Eukaryotic genes and viruses Flashcards
What is chromatin?
A complex of negative DNA and its associated positive proteins (histones)
What are nucleosomes and linker DNA in chromatin?
Nucleosomes are the DNA coiled around histones
Linker DNA is the uncoiled regions between them
What are nucleosomes?
The basic unit of chromatin
How does chromatin condensation affect gene expression
Condensed chromatin is transcriptionally inactive as it limits the access of proteins required for transcription
Relaxed chromatin is active as proteins required for transcription can access the DNA
What is the most condensed state of DNA?
Metaphase chromosome
What are exons and introns
Regions of DNA in pre-mRNA
Exons are coding regions and introns are non-coding regions
How are introns removed from pre-mRNA?
- through splicing
- spliceosome cuts them out
What is the function of topoisomerases I and II?
relieve torsional stress ahead of fork
What is the function of DNA helicase?
Unwinds parental strands by ATP hydrolysis
What happens in DNA replication in eukaryotes?
- replication originates at the autonomous replication sequences that recruits a complex of proteins known as the ORC
- DNA helicases unwind the DNA
- replication protein A binds and stabilises the DNA at the fork
What happens in replication priming?
- an RNA primer is required to initiate synthesis
- a complex of DNA polymerase a and primase creates a hybrid RNA/DNA primer
RNA polymerase adds a short stretch of RNA nucleotides which are then extended by DNA pol A
What are the roles of DNA polymerases alpha, delta and epsilon?
Alpha: extends the RNA primer with DNA but lacks proofreading
Delta: lagging strand DNA polymerase
Epsilon: leading strand DNA polymerase
What is processivity?
The ability of DNA pol to continuously synthesise DNA without frequent dissociation
What is the role of the clamp loader and PCNA clamp?
Clamp loader recruits the PCNA clamp at the function between the RNA/DNA primer and the template strand.
The clamp then forms a ring that displaces pol alpha and recruits delta or epsilon
How are the RNA primers removed on the lagging strand
Pol delta elongates the Okazaki fragments
When it encounters an RNA primer is displaces it to form a flap
FEN1 cuts the flap at the branch point
DNA ligase I seals the gap
What is the hayflick limit?
It isnt possible to add or remove RNA primers at telomeric ends and so the chromosome end shortens after each round of replication. The hayflick limit is where the telomeres become too short and the cell stops dividing
How does telomerase increase the telomere repeat length?
Telomerase RNA provides a template for extending DNA template strand.
Telomerase reverse transcriptase extends the DNA template
How does telomerase affect aging and cacner?
Telomerase is regulated in stem cells but inactivated during development. Telomere shortening is the sign of aging cells
In cancer, telomerase is inappropriately reactivated
What is transcripton?
The synthesis of an mRNA strand with the same sequence as the coding strand
What are distal control elements?
Molecules that function to enhance or repress transcription
What is the TATA box?
A site for recruitment of TAT binding protein
TBP binds to the core promoter TAT box.
TBP recruits other GTFs (general transcription factors) which recruit DNA polymerase II
What three processing steps does pre-mRNA go through to become mRNA
- 5’CAP
- Pre-mRNA splicing
- 3’ cleavage and polyadenylation
What is the process of 5’CAP
A methylated guanosine is added to the 5’ end of the pre-mRNA to promote stability and translational efficiency
What is polyadenylation?
Polyapolymerase adds a long string of residues called a poly(A) tail to the cleaved 3’ end
What is alternative splicing?
- multiple mRNAs can come from a single gene due to the joining of different exon combinations from the same mRNA
- this is where most human diversity comes from
How are mRNAs transported from the nucleus?
Transported from the nucleus to the cytoplasm through the nuclear pore
What is the structure of eukaryotic ribosomes?
a combination of rRNA dna proteins
80s
Composed of 60S and 40S subunits
What is codon degeneracy?
More than one codon can specify the same amino acid
tRNA recognises these codons and the 3’ most base binds less highly with the 5’ most anticodon to create the wobble effect
How are the ribosome subunits seperated?
By eIF3 and eIF6 (eukaryotic initiation factors)
What is the pre-initiation complex?
The 40S subunit, EIF3, tRNA bound to the p-site of 40S and other eIFs
How is translation initiated?
- the pre-initiation complex binds to mRNA at 5’
- methyl CAP-binding complex proteins recognise the methyl CAP and the pre-initiation complex binds to it
The pre-initiation complex is hydrolysed into its GTP form and all its initiation factors dissociate
The 60S subunit joins with the 40S subunit
What are EEFs?
eukaryotic elongation factors
How does translational elongation occur?
EEF-1a-GTP brings charged aa-tRNA to the A-site and is then hydrolysed into its GDP form.
A peptide bond is formed by the 28S and the peptidyl site transfers the peptide chain to the A site where it binds to the new amino acid.
EEF-2-GTP repositions tRNAs to open up the A site so a new codon can enter and start the process again
How does translational termination occur?
Stop codons recruit release factor eRF1 and eRF3-GTP.
The hydrolysis of eRFS-GTP causes the ribosome and peptide chain to dissociate
In what categories can viruses be classified? (5)
host, cell type, disease symptoms, genome, structure and shape
How can viruses be transmitted? (4)
Vertical (mother to child)
Horizontal (person to person)
Zoonosis (from an animal)
Body fluids (saliva, urine etc)
What is innate immunity? (3)
early, non-specific
phagocytic cells engulf the foreign antigens
What is adaptive immunity? (5)
1-2 weeks
highly antigen specific
memory based
B+T cells
Lymphocytes stay in a resting state until activated by antigens
Daughter cells can differentiate into effector or memory cells
What is T-cell mediated immunity? (2)
Cell mediated response
Cytotoxic T cells induce death of virus or pathogen infected cells
What is B-cell mediated immunity? (3)
Long term
Antibody based immunity
B cells are activated more quickly due to previous encounter with antigen
What is antigenic DRIFT? In the flue
Minor mutations in membrane envelope antigens due to the high mutation rate and lakc of proofreading in RNA genome replication.
This can change the level of immunity a host has
What is antigenic SHIFT? in the flu
Major change in membrane envelope antigen subtypes
Recombination or re-assortment of viral strains
Host has no immunity to this strain
What are nucleoside analogues?
They inhibit viral replication
E.G. AZT is a chain terminator that can be incorporated into the genome by reverse transcriptase
Why are nucleosides used in treatment rather than nucleotides?
Nucleotides contain charged phosphate groups that prevent them from crossing membranes but nucleosides don’t have this group
What are oncoviruses? What do they do?
Cancer causing viruses
Insert into the host genome to bring on a strong oncogene promoter and inactivate tumour suppressor genes
What is a proto-oncogene?
A cellular gene capable of causing cancer when dysregulated
