Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

PROTEIN METABOLISM > ALL THE THINGS > Flashcards

ALL THE THINGS Flashcards

1
Q

What are the 3 RNA species involved in translation?

A

tRNA
rRNA
mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What function/role do tRNAs play in translation?

A

function as adaptors between mRNA codons and specific amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What % of total cellular RNA is tRNA?

A

15%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What function/role do rRNAs play in translation?

A

form part of the structure of ribosomes and participate in protein synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What % of total cellular RNA is rRNA?

A

80%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What function/role do mRNAs play in translation?

A

code for proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What % of total cellular RNA do mRNAs play in translation?

A

5%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How many total codons are there in the Genetic Code?

A

64

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the start codon?

A

AUG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the 3 stop codons?

A

UAA, UAG, UGA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the Wobble Position?

A

means there is “steric freedom” at this site; other bases may pair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Codons that differ in the first two bases will have their own what?

A

tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How many reading frames are possible for a given mRNA?

A

3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What causes alteration of the reading frame?

A

non-N3 insertions/deletions cause alteration of the reading frame

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

When the tRNA arrives at the mRNA, pairing between what occurs?

A

pairing between codon and anticodon; antiparallel alignment

Codon is 5’-3’
Anticodon is 3’-5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

When the anticodon has an inosine at position 1, it can pair with how many different codons?

A

3

Position 1 is always at the 5’ end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are the 3 different mutations affecting translation?

A

Missense
Nonsense
Insertions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What types of insertions/deletions are possible?

A

Frameshift mutations

3n insertions/deletions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are silent mutations?

A

DNA base-pair substitutions that do not affect the amino acid coding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are a special class of insertions/deletions?

A

splicing errors caused by splice site mutations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Aminoacyl-tRNA synthetases are enzymes that carry out how many coupled reactions?

A

2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Describe the 2 coupled reactions carried out by aminoacyl-tRNA synthetases

A

(1) An amino acid is activated by reaction with ATP to give an aminoacyl-AMP intermediate
(2) Amino acids are coupled to tRNA’s by an ester linkage between the carboxyl group of the amino acid and the 2’ or 3’ OH of the 3’ A-residue of the tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Why do aminoacyl-tRNA synthetases have to be very precise?

A

they bridge between 3-letter codon code and specific amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Each aminoacyl-tRNA synthetase is specific for one what and one or more corresponding?

A

specific for one amino acid and one or more corresponding tRNAs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

tRNA specificity is based on what?

A

specific bases in the anticodon and other bases elsewhere in the tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is a “Charged tRNA?”

A

tRNA carrying an amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What are the 2 steps in aminoacylation of tRNA by aminoacyl-tRNA synthetases?

A

(1) amino acid activation by ATP with the release of phosphate
(2) binding of the activated amino acid to terminal A residue of the tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

tRNA synthetases can remove what kinds of errors?

A

coupling errors; if the incorrect amino acid binds the synthesis site, it gets moved to the editing site to be removed and replaced

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

The Initiator tRNA (tRNAf) is first charged with what?

A

methionine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

A formyl group is transferred to the methionyl - tRNAfMet from what?

A

N10 - formyltetrahydrofolate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What role does formylation of the amino group play?

A

the attached methionine can no longer be inserted in the interior of the polypeptide chain

All other methionines added will be devoid of the formyl group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Before translation begins in Prokaryotes, the 3’-end of mRNA must pair with what?

A

16S rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What is the pairing to the 16S rRNA mediated by in Prokaryotes?

A

the Shine-Dalgarno sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Where is the Shine-Dalgarno sequence in Prokaryotes?

A

6 bases upstream of the AUG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

After pairing with 16S RNA, what else must the mRNA pair with before translation begins in Prokaryotes?

A

the mRNA AUG must pair with the anticodon of the initiator methionyl-tRNAfMet

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What are the initiation factors for Prokaryotic translation?

A

IF1, IF2, IF3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Multiple internal Shine-Dalgarno sequences are located where?

A

near the start sites for each of the encoded proteins in a polycistronic mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What are the 2 ribosomal subunits in Prokaryotes?

A

Small 30S
Large 50S

Together make the 70S ribosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

In the first step of bacterial translation initiation, what does IF3 prevent?

A

the 30S and 50S subunits from combining prematurely

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

In the first step of bacterial translation initiation, what does IF1 prevent?

A

prevents the use of the A site in initiation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

In the second step of bacterial translation, what does IF2 do?

A

binds to an initiator tRNA and controls the entry of tRNA onto the P-site. IF2 bound to GTP binds to the 30S P-site.

IF2 allows addition of the initiator methionyl-tRNAfMet to the P-site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

In the third step of bacterial translation, what happens?

A

50S subunit binds. It hydrolyzes GTP bound to IF2 and leads to the release of all the IFs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

During protein synthesis, the nascent protein is always covalently bound to what?

A

a tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What does bacterial protein synthesis begin with?

A

a peptidyl-tRNA in the P-site. An aminoacyl-tRNA guided by EF-Tu binds the A-site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

In bacterial elongation, with both P & A sites occupied, what is formed and what catalyzes its formation?

A

a new peptide bond catalyzed by 23S rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

23S rRNA is a known what with what kind of activity?

A

ribozyme with peptidyl-transferase activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

In bacterial elongation, what translocates the ribosomal subunits to move the deacylated tRNA to the E-site?

A

elongation factor G

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

Once in the E-site, the deacylated tRNA is free to do what in bacterial elongation?

A

dissociate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Peptide bond formation in bacterial elongation is followed by shifting a tRNA position on the 50S subunit. What kind of binding state is formed?

A

hybrid binding state

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

In the Translocation step of bacterial elongation, energy from the hydrolysis of what bound to what drives the step?

A

GTP bound to EF-G

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Termination of translation in bacteria is by what?

A

by release factors that are proteins with tRNA shapes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

Binding of release factors force the peptidyl transferase to add what to the peptidyl tRNA?

A

to add water instead of an amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Two high energy bonds of what are cleaved when charging tRNA with an amino acid?

A

ATP

54
Q

To the bind the charged tRNA to the ribosomal A-site, one high end energy bond of what is cleaved?

A

GTP

55
Q

What is cleaved for the translocation step in bacteria?

A

GTP

56
Q

For each amino acid incorporated in translation, how many total bonds are consumed?

A

4

57
Q

What are the ribosomal functional sites?

A

A site
P site
E site

58
Q

What is the A-site?

A

acceptor site; associated with mRNA codon

59
Q

What is the P-site?

A

peptidyl transferase site, associated with mRNA codon

60
Q

What is the E-site?

A

exit site, not associated with mRNA codon, less well defined in Eukary ribosomes

61
Q

Both large and small ribosomal subunits contribute to form which sites?

A

A and P-sites

62
Q

Where is the complementary sequence for the Shine-Dalgarno sequence?

A

withi the 16S rRNA

63
Q

In the 50S subunit, what rRNA is the peptidyl transferase (ribozyme)?

A

23S rRNA

64
Q

What rRNA is the peptidyl transferase in Eukary and which subunit is it found in?

A

28S rRNA

60S subunit

65
Q

In bacteria, what ion is associated with activation of amino acids, initiation, and elongation?

A

Mg2+

66
Q

What are the 5 agents mentioned in class that inhibit protein synthesis?

A 
Streptomycin
Puromycin
Tetracyclin
Chloramphenicol
Eryhtromycin
67
Q

How does Streptomycin inhibit protein synthesis?

A

binds to 30S subunit and causes misreading of the genetic code and inhibits initiation of translation at higher concentrations

68
Q

How does Puromycin inhibit protein synthesis?

A

structurally similar to the 3’-end of aminoacyl tRNA

binds to the A site and participates in peptide bonding: peptidyl puromycin — prematurely ending synthesis

69
Q

How does Tetracyclin inhibit protein synthesis?

A

blocks A-site

70
Q

How does Chloramphenicol inhibit protein synthesis?

A

binds to the large ribosomal subunit and blocks bacterial peptidyl transferase

71
Q

How does Erythromycin inhibit protein synthesis?

A

binds to the large ribosomal subunit, blocking translocation

72
Q

Which agents specifically inhibit the 50S ribosomal subunit?

A

Erythromycin

Chloramphenicol

73
Q

Which agents specifically inhibit the 30S ribosomal subunit?

A

Tetracyclin

Streptomycin

74
Q

Bacterial resistance to antibiotics is mediated by what?

A

plasmids encoding enzyme(s) — which alter the host

75
Q

Staphylococcal resistance to erythromycin is the result of what?

A

conversion of a single adenosine in 23S rRNA to N6-dimethyladenosine, so that erythromycin can no longer bind

76
Q

The conversion of the adenosine to N6-dimethyladenosine is mediated by what plasmid borne enzyme?

A

RNA methylase

77
Q

What are the eukaryotic orthologs of EF-Tu and EF-G initiation factors?

A

eEF1

eEF2

78
Q

When forming the eukary initation complex, what binding protein is bound to the 3’-end of the mRNA?

A

PABP - poly(A) binding protein

79
Q

With PABP bound, what binds to the 5’-cap in eukaryotic initiation?

A

eIF4E

80
Q

With eIF4E bound to the cap and PABP at the 3’-end, what binds next to tie the ends of the mRNA together?

A

eIF4G

81
Q

The eIF proteins are also involved in the binding of the initiation complex to what ribosomal unit?

A

40S subunit

82
Q

Another eIF protein scans the mRNA with the 40S subunit for what codon?

A

AUG codon

83
Q

In order to find the AUG, what does the eIF protein need to have to resolve secondary structure in the 5’UTR of the mRNA?

A

it needs to have helicase activity; it also NEEDS ATP

84
Q

In eukaryotic initation, is the methionine bound to the initiator tRNAMet formylated?

A

No

85
Q

What are the two potent toxins that affect Eukaryotic protein synthesis?

A

Diptheria toxin

Ricin

86
Q

What does Diptheria toxin do/cause?

A

inactivates eukary elongation factor 2 (eEF2, similar to bacterial EF-G) by modification of a histidine residue (by ADP-ribosylation)

87
Q

What kind of illness is Diptheria?

A

respiratory track illness

88
Q

What Ricin do/cause?

A

depurinates a specific adenosine residue in the 28S rRNA, thereby inactivating its peptidyl transferase activity

89
Q

What are heat shock proteins?

A

synthesized upon cellular heat exposure. Hsp’s have affinity for exposed hydrophobic patches of incompletely folded proteins and use ATP for binding and release of these patches

90
Q

Both Hsp 60 & 70 use lots of what to ensure correct protein folding?

A

ATP

91
Q

Where can you find chaperones like Hsp 60 & Hsp 70?

A

in both the cytoplasm and inside organelles

92
Q

What are some of the modifying groups involved in posttranslational modifications?

A

Phosphate on Ser, Thr, or Tyr

Methyl on Lys

Acetyl on Lys

Palmityl on Cys

N-acetylglucosamine on Ser or Thr

Ubiquitin on Lys

93
Q

What affect does the phosphate on Ser, Thr, or Tyr have? (Function of the modification)

A

drives the assembly of a protein into larger complexes

94
Q

What effect does methylation of Lys have (Postranslationally)

A

Helps to create histone code in chromatin through forming either mono-, di-. or tri-methyl lys

95
Q

What effect does an acetyl group have on lys? (Postranslationally)

A

Helps to create histone code in chromatin

96
Q

What effect does a palmityl group on Cys have? (Postranslationally)

A

this fatty acid addition drives protein association with membranes

97
Q

What effect does N-acetylglucosamine have on Ser or Thr? (Postranslationally)

A

controls enzyme activity and gene expression in glucose homeostasis

98
Q

Ubiquitin on Lys will have what affect postranslationally?

A

Monoubiquitin addition regulates the transport of membrane proteins in vesicles

A polyubiquitin chain targets a protein for degradation

99
Q

In the formation of the functional final protein, what is removed?

A

the formyl group in prokaryotes, the amino terminal methionine, and often additional amino terminal terminal amino acids

100
Q

In 50% of eukary proteins, the amino group of the N-terminal residue is what? (How is it modified)

A

N-acetylated

101
Q

Are carboxy terminals susceptible to terminal modifications?

A

they may be trimmed and modified

102
Q

How are proteins targeted to intracellular organelles or for secretion?

A

they lose their signal sequences often through cleavage at a specific site

103
Q

What enzyme acts to cleave the signal sequence on a growing polypeptide chain?

A

signal peptidase - specific N-terminal aa sequence is cleaved off

104
Q

What are the 3 common phosphorylated amino acids discussed in class?

A

Phosphoserine
Phosphothreonine
Phosphotyrosine

(All these groups have an OH in their side chains ;] )

105
Q

What do protein kinases and phosphatases do?

A

Protein Kinases add a phosphate group via an ATP molecule

Phosphatases remove phosphate groups

106
Q

Protein phosphorylation and dephosphorylation acts like what kind of switch?

A

They act like on/off switches.

The example given in class was with Casein. When the Ser residue on Casein is phosphorylated it is turned on and does its function. When acted on by a phosphatase, it is switced off

107
Q

Carboxylation is an enzymatic mechanism dependent on what vitamin?

A

Vitamin K

108
Q

Where is carboxylation an important modification?

A

at the Glutamate residue in the Gla region of certain blood-clotting factors

109
Q

In blood clotting, what does modification via vitamin-K dependent carboxylation confer?

A

confers membrane binding properties required for proper functioning of the blood clotting cascade

110
Q

Vitamin-K antagonists would do what?

A

slow down clotting

111
Q

Hydroxylation of a proline residue to make hydroxylated proline is an important constituent of what?

A

fibrillar collagen

112
Q

What are the two types of oligosaccharide linkages found in glycoproteins?

A

N-linked oligosaccharides: carbohydrate side chains are enzymatically attached to the amide nitrogen of an Asn residue

O-linked oligosaccharides: carbohydrate side chains can be attaced to the hydroxyl of Ser or Thr residues

113
Q

What kinds of proteins contain oligosaccharide side chains?

A

proteins that function extracellularly like plasma proteins and lubricating proteoglycans

114
Q

Acetylation of lysine regulates the interaction of histones with?

A

DNA

115
Q

Methylation of lysine regulates the interaction of histones with other proteins, mainly what?

A

transcription factors

116
Q

Which modification removes the positive charge on Lysine?

A

acetylation

117
Q

The Hsp 70 chaperone system is working how? Hsp 60 system what?

A

Hsp 70 works co-translationally

Hsp 60 uses a folding chamber

118
Q

Addition of fatty acids to amino terminal amino or cystein groups does what?

A

anchors proteins to membranes

119
Q

Many enzymes are synthesized as inactive precursors that are activated how? BONUS: What are the inactive forms of the proteins called?

A

by proteolysis

BONUS: Zymogens

120
Q

The binding and tagging of a target protein is carried out by what?

A

ubiquitin ligase

121
Q

Ubiquitin is how many amino acids long?

A

76

122
Q

Target proteins for ubiquitin ligase first undergo what to mark them for polyubiquitylation?

A

phosphorylated

123
Q

A polyubiquitin chain on a lysine residue directs protein to what for degradation?

A

the proteasome

124
Q

What is a proteasome?

A

a cylindrical ATP-dependent protease

125
Q

A target protein with a polyubiquitin chain is degraded where in the proteasome?

A

it is brought through the active site.

the ubiquitin residues are removed before entering the active site

126
Q

Protein folding diseases are caused by misfolding due to mutations and subsequent aggregation in protease resistant protein aggregates like amyloid. Name some of these diseases.

A

These are dominant diseases:

Sickle Cell Anemia
Alpha-1-antitrypsin deficiency

Huntington’s and Alzheimer’s

127
Q

Changes in what structure can cause proteins to resist proteolysis?

A

Changes in secondary protein structure

128
Q

Prion diseases are caused by what and what?

A

misfolding and aggregation of prion proteins

129
Q

Prion diseases are described as having a highly ____ nature.

A

infectious

130
Q

What are some common prion diseases?

A

CJD: Creutzfeldt-Jacob disease in humans

BSE: Bovine spongiform encephalopathy in cattle

Scrapie in sheep

131
Q

Protein misfolding diseases all result in conversion of protein secondary structure into what?

A

beta sheets which stack one above another

PROTEIN METABOLISM (1 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions