Lecture 4: Structure and Proteins- AA

Question 1

Hydrophobic AA’s

Answer 1

Glycine 
Alanine
Proline
Valine
Leucine
Isoleucine
Methionine
Tryptophan
Phenylalanine

Question 2

Polar AA’s

Answer 2

Serine
Threonine
Asparagine (Asn) - N
Gluatamine (Gln) - Q
Cysteine

Question 3

Charged (+) AA’s

Answer 3

Lysine
Arginine (Arg) - R
Histidine

Question 4

Charged (-) AA’s

Answer 4

Aspartate (Asp) - D

Glutamate (Glu) - E

Question 5

pKa’s of Ionizing Side Chain

Answer 5

Arginine (12.5)
Aspartic Acid (4.1)
Cysteine (8.3)
Glutamic acid (4.1)
Histidine (6.0)
Lysine (10.8)
Tyrosine (10.9)

Question 6

Tiny AA’s

Answer 6

A, G, C, S

Question 7

Small AA’s

Answer 7

P, T, D, N

Question 8

Medium AA’s

Answer 8

V, E, H, Q

Question 9

Large AA’s

Answer 9

I, L, K, R, M

Question 10

Very Large

Answer 10

Y, F, W

Question 11

Essential AA’s

Answer 11

[Humans cannot synthesize]:
H, I, L, K, F, T, W, V
[Consumption>Production]:
R, M

Question 12

Non-essential AA’s

Answer 12

[Humans can synthesize de novo]:
D, A, N, C, Q, E, G, P, S
[Secondary synthesis]:
Y

Question 13

Essential AA’s (mnemonic)

Answer 13

P - phenylalanine
V - Valine
T - Tryptophan

T - Threonine
I - Isoleucine
M - Methionine

H - Histidine
A - Arginine
L - Lysine
L - Leucine

Question 14

Selenocysteine (Sec, U) - 21st AA

Answer 14

• pKa= 5.2
• Synthesized from Serine
• Processed to selenomethionine in plants, algae, and yeast; Alanine in animals
• 21st AA

Question 15

Stop codons

Answer 15

UGA, UAA, UAG

Question 16

Selenocysteine (Sec, U) and uses of UGA (opal)

Answer 16

-Within mitochondria, UGA = W codon
-In some ciliates, UGA = C codon
-Found in ALL 3 domains of life
-Uses own tRNA and SECIS
[Selenocysteine Insertion]

Question 17

Selenoproteins

Answer 17

Proteins that incorporate Secs

Question 18

Why are selenoproteins important for good health?

Answer 18

1. Reduce oxidative stresses in conjunction with Vitamine E
2. Required in cerebellum neurons (growth and coordination)
3. Moderate inflammatory responses - can reduce IBS

Question 19

Selenium deficiences result in

Answer 19

1. Myopathies (Keshan disease- cardiomyopathy and Statin intolerance- rhabdomyolysis)
2. Immune-incompetence

Question 20

Keshan disease (Cardiomyopathy)

Answer 20

[Myopathy]

• Caused by not enough selenium in diet
• Oxidative stress is disinhibited
• Treated with Se supplements

Question 21

Statin-intolerance (Rhabdomyolysis)

Answer 21

• Statins inhibit Sec-tRNA

- Treated by discontinuing statin

Question 22

Statins

Answer 22

Block formation of cholesterol in the liver

Question 23

Too much Selenium

Answer 23

• Hair and nail brittleness (Garlic breath)
• GI/Neuro lesions
• Myopathies, renal failure, and death

Question 24

Pyrrolysine (Pyl, O)

Answer 24

• Made by combining 2 lysisines
• Found only in some prokaryotes, all are methanogens
• Uses own tRNA
• Named 22nd AA

Question 25

Pyrrolysine (Pyl, O) and uses of UAG (amber)

Answer 25

- Usually UAG and UAA are reprogrammed togetherr | - UAG can also be an L or Q codon in some organisms

Question 26

Pyrrolysine - human intestinal microbe make/use Pyl

Answer 26

1. Methanomassiliicoccus luminyensis (Archae) | 2. Bilophila wadsorthia (Euchbacteria)

Question 27

Methanomassiliicoccus luminyensis (Archaea)

Answer 27

-Methanogen, Gram-neg, non-motile, coccoid

Question 28

Bilophila wadsorthia (Euchbacteria)

Answer 28

- Opportunistic pathogen, Gram-neg, anaerobic, rod - Penicillin-resistant - Common in gangrenous and abscessed tissues/organs - Overabundance may be linked to IBD/colitis - In mice, fish oil (unsat fats) decreases blooms but lard/milk fats (sat fats) increases blooms

Question 29

Non-proteinogenic AA's

Answer 29

1. Post-translational additions to proteinogenic AA's (Addition of phosphate grp) 2. D-entantiomers (bacterial peptidoglycan walls often contain D-Ala and D-glu) 3. Metabolism intermediates (ornithine and citrulline in the urea cycle) 4. Pre-biotic or extraterrestrial origin (Rudimentary AA's that did not make it into the genetic code, like alpha, gamma-diaminobutyric acid (DAB)

Question 30

NRPS (Non-ribosomal protein synthesis)

Answer 30

NRPS can make proteins and ANTIBIOTICS 1. A/Adenylation- activate carboxyl 2. PCP/Peptidyl Carrier Protein (T/Thiolation) - elongation intermediate 3. C/Condensation- peptide bond formation 4. TE/Thioesterase - release or cyclization

Question 31

Antibiotics are made by

Answer 31

``` NRPS !!! First Abx= B-lactams like pencillin An AVC tripeptide= L-alpha-aminoadipate-L-Cys-D-Val Newest class of Abx= Odilorhabdins (Lys- DAB (BOH)-DAB (BOH)- Gly-Orn-Pro-His -Dhl-Dha-Dhl-Dbt) ```

Question 32

Statins are made by

Answer 32

Polyketide synthesis (PKS)

Question 33

Primary structure

Answer 33

A linear chain of AA's

Question 34

Secondary structure

Answer 34

Local folding of the polypeptide chain, connected by Hydrogen bonds; Repetitive arrangements of amino acids that are near each other in the linear sequence

Question 35

Tertiary structure

Answer 35

Folding of the secondary structure, connected by disulfide linkages; Overall folding of a single polypeptide chain, which can include α-helical and/or β-sheet structures

Question 36

Quaternary structure

Answer 36

Interaction of multiple peptides; Association of at least 2 protein subunits

Question 37

Single bonds means

Answer 37

Rotation is possible (cis and trans)

Question 38

Peptide bond exists between

Answer 38

Carboxyl carbon (attached to double bonded O) and NH (in amine)