genome structure Flashcards
1
Q
what is DNA?
A
- DNA is deoxynucleic acid
- macromolecule consisting of linear strand of nucleotides
- single linear strands bind to complementary strands to form double stranded DNA.
2
Q
What are constitutes of DNA?
A
- nitrogenous base
- ribose sugar
- phosphate group
3
Q
which direction is DNA transcribes?
A
- 5’ to 3’
- DNA polymerase only works in 5’ to 3’ direction.
4
Q
Which bases are purines and which are pyrimidines?
A
- purines = G, A,
- pyrimidines = C, T, U
uracil replaces thymine so its also a pyrimidine
5
Q
How many hydrogen bonds do AT and CG have?
A
- AT = 2 H bonds
- CG = 3 H bonds
6
Q
What are features of 3D structure of DNA?
A
- 2 antiparallel strands
- bases are stacked
- 2 grooves = major groove and minor groove
7
Q
outline human genome variation.
A
- 3x10^9 base pairs - 3Gbp
- about 20, 000 genes
- normally smaller organisms have fewer genes BUT this is not always the case
8
Q
How does 2 meter of DNA fit in 50 micrometer diameter cell?
A
- histones and DNA packaging in coils.
9
Q
what are histones?
A
- basic (-ve charged) proteins that bind to DNA.
- 10 nm molecules
- 146 bp of DNA wind around the histone core octomer.
10
Q
How many histones form nucleosome?
A
- 8 histones
- 2x (H2A) , (H2B) , (H3), (H4) .
11
Q
Which histone binds to the linker DNA?
A
- histone 1 binds to the linker DNA
12
Q
What are the 6 stages of DNA packaging?
A
- DNA double helix
- nucleosome
- chromatin fibre
- extended section of chromosome
- loops of chromatin fibre
- metaphase chromosome (densest form)
13
Q
What are 3 chromosome structures?
A
- metacentric : equal long and short arm.
- submetacentric : long long arms and short short arms
- acrocentric : no short arm at all.
14
Q
What are the 2 main features of chromosome?
A
- centromere = holds the chromatin arms in place at the centre
- telomeres = ends to the chromatin, prevents eroding of genetic material.
15
Q
What is human karyotype?
A
- process of pairing and ordering all chromosomes of an organism shows bonding patterns, size differences etc.
16
Q
What is a genome?
A
- The primary DNA sequence encodes all the gene products necessary for a human
- primary DNA sequence also includes a large number of regulatory signals
- much of the DNA sequence does not have an assigned function yet.
17
Q
What is an exome?
A
- regions of the gene that encode for protein
- 1- 2% of the genome is exome.
18
Q
How do we define genome?
A
- 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.
19
Q
What are intergenic regions and what do they contain?
A
- DNA sequences , endogenous retroviruses, pseudogenes etc.
- regions between genes.
- 98% of the genome
20
Q
What do gene clusters reflect?
A
- allows for co-ordinated gene regulation
- may just reflect evolutionary history
21
Q
What is the purpose of introns?
A
- used in splicing to form a variety of exons
- used in evolution to form new genes
22
Q
What is the function of the promoter?
A
- promoters recruit RNA polymerase to a DNA template
- RNA polymerase binds asymmetrically to the promoter and can only move 5’ to 3’
- regulation occurs via transcription factors.
23
Q
What are the different structures that make up a gene?
A
- promotor
- transcription unit
- initiation
- exon
- intorns
- termination
24
Q
What is the function of enhancers?
A
- upregulate gene expression (activators)
- they are short sequences that can be in the gene or many kilobases distant.
- they are targets for transcription factors
25
What is the function of silencers?
- downregulate gene expression (repressors)
| - they are also position - independent and are also targets for transcription factors
26
What is the function of insulators?
- short sequences that act to prevent enhancers/ silencers influencing other gene
27
What is transcription?
- process of copying DNA sequence to RNA.
28
What catalyses the synthesis of messenger RNA?
- RNA polymerase II
| - RNA polymerase II recognises promoter efficiently with assistance of many other transcription factors.
29
What direction does RNA polymerase II transcribe in?
- 5' to 3' direction
| - transcribes everything after the transcription start site (exon and introns)
30
Describe the steps of transcription.
1. RNA polymerase recruited (closed complex).
2. DNA helicase locally unwound.
3. RNA synthesis occurs
3. Elongation
4. termination
5. RNA polymerase dissociates.
31
What are 3 post transcriptional modifications?
1. capping
2. splicing
3. polyadenylation
32
Describe the process of capping.
1. after 25- 30 nts synthesised a methylated cap is added to the 5' end by 3 enzyme activities
2. 5' to 5' triphosphate bridge added by RNA 5' triphosphatase.
3. guanosine added by guanylytransferase
4. which is methylated by N7G- methyltransferase at position 7
33
What are the 3 enzymes involved in capping?
1. RNA 5' triphosphatase
2. guanyltransferase
3. N7G- methyltransferase
34
Describe the process of splicing.
- process of removing introns, using spliceosomes.
1. spliceosome catalyses the connection of one exon to another.
2. creates a 2' - 5' linkage
3. intron is a lariat structure (loop)
35
Why is splicing important?
- splicing allows target mRNAs for nuclear export
36
Describe polyadenylation.
- addition of poly A tail in the 3' .
1. CPSF(cleavage and polyadenylation stimulating factors) recognises the PAS (poladynlation signal) and acts on cleavage site.
2. CSTF (cleavage stimulating factor) recognises GU- rich down stream element (DSE)
3. PAP (poly A polymerase) is recruited and adds multiple A bases after cleavage site.
37
Describe translation.
- once mRNA is exported from nucleus into cytoplasm via nuclear pore
- ribosome picks it up and starts translating the mRNA -> protein
38
What is the point of alternative splicing?
- splicing is the process of removing introns
- alternative splicing: splicosomes cuts at different length of the DNA sequence making a variety of exons
- variety of exons = variety of proteins (isoforms) from the same gene.
39
What 2 compartments can genome be separated into?
- compartment A : transcriptionally active histone modification
- Compartment B:
transcriptionally repressed with repressive histone modification
(same compartments brought together in 3D structure)
40
What are topologically - associated domains (TADs)
- individual compartments made up of several non- interacting sub - compartments
- TADs are usually separated by the transcriptional repressor CTCF protein.
41
What is cohesion regulated chromatin loop extrusion?
- separating parts of DNA
| - enhancer and promoter close together = strong transcription and translation and vice versa.
42
What different colours in 3D structure show active and inactive genes?
- regions of chromosomes where genes are active are BLUE.
| - regions which are inactive are YELLOW
