Biochemistry - First Half

Question 1

Non-Polar Amino Acids

Answer 1

A, V, I, L M, F

Question 2

Moderately Non-Polar AA

Answer 2

Y, W, C, G, P

Question 3

Polar AA

Answer 3

S, T, N, Q

Aparagine, Glutamine

Question 4

Positive AA

Answer 4

H, R, K

Question 5

Negative AA

Answer 5

D,E
Aspartate, Glutamate

Question 6

AA that can accept or donate H+ from their sidechains

Answer 6

S, T, C, Y, D, E

Question 7

AA with Ionizable Side Chains

Answer 7

D, E, Y, C, R, H, K
- positives
- negatives
- and cysteine and tyrosine

Question 8

Partition CT

Answer 8

• Silica gel (polar)
• np out first

Question 9

Thin Layer CT

Answer 9

• in lab
• ninhydrin
• silica gel
• np go further

Question 10

Ion Exchange CT

Answer 10

Cation - bind +
Anion - bind -
change pH or outcompete

Question 11

Affinity CT

Answer 11

Ligand attach to beads in column
- prots bind to ligand
- add salt to weaken bond to ligand
- can add a tag to bind the ligand with more specificity

Question 12

Immobilized Metal CT

Answer 12

• Ni2+ resin
• cluster of His bind tightly
• change prot structure
• add imidazole to elude

Question 13

Gel Filtration CT

Answer 13

• size
• polymeric gels
• large out first
• antilog of y axis to find molar mass

Question 14

Electrophoresis

Answer 14

size shape charge
- use electric field to differ based off charge
- speed depends on size
- uses polyacrylamide gel
- visualize with Coomassie blue

Question 15

Isoelectric Focusing

Answer 15

pH gradient
- stops where isoelectric point = 0

Question 16

SDS - electrophoresis

Answer 16

• partially unfolds
• large negative charge
• uniform charge per unit size
• based on weight

Question 17

2D gels

Answer 17

• separate by isoelectric point then weight
• SDS-PAGE and isoelectric focusing

Question 18

Mass Spectrometry

Answer 18

• vaporize with lazar
• charged particles to detector
• faster = smaller

Question 19

Sanger Method

Answer 19

Fluorodinitrobenzene
- reacts with Nterm - NH2 is nucleophile (basic)
- - attacks at C-F which is electrophile
- HF as leaving agents
- destroys rest of chain (because acid hydrolysis breaks all peptide bonds)
- Nterm with Dinitrobenzene is yellow so easily found

Question 20

Edman degradation

Answer 20

a) coupling with PITC - done in basic conditions so NH2 is deprotonated and can act as a nucleophile
b) cyclization - so acts as an acid a protonates - causing cyclization
- increases strength of S bond (nucleophile) and cycles up to C=O
- - breaking bond to next NH to restart

Question 21

trypsin

Answer 21

• Arg, Lys
• not with proline to the right
• always cterm is Lys and Arg

Question 22

chemotrypsin

Answer 22

• Phe, Trp, Try
• not with proline
• on right side

Question 23

cyanogen bromide

Answer 23

• Met
• yes with proline
• converts Met to Homocystein (Hse)

Question 24

Linus Pauling

Answer 24

• peptide bond has double bond character
• CN is planar and cannot rotate
• can rotate at C-C so planes can rotate

Question 25

Helical

Answer 25

- 3.6 aa per turn - 5.4 A long each turn - Carboxylate of 1 lines up with Amide of 5

Question 26

Beta

Answer 26

- space for bulky side chains - WYF needs VIT C

Question 27

Urea

Answer 27

- weakens the hydrophobic effect - denaturing agent

Question 28

2-mercaptoethanol

Answer 28

- converts disulfide bonds back to their regular seperate cystein groups - disulfide reducing agent

Question 29

Common FA

Answer 29

- unbranched - even number of carbons - cis bonds - methylene bridged

Question 30

Let my pal stay around

Answer 30

Laurate 12 Myristate 14 Palmitate 16 Stearate 18 Arachidate 20

Question 31

Phosphate head group

Answer 31

Phosphatidic Acid - just an H -2 or about -1.5 (resonance) Choline - 0 Ethanolamine - 0 Serine - (-1) Glycerol - (-1)

Question 32

Absorption Chromatography

Answer 32

- neutral eludes first - then polar - then charged

Question 33

Analysis of FA

Answer 33

Transesterification to FA methyl esters (volatile) - seperated based on size and degree of unsat - mass spec - FAME can be used in gas-liquid chromatography or high performance liquid chromatography

Question 34

Enantiomers

Answer 34

Differ at ALL chiral carbons - identical chem properties

Question 35

Diastereomers

Answer 35

Differ at more than 1 chiral C - not identical chem properties

Question 36

Epimers

Answer 36

A diastereomer that differs at ONLY 1 chiral C

Question 37

Chiral Carbons of Aldoses vs Ketoses

Answer 37

- ketoses - have isomers chiral carbons with same C amount - aldoses have more b/c they are on the end 2^n - n is the number of chiral centers

Question 38

Anomers

Answer 38

Differ in orientation at the anomeric carbon

Question 39

Glycoside

Answer 39

- a sugar component bonded to a non-sugar component via a glycosidic linkage

Question 40

A-T

Answer 40

- 2 H bonds

Question 41

G-C

Answer 41

- 3 H bonds

Question 42

DNA

Answer 42

- antiparallel - right handed - major minor groove - bases 3.4 A apart - one turn 10A Major Groove - more accessible to interactions w proteins that recognize a specific DNA sequence

Question 43

ATP to ADP and Pi

Answer 43

1) releases electrostatic repulsion 2) Pi has more resonance stability than ATP - further releasing PPi to 2 Pi releases more electrostatic repulsion

Question 44

CoA

Answer 44

comes from pantothenic acid (B5) - carriers acids (acyl groups)

Question 45

Acetyl CoA

Answer 45

is acetone with a CoA

Question 46

NAD+ and NADP+

Answer 46

from Niacin (B3) - accept hydride ion H- - redox at nicotinamide ring

Question 47

FAD and FNM

Answer 47

from vitamin riboflavin (B2) - prosthetic groups - accept 1 or 2 H atoms - can form a semiquinone radical

Question 48

Rotenone

Answer 48

inhibits C1

Question 49

barbiturates

Answer 49

inhibits C1

Question 50

antimycin A

Answer 50

inhibits C3

Question 51

CN- or CO

Answer 51

inhibits C4

Question 52

Add ADP and Pi

Answer 52

increases ATP synthase

Question 53

Add succinate

Answer 53

increases ETC

Question 54

Venturicidin or Oligomycin

Answer 54

inhibit ATP synthase