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Metabolism, Molecular, and Pharmacogenomics (MMP) > Molecular Biology (Quiz 2 Chp 12, 13, 15) > Flashcards

Molecular Biology (Quiz 2 Chp 12, 13, 15) Flashcards

1
Q

What are the stages of prokaryotic protein translation?

A
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2
Q

What are the stages of eukaryotic protein translation?

A
  1. Pre-initiation
  2. Initiation
  3. Elongation
  4. Termination
  5. Post-translational processing
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3
Q

mRNA is read for protein translation for _______ to ________.

A

5’ to 3’

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4
Q

Why is mRNA reading different from DNA replication and DNA transcription?

A

mRNA is read from 5’ to 3’ for transcription while DNA is read from 3’ to 5’ for both replication and transcription.

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5
Q

What is genetic code?

A

The genetic code determines what amino acid in encoded within the 3 nucleotide sequence (codon)

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6
Q

Most amino acids are determined by more than 1 codon. However, which two amino acids are only determined by 1 codon?

A

Methionine and Tryptophan

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7
Q

What is a codon?

A

This is the set of 3 nucleotides that code for an amino acid

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8
Q

The genetic code is ________ and _________.

A

Unambiguous and degenerate

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9
Q

What does it mean that the genetic code is unambiguous?

A

This means that only 1 amino acid is indicated by each of the 61 codons. There is not more than 1 amino acid for a codon.

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10
Q

What does it mean that the genetic code is degenerate?

A

This means that each amino acid is encoded by two or more codons with exceptions for Tryptophan and Methionine which are encoded by 1 codon only.

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11
Q

The genetic code provides ________ unique codon combinations of nucleotides that will code for amino acids.

A

64 (61 encode for actual amino acids while 3 encode are nonsense and stops codons)

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12
Q

What is an anti-codon?

A

This is a sequence of 3 nucleotides in tRNA that match the complementary codon in mRNA.

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13
Q

What is the “Wobble” hypothesis for tRNA?

A

This is the reason why tRNA can encode for more than one codon on mRNA.

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14
Q

What are the characteristics behind the wobble hypothesis for tRNA?

A
  • The first two base pairs between codon and anticodon from the strongest and standard base pairs

-the wobble position is at the 3’end of the codon and the 5’ end of the anticodon which is a weaker bond

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15
Q

Why can tRNA recognize more than 1 codon?

A
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16
Q

What is a reading frame?

A

This is the way of dividing and reading the sequence of nucleotides in DNA or RNA molecules into a continuous set of NON-OVERLAPPING triplets.

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17
Q

What do all reading frames start with?

A

The AUG initiation codon. This encodes for methionine.

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18
Q

Are DNA mutations random or non-random?

A

DNA mutations are random.

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19
Q

DNA mutations are in the chantes in nucleotides sequences in DNA strands. A mutation __________ be repaired. Therefore, they are ________ when the cell divides.

A

CANNOT
Replicated

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20
Q

What are the differences between DNA damage and DNA mutations?

A

DNA damages can be repaired so they are temporary. DNA mutations cannot be repaired so they are permanent and are most likely derived from DNA damage.

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21
Q

Which direction is a polypeptide synthesized?

A
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22
Q

What are the 3 types of DNA mutations?

A
  1. Point mutation
  2. Insertion
  3. Deletion
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23
Q

What are the two types of the DNA mutation known as a point mutation?

A

Transition and Transversion mutations

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24
Q

What is a transition point mutation in DNA mutations?

A

This is when 1 purine (or pyrimidine) is replaced by another purine (or pyrimidine).

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25
Q

What is a transversion point mutation in DNA mutations?

A

THis is when 1 purine is replaced by a pyrimidine or vice versa.

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26
Q

What are the 3 consequences of a point mutation?

A
  1. Silent mutation
  2. Missense mutation
  3. Nonsense mutation
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27
Q

What is a ‘silent’ consequence of a point mutation?

A

The point mutation specifics for the same amino acid.

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28
Q

What is a ‘missense’ consequence of a point mutation?

A

The point mutation specifies a different amino acid.

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29
Q

What is a ‘nonsense’ consequence of a point mutation?

A

The point mutation specifies for a stop codon which makes the protein polypeptide shorter.

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30
Q

What is the DNA mutation known as an insertion?

A

A nucleotides is added and the reading sequence in changed. It could add 3 nucleotides which would not impact the reading sequence as much.

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31
Q

What is the DNA mutation known as a deletion?

A

A nucleotide is deleted and the reading sequence it changed.

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32
Q

What is a frameshift mutation?

A

This occurs when the number of nucleotides inserted or deleted is not a multiple of 3 and the reading frame shifts.

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33
Q

What are the major structural features of tRNA?

A
  • 3 hairpin turns
  • free P group at 5’ end
  • CCA group at 3’ end
  • extensive internal base pairing
    -nucleotide modifications
    -anticodon arm
  • amino acid arm
  • D arm
  • TC arm
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34
Q

What is the anticodon arm on tRNA?

A

This portion contains that anticodon which will directly interact with an mRNA complementary codon sequence.

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35
Q

What is the amino acid arm on tRNA?

A

This is the site that carries the specific amino acid.

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36
Q

tRNA has extensive _________ _____ pairing and ________ modification.

A

Internal base
Nucleotide

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37
Q

All mature tRNAs have _______ at the 3’ end.

A

CCA

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38
Q

How does a tRNA become charged?

A

A methionine is attached to the 3’ CAA portion with the use of energy.

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39
Q

What are the two pre-initation events for protein translation?

A
  1. tRNA charging
  2. Dissociation of ribosome subunits/ ribosome recycling
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40
Q

How is a tRNA charged with an amino acid?

A
  1. An amino acid and ATP come together to form an aminoacyl-AMP (adenylate) via the enzyme aminoacyl-tRNA synthetase.
  2. Aminoacyl-AMP and tRNA come together to form the aminoacyl-tRNA
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41
Q

What enzyme catalyzes the combination of an amino acid with ATP to form the aminoacyl-AMP?

A

Aminoacyl-tRNA synthetase

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42
Q

Where does tRNA charging take place in the cell?

A

Cytosol

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43
Q

What bond type connects the newly charged tRNA with the amino acid?

A

Ester bond

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44
Q

Is aminoacyl-tRNA synthetase specific?

A

Yes. Each synthetase recognizes a specific amino acid and the tRNAs that carry it. There are 20 different synthetases for all 20 different amino acids.

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45
Q

What is ribosome recycling?

A

This is a process where ribosomes assemble after protein synthesis to make ribosomal subunits for new rounds of translation.

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46
Q

What are the main characteristics of the ribosomes and rRNA in prokaryotes?

A

-70s ribosome splits into a large 50s and small 30s subunit.
- 50s subunit splits off into many rRNAs
- 30s subunit makes 1 rRNA called 16s

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47
Q

What are the main characteristics of the ribosomes and rRNA in eukaryotes?

A

-80s ribosome splits into a large 60s and a small 40s subunit.
-60s subunit splits into many rRNAs
-40s subunit splits into 1 rRNA

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48
Q

rRNA has extensive ______ base pairing and complexes with proteins to form ribonucleoprotein particles called _________.

A

internal
ribosomes

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49
Q

A ribosome is a supramolecular complex that contains both ________ and ______.

A

Proteins
RNA

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50
Q

What is the main function of the ribosomes?

A

They catalyze the peptide bond formation between amino acids

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51
Q

What are the 3 tRNA binding sites on the ribosome?

A

A site
P site
E site

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52
Q

What is the function of the A site on the ribosome that binds tRNA?

A

The A-site tRNA carries the amino acids

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53
Q

What is the function of the P-site on the ribosome that binds tRNA?

A

The P-site carries the polypeptide chain

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54
Q

What is the function of the E-site on the ribosome that binds tRNA?

A

The E-site is empty and carries nothing

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55
Q

Where is the initiating AUG sequence found in bacteria for protein translation?

A

The Shine-Dalgarno sequence. This area is high in G and A nucleotides.

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56
Q

Why is 16s rRNA important in initiating protein translation in prokaryotes?

A

The 3’ end of 16s identifies the shine-dalgarno sequence.

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57
Q

How many tRNAs are used for initiation in prokaryotes and what are their functions?

A

2 tRNA for initiation in prokaryotes. One tRNA is used for initiation at the AUG site while the other take care of all the other AUG/methionine within the mRNA.

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58
Q

What is unique about prokaryotic protein translation in terms of formylation?

A

The first methionine (AUG start codon) is formylated after it is on the tRNA.

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59
Q

What is the initiation sequence for protein translation in eukaryotes called?

A

Kozak sequence and AUG is imbedded within it.

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60
Q

T or F: Methionine is formylated at the beginning of protein translation in eukaryotes.

A

False. This only occurs in prokaryotes.

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61
Q

What 3 initiation factors are required for protein translation initiation in prokaryotes?

A

IF1, IF2, and IF3

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62
Q

What initiation factor is required for the initiation of protein translation in eukaryotes?

A

eIFs

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63
Q

What is the 1st step of initiation of protein translation in eukaryotes?

A

eIF3 prevents the binding to the 40s and 60s ribosomes units early.

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64
Q

What is the 2nd step of initiation of protein translation in eukaryotes?

A

eIF2 with GTP recruits the charged tRNA (Met-tRNA) to the 40s subunits making it 43s subunit.

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65
Q

What is the 3rd step of initiation of protein translation in eukaryotes?

A

5’ capped mRNA binds to a separate eIF4F complex which then binds to the previous 43s subunit to make a 48s subunit. The mRNA is then scanned for the AUG start site within the Kozak sequence

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66
Q

What is the 4th step of initiation of protein translation in eukaryotes?

A

Once the AUG start is found, the 60s subunit binds, GTP from the eIF2 is hydrolyzed and eIF factors leaved. This is now an 80s subunit.

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67
Q

Know the differences in the initiation of protein synthesis in eukaryotes and prokaryotes.

A
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68
Q

What are the 3 steps of protein elongation?

A
  1. Decoding
  2. Transpeptidation
  3. Translocation
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69
Q

Describe the first step of protein elongation known as decoding.

A

This is when the correct AA-tRNA based on codon/anticodon base-pairing binds to the A-site on the ribosome based on the next codon.

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70
Q

Describe the second step of protein elongation known as transpeptidation.

A

This is when the existing AA on P-site forms the peptide bonds between the income AA on tRNA in the A-site.

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71
Q

Describe the third and final step of protein elongation known as translocation.

A

This is when EF-G binds to the A-site and displaces the tRNA there to shift it left into the Psite and Esite. This allows the next aminoacyl-tRNA to bind to the A-site so the elongation process can continue.

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72
Q

What are the 3 protein elongation factors in prokaryotes?

A

EF-Tu- delivers AA-tRNA
EF-Ts- regnerates EF-Tu
EF-G- promotes translocation

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73
Q

What are the 3 protein elongation factors in eukaryotes?

A

eEF-1A- delivers AA-tRNAs
eEF-1B- regnerates eEF-1A
eEF-2- promotes translocation

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74
Q

How does the ribosome monitor correct codon-anticodon base pairing?

A

During elongation, ribosome does error checking by checking if the base pairing between the codon on mRNA and anticodon on tRNA are correct. It does not check to see if the right AA was added.

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75
Q

What is the second error checking step in protein elongation?

A

When a new tRNA is added to the A-site

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75
Q

What triggers the termination of translation?

A

Stop codons (UAA, UAG, or UGA) entering the A-site in ribosome

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75
Q

What adds the polypeptide chain to the new amino acid?

A

Peptidyltransferase. This is not a protein, it is the rRNA of the large ribosomal subunit.

Polypeptide in P site is added to amino acid in A-site

75
Q

How does the ribosome catalyze peptide bond formation?

A

Through transpeptidation in the elongation steps, the ribosome creates the peptide bond between the existing chain in the P-site and the incoming AA in the A-site.

76
Q

What is the major point of regulation for translation in prokaryotes?

A

Initiation controlled at the Shine-Dalgarno sequence

76
Q

How is translation terminated?

A

A stop codon shows up in the A-site which triggers release factors to bind to the stop codons. This activates peptidyl transferases to hydrolyze the bond between the peptide chain and tRNA.

76
Q

What enzyme hydrolyses the bond between the peptide chain and tRNA in termination of protein translation?

A

Peptidyltransferase

76
Q

What happens to the ribosome during termination of protein translation?

A

The ribosome dissociates into its individual 2 subunits releasing the mRNA.

76
Q

What is a polysome?

A

When many ribosomes are on a single mRNA to translate it into protein. The complex this forms is called a polysome.

76
Q

For eukaryotes, if the initiation factors are phosphorylated this will _______ protein synthesis.

A

Decrease

76
Q

What enzyme folds proteins for post-translational modifications in both eukaryotes and porkaryotes?

A

Chaperones

76
Q

____________ cannot happen after the formation of the peptide bond between two AA.

A

Proofreading

76
Q

What are the 4 major points of translation regulation in eukaryotes?

A
  • mRNA export into cytoplasm
  • mRNA stability
  • negative translation control (binding of proteins near 5’ end inhibits initiation)
  • initiation factor phosphorylation- decreases protein synthesis
76
Q

For eukaryotes, the binding of proteins near the ________ end of mRNA inhibits translation

A

5’

76
Q

What are 4 antibiotics that target protein translation therefore inhibiting bacterial infections?

A
  1. Streptomycin
  2. Tetracycline
  3. Erythromycin
  4. Chloramphenicol
76
Q

What is a post translational modification of proteins that occurs in both eukaryotes and prokaryotes?

A
  1. Protein folding
  2. Peptide removal to convert proteins to more active forms
  3. Phosphate group addition to change function
  4. conjugation (adding lipids or carbs)
  5. Removal of signal peptides after entrance into cellular compartment of need
76
Q

What is a trigger factor and what is its function?

A

A trigger factor is a ribosome associated chaperone seen in prokaryotes. It is needed in prokaryotes for protein folding of the new polypeptide chain.

76
Q
A
76
Q
A
77
Q

What is a type of post-translational modification that alters the function of a polypeptide?

A

Amino acid modification through the addition of a phosphate group.

77
Q

What is a type of post-translational modification that only occurs in prokaryotes?

A

Methionine removal

77
Q

Is DNA replication a part of gene expression?

A

No only transcription and translation

77
Q

Genotype determines _________.

A

Phenotype

77
Q

What is the major mechanism that regulates gene expression in prokaryotes?

A

Transcription

77
Q

What is an operon?

A

An operon is in a prokaryote. It is a cluster of genes that share a single promoter that regulates transcription. An operon allows bacteria to express several genes at the same time!

77
Q

What is the regulatory advantage of arranging genes into an operon?

A

Most genes in an operon perform related functions. There 1 promoter coordinating the transcription of related genes allows for the needed to be made all at once.

77
Q

How are operons regulated?

A
  1. Positive control
  2. Negative control
77
Q

What is positive control in regulation of an operon?

A

This is when transcription is turned on in the presence of an activator (regulatory protein). These bind to the regulatory sequence on DNA.

78
Q

What is negative control in regulation of an operon?

A

This is when transcription is turned off in the presence of a repressor. These bind to the regulatory sequence on DNA.

79
Q

For both the positive and negative control in the regulation of an operon, those mechanisms can also be regulated. What two things do this?

A

The regulatory proteins (repressor or activator) bind to small molecules that are either inducers or co-repressors. An inducer increases transcription while a co-repressor decreases transcription.

80
Q

What is the major means to regulate gene transcription in prokaryotes?

A

Through repressors

81
Q

What is the lac operon?

A

These are the genes necessary for bacteria to use lactose as an energy source.

82
Q

What happens to the lac operon if no lactose is present?

A

The repressor binds to the operator site on promoter to inhibit transcription of the lac operon.

83
Q

What happens to the lac operon is lactose becomes available?

A
  1. Lactose is the inducer here and it binds to the repressor. This induces a confirmation change on the repressor to make its inactive and therefore no longer able to bind to DNA.
  2. This allows RNA polymerase to bind and transcribe the lac operon genes.
  3. However, the lac promoter is weak and needs more to start transcription
  4. It requires cAMP binding to Catabolite Gene Activator Protein (CAP) to stimulate transcription
84
Q

The lac operon does not work when ______________ is high unless CAP can bind with cAMP.

A

Glucose

85
Q

What happens to lac operon transcription is glucose levels are high?

A

This results in decreased cAMP soit will not bind to CAP protein and therefore remains inactive and none of the lac operon will be transcribed.

86
Q

What happens to the lac operon is glucose levels are low and lactose is available?

A

This increases cAMP concentration therefore it binds to CAP and and that complex binds to 5’ end of promoter and help RNA polymerase bind to transcribe the lac operon.

87
Q

T or F: Even if prokaryote cells are full of lactose, they will not transcribe the lac operon if there is enough glucose present.

A

True

88
Q

What happens to the lac operon if there is high glucose and no lactose.

A

No lac operon transcribed

89
Q

What happens to the lac operon if there is no glucose and no lactose?

A

No lac operon transcribed

90
Q

What happens to the lac operon if there is high glucose and high lactose?

A

No lac operon transcribed

91
Q

What happens to the lac operon if there is no glucose and high lactose?

A

The lac operon will be transcribed

92
Q

What is the Trp operon?

A

This is the operon the produces the enzymes needed to produce the tryptophan essential amino acid.

93
Q

How do a co-repressor and repressor act together?

A

When a co-repressor binds to an inactive repressor, it changes it confirmation allowing it to bind to the operon and inhibit transcription.

94
Q

What is the Trp repressor and how does it relate to the Trp operon?

A

The final product tryptophan is a corepressor that binds to the inactive reporessor allowing it to change conformation and bind to the trp operon operator, inhibiting an further transcription of the trp operon.

95
Q

The Trp repressor protein is normally __________.

A

inactive

96
Q

What is chromatin remodeling?

A

This is the activation of a gene for transcription which requires changes to the chromatin structure. It can become euchromatin or heterochromatin.

97
Q

Why is chromatin remodeling needed for efficient eukaryotic gene expression?

A

This is all done to rearrange the nucleosome to expose the promoter region of DNA for gene expression. It allows specific DNA sequences to be transcribed.

98
Q

What is a euchromatin?

A

This is a lightly packed chromatin and it ready and active for transcription

99
Q

What is a heterochromatin?

A

This is a tightly packed chromatin that is not ready and inactive for transcription.

100
Q

What are the ways in which histones can be modified?

A
  1. Methylation
  2. Acetylation
  3. Phosphorylation
101
Q

What happens when histones are modified?

A

Methylation increases the positive charge. Acetylation decreases positive charge. Phosphorylation increases negative charge.

102
Q

What is lysine acetylation for histone modification?

A

Protein called histone acetyltransferase adds an acetyl group onto a histone tail sticking out of the nucleosome and makes its lose it negative charge so that the nucleosome loses its grip on DNA and that promotes gene transcription.

103
Q

Is histone acetylation reversible?

A

Yes. Acetyls are added by histone acetyltransferases and removed by histone deacetylases.

104
Q

What are CpG islands?

A

This is another name for the promoter region on DNA that has lots of C and G bases next to eachother.

105
Q

What is the goal of DNA methylation for histone modification?

A

The goal is to silence gene expression but methylated the promoter region of DNA. This is catalyzed by DNA methyltransferases which take a methyl group from SAM.

106
Q

DNA methylation has been implicated in _____________ ___________.

A

Genomic imprinting.

107
Q

What is genomic imprinting?

A

This is a process that controls the genes to be expressed in a parent-specific manner.

108
Q

How many ways can eukaryotic gene expression be regulated?

A

4 ways

109
Q

What are the 4 ways in which eukaryotic gene expression is regulated?

A
  1. Availability of the genes
  2. At the level of transcription
  3. Post-transcriptional processing of RNA
  4. At the level of translation
110
Q

At the level of transcription, what regulates gene expression in eukaryotes?

A

Transcriptional factors and regulatory proteins

111
Q

What is the transcription factor IID?

A

This transcription factor binds to the promoter region of DNA and recognizes the TATA box to bring in the other 5 transcription factors.

112
Q

Activator proteins bind to the _________ region on the DNA sequence.

A

Enhancer

113
Q

Repressor proteins bind to the ________ region on the DNA sequence.

A

Silencer

114
Q

What is the basic structure of an upstream transcription factor?

A

There are 3 basic domains; DNA-binding domain (DBD), structural domain and transcription regulation which is the activation domain.

115
Q

What is a mediator protein at the level of regulation at transcription in eukaryotes?

A

Specific transcription factors bind the mediator protein which are coactivators or corepressors which then interact with the general transcription factors that are apart of the basal/general transcription complex.

116
Q

How do DNA-binding proteins interact with DNA?

A

They bind to the major groove of DNA

117
Q

What are the four motifs in which DNA-binding proteins interact with DNA?

A
  1. Zinc fingers
  2. Leucine zipper
  3. Helix-turn-helix
  4. Helix-loop-helix
118
Q

What type of receptors are the steroid hormone/thyroid hormone receptors?

A

Nuclear receptors

119
Q

What protein inactivates the steroid hormone receptor and how?

A

Heat shock protein. It binds the receptor and makes the nuclear localization signal (NLS).

120
Q

What are the 6 major domains of the steroid-hormone/thyroid receptors?

A
  1. TAD- transactivation domain. It binds to and activates transcriptional regulators
  2. DBD- DNA binding domain- binds to DNA
  3. NLS- nuclear localization signal- signal that goes into nucleus
  4. LBD- ligand binding domain
  5. IBS- inhibitor binding domain
  6. DS- dimerization site
121
Q

What happens to the steroid hormone receptor in the presence of a glucocorticoid like cortisol?

A

Cortisol releases heat shock protein allowing the receptor to dimerize and translocate into the nucleus. It binds to a segment of DNA called GRE.

122
Q

What is GRE?

A

This is where the nuclear receptor binds once it translocates into the nucleus. This is a hormone response element (HRE) portion of DNA.

123
Q

What is a hormone response element (HRE)?

A

This is a specific DNA sequence that nuclear receptors recognize with increased affinity.

124
Q

What does the thyroid hormone receptor form a heterodimer with?

A

Retinoid and receptor RXR

125
Q

How is the thyroid hormone receptor inactivated?

A

The dimer (retinoid and receptor RXR) bind the hormone response element (HRE) and a corepressor complex to inhibit gene expression. HDAC also removes acetyl group to make the histone/DNA complex tighter to reduce gene expression.

126
Q

How is the thyroid hormone receptor activated?

A

When thyroid hormone binds to the thyroid hormone receptor it causes a conformational changes and releases the corepressors and now binds coactivators. This activates gene transcription. HAT adds an acetyl group here too to loosen the tightness between histone/DNA complex and increase gene expression.

127
Q

JAK-STAT pathway relays ________ based signals.

A

Cytokine

128
Q

What type of receptor is used in the JAK-STAT pathway?

A

Tyrosine kinase receptor

129
Q

_______ activity is a major way to turn on signal transduction.

A

Kinase. It adds a phosphate to STAT in JAK-STAT pathway which can translocate into the nucleus to act as a transcription factor.

130
Q

cAMP stimulates ____________ which phosphorylates CREB.

A

Protein Kinase A (PKA)

131
Q

Once CREB is phosphorylated by PKA, what happens to gene expression?

A

CREB binds to DNA on CRE site and acts as a transcription factor to activate gene expression.

132
Q

If a cell upregulates or downregulates it synthesis of ______________, the rate of transcription can also be increased or decreased.

A

Coactivators

133
Q

The thyroid hormone receptor is critically dependent on the concentration of ___________ receptor to provide a dimer partner.

A

Retinoid

134
Q

What is immature mRNA that is the product right after transcription and no post-transcriptional modifications have occured yet?

A

hnRNA

135
Q

What is alternative splicing?

A

This is changing where hnRNA is spliced which can produce different gene products.

136
Q

What is alternative polyadenlyation?

A

This adds a poly A tail onto different sections which can produce different gene products.

137
Q

What is RNA editing?

A

This is when nitrogenous bases are altered, or nucleotides are added or deleted after the RNA transcript is synthesized so the mature mRNA and final protein products differ in different tissues.

138
Q

Can RNA transport out of the nucleus and into the cytoplasm be regulated?

A

Yes! The binding proteins on mRNA to protect it and proteins on the nuclear pore allow it out and those can be regulated.

139
Q

How is mRNA degradation regulated?

A
140
Q

How is microRNA synthesized?

A
  1. A short peice of mRNA is made
  2. In nucleus, an RNA-specific nuclease (Drosha) creates a stem-loop Pre-miRNA of 70-80 nucleotides.
  3. Pre-miRNA is exported out the nucleus and interacts with a Dicer complex.
  4. Dicer process the pre-miRNA to mature miRNA.
141
Q

How does microRNA regulate gene expression?

A

microRNAs regulate protein expression at the post transcriptional level. A microRNA can either induce the degradation of a target mRNA or block the translation of the target mRNA.

Mature miRNA binds to RNA-induced silencing complex (RISC). The miRNA direects the complex to a complementary sequence and that target can be silenced or repressed.

142
Q

How is mRNA translation controlled?

A
  1. Negative translation control- if proteins bind near the 5’ end of mRNA, translation is inhibited
  2. covalent modification of translation factors controls which mRNAs are translated.
143
Q

When heme levels are high, what happens to heme-regulated inhibitor kinase (HRI)?

A

Inhibition of HRI: When heme levels are sufficient, heme binds to HRI and inhibits its kinase activity. This means HRI does not phosphorylate eIF2α.

eIF2 Remains Active: Without phosphorylation, eIF2 remains active and can bind GTP, forming the eIF2-GTP-tRNA complex necessary to start translation.

Protein Synthesis: With active eIF2, translation proceeds normally, allowing for the production of globin and other proteins. This is essential in erythroid cells, where balanced heme and globin production are critical for hemoglobin assembly.

144
Q

When heme levels are low, what happens to heme-regulated inhibitor kinase (HRI)?

A

Activation of HRI: In low heme conditions, HRI is active and auto phosphorylates itself. Active HRI then phosphorylates eIF2α.

Inhibition of eIF2: Phosphorylated eIF2α cannot effectively bind GTP. This prevents the formation of the eIF2-GTP-tRNA complex, which is necessary for initiating translation.

Suppression of Protein Synthesis: With eIF2 inactivated, global translation is reduced, leading to decreased synthesis of globin and other proteins. This protects the cell from accumulating unbound globin chains, which could be toxic.

145
Q

What happens to the transferrin receptor and ferritin production in the when iron is low in the cell?

A

Transferrin Receptor (TfR) Production Increases:

The transferrin receptor (TfR) is a membrane protein responsible for importing iron into the cell by binding to transferrin, the iron-carrying protein in the blood.

In low iron conditions, iron regulatory proteins (IRPs) bind to IREs located in the 3’ untranslated region (UTR) of the TfR mRNA.This binding stabilizes the TfR mRNA, preventing its degradation and increasing TfR synthesis.

Increased TfR on the cell surface enhances iron uptake by increasing transferrin binding, thus helping the cell acquire more iron.

Ferritin Production Decreases:

Ferritin is an intracellular protein that stores iron safely within the cell.
When iron is scarce, IRPs bind to IREs in the 5’ UTR of ferritin mRNA, blocking ribosome access and preventing its translation.
Reduced ferritin production means less iron is sequestered within the cell, keeping more iron available for essential metabolic processes.

146
Q

When heme levels are high, what happens to heme-regulated inhibitor kinase (HRI)?

A

Inhibition of HRI: When heme levels are sufficient, heme binds to HRI and inhibits its kinase activity. This means HRI does not phosphorylate eIF2α.

eIF2 Remains Active: Without phosphorylation, eIF2 remains active and can bind GTP, forming the eIF2-GTP-tRNA complex necessary to start translation.

Protein Synthesis: With active eIF2, translation proceeds normally, allowing for the production of globin and other proteins. This is essential in erythroid cells, where balanced heme and globin production are critical for hemoglobin assembly.

147
Q

What happens to the transferrin receptor and ferritin production in the when iron is high in the cell?

A

Transferrin Receptor (TfR) Production Decreases:

When there is ample iron, iron binds to IRPs, causing them to undergo a conformational change that prevents their binding to IREs.Without IRP binding, the TfR mRNA in the 3’ UTR is no longer stabilized, leading to its degradation.
Reduced TfR production means less iron is taken up, helping to avoid iron overload in the cell.

Ferritin Production Increases:

In high iron conditions, IRPs do not bind to the IREs in the 5’ UTR of ferritin mRNA, allowing translation to proceed.
As a result, ferritin synthesis increases, enabling the cell to store the excess iron safely.

148
Q

If the mRNA codon is 5’ CUG 3’, the tRNA that would pair is _____________.

A

CAG (the same but U becomes A)

149
Q

Which of the following statement about the genetic code is false?

A. Codons in mRNA are “read” by base pairing
with anticodons in tRNA.

B. The genetic code is described as degenerate
because multiple codons can code same
amino acid.

C. AUG encodes methionine and is only used
as the start codon for translation.

D. Tryptophan has one codon

A

C

150
Q

Which of the following is true regarding the Shine-Dalgarno sequence?

A. It is a nucleotide sequence involved in termination of
translation.
B. It is a nucleotide sequence involved in initiation of
translation.
C. It functions as a promoter sequence which
recognizes and bonds the sigma factor.
D. It is part of rRNA sequence used to control
translation.

A

B.

151
Q

In eukaryotes, translocation requires the binding of which elongation factor?

A. IF1
B. eEF-2
C. eIF4F
D. EF-G

A

B. eEF-2

In eukaryotes, translocation, which is the process of moving the ribosome along the mRNA to the next codon during protein synthesis, requires the elongation factor eEF-2. This factor binds to the ribosome and, with the hydrolysis of GTP, facilitates the movement of the ribosome, allowing translation to proceed to the next codon.

Here’s a quick breakdown of the other options for clarification:

A. IF1: This is an initiation factor in prokaryotes, not involved in eukaryotic translocation.
C. eIF4F: This is a eukaryotic initiation factor involved in mRNA binding, not translocation.
D. EF-G: This is a prokaryotic elongation factor responsible for translocation in prokaryotes, equivalent to eEF-2 in eukaryotes.

152
Q

What is the term that describes “each codon only codes for one specific amino acid?”

A

Unambiguous

153
Q

Which is not an essential component during the formation of aminoacyl-tRNAs?

A. Amino acids
B. ATP
C. tRNA
D. GFP

A

D. GFP

Green fluorescent protein (GFP) is not involved in the formation of aminoacyl-tRNAs. GFP is a protein commonly used as a fluorescent marker in various biological experiments but has no role in the aminoacylation process.

The other components are essential in the formation of aminoacyl-tRNAs:

A. Amino acids: Needed as the building blocks that are attached to tRNAs.
B. ATP: Required as an energy source for the aminoacyl-tRNA synthetase to catalyze the reaction.
C. tRNA: The molecule that carries the amino acid to the ribosome during translation.
Aminoacyl-tRNA synthetases catalyze the attachment of amino acids to their corresponding tRNAs using ATP, forming aminoacyl-tRNAs that are essential for protein synthesis.

154
Q

The Shine-Dalgarno sequence interacts with the …

A. 16S rRNA of the 30S ribosome subunit
B. 50S ribosome subunit
C. 40S ribosome subunit
D. eIF4F

A

A. 16S rRNA of the 30S ribosome subunit

155
Q

Which of the following is true regarding the Shine-Dalgarno sequence?

A. It is a nucleotide sequence involved in
termination of translation.
B. It is a nucleotide sequence involved in
initiation of translation.
C. It functions as a promoter sequence which
recognizes and bonds the sigma factor.
D. It is part of rRNA sequence used to control
translation.

A

B. It is a nucleotide sequence involved in the initiation of translation

Why the other answers are not correct:
A. It is a nucleotide sequence involved in termination of translation: The Shine-Dalgarno sequence is not involved in termination; it functions at the initiation stage.
C. It functions as a promoter sequence which recognizes and bonds the sigma factor: Promoter sequences and sigma factors are part of transcription initiation, not translation initiation.
D. It is part of rRNA sequence used to control translation: The Shine-Dalgarno sequence is part of the mRNA, not the rRNA, though it pairs with the rRNA during initiation.

156
Q

Bacteria can coordinately express several genes simultaneously. What explains why several different proteins can be synthesized from a typical prokaryotic mRNA?

A

Bacteria groups together related genes in a structure called an operon.

157
Q

E. Coli will only express genes for lactose metabolism when lactose is present. In E. Coli, under high lactose and high glucose conditions, what could lead to maximal transcription activation of the lac operon?

A

A mutation leading to enhanced cAMP levels.

This is because the lac promoter is weak and it requires cAMP and CAP binding together and lactose acting as an inducer to get rid of the repressor to initiate gene expression of the lac operon.

158
Q

T or F: Translation is the major step to regulate gene expression in prokaryotic cells.

A

False. It is transcription.

159
Q

What is the name of a molecule that binds to the repressor, which is in an inactive form, causing it to change the conformation and bind to the operator, thereby inhibiting transcription?

A

Co-repressor

160
Q

Which of the following best describes the mechanism describes the ability of a normal cell to become a cancer cell via a variety of mechanisms?

A

Clonal expansion allows a mutated cell to accumulate multiple mutations in proto-oncogenes and tumor suppressor genes and become a cancer cell

161
Q

The functions which have been identified for the proteins expressed by cellular proto-oncogenes include all of the following except:

A

Enzyme involved in DNA mismatch repair

162
Q

T or F: Caspases are used for death receptor-initiated apoptosis pathway but not in mitochondria-derived intrinsic apoptosis pathway.

A

False

163
Q

T or F: The mutations in DNA damage repair enzymes that contribute to the development of cancer are gain-of-function mutations.

A

False

164
Q

Which of the following statements about the genetic code is false?

A

Serine only has one codon

165
Q

The steps required for peptide elongation at the ribosome are?

A

Decoding, transpeptidation, and translocation

Metabolism, Molecular, and Pharmacogenomics (MMP) (5 decks)

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