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Lecture 2

BIOC12Fall2012 Lecture Week 2 Notes.docx

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Biological Sciences
Rongmin Zhao

BIOC12Fall2012 Lecture Week 2: Amino acids and peptide bonds (Chapter 4) General structure of standard amino acid structure o Chiral Carbon = attached to 4 different groups o Achiral = attached to same groups o o a carboxyl acid group and an amino group are bonded to the same carbon, and at least one of the other groups is a H o except for proline and its derivatives all of the amino acids commonly found in proteins possess this type of structure Structures and Properties of Amino Acids o carboxylic group is negatively charged so it can combine with the positively charged amino group on another amino acid to from a peptide bond through dehydration o inside a cell, under normal physiological coniditons (pH =7), the amino group is protonated because the pKa of the group is close to 9 and the carboxyl group is ionized because the pKa of that group is below 3 (acidic) 1 The 20 Common/Standard Amino Acids Nonpolar (hydrophobic) amino acids o methionine is always the first amino acid to be inserted into the polypeptide by the ribosome during protein synthesis o important for the processes that drive protein chains to fold  to form their natural structure o tryptophan is borderline in this group because it can sometimes interact with water via its N-H of the indole ring 2 Polar, Uncharged Amino Acids o except for glycine they all can form H bonds with water o play nucleophillic roles in enzyme reactions o glycine’s H as the R group does not form H-bonds with water, and glycine is soluble mainly due to the amino and carboxyl groups The Acidic Amino Acids o at pH =7, they have a net negative charge  so they are found in the form of aspartate and glutamate (-COO ) o important for proteins that bind metal ions 3 Basic Amino Acids o arginine is the most basic amino acid o net positive charges at pH=7 o at pH=7, histidine (pKa=6), only 10% is protonated  so they play important roles as proton donors and acceptors in many enzyme reactions o arginine and lysisne side chains which are protonated at pH=7 participate in electrostatic interactions in proteins Naming amino acids o o the alpha carbon is always next to the carboxyl group o in systematic names though, the carboxyl group C is always number 1 and the adjacent C are numbered sequentially o 4 The amino acids can be grouped by their side chains (R-group) o can be grouped as aliphatic, aromatic, sulphur containing amino acids, and small amino acids The aliphatic amino acids: (blue indicates the hydrophobic side chain) o The aromatic amino acids o  all 3 absorb UV light (used to measure protein []) o the R group is hydrophobic but both tyrosine and tryptophan also have hydrophilic proterties because of OH and NH groups o o phenylalanine has a benzyl side chain and is hydrophobic o tyrosine has a phenol side chain o tryptophan has a bicyclic indole as a side chain o both tyrosine and tryptophan have hydrophilic properties Sulfur containing amino acids: o o methionine contains a nonpolar thioether group (almost always the first amino acid in a protein, but may be cleaved) o cysteine has a somewhat hydrophobic side chain but the sulfur atom can from weak hydrogen bonds with O and N  the S also acts as a weak acid and can loose its H 5 o 2 cysteins for a disulfur bond which can be broken by a reducing agent Side chains with alcohol groups – aliphatic side groups o o threonine has 2 chiral centers o uncharged polar side chains contain B-hydroxyl groups o gives molecule hydrophilic character o hydroxyl groups have weak ionization properties o does not ionize in aqueous solution (at physiological condition at least) Acidic (carboxylate) R groups and Amine derivatives o these are dicarboxylic amino acids which are negatively charged, ionizable at neutral pH, have hydrophilic side chains o o at neutral pH they are in conjugated form, therefore called aspartate and glutamate rather than aspargine and glutamine o amides are uncharged and highly polar  they are usually on the surface of proteins and can interact with water as well as other polar amino acids through H bonds Proline o o proline is different than all other 19 chiral amino acids in that is delta carbon side chain form a bond with the N of the alpha amino group of the alpha carbon o the formation of the ring restricts side chain conformation 6 Overlap of Classification o C (H-H) refers to the reduced form of Cysteine o C (S-S) indicates that there are 2 Cys molecules linked together Several Amino Acids Occur Rarely in proteins – modified normal amino acids o selenocysteine o pyrolysine occurs in several archeal species o hydroxylsine, hydroxyproline occurs in collagen o carboxyglutamate – blood clotting proteins o pyroglutamate – in bacteriorhodopsin o GABA – epinephrine, histamine, serotonin act as neurotransmitters and hormones o Phosphorylated amino acids act as a signaling device o 7 The side chains of amino acids can be modified – rare amino acids in proteins o o the alcohol groups of Ser, Thr and Tyr are often phosphorylated o the E-NH2group of Lys is often acetylated (histone acetylation) o the hydroxyproline is a major amino acid in collagen o the modification of a side chain is a posttranslational event Many amino acid derivatives are bioactive molecules o GABA is a derivative of Glu by decarboxylation  it is a neurotransmitter o Histamine is a derivative of His by decarboxylation  local mediator of allergic reaction o Dopaime is a derivative of Tyr by decarboxylation  neurotransmitter o Thyroxine is a derivative of Tyr  hormone for metabolism Green fluorescent protein (GFP) is a commonly used reporter protein o From jelly fish  naturally fluorescent protein o Made up of 238 amino acids o The prosthetic (light emitting group) is an oxidative product of the sequence FSYGVQ 8 Mechanism of GFP
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