Isa Evangelista, Cj Gutierrez

(Content from Maam Sariles lectures and Maam Esmallas notes)

AMINO ACIDS
I. ALIPHATIC
A. STRAIGHT CHAIN
Glycine - Neutral, Non-polar
Gly - no chiral center
G - no asymmetric carbon
- less steric hindrance than
other AAs
Alanine - Neutral, Non-polar
Ala
A

B. BRANCHED CHAIN
Valine - Neutral, Non-polar
Val - Isopropyl
V - -branched
Leucine - Neutral, Non-polar
Leu - Isobutyl
L
Isoleucine - Neutral, Non-polar
Ile - Sec-butyl
I - 2 chiral carbons
- -branched

C. HO containing
Serine - Neutral, Polar
Ser - Primary Alcohol
S
Threonine - Neutral, Polar
Thr - Secondary Alcohol
T - Has two chirality centers
- -branched

D. S containing
Cysteine - Neutral, Polar
Cys - Has a thiol group
C - Weak acid
- Can form H-bonds
- ionized form is polar;
protonated form is less polar
than serine
- has ability to form covalent
bonds (disulfide bonds)
Methionine - Neutral, Non-polar
Met - hydrophobic
M - more hydrophobic than
cysteine
- thioether
 - start amino acid

E. ACIDIC AA
- carboxyl groups (weaker than -carboxyl group) in the R
- Ionic, Polar
- negatively charged at physiological pH
- present as conjugate bases
- carboxyl groups function as nucleophiles in some enzymatic reactions
Aspartate - Ionic, Polar
Asp - -carboxyl group
D - e-releasing inductive effect
decreases acidity; e-attracting
inductive effect increases
acidity
Glutamate - Ionic, Polar
Glu - -carboxyl group
E

F. AMIDIC AA
- Polar
- H-bonding
Asparagine - Neutral, Polar
Asn - capable of H-bonding
N - amide groups do not become
charged
Glutamine - Neutral, Polar
Gln - capable of H-bonding
Q - amide groups do not become
charged

G. BASIC AA
- hydrophilic nitrogenous bases
- positively charged at physiological pH
- protonated in solutions
- Ionic; electrostatic interaction
Lysine - has a 1 amino group
Lys - contains -amino group
K - diamino acid
- protonated at pH 7.0
- e-releasing inductive effect:
high basicity
Arginine - most basic amino acid
Arg - contains guanido group
R - guanidinium ion always
protonated
Histidine - heterocyclic ring side chain
His - not aromatic
H - contains imidazole
- only amino acid that
functions as buffer in
physiological range
II. AROMATIC
Phenylalanine - Neutral, Non-polar
Phe - Hydrophobic
F
Tyrosine - Neutral, Polar
Tyr - Hydrophobic
Y - H-bonding
- not very soluble in water, but
contains a polar hydroxyl
group in the para position of
the phenyl ring
- tyrosine hydroxyl is solvent-
exposed
Tryptophan - Neutral, Non-polar
Trp - Hydrophobic
W - has indole ring
- borderline hydrophobic /
polar
- proton attached to indole
nitrogen can act as H-bond
donor to water or other H-bond
acceptor
- majority or large trp side-
chain is non-polar

III. CYCLIC AA
H. IMINO ACID
Proline - Neutral, Non-polar
Pro - Hydrophobic
P - cyclic but not aromatic
- 2 -amino group or -imino
acid
- has a conformationally
restricted structure
- behaves more like a polar
amino acid since proline has
a fairly high tendency to
appear on the solvent-
exposed surface of
proteins

Selenocysteine
Sec
U

Essential Amino acids L, I, V, H, K, M, F, T, W (obtained from nutrition; cant be synthesized in

enough amt in the body)
Non-essential amino acids A, R, N, D, C, E, Q, G, P, S, Y (synthesized by the body)

Amino Acids with 3 pka values: 2 Acidic, 3 Basic, Cys, Tyr

TERTIARY STRUCTURES
- 3D Structures
- Types:
h bond Asn & Gln
ionic bond Lys & Glu
hydrophobic/ nonpolar Val & Leu
covalent Cys & Cys
stacking interaction/ pi-pi complexation Trp & Tyr

QUATERNARY STRUCTURES
- Interaction between subunit
- Denaturation: loss of different interactions
- Done through:
heat destroys Van der Waals
large changes in ph destroys side-chains
destroys hydrophobic reactions or ionic
detergent
reactions
urea/ guanidine destroys H-bonding
mercaptoethanol destroys disulfide bonds