Class Notes (837,698)
Canada (510,399)
BIOC12H3 (56)
Lecture 2

BIOC12FAll2012 Lecture Week 2 Notes

13 Pages
Unlock Document

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
More Less

Related notes for BIOC12H3

Log In


Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.