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Biochemistry 2 > Protein Metabolism > Flashcards

Protein Metabolism Flashcards

1
Q

Most pathways and systems of protein biosynthesis are?

A

highly conserved amongst organisms

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2
Q

How many enzymes and associated proteins are needed to make polypeptides?

A

300

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3
Q

What percentage of chemical energy in the cell does protein synthesis use?

A

90%

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4
Q

What percentage of the cell’s dry weight is related to the synthesis of proteins?

A

35%

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5
Q

Translation

A

process by which proteins are made
tRNA with amino acid reads mRNA code so rRNA can make a protein

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6
Q

Codon

A

nucleotide triplet on mRNA that encodes the amino acid

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7
Q

Amino acid sequence is determined by?

A

the codon sequence

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8
Q

How many codons encode amino acids?

A

61

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9
Q

Start codon

A

AUG

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10
Q

Stop Codons

A

UAA
UAG
UGA

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11
Q

alteration of the 3rd nucleotide

A

typically has no change for the amino acid it encodes

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12
Q

In a random sequence how many in 20 codons is a stop code?

A

1

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13
Q

open reading frame

A

reading frame with more than 50 codons and no stop codon

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14
Q

anti-codon

A

complementary sequence to codon on mRNA

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15
Q

The first two bases of the codon bind strongly while the third can?

A

wobble

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16
Q

If the wobble base is C or A

A

no wobble

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17
Q

If the wobble base is U or G

A

it can recognize 2

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18
Q

If the wobble base is I

A

it can recognize 3; A, U or C

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19
Q

missense mutation

A

most common, single alteration

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20
Q

silent mutation

A

nucleotide changes but amino acids encoded for remains the same

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21
Q

transition mutation

A

purine/pyrimidine swapped for a purine/pyrimidine

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22
Q

A change in the first nucleotide results in ?

A

a similar amino acid

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23
Q

Describe transitional frame shifting

A

ribosome will skip a stop codon and change reading frame to make a modified protein

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24
Q

How many reading frames are for every gene?

A

3

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25
Q

gRNA

A

guide RNA
acts as template for alterations when mRNA is edited before translation

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26
Q

Deamination can lead to?

A

an early stop codon and shorter peptide

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27
Q

Where does protein synthesis happen?

A

in the ribosome

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28
Q

Ribosome

A

supramolecular structure that doesn’t vary across organisms

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29
Q

5 stages of protein synthesis

A

activation
initiation
elongation
termination
folding and post translational modifications

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30
Q

Where are amino acids activated?

A

C-terminus

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31
Q

What is the link between the amino acid and mRNA code?

A

tRNA

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32
Q

How many tRNA synthetases per amino acid

A

1

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33
Q

tRNA synthetase

A

attaches amino acid to tRNA and proofreads it

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34
Q

amino acid arm

A

binds amino acid

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35
Q

anticodon arm

A

matches mRNA
tells which amino acid to bind

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36
Q

D arm

A

helps with folding

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37
Q

T Psi C arm

A

interacts with ribosome

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38
Q

extra arm

A

variable

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39
Q

Carboxylic acid attaches to ATP to form what?

A

an adenylyl end amino acid

40
Q

Class 1 Activation

A

2’ OH of tRNA binding arm attacks carbonyl, kicks off AMP as a leaving group

transesterification; amino acid moves from 2’ to 3’ OH

41
Q

Class 2 Activation

A

3’ OH of tRNA binding arm attacks carbonyl, kicks off AMP as a leaving group

42
Q

When does proofreading occur?

A

during amino acid tRNA attachment

43
Q

How does tRNA Synthetase proofread?

A

larger amino acid wont fit in active site
smaller amino acid will be hydrolysis off

44
Q

Which amino acid initiates protein synthesis in eukaryotes? Bacteria?

A

Met
FMet

45
Q

Steps of initiation in bacteria

A
  1. binding of initiation factors
  2. binding of FMet tRNA to start codon on mRNA
  3. assembly of active ribosome
46
Q

IF 1 binds

A

in A site

47
Q

IF3 binds

A

in E site, blocks large subunit

48
Q

mRNA binds with start codon near which site?

A

P site

49
Q

IF2 brings FMet-tRNA to bind where?

A

P site

50
Q

When 50s binds and kicks of the IFs what forms?

A

the active ribosome

51
Q

Exit Site

A

empty tRNA leaves from here

52
Q

Peptidyl Site

A

where peptide bond is made

53
Q

Aminoacyl site

A

incoming amino acid-tRNA enters

54
Q

Where is the AUG codon in eukaryotic initiation?

A

further up the mRNA strand

55
Q

Peptide bond steps

A
  1. binding of incoming amino acid tRNA
  2. bond formation
  3. translocation
56
Q

During elongation the next amino acid is brought by tRNA into the A site with?

A

EF-Tu

57
Q

Hydrolysis of GTP and removal alters?

A

the shape of tRNA so that a bond can be made between amino acid and peptide

58
Q

Does proofreading occur in elongation?

A

no

59
Q

How does EF-Tu dissociate?

A

slowly

60
Q

If the tRNA-mRNA interaction is incorrect what happens?

A

the tRNA-amino acid will leave without adding its amino acid

61
Q

During elongation what attacks what?

A

the amino terminus of the incoming amino acid attacks the C terminus of the peptide chain

62
Q

During elongation what happens to tRNA?

A

is removed from the P site
changes conformation- empty towards E site, tRNA with peptide towards P site

63
Q

EF-G

A

binds to the A site and shoves tRNAs over by 1 site

64
Q

When the stop codon is released what binds and what does it do?

A

releasing factor- cleaves the peptide chain from tRNA

65
Q

Each peptide bond formed requires the hydrolysis of 4 nucleotide triphosphates which are?

A

1 ATP
3 GTP

66
Q

What is termination regulated by?

A

ribosomal recycling factors

67
Q

Polysome

A

multiple ribosomes on the same mRNA; allows for rapid and high levels of protein expression in bacteria

68
Q

How can proteins be post translationally modified?

A

amino and carboxy terminal modifications
loss of signal sequences
modification of amino acids
attachment of carbohydrates, isoprenyl groups, or prosthetic groups
proteolytic processing
disulfide cross-links

69
Q

Which amino acids are likely to get phosphorylated?

A

Tyr
Thr
Ser

70
Q

Which amino acid is likely to get carboxylated?

A

Glu

71
Q

Which amino acids are likely to get methylated?

A

Lys, Arg

72
Q

Which amino acids can make O-linked glycoproteins?

A

Ser, Thr, Tyr

73
Q

Which amino acids can make N-linked glycoproteins?

A

Asn, Arg

74
Q

Isoprenes attach to which amino acid?

A

Cys

75
Q

Isoprenylation of Ras is?

A

oncogenic

76
Q

What are some examples of prosthetic groups?

A

heme, biotin

77
Q

Proteolytic processing

A

when a larger protein is cut into a smaller one for function

78
Q

Disulfide cross links

A

Cys-Cys
help hold protein in folded shape

79
Q

Puromycin

A

mimics amino acid attached to tRNA
enters the A site and makes a peptide bond
causes early termination
antibiotic

80
Q

Tetracyclines

A

bind in the A site and block tRNA from binding
causes early termination
antibiotic

81
Q

Cycloheximide

A

toxin that blocks translation of tRNA

82
Q

Ricin

A

Toxin that is a large protein that inactivates the large subunit of the ribosome

83
Q

Where does posttranslational modification occur?

A

endoplasmic reticulum

84
Q

Signal sequence brings the ribosome to the ER using?

A

signal recognition particles

85
Q

Where does glycosylation start?

A

in the endoplasmic reticulum

86
Q

Where is the protein transported from the endoplasmic reticulum?

A

the golgi complex

87
Q

Lysosome

A

enzyme breaks down proteins

88
Q

Secretory granules are used for?

A

extracellular release

89
Q

Transport vesicles are used for?

A

intracellular release

90
Q

Are signal sequences for nuclear transport cleaved?

A

no

91
Q

Where do nuclear localization sequences occur?

A

internal site of the peptide

92
Q

How can cells import proteins?

A

endocytosing

93
Q

Proteosome

A

enzyme that degrades proteins

94
Q

The longer a protein is in a cell, the more it collects ?

A

ubiquitin

95
Q

The level of ubiquitination is highly influenced by?

A

the N-terminal amino acid

96
Q

Stabilizing amino acids

A

Ala, Gly, Met, Ser, Thr, Val

97
Q

Destabilizing amino acids

A

Gln, Ile, Glu, Tyr, Pro, Asp, Leu, Lys, Phe, Arg

Biochemistry 2 (11 decks)

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