AMINO FUCKING ACIDS

Question 1

Glycine

Answer 1

Gly
G
-H
no steric hinderance

Question 2

Alanine

Answer 2

Ala
A
-CH3

Question 3

Valine

Answer 3

Val
V
-

Question 4

Isoleucine

Answer 4

Ile

I

Question 5

Leucine

Answer 5

Leu

L

Question 6

Phenylalanine

Answer 6

Phe
F
Planar, bulky, polar b/c conjugated ring

Question 7

Tyrosine

Answer 7

Tyr
Y
10
Can become phosphorylatied

Question 8

Tryptophan

Answer 8

Trp
W
Planar, bulky, polar b/c conjugated ring

Question 9

Methionine

Answer 9

Met
M
inert sulfur

Question 10

Histidine

Answer 10

His
H
6.0
very dependent on pH
Usually coupled with pH dependent regulation

Question 11

Serine

Answer 11

Ser
S
Sterically open OH group
O-link glysocidation
Can become phosphorylatied

Question 12

Threonine

Answer 12

Thr
T
Sterically open OH group
O-link glysocidation
Can become phosphorylatied

Question 13

Cysteine

Answer 13

Cys
C
8.3

Can make covalent cross links
(S-S) bonds-only in oxidizing env-like outside cell (inside is reducing)

Question 14

Asparagine

Answer 14

Asn
N
N-linked glycosylation

Question 15

Glutamine

Answer 15

Glu
X
4

Question 16

Proline

Answer 16

Pro
Z
Has NH2-imino acid
Can get linked together NH2 to NH and bond to carboxyl-multimerize
Bulky-seen on surfaces (not in sheets or helices cuz bulk)
Can be cis (15%) but mostly trans
kink-destabilitzes protein

Question 17

Aspartic Acid

Answer 17

Asp
D
4

Question 18

Glutamic Acid

Answer 18

Glu
E
4
role as N donor in metabolis

Question 19

Lysine

Answer 19

Lys
K
10
FLoppy cjain-tries to interact with water

Question 20

Arginine

Answer 20

Arg
R
12
Numerous sites for H bonding

Question 21

AA structure

Answer 21

PAPER NC’s

H3N(+)-C(HR)-COO(-) (pka=9) (pka=2)

Question 22

pH

Answer 22

COOH and NH3(+)

Question 23

pH>pKa

Answer 23

COO(-) and NH2

Question 24

Peptide bond formation

and characteristics

Answer 24

H3N(+)-C(HR)-COO(-)
\+
H3N(+)-C(HR)-COO(-)
=
H3N(+)-C(HR)=COO-N(+)-C(HR)etc

PLANAR (b/c steric hinderance) AND POLAR
ALL CIS EXCEPT PROLINE (15% of time)

Alpha carbons are on op corners of plane

N terminus to C terminus

Question 25

L configuration

Answer 25

H in front-CORN

Question 26

Xylate acid vs exlate

Answer 26

COOH vs COO-

Question 27

SELF STUDY/WORKSHOPS

Answer 27

DO THEM AT SOME POINT

Question 28

phi and psi function

Answer 28

specific path of polypeptide backbone

generate alpha helices and beta sheets

only two sets of phi/psi angles can be repeated without collision

Question 29

Primary, secondary, tertiary, quat

Answer 29

sequence, disulfide bridges, covalent bonds

local arrangements, peptide bonds, H bonds (helices and sheets)

Tertiary-domain

Multidomain

Question 30

Alpha helix

Answer 30

right handed 
carbonyl carbons on axis
NH groups down
=O grouops face up
H bonds between C=O---H-N
    -neutralizes polar character in up down direction
Residue every 100 degrees, 3.6/turn

polar side chains outside
nonpolar inside

Question 31

right handed

Answer 31

look in, goes clockwise

Question 32

Beta sheet polarity and where is loop

Answer 32

Parallel=NONPOLAR
-no loop necc
Anti=ALT POLAR/NON
-loop goes out of plane

Question 33

Beta sheet characteristics

Answer 33

pleat b/c poly peptide backbone is trans

side chains are above/below sheet

H bonds between strands

3.5 residues from top amplitude to bottom

Question 34

Turns/Loops

Answer 34

Where functional sites are

Between antiparallel beta strand=beta hairpin

beta, alpha, beta

helix loop helix

4 residue beta bend-holds beta strand (anti parallel) together
H bond between 1 and 4-greek key-very stable-in immunoglobulins

robust, stable, and common

Question 35

Forces that stabilitze proteins

5

Answer 35

VDW-interactions from close atoms
Hydrophobic
H bonds
Ionic interactions
Disulfide bridges

Question 36

Are domains contigous

Answer 36

not always-and can also be folded seprately

Question 37

Folds in regard to alpha and beta

Answer 37

Can have different proportions of both