EC1: RNA, Transcription, and Promoters Flashcards
Where in the cell are genes found?
Nucleus
Where are proteins made?
Cytoplasm of ribosomes
What carries the ‘message’ from the nucelus (or wherever the genes are made) to the ribosome?
mRNA
What do the arrows represent in this diagram?
The flow of information in a biological system
What is transcription, and what enzyme is involved?
DNA-dependent mRNA synthesis; RNA polymerase
What is translation, and what enzyme is involved?
mRNA-depended protein synthesis; ribosome
What is this molecule and where is it found? What is the numbering system of carbons around this ring?
Ribose
Found in RNA
What is this molecule and where is it found?
Deoxyribose
Found in DNA
What are the four bases in RNA? Which ones are shared with DNA?
Adenine (A) – shared with DNA
Guanine (G) – shared with DNA
Cytosine – shared with DNA
Uracil (U) – unique to RNA
What’s the difference between the RNA base uracil and the DNA base thymine?
Thymine is 5-methyl-U, i.e. has a methyl group on the fifth carbon of uracil
Which bases (DNA and RNA) are purines and which are pyrimidines?
Purines: adenine, guanine
Pyrimidines: thymine, cytosine, uracil
Is RNA in cells single- or double-stranded? What is the exception?
It is single-stranded, but some viruses have dsRNA
Is there base equivalence in RNA?
No – the amounts of the four bases vary independently
How does ssRNA form a secondary structure? What is the name of this structure?
It folds back on itself, forming non-standard pairs in step-loop structures, resulting in partial double-stranded regions
How many base pairs have a folded piece of RNA and a folded piece of DNA per 360° turn?
RNA: 11 base pairs
DNA: 10 base pairs
Are all enzymes proteins?
No – some can be made of RNA
What are the major types of RNA and what is their approximate relative proportions in a cell?
messenger RNA (mRNA) – approx. 5%
ribosomal RNA (rRNA) – approx. 80%
transfer RNA (tRNA) – approx. 15%
What are the purposes of mRNA?
It carries genetic information that is copied from the gene (DNA)
It is used as a template for translation by ribosomes
Differentiate between bacterial and eukaryotic rRNA.
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
How long is tRNA?
Approx. 76 nucleotides
What is the role of tRNA?
It carries amino acids to the ribosomes for protein synthesis
Define ‘proteinogenic amino acid’.
An amino acid that goes into a protein
How many tRNAs are dedicated to each proteinogenic amino acid?
One
What is the standard abbreviation for RNA polymerase?
RNAP
What is the general equation for RNA synthesis (transcription)?
(RNA)n + NTP ⇌ (RNA)n+1 + PPi
(PPi → 2Pi)
What catalyses RNA synthesis?
RNA polymerase
What drives RNA synthesis?
Cleavage of inorganic pyrophosphate (PPi) by pyrophosphatase
What does the synthesis of RNA require?
Nucleoside triphosphates (NTPs)
Mg2+
dsDNA template
In which direction are all nucelic acids made?
5’ → 3’
How processive is RNA synthesis?
Very
How does RNA synthesis differ from DNA synthesis? (x4)
- 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
Is transcribed RNA made parallel or anti-parallel to a DNA strand?
Anti-parallel
How does RNAP know:
- which strand to transcribe
- where to start?
Using promoters:
- The RNA polymerase looks for promoters
- Promoter is directional
What is a promoter?
A specific binding site for RNA polymerase
How does a promoter work?
It is directional and ‘catches’ and ‘orientates’ the RNAP
RNAP opens the promoter
RNAP then transcribes the 3’→5’ strand
To which part of the DNA strand do the terms ‘upstream’ and ‘downstream’ refer?
The coding region
Is the promotor upstream or downstream of the coding region?
Upstream
Is the promoter transcribed in RNA transcription?
No
How do we find promoters?
Footprinting: the sequences is protected from digestion by RNAP
What are the benefits of having different sequences for promoters?
- 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
What do promoters look like?
They all differ, but the best guess is a ‘consensus sequence’.
What is a strong promoter?
A promoter that generates more of their product
