AMINO FUCKING ACIDS Flashcards by Daniel Marino | Brainscape

Q

Glycine

A

Gly
G
-H
no steric hinderance

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Q

Alanine

A

Ala
A
-CH3

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Q

Valine

A

Val
V
-

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Q

Isoleucine

A

Ile

I

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Q

Leucine

A

Leu

L

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Q

Phenylalanine

A

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

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Q

Tyrosine

A

Tyr
Y
10
Can become phosphorylatied

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Q

Tryptophan

A

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

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Q

Methionine

A

Met
M
inert sulfur

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Q

Histidine

A

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

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Q

Serine

A

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

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Q

Threonine

A

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

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Q

Cysteine

A

Cys
C
8.3

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

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Q

Asparagine

A

Asn
N
N-linked glycosylation

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Q

Glutamine

A

Glu
X
4

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Q

Proline

A

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

Q

Aspartic Acid

A

Asp
D
4

Q

Glutamic Acid

A

Glu
E
4
role as N donor in metabolis

Q

Lysine

A

Lys
K
10
FLoppy cjain-tries to interact with water

Q

Arginine

A

Arg
R
12
Numerous sites for H bonding

Q

AA structure

A

PAPER NC’s

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

Q

pH

A

COOH and NH3(+)

Q

pH>pKa

A

COO(-) and NH2

Q

Peptide bond formation

and characteristics

A

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

Q

L configuration

A

H in front-CORN

Q

Xylate acid vs exlate

A

COOH vs COO-

Q

SELF STUDY/WORKSHOPS

A

DO THEM AT SOME POINT

Q

phi and psi function

A

specific path of polypeptide backbone

generate alpha helices and beta sheets

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

Q

Primary, secondary, tertiary, quat

A

sequence, disulfide bridges, covalent bonds

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

Tertiary-domain

Multidomain

Q

Alpha helix

A

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

Q

right handed

A

look in, goes clockwise

Q

Beta sheet polarity and where is loop

A

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

Q

Beta sheet characteristics

A

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

Q

Turns/Loops

A

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

Q

Forces that stabilitze proteins

5

A

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

Q

Are domains contigous

A

not always-and can also be folded seprately

Q

Folds in regard to alpha and beta

A

Can have different proportions of both