amino acid structure and function

Question 1

what isomers are usually dealt with in biology

Answer 1

L isomers

Question 2

hydrophobic amino acids

Answer 2

glycine
alanine
proline
valine
leucine
isoleucine
methionine
tryptophan
phenylalanine

Question 3

polar amino acids

Answer 3

serine
threonine
tyrosine
asparagine
glutamine
cysteine

Question 4

which amino acids can participate in redox rxns?

Answer 4

cysteine

disulfide linkages

Question 5

charged (+) amino acids

basic

Answer 5

lysine
arginine
histidine

Question 6

charged (-) amino acids

acidic

Answer 6

aspartate (aspartic acid)

glutamate (glutamic acid)

Question 7

small amino acids

Answer 7

alanine
glycine
cysteine
serine

proline
threonine
aspartic acid
asparagine

Question 8

medium amino acids

Answer 8

valine
histidine
glutamic acid
glutamine

Question 9

large amino acids

Answer 9

isoleucine
leucine
methionine
lysine
arginine 

tyrosine
tryptophan
phenylalanine

Question 10

essential amino acids

Answer 10

humans cannot synthesize; cannot make or cannot make enough

histidine
lysine
tryptophan
isoleucine
phenylalanine
valine
leucine
threonine

consumption > production:
arginine
methionine

Question 11

nonessential amino acids

Answer 11

humans can synthesize dev novo

alanine
cysteine
glycine
asparagine
glutamine
proline
aspartic acid
glutamic acid 
serine

secondary synthesis:
tyrosine (can make it, but make it from a nonessential amino acid-phenylalanine

Question 12

mnemonic for essential amino acids

Answer 12

Pvt Tim Hall (first letter of full name)

P henylalanine (Phe, F)
V aline (Val, V)
T ryptophan (Trp, W)

T hreonine (Thr, T)
I soleucine (Ile, I) 
M ethionine (Met, M)

H istidine (His, H)
A rginine (Arg, R)
L ysine (Lys, K)
L eucine (Leu, L)

Question 13

proteinogenic amino acids

Answer 13

are used to make proteins from the genetic code

Question 14

nonproteinogenic amino acids

Answer 14

are not decoded from the genome

e.x. post-translational modifications (phosphorylation for example)

Question 15

21st amino acid

Answer 15

Selenocysteine (Sec, U)

pKa = 5.2
synthesized from serine

Question 16

selenocysteine can be processed to:

Answer 16

selenomethionine in plants, algae, and yeast

and alanine in animals

Question 17

stop codon for selenocysteine

Answer 17

UGA (opal)

Question 18

selenocysteine is found in

Answer 18

all 3 domains of life (bacteria, archea, and eukaryea)

Question 19

selenocysteine uses its own

Answer 19

tRNA and SECIS (selenocysteine insertion sequence)

Question 20

proteins that incorporate Sec are called

Answer 20

selenoproteins

Question 21

selenoproteins are important for good health:

Answer 21

reduce oxidative stresses in conjunction with vitamin E

required in cerebellum neurons (growth and coordination)

moderate inflammatory responses (may reduce IBD)

Question 22

what happens to a selenoprotein when Sec is not available

Answer 22

usually a stop codon –> proteins ends up truncated

Question 23

selenium deficiency results in

2.

Answer 23

1. myopathies

keshan disease (cardiomyopathy

• caused by not enough selenium in the diet
• oxidative stress is disinhibited
• treated with Se supplements

statin intolerance (rhabdomyolysis-muscle death)

• statins inhibit Sec-tRNA
• treated by discontinuing statin

2. Immune-incompetence

Question 24

statins are drugs that

Answer 24

block the formation of cholesterol in the liver

Question 25

too much selenocysteine results in

Answer 25

hair and nail brittleness, “garlic breath”

gastrointestinal/neurological leions

myopathies, renal failure, and death

Question 26

22nd amino acid

Answer 26

pyrrolysine (Pyl, O)

made by combining 2 lysines

Question 27

stop codon for pyrrolysine

Answer 27

UAG (amber)

Question 28

pyrrolysine is found

Answer 28

in some prokaryotes, all are methanogens

Question 29

pyrrolysine uses its own

Answer 29

tRNA

Question 30

several members of the human intestinal microbiome make/use Pyl) including

Answer 30

methanomassiliicoccus luminyensis (arahaea)

bilophila wadsorthia (eubacteria)

Question 31

nonproteinogenic amino acids include

Answer 31

post-translation additions to proteinogenic amino acids

D-enantiomers

metabolism intermediates

pre-biotic or extraterrestrial origin

proteins made by non-riboosomal protein synthesis

Question 32

A/Adenylation

Answer 32

activation carboxyl

Question 33

PCP/Peptidyl carrier

Answer 33

elongation intermediate

Question 34

C/Condensation

Answer 34

peptide bond formation

Question 35

TE/Thioesterase

Answer 35

release of cyclization

Question 36

most antibiotics are made by

Answer 36

non-ribosomal protein synthesis

Question 37

newest class of antibiotics

Answer 37

odilorhabdins

Question 38

statins are made by

Answer 38

polyketide synthesis (PKS)

Question 39

primary structure

Answer 39

chain of amino acids

Question 40

secondary structure

Answer 40

local folding of the polypeptide chain, connected by hydrogen bonds

alpha helices and beta sheet

Question 41

tertiary structure

Answer 41

folding of the secondary structure, connected by disulfide linkages

Question 42

quaternary structure

Answer 42

interaction of multiple peptides

Question 43

polypeptide chains start from _____ and go towards _____

Answer 43

amino side

carboxyl side

Question 44

peptide bond

Answer 44

bond between carbon and nitrogen

Question 45

because amino acids are joined by a single bond,

Answer 45

rotation is possible