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BS1030: Biochemistry > EC1: RNA, Transcription, and Promoters > Flashcards

EC1: RNA, Transcription, and Promoters Flashcards

1
Q

Where in the cell are genes found?

A

Nucleus

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2
Q

Where are proteins made?

A

Cytoplasm of ribosomes

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3
Q

What carries the ‘message’ from the nucelus (or wherever the genes are made) to the ribosome?

A

mRNA

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4
Q

What do the arrows represent in this diagram?

A

The flow of information in a biological system

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5
Q

What is transcription, and what enzyme is involved?

A

DNA-dependent mRNA synthesis; RNA polymerase

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6
Q

What is translation, and what enzyme is involved?

A

mRNA-depended protein synthesis; ribosome

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7
Q

What is this molecule and where is it found? What is the numbering system of carbons around this ring?

A

Ribose

Found in RNA

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8
Q

What is this molecule and where is it found?

A

Deoxyribose

Found in DNA

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9
Q

What are the four bases in RNA? Which ones are shared with DNA?

A

Adenine (A) – shared with DNA

Guanine (G) – shared with DNA

Cytosine – shared with DNA

Uracil (U) – unique to RNA

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10
Q

What’s the difference between the RNA base uracil and the DNA base thymine?

A

Thymine is 5-methyl-U, i.e. has a methyl group on the fifth carbon of uracil

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11
Q

Which bases (DNA and RNA) are purines and which are pyrimidines?

A

Purines: adenine, guanine

Pyrimidines: thymine, cytosine, uracil

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12
Q

Is RNA in cells single- or double-stranded? What is the exception?

A

It is single-stranded, but some viruses have dsRNA

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13
Q

Is there base equivalence in RNA?

A

No – the amounts of the four bases vary independently

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14
Q

How does ssRNA form a secondary structure? What is the name of this structure?

A

It folds back on itself, forming non-standard pairs in step-loop structures, resulting in partial double-stranded regions

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15
Q

How many base pairs have a folded piece of RNA and a folded piece of DNA per 360° turn?

A

RNA: 11 base pairs

DNA: 10 base pairs

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16
Q

Are all enzymes proteins?

A

No – some can be made of RNA

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17
Q

What are the major types of RNA and what is their approximate relative proportions in a cell?

A

messenger RNA (mRNA) – approx. 5%

ribosomal RNA (rRNA) – approx. 80%

transfer RNA (tRNA) – approx. 15%

18
Q

What are the purposes of mRNA?

A

It carries genetic information that is copied from the gene (DNA)

It is used as a template for translation by ribosomes

19
Q

Differentiate between bacterial and eukaryotic rRNA.

A

Bacterial:

3 x rRNAs; two large, one small; 50 proteins in bacterial ribosome

Eukaryotic:

4 x rRNAs; two large, two small; 80 proteins in eukaryotic ribosome

20
Q

How long is tRNA?

A

Approx. 76 nucleotides

21
Q

What is the role of tRNA?

A

It carries amino acids to the ribosomes for protein synthesis

22
Q

Define ‘proteinogenic amino acid’.

A

An amino acid that goes into a protein

23
Q

How many tRNAs are dedicated to each proteinogenic amino acid?

A

One

24
Q

What is the standard abbreviation for RNA polymerase?

A

RNAP

25
Q

What is the general equation for RNA synthesis (transcription)?

A

(RNA)n + NTP ⇌ (RNA)n+1 + PPi

(PPi → 2Pi)

26
Q

What catalyses RNA synthesis?

A

RNA polymerase

27
Q

What drives RNA synthesis?

A

Cleavage of inorganic pyrophosphate (PPi) by pyrophosphatase

28
Q

What does the synthesis of RNA require?

A

Nucleoside triphosphates (NTPs)

Mg2+

dsDNA template

29
Q

In which direction are all nucelic acids made?

A

5’ → 3’

30
Q

How processive is RNA synthesis?

A

Very

31
Q

How does RNA synthesis differ from DNA synthesis? (x4)

A
  • No primers
  • Not semi-conservative, as the DNA template remains unchanged
  • No nuclease activities
  • Only one DNA strand copied in the complementary sense even though dsDNA is required
32
Q

Is transcribed RNA made parallel or anti-parallel to a DNA strand?

A

Anti-parallel

33
Q

How does RNAP know:

  1. which strand to transcribe
  2. where to start?
A

Using promoters:

  1. The RNA polymerase looks for promoters
  2. Promoter is directional
34
Q

What is a promoter?

A

A specific binding site for RNA polymerase

35
Q

How does a promoter work?

A

It is directional and ‘catches’ and ‘orientates’ the RNAP

RNAP opens the promoter

RNAP then transcribes the 3’→5’ strand

36
Q

To which part of the DNA strand do the terms ‘upstream’ and ‘downstream’ refer?

A

The coding region

37
Q

Is the promotor upstream or downstream of the coding region?

A

Upstream

38
Q

Is the promoter transcribed in RNA transcription?

A

No

39
Q

How do we find promoters?

A

Footprinting: the sequences is protected from digestion by RNAP

40
Q

What are the benefits of having different sequences for promoters?

A
  • Regulation: possibility of turning some promoters on and some off independently
  • Some promoters will catch RNAP more efficiently so functions more effectively than other promoters so more mRNA is made and more proteins are made
41
Q

What do promoters look like?

A

They all differ, but the best guess is a ‘consensus sequence’.

42
Q

What is a strong promoter?

A

A promoter that generates more of their product

BS1030: Biochemistry (21 decks)

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