Define genomics
Study of all the genes in an organism
Define genetics
Study of inheritance of genes
Define autosomal dominant and give 2 examples
Autosomal dominant allele is not sex linked and will express itself in heterozygous individual e.g huntingtons, hypercholesterdemia
Define autosomal recessive and give 3 examples
Both parents must be at least heterozygous, offspring must inherit two faulty copies e.g sickle cell, cystic fibrosis, phenylketonuria
What is X-linked recessive?
Most often expressed in males, on X chromosome, women must be homozygous. E.g haemophilia, colour blindness, duchenne muscualr dystrophy
Define gene
A segment of DNA encoding a polypeptide chain, including regulatory sequences, introns and exons
Molecular markers used to map disease loci are based on what?
Polymorphisms which are common differences in DNA sequence that vary between individuals e.g SNPs and SSRs
What does SNP stand for and give an example of when it occurs in a coding section of DNA
Single nucleotide polymorphism, A to T transversion in sickle cell
What does SSR stand for and what it is used for
Simple sequence repeat, tandem repeat of 2-8 base sequences, different individuals inherit different number of repeats at each loci, used in DNA sequencing
What’s the main problem with linkage mapping?
Narrows down to 10^5 base pairs BUT that’s still 10genes, don’t actually identify gene
Define alleles
Genes encoding for different polymorphic forms of proteins
Give 4 normal control mechanisms
1) heterozygosity
2) apoptosis
3) cell cycle control
4) regulation of gene transcription
How many mutations are needed in a growth cycle in each cell for cancer to occur?
3, notes Ras is a dominant mutation
Define oncogene
Mutated forms of proto-oncogenes which control cell growth (usually dominant mutation)
Define tumour suppressor genes and give 3 examples that act as cell cycle checkpoints
Exert negative effects on cell growth e.g pRb, p53, PTEN
‘Tumour suppressor genes are usually autosomal dominant’ true or false?
FALSE they are autosomal recessive
What is Li Fraumeni syndrome?
Inherited mutation in the tumour suppressor gene p53 which is the cause of many childhood tumours
What is pRB and what happens during a mutation?
Is the first tumour suppressor gene identified, regulator of cell division. Usually inherit one mutation but a mutation in the second allele leads to retinoblastoma (tumour of retina)
What are translocations?
Are aberrant cross overs between chromosomes during cell division. This can lead to genes normally regulated by one promoter being separated from this and instead being controlled by another.
Give an example of a translocation occurring
bcl-2 an anti apoptotic protein can be translocated to come under the control of Ig promoter, over expression in these cells with no apoptosis can result in tumour
What is chronic myeloid leukaemia (CML)
Caused by constitutive activation of c-abl tyrosine kinase by loss of N terminal regulatory domain increased cell signalling and growth
What happens in GAP1 phase of the cell cycle
Cell prepares for DNA synthesis:
Is it big enough?
Are there sufficient nutrients?
Are external growth stimuli present?
What happens in the S phase of the cell cycle?
DNA replicated/synthesised
What happens in Go and G2 phase of cell cycle
Go= resting phase Ill defined G2= cell prepares for division
What are the two families of proteins involved in the control of the cell cycle
1) cyclins (transcription dependent)
2) cyclin dependant kinases (activation dependent)
What is key in controlling the cell cycle?
Phosphorylation by cyclin dependent kinases CDKs
Name the two groups of CDK inhibitors
1) INK4- inhibit CDK4/6
2) CIP/Kip- inhibit all CDKs
What is the role of p53
Tumour suppressor protein, stabilised yh binding to damaged DNA, mediates increase in expression of CDKIs to halt cell cycle whilst DNA is repaired. If damage is too great it up regulates apoptotic proteins e.g bad, bax
Define transcription
Synthesis of RNA from a DNA template, it requires RNA polymerase, transcription factors and specific transcriptional control sequences
How many mammalian RNA polymerases are there and what are they called?
THREE-
RNA pol1 = rRNA
RNA pol2 = mRNA
RNA pol3 = tRNA
What binds two ribonucleotide triphosphates together?
Phosphodiester bond
Where does synthesis of an mRNA begin?
NUCLEUS
What makes up a transcription initiation complex?
1) transcription factors
2) co activators
3) enhancer sequences
4) general transcription factors e.g SRBs and RNA pol 2
5) promoter region
What protects the 5’ end of the growing mRNA from 5’exonucleases?
Cap of methyl G
What two things protect and aid the transport of mRNA into the cytoplasm?
1) cap binding complex
2) poly-A-binding protein (Pab2)
Name three main sites on a ribosome that are involved in protein synthesis
1) P site
2) A site
3) E site
What amino acid do all human genes start with?
Methionine- MET
Define promoter
DNA sequence that determines the site of transcription initiation for an RNA polymerase
What do inducible transcription factors bind to?
Response elements of promoter
What are inducible transcription factors regulated by?
Extracellular stimuli
Name 5 inducible transcription factors
1) steroids
2) NFkB
3) AP-1
4) CREB
5) STATS
What are steroids and where do they act?
Lipophilic hormones that diffuse through bloodstream to site of action of which being intracellular receptors
Name 5 steroids in the Body
1) glucocorticoid
2) aldosterone
3) testosterone
4) b-estradiol
5) vitamin D
Where are steroid response elements often found?
In the enhancers which activate nearby promoters
Name one steroid hormone inhibitor
HSP90
Where are homodimers located?
Cytoplasm and nuclear
Where are heterodimers located?
Nuclear location
What explains the anti inflammatory proteins of steroids?
Steroid activated glucocorticoid receptor- inhibits expression of IL-1
What does NFkB stand for and what is it?
Nuclear factor kappa B, family of dimeric transcription factors (five members)
What do all NFkB members contain?
Conserved 300 amino acid rel-homology domain
What 3 things is the Rel-homology domain on NFkB involved in?
1) DNA binding
2) dimerisation
3) interaction with IkB
Name two inducible transcription factors that are regulated by seeing phosphorylation
1) CREB
2) AP-1
Phosphorylation CREB binds to what response element?
Binds to cAMP response element- CRE on DNA
CREB binds what co-activator and what does it interact with?
Co activator- CBP/p300
Interacts with basal transcriptional machinery
What does AP-1 inducible transcription factor contain?
Leucine zippers
Name two members of the Fos family
C-Fos
Fra-1
Name 3 members of the jun family
C-Jun
Jun-B
Jun-D
Name two ways in which the activity of the inducible transcription factor AP-1 is regulated
1) regulation of c-Fos promoter
2) phosphorylation of c-Jun
What two serines on C-Jun are targets for phosphorylation by JNK (jun N terminal kinase)
Serine 63 and 73
What does STAT stand for and how many members are there?
Signal transducers and activators of transcription, 7
Name the 7 members of STAT
STAT 1-4
5a, 5b and 6
Name the inducible transcription factor that is regulated by tyrosine phosphorylation
STATs
Give an example of a reporter assay
Luciferase assay- enzyme derived from fireflies gives the glowing light, light is measured
Histone acetylation blocks the ability to bind DNA by masking what?
Positive charge
What is heterochromatin
Densely packed nucleosomes
Condensed
Not actively transcribed
Deacetylated histones
What is euchromatin
Extended beads on a string appearance
Being actively transcribed
Acetylated histones
How many base pairs does the TATA box consist of?
6bp, TATAAA
What binds to the TATA box first and what is it?
TFIID- multimeric protein complex comprising:
TATA binding protein (TBP)
TBP-associated factors (TAFs)
TBP binding to the TATA box does what to the structure?
Distorts it- considerable bending
TBP binds to what of the TATA box in DNA?
Minor groove
List the order in which the transcription initiation complex forms
1) TFIID
2) TFIIA
3) TFIIB
4) TFIIF (+pol II)
5) TFIIE
6) TFIIH
What’s the role of TFIIH in the transcription initiation complex
Has helicase activity- unwinds DNA
Has kinase activity- phosphorylates carboxyl terminal domain CTD of RNApol II
Name 4 DNA binding motifs
1) zinc finger proteins
2) helix-turn-helix
3) helix-loop-helix
4) leucine zipper
What’s RNA interference
Post transcriptional regulation of gene expression by double stranded RNA molecule in a sequence specific manner
What does RISC stand for
RNA interference silencing complex
Name two important molecules in RNA interference
siRNA and microRNA
What is gene therapy?
Introduction of genetic material into a persons cells to fight disease
Define pharmacogenetics
The influence of an individual’s genetic profile on medicine efficacy and safety
Define pharmacogenomics
Using genomic information in the discovery of new medicines and targets