[2] Class 6: Nucleotide Structure/ Metabolism

Question 1

DNA 5’ to 3’ gives:

Answer 1

Directionality

Question 2

Which carbon of the ribose is deoxy in DNA:

Answer 2

2’

Question 3

What type of bonds form between A-T and C-G

Answer 3

H bonds

Question 4

DNA helix structure

Answer 4

R handed antiparallel 5’-3’

Question 5

A-T how may h bonds?

Answer 5

2 h bonds

Question 6

How many h bonds c-g

Answer 6

3 h bonds

Question 7

Phosphodiester bond, where is it in dna?

Answer 7

Between 3’ carbon of ribose and 5’ methyl grp on other ribose (below)

Question 8

Who observed nucleotides in DNA? Who received credit?

Answer 8

Rosalind franklin,

Watson and crick received the prize for it though

Question 9

How many nucleotides in our genome?

Answer 9

3 billion

Question 10

How is DNA condensed to fit in our cells?

Answer 10

DNA binding proteins (histones and non-histones) allows for dynamic state between condensation and rapid access for gene expression

Question 11

Protein+Nuclear DNA=

Answer 11

Chromatin

Question 12

Phosphate esters of nucleosides

Contain base, sugar and phosphate

Answer 12

Nucleotide

Question 13

Base + sugar

Answer 13

Nucleoside

Question 14

WHat type of bond is between the purine/pyramidine base and the ribose sugar?

Answer 14

Beta glycosidic linkage

Question 15

Big ring:

Small ring:

Answer 15

Small name: purine

Big name: pyrimidine

Question 16

Purine nucleotide base:

Nucleosides?

Answer 16

Adenine; guanine

Adenosine;guanosine

Question 17

Pyramidine nucleotide base:

Nucleoside:

Answer 17

Cytosine, Uracil, thymine

Cytidine, uridine, thymidine

Question 18

Difference in thymine and uracil?

Answer 18

2’ methyl on thymine,

H on uracil

Question 19

What are the other purines?

Answer 19

Hypoxanthine, inosine, xanthine, xanthosine

Question 20

How can you go from a nucleotide to a DEOXYnucleotide?

Answer 20

Ribonucleotide reductase

Question 21

What stimulates and inhibits ribonucleotide reductase?

Answer 21

ATP stimulates ribonucleotide reductase,

dATP nucleotides inhibits ribonucleotide reductase

Question 22

Bonds of the 3 phosphates in ATP:

Answer 22

Ester bond on the alpha phosphate and 2 anhydride bonds on beta and gamma phosphates

Question 23

4 specific roles of nucleotides:

Answer 23

ATP, CoA, NAD+, FAD

Question 24

DNA bonded together is a phosphodiester bond: another name for this is

Answer 24

A covalent bond

Question 25

DNA measurements:

Answer 25

``` Length between 1 full turn: 34å 10 basepairs /turn Base pairs are separated by 3.4 å, 36º turn w/ each rotation of a new base pair. 20Å width of DNA ```

Question 26

Why is DNA typically in B form: long and slender?

Answer 26

B/c it is typically hydrated in the cell

Question 27

DNA is more stable w/ more o which base pair?

Answer 27

C-G b/c there are 3 H bonds

Question 28

Catalyzes the formation of a phosphodiester bridge:

Answer 28

DNA polymerase

Question 29

RNA of retrovirus is converted to DNA by what enzyme, and subsequent synthesis of DNA strand?

Answer 29

Reverse transcriptase

Question 30

What enzyme is responsible for cutting long chain RNA/DNA to short oligomers?

Answer 30

(Deoxy)ribonucleases

Question 31

CLeaves oligomers into nucleotides

Answer 31

Phosphodiesterase

Question 32

Cleaves nucleotides to nucleosides

Answer 32

Nucleotidase

Question 33

Cleaves Nucleoside to (deoxy)ribose and base

Answer 33

Nucleosidase

Question 34

What enzyme can be used to make Uric acid soluble?

Answer 34

URate oxidase makes it into allantoin

Question 35

Allopurinol inhibits

Answer 35

Xanthine oxidase

Question 36

Structure of xanthine oxidase

Answer 36

2 FADs 2 Mo atoms 8 Fe atoms

Question 37

Colchicine helps w/ gout by:

Answer 37

Decreasing movement of granulocytes to affected area

Question 38

Norma serum uric acid 4-8.6 mg/dL What is the increased risk of gout measurement?

Answer 38

>9 mg/dL

Question 39

Which bases are converted to Glucogenic and ketogenic metabolites

Answer 39

Pyrimidines

Question 40

5 components that form purines: 5 components of pyrimidines:

Answer 40

CO2, Gln, Asp, N10-formyl-THF HCO3, Gln, Asp, N5, N10-methylene THF

Question 41

What is the committed step in purine synthesis?

Answer 41

The formation of phosphoribosyl amine (PRA)

Question 42

Do you commonly see inosinate in DNA or RNA?

Answer 42

No it is converted to guanosine monophosphate and AMP

Question 43

2 salvage enzymes in purine:

Answer 43

HGPT and APT

Question 44

Central constituent of nucleotide metabolism Synthesized from ribose phosphate and ATP.

Answer 44

Phosphoribosyl pyrophosphate PRPP

Question 45

Which ring is synthesized attached to ribose phosphate?

Answer 45

Purine ring

Question 46

When purines are synthesized onto a ribose sugar...what initially contributes to the ribose sugar?

Answer 46

PRPP

Question 47

What is the committed step in purine synthesis ?

Answer 47

Formation of PRA

Question 48

PRPP + glutamine =

Answer 48

PRA

Question 49

Purine synthesis key step and is inactivated w/ methotrexate:

Answer 49

THF closes the base ring

Question 50

Methotrexate targets what enzyme that results in inhibiton of DNA replication

Answer 50

Dihydrofolate reductase It is an analog of folate substrate

Question 51

TCA intermediates made in purine synthesis:

Answer 51

Fumarate and adenylsuccinate

Question 52

Synthesis of purine nucleotides is controlled by ______________________ at several sites to balance the productions of purine

Answer 52

feedback regulation

Question 53

If PRPP is made then inhibited what other 2 molecule would it become?

Answer 53

Histidine and pyrimidine nucleotides

Question 54

AMP and GMP synthesis is stimulated by: Synthesis of PRPP, PRA, and GMP and AMP from IMP is

Answer 54

feedback inhibited

Question 55

Pyramiding is synthesized from:

Answer 55

carbamoyl phosphate

Question 56

Synthesized from carbamoyl phosphate and aspartate by aspartate-transcarbamoylase

Answer 56

Pyrimidine ring

Question 57

What is the first and committed step of pyramiding synthesis:

Answer 57

Formation of carbomoyl aspartate and carbamoyl phosphate

Question 58

What happens before the rxn w/ PRPP in pyramiding synthesis? It is catalyzed by orate phosphoribosyl transferase

Answer 58

The ring forms

Question 59

Human hereditary disorder involving the synthesis of pyrimidine nucleotides

Answer 59

Orotic aciduria Tx: oral uridine

Question 60

Formed from the ribonucleotides by the reduction of the ribonucleoside diphosphates

Answer 60

Deoxyribonucleotides

Question 61

Ribonucleotide diphosphate to deoxyribonucleotide by ribonucleotide reductase...what is the H donor for the reduction?

Answer 61

Thioredoxin or glutaredoxin

Question 62

2 major control points of pyrimidine biosynthesis:

Answer 62

1. Carbamoyl phosphate synthetase is hibited by UMP and purines BUT stimulated by PRPP 2. Asp transcarbamoylase is feedback inhibited by CTP

Question 63

DNA is synthesized from dATP,dCTP,dGTP, and dTTP. The [ ] of which is limiting factor?

Answer 63

dTTP

Question 64

Salvage pathway

Answer 64

Base by self needs to be put back on sugar...this is cheaper then remaking the base

Question 65

Purine salvage enzymes (2):

Answer 65

Adenine phosphoribosyl-transferase (APRT) Hypoxanthine guanine phosphoribosyl transferase (HGPRT)

Question 66

Pyrimidine nucleotide salvage enzymes (2):

Answer 66

Uridine phosphoprylase Thymidine phosphoprylase