Proteins

The word protein is derived from the Greek word “proteios” The word protein is derived from the Greek word “proteios”. Which means primary or of prime importance. Proteins are composed of long chains of amino acids joined together via peptide bonds. A polypeptide with more than 100 amino acid residues, having molecular mass more than 10,000u is called a protein.

Amino Acids Amino acids are derivatives of carboxylic acids formed by substitution of -hydrogen for amino functional group. COOH NH2 C R H

AA are optically active molecules due to the presence of a chiral carbon (except in the case of glycine where the R-group is hydrogen) According new IUPAC nomenclature L- D- forms were replaced for (S)- and (R)- system

Proteins play key roles in a living system Three examples of protein functions Catalysis: Almost all chemical reactions in a living cell are catalyzed by protein enzymes. Transport: Some proteins transports various substances, such as oxygen, ions, and so on. Information transfer: For example, hormones. Structural proteins: proteins with the primary purpose of producing the essential structural components of the cell. Alcohol dehydrogenase oxidizes alcohols to aldehydes or ketones Haemoglobin carries oxygen Insulin controls the amount of sugar in the blood

Amino acid: Basic unit of protein COOH NH2 C R H Different side chains, R, determin the properties of 20 amino acids.

Zwitter Ion A zwitter ion is a chemical compound that carries a total net charge of 0 and is thus electrically neutral, but carries formal charges on different atoms.

White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic 20 Amino acids Glycine (G) Alanine (A) Valine (V) Isoleucine (I) Leucine (L) Proline (P) Methionine (M) Phenylalanine (F) Tryptophan (W) Asparagine (N) Glutamine (Q) Serine (S) Threonine (T) Tyrosine (Y) Cysteine (C) Asparatic acid (D) Glutamic acid (E) Lysine (K) Arginine (R) Histidine (H) White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

Proteins are linear polymers of amino acids NH3＋ C COOー ＋ NH3＋ C COOー ＋ H H A carboxylic acid condenses with an amino group with the release of a water H2O H2O R1 R2 R3 NH3＋ C CO NH C CO NH C CO H Peptide bond H Peptide bond H The amino acid sequence is called as primary structure F T D A G S K A N G S

Classification of Proteins

Globular Proteins Proteins that consist of long chains of amino acids folded up into complex shapes. Globular proteins serve as, or form important components of, the following: Enzymes Hormones Antibodies Some structural proteins.

Structure of Insulin

Fibrous Proteins Proteins that tend to be insoluble and strong and so play a structural role in organisms for support or protection. They can be subdivided into several different types: keratins, found in hair, fingernails, and bird feathers collagens – the most abundant proteins in a vertebrate body – found in connective tissues such as cartilage elastins, found in ligaments, around blood vessels.

Structure of Keratin

DIFFERENCES BETWEEN GLOBULAR AND FIBROUS PROTEINS They are more or less spherical in shape. Globular proteins are usually soluble in water. They have polypeptide chains which lie side by side, held together by H-bonds and have thread like structure. Fibrous proteins are insoluble in water. Eg: insulin, albumins, etc. Eg: keratin, myosin, etc.

Structure of Proteins

Each Protein has a unique structure Amino acid sequence NLKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG Folding!

Basic Structural Units of Proteins

Primary Structure The sequence in which the amino acids are arranged in a polypeptide chain of a protein is called the primary structure of the protein.

Secondary structure There are two types of structural proteins: α-helix The peptide chain coils and the turns of the coil are held together by hydrogen bonds. β-pleated sheet Here the protein chains are not coiled but are stretched out.

α-helix β-sheet Secondary structures, α-helix and β-sheet, have regular hydrogen-bonding patterns.

Tertiary Structure Quaternary Structure Arises due to folding and coiling of secondary proteins. Quaternary Structure Composed of two or more polypeptide chains.

Three-dimensional structure of proteins Tertiary structure Quaternary structure

Hierarchical nature of protein structure Primary structure (Amino acid sequence) ↓ Secondary structure （α-helix, β-sheet） Tertiary structure （Three-dimensional structure formed by assembly of secondary structures） Quaternary structure （Structure formed by more than one polypeptide chains）

Close relationship between protein structure and its function Example of enzyme reaction Hormone receptor Antibody substrates A enzyme enzyme B Matching the shape to A Digestion of A! enzyme A Binding to A

Protein structure prediction has remained elusive over half a century “Can we predict a protein structure from its amino acid sequence?” Now, impossible!

Native State At normal pH and temperature, each protein will take up a shape which is energetically most stable. This shape is called the native state of a protein.

Protein denaturation Denatured state = unfolded state Native state = folded state Denaturation = heat, urea, salts

Summary Proteins are key players in our living systems. Proteins are polymers consisting of 20 kinds of amino acids. Each protein folds into a unique three-dimensional structure defined by its amino acid sequence. Protein structure has a hierarchical nature. Protein structure is closely related to its function. Protein structure prediction is a grand challenge of computational biology.

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