Review for Test #2

Question 1

All amino acids have a ____ carbon except glycine.

Answer 1

chiral

Question 2

All amino acids have a tetrahedral geometry except __________.

Answer 2

Proline

Question 3

Nonpolar Amino Acids: (7)

Answer 3

I = Isoleucine
L = Leucine
V = Valine
A = Alanine
G = Glycine
P = Proline
M = Methionine

Question 4

Smallest aa:

Answer 4

Glycine

Question 5

aa with a backbone:

Answer 5

Proline

Question 6

Methionine has:

Answer 6

no dipole moment b/t the carbon and the sulfur

Question 7

Non-polar Aromatic: (3)

Answer 7

W = Tryptophan
F = Phenylalanine
Y = Tyrosin

Question 8

Aromatic means:

Answer 8

can absorb light

Question 9

Most absorbant aa:

Answer 9

Tryptophan (Trp)

Question 10

Only weakly absorbent at 260nm:

Answer 10

Phenylalanine (Phe)

Question 11

Proteins ratio at 260/280 is typically:

Answer 11

0.5

Question 12

DNAs ratio at 260/280 is typically:

Answer 12

1.8-2.0

Question 13

Beer’s Law and definitions of constants:

Answer 13

A = Ɛlc

A = absorbance at 280 nm
Ɛ = extinction coefficient
c = protein concentration in M
l = pathlength of cuvette (distance light shines through the sample)

Question 14

Polar Amino Acids: (5)

Answer 14

Q = Glutamine
C = Cystine
T = Threonine
N = Asparagine
S = Serine

Question 15

Acidic Amino Acids: (2)

Answer 15

E = Glutamate
D = Aspartate

Question 16

Basic Amino Acids:

Answer 16

H = Histidine
R = Arginine
K = Lysine

Question 17

• Non polar aa are usually found ______ of the protein.
• Polar aa are usually found ______ of the protein.

Answer 17

• within the core
• on the surface

Question 18

Cystines -SH side group can ______________ which are important for ___________.

Answer 18

• oxidize to form disulfide bonds
• long range interactions for tertiary structures

Question 19

Acidic amino acids are typically (-) charged due to:

Answer 19

Deprotonated carboxyl group on the side chain

Question 20

Aspartate is the ________ version of the ________ _________.

Answer 20

• deprotonated
• protonated
• Aspartic acid

Question 21

This type of aa can form ____________ with _______.

Answer 21

• hydrogen bonds
• water
• polar amino acids

Question 22

The __________ on basic amino acids can be __________.

Answer 22

• extra amino group
• protonated to carry a (+) charge

Question 23

Least basic, basic aa with a sidechain pKa of 6:

Answer 23

Histidine

Question 24

Protonated amino acid –>

Answer 24

pH is lower than pKa

Question 25

Deprotonated aa -->

Answer 25

pH is higher than pKa

Question 26

AA are more likely to loose a H+ when _________.

Answer 26

- the environments pKa increases

Question 27

pKa < pH -->

Answer 27

molecule negatively charged/deprotonated

Question 28

pKa > pH -->

Answer 28

molecule positively charged/protonated

Question 29

more likely to loose H+ --> more _____ --> ______________

Answer 29

- more acidic - decrease in pKa

Question 30

less likely to loose H+ --> more _______ --> ____________

Answer 30

- more basic - increase in pKa

Question 31

Negative charge introduced --> _____________ Positive charge introduced --> _______________

Answer 31

- deprotonateed - protonated (with H+)

Question 32

Basic aa are typically _____ charged

Answer 32

- positively

Question 33

Peptide bond =

Answer 33

amide bond

Question 34

carboxyl reacts with ______ group to form a peptide bond

Answer 34

amide

Question 35

+ Gibbs free energy for condensation reaction means --> _________ so must be

Answer 35

not thermodynamically favorable - coupled to ATP hydrolysis during protein biosynthesis

Question 36

The partial double bond character is caused by

Answer 36

the delocalization of electrons

Question 37

Proteases:

Answer 37

enzymes that cleave specific peptide bonds

Question 38

R1 cleaves the bond _____ the aa R2 cleaves the bond _____ the aa

Answer 38

- after - before

Question 39

If ______ is the 2nd amino acid the protease will not cleave the bond.

Answer 39

Proline

Question 40

Amino acid residue name for alanine:

Answer 40

Alanyl

Question 41

Backbone for proteins is made up of:

Answer 41

peptide bonds (NCCNCCNCC)

Question 42

Free amino group at:

Answer 42

N-terminus

Question 43

Free carboxyl group at:

Answer 43

C-terminus