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
infectivity of TSE (reduced/not reduced) by NaOH, other protein denaturants
reduced
208 residue glycoprotein of unknown function expressed in brain and many other organs
prion protein
soluble, protease sensitive PrP
PrPc, non pathogenic
PrPc alpha helix: beta sheet ratio
lots of alpha: little beta
PrPsc alpha helix: beta sheet ratio
less alpha: more beta
insoluble, protease insensitive PrP
PrPsc
the two forms of PrPc and PrPsc interconvert with an eqbm that favors the ___ form
PrPc
when several molecules of ____ come in contact (very rare), they can bind via (alpha helix/beta sheet) interaction
PrPsc, beta sheet (blob tag)
result of PrPsc blob tag
stabilized beta sheet structure that does not dissociate readily and adds more converted monomers quickly
____ studies support protein-only model
transgenic
putting purified infectious amyloid protein into mouse
seeding of nucleus
why don’t we all have TSE’s
species barrier
what experiment proved the TSE species barrier
infecting healthy hamsters or mice with amyloid fibers taken from diseased hamsters or mice–wild type mouse was immune to hamster amyloid
transgenic mouse response to hamster amyloid
normal mouse except it has PrP hamster genes–not immune to hamster amyloid
molecular structure that is the culprit of TSE
beta sheet
potential therapy for TSE: made chimeric mice using stem cells expressing shRNA against PrPc (lentivirus vector)
siRNA silencing of PrPc
three potential therapies for TSE:
siRNA silencing of PrPc, stabilizing PrPc (prevent it from converting to toxic form), immunotherapy
how do you generate an immune response to PrP
use a PrP-PrP dimer, generates CD4 and CD8 T cell response in mice
what enzyme cleaves APP to yield an Alzheimer AB peptide
secretases
correctly cleaved APP eliminates possibility of (AB40/AB42)
AB42
Alzheimer plaques: virtually all amyloid fibers are (AB40/AB42)
AB42
triplication of the __ gene, either alone or with _____ (chromosomal abnormality), leads to AD
APP, trisomy 21
two hypotheses by which AB42 leads to neuronal cell death–what is the toxic species
1-the toxic species is made of small, soluble aggregates of the misfolded peptide that form before the mature fibril
2-the toxic species is the mature amyloid fibril
in the hypothesis that states that the toxic species in AD is made of small, soluble aggregates of the misfolded peptide that form before the mature amyloid fibril, what is the role of the amyloid fibril
by product of the disease or may even be protective
the structure of AB42 in its amyloid fibril form consists of (a parallel/an antiparallel) beta sheet
parallel in register beta sheet
stabilizing interactions in the AB42 beta sheet are (hydrophobic/hydrophilic)
hydrophobic
what is the target of Alzheimer treatments
eliminate AB42
mutations in (alpha/beta/gamma) secretases are associated with early onset AD
gamma
why did modulating gamma secretase activity not work as an effective treatment for AD
gamma secretase cleaves other important stuff
how would amyloid fibrils theoretically have a protective role
they would act as a sink for the real toxic species, the pre-fibrillar soluble aggregates
why are pigs resistant to diabetes
their islet amyloid polypeptide differs from human IAPP by ten amino acids
potential treatment for diabetes
transplantation of pig islet cells
structure of islet amyloid polypeptide in aqueous solution
no detectable structure
islet amyloid polypeptide is known to bind:
lipid bilayers
although islet amyloid polypeptide is structureless, it has ______ tendencies which give a hint about how it interacts with the membrane
helical–a hydrophobic face is apparent
how does a peptide inhibit the beta sheet from becoming the amyloid fibrillar state
caps the beta sheet by methylation before it reaches the fiber state–can no longer H bond with nearby side chains or peptides
soluble oligomers of IAPP (islet amyloid polypeptide) are (less/more) toxic than mature fibrils
more
how do the soluble oligos cause cell death–2 hypotheses
1-disrupts the integrity of the cell membrane–pokes a hole in the membrane which becomes leaky (PORE hypothesis)
2-binds to and stimulates glutamate receptor, leading to dendritic spine loss (RECEPTOR hypothesis)
what treatment reverses the physical and cognitive defects caused by soluble oligos in mice
glutamate receptor inhibitors
copying DNA into RNA
transcription
making RNA usable for protein synthesis
mRNA Processing
turning genes on/off
gene regulation
(all/not all) DNA is replicated; (all/not all) DNA is transcribed
all is replicated, but not all is transcribed
transcription occurs based on
needs of the cell
type of RNA that codes for proteins
mRNA
type of RNA that forms the core of the ribosome and catalyzes protein synthesis
rRNA
type of RNA that regulates gene expression
miRNA
type of RNA that serves as adaptors between mRNA and amino acids during protein synthesis
tRNA
two ways RNA is different from DNA
uracil, ribose rather than deoxyribose
RNA-RNA hybrids that can have catalytic activity
ribozymes
RNA-RNA hybrids that can serve a regulatory function
miRNAs
substrates for RNA synthesis
rNTPs
____ sequences in the DNA tell RNA Pol where to start
promoter
____ sequences in the DNA tell RNA Pol where to stop
terminator
step of transcription at which cells regulate which proteins are produced and at what rate
initiation
three steps of transcription
initiation, elongation, termination
two typical promoter sequences in bacterial genes
-35 box, TATA box
role of promoter sequences
recruits polymerase and tells it where to begin transcription
role of the 3’ untranslated region
regulates stability
genes can be coded on (only one/either) DNA strand
either
transcription (does/does not) require a primer
does not–occurs de novo
RNA Pol (has/does not have) exonuclease activity
does not have
RNA Pol (I/II/III) transcribes most rRNA genes
RNA Pol I
RNA Pol (I/II/III) transcribes protein-coding genes, miRNA genes
RNA Pol II
RNA Pol (I/II/III) transcribes tRNA genes, 5S rRNA gene
RNA Pol III
antibiotic that targets RNA Pol
rifampin
poisonous mushrooms inhibit eurkaryotic RNA Pol (I/II/III)
RNA Pol II
mRNA processing occurs (co-transcriptionally/post-transcriptionally)
co-transcriptionally
when mRNAs are covalently modified at the ends and undergo RNA splicing
mRNA processing
in bacteria, translation occurs (co-transcriptionally/post-transcriptionally)
co-transcriptionally
which enzyme recruits RNA processing enzymes
RNA Pol II
what is the purpose of the mRNA cap
protects RNA from being degraded
what is the purpose of the poly A addition signal
stability during export and translational efficiency
5’ cap
G nucleotide stuck on end of RNA backwards
type of linkage used to put on the 5’ cap
5’ > 5’
poly A tail and 5’ cap are (templated/not templated)
not templated
proteins that bind 5’ cap and 3’ poly A tail mediate: (2 things)
export out of nucleus and translation initation
junk sequences
introns
how are introns removed
splicing
difference between primary transcript and mature mRNA
introns have been removed
purpose of interrupted eukaryotic genes
expand the repertoire of gene products via alternative splicing, evolutionary diversity
what sequences indicate where introns should be removed
cis acting sequences
splicing enzymes
snRNPs-small nuclear ribonucleoprotein particles
excised intron
lariat RNA fragment
snRNPs recognize _____ and then cleave the RNA at the intron-exon borders and covalently link the exons together
cis acting sequences
proteins + uracil rich snRNAs
U-snRNPs
fate of the lariat
degraded in nucleus
unique linkage formed by formation of lariat
2’ > 5’
syndrome that results from errors in RNA splicing
Progeria syndrome; truncated protein results in devastating disease
in prokaryotes, the final amount of protein depends on:
the efficiency of each step of transcription and translation
in eurkaryotes, the final amount of protein depends on:
gene regulation–expression is varied based on cell’s needs
gene regulatory proteins that bind DNA and help regulate transcription
transcription factors
bacteria organize genes in ____
operons
how are bacterial genes switched on and off
activators/repressors
cis-acting sites in bacterial DNA
operators
proteins that start transcription of bacterial genes
trans-acting factors
what is the purpose of the two-half sites of the DNA binding sites on an activator protein
specificity–just one site wouldn’t be specific enough so they homodimerize
key structural feature of transcription regulatory proteins
alpha helix/recognition helix
purpose of recognition helix on transcription regulatory proteins
side chains interact in the major groove with a series of base pairs
DNA site recognition by transcription regulatory proteins is determined by ______ interactions
amino acid- nucleotide base interactions (does not have to unwind the DNA or disrupt base pairing)
a tumor suppressor protein whose loss of function mutations lead to a variety of cancers, beta barrel fits in with major groove
p53
p53 is a (negative/positive) transcription factor
negative
specific p53 amino acid that associates with DNA backbone
Arg
purpose of Zn finger in p53 structure
stabilizes the Arg residue
purpose of bacterial operon
efficiently make/regulate everything needed for one task (eg make Trp)
transcription of the five trp genes in the trp operon from a single promoter results in the formation of a single long transcript called a
polycistronic mRNA
when is the trp operon repressed by the repressor
when Trp is present already–why make more
the repressor in the trp operon
Trp itself
lac operon is repressed normally by
glucose
eukaryotic transcription factors are ____-the two main functions are separable
modular
two main functions of eukaryotic transcription factors
DNA binding and transcription activation/repression
purpose of the DNA binding domain of eukaryotic txn factors
provides specificity
purpose of the activator/repression domain of eukaryotic txn factors
provides function
risk associated with modular txn factor
fusion of different parts of different factors as a result of chromosomal translocation can result in a novel activity, sometimes with negative consequences (leukemia)
regulatory sequences in eukaryotes are called _____ and can be thousands of base pairs away from the promoter
enhancers
typical eukaryotic activators work via a large “______ complex” of about 25 proteins
mediator
enhancers are found (before/in/after) genes
all three
sequences that bind activators
cis acting
enhancers are (trans/cis) acting sequences
cis
how do enhancers function in a cell-type specific manner
the proteins that bind them are differentially expressed
how does overexpression of HOX11 that leads to lymphoblastic leukemia occur
translocation of enhancer region–usually the gene is off, the enhancer turns it on
two major types of chromatin modification
covalent histone modifications and ATP dependent nucleosome remodeling
which proteins bind to the nucleosome and open up the chromatin so RNA Pol can bind
transcription factors
major histone modification that leads to acetylation of Lys on H3 is (activating/repressing)
activating
major histone modification that leads to de-acetylation of Lys on H3 is (activating/repressing)
repressing
generally histone (acetyltransferases/deacetylases) activate transcription
acetyltransferases
generally histone (acetyltransferases/deacetylases) repress transcription
deacetylases
eukaryotic gene ____ proteins increase the rate of transcription initiation once bound to DNA
activator
two ways activator proteins increase the rate of txn of eukaryotic genes
1- acting directly on the txn machinery
2-changing local chromatin structure
a special class of ATPases that displace nucleosomes from promoters
chromatin remodeling enzymes
txn factors typically control (only one gene/multiple genes)
multiple genes
why txn factors can cause side effects of a drug
affects more than just its target gene
how can defects in txn programs block differentiation and contribute to cancer development
cell stays in immature state and continues to divide
test that measures the abundance of mRNAs in cells or tissues
gene expression profiling (txn profiling)
test that can measure relative mRNA levels, monitors hundreds of genes at once
DNA microarray
test that is a whole genome sequencing method that can measure the relative abundance of all RNAs made in the cell
RNA-seq
unique regulatory region that controls chromatin structure over entire domain
locus of control
what causes beta thalassemia (beta globin production is prevented)
deletion of LCR
two ways to remind cells of their cell type
1-autoregulation
2-epigenetic inheritance via modification of DNA and chromatin
when txn factor activates other genes but also its own gene
autoregulation
modification of histones (acetylation, methylation)
epigenetic inheritance-chromatin
exception to universal genetic code
mitochondria
multiple codons code for a single amino acid
degenerate code
most hydrophobic aa’s are on which side of the genetic code table
left
most charged aa’s are on which side of the genetic code
right
where are polar aa’s on the genetic code table
middle
how many start codons are there
one
how many stop codons are there
three
three terms that refer to stop codons
stop, nonsense, termination
how many potential reading frames are there for any given nucleic acid
three
how do you get a truncated protein from a mutation in translation
a stop codon is formed where there shouldn’t be one
what is the effect of silent mutations
rate of translation
antiparallel triplet of bases which can hydrogen bond to the codon
anticodon
tRNA molecule with aa attached to the 3’ OH
amino acyl tRNAs
enzyme that attaches the aa to the tRNA
amino acyl tRNA synthetases
what forms the acceptor or amino acid stem on tRNA
base pairing of 5’ and 3’ ends of the tRNA molecule
suggests that the first two bases of the codon: anticodon interaction are constrained by normal Watson-Crick base pairing but that the requirements for H-bonding at the third base are less stringent
wobble hypothesis
the two steps of the rxn catalyzed by aminoacyl tRNA synthetases
1-activation of aa by rxn with ATP to form aminoacyl adenylate
2-reaction of activated aa with 3’-OH of tRNA to form the aminoacyl-tRNA
energy cost of rxn catalyzed by aminoacyl tRNA synthetase
2 phosphoanhydride bonds (hydrolysis of ATP and PPi > 2Pi to push reaction forward)
the three sites on the ribosome and what they stand for
E-exit
P-peptidyl
A-aminoacyl
the mRNA binds to the (large/small) ribosomal subunit
small
what happens at the A site
incoming aminoacyl tRNAs attach
what happens at the P site
attachment of the peptidyl tRNA
what happens at the E site
harbors the spent tRNA prior to releasing it
enzyme that catalyzes peptide bond in protein elongation
peptidyl transferase (a ribozyme)
step of translation when mRNA binds and is aligned in correct reading frame, initiator aminoacyl tRNA binds, ribosome assembles from subunits
initiation
step of translation when aminoacyl tRNA binds and checks codon-anticodon match, new peptide bond is formed growing chain is translocated from A to P, and mRNA is pulled along
elongation
step of translation when release factors bound to GTP bind to stop codon in A site
termination
role of GTP hydrolysis in translation
releases peptide chain
5-10 nucleotide sequence in prokaryotes found 4-7bp’s upstream of the relevant AUG
Shine-Delgarno sequence
this sequence in prokaryotes is complementary to the 3’ end of the 16s rRNA and H-bonds with it, aligning the mRNA
Shine-Delgarno sequence
multiple proteins can be translated from the same mRNA after alignment of the ribosome at different Shine-Delgarno sequences within the mRNA
bacteria have polycistronic messages
which tRNA is used to start translation
tRNA-met
factors that help assemble and disassemble transient translation complexes
initiation factors
how does GTP accelerate translation
GTP causes conformational changes in components of the ribosome and its hydrolysis to GDP + Pi forces reactions to be irreversible
energy cost of initiation
1 GTP hydrolysis
energy cost of elongation per aa added
2 GTP hydrolysis
energy cost of releasing polypeptide
1 GTP hydrolysis
energy cost of proofreading (wrong tRNA ends up in the ribosome)
2 high energy phosphoanhydride bonds
what are stop codons recognized by
release factors
what do release factors carry with them
bound-GTP
how does binding of the release factor alter the activity of peptidyl transferase
causes it to add H2O instead of an aa to the peptidyl-tRNA, removing the peptide from the tRNA
translation proofreading has high (efficiency/fidelity)
fidelity
sources of error in translation (2)
1-attachment of wrong aa to the tRNA
2-incorrect base pairing of tRNA to codon
two stages of translation when proofreading occurs
1-aminoacyl tRNA synthetase
2-when aminoacyl-tRNA first binds to A site of ribosome
prooreading activity of aminoacyl tRNA synthetase
two active sites–one to recognize correct aa, other to recognize and cleave the incorrect aa (hydrolysis of GTP)
energy cost if the wrong tRNA-aa gets into the A site during elongation
one phosphoanhydride bond
at which step of translation is translation usually controlled and why
initiation because it is so expensive energetically
which translation factor controls initiation
availability of eIF-2
what is the action of eIF-2
carries GTP and initiator tRNA to the ribosome
(phosphorylation/dephosphorylation) of eIF-2 by specific protein (kinases/phosphatastes) decreases the rate of protein synthesis
phosphorylation by protein kinases decreases the rate of protein synthesis
if the eIF-2 GDP is not phosphorylated, what is its normal fate
it is recycled to eIF-2 GTP
when eIF-2 GDP is phosphorylated, what is the result
phosphorylation locks eIF-2/eIF-2B complex in the inactive, GDP bound form
when does synthesis of globin in reticulocytes occur
only when heme is available for assembly into hemoglobin
in the absence of heme, cells activate Heme Controlled Inhibitor which (phosphorylates/dephosphorylates) eIF-2
phosphorylates
heme (activates/inhibits) the change from pro-HCI (inactive) to HCI (active)
inhibits
protects 5’ end of RNA from ribonucleases and allows eukaryotic cells to distinguish between mRNA and other types of RNA
5’ cap
5’ untranslated region often contains sequences important for translational (fidelity/efficiency)
efficiency
can contain signal sequences that target the mRNA to be translated at specific places in the cell or to be transported to particular locations within the cell
3’ untranslated region
poly A tail is added (co/post) transcriptionally
post
purpose of poly A tail
stabilizes the 3’ end
when iron levels are low, ferritin (is/is not) made and transferrin receptor (is/is not) made
ferritin is not made and the transferrin receptor is made
when there is excess iron, ferritin (is/is not) made and transferrin receptor (is/is not) made
ferritin is made, transferrin receptor is not made
iron response factor
aconitase
in the (presence/absence) of iron, aconitase binds to a specific stem-loop structure known as the Iron Response Element present in mRNA
absence of iron
how do endogenous siRNAs and miRNAs down regulate translation
by inducing mRNA degradation
RNAi
RNA interference–an important way to regulate protein synthesis
what happens to dsRNA to achieve RNAi
gets processed to siRNA
what happens to the host mRNA translation when cells are infected with poliovirus
host mRNA translation is strongly inhibited
dsRNA is a sign of what
viral infection
what does dsRNA presence in the cell cause the cell to secrete
interferons
what two enzymes are expressed when interferon binds to the surface of cells
1-ribosome-associated protein kinase (phosphorylates eIF-2 and prevents initiation of translation
2-2,5 A synthetase
what does 2,5 A Synthetase do
produces unusual polymers of ATP that activate an endoribonuclease that cuts in the middle of both mRNAs (cellular and viral) and rRNAs
how does 2,5 A Synthetase slow down protein synthesis (2 ways)
by loss of mRNAs to be translated and the loss of rRNA to make ribosomes
how do cells stop the spread of viral infection
they kill themselves or shut down protein synthesis
what drives the efficiency of protein synthesis
hydrolysis of co-factor GTP
property of mRNA that codes for proteins that are present at constant levels throughout the lifecycle of a cell
long half life
most common use of HW equation
find out carrier risk for a recessive disease
HW equation
p^2 + 2pq + q^2
2pq (>/<) q^2
2pq»q^2
when individuals choose mates that are more like themselves
assortative mating
assortative mating leads to more (heterozygosity/homozygosity)
more homozygosity
the ratio of heterozygotes (carriers) to homozygotes (affecteds) goes (up/down) as the frequency of the disease decreases
goes up
male birth rate for XLR represents (q/q^2)
q
female affected rate for XLR is represented by
q^2
female carrier rate for XLR is represented by
2pq
three no’s for HW to apply
no immigration, no mutation, no selection
p+q=1 represents (gene frequency/genotypes)
gene frequency
P + H + Q = 1 represents (gene frequency/genotypes)
genotypes
assume dominants are (heterozygous/homozygous)
heterozygous
assume parents of an autosomal recessive:
are both carriers
when any individual has an equal chance of mating with any other individual in the population
random mating
in theory, HW is achieved (over time/immediately) and is stable
immediately
affect of non random mating
increase homozygotes
allows uncommon alleles to become homozygous
consanguinity
coefficient of selection
s
genetic fitness
f
genetic fitness f=
1-s
the probability of transmitting genes to the next generation and of the survival in that generation to be passed on to the next, in relation to the average probability for the population
fitness
dominant lethals (persist/are removed)
are removed
small advantage to many carriers, big disadvantage to few homozygotes
heterozygous advantage/balanced selection
mutation rate (higher/lower) in mitochondria
higher
mutation rate (higher/lower) in Y chromosome
higher
equation for rare autosomal dominants mu=
mu= n/2N
in mu=n/2N, n=
number of affected patients born to unaffected parents
in mu=n/2N, N=
total number of births
in mu=n/2N, mu=
mutation rate
the same allele that confers an advantage when expressed in early development may be a disadvantage in adulthood
pleiotropy
arising by chance in close physical proximity to a gene with selective advantage and increasing in frequency as a result of selection on this neighboring gene
hitch hiking
de novo point mutations are more likely to be (maternally/paternally) inherited
paternally
two best known microdeletion syndromes
Prader Willi and Angelman
(prader willi/angelman) patients are small and hypotonic at birth, but then begin to gain weight rapidly. Developmentally delayed but do well in special ed
prader willi
(prader willi/angelman) patients are severely mentally retarded
angelman
(karyotype/FISH/population) studies show the cause of the deletion in prader willi and angelman syndromes
population studies
for a prader willi patient, the deletion is present on the (maternal/paternal) chromosome 15
paternal
for an angelman patient, the deletion is present on the (maternal/paternal) chromosome 15
maternal
why does maternal uniparental disomy also cause prader willi as well as paternal deletion
because the paternal information from chromosome 15 is missing
inheritance of a chromosome or chromosomes from 1 parent to the exclusion of the other parent
uniparental disomy
uniparental disomy (can/cannot) be detected by standard karyotype
cannot-homologs will look alike
tests that can determine uniparental disomy
molecular probe technology, microarray
duplication of 1 chromosome leading to lack of heterozygosity
uniparental isodisomy
2 different chromosomes from the same parent
uniparental heterodisomy
the zygote rescue solution to a monosomy is duplication of the one existing chromosome, leading to:
uniparental isodisomy
the zygote rescue solution to a trisomy is loss of one of the chromosomes, leading to (three options):
biparental heterodisomy--two different ways uniparental heterodisomy (when zygote deletes the wrong one)
the differential modification of the maternal and paternal genetic contributions to the zygote resulting in the differential expression of parental alleles during development and in the adult
imprinting
imprinting (is/is not) found on all chromosomes
is not
methylation involves adding methyl groups to (A/C/T/G) residues in the DNA
cytosine
pattern of methylation is (the same/different) between males and females
different
imprinting lasts (indefinitely/one generation)
one generation
correct methylation pattern is applied during (mitosis/meiosis)
meiosis
when some chromosomes in a male gamete retain the female methylation pattern
imprinting failure
result of an imprinting failure
one chromosome from each parent but both have female methylation imprint
the study of heritable changes in gene function that are not caused by change in the DNA sequence
epigenetics
methylation of genes turns them (on/off)
off
what is the mechanism of action of methylated DNA to repress transcription
blocks the binding of required co factors and activators
hypomethylation of (proto oncogenes/tumor suppressor genes) may cause cancer
proto oncogenes
hyper methylation of (proto oncogenes/tumor suppressor genes) may cause cancer
tumor suppressor genes
small, non coding RNAs that bind to mRNA to regulate gene expression to prevent translation or interfere with translation
miRNAs
(up/down) regulation of miRNA is reported in a number of tumors
down regulation
neurodevelopmental disorder, primarily affects females, seizures, variable phenotype, linked to mutations in the MECP2 txn factor
Rett Syndrome
normal function of MECP2 txn factor
development of neurons
what is disease severity linked to in Rett syndrome
X inactivation
