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ALL THE THINGS Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

What are the 3 RNA species involved in translation?

A

tRNA
rRNA
mRNA

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2
Q

What function/role do tRNAs play in translation?

A

function as adaptors between mRNA codons and specific amino acids

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3
Q

What % of total cellular RNA is tRNA?

A

15%

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4
Q

What function/role do rRNAs play in translation?

A

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

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5
Q

What % of total cellular RNA is rRNA?

A

80%

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6
Q

What function/role do mRNAs play in translation?

A

code for proteins

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7
Q

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

A

5%

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8
Q

How many total codons are there in the Genetic Code?

A

64

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9
Q

What is the start codon?

A

AUG

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10
Q

What are the 3 stop codons?

A

UAA, UAG, UGA

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11
Q

What is the Wobble Position?

A

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

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12
Q

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

A

tRNA

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13
Q

How many reading frames are possible for a given mRNA?

A

3

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14
Q

What causes alteration of the reading frame?

A

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

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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’

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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

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17
Q

What are the 3 different mutations affecting translation?

A

Missense
Nonsense
Insertions

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18
Q

What types of insertions/deletions are possible?

A

Frameshift mutations

3n insertions/deletions

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19
Q

What are silent mutations?

A

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

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20
Q

What are a special class of insertions/deletions?

A

splicing errors caused by splice site mutations

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21
Q

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

A

2

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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

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23
Q

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

A

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

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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

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25
Q

tRNA specificity is based on what?

A

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

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26
Q

What is a “Charged tRNA?”

A

tRNA carrying an amino acid

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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

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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

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29
Q

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

A

methionine

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30
Q

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

A

N10 - formyltetrahydrofolate

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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

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32
Q

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

A

16S rRNA

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33
Q

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

A

the Shine-Dalgarno sequence

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34
Q

Where is the Shine-Dalgarno sequence in Prokaryotes?

A

6 bases upstream of the AUG

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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

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36
Q

What are the initiation factors for Prokaryotic translation?

A

IF1, IF2, IF3

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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

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38
Q

What are the 2 ribosomal subunits in Prokaryotes?

A

Small 30S
Large 50S

Together make the 70S ribosome

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39
Q

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

A

the 30S and 50S subunits from combining prematurely

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40
Q

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

A

prevents the use of the A site in initiation

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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

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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

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43
Q

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

A

a tRNA

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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

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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

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46
Q

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

A

ribozyme with peptidyl-transferase activity

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47
Q

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

A

elongation factor G

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48
Q

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

A

dissociate

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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

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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

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51
Q

Termination of translation in bacteria is by what?

A

by release factors that are proteins with tRNA shapes

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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

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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

biology exam (6 decks)

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