Exam #1 Material

Question 1

Know the 20 Amino Acids

Answer 1

-

Question 2

If pKa is below given pH….

Answer 2

deprotonate (remove an H)

Question 3

If pKa is above given pH…

Answer 3

protonate (add an H)

Question 4

Cysteine pKa

Answer 4

8.18

Question 5

Lysine pKa

Answer 5

10.53

Question 6

Arginine pKa

Answer 6

12.48

Question 7

Histidine pKa

Answer 7

6.00

Question 8

Tyrosine pKa

Answer 8

10.07

Question 9

Aspartic Acid pKa

Answer 9

3.65

Question 10

Glutamate pKa

Answer 10

4.25

Question 11

C-term pKa

Answer 11

2.16

Question 12

N-term pKa

Answer 12

9.47

Question 13

pI calculation

Answer 13

-

Question 14

Question 1C about if the given ligand interacts with an amino acid what other sidechains would it interact with?

Answer 14

In our exam it talked about Futbahl binding to Tyr and can also interact with Glu because of the n+3 rule
In the old exam it talked about Ligandin and how His interacts with it and can also interact with Glu and Arg because they are hydrophilic, polar, and can also form Hydrogen bonds like Histidine.
CONSIDER THE STRUCTURES OF AMINO ACIDS WHEN DOING THIS QUESTION b/c it can help get at least partial discussing the properties of the amino acids

Question 15

Given an amino acid sequence, you have to compare them to HUMAN sequence
Which one is yeast?

Answer 15

The most different one from Human, so C

Question 16

Given an amino acid sequence, you have to compare them to HUMAN sequence
*Which one is macaque monkey”

Answer 16

The most similar one to Human, so B

Question 17

Boxed Amino Acids critical for ADH1’s chemistry in each species?

Answer 17

No, b/c there is significant variation in this region across the species

Question 18

Amino Acid interactions?

Answer 18

Hydrogen bond acceptor/donor, salt bridge, polar/hydrophilic

Question 19

Know thermodynamic equation and how to apply them and know the constants

Answer 19

-

Question 20

A negative delta G moves reaction to the…

Answer 20

right towards the products

Question 21

A positive delta G moves reaction to the…

Answer 21

left towards the reactants

Question 22

Joules Conversion

Answer 22

1 kJ=1000 J

Question 23

Know the Henderson-Hasselbach Equation

Answer 23

pH= pKa+log base/acid

Question 24

Normal pKa of Lysine not 7.1, what effect happened on Lys324?

Answer 24

pKa went down because normal pKa of Lysine is 10.53 and this happened due to another Lysine nearby which has a positive charge and an H-bond donor

Question 25

Protein Folding: Delta G

Answer 25

Delta G is smaller than a similarly sized completely folded protein b/c not all folded Delta G also negative b/c still mostly folded

Question 26

Protein Folding: Delta S

Answer 26

Delta S is negative and similar magnitude, becoming more ordered or "just as ordered"

Question 27

Protein Folding: Delta H

Answer 27

Delta H is negative and smaller than similar protein making favorable interactions

Question 28

Mutation of His64 (distal histidine) to Asn, effect on hemoglobin's overall affinity for oxygen?

Answer 28

No effect b/c Asn can also provide H-bond to O2 OR decrease because geometry is wrong of H-bond

Question 29

His2 and His143 involved in 2,3 BPG mutated to Leu, what's the effect on hemoglobin's overall affinity for oxygen?

Answer 29

Increase b/c mutations lower affinity for BPG which then increases affinity for oxygen

Question 30

The y subunit of the tribe's fetal hemoglobin is identical to the y subunit found in "normal" fetal hemoglobin, would a pregnant lady of this tribe be more, less, or equally effective at delivering oxygen to the developing fetus, when compared to mothers possessing "normal" hemoglobin?

Answer 30

Less effective b/c it lacks the difference in affinity between maternal and fetal hemoglobin

Question 31

Know the Kd equation

Answer 31

-

Question 32

100% bioavailability

Answer 32

Multiple Kd by 100

Question 33

Higher affinity between human and parasite

Answer 33

Whatever the higher number is

Question 34

Proximal Histidine mutated to Glycine less probable as compared to His to Ala mutation?

Answer 34

Less probable b/c Gly lacks R-group, unlike Ala which has an R-group like His

Question 35

Distal histidine replaced by similar alanine-imidazole combination, what effect would this have on hemoglobin's affinity for oxygen?

Answer 35

No effect b/c this new combo would still provide Hydrogen bond

Question 36

Positive cooperativity

Answer 36

initial binding increase affinity for other ligand nH>1

Question 37

Non-competitive cooperativity

Answer 37

Independence nH=1

Question 38

Negative cooperativity

Answer 38

Decreases affinity for other ligand nH<1

Question 39

Graph lines for cooperativity

Answer 39

Study page 7 of 463 EXAM #1 2023

Question 40

Hydrophobic interactions

Answer 40

Help stabilize neutral protonate form and destabilize (-) charged deprotonated form would increase pKa of Asp. Trp or Phe can help provide hydrophobic envt.

Question 41

It is reasonable to expect the sidechain of an aspartic acid to form a strong noncovalent interaction with the sidechain of:

Answer 41

Lysine and Asparagine

Question 42

To raise the pKa of a tyrosine sidechain, an enzyme could:

Answer 42

Put it in a hydrophobic pocket Put it near an aspartate Put it near an arginine?

Question 43

Bicarbonate is not a good buffer b/c...

Answer 43

Buffer works best when pH is equal to pKa, in this case it wasn't

Question 44

Replace Y w/ F,W, or H, why?

Answer 44

Histidine can replace Y due to its neutral state Y is big aromatic like F and W

Question 45

Beta Sheets are:

Answer 45

held together by hydrogen bonds between functional groups in the backbone

Question 46

Consider the sidechain of the amino acid tryptophan. Remember, the sidechain is the part of the amino acid that makes it different from the other amino acids- it begins just after the C alpha. Which of the follow interactions is it (reasonably) conceptually possible for the sidechain of tryptophan to make? Select all correct answers

Answer 46

Van der Waals interactions & Hydrogen bonds, as a hydrogen bond donor

Question 47

Consider the sidechain of the amino acid lysine Which of the follow interactions is it (reasonably) conceptually possible for the sidechain of lysine to make? Select all correct answers

Answer 47

Van der Waals interactions Hydrogen bonds, as a hydrogen bond donor Electrostatic interactions, as a cation