missed questions, topics needing review Flashcards
what would be the effect of a drug that inhibits the ligase activity of Topo I?
Topo I regulates superhelicity of DNA by creating/resealing ssDNA breaks to remove excess negative supercoils —> inhibiting ability to rejoin DNA would be converting Topo I into DNA breaking agent
ex: cancer drugs such as camptothecin
what would be the effect of a drug that inhibits 5’->3’ exonuclease activity of DNA pol I?
DNA pol I 5’-3’ exonuclease activity removes RNA primers —> drug would prevent transcription
(DNA pol I also has 3’-5’ exonuclease activity for proofreading)
what repair pathway is used to fix deaminated cytosines
BER
(don’t overthink it, it’s a broken base)
are the 5’UTR and 3’UTR sequences between or outside the start and stop codons?
OUTSIDE - they are not being translated (don’t overthink it)
mRNA from same gene in different tissues may be different sizes due to ___
alternative splicing
which can use RNA as a substrate: Northern blot, restriction enzymes
Northern blot
Western blotting vs immunoprecipitation
Western blotting: proteins blotted on paper and antibodies detected
Immunoprecipitation: antibody coupled to solid substrate, mixed with lysate and loaded onto gel
below their pKa, + amino acids are (+/-), and above their pKa, + amino acids are (+/-)
below their pKa, - amino acids are (+/-), and above their pKa, - amino acids are (+/-)
+ amino acids: [+] BELOW pKa, neutral above
- amino acids: neutral below their pKa, [-] ABOVE
how many genes does each chromosome have and how many total
each gene has ~1,000 genes
~22,000 genes total
how many base pairs in each copy of chromosomes
3.2e9 bp = C value
how precise is the resolution of G-banding
1 band = 4-7 Mb = 45 genes
each chromosome has ~1000 genes
how long is probe for FISH
10’s of bases long
this mutation affecting double strand break repair causes immune deficiency because it is involved in B/T cell differentiation. What is?
ATM mutation (causes AT)
mutation in HNPCC vs BER defect that causes colon cancer
MSH —> defective MMR —> HNPCC
MYH —> defective BER —> colon cancer
explain significance of location of Huntington’s TNR
first EXON of chromosome 4 —> causes protein aggregation
T/F: small G proteins like ras have intrinsic GAP activity
TRUE
most ras mutations affect its ability to turn itself off —> constitutively active
how are protein kinase receptors turned off
reversible phosphorylation of the receptor via phosphatase
proteins entering secretory pathway need what to be delivered to ER
SRP (signal receptor protein)
this junction structure has dense cytoplasmic plaques and intermediate filaments
spot desmosomes
_________ of myosin is located at globular head, _____ of myosin is at tail region
motor domain at globular head with ATPase activity
coiled coil domain that allows heavy chain to dimerization at tail region
lamins are ____ filaments that assemble as _____
lamin - intermediate filaments, assemble as coiled-coil dimers
mutation could cause muscle weakness
what is different in lamin A between normal and progeria patients?
altered RNA splicing of lamin A leads to shortened protein in progeria patients
consequence: upstream protease cleavage site is removed from primary sequence, and so a lipid attachment that should be removed is not
this lipid structure gets incorporated into the nuclear envelope, and proteins are mislocalized
how does lamin A mutation cause Werner’s syndrome (BER defect, MYH helicase mutation)?
lamin A mutation causes lipid region to remain attached (due to alternative splicing that removes cleavage site)
lamin A with lipid attachment gets incorporated into nuclear envelope
this disrupts Werner’s MYH helicase binding and it can’t perform its function (even though its there - it’s mislocalized)
how does mutation of coagulation proteins MCFD2 and LMAN cause a bleeding disorder?
if either protein is missing, clotting factors cannot be incorporated into COP-II (secretory pathway) vesicles
they bind each other and make functional dimer - need them both
mutations in Rab27a, Mlph, and Myo5A all cause what?
Griscelli syndrome - pigment abnormalities
(Mlph = melanophillin)
Griscelli I: myosin5a link to melanosome is absent
Rab27a binds melanosome when GTP bound, Rab “effector” melanophillin binds myosin
how do Rab27a, myosin5a, and melanophillin work together?
Rab27a binds melanosome when GTP bound
Rab “effector” melanophillin binds myosin
mutation in any of these 3 proteins causes Griscelli syndrome
in Griscelli Type I there is a neural phenotype, but in Type II there is an immune phenotype. give explanation
type I: myosin5a mutation (neural phenotype)
type II: Rab27a mutation (immune phenotype)
perhaps another Rab can substitute in brain, or maybe myosin has different function in brain that is unaffected by Rab absence
in immune cells, Rab27a needed to recruit vesicles to membranes (fusion of granules form lymphocyte with target cell membrane)
a newborn is born with a sacrococcygeal tumor containing skin derived from remnant epiblast cells. What developmental process failed?
incomplete primitive streak regression
blastocyst implantation occurs at the end of week ___
describe the process
blastocyst implantation occurs at end of week 1
trophoblast layer near embryonic pole attaches to uterine endometrium, which at this point has undergone decidual reaction
giveaway for connective tissue
relatively few cells compared to ECM
T/F: covalent attachment of lipid to Rab27 is necessary for effective melanosome transport
TRUE: Griscelli’s syndrome can develop if this is defective (cause by mutation in either Myosin5a, Rab27, or melanophillin)
what is the result of displacing a drug from albumin in the body
increased volume of distribution (Vd) - the drug can now enter more compartments than it could before
this will consequently also increase half life
which of these is a possible result of drug-drug interactions?
a. increased CLbody
b. decreased CLbody
drug-drug interactions could INCREASE CLbody (for example: pharmacological inhibition - causing other drug’s metabolism)
but will never decrease it
in humans, HPE due to ___ haploinsufficiency results in _______, but not _______
in humans, HPE due to SHH haploinsufficiency results in CNS/CRANIOFACIAL defects but NOT limb
(other Shh disease cause limb defects such as polydactyly though)
what does cyclopamine do and how does it work
treats Hh related disease that occur from Smo or more upstream defects
(NOT Gli defects)
Which of these helps prevent re-initiation of M phase?
a. Wee1
b. APC
APC ubiquitin ligase prevents re-initiation of M phase
the most common Phase I and Phase II drug metabolism reactions are, respectively:
Phase I: CYP3A
Phase II: glucuronidation
if a mouse is born with an extra cervical vertebrae but is missing a thoracic vertebrae, what Hox mutation occurred
LOF Hox mutation —> anterior transformation !!!!!!
GOF Hox mutation causes POSTERIOR transformation (ex - thoracic vertebrae where cervical should be)
competitive antagonism decreases apparent ____
potency
Nuclear lamina is composed of
Intermediate filaments
Which is the most direct consequence of progerin mutation?
a. Prevents intermediate filament formation from lamin monomers
b. Leads to atypical Werner’s because direct binding of a DNA helicase is altered
c. Prevents a proteolytic cleavage that would eliminate a lipid attachment that now becomes permanent
c. Prevents a proteolytic cleavage that would eliminate a lipid attachment that now becomes permanent
Lamin precursor protein is covalently coupled to a lipid chain, but it’s removed via proteolytic cleavage
Mutation causes abnormal splicing that eliminates proteolytic cleavage site —> lipid is incorporated into nuclear membrane
The most likely cause of coagulation factor deficit in multiple coagulation deficiency is that:
A. Factor V and Factor VIII cannot be incorporated into COP I vesicles
B. Each individual factor has a mutation that prevents recognition by a complex of LMAN and MCDF2
C. Either LMAN or MCDF2 are non-functional so transport from ER to Golgi is abolished
D. Formation of COP-II vesicles is prevented so that transport from ER to Golgi is abolished
C. Either LMAN or MCDF2 are non-functional so transport from ER to Golgi is abolished
*either of the 2 independent mutations can prevent assembly of 2 molecule complex that associates with COP-II to allow transport from ER in COP-II vesicles
The major cause of Griscelli type I is:
A. Myosin cannot directly bind Rab27
B. A 3 component system including myosin5a needed for melanosome movement cannot assemble properly
C. Dinosaurs
B. A 3 component system including myosin5a needed for melanosome movement cannot assemble properly
Myosin5a interacts with melanophillin (not Rab27 directly)
what are the TNR sequences in each of the TNR disorders (and where are the mutations found, and inheritance)
Fragile X: CGG, X dominant, 5’UTR
fraCture, fraGGile X
(also Cognition is fraGGile)
Huntington’s: CAG, aut dom, EXON
Friedrich’s Ataxia: GAA, aut recessive, intron
fredGggggerich’s AtaxiA
(also only one recessive, only one to start with G)
(also proGressive weakness And Ataxia)
Myotonic Dystrophy: CTG, aut dom, 3’UTR
Cataracts, myoTonia, Gait issues
(also Classic To Congenital - for levels of severity)
how long is the probe for FISH
10’s of bases long
what is CGH karyotyping good for
control patient + unknown problem
(colors fluoresce green yellow or red)
can only see how many copies there are of a gene - no orientation changes (balanced rearrangements)
why is it important that phosphatidyl-serine is found on the inner leaflet of the PM?
negative charge
needed for PKC
proteins for which of these targets go through the ER and Golgi?
a. lysosome
b. endosome
c. peroxisome
d. mitochondria
lysosome and endosome proteins go through ER/Golgi
peroxisomal proteins do NOT, neither do mitochondrial proteins
order these in location of where you would find them from hemidesmosomes to connective tissue:
collagen 7
collagen 17
collagen 4
hemidesmosomes
————————————
collagen 17 (XVII) (lamina lucida)
————————————
collagen 4 (IV) (lamina densa) + perlecan
————————————
collagen 7 (VII) (lamina reticularis) + proteoglycans
————————————
connective tissue
which cell junction contains dense cytoplasmic plaques and desmoglein (type of cadherin)
spot desmosomes/macula adherens
which of these is DNA, which protein?
homeobox
homeodomain
homeobox = DNA sequence
homeodomain = protein (ENCODED by the homeobox), 3 alpha helices - helix #3 contacts DNA at AT-rich binding sites (promoters and enhancers)
