genomics Flashcards

1
Q

how can shearing be achieved

A

chemically, enzymatically or physically

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2
Q

what are adaptors

A

collection of components that bind to dna library to allow library fragments to be sequenced

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3
Q

what are components of adaptor and what they do

A

Anchor: attach dna fragments to flow cell fo seq later

primer binding site: facilitate seq. y synthessi reation

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4
Q

is hybridization to flow cell a selective process

A

no is random

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5
Q

what type of amplification occurs during cluster generation

a. pcr amp
b. sonic amp
c. bridge amp
d. temporal amp

A

c

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6
Q

what are bases modified with

a. terminators, condensor
b. insulators, enhancers
c. instigators, histones
d. terminators, dye

A
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7
Q

what is one use of ngs

A

find variant comparing consensus seq( seq underwent ngs) with human sequence refernce

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8
Q

two differences between ngs V sanger

A
Ngs= consensus seq.... sanger= one seq read
ngs= digital readout .....sanger= analogue readout
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9
Q

in wes what captures target regions (exons)

A

baits. magnetic beads

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10
Q
during what step of wes polymorphisms found
a. seq read allignment
b.target coverage capture
c variant calling
d. variant annotation
A

c

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11
Q

ngs uses

A

disease gene identfication in famliy in wes

RNA seq-discover isoforms of genes dif exp and reg and so measure gene abundance

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12
Q

during dna seq what type of rpimer is only used

A

single forward primer making amp limited and not exponential

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13
Q

what does dna polymerase require to work

A

mg2+ cofactor
buffer for correct pH balance( need to increase pH due to h+ release during phosphodiester bond formation)
, DTP,
free 3’OH on primer. (form link with phospahte group of DNTP), template strand extending past primer

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14
Q

direction of elongation of strand
a. 5’ to 3’
b 3’ to 5’

A

a

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15
Q

what reaction happen in elongation ***

A

Hydrolysation of DnTP so phosphate bind to 3’OH primer forming a phosphodiester bond and as aresult release an inorganic pyrophospate and h+ from 3’oh

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16
Q

how elongation halted

A

incorporation of ddntp
polymerase cant distinguish between DNTP and DDNTP as both have triphosphate group and so a phosphodiester bond is formed between 3’oh and DDntp .
no more binding past this point as DDNTP has missing 2 OH group at 2’,3’ carbon where phoshodiester bond shoulf occur with 5’ triphoshate
BUT have low frequency of DDNTP and So low ratio compared to DNTP to decrease chance of termination

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17
Q

how sequence read

A

ddntp flouresce colour at end
all seq arranged in order of size
last dntp show which base is and what is bound to as is comp and so determine seq

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18
Q
which 3 are roles of cerebellum
a. refine learned movement patterns
b refine innate movement patterm
c. maintain balance
d. coordinates complex somatic motor patterns
A

a c d

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19
Q

what does brainstem do

A

acts as processing and relay centre for info passing to and from cerebrum and cerebellum

has reflex centres which are associated with respiratory and cardiovascular functions

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20
Q

what parts of brain make up diencephalon

A

dorsal thalamus

ventral hypothalamus

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21
Q

what arteries supply brain
a. 2 internal carotid, 2 vertebral arteries
b 2. external carotid, 2 vertebal arteries
c. 1 internal carotid, 1 vertebral arteries
d. 1 external carotid, 1 vertebral arterie

A

a

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22
Q

whayt does internal carotid bifurcate into

A

anterior and middle cerebrsl artieres

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23
Q

what does vertebral arteries bifuyrcate into

A

basilar artery

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24
Q

how vertebral artery acend to brain

A

in neck through foramina- into cranial cavity through foramen magnum

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25
Q

how internal carotid artery go ro brain level

A

neck to cranial cavity via carotid canal- into cavernous sinus- out sinus to opric chiasma

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26
Q

what does anterior communicating connect

A

both anterior cerebral arteries

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27
Q

what does posterior communicating connect

A

posterior cerebral artery which branches of basilar artyery with the internal carotid at point internal carotid bifurcates

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28
Q

what happens when cerebral blood flow is reduced

A

stimulates release of vasoactive substances to cause arterial dilatation

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29
Q

what is haemorrhagic stroke

A

weakened blood vessel in brain has burst

30
Q

where does anterior cerebral supply and what happens when block

A

supply primary motor cortex for lower limb

blockages/ no blood supply lead to incontinence(pee himself)as cant control pelvic floor muscle

31
Q

what does middle cerebral supply and what does blockage do

A

broca and wernickes, motor cortex
blockage= loss of sensation and motor function for everywhere except lower limb

effect speach and ability to understand speech

32
Q

what posterior cerebral supply and blockage affect

A

supply primary visual cortex, hippocampus

block- visual field defect and memory loss

33
Q

during implanation what hormone faciliatates increase in desidual cell size

A

progesterone

34
Q

when desidual cells enlarge what are the coated with

A

glycogen and lipid rich fluid

35
Q

how is blood exhnaged between mother and blastocyst

A

a region called junctional zone is created. it is composed of blastocyst surrounded by protrusions known as primary villi. between primary villi gaps are left called ‘Lucanae’ and blood fills here as veins and arteries connect to this point

36
Q

where does hcg come from

A

placenta

37
Q

when is hcg present during pregnancy

A

from fertilisation till 13 weeks very high then reduces and low throughout pregnancy

38
Q

what does hcg bind to

A

LH R of corpus leuteum and by doing so stimulates e2 and prog release in a low e2 ratio: high prog to mainatin pregnancy

39
Q

from 0-7 week what produces e2+ prog and after 7 weeks what does this too

A
0-7= corpus leuteum
7+= placenta
40
Q

placenta produce HPL- start at week 7- what does this do

A

countercat maternal insulin by downregulating it so more gluscose avb for foetus

41
Q

why during pregnancy mother develop diabetes

A

HPL can casue insulin resistance

42
Q

what makes placenta good at its job

A
  1. blood flow at low pressure allowing efficient filtration
  2. huge reserve of cholesterol which is a precursor for all hormones made here sent to mother except HPL
  3. large SA created by cotyledons
43
Q

what is placental previa

A

implant in lower uterus,
fully or partially covering the
internal cervical os

44
Q

risk factors of placental previa

A
RISK FACTORSPrevious caesarean delivery
Previous uterine/endometrial surgery
Uterine fibroids
Previous placenta previa 
Smoking & recreational drug use
Multiple gestation
Maternal age >35yo
45
Q

what is placetal abruption and what cuases

A
Premature separation 
of all or part of the 
placenta. 
aused by the degeneration of 
maternal arteries supplying blood to 
the placenta.

• Degenerated vessels rupture causing
haemorrhage and separation of the
placenta.

46
Q

riskn. factors of placental abruption

A

RISK FACTORS Blunt force trauma e.g. car crash, fall
 Smoking & recreational drug use – risk of
vasoconstriction and increased blood pressure.
 Multiple gestation
 Maternal age >35yo
 Previous placental abruption

47
Q

what is pre eclampsia and causes

A

inadequate
maternal blood flow to the placenta during pregnancy.
• Causes new onset maternal hypertension and
proteinuria.

48
Q

pre eclampsia risk factors

A
RISK FACTORS
First pregnancy
Multiple gestation
Maternal age >35yo
Hypertension
Diabetes
Obesity
Family history of pre-eclampsia
49
Q

outline what is required for implantation

A

thickened endometrium with increased embryo markers
fully developed blatocyst containing: trophoblast(become placenta), blastoceal(fluid), embryoblast ( foetus become) which has left zona peliculada as that has been digested by enzymes

50
Q

what are steps of implanataion

A

apposition, attachement, invasion

51
Q

what percent of genome codes for protein.

a. 3
b. 5
c. 2
d. 6

A

c

52
Q

how is snp generated

A

mismatch repair during DNA replication change parental allele instead and so passed onto daughter cell– next gen (metogenesis)

53
Q

where is snp mainly not found

A

exome

54
Q

what disease is both deliterious but also beenfical

A

sickle cell anemia as provide protection from malaria

55
Q

what is a microsatellite

A

short tandom repeat

56
Q

what causes microsatellite

A

polymerase slippage form bubble, when repaired bubble straightnened= elongation of genome

57
Q

example of microsatellite disease

A

huningtons disease

58
Q

cause of copy number variant

A

non-allelic recombination results in duplication/deletion and copy number change during meiosis( chunks of genome deleted or repeated)

59
Q

Most common variants not causing Mendelian, monogenic disorders.

Majority are probably neutral (particularly intergenic variants).- cnv
BUT!
May well impact upon complex, non-Mendelian disorders and undoubtedly
contribute to general individual variation (personality, sporting ability, looks etc)

A

cnv,microsattelites,snp

60
Q

why is newborn uterus larger than infant uterus

A

as a foetus was exposed to lots of e2 so lead to proliferation of endometrium

61
Q

where does fertilisation occur

A

ampulls

62
Q

how long does take for embryo to reach endometrium for implantation

A

5-6 days

63
Q

what size is oocyte

A

100 micro metres in size

64
Q

define tortosuity

A

ratio of actual flow path length to the straight distance between the ends of the flow path

65
Q

what alters the viccosity of cervix

A

Cervical mucus is less viscous in the absence of progesterone and high e2
allowing sperm to pass.

66
Q

what is puerperium

A

period after mother gives birth that body returns to normal

67
Q

what are the cascade of events following ovulation

A

– blood flow to the follicle increases dramatically
– appearance of apex or stigma on ovary wall
– Local release of proteases and inflammatory mediators
– Enzymatic breakdown of protein of the ovary wall

68
Q

what increases chance of dominant follicle surviving fsh intecycle

A

Increased sensitivity to FSH as more FSH R
more granulosa cells therefore produce more E2
LH R present- this occurs as FSH switches on the gene to do this

69
Q

overall role of HPG axis

A

instigate and coordinate puberty/ gonadarche and maintain fertility

70
Q

what type of bone does body mostly have

A

cortical- macroscrapic structure- highly calcified

71
Q

during bone resorption what breaks inorganic and organic portion of the bone

A

inorganic– acid

organic-enzyme