Exam #1 Material Flashcards
Know the 20 Amino Acids
-
If pKa is below given pH….
deprotonate (remove an H)
If pKa is above given pH…
protonate (add an H)
Cysteine pKa
8.18
Lysine pKa
10.53
Arginine pKa
12.48
Histidine pKa
6.00
Tyrosine pKa
10.07
Aspartic Acid pKa
3.65
Glutamate pKa
4.25
C-term pKa
2.16
N-term pKa
9.47
pI calculation
-
Question 1C about if the given ligand interacts with an amino acid what other sidechains would it interact with?
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
Given an amino acid sequence, you have to compare them to HUMAN sequence
Which one is yeast?
The most different one from Human, so C
Given an amino acid sequence, you have to compare them to HUMAN sequence
*Which one is macaque monkey”
The most similar one to Human, so B
Boxed Amino Acids critical for ADH1’s chemistry in each species?
No, b/c there is significant variation in this region across the species
Amino Acid interactions?
Hydrogen bond acceptor/donor, salt bridge, polar/hydrophilic
Know thermodynamic equation and how to apply them and know the constants
-
A negative delta G moves reaction to the…
right towards the products
A positive delta G moves reaction to the…
left towards the reactants
Joules Conversion
1 kJ=1000 J
Know the Henderson-Hasselbach Equation
pH= pKa+log base/acid
Normal pKa of Lysine not 7.1, what effect happened on Lys324?
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
Protein Folding: Delta G
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
Protein Folding: Delta S
Delta S is negative and similar magnitude, becoming more ordered or “just as ordered”
Protein Folding: Delta H
Delta H is negative and smaller than similar protein making favorable interactions
Mutation of His64 (distal histidine) to Asn, effect on hemoglobin’s overall affinity for oxygen?
No effect b/c Asn can also provide H-bond to O2 OR decrease because geometry is wrong of H-bond
His2 and His143 involved in 2,3 BPG mutated to Leu, what’s the effect on hemoglobin’s overall affinity for oxygen?
Increase b/c mutations lower affinity for BPG which then increases affinity for oxygen
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?
Less effective b/c it lacks the difference in affinity between maternal and fetal hemoglobin
Know the Kd equation
-
100% bioavailability
Multiple Kd by 100
Higher affinity between human and parasite
Whatever the higher number is
Proximal Histidine mutated to Glycine less probable as compared to His to Ala mutation?
Less probable b/c Gly lacks R-group, unlike Ala which has an R-group like His
Distal histidine replaced by similar alanine-imidazole combination, what effect would this have on hemoglobin’s affinity for oxygen?
No effect b/c this new combo would still provide Hydrogen bond
Positive cooperativity
initial binding increase affinity for other ligand nH>1
Non-competitive cooperativity
Independence nH=1
Negative cooperativity
Decreases affinity for other ligand nH<1
Graph lines for cooperativity
Study page 7 of 463 EXAM #1 2023
Hydrophobic interactions
Help stabilize neutral protonate form and destabilize (-) charged deprotonated form would increase pKa of Asp.
Trp or Phe can help provide hydrophobic envt.
It is reasonable to expect the sidechain of an aspartic acid to form a strong noncovalent interaction with the sidechain of:
Lysine and Asparagine
To raise the pKa of a tyrosine sidechain, an enzyme could:
Put it in a hydrophobic pocket
Put it near an aspartate
Put it near an arginine?
Bicarbonate is not a good buffer b/c…
Buffer works best when pH is equal to pKa, in this case it wasn’t
Replace Y w/ F,W, or H, why?
Histidine can replace Y due to its neutral state
Y is big aromatic like F and W
Beta Sheets are:
held together by hydrogen bonds between functional groups in the backbone
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
Van der Waals interactions & Hydrogen bonds, as a hydrogen bond donor
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
Van der Waals interactions
Hydrogen bonds, as a hydrogen bond donor
Electrostatic interactions, as a cation
