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Flashcards in DNA Deck (79)
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1
Q

Define genomics

A

Study of all the genes in an organism

2
Q

Define genetics

A

Study of inheritance of genes

3
Q

Define autosomal dominant and give 2 examples

A

Autosomal dominant allele is not sex linked and will express itself in heterozygous individual e.g huntingtons, hypercholesterdemia

4
Q

Define autosomal recessive and give 3 examples

A

Both parents must be at least heterozygous, offspring must inherit two faulty copies e.g sickle cell, cystic fibrosis, phenylketonuria

5
Q

What is X-linked recessive?

A

Most often expressed in males, on X chromosome, women must be homozygous. E.g haemophilia, colour blindness, duchenne muscualr dystrophy

6
Q

Define gene

A

A segment of DNA encoding a polypeptide chain, including regulatory sequences, introns and exons

7
Q

Molecular markers used to map disease loci are based on what?

A

Polymorphisms which are common differences in DNA sequence that vary between individuals e.g SNPs and SSRs

8
Q

What does SNP stand for and give an example of when it occurs in a coding section of DNA

A

Single nucleotide polymorphism, A to T transversion in sickle cell

9
Q

What does SSR stand for and what it is used for

A

Simple sequence repeat, tandem repeat of 2-8 base sequences, different individuals inherit different number of repeats at each loci, used in DNA sequencing

10
Q

What’s the main problem with linkage mapping?

A

Narrows down to 10^5 base pairs BUT that’s still 10genes, don’t actually identify gene

11
Q

Define alleles

A

Genes encoding for different polymorphic forms of proteins

12
Q

Give 4 normal control mechanisms

A

1) heterozygosity
2) apoptosis
3) cell cycle control
4) regulation of gene transcription

13
Q

How many mutations are needed in a growth cycle in each cell for cancer to occur?

A

3, notes Ras is a dominant mutation

14
Q

Define oncogene

A

Mutated forms of proto-oncogenes which control cell growth (usually dominant mutation)

15
Q

Define tumour suppressor genes and give 3 examples that act as cell cycle checkpoints

A

Exert negative effects on cell growth e.g pRb, p53, PTEN

16
Q

‘Tumour suppressor genes are usually autosomal dominant’ true or false?

A

FALSE they are autosomal recessive

17
Q

What is Li Fraumeni syndrome?

A

Inherited mutation in the tumour suppressor gene p53 which is the cause of many childhood tumours

18
Q

What is pRB and what happens during a mutation?

A

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)

19
Q

What are translocations?

A

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.

20
Q

Give an example of a translocation occurring

A

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

21
Q

What is chronic myeloid leukaemia (CML)

A

Caused by constitutive activation of c-abl tyrosine kinase by loss of N terminal regulatory domain increased cell signalling and growth

22
Q

What happens in GAP1 phase of the cell cycle

A

Cell prepares for DNA synthesis:
Is it big enough?
Are there sufficient nutrients?
Are external growth stimuli present?

23
Q

What happens in the S phase of the cell cycle?

A

DNA replicated/synthesised

24
Q

What happens in Go and G2 phase of cell cycle

A
Go= resting phase Ill defined 
G2= cell prepares for division
25
Q

What are the two families of proteins involved in the control of the cell cycle

A

1) cyclins (transcription dependent)

2) cyclin dependant kinases (activation dependent)

26
Q

What is key in controlling the cell cycle?

A

Phosphorylation by cyclin dependent kinases CDKs

27
Q

Name the two groups of CDK inhibitors

A

1) INK4- inhibit CDK4/6

2) CIP/Kip- inhibit all CDKs

28
Q

What is the role of p53

A

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

29
Q

Define transcription

A

Synthesis of RNA from a DNA template, it requires RNA polymerase, transcription factors and specific transcriptional control sequences

30
Q

How many mammalian RNA polymerases are there and what are they called?

A

THREE-
RNA pol1 = rRNA
RNA pol2 = mRNA
RNA pol3 = tRNA

31
Q

What binds two ribonucleotide triphosphates together?

A

Phosphodiester bond

32
Q

Where does synthesis of an mRNA begin?

A

NUCLEUS

33
Q

What makes up a transcription initiation complex?

A

1) transcription factors
2) co activators
3) enhancer sequences
4) general transcription factors e.g SRBs and RNA pol 2
5) promoter region

34
Q

What protects the 5’ end of the growing mRNA from 5’exonucleases?

A

Cap of methyl G

35
Q

What two things protect and aid the transport of mRNA into the cytoplasm?

A

1) cap binding complex

2) poly-A-binding protein (Pab2)

36
Q

Name three main sites on a ribosome that are involved in protein synthesis

A

1) P site
2) A site
3) E site

37
Q

What amino acid do all human genes start with?

A

Methionine- MET

38
Q

Define promoter

A

DNA sequence that determines the site of transcription initiation for an RNA polymerase

39
Q

What do inducible transcription factors bind to?

A

Response elements of promoter

40
Q

What are inducible transcription factors regulated by?

A

Extracellular stimuli

41
Q

Name 5 inducible transcription factors

A

1) steroids
2) NFkB
3) AP-1
4) CREB
5) STATS

42
Q

What are steroids and where do they act?

A

Lipophilic hormones that diffuse through bloodstream to site of action of which being intracellular receptors

43
Q

Name 5 steroids in the Body

A

1) glucocorticoid
2) aldosterone
3) testosterone
4) b-estradiol
5) vitamin D

44
Q

Where are steroid response elements often found?

A

In the enhancers which activate nearby promoters

45
Q

Name one steroid hormone inhibitor

A

HSP90

46
Q

Where are homodimers located?

A

Cytoplasm and nuclear

47
Q

Where are heterodimers located?

A

Nuclear location

48
Q

What explains the anti inflammatory proteins of steroids?

A

Steroid activated glucocorticoid receptor- inhibits expression of IL-1

49
Q

What does NFkB stand for and what is it?

A

Nuclear factor kappa B, family of dimeric transcription factors (five members)

50
Q

What do all NFkB members contain?

A

Conserved 300 amino acid rel-homology domain

51
Q

What 3 things is the Rel-homology domain on NFkB involved in?

A

1) DNA binding
2) dimerisation
3) interaction with IkB

52
Q

Name two inducible transcription factors that are regulated by seeing phosphorylation

A

1) CREB

2) AP-1

53
Q

Phosphorylation CREB binds to what response element?

A

Binds to cAMP response element- CRE on DNA

54
Q

CREB binds what co-activator and what does it interact with?

A

Co activator- CBP/p300

Interacts with basal transcriptional machinery

55
Q

What does AP-1 inducible transcription factor contain?

A

Leucine zippers

56
Q

Name two members of the Fos family

A

C-Fos

Fra-1

57
Q

Name 3 members of the jun family

A

C-Jun
Jun-B
Jun-D

58
Q

Name two ways in which the activity of the inducible transcription factor AP-1 is regulated

A

1) regulation of c-Fos promoter

2) phosphorylation of c-Jun

59
Q

What two serines on C-Jun are targets for phosphorylation by JNK (jun N terminal kinase)

A

Serine 63 and 73

60
Q

What does STAT stand for and how many members are there?

A

Signal transducers and activators of transcription, 7

61
Q

Name the 7 members of STAT

A

STAT 1-4

5a, 5b and 6

62
Q

Name the inducible transcription factor that is regulated by tyrosine phosphorylation

A

STATs

63
Q

Give an example of a reporter assay

A

Luciferase assay- enzyme derived from fireflies gives the glowing light, light is measured

64
Q

Histone acetylation blocks the ability to bind DNA by masking what?

A

Positive charge

65
Q

What is heterochromatin

A

Densely packed nucleosomes
Condensed
Not actively transcribed
Deacetylated histones

66
Q

What is euchromatin

A

Extended beads on a string appearance
Being actively transcribed
Acetylated histones

67
Q

How many base pairs does the TATA box consist of?

A

6bp, TATAAA

68
Q

What binds to the TATA box first and what is it?

A

TFIID- multimeric protein complex comprising:
TATA binding protein (TBP)
TBP-associated factors (TAFs)

69
Q

TBP binding to the TATA box does what to the structure?

A

Distorts it- considerable bending

70
Q

TBP binds to what of the TATA box in DNA?

A

Minor groove

71
Q

List the order in which the transcription initiation complex forms

A

1) TFIID
2) TFIIA
3) TFIIB
4) TFIIF (+pol II)
5) TFIIE
6) TFIIH

72
Q

What’s the role of TFIIH in the transcription initiation complex

A

Has helicase activity- unwinds DNA

Has kinase activity- phosphorylates carboxyl terminal domain CTD of RNApol II

73
Q

Name 4 DNA binding motifs

A

1) zinc finger proteins
2) helix-turn-helix
3) helix-loop-helix
4) leucine zipper

74
Q

What’s RNA interference

A

Post transcriptional regulation of gene expression by double stranded RNA molecule in a sequence specific manner

75
Q

What does RISC stand for

A

RNA interference silencing complex

76
Q

Name two important molecules in RNA interference

A

siRNA and microRNA

77
Q

What is gene therapy?

A

Introduction of genetic material into a persons cells to fight disease

78
Q

Define pharmacogenetics

A

The influence of an individual’s genetic profile on medicine efficacy and safety

79
Q

Define pharmacogenomics

A

Using genomic information in the discovery of new medicines and targets