bmsc exam 2 study guide

which molecule serves as the starting molecule for de novo purine nucleotide synthesis?

ribose-5-phosphate

in de novo purine synthesis, inosine monophosphate (IMP) serves as the precursor for:

AMP and GMP

which nucleotide is the first fully formed pyrimidine nucleotide produced in de novo synthesis?

UMP

which statement correctly compares purine and pyrimidine de novo synthesis?

purines are built on PRPP; pyrimidine are synthesized first and attached later.

the enzyme HGPRT salvages which purine bases?

guanine and hypoxanthine

the anticancer drug 5-fluorouracil (5-FU) inhibits this reaction:

dUMP to dTMP

which carbon of the ribose sugar is reduced by the enzyme ribonucleotide reductase?

2’

cytidine triphosphate (CTP) is synthesized directly from:

UTP

what are critical components of PCR?

two unique DNA primers, predefined DNA target sequence, thermostable polymerase.

which corresponds to the addition of a poly-A tail?

J

Which corresponds to the product of splicing?

K

which letter corresponds to helicase?

B

which letter corresponds to where irinotecan acts

A

which letter corresponds to the 3’ end of template DNA

F

which letter corresponds to the RNA primer

C

which letter corresponds to the okazaki fragment

D

which letter corresponds to leading strand synthesis

E

what nomenclature corresponds to sense

coding strand and nontemplate strand

what nomenclature corresponds to antisense

noncoding strand

if mRNA has the sequence 5’-AUUCAGCACC-3’, the corresponding antisense strand would read:

3’-TAAGTCGTGG-5’

which statement is false regarding nucleoside HIV reverse transcriptase inhibitors (NRTis)?

contain a 3’-OH group

the DNA content of an organism was found to contain 16% A. therefore, the % of G would be

34

upon heating a sample of DNA to around 95ºC a sharp increase in absorbance at 260nm wavelength reange indicates

DNA denaturing cerrelatin to double helix strand separation

which of the following matched pairs (process: initiator or process) is incorrect?

PCR: DNA primers + RNA primase

which statement is incorrect for mitochondrial DNA (mTDNA)

is linear dsDNA

which statement is false regarding mRNA transcription and processing?

exons are removed from pre mRNA by a process called splicing

what is a pyrimidines structure

a single heterocyclic ring

what is a purines structure

two fused heterocyclic rings

which bases are pyrimidines

c, t, u

which bases are purines

a, g

what is the composition of a nucleotide

nitrogenous base, pentose sugar, phosphate group

what is the composition of a nucleoside

nitrogenous base, pentose sugar

what is the distinction in structure between ribose and deoxyribose

2’ OH group

which carbon holds the nitrogenous base

1’

which carbon holds the phosphate group

4’

how is atp converted to cyclic AMP

adenylyl cyclase

what does kinase do

adds phosphate groups

what does phosphodiesterase do

remove phosphate groups

phosphodiesterase inhibitors are a buildup of what

cAMP

what do PDE-5 inhibitors do

increase GMP or AMP, all end in -afil

what is the mechanism of action for PDE inhibitors

inhibit phosphodiesterase enzymes, cAMP and gGMP levels increase, calciums levels decrease, vasodilation and smooth muscle relaxation.

de novo synthesis-

from scratch

salvage pathway-

recycling from other cells or tissues

how many steps does it take to construct purine rings

11

what are purine rings composed from

ribose-5-phosphate

what amino acids construct purine rings

aspartic acid, glycine, glutamine

how many ATP are required for purine ring formation

6

what is the first complete purine nucleotide formed

IMP (inosine monophosphate)

what is the central intermediate in all nucleotide biosynthesis

5-phosphoribosyl-1-pyrophosphate (PRPP)

how many ATP are used during the salvage pathway

1

the formation of AMP from adenine is from the catalyzation of what

APRT (adenine phosphoribosyltransferase)

what is the treatment of gout?

avoid food/drinks high in purines, drug therapy includes allopurinol.

allopurinol is what type of inhibitor of xanthine oxidase

competitive inhibitor

what does allopurinol do to uric acid

decreases formation

what are pyrimidine rings constructed from

glutamine, aspartic acid, and co2

how is the pyrimidine ring synthesized

free pyrimidine then incorporated into the nucleotide

how many steps does it take to construct pyrimidine rings

6

what is the first nucleotide formed in pyrimidine formation

UMP

what direction is DNA synthesized

5’-3’

what does annealing refer to

cooling a heated sample results in reformation of dsDNA

what does DNA topoisomerase do

release torsional strain in front of the replication fork, prevents supercoiling.

what does DNA helicase do

unwinds and unzips the double helix at replication fork-separates complimentary base pairs

what does DNA primase do

adds a short RNA primer to each DNA strand to initiate replication

what does DNA polymerase do

adds nucleotides to growing DNA strands- leading and lagging. some have endonuclease capability (proofreading to fix errors)

what does DNA ligase do

joins DNA fragments together by forming phosphodiester bonds between nucleotides

how do fluoroquinolone antibiotics work

they inhibit bacterial DNA topoisomerases

what is each fragment of the lagging strand called

an okazaki fragment

how many RNA primers does the leading strand need

1

how many RNA primers does the lagging strand need

many

what is the hayflick limit

the number of times a normal somatic, differentiated human cell population will divide before cell division stops.

a DNA sample contains 30% adenine. what percentage of guanine is present

20

how many h bonds are formed between a c-g pair

3

how many h bonds are formed between a t-a pair

2

a DNA strand has the sequence 5’-CCGTAAGC-3’. how many hydrogen bonds would form between this strand and its complementary strand.

21

a dna strand has the sequence 5’-ATGCCGTA-3’. what is the complementary DNA strand

3’-TACGGCAT-5’

this new strand is being synthesized in a continuous fashion

f

topoisomerase inhibitors act here

a

this is an okazaki fragment

c

this is where helicase primase inhibitors act

b

the 5’ end of a parent strand corresponds to letter

e

histone dynamics are controlled by what 2 enzymes

HAT (histone acetyltransferase) and HDAC (histone deacetylase)

what is happening to acetylated chromatin

it is open and transcriptionally active

what is happening to deacetylated chromatin

it is compact and transcriptionally repressed.

what suffix do HDAC inhibitors have

-inostat

what is the purpose of PCR (polymerase chain reaction)

quickly make many copies of a region of a DNA molecule

how many DNA primers are involved in PCR

2, 1 forward and 1 reverse

how many deoxynucleotide triphosphates are involved in PCR

4, dATP, dTTP, dGTP, dCTP

what thermostable DNA polymerase is used for PCR

Taq polymerase

what are the steps of PCR

denaturation, annealing, and extension

What happens during the denaturation step of PCR

heat the DNA to 95ºC, the dsDNA opens to ssDNA.

what happens during the annealing step of PCR

ssDNA primers bind to complementary single strand bases of denatured DNA

what happens during the extension step of PCR

taq polymerase attaches and starts copying the template. after 3 cycles, there are two new copies.

introns-

extra gene sequences, not expressed or translated into protein

exons

portions of a gene that are expressed and translated

what must first happen in order for RNA synthesis to begin

RNA polymerase must bind to dsDNA at the promoter region

during elongation what direction does RNA polymerase walk along on the template strand

3’ to 5’

what direction is the new mRNA strand synthesized in

5’ to 3’

what is the 5’-G cap made of

methylated guanosine

what is the purpose of the 5’-G cap

it protects mRNA from degradation by exonucleases, and assists in binding to ribosomes to initiate protein translation.

if mRNA has the sequence 5’- AUUCUGCACC-3’, how would the sense strand of DNA read

5’-ATTCTGCACC-3’