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genomics Flashcards

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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
how internal carotid artery go ro brain level
neck to cranial cavity via carotid canal- into cavernous sinus- out sinus to opric chiasma
26
what does anterior communicating connect
both anterior cerebral arteries
27
what does posterior communicating connect
posterior cerebral artery which branches of basilar artyery with the internal carotid at point internal carotid bifurcates
28
what happens when cerebral blood flow is reduced
stimulates release of vasoactive substances to cause arterial dilatation
29
what is haemorrhagic stroke
weakened blood vessel in brain has burst
30
where does anterior cerebral supply and what happens when block
supply primary motor cortex for lower limb | blockages/ no blood supply lead to incontinence(pee himself)as cant control pelvic floor muscle
31
what does middle cerebral supply and what does blockage do
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
what posterior cerebral supply and blockage affect
supply primary visual cortex, hippocampus block- visual field defect and memory loss
33
during implanation what hormone faciliatates increase in desidual cell size
progesterone
34
when desidual cells enlarge what are the coated with
glycogen and lipid rich fluid
35
how is blood exhnaged between mother and blastocyst
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
where does hcg come from
placenta
37
when is hcg present during pregnancy
from fertilisation till 13 weeks very high then reduces and low throughout pregnancy
38
what does hcg bind to
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
from 0-7 week what produces e2+ prog and after 7 weeks what does this too
``` 0-7= corpus leuteum 7+= placenta ```
40
placenta produce HPL- start at week 7- what does this do
countercat maternal insulin by downregulating it so more gluscose avb for foetus
41
why during pregnancy mother develop diabetes
HPL can casue insulin resistance
42
what makes placenta good at its job
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
what is placental previa
implant in lower uterus, fully or partially covering the internal cervical os
44
risk factors of placental previa
``` RISK FACTORSPrevious caesarean delivery Previous uterine/endometrial surgery Uterine fibroids Previous placenta previa Smoking & recreational drug use Multiple gestation Maternal age >35yo ```
45
what is placetal abruption and what cuases
``` 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
riskn. factors of placental abruption
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
what is pre eclampsia and causes
inadequate maternal blood flow to the placenta during pregnancy. • Causes new onset maternal hypertension and proteinuria.
48
pre eclampsia risk factors
``` RISK FACTORS First pregnancy Multiple gestation Maternal age >35yo Hypertension Diabetes Obesity Family history of pre-eclampsia ```
49
outline what is required for implantation
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
what are steps of implanataion
apposition, attachement, invasion
51
what percent of genome codes for protein. a. 3 b. 5 c. 2 d. 6
c
52
how is snp generated
mismatch repair during DNA replication change parental allele instead and so passed onto daughter cell-- next gen (metogenesis)
53
where is snp mainly not found
exome
54
what disease is both deliterious but also beenfical
sickle cell anemia as provide protection from malaria
55
what is a microsatellite
short tandom repeat
56
what causes microsatellite
polymerase slippage form bubble, when repaired bubble straightnened= elongation of genome
57
example of microsatellite disease
huningtons disease
58
cause of copy number variant
non-allelic recombination results in duplication/deletion and copy number change during meiosis( chunks of genome deleted or repeated)
59
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)
cnv,microsattelites,snp
60
why is newborn uterus larger than infant uterus
as a foetus was exposed to lots of e2 so lead to proliferation of endometrium
61
where does fertilisation occur
ampulls
62
how long does take for embryo to reach endometrium for implantation
5-6 days
63
what size is oocyte
100 micro metres in size
64
define tortosuity
ratio of actual flow path length to the straight distance between the ends of the flow path
65
what alters the viccosity of cervix
Cervical mucus is less viscous in the absence of progesterone and high e2 allowing sperm to pass.
66
what is puerperium
period after mother gives birth that body returns to normal
67
what are the cascade of events following ovulation
– 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
what increases chance of dominant follicle surviving fsh intecycle
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
overall role of HPG axis
instigate and coordinate puberty/ gonadarche and maintain fertility
70
what type of bone does body mostly have
cortical- macroscrapic structure- highly calcified
71
during bone resorption what breaks inorganic and organic portion of the bone
inorganic-- acid | organic-enzyme

genomics (1 decks)

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