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Biochemistry > Module 9: V1 - V5 > Flashcards

Module 9: V1 - V5 Flashcards

1
Q

How is DNA converted into a polypeptide chain?

A

DNA is converted into RNA during transcription and processing converts RNA into mRNA
mRNA is then converted into a polypeptide chain during translation

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2
Q

How is transcription similar to DNA replication?

A

a bubble opens up in the DNA where the two strands have separated and a new molecule is synthesised

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3
Q

How is transcription different to DNA replication?

A

there is a very small amount of base pairs open at any one point (17 bp)
RNA base pairs with a template strand

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4
Q

What is the nontemplate strand in transcription?

A

otherwise known as the coding strand which does not base pair with RNA during transcription

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5
Q

How many template strands are there during replication and transcription?

A

two during replication and one during transcription

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6
Q

Which enzyme relieves tension during transcription?

A

DNA topoisomerase

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7
Q

Which chemical reaction does RNA polymerase catalyse?

A

same chemical reaction as DNA synthesis in replication, the difference is that there is a growing RNA strand

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8
Q

Which substrate is added to the growing RNA strand during transcription?

A

NTP, not dNTP because these are used during replication

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9
Q

How is the backbone formed between NTP residues?

A

residues in the enzyme coordinate with Mg2+ ions which coordinate with phosphate groups that are used to form the backbone

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10
Q

In which direction does transcription occur?

A

in the 5’ -> 3’ direction

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11
Q

How many RNA polymerases do eukaryotes have?

A

three

RNA pol I which transcribes rRNA, RNA pol III which transcribes tRNA and rRNA and RNA pol II which transcribes mRNA

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12
Q

Where does RNA pol II recognise genes?

A

at the region of the promoter known as the TATA box

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13
Q

What allows there to be a lot more transcriptional regulation in eukaryotes? Why?

A

additional subunits
there are now a lot more proteins and protein complexes that can interact with RNA pol II to influence whether it will describe a gene or not

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14
Q

What is RNA polymerase responsible for?

A

expression of most genes

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15
Q

What is the structure of RNA polymerase II?

A

large and complex (12 subunits)

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16
Q

Is the template strand the same as the nontemplate strand?

A

no, it is the inverse of the nontemplate strand

this is because it is base pairing with the template strand (reverse complement)

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17
Q

Which strand looks identical to the RNA produced?

A

the coding (nontemplate) strand is the same except for U bases

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18
Q

Which strand are genes found on?

A

the coding (nontemplate) strand

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19
Q

What is a consensus sequence?

A

a sequence of DNA, RNA, or protein that represents aligned, related sequences
is normally defined by the most common nucleotide(s) or amino acid residue(s) at each position

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20
Q

Which regions exist on the E. coli promoter?

A

UP element, -35 region, -10 region, spacer, RNA start

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21
Q

What is the TATA box?

A

a sequence contained within a gene that is recognised RNA pol II
ensures that transcription occurs in the correct direction

22
Q

Are chromosomes able to be transcribed in different directions (right to left and left to right)?

A

yes

23
Q

What are the phases of transcription?

A

assembly, initiation, elongation and termination

24
Q

What are general transcription factors?

A

proteins which are required for the expression of all genes e.g. TFIIA, B, C, D, etc.
gene regulatory proteins are called transcription factors

25
Q

What does each transcription factor regulate?

A

the expression of a subset of genes

26
Q

What is TBP?

A

TATA box binding protein which is the first protein that binds to the promoter and recognises TATA boxes in promoters that are going to be transcribed by RNA pol II

27
Q

What is the role of TFIIB?

A

important role in bringing RNA pol II

28
Q

What is the role of TFIIH?

A

binds all of the other proteins for assembly resulting in a preinitiation complex

29
Q

What is required for transcription to begin?

A

DNA needs to be unwound: helicase activity of TFIIH protein and kinase activity phosphorylates a specific region of the RNA pol II protein known as the CTD

30
Q

What does phosphorylation of CTD result in?

A

firing off of enzymatic process of transcription -> production of RNA by RNA pol II -> elongation factors come in to assist -> elongation factors relieve and termination factors bind when RNA pol II reaches the end of the gene

31
Q

What does the primary transcript need to be converted into mature mRNA?

A

a 5’ cap, a poly-a tail and cleavage of introns

32
Q

What is a 5’ cap?

A

a modified nucleotide which is added to the 5’ end of the RNA (5’-5’ phosphate linkage)

33
Q

What is the role of the 5’ cap?

A

prevents degradation by endonucleases and allows this side of the mRNA to be recognised by the translational machinery

34
Q

Where does 5’ capping occur?

A

at the CTD of RNA polymerase II

35
Q

Why does splicing occur?

A

eukaryotic genes have sections that need to be removed from the primary transcript - introns are removed leaving only exons (coding sequences)

36
Q

What is splicing carried out by?

A

the spliceosome which is made of protein and RNA

the subunits of the spliceosome are called snRNPs

37
Q

How does splicing occur?

A

there are recognisable sequences in the intron at the very beginning and end and one short sequence in the middle
snRNPs recognise these sequences

38
Q

Where does splicing occur?

A

at the CTD of RNA pol II

39
Q

Where is the poly-a tail added? What is a poly-a tail?

A

at the CTD of RNA pol II
a large number of adenines added at the 3’ end
this is carried out by polyadenylate polymerase which adds 80-200 A’s

40
Q

How is the length of the poly-a tail related to the period of time a protein can be translated for?

A

the longer the poly-a tail, the longer the period of time a protein can be translated for

41
Q

What is a codon?

A

a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule

42
Q

Which codon is the start codon?

A

AUG - methionine

43
Q

Which codons are the stop codons?

A

UAA, UAG and UGA - stop

44
Q

Why is the genetic code degenerate?

A

because more than one codon can encode for the same amino acid

45
Q

What is a silent mutation?

A

a mutation in which changing of a single base pair results in no change to the amino acid and the polypeptide chain

46
Q

What is a missense mutation?

A

a mutation in which changing of a single base pair results in a change to the amino acid and may or may not change the polypeptide chain

47
Q

What is a nonsense mutation?

A

a mutation in which changing of a single base pair results in a stop codon, therefore a truncated protein is produced

48
Q

What are indel mutations?

A

mutations which involve either an insertion or deletion of a single base pair

49
Q

How can an insertion mutation result in frameshift?

A

results in addition of a single base pair which shifts the entire sequence to the right
this results in different codons and therefore translation of different amino acids

50
Q

How can a deletion mutation result in frameshift?

A

results in deletion of a single base pair which shifts the entire sequence to the right ∴ different codons which could result in a stop codon and a truncated protein

Biochemistry (30 decks)

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