Genome structure Flashcards
In what direction is a DNA strand by convention?
Sequence is 5’ to 3’ by convention
How does DNA exist in its 3D form?
- There are two antiparallel strands of DNA
- The bases are stacked
- There are two grooves ‘major and minor’
How many grooves does DNA have?
2 grooves -Major -Minor
How is DNA packaged?
DNA double helix–>Nucleosomes(Beads on string)–>Chromatin fibre –>Loops of chromatin fiber–>Metaphase chromosome
What is the function of histones?
Basic protein that bind DNA
How many histones form a nucleosome?
8 histones form a nucleosome
Which histone binds the linker DNA?
Histone 1 binds the linker DNA
Why do chromosomes come in different shapes? What are the three different types of chromosomes?
Chromosomes come in different shapes due to position of centromere
- Metacentric
- Submetacentric - small arms
- Acrocentric - satellite arms
What does the primary DNA sequence encode?
Primary DNA sequence encodes all the gene products necessary for an organism
What does the primary DNA sequence also contain a large number of?
Primary DNA sequence also includes a large number of regulatory signals
What is the definition of the exome?
Sum of all gene sequences
Definition of a gene
All of the DNA that is transcribed into RNA plus all of the cis-linked(local) control regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein
What do intergenic regions contain?
Contain sequences of no known function like:
- Repetitive DNA
- Endogenous retrovirus
- Pseudogenes
What do genes often cluster in? What does this allow?
- Genes often cluster in families e.g globin gene cluster
- Allows for co-ordinated gene regulation
- May just reflect evolutionary history
What does clustering of genes into families allow?
Allows for coordinate gene regulation
What does the promoter recruit and to where?
Promoter recruits RNA polymerase to DNA template
In what orientation does RNA polymerase bind and what direction does it only move in?
RNA polymerase binds asymmetrically and can only move from 5’ to 3’ direction
What are UTR’s a part of?
UTR’s are a part of the exons
Why is a TATA box needed?
Needed to recruit general transcription factors and RNA polymerase
Why is a regulatory element needed?
Needed to regulate recruitment of RNA polymerase
What does RNA polymerase 1 do?
Needed to transcribe rRNA genes
What does RNA polymerase 2 do?
Needed to transcribe mRNA
What does RNA polymerase 3 do?
Needed to transcribe tRNA and other small RNA’s
Process of transcription
1) RNA polymerase recruited (open complex)
2) DNA helix locally unwound (open complex)
3) RNA synthesis begins
4) Elongation
5) Termination
6) RNA Polymerase dissociates
What happens to mRNA after transcription?
mRNA is extensively modified after transcription:
1.Capped at 5’ end using 7-methylguanosine - makes resistant to digestion within the cell and nucleus which would degrade the message, transcription will continue to completion
2.Polyadenylated at 3’ end - cleavage factors bind and signal for cleavage to occur, poly A polymerase adds A bases to 3’ end
3.Removal of introns
When is the 5’ cap added and why?
After RNA polymerase begins transcription, a methylated cap is added to prevent digestion
What is 3’ poly A tail formed by?
Formed by: 1.Removal of G/U rich region by clevage factors 2.Polyadenylate polymerase adds many A bases forming poly A tail preventing degradation
What is splicing?
Splicing is removal of introns by spliceosome and by joining of exons
What is alternative splicing?
Exons can be skipped or added so different isoforms of protein can be produced from the same gene
How have pseudogenes lost their function?
Genes which are partially inactivated due to the loss or gain of a sequence which disrupts their correct transcription/ and or translation.
Processed pseudogenes have no promoter or exons as they are copied from mRNA by retrotransposition
List some regulatory regions in a gene and their function
- ENHANCERS = upregulate gene expression - short sequences that can be in the gene or many kilobases distant. They are targets for transcription factors (activators)
- SILENCERS = down regulate gene expression. They are also position-independant and are targets for transcription factors (repressors)
- INSULATORS = short sequences that prevent enhancers/ silencers influencing other genes
