genome structure Flashcards
what is DNA?
- DNA is deoxynucleic acid
- macromolecule consisting of linear strand of nucleotides
- single linear strands bind to complementary strands to form double stranded DNA.
What are constitutes of DNA?
- nitrogenous base
- ribose sugar
- phosphate group
which direction is DNA transcribes?
- 5’ to 3’
- DNA polymerase only works in 5’ to 3’ direction.
Which bases are purines and which are pyrimidines?
- purines = G, A,
- pyrimidines = C, T, U
uracil replaces thymine so its also a pyrimidine
How many hydrogen bonds do AT and CG have?
- AT = 2 H bonds
- CG = 3 H bonds
What are features of 3D structure of DNA?
- 2 antiparallel strands
- bases are stacked
- 2 grooves = major groove and minor groove
outline human genome variation.
- 3x10^9 base pairs - 3Gbp
- about 20, 000 genes
- normally smaller organisms have fewer genes BUT this is not always the case
How does 2 meter of DNA fit in 50 micrometer diameter cell?
- histones and DNA packaging in coils.
what are histones?
- basic (-ve charged) proteins that bind to DNA.
- 10 nm molecules
- 146 bp of DNA wind around the histone core octomer.
How many histones form nucleosome?
- 8 histones
- 2x (H2A) , (H2B) , (H3), (H4) .
Which histone binds to the linker DNA?
- histone 1 binds to the linker DNA
What are the 6 stages of DNA packaging?
- DNA double helix
- nucleosome
- chromatin fibre
- extended section of chromosome
- loops of chromatin fibre
- metaphase chromosome (densest form)
What are 3 chromosome structures?
- metacentric : equal long and short arm.
- submetacentric : long long arms and short short arms
- acrocentric : no short arm at all.
What are the 2 main features of chromosome?
- centromere = holds the chromatin arms in place at the centre
- telomeres = ends to the chromatin, prevents eroding of genetic material.
What is human karyotype?
- process of pairing and ordering all chromosomes of an organism shows bonding patterns, size differences etc.
What is a genome?
- 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.
What is an exome?
- regions of the gene that encode for protein
- 1- 2% of the genome is exome.
How do we define genome?
- 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 are intergenic regions and what do they contain?
- DNA sequences , endogenous retroviruses, pseudogenes etc.
- regions between genes.
- 98% of the genome
What do gene clusters reflect?
- allows for co-ordinated gene regulation
- may just reflect evolutionary history
What is the purpose of introns?
- used in splicing to form a variety of exons
- used in evolution to form new genes
What is the function of the promoter?
- 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.
What are the different structures that make up a gene?
- promotor
- transcription unit
- initiation
- exon
- intorns
- termination
What is the function of enhancers?
- upregulate gene expression (activators)
- they are short sequences that can be in the gene or many kilobases distant.
- they are targets for transcription factors
What is the function of silencers?
- downregulate gene expression (repressors)
- they are also position - independent and are also targets for transcription factors
What is the function of insulators?
- short sequences that act to prevent enhancers/ silencers influencing other gene
What is transcription?
- process of copying DNA sequence to RNA.
What catalyses the synthesis of messenger RNA?
- RNA polymerase II
- RNA polymerase II recognises promoter efficiently with assistance of many other transcription factors.
What direction does RNA polymerase II transcribe in?
- 5’ to 3’ direction
- transcribes everything after the transcription start site (exon and introns)
Describe the steps of transcription.
- RNA polymerase recruited (closed complex).
- DNA helicase locally unwound.
- RNA synthesis occurs
- Elongation
- termination
- RNA polymerase dissociates.
What are 3 post transcriptional modifications?
- capping
- splicing
- polyadenylation
Describe the process of capping.
- after 25- 30 nts synthesised a methylated cap is added to the 5’ end by 3 enzyme activities
- 5’ to 5’ triphosphate bridge added by RNA 5’ triphosphatase.
- guanosine added by guanylytransferase
- which is methylated by N7G- methyltransferase at position 7
What are the 3 enzymes involved in capping?
- RNA 5’ triphosphatase
- guanyltransferase
- N7G- methyltransferase
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)
Why is splicing important?
- splicing allows target mRNAs for nuclear export
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.
Describe translation.
- once mRNA is exported from nucleus into cytoplasm via nuclear pore
- ribosome picks it up and starts translating the mRNA -> protein
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.
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)
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.
What is cohesion regulated chromatin loop extrusion?
- separating parts of DNA
- enhancer and promoter close together = strong transcription and translation and vice versa.
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
