Isa Evangelista, Cj Gutierrez

(Content from Maam Sariles lectures and Maam Esmallas notes)

AMINO ACIDS
I. ALIPHATIC
A. STRAIGHT CHAIN
Glycine
Gly
G

Alanine
Ala
A
B. BRANCHED CHAIN
Valine
Val
V
Leucine
Leu
L
Isoleucine
Ile
I

C. HO containing
Serine
Ser
S
Threonine
Thr
T

D. S containing
Cysteine
Cys
C

Methionine
Met
M

- Neutral, Non-polar
- no chiral center
- no asymmetric carbon
- less steric hindrance than
other AAs
- Neutral, Non-polar

Neutral, Non-polar
Isopropyl
-branched
Neutral, Non-polar
Isobutyl

Neutral, Non-polar
Sec-butyl
2 chiral carbons
-branched
- Neutral, Polar
- Primary Alcohol
-

Neutral, Polar
Secondary Alcohol
Has two chirality centers
-branched

- Neutral, Polar
- Has a thiol group
- 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)
- Neutral, Non-polar
- hydrophobic
- 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
Asn
N
Glutamine
Gln
Q

G. BASIC AA
- hydrophilic nitrogenous bases
- positively charged at physiological pH
- protonated in solutions
- Ionic; electrostatic interaction
Lysine
Lys
K

Arginine
Arg
R
Histidine
His
H

- Neutral, Polar
- capable of H-bonding
- amide groups do not become
charged
- Neutral, Polar
- capable of H-bonding
- amide groups do not become
charged

- has a 1 amino group

- contains -amino group
- diamino acid
- protonated at pH 7.0
- e-releasing inductive effect:
high basicity
- most basic amino acid
- contains guanido group
- guanidinium ion always
protonated
- heterocyclic ring side chain
- not aromatic
- contains imidazole
- only amino acid that
functions as buffer in
physiological range

II. AROMATIC
Phenylalanine
Phe
F
Tyrosine
Tyr
Y

Tryptophan
Trp
W

III. CYCLIC AA
H. IMINO ACID
Proline
Pro
P

- Neutral, Non-polar
- Hydrophobic
- Neutral, Polar
- Hydrophobic
- H-bonding
- not very soluble in water, but
contains a polar hydroxyl
group in the para position of
the phenyl ring
- tyrosine hydroxyl is solventexposed
- Neutral, Non-polar
- Hydrophobic
- 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 sidechain is non-polar

- Neutral, Non-polar
- Hydrophobic
- 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 solventexposed 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
ionic bond
hydrophobic/ nonpolar
covalent
stacking interaction/ pi-pi complexation

Asn
Lys
Val
Cys
Trp

&
&
&
&
&

Gln
Glu
Leu
Cys
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