Basic and General Biochemistry Amino Acid and Protein PDF

Amino Acid & Protein Amino acid – is the basic unit of a Protein. Stereoisomerism (D / L):  Classification is based on the chemical properties of the “R” group of the amino acid. Whether it is polar or non polar, acidic or basic (i) Hydrophobic & non-polar (ii) Polar and uncharged (ii...

Amino Acid & Protein Amino acid – is the basic unit of a Protein. Stereoisomerism (D / L):  Classification is based on the chemical properties of the “R” group of the amino acid. Whether it is polar or non polar, acidic or basic (i) Hydrophobic & non-polar (ii) Polar and uncharged (iii) Polar and negatively charged (iv) Polar and positively charged  Amino acids can also be classified according to their “R” group in a different way, such as; (a) Aliphatic amino acids (leu, ile, ala, val). (b) Aromatic amino acids (phe, trp, tyr) (c) Amino acids containing sulphur (cys, met) (d) Amino acids containing a hydroxyl group (thr, ser). (e) Acidic amino acids (asp, glu) (f) Basic amino acids (lys, arg, his) (g) Imino acids (pro). Pro has a cyclic R group (h) Amides (Gln, Asn) Generally soluble in polar solvent (H2O) and insoluble in organic solvents because they have polar groups; some easier than others to dissolve. Aliphatic ones are soluble in organic solvents. High melting point (~300oC) because of their crystalline structure, highly charged, polar groups. Aromatic amino acids absorb UV light because of their conjugated double bonds in their R groups. Because of this proteins containing these amino acids can be detected in colorless solutions. Amino acids are amphoteric molecules and are called zwitterions because they contain both positive and negative charges depending on the functional groups present in the molecule. They are affected by pH of their surrounding environment and can become more positively or negatively charged due to the loss or gain of protons (H+). Amino acids which make up proteins may be positive, negative, neutral or polar in nature, and together give a protein its overall charge. Proteins are biopolymers of amino acids. They vary greatly in size; large proteins can have 1000-2000 amino acids (collagen) and the small ones have less than 100 amino acids (insulin has 51 amino acids). Myoglobin has 153 amino acids. The medium size ones have ~400-500 amino acids such as ADH (374) and hemoglobin (574). Two classes – Globular or Fibrous proteins. They function as enzymes or as a structure or for transport, as hormones, etc. Conjugated proteins – those that possess a non-protein moiety – ex hemoglobin has haem/heme The Primary structure – the linear sequence of amino acids in a protein. The Secondary structure – local conformations of the polypeptide chain formed as a result of the regular folding of backbone atoms without participation of side chain groups OR common folding patterns in protein structure OR structure of the polypeptide chain resulting from a lot of H bonding between neighboring peptide bonds. The Super Secondary Structures – the arrangement of secondary structures in a specific manner. The Tertiary structure – this is the 3-dimensional structure of the protein formed as a result of interactions between amino acids far away from each other in the primary sequence. The Quaternary structure – the association or arrangement of polypeptide chains (subunits) in an oligomeric protein. (a) The  - helix A lot of hydrogen bonding between C=O and N-H groups of neighboring peptide bonds Helix is Right Handed In a globular protein, on average there are ~11 amino acid (aa) in one helix (can be up to 53aa). (b) The -structure: like the alpha helix, has many hydrogen bonds between neighboring peptide bonds of the same or different chain. 2 types; Parallel (chains in same direction) or Anti-parallel (chain in different directions). Forms the -pleated sheet structure. In a globular protein there are 2-15 aa in this structure (average = 6). the anti-parallel is more commonly found. there is a slight right-handed twist. usually found in the central core of globular proteins. The -structure The 3-D structure of a particular protein /polypeptide. Some include the arrangement of secondary structures – Super secondary structures or motifs On average 27% are in alpha helix and 23% beta structures But there are exceptions – there is 75-80% alpha helix in Myoglobin and Hemoglobin Concanavalin A has only beta structures and no alpha helices. It is a lectin protein that binds selectively to carbohydrates (sugars, glycoproteins) found in plants, human etc. Usually all hydrophobic aa are found in the protein interior (val, leu, met) Polar and charged aa (glu, asp, his, lys) are found on the surface of the proteins – meets water molecules Polar aa with no charge can be found inside or on the surface of globular proteins (ser, asn, tyr) Usually globular proteins that are large (>200aa) have DOMAINs – for example, domain A & B (ex. The enzyme glyceraldehyde 3-P DH, phosphoglycerate kinase) (a) The Peptide bond – its geometry: The C=O, C-N atoms are planar. Degree of rotation depends on the size of the R groups of the amino acids in the peptide bond It has a double bond characteristic. The structure and geometry of the peptide bond limits the degree of rotation or conformational coiling that can take place. (b)The Hydrogen bond (c) Hydrophobic interactions Occurs between side chains (R) that are hydrophobic in nature Automatically/spontaneously avoids interaction with water (more stable) Usually in the core of globular proteins (d)Electrostatic interactions Occurs between side chains that are charged (ex: between -- COO- with --NH+ groups) 3 (e) Van der Waals interactions / dipole-dipole: Transient weak electrical attractions; electron clouds around molecule fluctuate and forms temporary electric dipoles (ex: between two methyl groups, –CH3) (f) Disulphide bond: Between side chains of cysteine residues linking together polypeptide chains (same or different chains) (--CH2-SH + --CH2-SH  --CH2-S-S-CH2--) Myoglobin Concanavalin A The fourth level of protein structure is concerned with the interaction of 2 or more polypeptide chains to associate to form a larger protein molecule. Proteins with more than one polypeptide chain are said to be oligomeric, and the individual chains are called subunits or monomers of the oligomer. The geometry of the molecule is its quaternary structure. Two subunits forms a dimer, three a trimer, four a tetramer etc. The subunits (polypeptide chains) may be identical (homogeneous) e.g. muscle creatine kinase is a dimer of 2 identical subunits or non-identical e.g. haemoglobin is a tetramer and contains 2 alpha + 2 beta subunits (heterogeneous).