genomics Flashcards
how can shearing be achieved
chemically, enzymatically or physically
what are adaptors
collection of components that bind to dna library to allow library fragments to be sequenced
what are components of adaptor and what they do
Anchor: attach dna fragments to flow cell fo seq later
primer binding site: facilitate seq. y synthessi reation
is hybridization to flow cell a selective process
no is random
what type of amplification occurs during cluster generation
a. pcr amp
b. sonic amp
c. bridge amp
d. temporal amp
c
what are bases modified with
a. terminators, condensor
b. insulators, enhancers
c. instigators, histones
d. terminators, dye
what is one use of ngs
find variant comparing consensus seq( seq underwent ngs) with human sequence refernce
two differences between ngs V sanger
Ngs= consensus seq.... sanger= one seq read ngs= digital readout .....sanger= analogue readout
in wes what captures target regions (exons)
baits. magnetic beads
during what step of wes polymorphisms found a. seq read allignment b.target coverage capture c variant calling d. variant annotation
c
ngs uses
disease gene identfication in famliy in wes
RNA seq-discover isoforms of genes dif exp and reg and so measure gene abundance
during dna seq what type of rpimer is only used
single forward primer making amp limited and not exponential
what does dna polymerase require to work
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
direction of elongation of strand
a. 5’ to 3’
b 3’ to 5’
a
what reaction happen in elongation ***
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
how elongation halted
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
how sequence read
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
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 c d
what does brainstem do
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
what parts of brain make up diencephalon
dorsal thalamus
ventral hypothalamus
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
whayt does internal carotid bifurcate into
anterior and middle cerebrsl artieres
what does vertebral arteries bifuyrcate into
basilar artery
how vertebral artery acend to brain
in neck through foramina- into cranial cavity through foramen magnum
how internal carotid artery go ro brain level
neck to cranial cavity via carotid canal- into cavernous sinus- out sinus to opric chiasma
what does anterior communicating connect
both anterior cerebral arteries
what does posterior communicating connect
posterior cerebral artery which branches of basilar artyery with the internal carotid at point internal carotid bifurcates
what happens when cerebral blood flow is reduced
stimulates release of vasoactive substances to cause arterial dilatation
what is haemorrhagic stroke
weakened blood vessel in brain has burst
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
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
what posterior cerebral supply and blockage affect
supply primary visual cortex, hippocampus
block- visual field defect and memory loss
during implanation what hormone faciliatates increase in desidual cell size
progesterone
when desidual cells enlarge what are the coated with
glycogen and lipid rich fluid
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
where does hcg come from
placenta
when is hcg present during pregnancy
from fertilisation till 13 weeks very high then reduces and low throughout pregnancy
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
from 0-7 week what produces e2+ prog and after 7 weeks what does this too
0-7= corpus leuteum 7+= placenta
placenta produce HPL- start at week 7- what does this do
countercat maternal insulin by downregulating it so more gluscose avb for foetus
why during pregnancy mother develop diabetes
HPL can casue insulin resistance
what makes placenta good at its job
- blood flow at low pressure allowing efficient filtration
- huge reserve of cholesterol which is a precursor for all hormones made here sent to mother except HPL
- large SA created by cotyledons
what is placental previa
implant in lower uterus,
fully or partially covering the
internal cervical os
risk factors of placental previa
RISK FACTORSPrevious caesarean delivery Previous uterine/endometrial surgery Uterine fibroids Previous placenta previa Smoking & recreational drug use Multiple gestation Maternal age >35yo
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.
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
what is pre eclampsia and causes
inadequate
maternal blood flow to the placenta during pregnancy.
• Causes new onset maternal hypertension and
proteinuria.
pre eclampsia risk factors
RISK FACTORS First pregnancy Multiple gestation Maternal age >35yo Hypertension Diabetes Obesity Family history of pre-eclampsia
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
what are steps of implanataion
apposition, attachement, invasion
what percent of genome codes for protein.
a. 3
b. 5
c. 2
d. 6
c
how is snp generated
mismatch repair during DNA replication change parental allele instead and so passed onto daughter cell– next gen (metogenesis)
where is snp mainly not found
exome
what disease is both deliterious but also beenfical
sickle cell anemia as provide protection from malaria
what is a microsatellite
short tandom repeat
what causes microsatellite
polymerase slippage form bubble, when repaired bubble straightnened= elongation of genome
example of microsatellite disease
huningtons disease
cause of copy number variant
non-allelic recombination results in duplication/deletion and copy number change during meiosis( chunks of genome deleted or repeated)
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
why is newborn uterus larger than infant uterus
as a foetus was exposed to lots of e2 so lead to proliferation of endometrium
where does fertilisation occur
ampulls
how long does take for embryo to reach endometrium for implantation
5-6 days
what size is oocyte
100 micro metres in size
define tortosuity
ratio of actual flow path length to the straight distance between the ends of the flow path
what alters the viccosity of cervix
Cervical mucus is less viscous in the absence of progesterone and high e2
allowing sperm to pass.
what is puerperium
period after mother gives birth that body returns to normal
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
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
overall role of HPG axis
instigate and coordinate puberty/ gonadarche and maintain fertility
what type of bone does body mostly have
cortical- macroscrapic structure- highly calcified
during bone resorption what breaks inorganic and organic portion of the bone
inorganic– acid
organic-enzyme
