Lecture 5

Question 1

Do AA sporcle quizzes

Answer 1

“He’s too dangerous to be kept alive……DEW IT”

Question 2

Explain the importance of understanding what the “R group” of AA’s looks like a physiologic pH.

Answer 2

AA’s at physiologic pH (7.4) are in their Zwitterionic form (means 2)

This means that there is a NH3+ group and a COO- group that cancel out the charges of one another.

Question 3

Explain the significance of the chiral center on 19 of the 20 AA’s. Which AA does not have a chiral center?

Answer 3

Having a chiral center means that there are 2 possible enantiomer forms of most AA’s

Lysine is the only AA without a chiral center

Question 4

Which is the physiologically relevant isomer of nearly all of the AA’s?

Answer 4

L (as opposed to D)

Question 5

State the single letter abbreviation of all hydrophobic (nonpolar) AA’s

Answer 5

GAPVLIMWF

GAVLIPMTP Mnemonic

Question 6

State the single letter abbreviation of all polar AA’s

Answer 6

STYNQC

STAGTW Mnemonic

Question 7

State the single letter abbreviation of all Charged AA’s (state the 2 negatively charged one’s first)

Answer 7

DEKRH

AGLAH Mnemonic

Question 8

Which of the following AA’s is the negatively charged one?

Glutamine or Glutamate

Answer 8

Glutamate

Question 9

Which AA has the potential to form disulfide bonds? how many of these must be present in order for a disulfide bond to occur?

Answer 9

Cysteine

anything with a disulfide bond, must have at least 2 cysteines

Question 10

State the AA’s that are long and linear in shape (“Large”)

Answer 10

R (arginine)

M (methionine)

I (isoleucine)

L (Leucine)

K (Lysine)

Question 11

State the AA’s that are aromatic (“Very Large”)

Answer 11

Y (Tyrosine)

F (Phenylalanine)

W (Tryptophan)

Question 12

State the essential AA’s (be sure to put the 2 “iffy” ones at the end

Answer 12

K (lysine)
F (phenylalanine)
H (histidine)
I (isoleucine)
L (leucine)
T (threonine)
W (tryptophan)
V (valine)
R (arginine)
M (methionine)

Mnemonic: “King Frank’s HILT Was Very Rad Man)

Question 13

State the non essential AA’s

Answer 13

C (cysteine)
A (alanine)
N (asparagine)
D (aspartic acid)
Y (tyrosine)
P (proline)
E (glutamic acid)
G (glycine)
S (serine)
Q (glutamine)

Mnemonic: “CANDY PEGS, Questions?”

Question 14

Name the 2 essential AA’s that are different than the others and explain why they are different.

Answer 14

R (arginine)
M (methionine)

These 2 are different bc humans ARE able to synthesize them, however we use them up at a much faster rate than we are able to synthesize them
(this issue is why they are still considered essential AA’s)

Question 15

Name the non-essential AA that is made via “secondary synthesis” and explain what this means

Answer 15

Y (tyrosine)

Tyrosine is synthesized by adding an OH group to phenylalanine, which is an essential AA

This means that you have to have enough excess phenylalanine around to create tyrosine and therefore muddies the water surrounding Tyrosine’s status as a non-essential AA.

Question 16

State the 21st AA and describe it (encoded by what sequence,type of RNA, sequence and reason for it, pka)

Answer 16

Selenocysteine

Encoded by a UGA stop codon (only AA encoded by stop codon)

It is synthesized on it’s own tRNA

has a pka lower than phys. pH, so it is deprotonated

Question 17

Explain what SECIS is and it’s purpose

Answer 17

SECIS (Selenocysteine Insertion Sequence) a necessary sequence in Selenocysteine forms a hairpin that “pauses the ribosome” in order to provide enough time for the proper tRNA to fall into place on the peptide chain

Question 18

Name 2 ailments that are results of selenium deficiency

Answer 18

Keshan disease (cardiomyopathy)

Statin Intolerance (rhabdomyolysis: “a breakdown of muscle tissue that causes kidney failure due to the release of a damaging protein into the blood”)

Question 19

Name the 22nd AA and describe it (codon, how it’s structure is related to other AA’s)

Answer 19

Pyrrolysine

uses UAG/amber codon (stop codon)

(has a stem loop sequence, however it isn’t a necessary mechanism)

it is basically 2 lysine’s stuck together

Question 20

Name the domains of living organisms that Selenocysteine and Pyrrolysine are found in

Answer 20

Selenocysteine: found in all 3 domains

Pyrrolysine: found in Prokaryotes only

Question 21

Pyrrolysine is found in Methanomassiliicoccus luminyensis and Bilophila wadsorthia. Explain why these prokaryotes are pertinent to humans.

Answer 21

Methanomassiliicoccus luminyensis: found in the intestinal biome and is a methanogen that reduces methanol by oxidizing hydrogen (in order to regulate pH)

Bilophila wadsorthia: found in the intestinal biome and is an opportunistic pathogen that is common in gangrenous/abscessed tissues.
(IN MICE unsaturated fats decrease severity while saturated fats increase it’s severity)

Question 22

Explain the relevance/application of the following statements about non proteinogenic AA’s

1. They can be used during non-ribosomal protein synthesis (NRPS)
2. They are NOT used to make proteins

Answer 22

1. NRPS is the method by which many antibiotics are made ex. penicillin
2. non proteinogenic AA’s can be metabolism intermediates, Extraterrestrial in origin, and play many physiological roles (such as bacteria cell walls, neurotransmitters, Toxins/antimicrobials)

Question 23

Explain the “up down up down” layout of AA’s that are connected via peptide bonds

Answer 23

basically means that the functional group on each carbon (opposite the H) alternates “up down up down”

(this contributes to the decreased window of preferred bond angles)

Question 24

True or False:

Peptide bonds are planar and linear in structure, which means that there is not any bond rotation that is occuring

Answer 24

False:

While peptides bonds are planar and linear in structure, there is still SOME bond rotation occurring.

Most peptide bonds between AA’s have a very small range of preferred bonding angles, which means they are just shy of having “no bond rotation”
(basically any single bond, which is what peptide bonds are, will have at least some slight bond rotation)

Question 25

Briefly state the 2 types of primary structure modifications that can be made to AA peptide chains AFTER translation

Answer 25

1. Enzymatic cleavage of signal sequences (“cut things off”)
2. Chemical modification of side chains (“add things on”)
   ex. phosphorylation, glycosylation, methylation, etc.