Amino Acids, Peptides, and Proteins

MCAT Prep: Biochemistry Part 1

amino acids

have an amino group, carboxylic acid, a hydrogen atom, and an R group attached to a central alpha-carbon

Glycine

3-letter code: Gly

1-letter code: G

pK_a: neutral

Group: small

Special Properties: not chiral; found in structural loops

Gly; G

Alanine

3-letter code: Ala

1-letter code: A

pK_a: neutral

Group: small, nonpolar

Ala; A

Serine

3-letter code: Ser

1-letter code: S

pK_a: neutral

Group: polar

Special Properties: can form H-bonds; can be phosphorylated to introduce a negative charge

Ser; S

Threonine

3-letter code: Thr

1-letter code: T

pK_a: neutral

Group: polar

Special Properties: can form H-bonds, can be phosphorylated to introduce a negative charge

Thr; T

Cysteine

3-letter code: Cys

1-letter code: C

pK_a: slightly basic

Group: polar

Special Properties: forms disulfide bridges, important for 3° and 4° structure

Cys; C

Valine

3-letter code: Val

1-letter code: V

pK_a: neutral

Group: nonpolar

Val; V

Leucine

3-letter code: Leu

1-letter code: L

pK_a: neutral

Group: nonpolar

Leu; L

Isoleucine

3-letter code: Ile

1-letter code: I

pK_a: neutral

Group: nonpolar

Ile; I

Methionine

3-letter code: Met

1-letter code: M

pK_a: neutral

Group: nonpolar

Special Properties: “start” amino acid (can also be found at other positions)

Met; M

Proline

3-letter code: Pro

1-letter code: P

pK_a: neutral

Group: nonpolar

Special Properties: the only cis-amino acid; side chain part of peptide bond; introduces kinks in alpha-helices; found in loops and turns

Pro; P

Phenylalanine

3-letter code: Phe

1-letter code: F

pK_a: neutral

Group: nonpolar

Special Properties: aromatic

Phe; F

Tyrosine

3-letter code: Tyr

1-letter code: Y

pK_a: neutral

Group: nonpolar

Special Properties: aromatic; can be phosphorylated to introduce a negative charge

Tyr; Y

Tryptophan

3-letter code: Trp

1-letter code: W

pK_a: neutral

Group: nonpolar

Special Properties: aromatic

Trp; W

Aspartate

3-letter code: Asp

1-letter code: D

pK_a: acidic

Group: negatively charged at physiological pH

Special Properties: side chain can form salt bridge

Asp; D

Glutamate

3-letter code: Glu

1-letter code: E

pK_a: acidic

Group: negatively charged at physiological pH

Special Properties: side chain can form salt bridge

Glu; E

Asparagine

3-letter code: Asn

1-letter code: N

pK_a: neutral

Group: polar

Special Properties: side chain can form H-bonds

Asn; N

Glutamine

3-letter code: Gln

1-letter code: Q

pK_a: neutral

Group: polar

Special Properties: side chain can form H-bonds

Gln; Q

Histidine

3-letter code: His

1-letter code: H

pK_a: slightly acidic

Group: polar

Special Properties: aromatic; can be positively charged at acidic pH

His; H

Lysine

3-letter code: Lys

1-letter code: K

pK_a: basic

Group: positively charged at physiological pH

Special Properties: side chain can form salt bridge; can be acetylated to mask the positive charge (important in DNA-protein interaction)

Lys; K

Arginine

3-letter code: Arg

1-letter code: R

pK_a: basic

Group: positively charged

Special Properties: side chain can form salt bridge

Arg; R

fully protonated

at low (acidic) pH

zwitterion

when pH = pI (a molecule that contains an equal number of positively and negatively charged functional groups)

fully deprotonated

at high (basic) pH

pI

is determined by averaging the pK_a values that refer to protonation and deprotonation of the zwitterion

condensation (dehydration)

Peptide bond formation is a ___________ reaction with a nucleophilic amino group attacking an electrophilic carbonyl.

hydrolysis

Peptide bonds are broken by ___________.

Primary structure

linear sequence of amino acids

Secondary structure

local structure stabilized by noncovalent bonds; includes alpha-helices and beta-sheets

Tertiary structure

three-dimensional structure stabilized by hydrophobic interactions, acid-base interactions (salt bridges), hydrogen bonding, and disulfide bonds

Quaternary structure

interactions between subunits

denaturation

Heat and solutes can cause ______________.