amino acid must knows

Defines the identity and chemical behavior of amino acid

R/side chain

Because the four groups attached to the α-carbon are DIFFERENT, this makes the a-carbon?

asymmetric or chiral

Something is ___ if its mirror image cannot be superimposed on the original (just like your left and right hands.)

chiral

amino acid enantiomers

L-amino acid (levorotatory) D-amino acid (dextrorotatory)

Proteins in humans and all living organisms are built only from?

L-amino acids

At pH < pI they’re

positively charged → move toward the cathode (–)

At pH > pI, they’re

negatively charged → move toward the anode (+)

At pH = pI

net charge = 0 → they don’t move (basis of isoelectric focusing).

Side chains mostly hydrocarbons

NONPOLAR ALIPHATIC

Contain benzene-like rings

NONPOLAR AROMATIC

Side chains can form H bonds but carry no net charge at physiologic pH

POLAR UNCHARGED

Side chains have -COOH that are deprotonated at physiologic pH, giving them negative charges (COO)

POLAR ACIDIC

Side chains have nitrogencontaining compounds that accept protons; positively charged at physiologic pH

POLAR BASIC

NONPOLAR ALIPHATIC

MPLIVAG

NONPOLAR AROMATIC

PTT

POLAR UNCHARGED

STAG CYST

POLAR ACIDIC

"-ATE"

POLAR BASIC

basic HAL

branched hydrocarbons; strongly hydrophobic

Leu, Ile, Val

smallest; only chiral AA

Gly

cyclic

Pro

Thioether (S-CH3)

Met

Indole ring

Trp

Phenol group

Tyr

Have hydroxyl groups (-OH); can form H bonds

Ser,Thy

Amide-containing

Asn,Gln

Imidazole ring

His

Guanidinium group

Arg

Hydroxyl (–OH) containing

Serine, Threonine, Tyrosine

Sulfur-containing

Cysteine, Methionine

Amide-containing

Asparagine, Glutamine

Imine / secondary amine

Proline

Small/special

Glycine

A

Alanine

R

Arginine

D

Aspartic Acid

N

Asparagine

C

Cysteine

E

Glutamic Acid

Q

Glutamine

G

Glycine

H

Histidine

I

Isoleucine

L

Leucine

K

Lycine

M

Methionine

F

Phenylalanine

P

Proline

S

Serine

T

Threonine

W

Tryptophan

Y

Tyrosine

V

Valine

greater Ka

stonger the acid

greater pKa

weaker the acid

low pH

The carboxyl (–COOH) keeps its hydrogen → neutral (no charge). The amino group (–NH₃⁺) has an extra hydrogen → positive.

The amino acid carries a positive charge

slowly increase the pH

Now the carboxyl is negative, while the amino group is still positive. ZWITTERION = ZERO NET CHARGE = ISOELECTRIC POINT

increase the pH further

Now the carboxyl group is negative while the amino group is neutral The amino acid now has a net negative charge (–1).

Peptide bond between the carboxyl group of one AA and the amino group of the next.

Primary Protein Structure

Hydrogen bonds between backbone atoms (not side chains).

Secondary Protein Structure

Side chain interactions: Hydrophobic interactions (main driver) Hydrogen bonds Ionic (salt) bridges Disulfide bonds (Cys–Cys) Van der Waals forces

Tertiary Protein Structure

Non-covalent forces ± disulfide bonds

Quarternary Protein Structure

The sequence determines shape and function.

Primary Protein Structure

Provides the protein’s basic shape framework (springs, folds, sheets).

Secondary Protein Structure

Myoglobin is an example of

Tertiary Protein Structure

Hemoglobin is an example of

Quarternary Protein Structure

right-handed spiral

a-Helix

helix breakers

proline and glycine

e chain is fully extended, not coiled

b-sheet

very short (4 amino acids) — make a tight 180° bend

b-turns

: longer, irregular connectors; found on the protein surface.

loops7