Nucleic Acids Flashcards
What is the first amino acid in a protein translated from mitochondrial mRNA?
Formylmethionine (fMet).
What is chromatin?
DNA + associated proteins
What are nucleosomes?
DNA wrapped around a core of histone proteins - an example of chromatin.
Name the purines
Adenine and guanine.
Describe charges in DNA.
Phosphate groups (backbone) negative Histones positive
What direction is DNA synthesised?
5’ to 3’ of new strand. dNTP added to 3’ end of primer.
What is DNA primase?
An RNA polymerase which produces an RNA primer.
How is an incorrect nucleotide removed?
3’ to 5’ exonuclease activity of DNA polymerase.
Which is the antisense strand?
The template strand.
What does RNA polymerase II do?
Transcribes encoding mRNA.
What is the promoter gene?
The DNA sequence at which the transcription complex assembles.
How do transcription factors facilitate transcription?
They remodel chromatin. Hyperacetylation = gene expression. Hypoacetylation = gene repression. (They upregulate or downregulate the basal transcription complex).
For stability, what 2 features are added to the primary transcript (pre-mRNA)?
A 5’ cap - a modified nucleotide (7-methylguanosine)
A polyA tail, 11-30 bases downstream of AAUAAA.
What is alternative splicing?
Some exons are ignored, e.g. a mutate exon in dystrophin which causes DMD is ignored.
What is a tRNA with an amino acid attached called?
Charged
Name the 2 sites of the large ribosomal subunit.
The P (peptidyl) site and A (amino acyl) site.
What are elongation factors (EFs)?
Proteins which promote the movement of ribosomes along mRNA using GTP.
Why is GTP used?
Increases efficient and accuracy of translation by providing pauses (GPT hydrolysis) allowing incorrect base pairs to dissociate.
What happens when a stop codon is recognised?
A release factor binds to the A site, causing the dissociation of the release factor and ribosomes.
What recognises the signal sequence on a protein destined for the ER?
A SRP (signal recognition particle).
Which enzyme cleaves the signal sequence of a protein being translated on the surface of the rER?
Signal peptidase
How are transmembrane proteins held in the membrane?
They encode one or more hydrophobic sequences.
What does the energy needed to break the H-bonds between DNA bases and hence denature the DNA depend on?
Strand length
Base composition (G-C = 3 H-bonds)
Chemical environment: monovalent cations stabilise the DNA duplex. Denaturants destabilise.
What is hybridisation stringency?
The power to distinguish between related sequences.
Which handed double helix is DNA and how many base pairs are there per helical turn?
Right-handed double helix. 10bp per helical turn.
What are teratogens?
Agents which interfere with normal embryonic or foetal development.
Roughly how many genes and proteomes are there in the human genome and proteome respectively?
25,000 genes: 1,000,000 proteins.
Describe the process of RNAi
dsRNAs and shRNAs are digested into fragments of 21-25bp by DICER using RNAse III like endonuclease activity, forming siRNAs.
siRNA guided endonuclease activity removes the passenger strand, requiring Argonaute-Piwi proteins.
This forms the RNA-induced splicing complex (RISC) which recognises and cleaves target mRNA molecules.
How are tRNAs charged?
Amino acid binds to aminoacyl tRNA synthetase, which cleaves pyrophosphate from ATP and binds the AMP to the AA: the AA is adenylated.
The adenylated AA is then attached to the tRNA: AMP and aminoacyl tRNA synthase detach leaving the charged tRNA.
What is breaking the hydrogen bonds to separate strands of DNA called? How can it be done?
What is encouraging the bonds to reform called?
MELTING.
High temperature of low salt environment.
REANNEALING.
How many base pairs wrap around a single histone octamer?
150bp.
Detail the macrostructure of DNA
Double helix: nucleosome: 30nm fibre: chromatin loops: chromosome.
What constitutes the gene promoter region?
The TATA box/ sequence and the transcription factor binding site.
What does TFII D do?
Contains TATA binding protein (TBP) and TBP accessory factors (TAFs).
Binds to TATA sequence and partially unwinds the DNA by widening the minor groove.
What does TFII F do?
Binds to RNA polymerase II which then binds to TFII B.
What does the splice donor site always start with and the splice acceptor site always end with?
GU
Pyrimidine 15 N C AG
What are the start and stop codons?
Start: AUG
End: UAA, UGA, UAG
