Biochem: Chpts 1-3

Components to Amino Acids

four groups attached to a central carbon

Amino group, carboxylic acid, hydrogen group, and R group

What is the purpose of the R group

determines chemistry and function of that amino acid

Stereochem of Amino Acids

stereochem for alpha carbon is L for all chiral amino acids in eukaryotes

D- amino acids can exist in prokaryotes

all chiral amino acids except cysteine have (S) configuration

all amino acids are chiral except glycine, which has a hydrogen atom as its R group

Nonpolar, nonarmoatic AA (7)

glycine, alanine, valine, leucine, isoleucine, methionine, proline

Aromatic AA (3)

tryptophan, phenylalanine, tyrosine

Polar AA (5)

serine, threonine, asparagine, glutamine, cysteine

Negatively charged (acidic) AA (2)

aspartate, glutamate

Positively charged (basic) AA (3)

lysine, arginine, histidine

Hydrophobic AA vs Hydrophilic

hydrophobic = long alkyl chains

hydrophilic = charges

Amphoteric definition

can accept or donate protons

pKa definition

pKa of a group is the pH at which half of the species are deprotonated

[HA] = [A^-]

AA excist in different forms at different pH values

low (acidic) → AA is fully protonated

pH near the pI → AA is neutral zwitterion

high (basic) → AA is fully deprotonated

Isoelectric point (pI) of AA without charged side chain

Averaging the two pKa values

Titration curve - flat vs vertical points

flat = at the pKa values of the AA

vertical = pI of AA

Isoelectric point (pI) of AA with charged side chains

additional pKa value

pI is calculated by averaging the two pKa values that correspond to protonation and deprotonation of the zwitterion

Isoelectric point (pI) to know

AA without charged have pI around 6

AA (acidic) have pI well below 6

AA (basic) have pI well above 6

Forming a peptide bond is…

condensation or dehydration reaction (releasing one molecule of water)

Hydrolysis

breaking a peptide bond

Primary Structure

linear sequence of amino acids in a peptide and is stabilized by peptide bonds

Secondary Structure

local structure of neighboring amino acids, stabilized by H-bonding between amino groups and nonadjacent carboxyl groups

alpha-helix = clockwise coils around a central axis

beta-pleated sheets = rippled strands that can be parallel or antiparallel

Proline with Secondary Structure

can interrupt secondary structure because of its rigid cyclic structure

Tertiary Structure

3D shape of a single polypeptide chain, stabilized by hydrophobic interactions, acid-base interactions (salt bridges), H-bonds, and disulfide bonds

Hydrophobic interactions → push hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs free energy

Quaternary Structure

interaction between peptides in proteins that contain multiple subunits

Conjugated Proteins

Proteins with covalently attached molecules called Prosthetic group

May be a metal ion , vitamin, lipid, carb, or nucleic acidD

Denaturation

both heat and increasing solute concentration can lead to loss of 3D protein structure