responsible for maintaining the primary structure. . The AA sequence must be written from the Nterminus to the C-terminus.§2. It is also called amino acid sequence.

Sickle cell anemia Hb A : Val-His-Leu-Thr-Pro-Glu-Glu-LysHb S : Val-His-Leu-Thr-Pro-Val -GluLys- .

Sickle cell anemia I’m hydrophilic! Just 1 out of 146 amino acids! But I’m hydrophobic! .

2 Secondary Structure The secondary structure of a protein is defined as a local spatial structure of a certain peptide segment. . that is.§2. the relative positions of backbone atoms of this peptide segment.

These structures arise due to the regular folding of the backbone of the polypeptide chain due to hydrogen bonding between C = O and –NH– groups of the peptide bond. .Secondary structure of protein The secondary structure of protein refers to the shape in which a long polypeptide chain can exist.

Repeating units of N(-H). and C(=O) constitute the backbone. C. The side chains are not considered. -helix -pleated sheet . H-bonds are responsible for stabilizing the secondary structure.

2. • Side chains of AA residues protrude outward from the helical backbone. .6 AAs per turn and a 0. creating a pitch of 0. • 3.§2.54 nm.15 nm vertical distance.a -helix • A helical conformation is right-handed. • The hydrogen-bonds are parallel to the helical axis.

Left-hand versus right-hand .

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5 nm (a) (b) .0.6 个残基 C原子 O原子 N原子 第n+3个肽键的H原子 H原子 第n个肽键的O原子 肽链走向 0.54 nm 3.

The -CO group of residue n is H-bonded to the NH group of residue (n+4). .

• The side chains of adjacent AAs protrude in opposite directions. • H-bonds are perpendicular to the backbone direction. • The adjacent protein backbones can be either parallel or anti-parallel. .-pleated sheet • An extended zigzag conformation of protein backbones • Protein backbones are arranged sideby-side through H-bonds.

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. the three-dimensional (3D) arrangement of all atoms.3 Tertiary Structure The tertiary structure is defined as the spatial positions of all atoms of a protein.e. . i.§2.

• hydrophobic interaction • ionic interaction • hydrogen bond • van der Waals interaction .Four types of interactions stabilize the protein tertiary structure.

.§2.4 Quaternary Structure The quaternary structure is defined as the spatial arrangement of multiple subunits of a protein.

and hydrophobic interactions. • Each individual peptide is called subunit. . trimer . ionic interactions.• Proteins need to have two or more polypeptide chains to function properly. • Polypeptide chains can be in dimer.. • These subunits are associated through H-bonds.or heteroform. as well as homo..

From primary to quaternary structure .

wool. Some common examples are • keratin (present in hair. • Such proteins are generally insoluble in water. . silk) and myosin (present in muscles). then fibre– like structure is formed. etc.Fibrous proteins • Fibrous proteins • When the polypeptide chains run parallel and are held together by hydrogen and disulphide bonds.

These are usually soluble in water. • Insulin and albumins are the common examples of globular proteins. .Globular proteins • Globular proteins • This structure results when the chains of polypeptides coil around to give a spherical shape.

ionic bonds. disulfide bridges • temperature • pH • salinity – alter 2° & 3° structure • alter 3-D shape – destroys functionality • some proteins can return to their functional shape after denaturation.Protein denaturation • Unfolding a protein – conditions that disrupt H bonds. many cannot .

.be susceptible to enzymatic digestion. . • The denatured proteins tend to .lose crystalizability. . .lose the biological activity. .increase the viscosity.Protein denaturation The process in which a protein loses its native conformation under the treatment of denaturants is referred to as protein denaturation.decrease in solubility.

Common examples of denaturationThe coagulation of egg white on boiling Curdling of milk which is caused due to the formation of lactic acid by the bacteria present in milk.• Denaturants physical: heat. bases. . organic solvents. ultraviolet light. detergents. During denaturation 2° and 3° structures are destroyed but 1º structure remains intact. violent shaking. … chemical: strong acids.

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H C H .