calm review quiz 1 8-27-08

8/8/2019 CALM Review Quiz 1 8-27-08

1/104


2/104

Unfortunately most of the class is

memorization

Mundane details will be tested

It is OK if you have not already taken abiochem/genetics course


3/104

Cancer

Accidents

Cerebrovascula...

Kidneydisease...

Chronic

respir...

13%

23% 23%

20%20%

1. Cancer

2. Accidents

3. Cerebrovascularincidents

4. Kidney diseases

5. Chronicrespiratory

diseases


4/104

Know the top causes of death in the US

1. Heart diseases

2. Cancer

3. Cerebrovascular incidents

4. Chronic respiratory diseases

5. Accidents


5/104

pH

lower,volu...

pH

lower,volu...

pHhigher,vol...

pHhigher,vol...

23%

30%

33%

13%

1. pH lower, volume lessin ICF

2. pH lower, volume

more in ICF3. pH higher, volume less

in ICF

4. pH higher, volume

more in ICF


6/104

Ion ECF ICF

Na+ 137 10

K+ 4.7 141

Ca++ 2.4 10-4

Mg++ 1.4 31

Cl- 113 4

HPO42-/HPO4

- 2 11

HCO3- 28 10Organic acids/esters 1.8 100

pH 7.4 6.5-7.5

Volume 15 25


7/104

I will try to hit all of the main points by

asking you questions about them

Explanations will follow

Getting questions wrong is a really goodway to learn something

It helps to come prepared, but is notabsolutely necessary


8/104

Join google group njmscalm2012 groups.google.com

Until I get access to post on WebCT

Might have to join google to join the

group


9/104

Southernblot

Findamarker...

Northernblot

Westernblot

Easternblot

23%

13%

27%

20%

17%

1. Southern blot

2. Find a marker

gene3. Northern blot

4. Western blot

5. Eastern blot


10/104

If a marker gene undergoes

independent assortment with a human

disease gene the marker is not close tothe marker

Linkage indicates you are close


11/104

Auto.Dom

.

Auto.Rec.

X-link.Dom.

X-link.Rec.

20%

30%

17%

33%1. Auto. Dom.

2. Auto. Rec.

3. X-link. Dom.4. X-link. Rec.


12/104

Nothing

Gain

offuncti...

Lossoffuncti...

Allof the

abo...

20%

27%

37%

17%

1. Nothing

2. Gain of function

3. Loss of function4. All of the above


13/104

SNP

RFLP

VNTR

SSR

CCV

30%

20%

17%

20%

13%

1. SNP

2. RFLP

3. VNTR4. SSR

5. CCV


14/104

Factor

Serotonin

transporter

Cyt.P-450

CYP2D

17

27

23

331. Factor V

2. Serotonin

transporter3. Cyt.P-450

4. CYP2D


15/104

P-450 is responsible for detoxification of

NSAIDs, anti-depressants, anti-

convulsants, etc.


16/104

Translocation...

Translocation...

Non-disjunctio...

Non-disjunctio...

23%

27%

20%

30%1. Translocation ofchrom. 9/22

2. Translocation ofchrom. 3/22

3. Non-disjunctionof chrom. 9

4. Non-disjunction

of chrom. 3


17/104

Securin

APC

CENtromere-ass...

Seperase

13

33

20

331. Securin

2. APC

3. CENtromere-associated

Protein-E

4. Seperase


18/104


19/104

True

False

50501. True

2. False


20/104


21/104

Leptotene

Zygotene

Pachytene

Diplotene+

Di...

27

23

27

23

1. Leptotene

2. Zygotene

3. Pachytene4. Diplotene +

Diakinesis


22/104


23/104

AutosomalRece...

AutosomalDomi...

Mitochondrial

-linkedReces...

-LinkedDomin...

3

17

2323

33

1. AutosomalRecessive

2. AutosomalDominant

3. Mitochondrial

4. X-linkedRecessive

5. X-LinkedDominant


24/104

1 2 3 4

17

27

30

27

1. 1

2. 2

3. 34. 4


25/104

1 2 3 4

17

3737

10

1. 1

2. 2

3. 34. 4


26/104

H1

H2A

H2B H

3H4

23

17 17

27

17

1. H1

2. H2A

3. H2B4. H3

5. H4


27/104

Changeprotein...

Changenucleos...

ChangeDNA

int...

Changenucleos...

33

13

20

331. Change protein

interactions

2. Changenucleosomepacking

3. Change DNA

interactions

4. Changenucleosome

stability


28/104


29/104

H1

H2A

H2B H

3H4

17

30

20

13

20

1. H1

2. H2A

3. H2B4. H3

5. H4


30/104


31/104

L1transposons

AluSines

Hypermethylati...

Crosslinking

30

27

23

20

1. L1 transposons

2. Alu Sines

3. Hypermethylation4. Crosslinking


32/104

ICF

Osteogenesisimperfecta

CHARGE

Syndrome

Microcephaly

Norelateddeficiencies

20

23

17

23

17

1. ICF

2. Osteogenesis

imperfecta3. CHARGE

Syndrome

4. Microcephaly5. No related

deficiencies


33/104

Individuals homozygous for de novo

methyltransferases (DNMT3B) suffer from

ICF (Immunodeficiency centromericregion instability and facial anomalies)


34/104

True

False

40

601. True

2. False


35/104

Alu must use a hijacked L1 transposon

integrase to insert itself into a

chromosome


36/104

Yes

No

43

57

1. Yes

2. No


37/104

Pseudo-Autosomal Region (PAR) on Y

chromosome allows crossing over

between the two


38/104

Dehydrated

ManyH20

interactions

CGRich

ATRich

20

13

33331. Dehydrated

2. Many H20

interactions3. CG Rich

4. AT Rich


39/104

Z-DNA is heavily methylated

DNA is methylated on C residues

A-DNA is dehydrated

B-DNA (normal form) has many

interactions with water


40/104

Interactwith

...

Bind

anamino...

Regulateamino

...

Binding

oftRN...

23

13

37

27

1. Interact withmRNA

2. Bind an aminoacid

3. Regulate aminoacid binding

4. Binding of tRNA

to ribosome


41/104


42/104

5AAC3

3AAC5

5CCA3

3CCA5

30

232323

1. 5AAC 3

2. 3AAC 5

3. 5CCA 34. 3CCA 5


43/104

Heatto100C

Coolto

0C

Treatwith

0.1...

Treatwith

0.1...

20

40

23

17

1. Heat to 100C

2. Cool to 0C

3. Treat with 0.1Macid

4. Treat with 0.1M

base


44/104

Facilitatethe...

Facilitatethe...

60

40

1. Facilitate theremoval of a PPifrom ATP

2. Facilitate theremoval of a PPifrom dNTP


45/104

Magnesiums two positive charges

stabilize the two negative charges on a

pyrophosphate molecule, facilitating itsrelease so that a deoxy-base may be

added to the growing chain with just

one phosphate group (phosphate

backbone)


46/104

Responsiblefordenaturi..

StabilizessDNA

Supercoiling

Primersynthesis

Seperatesreplicatedloo

..

30

27

17

1313

1. Responsible fordenaturing DNA

at Ori C

2. Stabilize ssDNA

3. Supercoiling

4. Primer synthesis

5. Seperates

replicated loopsof DNA


47/104

Supercoiling

JoinDNAends

StabilizesssD...

Seperatesrepl...

Responsiblef...

27

17

23

20

13

1. Supercoiling

2. Join DNA ends

3. Stabilizes ssDNA4. Seperates

replicated loops

of DNA

5. Responsible for

denaturing DNAat Ori C


48/104

Beginunwindin...

Ongoingunwind

...

Synthesisofp...

Removalofpri...

23

17

33

27

1. Begin unwinding

2. Ongoing

unwinding3. Synthesis of

primer

4. Removal ofprimer and gap

filling


49/104

None

3->5exonu...

5->3exonu...

3->5endon...

5->3endon...

27

17

20

27

10

1. None

2. 3 -> 5

exonuclease3. 5 -> 3

exonuclease

4. 3 -> 5endonuclease

5. 5 -> 3endonuclease


50/104

Primase

Repair

Replication

Mitonchondrial...

Replicationwi...

10

17

27

17

301. Primase

2. Repair

3. Replication4. Mitonchondrial

replication

5. Replication withPCNA


51/104

FEN-1

RPA

PCNA

23

27

23

27

1. FEN-1

2. DNAPol.

3. RPA4. PCNA


52/104

SSB (single stranded binding protein) is

equivalent to RPA


53/104

RBCs

Prokaryotes

Immaturelymph...

HI-infectedc...

10

30

33

27

1. RBCs

2. Prokaryotes

3. Immaturelymphocytes

4. HIV-infected

cells


54/104

Terminal deoxyribonucleotidyl

transferase is found mainly in

preimmunocytes Adds bases to ssDNA or dsDNA without a

template


55/104

Ciprofloxacin

Actino

mycin

Quinacrin

Cis-platin

33

23

17

27

1. Ciprofloxacin

2. Actinomycin

3. Quinacrin4. Cis-platin


56/104

ddC

Ciprofloxacin

Quinolones

Etoposide

17

30

2727

1. ddC

2. Ciprofloxacin

3. Quinolones4. Etoposide


57/104


58/104

Formula = 4# of bases


59/104

DNA

Polym

erase

Suppressorreg...

EcoRImethylas

...

T4DNA

ligase

23

3333

10

1. DNAPolymerase

2. Suppressorregion

3. EcoRI methylase

4. T4 DNA ligase


60/104

Water

CaCl2

NaCl

MgCl2

17

27

23

331. Water

2. CaCl2

3. NaCl4. MgCl2


61/104


62/104

DNA

Polym

erase

dNTP

ddNTP

T4DNA

ligase

20

40

17

23

1. DNAPolymerase

2. dNTP

3. ddNTP4. T4 DNA ligase


63/104

Hold

strandof...

Regulatoryrol...

Putsakinkin...

Recognize prom...

23

13

33

30

1. Hold strand ofDNA in place

2. Regulatory role

3. Puts a kink in

DNA

4. Recognizepromoter

sequence


64/104


65/104

Rifampin

Aptamers

Actino

mycin

Etoposide

23

30

27

20

1. Rifampin

2. Aptamers

3. Actinomycin4. Etoposide


66/104


67/104

Rifamptin blocks initiation by binding to

the B and B subunits to cause a

conformational change


68/104

Boundlacrepr...

LowcAMP

High

cAMP

FreeCAP

23

40

20

17

1. Bound lacrepressor

2. Low cAMP

3. High cAMP

4. Free CAP


69/104


70/104

RNA

Pol.I

RNA

Pol.II

RNA

Pol.III

RNA

Pol.I

+I...

RNA

Pol.I

+I...

13

33

17

10

27

1. RNAPol. I

2. RNAPol. II

3. RN

APol. III4. RNAPol. I + II

5. RNAPol. I + III


71/104

RNA

Pol.I

RNA

Pol.II

RNA

Pol.III

RNA

Pol.I

+I...

RNA

Pol.I

+I...

13

23

37

17

10

1. RNAPol. I

2. RNAPol. II

3. RN

APol. III4. RNAPol. I + II

5. RNAPol. I + III


72/104


73/104


74/104


75/104

RNA

Pol.I

RNA

Pol.II

RNA

Pol.III

13

27

37

23

1. DNAPol.

2. RNAPol. I

3. RN

APol. II4. RNAPol. III


76/104

RNAPol. II is strongly inhibited by -

amanitin; contained in the mushroom

Amanita phalloides RNAPol. III is inhibited at very high

concentrations


77/104

TFIIF

TFIIB

TFIIE

TFIIH

23

2727

23

1. TFIIF

2. TFIIB

3. TFIIE4. TFIIH


78/104


79/104

TFIIB binds TBP after it has already bound

to DNA

It recruits the RNAPol. II complex (RNAPol. II w/ CTD, TFIIF)


80/104


81/104

A zinc finger is a large superfamily of proteindomains that can bind to DNA.A zinc fingerconsists of two antiparallel strands, and an

helix. The zinc ion is crucial for the stability of this

domain type - in the absence of the metalion the domain unfolds as it is too small to

have a hydrophobic core.

wikipedia


82/104

PKA

cAMP

CREB

CBP

CRE

33

27

10

7

23

1. PKA

2. cAMP

3. CREB4. CBP

5. CRE


83/104

A mutation in CREB binding protein (CBP)

leads to this syndrome

Characterized by large flat digits, mentalretardation, and congenital heart

defects


84/104

Leydenreduces...

Brandenburgaf...

Leydenresolve

...

Brandenburgin...

20 20

27

331. Leyden reduces

HNF4 binding

2. Brandenburg

affects Factor IX

3. Leyden resolvesat puberty

4. Brandenburg

involvesandrogen

receptor binding


85/104

Both involve Factor IX

Leyden involves androgen receptor

binding -> gets better at puberty Brandenburg involves HNF4 binding and

never resolves throughout life


86/104

Methylation

Acetylation

Calcification

TdTupregulati...

30

33

10

27

1. Methylation

2. Acetylation

3. Calcification4. TdT upregulation


87/104

Largeform

Smallform

43

57

1. Large form

2. Small form


88/104


89/104

alGlu

Glual

Glyal

alGly

33

17

20

30

1. Val Glu

2. Glu Val

3. Gly Val4. Val Gly


90/104

a

17

20

27

20

17

1. a

2.

3.

4.

5.


91/104

Lossof1a-su...

Lossof2a-su...

Lossof3a-su...

Lossof4a-su...

7

20

50

23

1. Loss of 1 a-subunit gene

2. Loss of 2 a-

subunit genes

3. Loss of 3 a-subunit genes

4. Loss of 4 a-subunit genes


92/104

Loss of 3 alpha subunits will result in HbH

symptoms

You have 4 copies of the alpha subunitgene; 2 on each chrom.16

Only need 2 good copies to produce

alpha chain

Loss of all 4 = hydrops fetalis


93/104

37

27

37

1. +/+

2. +/0

3.

0

/

0


94/104


95/104

Interphase

Replication

MeiosisI

MeiosisII

Non-disjunctio...

23 23

13

17

23

1. Interphase

2. Replication

3.Meiosis I

4. Meiosis II

5. Non-disjunction


96/104

Thereisamut...

Thereisan au...

Oxygenated hem

...

Avalinerepla...

23

37

2020

1. There is a mutation inthe alpha globin gene

2. There is an autosomaldominant inheritance

3. Oxygenatedhemoglobin is prone

to form insoluble fibers

4. A valine replaces

glutamate in twochains


97/104

Remember there are two alpha and two

beta chains in Hb


98/104

The2hydroxy...

Thebaseuraci...

Alackofthym

...

Aclover-leaf...

Thelackofhy...

17

33

10

27

13

1. The 2 hydroxyl

2. The base uracil

3. A lack of

thymine4. A clover-leaf

structure

5. The lack ofhydrogenbonding


99/104

mRNAprobesar...

Thedisease-ca...

Proteinsofm

u...

Mutationsare...

Restrictionfr...

13

30

17

23

17

1. mRNA probes are used in

combination with antibodies

2. The disease-causing mutationis at or closely linked to an

altered restriction site

3. Proteins of mutated andnormal genes migratedifferently upon gel

electrophoresis

4. Mutations are outside ofrestriction sites so that

cleaving still occurs5. Restriction fragments remain

the same size but their charge

changes


100/104


101/104

NuclearDNA

Ribo

somalRNA

MessengerRNA

Mitochondrial

...

TransferRNA

17 17

13

20

33

1. Nuclear DNA

2. Ribosomal RNA

3. Messenger RNA

4. Mitochondrial

DNA

5. Transfer RNA


102/104

Seperationof...

Annealingoft...

Methylation

of...

Extensionoft...

Activationof...

20

13

27

13

27

1. Seperation of theDNA strands

2. Annealing of theprimers

3. Methylation of theDNA strands

4. Extension of theDNA strands

5. Activation of theDNA polymerase


103/104

Lysylhydroxyl...

Protein

kinase

Protein

phosph...

Histoneacetyl...

RNA

polym

erase

17

13

23

20

27

1. Lysyl hydroxylase

2. Protein kinase

3. Protein

phosphatase4. Histone

acetyltransferase

5. RNA polymerase


104/104

ownsyndrome

it.Dresista...

hennemuscu...

Cysticfibrosi...

hondroplasia...

3

23

30

17

27

1. Down syndrome

2. Vit. D resistantrickets

3. Duchenne

musculardystrophy

4. Cystic fibrosis

5. Achondroplasia

calm review quiz 1 8-27-08

Documents