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Biochemistry 2 > Protein Metabolism > Flashcards

Protein Metabolism Flashcards

(97 cards)

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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
gRNA
guide RNA acts as template for alterations when mRNA is edited before translation
26
Deamination can lead to?
an early stop codon and shorter peptide
27
Where does protein synthesis happen?
in the ribosome
28
Ribosome
supramolecular structure that doesn’t vary across organisms
29
5 stages of protein synthesis
activation initiation elongation termination folding and post translational modifications
30
Where are amino acids activated?
C-terminus
31
What is the link between the amino acid and mRNA code?
tRNA
32
How many tRNA synthetases per amino acid
1
33
tRNA synthetase
attaches amino acid to tRNA and proofreads it
34
amino acid arm
binds amino acid
35
anticodon arm
matches mRNA tells which amino acid to bind
36
D arm
helps with folding
37
T Psi C arm
interacts with ribosome
38
extra arm
variable
39
Carboxylic acid attaches to ATP to form what?
an adenylyl end amino acid
40
Class 1 Activation
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
Class 2 Activation
3’ OH of tRNA binding arm attacks carbonyl, kicks off AMP as a leaving group
42
When does proofreading occur?
during amino acid tRNA attachment
43
How does tRNA Synthetase proofread?
larger amino acid wont fit in active site smaller amino acid will be hydrolysis off
44
Which amino acid initiates protein synthesis in eukaryotes? Bacteria?
Met FMet
45
Steps of initiation in bacteria
1. binding of initiation factors 2. binding of FMet tRNA to start codon on mRNA 3. assembly of active ribosome
46
IF 1 binds
in A site
47
IF3 binds
in E site, blocks large subunit
48
mRNA binds with start codon near which site?
P site
49
IF2 brings FMet-tRNA to bind where?
P site
50
When 50s binds and kicks of the IFs what forms?
the active ribosome
51
Exit Site
empty tRNA leaves from here
52
Peptidyl Site
where peptide bond is made
53
Aminoacyl site
incoming amino acid-tRNA enters
54
Where is the AUG codon in eukaryotic initiation?
further up the mRNA strand
55
Peptide bond steps
1. binding of incoming amino acid tRNA 2. bond formation 3. translocation
56
During elongation the next amino acid is brought by tRNA into the A site with?
EF-Tu
57
Hydrolysis of GTP and removal alters?
the shape of tRNA so that a bond can be made between amino acid and peptide
58
Does proofreading occur in elongation?
no
59
How does EF-Tu dissociate?
slowly
60
If the tRNA-mRNA interaction is incorrect what happens?
the tRNA-amino acid will leave without adding its amino acid
61
During elongation what attacks what?
the amino terminus of the incoming amino acid attacks the C terminus of the peptide chain
62
During elongation what happens to tRNA?
is removed from the P site changes conformation- empty towards E site, tRNA with peptide towards P site
63
EF-G
binds to the A site and shoves tRNAs over by 1 site
64
When the stop codon is released what binds and what does it do?
releasing factor- cleaves the peptide chain from tRNA
65
Each peptide bond formed requires the hydrolysis of 4 nucleotide triphosphates which are?
1 ATP 3 GTP
66
What is termination regulated by?
ribosomal recycling factors
67
Polysome
multiple ribosomes on the same mRNA; allows for rapid and high levels of protein expression in bacteria
68
How can proteins be post translationally modified?
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
Which amino acids are likely to get phosphorylated?
Tyr Thr Ser
70
Which amino acid is likely to get carboxylated?
Glu
71
Which amino acids are likely to get methylated?
Lys, Arg
72
Which amino acids can make O-linked glycoproteins?
Ser, Thr, Tyr
73
Which amino acids can make N-linked glycoproteins?
Asn, Arg
74
Isoprenes attach to which amino acid?
Cys
75
Isoprenylation of Ras is?
oncogenic
76
What are some examples of prosthetic groups?
heme, biotin
77
Proteolytic processing
when a larger protein is cut into a smaller one for function
78
Disulfide cross links
Cys-Cys help hold protein in folded shape
79
Puromycin
mimics amino acid attached to tRNA enters the A site and makes a peptide bond causes early termination antibiotic
80
Tetracyclines
bind in the A site and block tRNA from binding causes early termination antibiotic
81
Cycloheximide
toxin that blocks translation of tRNA
82
Ricin
Toxin that is a large protein that inactivates the large subunit of the ribosome
83
Where does posttranslational modification occur?
endoplasmic reticulum
84
Signal sequence brings the ribosome to the ER using?
signal recognition particles
85
Where does glycosylation start?
in the endoplasmic reticulum
86
Where is the protein transported from the endoplasmic reticulum?
the golgi complex
87
Lysosome
enzyme breaks down proteins
88
Secretory granules are used for?
extracellular release
89
Transport vesicles are used for?
intracellular release
90
Are signal sequences for nuclear transport cleaved?
no
91
Where do nuclear localization sequences occur?
internal site of the peptide
92
How can cells import proteins?
endocytosing
93
Proteosome
enzyme that degrades proteins
94
The longer a protein is in a cell, the more it collects ?
ubiquitin
95
The level of ubiquitination is highly influenced by?
the N-terminal amino acid
96
Stabilizing amino acids
Ala, Gly, Met, Ser, Thr, Val
97
Destabilizing amino acids
Gln, Ile, Glu, Tyr, Pro, Asp, Leu, Lys, Phe, Arg

Biochemistry 2 (11 decks)

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