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Nucleic Acid Biochem III > Final Review Session > Flashcards

Final Review Session Flashcards

1
Q

What does a signal peptide signal for when attached to a polypeptide?

A

Migration to the ER pathway

eg. ER to Golgi etc.

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2
Q

What do hydrophobic stretches on polypeptides signal for?

A

That the protein will be embedded in a membrane

Perhaps to stay, or to become part of a vesicle for migration to Golgi etc. if there is no other sign for permanent embedment

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3
Q

What does a basic bipartite NLS signal for?

A

Nuclear localisation signal

Shuttle protein to nuclear pore so that protein can become nuclear protein

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4
Q

What does a signal peptidase site signal for when part of a protein?

A

Will be contained inside vesicles and then released to the exterior of the cell

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5
Q

What does an Asn-X-Ser signal for when part of a protein?

A

Asparagine-x-Serine

Signals for glycosylation of the protein, but the protein will only be glycosylated if in the ER. Asn-X-Ser means nothing in the cytoplasm.

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6
Q

What do signals for the mitochondrial outer or inner membrane signal for when part of a protein?

A

Outer: Shuttle to intermembrane space

Inner: Shuttle to mitochondrial matrix (outer membrane signal must be present for this to happen)

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7
Q

When there is a signal peptide that makes a protein go to the ER, what happens to the mitochondrial membrane signals on proteins?

A

They are ignored, as these only make sense when protein is in cytoplasm, there is no correct mechanism for transport to mitochondria in ER

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8
Q

Where does glycosylation take place?

A

The ER

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9
Q

What does a KDEL signal for when it is part of a protein?

A

It is a retention signal that is relative to having a signal peptide. When a signal peptide is present with a KDEL, the protein will stay in the ER. Not meaningful in cytoplasm.

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10
Q

What does PTS signal for when part of a protein?

A

Transfer to peroxisome

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11
Q

If you see a signal peptide along with other shuttling signals (eg. NLS), where does the protein go?

A

To the ER pathway. Signal peptide is strongest signal.

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12
Q

Deamination of a c makes a _?

A

U

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13
Q

What are the three possible stop codons (in RNA)?

A

UGA
UAA
UAG

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14
Q

What codon codes fort Met (start) in RNA?

A

AUG

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15
Q

Why are substitutions in the 3rd base of a codon silent?

A

Degeneracy of the genetic code

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16
Q

What type of genes can miRNA repress the translation of?

A

Endogenous (eg. transposons) and exogenous (eg. viral)

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17
Q

For a gene that has multiple introns, introns are spliced ___

A

Sequentially starting from the 5’ end

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18
Q

What structure does trans splicing generate in the intermediate?

A

Y molecule

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19
Q

What is trans/cis splicing?

A

trans: exons from different genes attach
cis: exons in same gene

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20
Q

The final step in translation initiation in bacteria is:

A

association of mRNA with the 30S ribosomal subunit

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21
Q

The final step in translation initiation in bacteria is:

A

Disassociation of IF-3 from the 30S ribosomal subunit

22
Q

During translation, which ribosome subunit(s) directly interact with the mRNA? Do initiation factors precede this step?

A

30S

Initiation factors bind to 30S before mRNA!

23
Q

Which initiation factor, when released from the 30S ribosome subunit, allows the 50S subunit to join the complex?

A

IF3

24
Q

The Shine-Dalgarno sequence occurs in what location in a bacterial mRNA molecule?

A

About 10 bases upstream of the AUG initiation codon

25
Q

What does edeine do?

A

Binds to E and P sites, prevents stabilization of initiator aminoacyl-tRNA

26
Q

What does avilamycin do?

A

Binds to large subunit of ribosome, prevents assembly with small subunit.

27
Q

What does aminoglycosidase do?

A

Binds to A site of ribosome, induces incorrect codon-anticodon recognition

28
Q

What does streptomycin do?

A

Binds S12 protein, affects specificity when loading aa-tRNA into the A site

29
Q

What does chloramphenicol do?

A

Binds A site, inhibits peptidyl transferase reaction.

30
Q

What does micrococcin do?

A

Binds the A site, interferes with binding of initiation and elongation factors, affecting both initiation and translocation.

31
Q

What does fusidic acid do?

A

Prevents translocation by binding EF-G when complexed with the ribosome .

32
Q

The 23S rRNA of the large subunit of bacterial ribosomes interacts with?

A

The 3’ CCA terminus of peptidyl tRNA in the P and A sites

33
Q

What experiment showed that protein synthesis doesn’t need DNA? What else did it show?

A

The one where they incubate E. coli extract in the presence or absence of DNAse. With DNAse, sysnthesis of proteins continued, indicating that DNA is not required. However, RNA needs to be added some time after because it gets degraded.

34
Q

What does polynucleotide phosphorylase do? How did it help elucidate the genetic code?

A

This enzyme ‘builds’ RNA when free ribonucleosides are provided. It was essential to conduct the many experiments with RNA to decipher the code.

35
Q

True or false? Ribosomes are assembled with ATP spending by a specific set of enzymes and chaperones

A

False. No ATP required and no additional proteins.

36
Q

True or false? Peptide bond synthesis at the P site of the ribosome is catalysed by specific bases of the ribosomal RNA and specific amino acids of a ribosomal protein located within the P site

A

FALSE. No proteins are invoved in catalysis of the peptide bond. Only rRNA.

37
Q

True or false? Genes for rRNA subunits are usually processed post— transcriptionally by splicing, just like mRNA transcripts

A

False. They are processed posttranscriptionally but NOT by splicing.

38
Q

True or false? All organisms use formyl—methionine as the initiation amino acid but in eukaryotes the formyl group is removed post— translationally

A

FALSE. Eukaryotes use Met.

39
Q

True or false? Translation initiation factors are needed for accuracy in pairing a tRNA with its correct amino acid

A

FALSE. This is job of elongation factors.

40
Q

True or false? EF-G mimics the conformation of EF-TU complexed with tRNA+amino acid

A

True

41
Q

True or false? Incorporation of an incorrect amino acid elicits the NMD response to eliminate the faulty protein

A

FALSE. Presence of premature stops codons does this. What is eliminated is the faulty mRNA.

42
Q

True or false? Ribosomes in the rough ER synthesize all proteins that are not cytoplasmic

A

FALSE. Only those that go through the secretory pathway via the ER.

43
Q

True or false? “Signal peptide” refers to the region of a protein that contains the information needed to reach its final cellular destination

A

FALSE. Contains the info to go to the secretory pathway via ER. Many destinations do not use signal peptide.

44
Q

True or false? RNAse P is a protein that cleaves the 5’ end of a maturing tRNA

A

True

45
Q

True or false? RNA editing corrects the mistakes made by the RNA polymerase by restoring the correct base in the mRNA

A

FALSE. RNA modifies nucleotides in the RNA but it is not a mechanism to correct errors.

46
Q

Describe potential effects of a mutation that impedes modification of the 5’ base at the anticodon of tRNAs.

A

The tRNA will not pair with certain codon with which it should.

47
Q

What is the effect of “long range base pairing” in tRNA and rRNAs?

A

Needed to achieve the final secondary and tertiary structure, essential for function.

48
Q

Describe the comparative phylogenetic approach to study the conformation of rRNA molecules

A

Basically compare sequence across species and look at conserved regions. Implies that sequence conservation reflects important function.

49
Q

What is the “universal core” in LSU and SSU rRNA?

A

The regions of the rRNA that are conserved across distantly related organisms.

50
Q

How would you draw a typical bacterial transcript with 3 protein—coding regions and indicate all elements that influence translation and their roles?

A

Indicate ORFs, start and stop codons, UTR (untranslated regions), shine dalgarno sequences.

51
Q

What is the 5’ UTR (untranslated region)?

A

The five prime untranslated region (5’ UTR) (also known as a Leader Sequence or Leader RNA) is the region of an mRNA that is directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. While called untranslated (or in other words doesn’t create a protein product), the 5’ UTR or a portion of it is often translated into a protein product. This product can then regulate the translation of the main coding sequence of the mRNA. In many other organisms however, the 5’ UTR is completely untranslated, instead forming complex secondary structure to regulate translation.

52
Q

What are guide RNA? Briefly describe possible effects when one guide RNA is missing

A

They are small RNA molecules that serve as templates to guide the editosome when adding or deleting bases in the mRNA. If absent, editing will fail, resulting in an incorrect transcript.

Nucleic Acid Biochem III (10 decks)

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