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MCAT Biomolecules > Amino Acids and Proteins > Flashcards

Amino Acids and Proteins Flashcards

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1
Q

Reverse transcriptase:
violates ________
RNA –> ???
replication of?

A
  • violates central dogma
  • RNA –> cDNA (complimentary)
  • replication of retroviruses (HIV)
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2
Q

ncRNA:
skips _____
ex?

A

noncoding RNA
skips translation
tRNA, rRNA

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3
Q

Epigenetics:

ex?

A
  • different phenotypes without making changes to the underlying DNA sequence
  • can have the same DNA in all body cells but not all cells look or behave exactly the same
  • DNA methylation, histone modification
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4
Q

peptide bond?
^ makes aa-aa-aa-aa-aa-aa?
^ makes what?

A

between 2 amino acids
polypeptide
protein

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5
Q

peptide bond formed by

A

nucleophilic addition-elimination rxn b/w carboxylic acid group of aa 1 and amino group of aa 2 creating amide bond

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6
Q

peptide bond cleaved/broken by?

A

acid hydrolysis and proteolysis

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7
Q

acid hydrolysis

A
  • heat + acid

- nonspecific form of cleavage of peptide bond

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8
Q

proteolysis

A

uses enzyme protease

specific

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9
Q

what are the special aa?

A

histidine, proline, glycine, cysteine

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10
Q

pH < pKa: protonation or deprotonation?

pH > pKa: protonation or deprotonation?

A

protonation

deprotonation

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11
Q

why is histidine a special aa?

A

pKa of side chain = 6.5 = physiological pH so it exists in the protonated and deprotonated state so it can stabilize or destabilize an active side of a protein

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12
Q

why is proline a special aa?

A

has a secondary alpha amino group (the side chain forms a 2nd bond w N on amino group)

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13
Q

why is glycine a special aa?

A

it has the simplest side chain
no chiral alpha C
flexible/free rotation around alpha C

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14
Q

why are proline and glycine special in terms of secondary protein structure?

A

proline and glycine cause the alpha-helix structure to “kink” = ALPHA HELIX BREAKERS

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15
Q

cysteine vs cystine

A

cysteine: reduced form (e for e- so have e- in reduced form); thiol- (SH)
cystine: oxidized form; 2 cysteines come together via disulfide bridge

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16
Q

how to form cystine?

A

2 cysteines: reducing –> oxidizing

-gain e- by loss of H and bond form b/w 2 sulfurs (disulfide bridge)

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17
Q

extracellular space: reducing or oxidizing? thiol or disulfide form?
intracellular space: reducing or oxidizing? thiol or disulfide form?

A

extra: oxidizing, disulfide
intra: reducing, thiol (antioxidants are inside the cell)

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18
Q

what is hemoglobin?

A

a protein (made of aa) that transports oxygen to tissues which creates ATP and energy

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19
Q

if amino group (NH2) is on the left for a fischer projection of an aa, what is its configuration?
if on the right?

A

L-aa

D-aa

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20
Q

what is the configuration found in humans?

A

L

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21
Q

L and D configurations are ______ b/c they are mirror images that are not _______

A

enantiomers

superimposable

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22
Q

what is an alkyl group?

A

CnH2n+1

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23
Q

classification of aa?

A

NP, hydrophobic

Polar, hydrophilic

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24
Q

NP, hydrophobic splits into which 2 functional group classifications?

A

alkyl and aromatic

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25
Q

what are the 7 NP, hydrophobic, alkyl aa?

A 
Glycine
Alanine
Valine
Methionine
Leucine
Isoleucine
Proline
26
Q

glycine?

A

NP, hydrophobic, alkyl

side chain: -H

27
Q

alanine?

A

NP, hydrophobic, alkyl

side chain: CH3

28
Q

valine?

A

NP, hydrophobic, alkyl

side chain: -CH(CH3)2

29
Q

methionine

A

NP, hydrophobic, alkyl

side chain: -CH2CH2SCH3

30
Q

leucine?

A

NP, hydrophobic, alkyl

side chain: -CH2CH(CH3)2

31
Q

isoleucine?

A

NP, hydrophobic, alkyl

side chain: -CH(CH3)CH3CH2

32
Q

proline?

A

NP, hydrophobic, alkyl

side chain: secondary alpha N

33
Q

what are the 2 NP, hydrophobic, aromatic aa?

A

phenylalantine

tryptophan

34
Q

phenylalantine?

A

NP, hydrophobic, aromatic

side chain: -CH2aromaticring

35
Q

tryptophan?

A

NP, hydrophobic, aromatic

side chain: 2 rings –> first ring looks like side chain of proline (NH) and second ring is aromatic

36
Q

polar, hydrophilic splits into what 3 categories?

A

neutral
acid
base

37
Q

what are the 6 neutral aa?

A 
Serene
Threonine
Asparagine
Glutamine
Cysteine
Tyrosine
38
Q

serene?

A

Polar, hydrophilic, neutral

side chain: CH2OH

39
Q

threonine?

A

Polar, hydrophilic, neutral

side chain: CH(OH)CH3

40
Q

asparagine?

A

Polar, hydrophilic, neutral

side chain: CH3CONH2

41
Q

glutamine?

A

Polar, hydrophilic, neutral

side chain: CH2CH2CONH2

42
Q

cysteine

A

Polar, hydrophilic, neutral

side chain: CH2SH

43
Q

tyrosine?

A

Polar, hydrophilic, neutral

side chain: -C-aromaticring-OH

44
Q

why are S,T,A,G,C,T neutral aa?

A

the side chain contains an O or an S which has a localized - charge and the rest of the side change has a + charge

45
Q

what are the 2 polar, hydrophilic, acidic aa?

A

Aspartic acid

Glutamic Acid

46
Q

aspartic acid?

A

Polar, hydrophilic, acidic

side chain: -CH2COOH

47
Q

glutamic acid?

A

Polar, hydrophilic, acidic

side chain: -CH2CH2COOH

48
Q

what makes aspartic acid and glutamic acid acidic?

A

they have a carboxylic group in their side chain = strong H donor

49
Q

after donating H, what do aspartic acid and glutamic acid become when in anion form?

A

aspertate

glutamate

50
Q

what are the 3 polar, hydrophilic, basic aa?

A

Histidine
Lysine
Arginine

51
Q

histidine?

A

polar, hydrophilic, basic

side chain: -C-ringwNandN

52
Q

lysine?

A

polar, hydrophilic, basic

side chain: -CH(CH2)3NH2

53
Q

arginine?

A

polar, hydrophilic, basic

side chain: -CH2(CH3)2N(NH2 and NH)H

54
Q

why are histidine, lysine, and arginine basic?

A

their side chain has N atoms = strong H acceptor

55
Q

primary structures for proteins determines what?

primary structure is stabilized by?

A

aa sequence

peptide bond

56
Q

secondary structures for proteins is?

secondary structure is stabilized by?

A

backbone interactions

H bonds

57
Q

two types of secondary structures?

A 
alpha helix (coiled spring)
beta pleated sheet (parallel or anti-parallel depending on if amino ends and carboxyl ends line up with themselves or each other)
58
Q

tertiary structures determined by?

stabilized by?

A

distant group interactions

H bonds, vander waals forces, disulfide bridge (cys aa), hydrophobic packing

59
Q

quaternary structure determined by?

stabilized by?

A

bonding b/w multiple polypeptides

same interactions that determine tertiary structure

60
Q

an individual polypeptide in a group of folded polypeptides is called?

A

subunit

MCAT Biomolecules (1 decks)

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