Protein Chemistry Pt. 1 PDF

PROTEIN CHEMISTRY PT.1 Building blocks of proteins. Most of the amino acids found in WHAT ARE PROTEINS? protein, except proline, are alpha- Large molecules...

PROTEIN CHEMISTRY PT.1 Building blocks of proteins. Most of the amino acids found in WHAT ARE PROTEINS? protein, except proline, are alpha- Large molecules amino acids. Made up of chains of amino acids Alpha – because the amino group linked together in a long chain. is attached to α carbon atom, Amino acids are linked by a adjacent to the carboxyl group. peptide bond or amide bond. GENERAL FORMULA OF AMINO Found in every cell in the body. ACID Involved in most of the body’s functions and life processes. Name derived from Greek word "Proteios," which means “holding first place.” The R group is different for each STRUCTURE OF PROTEINS amino acid, and it is the group Made up of chains of amino that defines the amino acid. acids; classified by number of Amino acid side chain is not amino acids in a chain: restricted to alkyl groups; may Peptides: fewer than 50 amino contain: acids 1. Open-chain, cyclic, or Dipeptides: 2 amino acids aromatic HC groups Tripeptides: 3 amino acids 2. Additional amino or carboxyl Polypeptides: more than 10 groups amino acids 3. Hydroxyl groups Proteins: more than 50 amino 4. S-containing groups. acids Typically, 100 to 10,000 amino acids linked together OPTICAL ACTIVITY OF AMINO ACIDS AMINO ACID All 20 AAs, except glycine, have at least one asymmetric or chiral Amino acids are composed of carbon atom. carbon, hydrogen, oxygen, and Glycine, the simplest amino acid, nitrogen. is optically inactive. An organic compound that Amino acids in proteins are L- contains two functional groups: configurated. an amino group (-NH2) and carboxyl group (-COOH).  Only L-amino acids are Examples: phenylalanine, valine, manufactured in cells and threonine, methionine, arginine assembled into proteins. (required for the young, but not L-amino acid refers to a for adults), tryptophan, histidine, stereoisomer of a particular isoleucine, lysine & leucine. amino acid whose amino group 2. Non-essential amino acids is on the left side in its Fisher Amino acids which can be projection. (-NH2 is to the left of synthesized by the human body. the α-carbon) There are 11 nonessential amino L-α glycine, the only achiral acids: alanine, arginine, amino acid. It is achiral because asparagine, aspartic acid, of the identical H attached to cysteine, glutamic acid, penultimate carbon. glutamine, glycine, proline, L-α alanine, its C2 is an serine, and tyrosine. asymmetric carbon because there are 4 different groups CLASSIFICATION OF AMINO ACIDS attached to it. These are -COOH, ACCORDING TO SIDE CHAIN -H, CH3 and –NH2. POLARITY L-α-valine, its C2 is an asymmetric carbon because 1. Non-polar Amino Acids there are four different groups R is an alkyl hydrophobic group attached to it. These are –COOH, which can’t hydrogen bond with -H, -CH(CH3)2 and –NH2 H2O. Absence of chiral carbon There are 9 non-polar amino makes glycine optically acids: Ala, Gly, Ile, Leu, Met, Trp, inactive while alanine & valine Phe, Pro, Val. both have chiral centers and 2. Polar Neutral Amino Acids are therefore optically active. R contains polar hydrophilic group so can form hydrogen bond with H2O. CLASSIFICATION OF AMINA ACIDS In those amino acids, R may ACCORDING TO HUMAN BODY contain: NEEDS - OH: ser, thr, tyr - SH: cys 1. Essential amino acids - Amide group: gln, asn Amino acids which organisms need to ingest because they are 3. Polar, Positively Charged necessary for nutrition and Amino Acids cannot be synthesized in the are the Basic amino acids body. lys, arg, his.  4. Polar, Negatively Charged 3. Tyrosine Amino Acids 4. Cysteine are the Acidic amino acids 5. Glutamine asp, glu. 6. Asparagine CLASSIFICATION OF AMINO ACIDS Polar, negatively charged amino BASED ON SIDE-CHAIN POLARITY acids (Acidic Amino Acids) Non-polar side chains (Hydrophobic): 1. Aspartic Acid 2. Glutamic Acid 1. Glycine – simplest AA, optically inactive (absence of chiral C) Polar, positively charged amino acids 2. Alanine: R = -CH3, methyl (Basic Amino Acids) 3. Valine: R = isopropyl 1. Lysine 4. Leucine: R = isobutyl 2. Histidine 5. Isoleucine 3. Arginine 6. Proline – an amino acid proline’s amino group is cyclical INTERACTION EXHIBITED BY R- Found at the beginning of protein GROUPS OF AMINO ACIDS or sides of helices which allows 1. Hydrophobic Interaction- protein to twist exhibited by amino acid if the R- 7. Methionine group is mainly hydrocarbon such Methionine is the metabolic as in ala, val, phe, leu, ile. precursor for cysteine; side chain 2. Ionic Interaction - exhibited by has S. acidic amino acid after 8. Phenylalanine deprotonation and by basic 9. Tryptophan amino acid upon protonation. Example: lys + asp 3. Hydrogen bonding - exhibited Only female mosquitoes bite by –OH & -SH containing amino people. They are searching for acids. Formed from amino acid isoleucine. electronegative atoms (F>O>N) with electropositive hydrogen. 4. Disulfide bond – a strong covalent bond formed when two Polar Neutral Amino Acids molecules of cysteine are (Hydrophilic) oxidized to cystine unit. 1. Serine 5. Stacking interaction or pi-pi 2. Threonine complexation – a weak attractive, non-covalent  interaction between aromatic At isoelectric point, almost all rings. Aromatic amino acids are amino acids in a solution are in phe, trp, tyr their zwitterion form. ACID-BASE PROPERTIES OF AMINO ACIDS ELECTROPHORESIS Amino acids have both a basic A method used to separate amino group and an acidic amino acids in an electrical field. carboxylic group (amphoteric The (+) charged AAs move property). toward the negative electrode They are acids when they are (Cathode). proton donors and bases when The (-) charged AAs move they are proton acceptors. toward the positive electrode At physiological pH (7.38), the (anode). carboxylic group loses a proton An amino acid at its pI does not while the amino group accepts a migrate. proton to form zwitterion or dipolar ions. PEPTIDE BOND Zwitterion Also known as amide bond. A molecule that has a (+) charge A chemical bond formed between on one atom and a (-) charge on two molecules when the carboxyl another atom, thus its net charge group of one amino acid reacts is 0. with the amino group of the other molecule, releasing a molecule of At lower pH value, zwitterion’s H2O. carboxyl grp. is protonated to form a positively charged amino It is a strong bond due to the acid double bond character of the C-N bond because of pi electron At higher pH value, zwitterion’s delocalization. amino group is deprotonated to form a negatively charged amino Links amino acids in a dipeptide, acid. tripeptide, and polypeptides. ISOELECTRIC POINT The pH at which an amino acid exists in its zwitterion form.