Biochemii Week 3

Front 1

The interconversion between mono and diphoshpate nucleotides if mediated by _____________________________>

Back 1

specific nucleoside monophosphate kinases (one for every base)

Front 2

The interconversion between di- and triphosphates is mediated by ___________________, called ____________________.

Back 2

a single kinase, nucleoside diphosphate kinase (NDPK)

Front 3

CTP is created from UTP with which enzyme? how is this enzyme regulated?

Back 3

cytidine triphosphate synthetase (cytidylate synthetase), CTP is the feedback inhibitor

Front 4

In pyrimidine biosynthesis carbamoyl phosphate and aspartate synthesize ______________ _______________. What is the name of the enzyme? How is it regulated?

Back 4

carbamoylaspartate, enzyme= aspartate transcarbamoylase , regulated by CTP

Front 5

Where does the amine group on the 4C of CTP come from?

Back 5

Gln, Q

Front 6

ATCase? what is it? how is it regulated?

Back 6

carbamoyl apartate, makes carbamoyl aspartate from
carbamoyl phosphate, it is down regulated by CTP, upregulated by ATP in the presence of CTP

Front 7

Back 7

CO2

Front 8

Back 8

Glycine

Front 9

Back 9

n10-fomyltetrahyrofolate

Front 10

Back 10

glutamine

Front 11

Back 11

aspartate

Front 12

Back 12

glutamine

Front 13

Back 13

n10- formyltetrahydrofolate

Front 14

Back 14

glutamine

Front 15

Back 15

CO2

Front 16

Back 16

Aspartate

Front 17

Draw this.

Back 17

Front 18

Draw this.

Back 18

Front 19

Back 19

PRPP amidotransferase

Front 20

Back 20

Gln+H2O ----> Glu + NH3

Front 21

Back 21

5-phoshoribosyl-1-amine

Front 22

Back 22

committed step

Front 23

Turning PRPP into 5-phosphoribosyl-1-amine is done by which enzyme? how is it regulated?

Back 23

PRPP amidotransferase
regulation
partial- GTP
ATP
total - GTP & ATP
IMP

Front 24

enzyme? regulation?

Back 24

ribose phosphate pyrophosphokinase , downregulated by ADP

Front 25

Who performed the S & R experiment? what was the main conclusion of the experiment?

Back 25

Griffith, genetic material can be transferred between cells

Front 26

Who performed the "ase" tests? What was the main conclusion of the experiment?

Back 26

Avery, McLeod, McCarty, DNA is the "transforming principle"

Front 27

Who performed the virus experiment? What was the main conclusion from the experiment?

Back 27

Hershey, Chase, Solidified that DNA is the genetic material

Front 28

Back 28

adenylosuccinate synthetase

Front 29

Back 29

inosinate (IMP)

Front 30

Back 30

Inosinate (IMP) dehydrogenase

Front 31

Allosteric feedback regulation of purine ribonucleotide synthesis occurs at four places. Name the enzymes.

Back 31

PRPP synthetase, glutamine-PRPP amidotransferase, adenylosuccinate lyase, IMP dehydrogenase

Front 32

Name the endproducts, missing enzymes, and draw the regulation of this pathway.

Back 32

Front 33

In the purine ribonucleotide biosynthesis pathway ribose 5-phosphate is converted to PRPP. Name the enzyme, and the regulation.

Back 33

PRPP synthetase, downregulated by ADP

Front 34

In the purine ribonucleotide biosynthesis pathway PRPP is converted to 5-Phosphoribosylamine. Name the enzyme, and the regulation.

Back 34

glutamine-PRPP amidotransferase,
regulation
partial- GTP
ATP
total - GTP & ATP
IMP

Front 35

In the purine ribonucleotide biosynthesis pathway IMP is converted to AMP. Name the regulated enzyme, and the regulation.

Back 35

adenylosuccinate synthetase, down regulated by AMP

Front 36

In the purine ribonucleotide biosynthesis pathway IMP is converted to GMP. Name the regulated enzyme, and the regulation

Back 36

IMP dehydrogenase, downregulated by GMP

Front 37

Name the enzyme reponsible for converting ribonucleotides into deoxyribonucleotides.

Back 37

ribonucleotide reductase

Front 38

Ribonucleotide reductase use _________________________ as substrates.

Back 38

ribonucleoside diphosphates

Front 39

Ribonucleotide reductase catalyzation involves a _______________ reduction. The source of these electrons is ___________________.

Back 39

2 electron, NADPH

Front 40

The regulation of ribonucletoide reductase maintains a balance of ______________________ ______________________.

Back 40

deoxynucleotide concentrations

Front 41

Regulation of _________________ ________________ maintains a balance of deoxynucleotide concentrations.

Back 41

ribonucleotide reductase

Front 42

Name this enzyme. What does it do?

Back 42

Ribonucleotide reductase
converts RNA to DNA

Front 43

Back 43

Substrate specificity site - top
Primary regulation site - bottom

Front 44

Back 44

active site

Front 45

Back 45

ATP, dATP, dGTP, dTTP

Front 46

Back 46

ATP, dATP

Front 47

Back 47

ADP, CDP, UDP, GDP

Front 48

The primary regulation switch on ribonucleotide reductase is an ON/OFF switch regulated with ATP, dATP. Which substrate in on, off?

Back 48

on-ATP
off-dATP

Front 49

The primary regulation switch on ribonucleotide reductase is an _________ - _________ switch.

Back 49

on/off

Front 50

The primary regulation switch on _______________ _______________ is an ON/OFF switch regulated with ATP, dATP. Which substrate in on, off?

Back 50

ribonucleotide reductase
on-ATP
off-dATP.

Front 51

The primary regulation switch on ribonucleotide reductase is an ON/OFF switch regulated with what substrates?

Back 51

on-ATP
off-dATP

Front 52

The substrate specificity site on ribonucleotide reductase works by ________________ regulation.

Back 52

reciprocal

Front 53

The substrate specificity site on ribonucleotide reductase works by reciprocal regulation. Explain.

Back 53

If a purine is in the substrate specificity site than a primidine is in the active site and vica versa.

Front 54

The reaction in the active site of ribonucleotide reductase occurs via a ____________ _____________. Which is pointed out because there are not many of these in the human body.

Back 54

radical intermediate

Front 55

draw the regulation for Ribonucleotide reductase.

Back 55

Front 56

dTMP is derived from d_______.

Back 56

UMP

Front 57

Back 57

Front 58

Fill in the blanks of this pathway for dTMP.

Back 58

Front 59

_____________ ______________ catalyzes the last step in dTMP pathway, the reaction uses THF as the cofactor to add a ____________ ____________ to C5. It converts d_____ to dTMP.

Back 59

Thimidylate Synthase
methyl group

Front 60

This pathway is the target for several ___________ and ______________ drugs.

Back 60

cancer, autoimmune

Front 61

____________ aa residue methylates Tetrahydrofolate.

Back 61

Serine

Front 62

Many types of cancers are defined by _____________ ___________ cells.

Back 62

rapidly dividing

Front 63

Cell division requires replication of ____________ ________, thus cancer (or rapidly dividing cells have a heightened need for _______________.

Back 63

genomic DNA, nucleotides

Front 64

Failure to replicate DNA during the cell cycle is detected by the DNA replication checkpoint resulting in _____________ _____________ ___________ and/or ______________.

Back 64

cell cycle arrest, apoptosis (programmed cell death)

Front 65

Because cancer is often rapidly dividing, blocking ___________ precursors is an effective strategy to arrest the cell cycle and/or cause apoptosis.

Back 65

nucleotide precursors

Front 66

Two specific strategies of blocking nucleotide precursors to eliminate cancer are?

Back 66

1. Block (Q) PRPP amidotransferase by using Q analogs, halting purine production
2. Block thymidylate synthase, stopping dTMP production.

Front 67

Describe how Fluorouracil halts nucleotide metabolism.

Back 67

Fluorouracil becomes FdUMP though the de novo pyrimidine pathway covalently binding to thymidylate synthetase halting the production of dTMP.

Front 68

Describe how Methotrexate inhibiits nucleotide metabolism.

Back 68

Methotrexate halts the methylation of THF that produces N5,N10 methylene THf. It does this by having a higher binding affinity for dihydrofolate reductase than it's substrate. Thus halting the production of dTMP.

Front 69

Name the two cancer treatment drugs that inhibit dTTP production.

Back 69

Fluorouracil
Methotrexate

Front 70

Name the two cancer treatment drugs that inhibit purine biosynthesis.

Back 70

azaserine
avicin

Front 71

Free __________ and ___________ bases can be salvaged from degraded DNA and RNA.

Back 71

purine, pyrimidine

Front 72

In the salvage pathway for purines.

Back 72

Adenosine phosphoriboysltransferase

Front 73

In the salvage pathway for purines Guanine or (hypoxyanthine) + PRPP --> GMP or XMP + PPi is catalyzed by ______________ _______________________(H/GPRT).

Back 73

hypoxanthine/guanine phosphoribosyltranferase.

Front 74

the best studied are ___________ salvage pathways which use specific __________________________ to join PRPP to free purine bases to form nucleotide monophosphates.

Back 74

purine, phosphoribosyltransferases

Front 75

In the catabolism and salvage of nucleotides pathway, guanylate and adenylate have a shared breakdown product in _______________.

Back 75

xanthine

Front 76

In the catabolism and salvage of nucleotides pathway, _______________ and ______________ have a shared breakdown product in xanthine.

Back 76

guanylate and adenylate

Front 77

In the catabolism and salvage of nucleotides pathway, guanosine cleavage from ribosyl produces the free base ____________, which is then deaminated to form ____________.

Back 77

guanine, xanthine

Front 78

In the catabolism and salvage of nucleotides pathway, adenosine is deaminated to form ___________. Separation from ribose yields _______________, which is oxidized to form _____________.

Back 78

inosine, hypoxanthine, xanthine

Front 79

The end product of the degradation of purines is?

Back 79

uric acid

Front 80

________ is the swelling of joints resulting from a build-up of urate in the form of sodium urate crystals.

Back 80

Gout

Front 81

Gout is the swelling of joints resulting from a build-up of ________ in the form of __________ __________ crystals.

Back 81

urate, sodium urate

Front 82

Gout is caused by the ________________ of uric acid.

Back 82

undersecretion or overproduction

Front 83

Gout, which is caused by undersecretion of uric acid is the result of a genetic defect. This defect is not known but is likely related to improper _______________ balance.

Back 83

purine

Front 84

What drug is used in the treatment of gout?

Back 84

Allopurinol

Front 85

The gout treatment drug Allopurinol is an anolog to _________________.

Back 85

Hypoxyanthine

Front 86

Allopurinol metabolizes to ____________, it is catalyzed by xanthine oxidase. ____________ binds tightly to ____________ ____________ effectively blocking the active site.

Back 86

oxypurinol, xanthine oxidase

Front 87

The cancer treatments and gout treatments talked about in class are called _____________________________. (general name)

Back 87

mechanism based inhibition or suicide substrate inhibition

Front 88

Define phenotype?

Back 88

the observable characteristics of an organism

Front 89

Define gene?

Back 89

a chromosomal segment that codes for a single functional polypeptide chain or RNA molecule

Front 90

Define chromosome?

Back 90

a single large DNA molecule and its associated proteins (contains many genes)

Front 91

Define karyotype?

Back 91

the number and visual appearance of the chromosomes in the cell nuclei of an organism or species

Front 92

Define genome?

Back 92

all the genetic information encoded in a cell or virus

Front 93

Back 93

m-phase, chromatids, centromer, condensed

Front 94

What is the c-value enigma?

Back 94

Front 95

Back 95

Telomeres

Front 96

Back 96

Centromere

Front 97

Back 97

genes, repeats, origins of replication

Front 98

Back 98

Front 99

Current estimates are that ______% of the genome codes for genes. ______% is noncoding.

Back 99

30 , 70

Front 100

Of the 30% that encodes for genes, only _____% is actually coding sequence, the remaining ______% consists of ___________ which are removed after transcription.

Back 100

1.5 , 28.5 , introns

Front 101

Approximately ____% of our genome is transposons.

Back 101

45%

Front 102

Evidence for non-coding, repeated elements in the DNA comes from?

Back 102

FISH analysis, Cot curves, Genome sequencing

Front 103

In DNA supercoiling these two are called?

Back 103

twist and writhe

Front 104

For B-form dsDNA any deviation from a helical twist of 10.5bp/turn represents a ____________ ____________.

Back 104

strained conformation

Front 105

Most dsDNA in a cell is _______________ resulting in writhe.

Back 105

underwound

Front 106

In supercoiling, _________ is the number of turns of the DNA double helix.

Back 106

twist

Front 107

In supercoiling, ______________ is the munber of times a dsDNA molecule is coiled or crosses over itself.

Back 107

writhe

Front 108

Back 108

Front 109

Why is it that many circular DNA molecules remain supercoiled when extracted from cells and free of protein and other cellular components?

Back 109

because the dsDNA is underwound

Front 110

Back 110