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Genomemetronomechickenboneashytone ass nigga Flashcards

1
Q

where are chromosomes located

A

nucleoplasm

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2
Q

what are the closed and open chromatid regions in interphase chromosomes called

A

closed - heterochromatin

open - euchromatin

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3
Q

out of euhcromatin and heterochtomatin, which one transcribed and why

A

euchromatin is typically transcribed because it is relaxed and open

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4
Q

what is the function of chromosomal territories (TAD’s)

A

topologically associated domains help separate heterochromatic and euchromatic regions

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5
Q

what determines wether a chromatin is open or closed

A

histone modifications dictate wether the chromatid is a eu/heterochromatid

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6
Q

difference between cis/trans-acting non-coding regions

A

cis - is not transcribed

trans - are transcribed - RNA

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7
Q

what are the 4 flavours of gene variations

A

SNP - single nucleotide polymorphisms
IDP - insertion deletion polymorphisms
SSR - simple sequence repeats
CNV - copy number variants

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8
Q

why do CNV class of mutations occur and what are the consenquences

A

unequal crossing over during mitosis 1

phenotypes can vary tremendously

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9
Q

Mendel’s first postulate

A

an organism inherits 2 alleles for each gene, one from each parent

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10
Q

Mendel’s second postulate

A

if the alleles are heterozygous, the dominant allele determines the phenotype

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11
Q

Mendel’s 3rd postulate, 1st law

A

during gamete formation, the two alleles segregate randomly, one to each pole
if they are homozygous them all the gametes will contain the same allele
if heterozygous, the half of the gametes will contain one and the other half will contain the other allele

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12
Q

what is the genotypic and phenotypic ratio of F2 of parents that are homozygous recessive and the other homozygous dominant

A

genotypic ratio - 1:2:1

phenotypic ratio - 3:1

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13
Q

Mendel’s 4th postulate, 2nd law

A

independent assortment - genes on a chromosome assort independently on their gene locus to other genes on different loci
evident in dihybrid inheritance

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14
Q

in dihybrid inheritance with parents with both genes heterozygous (TtRr x TtRr) what is the phenotypic ratio

A

9:3:3:1

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15
Q

what is reciprocal recessive epistasis, and what is the ratio

A

in dihybrid inheritance, a dominant allele must be present in both genes for the gene to be expressed
9:7

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16
Q

what is dominant epistasis, and the ratio

A

one dominant allele on one gene produces the same phenotype regardless of the status of the alleles on the other gene
12:3:1

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17
Q

what are duplicate dominant genes with cumulative effects and the phenotypic ratio

A

when a single dominant allele on a gene changes supresses a specific phenotype, both alleles on a single gene must be recessive for the gene to be expressed,
when both genes are homozygous recessive, it produces another phenotype
AaBb - 9
Aabb/BBaa - 6
aabb - 1

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18
Q

dominant and recessive, and the ratio

A

dominant allele from one gene and a recessive allele from the other gene produce the same phenotype
13:3

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19
Q

difference between differentiation and determination

A

determination - internal mechanisms determine the identity of the cell
differentiation - changes in cell morphology and other characteristics to become specialised

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20
Q

difference between pluri/multipotent cells and totipotent

A

pluripotent - can become several cells

totipotent - can become all cell types

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21
Q

what is loose binding

A

the core of RNA polymerase has a specificity for DNA

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22
Q

in bacterial RNA polymerase what is the function of the alpha sub-units

A

enzyme assembly
promotor recognition
binds to some activators

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23
Q

what is the function of the beta sub-units in bacterial RNA polymerase

A

they are the catalytic centre of the enzyme

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24
Q

what is the function of the sigma sub-unit in bacterial RNA polymerase

A

promoter specificity, ensures binding at promoter sequence only

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25
Q

what sub-unit of bacterial RNA polymerase is required for the initiation step

A

sigma

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26
Q

what part of bacterial RNA polymerase is required for elongation

A

core enzyme

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27
Q

what is sigma sub-unit 32 induced by

A

high temperatures

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28
Q

what sigma sub-units are for general use and nitrogen

A

general - sigma sub-unit 70

nitrogen - sigma sub-unit 54

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29
Q

when a promotor region is poorly recognised by RNA polymerase, what is used to activate it

A

catabolic activator protein (CAP)

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30
Q

how does glucose affect the lac operon

A

high glucose leads to low cAMP which leads to low CAP leading to no transcription
vice versa for low glucose levels

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31
Q 
out off the following, which is the only one that would lead to an active lac operon
low glucose, low lactose
high lactose, low glucose
high lactose, high glucose
high glucose, low lactose
A

high lactose, low glucose

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32
Q

how does lactose affect the lac operon

A

high lactose leads to lactose binding to the repressor protein, inactivating it, activating the lac operon
vice versa for low lactose

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33
Q

what is SP1, where is it found and what does it bind to

A

a transcriptional activator that confer general expression
found in all cell types
binds to GGGCGG

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34
Q

what is MyoD, where is it found and what does it bind to

A

a transcriptional activator that confers tissue specific expression
muscle-specific
binds to CANNTG

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35
Q

name a transcriptional factor that confers response to specific stimuli

A

oestrogen

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36
Q

how do histone acetyl transferase allow RNA polymerase to bind to a histone

A

acetylation of the lysines in the tail of the histone neutralises the charge
leads to a reduced affinity in the tail for DNA
opens up DNA for RNA polymerase to bind

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37
Q

what are the 2 domains of a histone

A

amino-tail

globular

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38
Q

purpose of histone de-acetylase

A

removes the acetyl group from the lysines in the tail to restore affinity and close down the DNA
preventing RNA polymerase from binding

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39
Q

what base is usually methylated in DNA

A

C

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40
Q

what is the gene number and genome size of humans

A

gene number - 31,000

genome size - 3,200

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41
Q

what is the gene number and the genome size of bacteria

A

gene number - 4000

genome size - 4

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42
Q

what is gene density

A

number of genes per genome size(mb)

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43
Q

what are the gene densities of human, mice, fly, yeast

A

human - 9
mice - 14
fly - 83
yeast - 512

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44
Q

what can causes chromosomal abnormalities

A

chemicals
radiation
errors in replication

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45
Q

what is monosomy

A

loss of a single chromosome

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46
Q

what is cri-du-chat syndrome

A

missing a small part of chromosome 5
1/50,000 infants
severe mental retardation
physical abnormalities

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47
Q

what is trisomy

A

gain of chromosome to a diploid chromosome

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48
Q

what causes down syndrome and the effects

A

trisomy at chromosome 21, only trisomy with a longer survival rate
respiratory diseases
heart malformations
15x higher leukemia rate

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49
Q

what are spontaneous causes for mutation

A

replication errors
deamination
tautomerisation

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50
Q

induced causes of mutation

A

radiation/UV
base analogues
intercalating agents

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51
Q

what are the chances normal replication will introduce an incorrect base

A

once every 10 to the power of 10

good chance it gets repaired as well

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52
Q

what are spontaneous structural alterations in DNA bases called

A

tautomerizations

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53
Q

what does the amino group of A and C tautomerize into

A

NH, imino group

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54
Q

what does the C=O, keto group of G and T tautomerize into, and what are the effects

A

C-OH, enol group

enol group binds a G instead of an A

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55
Q

example of an intercalating agent

A

ethidium bromide

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56
Q

example of a base analogue

A

bromouracil (T analogue)

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57
Q

what does CFTR (cystic fibrosis transmembrane conductance regulator) encode for

A

Cl- ion transporter

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58
Q

what does a mutant CFTR cause

A

doesn’t allow transport of chlorine ions out the cell which causes sticky mucus to build up around the cell

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59
Q

what is the location and name of the amino acid that is deleted that causes cystic fibrosis

A

deletion of phenylalanine at 508

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60
Q

what causes huntington’s disease

A

a tri-nucleotide repeat

inheritance of a defective huntingtin gene

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61
Q

what trinucleotide is repeated that causes huntingon’s disease

A

CAG

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62
Q

what type of genetic disease is huntington’s and cystic fibrosis

A

huntington’s - dominant autosomal

cystic fibrosis - recessive autosomal

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63
Q

what mutation causes breast cancer

A

mutation in BRAC1 or 2

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64
Q

where are BRAC1 and 2 located

A

BRAC2 - chromosome 13

BRAC1 - chromosome 17

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65
Q

what does the lack of factor VIII cause

A

haemophilia

66
Q

how can chromosomes be visualised for a light microscope

A

giemsa stain

67
Q

definition of epigenetics

A

processes that induce long term and stable changes in gene activity without a change in gene sequence

68
Q

what diseases does DNA methylation cause

A 
obesity
cancer
depression
heart disease 
hypertension
anxiety
69
Q

what % of breast cancer is inherited

A

5%

70
Q

what causes sporadic breast cancer

A

DNA hypermethylation of BRAC1

71
Q

what is the warburg effect

A

when cancer cells use glycolysis regardless of oxygen levels

72
Q

what is aneuploidy

A

chromosome instability, causes more mutations

73
Q

difference in growth type between benign and malignant tumours

A

benign - expansive

malignant - infiltrative

74
Q

difference in outcomes from spontaneous evolution between benign and malignant tumours

A

benign - usually favourable outcomes

malignant - always fatal

75
Q

what do tumours consist of

A

malignant cells
host cells
secreted factors
extracellular matrix protein

76
Q

what is the normal and mutated function of proto-oncogenes and their genetic properties

A

normal - promote cell survival and proliferation
mutated - normal function but amplifies and unregulated
dominant

77
Q

what is the genetic properties of a tumour suppressant gene

A

recessive

78
Q

what is the normal and mutated function of a care taker gene and its genetic properties

A

normal - repair/prevent DNA damage
mutated - loss of functions allows accumulation of mutations
recessive

79
Q

why is C-Myc highly regulated

A

its mRNA is short lived and protein levels are low

80
Q

where does translocation of c-myc occur and what does it cause

A

burkitt’s lymphoma

enhanced expression

81
Q

where is c-myc translocated from and to

A

from chromosome 8 to chromosome 14, near an antibody gene enhancer

82
Q

what is HER2

A

type 1 transmembrane growth factor receptor

83
Q

what happens upon ligand binding of HER

A

HER proteins undergo dimerization and transphosphorylation of their intracellular domains

84
Q

what promotes receptor dimerization and activity in HER

A

a V664E mutation

85
Q

what are the 5 classes of tumour suppressant genes

A 
proteins that arrest cell cycle
enzymes that check and repair DNA
proteins that promote apoptosis
checkpoint control proteins
receptors/hormones that function to inhibit cell proliferation
86
Q

where is p53 located

A

chromosome 17

87
Q

how does p53 regulate cell division

A

binds DNA, stimulating p21 which binds to CDK-cyclin complex - inactivating it

88
Q

what is loss of heterozygosity

A

when there is an inherited mutation in a tumour suppressant gene but the other copy is normal
loss of the remaining functional allele of that gene is LOH

89
Q

what does LOH cause

A

breast cancer
colon cancer
retinoblastoma

90
Q

what causes retinoblastoma

A

mutation in the RB gene

91
Q

function of RB

A

regulates cell cycle entry

92
Q

genetic properties of RB

A

can be hereditary but is recessive

93
Q

what happens if LOH occurs to an individual with hereditary mutation in their RB gene

A

they become homozygous for the mutant RB gene and develop a tumour in the retina

94
Q

what is a direct acting mutagen

A

chemicals that react with nitrogen and oxygen in DNA to alter base pairing

95
Q

what is an indirect acting mutagen

A

has little mutagenic effect until modified by cellular enzymes

96
Q

where does squamous cell carcinomas arise from and what are the causes and a common element between them

A

arises from stratified squamous and non-squamous epithelial cells
alcohol, smoking, UV
oxidative stress

97
Q

what is a retrovirus and an example that causes cancer

A

RNA viruses that incorporate into the genome of the host

HTLV-1

98
Q

how is devil facial tumour spread

A

tumour cells passage between individuals during biting behaviours

99
Q

what can gene therapy do for cancer treatment

A

target cancer cells or surrounding cells

100
Q

what has accelerated cancer gene therapies

A

CRSPR/Cas9

101
Q

what is the difference between germ-line and somatic gene therapy in terms of offspring

A

unlike germ-line therapy, somatic gene therapy doesn’t pass on the permanent changes down to offspring

102
Q

what are the 2 strategies used to deal with diseases

A

1 - modify diseased cells to alleviate disease

2 - kill diseased cells

103
Q

when is gene augmentation implemented to treat disease

A

when the diseased cell is altered due to a loss of function mutation

104
Q

when is gene silencing used to treat diseases

A

when the diseased cell is altered due to a gain of function mutation

105
Q

how is gene silencing achieved

A

turning off gene transcription of the harmful gene

106
Q

what is gene repair

A

restoring normal gene function or to minimize effect of mutation

107
Q

how do you directly kill cells

A

directly targeting the harmful cells with a gene that will kill them - suicide gene

108
Q

explain indirect cell targeting

A

enhancing the immune systems response to the harmful gene - initiating cell death

109
Q

what are the 2 general methods for gene delivery

A

in-vivo - directly

ex-vivo - cell-based delivery

110
Q

why do short lived cells pose a challenge to gene therapy

A

short lived cells need to divide more often, and they may not pass on the desired genetic material leading to:
loss of therapeutic effectiveness

111
Q

what is a non-viral vehicle for gene delivery

A

liposomes

112
Q

what are the viral vehicles for gene therapy

A

retrovirus
lentivirus
adenovirus
adeno-associated virus

113
Q

what is needed to achieve high levels of expression

A

gene needs to be place in a plasmid expression vector

114
Q

why is the cytomegalovirus (CMV) promotor used in expression vectors

A

strongest promotor
drives transcription
works in all eukaryotic cells

115
Q

what is the polyadenylation (A) site for

A

efficient termination of transcription

116
Q

what expression vector contains cytomegalovirus promotor

A

pJ7

117
Q

what happens when the plasmid enters the nucleus

A

RNA polymerase binds to cytomegalovirus transcription
the RNA is cleaved and polyadenylated
then its spliced

118
Q

why is plasmid entry into the nucleus very inefficient

A

due to the plasmid size it cannot pass through the nuclear pores

119
Q

what are the methods used to get plasmids to enter the nucleus

A
  • conjugating specific DNA or protein sequences that are known to facilitate nuclear transport
  • compacting the DNA so that its small enough to enter via the nuclear pores
120
Q

how many people does cystic fibrosis affect

A

1/2500

121
Q

what are the disadvantages of using liposomes for gene transfer

A
  • inefficient transfer of DNA to target cells
  • cannot target particular cell types
  • poor expression
122
Q

what is a capsid

A

surrounds genetic material in a virus

123
Q

what is the retrovirus genome

A

ssDNA

7-9Kb

124
Q

in a retrovirus what do the 3 regions code for
GAG
POL
ENV

A

GAG - capsid proteins
POL - reverse transcriptase
ENV - envelope proteins

125
Q

what are most retrovirus used for gene therapy used for

A

moloney murine leukaemia virus (MoMLV)

126
Q

how is a viral vector packaged

A

using a packaging line

127
Q

what is ADA deficiency

A

defective adenosine deaminase gene

ADA codes for a gene in the purine salvage pathway

128
Q

what is most affected by dATP

A

T-lymphocytes

129
Q

advantages of retroviral vectors

A

high efficiency of gene transfer

high levels of expression

130
Q

disadvantages of retroviral vectors

A

max insert is 7-7.5kb
only infects dividing cells
toxic - insertional mutagenesis

130
Q

disadvantages of retroviral vectors

A

max insert is 7-7.5kb
only infects dividing cells
toxic - insertional mutagenesis

131
Q

what is a risk of being treated for severe combined immunodeficiency using retroviral vectors

A

high level of constitutive expression of proto-oncogenes

causes cancer

132
Q

what is the genome of lentivirus

A

ssRNA

around 9Kb

133
Q

how is the safety profile of lentiviruses increased compared to retroviruses

A

engineered to reduce the strength of promotors and enhancers to reduce the risk of proto-oncogene expression

134
Q

what is the genome of adenovirus

A

dsDNA

around 36Kb

135
Q

what is the life cycle of adenoviruses

A

1 - early genes are expressed E1a and E1b
2 - expression of E1-E4 followed by viral DNA replication
3 - expression of late genes
4 - packaging of new virus particles and cell lysis

136
Q

what happens to first generation adenoviral vectors

A

E1 and E3 removed to allow insertion of transgene and to stop viral replication
low level transcription of viral genes
led to innate host response
cloning capacity of 7.5Kb

137
Q

what happens to second generation adenoviral vectors

A

all early genes deleted
have decreased toxicity and prolonged gene expression
cloning capacity of 35Kb

138
Q

disadvantages of adenoviral vectors

A

do not insert genes into host chromosome
temporary protein expression
doesn’t work well on dividing cells
requires repeat treatment

139
Q

what naturally occurring mechanism does gene silencing take advantage of

A

RNA interference (RNAi)

140
Q

what triggers gene silencing

A

double stranded RNA

141
Q

what are the components of gene silencing

A

ribonuclease - dicer
siRNA - short interfering RNA
RISC - RNA induced silencing complex

142
Q

what is direct siRNA therapy

A

synthesis of RNA oligonucleotides that are complementary to the target transcript
formation of a double stranded siRNA duplex
packaged into a liposome for delivery across the lipid bilayer

143
Q

how is shRNA converted into siRNA

A

a gene with inverted repeats is transcribed in the nucleus as short hairpin RNA
dicer cleaves it to create siRNA

144
Q

disadvantages of RNAi therapy

A

risk of off-target effects

delivering sufficient RNA to target cells can be difficult

145
Q

what model organism is used for cancer

A

oryzias latipes

146
Q

what model organisms are used for behaviour

A

rattus norvegicus

macaca mulatta

147
Q

what model organism is a gram negative gut bacteria

A

escherichia coli

148
Q

how many genes does eschericha coli have

A

4500

149
Q

what is the life cycle of eschericha coli

A

20 minutes

at 37 degrees

150
Q

what is the yeast model organism

A

saccharomyces cerevisiae

151
Q

what is the life cycle and gene number of saccharomyces cerevisiae

A

6000

1.5-2 hour life cycle

152
Q

what is the chromosome number and gene number size of caenorrhabditis elegans

A

6 chromosomes

20,000

153
Q

what is the life cycle of caenorrhabditis elegans

A

3 days

154
Q

how many chromosomes and what is the gene number of the drosophila melanogaster

A

4 chromosomes

14,000 genes

155
Q

what is the life cycle of the drosophila melanogaster

A

10-14 days

156
Q

what is the danio rerio model

A

a fish

157
Q

what is the gene number and chromosome number of a danio rerio

A

25

26,000

158
Q

what is the life cycle of the danio rerio

A

3 months

159
Q

chromosome number and gene number of mus muculus

A

20

23,000

160
Q

life cycle of the mus musculus

A

2 months

Biomed (9 decks)

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