MCAT Biochemistry Chapter 1

Amino Acid functional groups

Carboxyl and amino group

R group

Determines chemical properties of amino acid

Proteinogenic amino acids

Have the R group, caroxyl, amino group all bonded to one alpha carbon

Chiral/stereogenic AA

All, except achiral glycine

Configuration of AA

All L

All S except for cysteine

Non polar, nonaromatic AA

Glycine, alanine, valine, leucine, isoleucine, methionine, proline

Aromatic AA

Tryptophan, phenylalanine, tyrosine

Polar AA

Serine, cysteine, threonine, glutamine, asparagine,

Acidic AA, negatively charged

Aspartate, glutamate

Basic AA, postively charged

Arginine, lysine, histidine

Hydrophobic AA

Interior proteins

Alanine, leucine, isoleucine, valine, phenylalanine

Hydrophilic AA

Exterior proteins

Histidine, arginine, lysine, glutamate, aspartate, asparagine, glutamine

Site directed mutagenesis W53Y

53rd amino acid tryptophan mutated to tyrosine

Most acids in the body are

Deprotonated

Arginine postive charge

Delocalized across guanidine

Histidine protonation

Imidizole can be protonated in acidic conditions

Proline flexibility

Decreased due to cyclic formation

Arginine and glutamine amine groups

Are not protonated with pH changes

Serine and threonine

Very polar hydroxyl group

Cysteine

Less electronegative than oxygen

Amphoteric amino acids

Can donate or accept protons due to acidic carboxylic group, basic amino group

pKa

pH when half would be protonated

pH > pKa

More deprotonated molecules

pH < pKa

More protonated molecules

All AA have at least_ pKa’s

Ionizable AA have _

2; 3

pKa₁

Carboxyl, 2

pKa₂

Amino group, 9, 10

At an acidic pH, amino acids are usually __

At a basic pH, amino acids are usually __

positive, negative

Zwitterions

Amino acids at physiologic pH, has both positive and negative charge

pI

Isoelectric point, when molecule is electrically neutral

When pH is near pKa, solution

Acts as a buffer

At pI, solution

Is very sensitive to changes in pH

pI for amino acids without an ionizable side chain

Approximately 6

When pH is below pKa₁

Amine and carboxyl group are protonated

When pH is above pKa₂

Amine and carboxyl group are deprotonated

When pH is around pI

Amine is protonated, carboxyl is deprotonated

pI is typically equal to

(pKa₁+ pKa₂)/2

pI for acidic amino acids equals

(pKa of R group + pKa of carboxyl group)/2

pI for basic amino acids equals

(pKa of R group + pKa amine group)/2

pI of acidic amino acid

below 6

pI of basic amino acid

above 6

Residues

Amino acid subunits, make up peptides

Oligopeptide

Polypeptide

Under 20 residues

Over 20 residues

Peptide bond

Formed by a condensation/dehydration/acyl substitution rxn between amino and carboxyl group

Peptide bond formation

1. electrophilic carboyl attacks nucleophilic amino group

2. Hydroxyl of carboxylic acid becomes water, is removed

Amide group resonance

Has delocalized pi electrons, the C=O double bond can switch to a C-O single bond and C=N double bond

Limits rotation

Peptides are synthesized from

N to C terminus, by ribosomes

Peptide bond breakers

Hydrolysis by trypsin at C terminus of R, K and by chymotrypsin at C terminus of F, W, Y

Adds OH to carbonyl and H to amide

Primary structure of peptides

Amino acid sequence from N to C

Secondary structure of peptides

Hydrogen bonds between R groups, making alpha helixes, beta sheets

Alpha helix

H bond between carbonyl oxygen and amide hydrogen 3 residues apart, with side chains facing out

Beta sheets

H bond between amino acids across from each other

Can be parallel, antiparallel

Turns

Join secondary structures together

Beta are most common, between amino acids 3 residues apart

Proline in secondary structures

Causes kinks, usually in turns and at the beginning of alpha helices that cross the cell membrane

Rare in beta sheets

Fibrous proteins

Sheets or long strands

Globular proteins

Spherical

Tertiary structures of peptides

3-D structure determined by h-phobic and h-philic interactions of R groups and acid-base interactions

Salt bridges and Disulfide bonds

Salt bridge

Hydrogen and ionic bond

Disulfide bond

Oxidation bond between two cysteins, loss of 2 electrons and protons

Form loops, curlier hair has more bonds

Protein formation

Secondary structure form, moten globules form in intermediate states, collapse into tertiary structures

Denaturation

Loss of tertiary structure, loss of function

Solvation layer

Solvent molecules surrond the solute

Water molecules rearrange to maximize hydrogen bonding, nonspontaneous due to less disorder and decreased entropy

Entropy in h-philic R groups

Increased, spontaneous, more stable

Max stability

H-phobic R groups are away from water

H-philic R groups are interacting with water

Quaternary peptide structure

Only with multiple peptide chains

Brings catalytic sites together

Induces cooperativity - changes in one subunit can influence the other

Quaternary peptide formation

Smaller globular peptide subunits aggregate, reduces surface area

Conjugated proteins

Function/delivery location determined by prosthetic groups

Lipoprotein: ___ prosthetic group

Glycoprotein: ___ prosthetic group

Nucleoprotien: ___ prosthetic group

Lipid; carbohydrate; nucleic acid

Hemoglobin

4 pyrrole (heterocyclic aromatic) rings

Nitrogen of each ring attaches to central Fe

Denaturation occurs through

Heat - increases energy, decreases bonds between amino acids and hydrophobic interactions

Solutes - urea, SDS interfere with h-bonds, noncovalent bonds

C_M

Concentration when half the species is denatured

T_M

Melting point when half the species is denatured