Lecture 4 - Amino Acids

draw glycine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Gly, G, nonpolar side chain, hydrophobic

draw alanine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Ala, A, non-polar side chains, hydrophobic

draw Valine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Val, V, non-polar side chains, hydrophobic

draw leucine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Leu, L, nonpolar side chains, hydrophobic

draw isoleucne structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Ile, I, nonpolar side chains, hydrophobic

draw methionine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Met, M, nonpolar side chains, hydrophobic

draw Proline structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Pro, P, nonpolar side chains, hydrophobic

draw phenylalanine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Phe, F, nonpolar side chains, hydrophobic

draw Tryptophan structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Trp, W, nonpolar side chains, hydrophobic

draw serine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Ser, S, uncharged polar side chains, hydrophilic

draw threonine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Thr, T, uncharged polar side chains, hydrophilic

draw asparagine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Asn, N, uncharged polar side chains, hydrophilic

draw Glutamine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Gln, Q, uncharged polar side chains, hydrophilic

draw Tyrosine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Tyr, Y, uncharged polar side chains, hydrophilic

draw Cysteine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Cys, C, uncharged polar side chains, hydrophilic

draw Lysine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Lys, K, +ve charged (basic) polar side chains, hydrophilic

draw Arginine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Arg, R, +ve charged (basic) polar side chains, hydrophilic

draw Histidine structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

His, H, +ve charged (basic) polar side chains, hydrophilic

draw Aspartic Acid structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Asp, D, -ve charged (acidic) polar side chains, hyrdrophilic

draw Glutamic Acid structure, name its 3 letter name, 1 letter name, and polarity/charge of side chains, and hydrophobic/hydrophilic

Glu, E, -ve charged (acidic) polar side chains, hydrophilic

what are the amino acids with charged polar side chains often used in

catalysis by enymes

how many amino acids out of the 20 important ones are nonchiral (and which)

Glycine is the ONLY nonchiral amino acid out of the 20 important ones

Amino Acids

make up proteins

• made unique by their R groups

• all are chiral EXCEPT glycine

zwitterion

neutral compound having formal unit electrical charges of opposite sign

• neutral because has equal number of +ve and -ve charges on diff atoms on the compound

stereoisomers (and 2 types)

molecules with same formula and atom connections but different 3D shapes

• 2 types

  • enantiomers

  • diastereomers

RS system

ranks atoms around chiral carbon from highest atomic number to lowest

• then rotation of the direction they go is determined

enantiomers

non-superimposable mirror images

• same physical properties (except polarization) but differ in 3D shape

  • therefore different biological properties

• EVERY chiral center is inverted

  • ex. (R,S) → (S, R)

diastereomers

stereoisomers that are not enantiomers (they are NOT mirror images)

• occur when molecules has more than one chiral carbon

• same atomic connectivity but differ in spatial arrangement of some (but not all) of their stereocenters

• AT LEAST ONE chiral center (but not all) is inverted/changed

  • ex. (R,S) → (R,R)

stereocenters vs chiral center

• chiral center - carbon with 4 unique groups attached

  • swapping any 2 groups in the molecule gives new enantiomer

• stereocenters - any point on molecule where swapping 2 groups gives new stereoisomer (enantiomer or diastereomer)

Racemate

mixture of equal portions of enantiomers

• equal portions of R and S

Chiral molecules and polarized light

• chiral molecules are called optically active

  • because they rotate plane of polarized light

  • (-) means that molecules rotate light counter-clockwise

  • (+) means that molecules rotate light clockwise

does absolute configuration (R/S) and fisher notation (D/L) correlate to optical rotation (+/-)

NO they do not correlate

why is Fisher notation still used

because in absolute configuration (R/S), all L-amino acids are S enantiomers

• EXCEPT cystine (R config)

what is the one L-amino acid that is R config and why?

cysteine because it contains a sulfur atom

• bigger atom so it outranks the other groups and changes the config direction

L-amino acids

all natural amino acids have same relative config as L-glyceraldehyde

• so they are called L-amino acids by Fischer convention

Fischer projection

drawing that shows 3D molecules in 2D

• horizontal lines - projecting up from plane of paper

  • horizontal lines come out of paper to hug you

• vertical lines - projecting down from plane of paper

Fischer convention

designates chiral centers based on config relative to glyceraldehyde

• L - levorotatory (rotating to left or CCW)

• D - dextrorotatory (rotating to right or CW)

fischer and structure of chiral center

based his nomenclature on optical rotations for glyceraldehyde and had a 50% chance of getting the right structure for chiral centers

• guessed L and he got it right

2 ways to make a specific enantiomer

1. use enzymes because they invariably make only 1 enantiomer as a product

2. use fancy stereochemistry in the lab that will only make 1 enantiomer as a product

ambiguous notation

3 letter abbreviation for amino acids

• “Asx” means amino acids that is either Asp or Asn

• “Glx” means amino acids that is either Glu or Gln

• created because Asn can be hydrolyzed to Asp and Gln can be hydrolyzed to Glu depending on pH

peptide bonds

formed between condensation reaction between 2 amino acids

• catalyzed by rRNA, not proteins

• peptides are named in the N to C direction

amino acid residues

amino acids inside of peptides

disulfide bond

bond formed between two cysteine residues by oxidation reaction

• oxygen is reduced in the process

• often found in centre of a protein which can restrict molecular motion of that part of protein

amphoteric molecule

molecule that can act as both an acid and a base

are amino acids amphoteric? (and why)

Amino acids are amphoteric because the amino group is basic and carboxy group is acidic

• at low pH: both groups are protonated

• at intermediate pH - both groups are charged

• at high pH - both groups are deprotonated

isoelectric point (pI)

pH at which overall ionic charge on molecule is zero

• can be estimated by taking average of two pKa/s that involve neutral species

• pH < pI

  • net +ve charge

• pH > pI

  • net -ve charge

ibuprofen and thalidomide (and why chirality is important)

chirality is important because certain enantiomers can cause harm

• ibuprofen is made as a racemic mixture using conventional chemistry

  • but only one of its enantiomers is active

• thalidomide

  • (R) Thalidomide is a mild sedative, while (S) Thalidomide is a teratogen (causes birth defects)