Bch Nucleotides

Front 1

What is a redox pair? lippincott

Back 1

Oxidation (loss of electrons) of one compound is always accompanied by reduction (gain of electrons) of another substance (LEO says GER)

Front 2

What is an oxidative agent? lippincott

Back 2

Substances that have the ability to oxidize other substances. Oxidants remove electrons from another substance, and is thus itself reduced. And, because it “accepts” electrons, it is also called an electron acceptor

Front 3

What is a reducing agent? lippincott

Back 3

Substances that have the ability to reduce other substances. Reductants transfer electrons to another substance, and is thus itself oxidized. And, because it “donates” electrons it is also called an electron donor.

Front 4

Cellular respiration depends heavily on what redox reaction? lippincott

Back 4

The process of cell respiration depends heavily on the reduction of NAD+ to NADH and the reverse reaction (the oxidation of NADH to NAD+)

Front 5

What is a reducing equivalent? lippincott

Back 5

In biochemistry, the term reducing equivalent refers to any of a number of chemical species that transfer the equivalent of one electron (typically in the form of a hydrogen ions)

Front 6

Give some examples of reducing equivalents. lippincott

Back 6

A lone electron (for example, in reactions involving metal ions), a hydrogen atom (consisting of a proton and an electron), a hydride ion (:H-) that carries 2 electrons (for example in reactions involving NAD)

Front 7

What happens to the nitrogenous bases when nucleotides are digested? Pg 6

Back 7

Most bases are degraded to uric acid. Some are recycled in the salvage pathway.

Front 8

Where are nucleases made, and what is it’s end-product? Pg 6

Back 8

Pancreas, break down denatured nucleic acids to oligonucleotides, which are further digested by phosphodiesterases (also made by the pancreas), nucleotidases, and nucleosidases

Front 9

Why don’t PRPP deficiencies cause genetic problems? Pg 7

Back 9

You’re not alive without PRPP.

Front 10

How is PRPP different from a typical nucleotide? Pg 7

Back 10

PRPP has 2 phosphates in the 1’ position (in place of a typical nitrogenous base) and a single phosphate in the 5’ position.

Front 11

NADPH is often used in what type of reaction? Slide 34

Back 11

Mostly for biosynthesis.

Front 12

NADH is often used in what type of reaction? Slide 34

Back 12

Mostly used for degradation or oxidation.

Front 13

What are the 3 sources of nucleotides as discussed in this lecture? Slide 4

Back 13

Digestion, synthesis (de novo), & salvage pathway

Front 14

What 3 co-factors are needed specifically for thYmine synthesis (a pYrimidine) via one-carbon metabolism? Slide 5

Back 14

Folic acid, vitamin B12, SAM

Front 15

What does NAD stand for? Slide 8

Back 15

Nicotinamide adenine dinucleotide

Front 16

What does FAD stand for? Slide 9

Back 16

Flavin adenine dinucleotide

Front 17

The B5 vitamin is also known as? Slide 10

Back 17

Pantothenic acid

Front 18

The B12 vitamin is also known as? Slide 11

Back 18

Cobalamine. Named so because there is a cobalt molecule in the center.

Front 19

What are the 3 COMMON inherited disorders associated with nucleotide irregularities? Slide 13

Back 19

Gout, immunodeficiencies, renal stones

Front 20

De novo synthesis of nucleotides occurs when there is _ intake of nucleotides in the diet. Slide 14

Back 20

Decreased

Front 21

Salvage of nucleotides (esp. in enterocytes) occurs when there is _ intake of nucleotides in the diet. Slide 14

Back 21

Increased

Front 22

Ribose-5-phosphate is the substrate for PRPP synthetase. Where does the substrate come from? Slide 16

Back 22

Pentose phosphate pathway (PPP), off the glycolysis cycle.

Front 23

In addition to ribose-5-phosphate, what does PRPP synthetase require to function correctly? Slide 16

Back 23

ATP for the 2 additional phosphate groups

Front 24

Genetic problems with PRPP typically are due to what dysfunction? Slide 16

Back 24

Due to a defect in feedback inhibition (regulation). Not an enzymatic deficiency of PRPP synthetase because deficiencies of PRPP would result in death shortly after fertilization.

Front 25

What clinical disorder is MOST COMMONLY associated with a defect in PRPP synthetase? Pg 5

Back 25

Gout (mainly due to the lack of product inhibition)

Front 26

During de-novo synthesis of purines, how many molecules are added at a time? Slide 17

Back 26

One

Front 27

Explain how the [PRPP] regulates the rate of de-novo synthesis of purines.

Back 27

The more PRPP (substrate) you have, the more the reaction will be pushed to create more purines (products). Le Chatelier’s principle

Front 28

A gene on chromosome 21 codes for a tri-functional enzyme. Name the enzyme and its significance in down’s syndrome. Slide 17

Back 28

GARS-AIRS-GART. The enzyme is used until birth in the de-novo synthesis of purines, when it normally becomes downregulated. This downregulation does not occur in down’s syndrome.

Front 29

Explain the energy requirements for the de-novo synthesis of purines. Slide 17

Back 29

GTP is required for the synthesis of AMP. ATP is required for the synthesis of GMP. This acts to ensure an equal amount of each purine is created.

Front 30

Describe the “purine nucleotide cycle” that occurs in the de-novo synthesis of purines. Slide 18

Back 30

IMP -> (aspartate donates a “N”) → adenylosuccinate -> (fumarate released to replenish TCA cycle intermediates) -> AMP -> (AMP deaminase) -> IMP

Front 31

Describe the reaction AMP deaminase catalyzes and the pathology associated with its deficiency. Slide 18

Back 31

AMP -> IMP. Deficiency of the muscle-specific ISOenzyme is apparently a common cause of exercise-induced myopathy and probably the most common cause of metabolic myopathy in the human.

Front 32

What critical reaction does thymidylate synthase catalyze in the de-novo synthesis of pyrimidines? Slide 19

Back 32

A very important enzyme involved in one-carbon metabolism (FH4) that forms dTMP from dUMP. Thymidylate synthase is REQUIRED for the de-novo synthesis of thymidine (a pyrimidine).

Front 33

Describe how the 1st allosteric enzyme discovered changes in response to increased levels of ATP and CTP. Slide 20

Back 33

Aspartate transcarbamoylase (ATCase) found in the de-novo synthesis of pyrimidines is the MAJOR enzyme responsible for ensuring an equal amount of pyrimidines and purines are produced. High levels of ATP (as from de-novo synthesis of purines) causes the reaction rate of ATCase to increase. High levels of CTP (as from de-novo synthesis of pyrimidines) causes the reaction rate of ATCase to decrease.

Front 34

Compare and contrast purine and pyrimidine de-novo synthesis. Slide 21 & 22

Back 34

See the chart in the study guide!!!

Front 35

What are the 3 kinds of molecules used for one-carbon metabolism? Slide 23

Back 35

THF/FH4 (tetrahydrofolate) & SAM (SAM also imprints DNA), folate

Front 36

One carbon metabolism is crucial for the formation of what pyrimidine? Slide 23

Back 36

Thymine (dUMP -> dTMP) via thymidylate synthase

Front 37

Briefly explain what is the salvage pathway. Slide 23

Back 37

Recycling bases by adding them to PRPP to make nucleotides

Front 38

What reaction does ribonucleotide reductase catalyze? Slide 23

Back 38

XDP -> dXDP (forms a deoxyribose by reducing the ribose sugar)

Front 39

What 2 enzymes are upregulated and required during DNA replication in the cell cycle? Slide 25

Back 39

Thymidylate synthase (TS) is required to form dTMP. Dihydrofolate reductase (DHFR) is an enzyme that helps regenerate the FH4 required for thymidylate synthase to function.

Front 40

What is the relationship between folate and methionine in one-carbon metabolism? Slide 26

Back 40

Methyl-THF (a form of folate) is “stuck” without methionine synthase + B12. In the presence of methionine synthase & vitaB12, methionine & folate are produced

Front 41

In regards to one-carbon metabolism, what clinical symptoms does a deficiency of folic acid and vitamin B12 cause? Slide 28

Back 41

Macrocytic anemia (also known as megaloblastic anemia). Cells grow, but don’t divide because there is not enough material to replicate DNA (No methylene-THF = no dUMP -> dTMP). If there is not folic acid, there will be a higher risk for neural tube defects because folic acid helps to replenish methlyene-tetrahydrofolate.

Front 42

Where can folic acid and vitamin B12 be found in diets? Slide 28

Back 42

Folic acid = liver, green leafy veggies (also breads, cereals, flours, rice are fortified with folate). VitaB12 = animal protein, liver, milk, eggs (vegetarians may have a hard time eating enough B12)

Front 43

What is methotrexate (MTX)? What happens in MTX resistant cells? Slide 29

Back 43

An analogue of FH4 that is a potent competitive inhibitor of dihydrofolate reductase (DHFR). MTX will act to inhibit thymidylate synthase indirectly. In MTX resistant cells, the gene for DHFR is induced and amplified.

Front 44

A high level of homocysteine in the blood is an indicator of what clinical disease? Slide 31

Back 44

CAD

Front 45

What type of reaction and cofactor is responsible for eliminating excess homocysteine? Slide 31

Back 45

Homocysteine is eliminated by a transaminase reaction by vitamin B6

Front 46

Name the associated enzymes that require the following to function: folate, vitamin B12, vitamin B6. Slide 31, 25

Back 46

Folate = methionine synthase & DHFR, vitamin B12 = methionine synthase, vitamin b6 = transaminase reaction to eliminate homocysteine

Front 47

What is the purpose of SAM (SAMe) in one carbon metabolism? Slide 32

Back 47

A cofactor which donates methyl groups to become SAH

Front 48

What molecule is responsible for methylating nucleotides in DNA? Slide 33

Back 48

SAM. This is another example of the importance of one-carbon metabolism.

Front 49

What 2 enzymes (and their products) are required to make DNA from RNA? Slide 34

Back 49

Thymidylate synthase (producing dTMP) and ribonucleotide reductase (producing dADP, dGDP, or dCDP). Remember RR does not form dTMP (dTMP is so special it is formed by an enzyme named after itself).

Front 50

Describe which ribonucleotides are the substrates for ribonucleotide reductase? Slide 34

Back 50

ADP, GDP, CDP, but NOT TDP

Front 51

What are the products of ribonucleotide reductase? Slide 34

Back 51

Deoxynucleotide diphosphates (dADP, dGDP, dCDP)

Front 52

Describe the 2 regulatory sites on ribonucleotide reductase. Slide 35

Back 52

1.Activity sites: ATP increases overall activity and dATP (product) decreases overall activity. 2.Substrate specificity site: all the products (dADP, dGDP, and dCDP) have feedback inhibition on RR.

Front 53

Explain hydroxyurea’s action on ribonucleotide reductase. Slide 35

Back 53

Hydroxyurea inhibits RR. Hydroxyurea is upregulated in patients with sickle cell and increases [Hb F]. People with sickle cell will have less deoxynucleotide diphosphates.

Front 54

What if a cell already has the bases it needs to make additional copies of DNA? Slide 36

Back 54

It can recycle the bases via the “salvage” pathways.

Front 55

How would a defect in salvage lead to increased PRPP levels? Slide 36

Back 55

The enzyme xPRT uses PRPP and a base to form nucleotides. If the salvage pathway was defective, then no PRPP would be used by xPRT, resulting in an increased [PRPP]

Front 56

What 4 nucleotides can be made with the salvage pathway? Slide 36

Back 56

AMP, GMP, IMP, OMP

Front 57

What tissues in the body undergo extensive salvage of nucleotides? Slide 35

Back 57

Brain, immune cells (B &T), enterocytes

Front 58

Name the 3 salvage enzymes discussed in lecture and their substrates. Slide 35

Back 58

APRT = adenine, OPRT = orotic acid, HGPRT = guanine or hypoxanthine. (all 3 enzymes are types of phosphoribosyltransferases = xPRT)

Front 59

Mutated APRT results in? Slide 35

Back 59

Renal stones

Front 60

Mutated OPRT results in? Slide 35

Back 60

Orotic acid crystals

Front 61

Mutated HGPRT results in? Slide 35

Back 61

Gout (partial) or Lesch-Nyhan disease

Front 62

What is Lesch-Nyhan disease? Slide 37

Back 62

X-linked disorder, and thus, often affects males. Starting around age 2, the boys will self-mutilate themselves. This illustrates the importance of the salvage pathway in the brain.

Front 63

Explain how nucleoside kinases help with further recycling? Slide 38

Back 63

Nucleoside kinase help recycle nucleosides. They add a phosphate group to the nucleoside to convert it into a nucleotide. This requires ATP. Examples include: uridine kinase, cytidine kinase, thymidine kinase, deoxycytodine kinase, adenosine kinase.

Front 64

What is the main product produced in purine degradation & not pyrimidine degradation? Slide 41

Back 64

Uric acid, with is fairly insoluble (we are close to the solubility constant)

Front 65

What molecule is responsible for inhibiting xanthine oxidase, an enzyme found in the purine degradtion pathway, and why is this significant? Slide 41

Back 65

Allopurinol is a “suicide inhibitor”. This analog of hypoxanthine acts in the purine degradation pathway to help to prevent gout because the other products are much more soluble

Front 66

What is thought to play a larger role in gout, genetics or environment? Slide 41

Back 66

Genetics

Front 67

Why is uric acid a benefit to our bodies as long as it doesn’t crystallize? Slide 41

Back 67

It is an antioxidant in the non-crystalline state.

Front 68

Gout is caused by the accumulation of uric acid. Mechanistically, what are the 3 major theories? Slide 42

Back 68

1.Increased PRPP (due to increased PRPP synthetase activity, decreased salvage pathway activity, and/or increased pentose phosphate pathway). 2. Increased purine breakdown. 3.Decreased uric acid excretion

Front 69

Describe a theoretical sequelae for the development of gout that was discussed in lecture. Slide 44

Back 69

Excessive alcohol consumption at night results in dehydration -> the loss of H20 moves uric acid closer to its solubility constant -> take asprin in the morning for hangover -> ASA and uric acid compete for the same transporter to be excreted -> more uric acid stays in the body -> gout

Front 70

Explain why a high concentration of purines can lead to gout. Slide 42

Back 70

High purines -> increased breakdown -> increased uric acid -> gout

Front 71

What are the 3 genetic causes of gout? Slide 45

Back 71

1.Deficiency of G6Phosphatase (Von Gierke’s glycogen storage disease)- High levels of G6P buildup and is then forced into PPP to make ribose-5-P. 2.Disorders of PRPP synthetase- lack of feedback inhibition resulting in high amounts of PRPP, Km or Vmax may be changed from normal. 3.Partial or complete deficiency of HGPRT (salvage enzyme)

Front 72

What 2 enzymatic deficiencies result in SCID (severe combined immunodeficiency)? Slide 46

Back 72

ADA deficiency (adenosine deaminase), PNP deficiency (purine nucleoside phosphorylase)

Front 73

What disease is associated with the “bubble boy” and was the first disease treated by somatic cell gene therapy? Slide 48

Back 73

Adenosine deaminase deficiency

Front 74

What is the result of an ADA deficiency? Slide 48

Back 74

Increase in dATP. This will affect BOTH types immune cells (T & B cells) leading to SCIDS

Front 75

What are the 3 possible causes of ADA? Which is the most likely cause? Slide 49

Back 75

1.increased [cAMP] causing overactivity 2.increased [SAH] leading to increased [homocysteine] 3.increased [dATP] will inhibit ribonucleotide reductase leading to decreased DNA synthesis (this is probably what happens)

Front 76

Why do pyrimidines not have any degradation problems? Slide 51

Back 76

The end-products are highly water soluble. In addition, nitrogen is excreted as part of urea and the carbon skeletons enter the TCA cycle.

Front 77

Name 4 antimetabolites discussed in class. Slide 52

Back 77

Beta-D-arabinofuranosylcytosine. 5-fluorouracil. 6-mercaptopurine. 2’,3’-dideoxy-3’-azidothymidine (AZT)

Front 78

What is the drug combivir? Slide 53

Back 78

A combination of lamivudine (epivir) & zidovudine (retrovir). Both are nucleoside analogues used to treat, in combination, HIV