Protein Chemistry and Functions

Proteins are the most abundant organic molecules of the living system; they occur in every part of the cell and constitute about 50% of cellular dry weight. Protein Chemistry MB59.pdf

Proteins form the fundamental basis of the structure and function of life.

Abnormalities in protein structure can lead to molecular diseases with profound alterations in metabolic functions.

Proteins are polymers of amino acids linked together by peptide bonds. Protein Chemistry MB59.pdf

Catalytic, structural, contractile, transport, regulatory/hormonal, genetic, and protective proteins.

Proteins that catalyse reactions; example: enzymes.

Proteins involved in structure; examples: collagen and elastin.

Proteins involved in contraction; examples: myosin and actin.

Proteins involved in transport; examples: haemoglobin, myoglobin, albumin and transferrin.

Proteins involved in regulation; examples: ACTH, insulin and growth hormone.

Proteins associated with genetic material; example: histones.

Proteins involved in protection; examples: immunoglobulins, interferons and clotting factors.

They are classified as simple, conjugated and derived proteins. Protein Chemistry MB59.pdf

Proteins composed only of amino acid residues.

Proteins containing amino acids plus a non-protein moiety known as a prosthetic group or conjugating group.

Degradation products of native proteins.

Progressive hydrolysis produces smaller and smaller chains.

They are classified as globular proteins and fibrous/sclero proteins. Protein Chemistry MB59.pdf

They are spherical or oval in shape and easily soluble.

Albumins, globulins and protamines.

They are elongated or needle-shaped, have minimum solubility and resist digestion.

Collagen, elastin and keratins.

Globular proteins are sphericaloughly globular and compact; fibrous proteins are long, elongated, thread-like or rope-like.

Globular proteins fold into a compact 3D structure; fibrous proteins have parallel polypeptide chains that are often coiled or cross-linked.

Globular proteins are generally soluble; fibrous proteins are generally insoluble.

Globular proteins mainly have dynamic/metabolic roles such as catalysis, transport, signalling and immune defence; fibrous proteins mainly have structural/mechanical roles such as support, protection and tensile strength.

Globular proteins are easily denatured by heat, pH change or chemicals, whereas fibrous proteins are more resistant to denaturation.

Globular proteins.

Primary, secondary, tertiary and quaternary structures. Protein Chemistry MB59.pdf

The number and sequence of amino acid residues from the N-terminal to the C-terminal.

The folding of the polypeptide chain formed by interactions between amino acids relatively close to each other in the primary structure.

Further folding of the secondary structure to form a functionally active three-dimensional conformation.

The spatial arrangement of the subunits of an oligomeric protein.

A monomeric protein shows only up to tertiary structure.

Quaternary structure.

Strong covalent peptide bonds.

Because it is maintained by strong covalent peptide bonds.

They are arranged in a linear chain.

The genes contained in DNA.

Biological activity depends on the primary structure, and even a slight change may result in loss of biological activity.

Glutamic acid at the 6th position of the globin chain is replaced by valine.

A covalent bond formed between the carboxyl group of one amino acid and the amino group of the succeeding amino acid, with loss of a water molecule.

They are formed by the loss of a water molecule.

A dipeptide.

One peptide bond.

A tripeptide.

Two peptide bonds.

A tetrapeptide.

Three peptide bonds.

A peptide consisting of a few amino acids.

A combination of 10–50 amino acids.

A big polypeptide chain containing more than 50 amino acids.

The amino terminal (N-terminal) end and the carboxy terminal (C-terminal) end.

It has a free alpha-amino group and contributes the first amino acid.

On the left-hand side.

From the N-terminal to the C-terminal.

The end with a free alpha-carboxyl group contributed by the last amino acid.

They are involved in peptide bond formation.

It starts from the amino terminal end.

A peptide bond forms, water is removed, and the remaining amino acid portion is called a residue.

Their suffixes are changed to -yl, except for the free C-terminal amino acid.

Valylglycylleucine.

A tripeptide composed of glutamyl, cysteinyl and glycine residues; chemically, gamma-glutamyl-cysteinyl-glycine.

It is involved in erythrocyte membrane integrity.

Glu-His-Pro.

Three amino acids; it is a tripeptide.

Nanopeptides containing 9 amino acids.

The posterior pituitary.

Angiotensin I has 10 amino acids; angiotensin II has 8 amino acids.

It elevates blood pressure.

It is generally a right-handed, stable spiral conformation of a polypeptide chain.

The polypeptide bonds form the backbone.

They extend outward.

Hydrogen bonds between NH and C=O groups of the main chain.

3.6 residues per turn.

1.5 Å.

A triple helical structure.

The polypeptide chains are almost fully extended.

3.5 Å.

Hydrogen bonds between NH and C=O groups of neighboring polypeptide segments.

Parallel and antiparallel beta sheets.

Adjacent strands run in the same direction with regard to their amino and carboxy terminal ends.

Adjacent strands run in opposite directions with regard to their amino and carboxy terminal ends.

Silk fibroin.

Flavodoxin.

Flavodoxin and carbonic anhydrase are stated in the lecture as examples involving beta-sheet arrangements.

Segments that connect the ends of adjacent strands of antiparallel beta-pleats.

Four amino acids.

Proline or glycine.

A hydrogen bond between the first and fourth amino acid residues.

It produces a firm 180° turn in the polypeptide chain.

The folding of amino acids that are far apart in the linear primary structure, bringing them closer together.

Hydrophobic side chains are oriented toward the interior, while hydrophilic side chains are oriented toward the exterior surface.

A compact, independently folding region of a polypeptide chain that often carries out a specific function.

Ligand binding, catalysis, protein-protein interaction or DNA binding.

Calmodulin.

It is a calcium-binding regulatory protein that regulates intracellular calcium levels.

The arrangement/aggregation of certain polypeptide subunits to form one functional protein.

The protein loses its function.

Each individual polypeptide chain.

A protein consisting of one polypeptide chain.

Myoglobin.

A protein consisting of two polypeptide chains; example: creatine kinase (CK).

A protein consisting of four polypeptide chains; examples: haemoglobin, immunoglobulin and lactate dehydrogenase (LDH).

Myoglobin is a monomeric protein with one polypeptide chain.

Haemoglobin is an oligomeric protein composed of 2α and 2β subunits.

Each monomeric unit forms its own tertiary structure, then the monomeric units interact to form the functional tetrameric haemoglobin.

Hydrophobic bonds, hydrogen bonds, ionic bonds, van der Waals forces and disulfide bonds.

Interactions involving nonpolar side chains.

Polar groups.

An interaction between charged groups such as -COO⁻ and -NH₃⁺.

Forces between two neutral amino acids.

A covalent linkage formed between the sulfhydryl (-SH) groups of two cysteine residues, producing a cystine residue.

The disorganization of native protein structure involving loss of secondary, tertiary and quaternary structures without breaking the primary structure. Protein Chemistry MB59.pdf

Secondary, tertiary and quaternary structures.

Primary structure.

The lecture states that denaturation occurs without breaking the primary structure.

Heat, UV radiation, X-ray, ultrasound and pressure.

Acids, alkalies, organic solvents such as ether and alcohol, urea, salicylate and heavy metals such as lead and mercury.

They unfold or become disorganized.

It decreases solubility.

It increases precipitability.

Biological activity is lost.

Denatured proteins become easily digestible.