Unit 2 Part II Flashcards
a parent is a known carrier of a structural chromosome rearrangement or there is a previous child with a chromosome abnormality
familial abnormality
ONTD
open neural tube defect
recurrence risk if you already have one child with ONTD
2-5% (multifactorial, genetic component
largest portion of abortuses are due to which chromosome abnormality
trisomies, followed by 45, X
what is the trisomy that causes the most abortuses
trisomy 16
what percentage of 45, X conceptions spontaneously terminate
95%
two types of non invasive prenatal tests
examination, ultrasound
three types of invasive prenatal tests
cytogenetics, biochemical, molecular studies
this test can: detect multiple pregnancy, determine gestational age, determine the sex, identify possible abnormalities, may indicate further testing is needed
ultrasound
when is ultrasound usually performed during the pregnancy
18 weeks gestation
what is a nuchal translucency thickness of 6mm observed by ultrasound associated with
Down Syndrome
what test is used to detect a cleft lip
ultrasound
absence of brain caused by severe ONTD
anencephaly
brain outside of head caused by severe ONTD
encephalocele
MSAFP
maternal serum alpha fetal protein, an albumin produced by fetal liver
how is AFP detected in the maternal circulation
it crosses the placenta from the fetus into the mother
AFP level is likely to be (higher/lower) in a heavy set woman because the assay gives a result in amount per unit volume
lower
factors that affect MSAFP
gestational age (usually do it at 16-18 weeks), mother’s weight, maternal diabetes, diabetic status, race
low levels of MSAFP may risk of
Down syndrome and other chromosome abnormalities
high levels of MSAFP may risk of
ONTD
maternal serum quad test performed at 15-21 weeks
since AFP tests only give risks, combine with other tests to get closer to a diagnosis
PAPP test performed at 10-13 weeks, when low, is associated with risk of
Down Syndrome
non invasive prenatal screening uses _____ for testing
cell free placental DNA–free floating DNA comprised of DNA from mother and fetus
what percent of the cfpDNA is from fetus
about 15%
detection of anuesomy using cfpDNA is a (screening/diagnostic) test
screening
2 confirming diagnostic tests when the result is out of the normal range for a cfpDNA test
FISH, karyotype analysis performed on amniotic fluid collected by amniocentesis
a procedure where a needle is inserted through the abdomen into the amniotic cavity and withdrawing amniotic fluid
amniocentesis
at what age is amniocentesis usually performed
16-18 weeks
what is the risk of doing amniocentesis early at 13 weeks
less fluid in the cavity, removing fluid can limit the mobility of the fetus, could lead to developmental defects
AFAFP
amniotic fluid alpha fetal protein
low AFAFP levels indicate
chromosomal abnormalities
elevated AFAFP levels indicate
ONTD, MZ twins, fetal death, body wall defect, anencephaly
elevated MSAFP levels but not elevated AFAFP levels
DZ twins, small mother
closed neural tube defects present as (high/normal/low) AFP levels in mom and amniotic fluid
normal
confirmatory test if you see elevated AFP
acetylcholinesterase
why would acetylcholinesterase be present in amniotic fluid
if there is a defect in the neural tube
confirmatory test if you see low AFP
karyotype analysis
CVS testing
chorionic villi sampling
risk of fetal loss in CVS testing
1 in 100
what does the CVS sample
the placenta
how do you confirm abnormal CVS result
amniocentesis
if a mosaicism occurs, what makes it possible that CVS will work
the mosaicism must occur in both placental and fetal cells
when only part of the placenta has a mutation and the mutation is not in the fetus
confined placental mosaicism
implications of CVS testing with a confined fetal mutation mosaic
the CVS testing may miss the mutation
when is CVS the method of choice despite risks
if you want to know early on if there is a problem so you have the option to terminate the pregnancy
when would a trisomy in an uncle not affect the fetus
if it’s a nondisjunction error and not heritable
when would a trisomy in an uncle affect the fetus
if there’s a Robertsonian translocation and heritable
why use polar body analysis
when it is known that one or both partners carry a gene mutation, like with CF. the mutation may be in the polar body, so then you can use the egg. if it’s not in the polar body, then it’s in the egg, so don’t use that egg.
preimplantation genetic diagnosis
test the 8 cell stage of the developing embryo–take one cell out and do the general assay to look for chromosomal aneuploidies
what to do if mom has known mitochondrial disease
enucleate a donor egg and use donor cytoplasm, mom’s nucleus
risky prenatal tests
amniocentesis, CVS
why would you perform a risky prenatal test
if a parent has a structural abnormality
a dizygotic twin pregnancy (does/does not) elevate amniotic fluid alpha fetoprotein
does not
prenatal diagnosis (can/cannot) identify males with huntington disease
cannot
when do most couples learn that they are both carriers for CF
after they have an affected child
tumors such as leukemias are known as ___ tumors
dispersed
uncontrolled cell growth characterized by a change in the normal organizational pattern of tissues or cells
malignancy
when cells become invasive or migrate to another site
metastasis
cancer of mesenchymal tissue (bone, cartilage, muscle, fat)
sarcoma
cancer of epitheloid tissues
carcinoma
cancer of bone marrow
leukemia
cancer of lymph and spleen
lymphoma
a primary cancer in a secondary location is known by the __classification
primary
gain, loss, or rearrangement of chromosomes
chromosome instability CIN
a dominantly acting gene involved in unregulated growth and proliferation
oncogene
how are oncogenes carried
by viruses
two ways to get an oncogene
mutation of proto-oncogene, from virus
structurally important “housekeeping genes” involved in cell proliferation and development
proto oncogene
proto oncogenes code for: (five things)
growth factors, cell surface receptors, intracellular signal transduction, DNA binding proteins (transcription), regulation of cell cycle
activation of proto-oncogene
mutation to its oncogene potential
(gain/loss) of function mutation in proto oncogene tumorigenesis
gain of function
number of alleles that must be mutated to activate a proto oncogene
one
genetic marker associated with chronic myelogenous leukemia
translocation between chromosome 9 and 22
type of translocation involved in chronic myelogenous leukemia
imbalanced–breaks within two genes and gets rearranged, promoter from one gene and coding from another > chimera
diagnostic marker of chronic myelogenous leukemia
Philadelphia chromosome
what does the 9;22 translocation in chronic myelogenous leukemia produce
an abnormal tyrosine kinase
how have negative side effects been minimized in chronic myelogenous leukemia
drug that targets aberrant tyrosine kinase specifically (targeted to a specific genetic lesion)
how is acute promyelocytic leukemia detected
FISH probe flanks break point of translocation
positive FISH result that indicates acute promyelocytic leukemia
yellow fusion signal
genetic element whose loss or inactivation allows the cell to display an alternate phenotype leading to neoplastic growth
tumor suppressor
(gain/loss) of function in tumor supressor gene tumorigenesis
loss of function
number of alleles that must be mutated to lose function in a tumor suppressor
two (recessive)
type of tumor suppressor gene that suppresses tumors by regulating cell cycle or growth inhibition
gate keeper
type of tumor suppressor gene that repairs DNA damage and maintains genomic integrity
caretaker
why is effect of loss of function of a tumor suppressor indirect
loss of this function may not be directly linked to disease
tumor suppressor genes are usually involved in growth of ____ tumors (solid/dispersed)
solid
classic gatekeeper mutation, functions in regulation of cell cycle, controls progression from G1 to S
Rb1
disease caused by mutation of Rb1 on chromosome 13
retinoblastoma
onset of retinoblastoma
prenatal-5 years old
sporadic mutations of Rb1 usually result in (uni/bi) lateral retinoblastoma
unilateral
inherited mutations of Rb1 often result in (uni/bi) lateral retinoblastoma
bilateral
secondary cancer caused by Rb1 mutation
osteosarcoma (teen years)
if someone has one mutation inherited for Rb1, it is likely that the second mutation will be (somatic/inherited)
somatic
although only a single mutation of Rb1 is inherited, there is a high likelihood that a second mutation will occur, giving rise to a cell with 2 mutations. this gives the pedigree the appearance of dominance, when really the MOI is recessive
Knudson’s Two Hit Hypothesis
somatic mutations of tumor suppressor genes usually result in (older/younger) age of onset
older
familial mutations of tumor suppressor genes usually result in (older/younger) age of onset
younger
familial cancer syndrome, mutation of p53, associated with many different cancers
Li Fraumeni
why is breast cancer so devastating in males
they have no idea what’s happening
BRCA mutations are (gatekeeper/caretaker) mutations
caretaker
five breakage syndromes
fanconi anemia, bloom syndrome, ataxia telangiectasia, xeroderma pigmentosum, cockayne syndrome
moi breakage syndrome
recessive
why are breakage syndrome chromes so unstable
they lack DNA repair
type of malfunction in hereditary non polyposis colon cancer
MMR
indirect testing for hereditary non polyposis colon cancer uses
microsatellites
why is testing for hereditary non polyposis colon cancer indirect
don’t know where the mutations are
why is hereditary non polyposis colon cancer NOT a gene mutation
it is a malfunction in a normal cellular process (MMR) that in and of itself is not deleterious
why does Down syndrome increase risk for leukemia
AML gene is located on chromosome 21
two problems with allogenic stem cell use
graft v host, immunosuppression
NF1
inherited tumor suppressor
the stalk domain of influenza haemagglutinin is embedded into:
the surface of the viral capsid
two major antigenic proteins in the influenza virus
haemagglutinin and neuraminidase
purpose of influenza haemagglutinin
molecular harpoon–how flu virus binds to the surface of cells (via head domain)
other viruses that use harpooning mechanisms to gain entry to cells (influenza and….)
HIV, SARS, ebola
the mechanism of entry using a molecular harpoon
membrane distortion
____ ____ _____ can be developed that specifically target different steps in virus entry by harpooning mechanism
small molecule inhibitors
purpose of mirror image peptide
inhibits gp41, the harpoon in HIV
degrades proteins
proteasome
only functional form of the protein
folded (native) form
the information necessary for a protein to fold to its native three dimensional conformation is where
encoded in its amino acid sequence
to random coil and back to biologically active structure
reversible denaturation
protein is vulnerable to _____ when it is in partially folded conformations because they expose hydrophobic residues that have not yet been buried in the hydrophobic core
aggregation
monomeric collapse is driven largely by:
hydrophobic effect
folding defects can affect: (2 things)
the properties of N (structure or stability) or the pathway the unfolded molecule takes to reach N (N=native form)
hsp60
60 kilo dalton heat shock protein–chaperone
how does hsp70 chaperone protein folding
binds to proteins as they are being synthesized by ribosomes and protect against aggregation by covering up sticky hydrophobic pathes
how does hsp60 chaperone protein folding
monomers make a large donut, misfolded proteins enter the cavity. In the cavity, ATP hydrolysis is used to physically unfold the misfolded protein. Protein can refold properly while protected inside the cavity
type of proteins that require chaperones to fold
large, multidomain proteins
unfolding enzyme that combines isolation, forced unfolding, and confinement
GroEL/GroES
most common natural substrates for GroEL/GroES
mixed alpha/beta secondary structures
ubiquitin/proteasome pathway
regulates protein turnover/degradation
role of ubiquitin
targets proteins for degradation by covalent ligation
covalent ligation by ubiquitin requires
ATP
E (1/2/3) activates ubiquitin in an ATP driven reaction that creates a high energy, covalent, thioester bond
E1
E (1/2/3) transfers the activated ubiquitin to the target protein via a thioester intermediate
E2
E (1/2/3) catalyzes the final transfer to the epsilon amino group of one or more specific lysine residues on the target protein. Repeated to generate polyubiquitin chains of various lengths
E3
core structure of proteasome
double donut
regulatory particles on proteasome
caps
where polyubiquitinated proteins bind on the proteasome
the cap
four types of diseases of the ubiquitin proteasome pathway
cancer, neurodegenerative diseases (AD, Parkinson, HD), CF, autoimmune
improper processing of peptide antigens–ubiquitin proteasome pathway defect
autoimmune disease
diseases in which ubiquintinated proteins are observed in plaques, Lewy bodies…
neurodegenerative (AD, HD..)
diseases in which there is increased degradation of p52, p27
cancers (those are tumor suppressors)
a mutation of a residue that is essential for function
direct knockout
mutation that pushes the equilibrium toward the unfolded state
destabilization
mutation shifts the conformational eqbm to an incorrectly folded state
toxic conformation
transcription factor, activated by DNA damage, triggers cell cycle arrest or apoptosis, prevents accumulation of chromosomal mutations
p53
where most mutations on p53 are found that cause it to lose function
DNA binding domain
Zinc ion role in p53
necessary for site specific DNA binding
where does the p53 zinc ion fit into the DNA
minor groove
___-___ provides scaffold for helix and loop on p53
beta-clam
__ ___ ___ alter side chains that directly bind to DNA and act by reducing DNA binding without changing overall protein structure or stability
DNA contact mutants
(stability/contact) mutants do not change DNA binding residues, often very distant from binding site. They decrease thermodynamic stability by disrupting hydrophobic, vdw, electrostatic, H-bond interactions
stability
destabilizing mutations often cause proteins to _____
aggregate
most common outcome of missense mutations
loss of thermodynamic stability (eqbm constant between native and unfolded/partially folded forms of the protein)
why do destabilized p53 mutants accumulate in cancer cells to abnormally high levels
p53 activates transcription of its own E3 ubiquitin ligase, MDM2
p53’s own E3 ubiquitin ligase
MDM2
what is the purpose of the p53 negative feedback loop with MDM2
keeps p53 levels very low in healthy cells with wild type p53
how can cancer be treated using p53
restoring proper p53 expression leads to regression of a variety of lymphomas and sarcomas without affecting normal tissues (mouse model)
crevice binders
small molecules that stabilize mutant proteins by associating with a specific nook in a protein’s native structure
crevice binders are (specific/non specific) protein stabilizers
specific
small molecule action in blocking the interaction between p53 and MDM2
can bind either MDM2 side or p53 side–suppresses degradation of p53; a rising tide floats all boats–brings the overall p53 activity back up by raising the number, even if individually they don’t work that well
70% of CF cases are caused by deletion of:
Phe508 in the CF transmembrane conductance regulator
CF transmembrane conductance regulator function
gated chloride channel
in CF, Phe508 CFTR is (overexpressed/missing) in target tissues
missing
structure and function of wild type CFTR and the CFTR missing Phe508 are (similar/different)
similar–the mutant is just missing that one residue and there are a few turns that are different
primary defect caused by mutant -Phe508 in CF
alters the pathway by which CFTR folds and assembles
family of membrane proteins that CFTR belongs to
ABC transporters (ATP binding cassette)
where is protein folding arrested prematurely in the mutant CFTR
ER–which then tags it for degradation by the proteasome
treatment options for mutant CFTR
none yet–the proteins fold better at 25C but you’re already dead by then…other possibilities: small organic molecules, overexpressing chaperones, inhibiting degradation by ubiquitin-proteasome pathway, stimulating CFTR function
serine protease inhibitor
serpin
anitrypsin deficiency causes:
emphysema
principle target of serpin in anitrypsin
neutrophil elastase
where is neutrophil elastase released
sites of inflammation
how does unchecked neutrophil elastase activity lead to emphysema
excessive connective tissue damage occurs
bind to target protease and prevent it from binding substrate
serpins
mechanism of serpin
molecular mousetrap–uses stored energy to trap its target
(uncleaved/cleaved) antithrombin has tumor suppressing activity by inhibiting angiogenesis
cleaved
(uncleaved/cleaved) antithrombin has protease activity
uncleaved
where does the reactive center loop on a1-anitrypsin want to end up after cleaving
on the inside–wants to be a beta strand, not on the outside
S-type a1-anitrypsin mutation results in:
protein not being able to H-bond, makes beta sheet more vulnerable to misinsertion
how does polymerization of mutant a1-anitrypsin occur in the liver
central beta sheet aberrantly opens and allows part of the reactive loop of a second protein to insert into the lower portion of the sheet
insertion of the RCL (reactive center loop) of a1-anitrypsin is (reversible/irreversible)
irreversible–once inserted, it never comes back out
how do mutant a1-anitrypsin polymers cause disease in the liver
these polymers cannot be cleared from the liver and accumulate, eventually causing liver failure
how can a1-anitrypsin polymer formation be blocked/reversed?
by peptides that correspond to portions of the reactive center loop–they bind the beta sheet where part of the RCL from a second antitrypsin molecule would occupy
a group of fatal, progressive, degenerative diseases of the central nervous system by infection with a prion
transmissible spongiform encephalopathies
an alternate form of a normal brain protein
prion
most definitive test of most neurogenerative diseases
post-mortem staining (reveals amyloid plaques)
infectivity of TSE (reduced/not reduced) by irradiation, heat
not reduced
