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Boston College
CHEM 4465

PROTEINS – STRUCTURE AND FUNCTION (DR. TRAISH) Introduction to Proteins - Proteins are abundant and functionally diverse molecules - They participate in cell regulation at all levels - They share a common structural feature: all are linear polymers of amino acids - Examples of protein function: catalysis, transport and storage, coordinated motion, mechanical support (why we don’t dissolve), organism host defenses, growth and differentiation, communication Structure and Function H H O I. AMINO ACIDS HNCC H R O - a. Chemical Structure i. Alpha carbon is bound to an amino group, a carboxyl group, and a side chain b. Classification – based on characteristics of side chains i. Aliphatic, non-polar (alkyl) – hydrophobic, usually located on interior of protein 1. Gly – smallest amino acid; can be inside or outside 2. Ala 3. Val 4. Leu 5. Ile – side chain important for protein stability 6. Pro – shares many properties with aliphatic group  Alkyl chain is cyclized(imino acid)unique properties ii. Aliphatic, polar – hydroxyl- or sulfur-containing side chains 1. Ser = Alanine + hydroxyl  polar, hydrophilic (can participate in H bonding); can be site of phosphorylation 2. Thr – has secondary alcohol group  hydrophilic, polar (H-bonding); can be found on the outside of a protein because hydrophilic 3. Cys – thiol (SH) group instead of hydroxyl = more acidic more reactive  an enzyme with a lot of cysteine can form disulfide bridges  can exist at high temperatures 4. Met – hydrophobic  found on interior iii. Aromatic Amino Acids – bulky side chains; mostly nonpolar and hydrophobic 1. Phe – very hydrophobic  very important in folding (found on inside) 2. Tyr = Phe + hydroxyl group – can participate in H-bonding, but still hydrophobic (only ionizes at a high temperature) 3. Trp – has indole substituent  Deficiency of Trp  belagra (type of dermatitis) iv. Acidic side chains – have COOH group 1. Asp -  and  COOH groups  2 negative charges  acid (polar, hydrophilic) 2. Asn – replaces COOH with NH gr2up – amide of Asp PROTEINS – STRUCTURE AND FUNCTION (DR. TRAISH) 3. Glu – like Asp but with an extra methyl (so gamma COOH) 4. Gln – like Glu but COOH replaced with NH grou2 (doesn’t ionize but participates in H-bonding v. Basic Amino Acids – accept proton; each plays a critical role in protein structure and function 1. His – hydrophilic, basic, found on outside of protein  has imidazole (ring with 2 N)  can donate or receive H functions in acid/base catalysis, found in enzymes  can bind to metal ions + 2. Lys – has NH at3epsilon C  highly protonated  doesn’t lose H until very high pH; found in histones (bind DNA) 3. Arganine – side chain has quanidino group  Arg + O s nitric oxide, a vasodilator c. Ionic properties of Amino Acids i. Amino acids are ampholytes – they have both acidic and basic weakly ionizable groups ii. at a low pH, net charge is positive; at a high pH, net charge is negative iii. but mostly they exist at a physiological pH: 1. COOH ionizes and gives a H and a conjugate base (COO ) - + 2. amino ionizes and retain a H 3. this is called a zwitterion iv. an ampholyte’s isoelectric point (point at which net charge is zero) = average of pKa 1nd pKa 2 **The side chains of Amino Acids make them chemically diverse** II. ORDERED STRUCTURE OF PROTEINS a. Overview i. Primary Structure 1. linear sequence of amino acids in a polypeptide chain 2. Convention: amino terminus on the left (N-terminal), COOH terminus on the right (C-terminal) ii. Secondary Structure 1. Local folding of amino acids in primary sequence into a specific arrangement 2. Different regions of the polypeptide can be different conformations – doesn’t have to be all one or the other 3. Carbonyl and amide groups of backbone are linked by hydrogen bonds, stabilizing the secondary conformation iii. Tertiary Structure PROTEINS – STRUCTURE AND FUNCTION (DR. TRAISH) 1. Spatial arrangement of various secondary structures (relationship of domains); the complete 3-D structure of polypeptide units 2. hydrogen bonding, hydrophobic interactions, electrostatic interactions, van der Waals’ forces all stabilize conformation 3. For many proteins, tertiary is the highest level of structure iv. Quaternary Structure 1. When there is more than one subunit (even if they are all the same) 2. Structure formed by monomer-monomer interaction in an oligomeric protein (can be hetero- or homo-oligomers) 3. Forces: charge-charge, van der Walls, 4. Example: hemoglobin: 2 and 2 subunits b. Primary Structure – What is a Peptide Bond? i. A condensation reaction between the amino group of one amino acid to the COOH group of another ii. Delocalization of  electrons over O, C, N: 1. Partial double bond character of CN and little twisting about CN bond 2. C=O and CN bonds are nearly parallel 3. O, C, N, and H are nearly coplanar – the trans form
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