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Biochemistry > Exam 3 December 7 Lecture > Flashcards

Exam 3 December 7 Lecture Flashcards

1
Q

What is a nucleoside?

A

ribose + nucleobase

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2
Q

What is a nucleotide?

A

nucleoside + phosphate

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3
Q

What are the different nucleobases, nucleosides (sugar is added), mononucleotides (phosphate is added), and types?

A 
adenine → adenosine → AMP → purine
guanine → guanosine → GMP → purine
cytosine → cytidine → CMP → pyrimidine
uracil → uridine → UMP → pyrimidine
hypoxanthine → inosine → IMP → purine
xanthine → xanthosine → XMP → purine
orotate → orotidine → OMP → pyrimidine
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4
Q

Hypoxanthine and xanthine have a similar structure to what other nucleobase?

A

guanine

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5
Q

What is the difference between hypoxanthine and xanthine?

A

hypoxanthine is missing an extra oxygen that xanthine has

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6
Q

What is orotate?

A

an intermediate in pyrimidine base synthesis

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7
Q

What is the de novo synthesis of purine bases?

A
  1. makes purine bases from scratch
  2. utilizes amino acids (glutamine, glycine, aspartate) as carbon and nitrogen donors
  3. costly in terms of energy → uses ATP in several steps
  4. PRPP (5-phosphoribosyl-1-pyrophosphate) is the key starting material
  5. the first step is the commitment step (and is regulated)
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8
Q

What is the first step of de novo synthesis of purine bases?

A

PRPP → 5-phosphoribosylamine (by PRPP-amidotransferase that changes glutamine to glutamate which is the nitrogen source and a phosphate group is lost)

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9
Q

What does the pentose phosphate pathway do?

A

makes ribose from glucose

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10
Q

What is the common intermediate for both AMP and GMP synthesis?

A

IMP

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11
Q

How is the commitment step for de novo purine synthesis regulated?

A

suppressed by AMP, GMP, and IMP

stimulated by PRPP

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12
Q

What is the delicate feedback loop involving IMP, GMP and AMP?

A

AMP and GMP suppress their own synthesis from IMP

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13
Q

How is GDP and GTP produced?

A

produced from GMP using ATP as a phosphate donor

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14
Q

What is the overall process of de novo synthesis of purine bases?

A

PRPP → 5-phosphoribosylamine → IMP → (XMP → GMP) OR (adenylosuccinate → AMP)

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15
Q

What is the de novo synthesis of pyrimidine bases?

A
  1. make the nucleobase first and then attach to the ribose
  2. orotate is synthesized from amino acids (glutamine and aspartate) and HCO3-
  3. OMP is synthesized from orotate and PRPP which is analogous to the salvage pathway
  4. UDP and UTP are produced from UMP using ATP as a phosphate donor
  5. CTP is produced from UTP
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16
Q

What is the main process of synthesizing pyrimidine bases?

A

orotate → OMP (PRPP comes in and phosphate group leaves) → UMP (by decarboxylation)

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17
Q

What is the importance of the salvage pathway?

A

making nucleotides is expensive → if nucleotides are recycled or come from the diet, the salvage pathway will occur since we don’t need to build it from scratch

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18
Q

The salvage pathway makes what?

A

nucleotides!! (not nucleosides)

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19
Q

What are the 3 examples of the salvage pathway?

A
  1. hypoxanthine-guanine phosphoribosyl transferase (HGPRTase): hypoxanthine + PRPP ↔ IMP + PPi AND guanine + PRPP ↔ GMP + PPi
  2. adenine phosphoryl transferase (APRTase): adenine + PRPP ↔ AMP + PPi
  3. pyrimidine phosphoryl transferase
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20
Q

What do both de novo synthesis and salvage pathways generate?

A

nucleoside monophosphate (NMP)

21
Q

What do nucleotide kinases do?

A

they add phosphate groups to NMP and NDP

22
Q

What is the major phosphate donor?

23
Q

What is the overall process of adding phosphate groups?

A

NMP → NDP → NTP

24
Q

How are purine bases degraded?

A

purine nucleoside phosphorylase removes nucleobases from nucleosides (examples are: 1) inosine + Pi ↔ hypoxanthine + ribose I-P 2) guanosine + Pi ↔ guanine + ribose I-P) → the end product of purine nucleobases is uric acid

25
How is adenosine degraded?
adenosine → inosine → hypoxanthine (by purine nucleoside phosphorylase) → xanthine (by xanthine oxidase) → uric acid (by xanthine oxidase)
26
How is guanosine degraded?
guanosine → guanine (by purine nucleoside phosphorylase) → xanthine (by xanthine oxidase) → uric acid (by xanthine oxidase)
27
What is the role of a purine nucleoside phosphorylase?
removes the nucleobase from the ribose ring (aka nucleoside)
28
What is the role of xanthine oxidase?
adds an oxygen
29
What is uric acid?
1. not very soluble 2. can form needle like sodium urate crystals that precipitate when there is too much urate in the body 3. the deposition of sodium urate crystals in the joints causes gout (severe inflammation) 4. called an acid because of tautomerization (uric acid ↔ tautomerized form of uric acid ↔ urate + H+)
30
What is gout and how is it presented?
patients have elevated levels of uric acids (hyperuricemia)
31
What are the causes of gout?
1. overproduction of purine bases by de novo synthesis 2. decreased excretion of uric acid (because of kidney issues) 3. alcohol (aka beer) and high fructose diet + red meats
32
What is allopurinol?
1. used to treat gout since it is a structural isomer of hypoxanthine 2. xanthine oxidase inhibitor (inhibits the production of uric acid) 3. reduces the production of uric acid 4. increases the utilization of hypoxanthine through the salvage pathway which reduces de novo purine synthesis → to make IMP (which is a key intermediate that suppresses the commitment step)
33
How are deoxyribose nucleotides synthesized?
1. dNTP is necessary for DNA replication and repair 2. ribonucleotide reductase converts NDP to dNDP which is the rate limiting step for dNTP synthesis 3. ribonucleotide reductase is allosterically regulated by many NTPs and dNTPs 4. NADPH is used as a reducing cofactor
34
What is the rate limiting step for dNTP synthesis?
the conversion of NDP to dNDP
35
What is the role of ribonucleotide reductase?
converts ribose to deoxyribose (NDP to dNDP)
36
What is NAD+?
nicotinamide adenine dinucleotide (has 2 phosphate groups) → nicotinamide is a vitamin (niacin aka vitamin B3)
37
How is NAD+ synthesized?
the first step is analogous to the salvage pathway in which PRPP acts as a ribose 5-phosphate donor (nicotinamide → nicotinamide mononucleotide → NAD+)
38
What is 6-mercaptopurine (6-MP)?
1. an antitumor drug 2. converted to a mononucleotide through the salvage pathway 3. the mononucleotide is a potent negative regulator of PRPP-amidotransferase which is the enzyme that catalyzes the commitment step of de novo purine synthesis 4. metabolized to 6-thiouric acid by xanthine oxidase 5. allopurinol is used together to potentiate the drug activity by inhibiting degradation
39
What is the basic function/role of 6-MP?
a mononucleotide that suppresses purine synthesis so it can block the synthesis of nucleotides so that cancer cells cannot divide
40
What is 5-fluorouracil?
1. an antitumor drug 2. analog of uracil 3. converted to FUMP and FdUMP in cells 4. FUMP is incorporated into RNA and interferes with RNA processing 5. FdUMP inhibits thymidylate synthase (synthesizes thymidine) irreversibly by forming a covalent bond 6. without dTTP, cells undergo "thymineless death"
41
What is the basis of 5-fluorouracil?
is like an isotere since it resembles uracil and interferes of the conversion of FUMP to FdUMP which makes dTTPs but without dTTPs, DNA cannot be made and cancer cells will die
42
What is acyclovir?
1. an antiviral drug that is used to treat herpes simplex virus (HSV) infections 2. converted to the monophosphate by a HSV-thymidine kinase which exists only in the infected cells 3. the triphosphate is used as a substrate for the HSV DNA polymerase that causes chain termination
43
What is the basis of acyclovir?
has a guanine ring but no ribose ring structure and once it is added to the growing chain, it blocks the replication of viral DNA → safe to human cells since it is only activated in virally infected cells → has a hydroxyl group on it that decreases its oral bioavailability
44
What is valacyclovir?
an esterified version of acyclovir with valine → a prodrug with greater oral bioavailability than acyclovir
45
What is sofosbuvir?
1. brand name is Sovaldi 2. antiviral drug used to treat hepatitis C → disease was not curable before this drug so it is the first drug of its class 3. prodrug → is rapidly converted to the active agent in vivo 4. activation of the corresponding nucleoside is much slower 5. the active agent is a potent inhibitor of NS5B which is a RNA-dependent RNA polymerase
46
What is the basis of sofosbuvir?
has groups that cover up and block the phosphate group and once the drug is in the body, the extra groups are removed to show the phosphate group → aka a prodrug
47
What is the basis of having a nucleotide analog as a drug?
has a phosphate group but can't enter the body well because of the charge on it → needs to act like a prodrug
48
Why are nucleotide analogs better drugs than nucleoside analogs?
nucleotide analogs works much better because of the phosphate group while nucleoside analogs will be degraded in the body and it is rarely converted to the nucleotide

Biochemistry (18 decks)

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