BCH3004 Principles In Biochemistry PDF

BCH3004 PRINCIPLES IN BIOCHEMISTRY 4(3+1) TS. DR. AZZREENA MOHAMAD AZZEME DEPARTMENT OF BIOCHEMISTRY, FACULTY OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES, UPM Proteins ▪ Proteins ▪ Peptide and polypeptide: characterization, structure and function ▪ Protein classificati...

BCH3004 PRINCIPLES IN BIOCHEMISTRY 4(3+1) TS. DR. AZZREENA MOHAMAD AZZEME DEPARTMENT OF BIOCHEMISTRY, FACULTY OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES, UPM Proteins ▪ Proteins ▪ Peptide and polypeptide: characterization, structure and function ▪ Protein classification ▪ Protein content, structure and sequence determination LEARNING OUTCOMES Students are able to: 1. explain type, structure, classification and function of proteins Protein Structure and Function ❑ Proteins → polymers consisting of amino acids linked by peptide bonds ❑ Four level of structure: i. Primary structure ii. Secondary structure iii. Tertiary structure iv. Quaternary structure Primary Structure ❑ The order in which the amino acids are covalently linked together e.g. Leu-Gly-Thr-Val-Arg-Asp-His Val-His-Asp-Leu-Gly-Arg-Thr Why is it important to know primary structure? e.g. Sickle anemia ▪ Red blood cells cannot bind oxygen efficiently ▪ Sickle cells tend to become trapped in small blood vessels, cutting of circulation and thereby organ damage ▪ Change in one amino acid residue in the sequence of primary structure Secondary Structure ❑ Hydrogen-bonded arrangement of the protein backbone ❑ The nature of the bonds in the peptide backbone plays an important role ❑ Within each amino acid residue are 2 bonds with reasonably rotation i. the bond between the α-carbon and the amino nitrogen of that residue ii. The bond between the α-carbon and the carboxyl carbon of that residue ❑ The combination of planar peptide group and the freely rotating bonds has important implication for the 3-D conformation of peptides and proteins Psi (Ψ) & Phi (ϕ) are called Ramachandran angles (after their originator, G. N. Ramachandran) The conformation of the chain shown corresponds to ϕ = +180 and Ψ = +180 ❑ The side chains also play a vital role in determining 3-D shape of a protein, but only the backbone is considered in the secondary structure ❑ 2 kinds of secondary structures that occur frequently in proteins are repeating α helix and β-pleated sheet (or β-sheet) hydrogen-bonded structures The α-Helix ❑ Stabilized by hydrogen bond parallel to the helix axis Why is the α-helix so prevalent? ❑ The helical conformation allows a linear arrangement of the atoms involved in their hydrogen bonds, which gives the bonds maximum strength → helical conformation very stable ❑ 3.6 residues of a.a for each turn of the helix and the pitch (vertical distance between one consecutive turn of the helix) of the helix is 5.4 Å (0.54 nm or 540 pm) ❑ Angstrom unit, 1 Å = 10-8 cm = 10-10 m, used for interatomic distances in molecules 3.6 residues/turn (5.4 Å) Factors disrupting α-helix 1. Proline - creates a bend in the backbone because of its cyclic structure - Cannot fit into the α-helix because i. rotation around the bond between nitrogen and the α-carbon is restricted ii. proline’s amino group cannot participate in intrachain hydrogen bonding 2. Strong electrostatic repulsion due to proximity of several charged group of the same sign e.g. lysine and arginine glutamate and aspartate  The β-Pleated Sheet ❑ The peptide backbone in the β-sheet is almost extended ❑ Hydrogen bonds can be formed between different parts of a single chain that is doubled back on itself (intrachain bonds) or between different chains (interchain bonds) Run the same direction → Parallel Run in opposite directions → β-pleated sheet Antiparallel β-pleated sheet ❑ The hydrogen bonding between peptide chains in the β- pleated sheet gives rise to a repeated zigzag structure ❑ Hydrogen bonds are perpendicular to the direction of the protein chain Supersecondary Structure and Domains ❑ Combination of α-helix, β-sheet and other secondary structures to form a protein ❑ α-helix + β-sheet + β-sheet = βαβ unit βαβ unit → two parallel strands of β-sheets are connected by a stretch of α-helix ❑ αα unit (helix-turn-helix) consists of two antiparallel α- helices ❑ Energetically favorable contacts exist between the side chains in the two stretches of helix ❑ β-meander unit, an antiparallel sheet is formed by a series of tight reverse turns connecting stretches of the polypeptide chain ❑ Greek key → antiparallel sheet → Polypeptide chain doubles back on itself ❑ Protein sequences that allow for a β-meander or Greek key can often be found arranged into a β-barrel in the tertiary structure of the protein  Fibrous proteins - usually perform structural role - e.g. collagen, keratin, fibroin - Silk fibers consist largely of protein fibroin, which, like collagen, but consists largely of β-sheet Keratin - α and β keratins - α-keratins are the major proteins of hair and fingernails, and comprise major fraction of animal skin - β keratins are found mostly in birds and reptiles I structures like feathers and scales Fibroin - β-sheet structure produced by silkworm and spiders - Silkworm fibroin contains long regions of stacked antiparallel β-sheets, with the polypeptide chain running parallel to the fiber axis - The stacked sheets are held together by noncovalent interactions between interdigitated side chains - The β-sheet regions comprise multiple repetition of the sequence - Silkworm fibroin → every residue is glycine, which usually followed by alanine and serine residues The arrangement of sheets results in a fiber that is strong and incapable of being stretched because the covalently bonded chains are already stretched to nearly maximum possible length Collagen - Most abundant single protein in most vertebrates - Collagen fibers constituent the major portion of tendons, and network of collagen fibers is an important constituent of skin - The basic unit of collagen fiber is the tropocollagen molecule, a triple helix of 3 polypeptide chains, each about 1000 residues in length  Globular proteins - the backbone folds back on itself to produce a more or less spherical shape - water soluble proteins - compact structure - e.g. myoglobin Tertiary Structure ❑ 3-D arrangement of all the atoms in the molecule ❑ Conformation of the side chains and the positions of any prosthetic groups Forces Involved in Tertiary Structure ❑ Noncovalent interactions Quaternary Structure ❑ Proteins that consist of more than one polypeptide chain ❑ Each chain is called subunit ❑ The number of chains can range from 2 to more than a dozen ❑ The chains may be identical or different ❑ Commonly occurring examples are dimers, trimers and tetramers, consisting of 2, 3 and 4 polypeptide chains, respectively → called oligomer ❑ The chains interact with one another noncovalently via electrostatic attractions, hydrogen bonds and hydrophobic interaction Allosteric proteins ❑ Not all multisubunit proteins exhibit allosteric effects, but many do ❑ Subtle changes at one site on a protein molecule may cause drastic changes in properties at a distant site The structure of hemoglobin. Hemoglobin (α2β2) is a tetramer consisting of four polypeptide chains (two α-chains and two β- chains