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Biochemistry - Real One > Lecture 16: Nucleotide Structure, Function, and Metabolism > Flashcards

Lecture 16: Nucleotide Structure, Function, and Metabolism Flashcards

1
Q

Jump right in. What joins individual nucleotides together in DNA?

A

Phosphate bonds between the sugars. (Hydrogen bonds connect the two strands together)

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2
Q

How many hydrogen bonds are there between the two types of nucleotides joining between two strands?

A

When C joins with G, 3 hydrogen bonds

When A joins with T, 2 hydrogen bonds

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3
Q

How do we fit all that DNA in our body

A

Mitotic chromosomes are condensed 500 times smaller than interphase DNA. The dynamic situation is they need to be allowed to rapidly access it for gene expression.
- Protein + Nuclear DNA = Chromatin

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4
Q

In one sentence, difference between nucelotide and nucleoside?

A

Nucleotides have the phosphate added on.

Nucleic Acids are multiple nucleotides

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5
Q

What’s the difference (in some cases, whenenver they feel like it) between Beta and Alpha

A

Beta is the “top face”. Alpha is the “bottom” or underface of the ring.

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6
Q

Let’s get this bullshit over with…learn how to recognize Purines vs. pyramidines.

A

Start with the basic version of each on slide 15. Presumably the rest are just variations of that one.

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7
Q

Draw Adenine. Where does it connect.

A

Do it

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8
Q

Draw Thymine. Where’s that one connect?

A

Do it.

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9
Q

Guanine?

A

Do it.

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10
Q

Cytosine?

A

Do it.

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11
Q

Uracil?

A

I hate everything.

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12
Q

There are two other purines that don’t appear in DNA or RNA. Name both bases and their nucleoside/nucleotide counterpart.

A
  • Base: Hypoxanthine
  • Nucleoside: Inosine (I)
  • Nucleotide: IMP
  • Base: Xanthine (Xan)
  • Nucleoside: Xanthosine (X)
  • Nucleotide: XMP
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13
Q

Know how to recognize ribose and deoxyribose

A

Do it!

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14
Q

What enzyme and coenzyme are needed to reduce an oxyribose down to deoxyribose

A
  • Ribonucleotide reductase and an NADPH coenzyme.

- ATP enhances this process, dATP inhibits it.

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15
Q

On slide 22, be able to recognize where on an ATP the
N-glycosidic bond is,
The phophoric acid ester bond, and
The Phophoric Acid Anhydride Bonds

A

N-glycosidic bond connects the base to the sugar
Phophoric acid ester bond connects the alpha phosphorous to the O in the sugar bond
Phophoric acid anhydride bonds connect the alpha phosphorous to the beta phosphorous, and the beta phosphorous to the gamma phosphorous.

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16
Q

How many Base pairs are there in every DNA strand turn

A

10 base pairs per turn (every turn is 3.4 angstroms)

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17
Q

What form is DNA most commonly in.

A

B-form is the hydrated form, and is longer and narrower than the A-form.

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18
Q

Name the general type of enzyme responsible for breaking down DNA or RNA into it’s base

A
  • Ribonuclease or Deoxyribonuclease would shorten the chain into shorter chains (oligomers).
  • Phophodiesterase would sever phosphourous bonds joining the oligomers. (Now they’re in NMP form)
  • Nucleotides are broken down by cutting the remaining phosphorous off with nucleotidase
  • Nucleosidase cuts the base off of the ribose or deoxribose.
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19
Q

Explain how GMP is broken down into uric acid.

A
  1. GMP loses a phosphorous with nucleotidase to become the nucleoside Guanosine.
  2. Guanosine is broken down with PNP enzyme (coenzyme Pi is converted to Ribose 1-P in the process) into Guanine.
  3. Guanine is broken down into Xanthine with Guanine Deaminase.
  4. Xanthine is broken down into Uric acid with Xanthine Oxidase.
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20
Q

Following the “IMP” pathway, explain how AMP is broken down into uric acid.

A
  1. AMP broken converted into IMP via AMP deaminase
  2. IMP loses Pi to become inosine.
  3. Inosine is converted into Hypoxanthine via purine nucleoside phosphorylase (PNP). In the process, Ribose becomes phosphorylated (Ribose 1-P)
  4. Hypoxanthine is broken down into Xanthine via Xanthine Oxidase. Allopurinol can inhibit this.
  5. Xanthine is broken down into Uric Acid with Xanthine Oxidase.
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21
Q

Following the “Adenosine pathway”, how can AMP also be broken down into Inosine?

A
  1. AMP is dephosphorylated by nucleotidase into Adenosine.

2. Adenosine is broken down into Inosine with adenosine deaminase.

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22
Q

How is Xanthine prepared?

A

Sounds like it’s a combination of Guanine and Hypoxanthine. Allopurinol can inhibit hypoxanthine from forming into xanthine. And it can also preven Xanthine from being oxidased into uric acid.

23
Q

What is allantoin?

A

I don’t know. But Urate Oxidase seems to catabolize uric acid into that.

24
Q

Describe Xanthine Oxidase

A
  • Catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid.
  • Has 2 flavin adenine dinucleotides (FADs), 2 Mo atoms, and 8 Fe atoms per molecule of enzyme.
  • Drug target for the treatment of gout.
25
Q

Describe Gout

A

Derived from latin word “gutta” (drop of discharge)

  • Hurts like hell in inflamed joints.
  • Was once thought of as rich people disease.
  • Big toe is most commonly affected area.
  • Can result from too much uric acid, or insufficient excretion of it. Primary is overproduction. Secondary is under-excretion.
  • Hyperuricemia: Uric acid exceeds plasma solubility
  • Sodium urate is crysalized in joints
  • Can cause kidney damage if deposited into kidney
  • Caused by purine-rich diet.
  • Treatment is Colchicine (Decreases movement of granulocutes to the affected area), and allopurinol that inhibits xanthine oxidase to form hypoxanthine.
26
Q

Describe how UMP, UDP, UTP, dUMP, dUDP, and dUTP are broken down into Malonyl CoA

A
  1. Fuck my life. So all those things are broken down by nucleotidase into uridine, or Deoxyuridine.
  2. Uridine Phosphorylase Phosphorylates another ribose in order to produce Uracil.
  3. Uracil goes through some stuff to become Beta-Alanine, and Beta-Alanine goes through some stuff to become Malonyl CoA. (which is ketogenic)
27
Q

How is CDP/CTP/etc. broken down into Malonyl CoA

A
  1. CDP/CTP/etc. are broken down into cytosine with nucleotidase.
  2. Cytosine, or deoxycytosine are broken down with aminohydrolase into Uridine, or deoxyuridine.
  3. From there, uridine follows the same pathway into malonyl CoA as UMP does.
28
Q

How is dTDP and dTTP broken down?

A
  1. dTDP and dTTP are broken down with nucleotidase into Deoxythymidine.
  2. Uridine phosphorylase converts (with another Pi transfer) the Deoxythymidine into Thymin.
  3. Thymine goes through some stuff to become Beta-aminoisobutyrate.
  4. Beta-aminoisobutyrate goes through some more stuff to become Methylmalonyl CoA, or Succinyl CoA. (Both of which are involved in the glucogenic pathway)
29
Q

What is the source of all of the components of the purine bases (in the ring)?

A

CO2, Glutamine, Glycine, Aspartate, N10-formyl THF

And yes, you ntk that.

30
Q

What is the source of the ring atoms in pyriidine bases?

A

HCO3-, Glutamine, Aspartate, N5, and N10-methylene THF.

31
Q

What are noteworthy features of purine biosynthesis?

A
  • The committed step in the purine synthesis is the formation of the Phosphoribosyl Amine.
  • The molecule formed is hypoxanthine ribose phosphate or Inosine Monophosphate.
  • The inosinate is not commonly found in DNA or in RNA. It is converted into Guanosine monophosphate and Adenosine monophosphate.
  • . There are two salvage enzymes:
    a. Hyponxanthine guanine phophoribosyl transferase.
    b. Adenine phosphoribosyl transferase
32
Q

Using the slide on 49, which carbon and nitrogens of purines belong to each respective portion.

A 
N1 is from Aspartate
C2 is from Tetrahydrofolate
N3 and N9 are from glutamine
C4, C5, and N7 are from Glycine
C6 is from Carbon Dioxide (Sections 1-6 are part of the hexagon)
C8 is from the another tetrahydrofolate
(Sections 4-9 compose the Pentagon)
33
Q

Describe Phase I of the De Novo Synthesis of Purines

A

Phase I: Ribose 5P Activation

  1. From the pentose phosphate pathway, an alpha-ribose 5-phosphate is introduced.
  2. An ATP reaction assists PRPP synthetase in converting the ribose phosphate into 5-phospho-alpha-ribosyl-1-pyrophosphate (PRPP)
34
Q

Describe the phase II portion of the De Novo Synthesis of purine nucleotides

A

Phase II: Convert PRPP to PRA

  1. PRPP undergoes a committed step where a glutamine is converted into a glutamate, a PPi is lost, and glutamine-phosphoribosyl pyrophosphate amidotransferase. (This mechanism is activated by the presence of PRPP and inhibited by existing purines)
  2. Finished Product (For this phase): PRA
35
Q

Describe Phase III of the De Novo synthesis of purines.

A

Phase III: Constructing the IMP ring.
1. CO2, Glycine, Glutamine, Aspartate, and N10 THF are thrown in there to construct IMP. Not too concerned with the how. Oh and Methotrexate inhibits this process.

36
Q

Describe the process IMP undergoes in order to become ATP or any of it’s derivatives.

A

Phase IV: Converting IMP to adenosine constructs

  1. IMP is converted to adenylosuccinate monophosphate through adenylosuccinate synthetase.
  2. Adenylosuccinate…whatever is converted to AMP through adenylosuccinase. A fumarate is lost duriing this point.
37
Q

Describe the process IMP undergoes Phase IV to become GTP

A

Phase IV: Converting IMP to guanosine products

  1. IMP dehydrogenase converts IMP to Xanthosine Phosphate (XMP). Nad+ is hydrated during this step.
  2. GMP synthetase causes Gln, ATP, to become AMP and Glutamate. Finished products is GMP…sort of.
38
Q

What is PRA (Don’t have to draw it, but it should be pretty easy to)

A

Phosphoribosylamine - Phosphorylated Sugar ribose with an amine where it’s N-base should be.

39
Q

Describe methotrexate

A
  • Antineoplastic agents such as methotrexate target dihydrofolate reductase that converts in the liver
  • This inhibition disrupts DNA replication in rapidly dividing cells
  • Efficacy depends on selective drug uptake by cancer cells versus normal cells.
  • It can inhibit DNA synthesis
  • Binds Dihydrofolate reductase 100 fold more tightly than whatever it was supposed to bind to.
40
Q

What’s unique to purines over pyramidindes regarding the base and the sugar.

A

In purine synthesis, the Base is built Onto the sugar.

In pyrimidines, The sugar is built onto the base i think

41
Q

Where is adenylosuccinate used?

A

In the TCA cycle? I think

42
Q

In purine synthesis, what steps are able to be feedback inhibited?

Where is it stimulated?

A

The One between PRPP and PRA.
The One between IMP and AMP/GMP

That second question gets weird.
GTP stimulates the production of more AMP
ATP stimulates the production of more GMP

43
Q

What does UMP require to upgrade up through UTP?

A

ATP is reduced in the production of UDP from UMP.

And then a second ATP is needed to bring it up again to UTP. It’s possible that this can be performed backwards too.

44
Q

Where are the components of the pyrimidine ring from?

A

C2, and N3 are from Carbamoyl Phosphate

The other 4 (including N1) is from Aspartate

45
Q

Describe the first Phase of De Novo Pyrimidine Synthesis

A
  1. Glutamine is converted with carbamoyl phophate synthetase II (at the expense of 2 ATP and an HCO30) into carbamoyl phosphate. PRPP can stimulate this step. UTP inhibits it.
  2. Carbamoyl phophate is converted with aspartate transcarbamoylase (at the expense of an aspartate) into Carbamoyl Aspartate.
  3. Carbamoyl Aspartate is converted with dihydroorotase into Dihydro Orotate.
46
Q

Describe the Second Phase of De Novo Pyrimidine Synthesis

A

Phase II attaches PRPP to make UMP

  1. Dihydroorotate uses dihydroorotate dehydrogenase into plain orotate IN THE MITOCHONDRIA. The rest of this shit takes place in the cytosol.
  2. Orotate uses UMP synthase to attach a PRPP to it, forming OMP.
  3. OMP uses UMP synthase to convert into a UMP
47
Q

Describe the third phase of De Novo Synthesis of Pyrimidine Nucleotides

A

Phase III Converts UMP to all the stuff we want.

  1. UMP is phophorylated to UDP (remember how?)
  2. Ribonucleotide reductase converts UDP into dUDP, dUTP, and dUMP.
  3. dUMP uses thmidylate synthase to convert itself into dTMP, where it goes into it’s respective thymidine product. This can be inhibited by 5-flurouracil. A N5,N10mTHF is utilized here.
  4. Alternatively, the UDP from Step 1 can be converted into CTP with CTP synthase. From there ribonucleotide reductase can convert it to dCDP.
48
Q

Where is the committed step in pyrimidine synthesis?

A

The formation of n-carbamoyl aspartate from aspartate and carbamoyl phosphate.

49
Q

What is orotic aciduria?

A

Human hereditary disorder involving the synthesis of the pyrimidine nucleotides.
- Usually treated with oral uridine.

50
Q

What is required in the formation of deoxyribonucleotides from ribonucleotides?

A

Deoxyribonucleotides are formed by the reduction of the ribonucleoside diphosphates. The immediate hydrogen donor for the reduction of ribonucleoside diphosphate is reduced THIOREDOXIN OR GLUTAREDOXIN.

51
Q

What are the two major control points of pyrimidine biosynthesis?

A
  1. Carbamoyl phosphate synthetase is inhibited by UMP and purines and stimulated by PRPP.
  2. Aspartate transcarbamoylase is feedback inhibited by CTP.
52
Q

What is usually the limiting factor in the construction of DNA?

A

dTTP. Which makes sense when you consider it’s only required for DNA.

53
Q

What is the purine nucleotide salvage pathway?

A

I don’t know.

  1. But one picture shows adenine phosphoribosyl-transferase (or APRT) and requires a PRPP to convert adenine into AMP.
  2. The other part shows Hypoxanthine Guanine Phophoribosyl-transferase (HGPRT) to convert Guanine and Hypoxanthine into GMP or IMP.
54
Q

What is the pyrimidine salvage pathway?

A
  1. Uracil is converted to Uridine with uridine phosphorylase at the expense of Ribose 1-P. The nucleoside product, Uridine uses kinases to convert into UMP UDP or UTP.
  2. Thymine Uses thymidine phosphorylase at the expense of 2-deoxyrobose 1-P to convert Thymine into Deoxythymidine. Deoxythymidinie can continue to be converted via thymidine kinase into dTMP, dTDP, or dTTP.

Biochemistry - Real One (25 decks)

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