Amino Acid Lecture 4 Questions

Question 0

For a solution pH above the pKa, the ____ form predominates.

Answer 0

unprotonated conjugate base (B-)

Question 1

For a solution pH below the pKa, the _____ form predominates.

Answer 1

protonated (AH)

Question 2

What is the definition of pKa?

Answer 2

the pH at which the concentrations of [AH] and [B-] are equal; the optimal buffer condition too

Question 3

What is the henderson-hasselbalch equation?

Answer 3

pH= pKa + log [A-]/[HA]

Question 4

At what pH are both charged groups (carboxy and amino groups) of amino acids protonated?

Answer 4

pH < 3.1

Question 5

At what pH will an amino acid with no ionizable side chains be in zwitter ion form?

Answer 5

3.1< 8

Question 6

At what pH will an amino acid with no ionizable side chain have both the carboxy and amino group deprotonized?

Answer 6

pH>8

Question 7

What is the isoelectric point (pI)?

Answer 7

the pH where the net charge on the amino acid is zero

Question 8

how do you calculate pI for an amino acid that doesn’t have a side chain with an ionizable group?

Answer 8

average the alpha amino and alpha carboxy group pKa’s

(3.1+8)/2 = 5.55

Question 9

how do you calculate the pI for amino acids with acidic side chains?

Answer 9

average the side chain pKa with the carboxy group pKa (3.1)

this applies for glutamate and aspartate

Question 10

how do you calculate the pI for amino acids with basic side chains?

Answer 10

average the side chain pKa with the amino group pKa (8)

applies to arginine, histidine, and lysine

Question 11

how do you calculate the pI for amino acids with side chains that don’t fall into the acidic or basic category? (tyr, cys)

Answer 11

average the side chain pKa with the carboxy group pKa (3.1)

Question 12

according to the powerpoint, what is the general rule to calculate pI?

Answer 12

pick the pKa above and below where the charge is zero and average them

Question 13

The ratio of unprotonated to protonated R group changes by _____ with each change in ____ relative to ___.

Answer 13

an order of magnitude
pH unit
pKa

Question 14

if pKa is 10.8, what is the ratio of unprotonated to protonated R group at the pH of 8.8?

Answer 14

1:100

Question 15

what is the R group on arginine called?

Answer 15

guanidino group

Question 16

what is the R group on histidine called?

Answer 16

imidazole ring

Question 17

a protein’s pKa can be influenced by ___

Answer 17

the local environment

Question 18

-SH is a ___. The ionized form (S-) is called a ____.

Answer 18

thiol; thiolate

Question 19

Which is a better acid at pH 7.8? Lys or Asp?

Answer 19

Lysine is a better proton donor at pH 7.8 because at that pH, a few lysine still have a proton to donate. Aspartate at pH 7.8 won’t have any proton to donate because it lost its proton at pH 4.1

Question 20

____ are pH sensitive and form between ___ and ___. The protonation state depends on the _______ of both groups. At physiological pH, ____ makes a great pH sensitive switch.

Answer 20

salt bridges; asp; his; microscopic pKa; histidine

Question 21

What did Gerhardus Johannes Mulder do?

Answer 21

• calculated the molecular formula of egg and serum albumin
• proposed that proteins were made of smaller building blocks called grundstoff
• essentially discovered amino acids

Question 22

What did Anselme Payen do?

Answer 22

• discovered the first enzyme (amylase) in beer
• this was before people knew about proteins
• amylase turns starch into glucose

Question 23

amino acid sequences are written from ___ terminus to ___ terminus.

Answer 23

N; C

Question 24

What did Frederick Sanger do?

Answer 24

• won the nobel prize in 1958 for sequencing insulin
• proved that proteins had a defined “primary” structure
• won second nobel in 1980 for sequencing DNA

Question 25

trypsin cleaves after ____

Answer 25

R/K residues (arginine/ lysine)

Question 26

chymotrypsin cleaves after ___

Answer 26

bulky hydrophobic AA’s

Question 27

where does cyanogen bromide cleave? what does it produce?

Answer 27

• CNBr cleaves the polypeptide at the C-terminal side of methionine
• peptidyl homoserine lactone

Question 28

how do we sequence proteins today?

Answer 28

mass spectroscopy

Question 29

what is the central dogma for protein sequencing from a DNA sequence?

Answer 29

DNA makes RNA makes Protein