missed questions, topics needing review

Question 1

what would be the effect of a drug that inhibits the ligase activity of Topo I?

Answer 1

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

Question 2

what would be the effect of a drug that inhibits 5’->3’ exonuclease activity of DNA pol I?

Answer 2

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)

Question 3

what repair pathway is used to fix deaminated cytosines

Answer 3

BER

(don’t overthink it, it’s a broken base)

Question 4

are the 5’UTR and 3’UTR sequences between or outside the start and stop codons?

Answer 4

OUTSIDE - they are not being translated (don’t overthink it)

Question 5

mRNA from same gene in different tissues may be different sizes due to ___

Answer 5

alternative splicing

Question 6

which can use RNA as a substrate: Northern blot, restriction enzymes

Answer 6

Northern blot

Question 7

Western blotting vs immunoprecipitation

Answer 7

Western blotting: proteins blotted on paper and antibodies detected

Immunoprecipitation: antibody coupled to solid substrate, mixed with lysate and loaded onto gel

Question 8

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 (+/-)

Answer 8

+ amino acids: [+] BELOW pKa, neutral above

• amino acids: neutral below their pKa, [-] ABOVE

Question 9

how many genes does each chromosome have and how many total

Answer 9

each gene has ~1,000 genes
~22,000 genes total

Question 10

how many base pairs in each copy of chromosomes

Answer 10

3.2e9 bp = C value

Question 11

how precise is the resolution of G-banding

Answer 11

1 band = 4-7 Mb = 45 genes

each chromosome has ~1000 genes

Question 12

how long is probe for FISH

Answer 12

10’s of bases long

Question 13

this mutation affecting double strand break repair causes immune deficiency because it is involved in B/T cell differentiation. What is?

Answer 13

ATM mutation (causes AT)

Question 14

mutation in HNPCC vs BER defect that causes colon cancer

Answer 14

MSH —> defective MMR —> HNPCC
MYH —> defective BER —> colon cancer

Question 15

explain significance of location of Huntington’s TNR

Answer 15

first EXON of chromosome 4 —> causes protein aggregation

Question 16

T/F: small G proteins like ras have intrinsic GAP activity

Answer 16

TRUE

most ras mutations affect its ability to turn itself off —> constitutively active

Question 17

how are protein kinase receptors turned off

Answer 17

reversible phosphorylation of the receptor via phosphatase

Question 18

proteins entering secretory pathway need what to be delivered to ER

Answer 18

SRP (signal receptor protein)

Question 19

this junction structure has dense cytoplasmic plaques and intermediate filaments

Answer 19

spot desmosomes

Question 20

_________ of myosin is located at globular head, _____ of myosin is at tail region

Answer 20

motor domain at globular head with ATPase activity

coiled coil domain that allows heavy chain to dimerization at tail region

Question 21

lamins are ____ filaments that assemble as _____

Answer 21

lamin - intermediate filaments, assemble as coiled-coil dimers

mutation could cause muscle weakness

Question 22

what is different in lamin A between normal and progeria patients?

Answer 22

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

Question 23

how does lamin A mutation cause Werner’s syndrome (BER defect, MYH helicase mutation)?

Answer 23

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)

Question 24

how does mutation of coagulation proteins MCFD2 and LMAN cause a bleeding disorder?

Answer 24

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

Question 25

mutations in Rab27a, Mlph, and Myo5A all cause what?

Answer 25

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

Question 26

how do Rab27a, myosin5a, and melanophillin work together?

Answer 26

Rab27a binds melanosome when GTP bound

Rab “effector” melanophillin binds myosin

mutation in any of these 3 proteins causes Griscelli syndrome

Question 27

in Griscelli Type I there is a neural phenotype, but in Type II there is an immune phenotype. give explanation

Answer 27

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)

Question 28

a newborn is born with a sacrococcygeal tumor containing skin derived from remnant epiblast cells. What developmental process failed?

Answer 28

incomplete primitive streak regression

Question 29

blastocyst implantation occurs at the end of week ___

describe the process

Answer 29

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

Question 30

giveaway for connective tissue

Answer 30

relatively few cells compared to ECM

Question 31

T/F: covalent attachment of lipid to Rab27 is necessary for effective melanosome transport

Answer 31

TRUE: Griscelli’s syndrome can develop if this is defective (cause by mutation in either Myosin5a, Rab27, or melanophillin)

Question 32

what is the result of displacing a drug from albumin in the body

Answer 32

increased volume of distribution (Vd) - the drug can now enter more compartments than it could before

this will consequently also increase half life

Question 33

which of these is a possible result of drug-drug interactions?
a. increased CLbody
b. decreased CLbody

Answer 33

drug-drug interactions could INCREASE CLbody (for example: pharmacological inhibition - causing other drug’s metabolism)

but will never decrease it

Question 34

in humans, HPE due to ___ haploinsufficiency results in _______, but not _______

Answer 34

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)

Question 35

what does cyclopamine do and how does it work

Answer 35

treats Hh related disease that occur from Smo or more upstream defects

(NOT Gli defects)

Question 36

Which of these helps prevent re-initiation of M phase?
a. Wee1
b. APC

Answer 36

APC ubiquitin ligase prevents re-initiation of M phase

Question 37

the most common Phase I and Phase II drug metabolism reactions are, respectively:

Answer 37

Phase I: CYP3A
Phase II: glucuronidation

Question 38

if a mouse is born with an extra cervical vertebrae but is missing a thoracic vertebrae, what Hox mutation occurred

Answer 38

LOF Hox mutation —> anterior transformation !!!!!!

GOF Hox mutation causes POSTERIOR transformation (ex - thoracic vertebrae where cervical should be)

Question 39

competitive antagonism decreases apparent ____

Answer 39

potency

Question 40

Nuclear lamina is composed of

Answer 40

Intermediate filaments

Question 41

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

Answer 41

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

Question 42

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

Answer 42

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

Question 43

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

Answer 43

B. A 3 component system including myosin5a needed for melanosome movement cannot assemble properly

Myosin5a interacts with melanophillin (not Rab27 directly)

Question 44

what are the TNR sequences in each of the TNR disorders (and where are the mutations found, and inheritance)

Answer 44

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)

Question 45

how long is the probe for FISH

Answer 45

10’s of bases long

Question 46

what is CGH karyotyping good for

Answer 46

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)

Question 47

why is it important that phosphatidyl-serine is found on the inner leaflet of the PM?

Answer 47

negative charge

needed for PKC

Question 48

proteins for which of these targets go through the ER and Golgi?
a. lysosome
b. endosome
c. peroxisome
d. mitochondria

Answer 48

lysosome and endosome proteins go through ER/Golgi

peroxisomal proteins do NOT, neither do mitochondrial proteins

Question 49

order these in location of where you would find them from hemidesmosomes to connective tissue:
collagen 7
collagen 17
collagen 4

Answer 49

hemidesmosomes
————————————
collagen 17 (XVII) (lamina lucida)
————————————
collagen 4 (IV) (lamina densa) + perlecan
————————————
collagen 7 (VII) (lamina reticularis) + proteoglycans
————————————
connective tissue

Question 50

which cell junction contains dense cytoplasmic plaques and desmoglein (type of cadherin)

Answer 50

spot desmosomes/macula adherens

Question 51

which of these is DNA, which protein?
homeobox
homeodomain

Answer 51

homeobox = DNA sequence

homeodomain = protein (ENCODED by the homeobox), 3 alpha helices - helix #3 contacts DNA at AT-rich binding sites (promoters and enhancers)