Biochemistry I Exam Iii

Front 1

What are the overall anabolic and catabolic pathways involved in nucleotide metabolism?

Back 1

Synthesis and Salvage (anabolic) Degradation ( catabolic)

Front 2

What major difference is there between purine and pyramidine synthesis in terms of when and how the ring is added? Both purine and pyramidine synthesis involve a molecule in common , what is it?

Back 2

Purines get converted to PRPP first from ribose-5-phosphate then have the ring added. Pyramidines do the opposite. PRPP

Front 3

3) What molecule is utilized in the start of the purine synthesis pathway? What molecule is formed by purine synthesis pathway? What is the name of the enzyme that catalyzes the addition of the first component of the purine ring? What nitrogen-containing amino acid donates the first part of the ring?

Back 3

PRPP goes to IMP. Gln-PRPP aminotransferase, Glutamine

Front 4

4) How many enzymatic steps are required to synthesize IMP from PRPP in humans? What is the cellular localization of all the enzymes that carry out these steps?

Back 4

10, in the cytosol

Front 5

What carrier is utilized in 2 different steps to add to the ring? What vitamin is it derived from? What atom does it donate?

Back 5

N-10 formyl THF, from vitamin B (folate), the first carbon

Front 6

What is the name of the enzyme required to turn folate into the form used in purine synthesis? How many steps? What chemical changes does it make in folate? Where in purine and pyramidine synthesis does inhibition of this enzyme have an effect?

Back 6

DHFR, 3, reduces folate to DHF and THF, steps 1 and 2 of pyrimidine synthesis.

Front 7

The pathway that is most affected by sulfa drugs is :

Back 7

Prokaryotic purine synthesis

Front 8

What nucleotides are formed from IMP?

Back 8

GMP and AMP

Front 9

9) What is the only enzyme that is known to be regulated in the steps of forming IMP from PRPP? What are the allosteric activators of this enzyme? What are the allosteric inhibitors of this enzyme?

Back 9

Glutamine PRPP aminotransferase. PRPP activates. AMP, GMP, IMP inhibit

Front 10

10) What is the allosteric inhibitor of adenylosuccinate synthetase? What is the allosteric inhibitor of IMP dehydrogenase?

Back 10

AMP inhibits adenylosuccinate synthetase, GMP inhibits IMP-DH

Front 11

11) What’s the difference in mechanism between inhibition by thio-IMP of 1) glutamine –PRPP aminotransferase 2) adenylsuccinate synthetase and IMP-DH

Back 11

1) Allosteric 2) competitive

Front 12

12) Can 6-mercaptopurine be incorporated into DNA and if so what is the effect?

Back 12

Yes, it blocks replication

Front 13

13) What do the acronyms HGPRT and APRT stand for and what do they do? What disease results from HGPRT deficiency? What are the symptoms? What is the reason for the increase in uric acid levels of the HGPRT deficient patient? What is their usual cause of death? Why do you need to ask 18 questions in one?

Back 13

APRT is adenine phosphoribosyltransferase turns adenine and PRPP into AMP. HGPRT is hypoxanthine-guanine phosphoribosyltransferase and turns guanine and PRPP into GMP. Deficiency leads to Lesch-Nyhan syndrome which causes mental retardation, self mutilation, and spasticity. Uric acid builds up because it leads to increased turnover of purines thus an increase in the rate of purine synthesis leading to a buildup of uric acid. People with Lesch-Nyhan die of renal failure

Front 14

14) If there were no salvage pathways in purine metabolism, would 6-mercaptopurine be effective as a chemotherapy agent?

Back 14

Yes because it inhibits Gln-PRPP-AT which is used in purine synthesis so it would still be effective.

Front 15

15) 6-mercaptopurine itself doesn’t inhibit enzymes, but is the precursor to what molecule that is?

Back 15

Thio-IMP

Front 16

16) How many enzymatic steps are required to synthesize OMP from glutamine and PRPP in humans? What is the cellular localization of all but one of the enzymes that carry out all these steps?

Back 16

4. cytosol

Front 17

) What cytosolic enzyme that catalyzes an ATP-requiring step of pyrimidine synthesis has an analogous mitochondrial that participates in the urea cycle? What is an enzyme that catalyzes the first step of pyrimidine synthesis? What are important differences between cytosolic and mitochondrial enzymes? Which enzyme of pyrimidine synthesis is found only in the mitochondria? Why is it advantageous that it is a mitochondrial enzyme?

Back 17

CPS II has an analog in the mitochondria (CPS I). Mitochondrial proteins usually can’t leave the mitochondria. Tight regulation of CPS II and not of CPS I. This is important to keep different parts of the cell cycle separate. Dihydroorotate Dehydrogenase is found exclusively in the mitochondria where conditions are appropriate.

Front 18

18) Why does excessive amounts of NH4 lead to elevated levels of orotic acid in the urine? Why does this primarily affect the liver?

Back 18

Because there’s too much ammonium which leads to less regulation of CPS I which leads to excess orotate. Primarily affects the liver because that’s where it detoxifies stuff.

Front 19

19) What enzyme is present in low levels in e-coli lab strains?

Back 19

Orotate PRT, certain e-coli is deficient here and cannot live in humans.

Front 20

20) What are the sources of carbon and nitrogen atoms in the pyrimidine ring?

Back 20

Glutamine and CO2

Front 21

21) What molecule is formed by the pyrimidine synthesis pathway?

Back 21

UMP

Front 22

22) How is the pyrimidine synthesis pathway like a salvage pathway?

Back 22

They both end up with UDP by dephosphorylating ATP

Front 23

23) Are other pyrimidine bases than orotate salvaged? Why are salvage pathways useful?

Back 23

Uridine and thyamidine are NOT CYTOSINE. Because they conserve energy by breaking down into stuff the cell needs and other stuff can be created easier.

Front 24

24) What purine triphosphate activates pyramidine synthesis?

Back 24

ATP

Front 25

25) How is cytidine monophosphate (CMP) formed?

Back 25

Its not formed. Its found in RNA????? Or it doesn’t exist???

Front 26

26) What purine triphosphate allosterically activates pyrimidine synthesis?

Back 26

ATP

Front 27

27) How is thymidine monophosphate (TMP) formed?

Back 27

From Ts Folate and UMP give dUMP as an intermediate

Front 28

28) What carrier donates a carbon to form TMP from dUMP? What is the enzyme that catalyzes the reaction?

Back 28

N5-N10 methylene THF. Ts is the enzyme.

Front 29

29) If there were no salvage pathways in pyrimidine metabolism, would 5-flourouracil be as effective as a cancer chemotherapeutic?

Back 29

Yes because it inhibits TMP synthesis causes suicide at fdUMP???????

Front 30

30) 5-flourouracil itself doesn’t inhibit enzymes but is the precursor to what enzyme that does?

Back 30

FdUMP

Front 31

31) What type of inhibition does flouro-deoxyuridine monophosphate have on thymidylate synthase?

Back 31

irreversible

Front 32

32) Can 5-flourouracil be incorporated into DNA? What’s the effect?

Back 32

Yes. Probably blocks synthesis of thymidine which is required for DNA synthesis

Front 33

33) What are some strategies cancer cells have been observed to adopt to exhibit methotrexate resistance?

Back 33

??????????

Front 34

34) What is the mechanism of ICI D1694? Considering that it could be said that ICI D1694 resembles methotrexate would it be expected to cause the same, fewer or more side effects?

Back 34

Inhibits N5N10 methylene THF. Similar effects as methotrexate

Front 35

35) How is the use of leucovorin and methotrexate different from the use of leucovorin with 5-flouro-uracil?

Back 35

Leucovorin is antagonistic of methotrexate. 5-flouro-uracil is an agonist of leucovorin.

Front 36

36) What do nucleotide kinases do? What do nucleotide diphosphate kinases do? What nucleotide can also do this by glycolysis or oxidative phosphorylation?

Back 36

Phosphorylate things, dephosphorylate things. Similar to glucokinase and hexokinase.

Front 37

37) What is the name of the enzyme that converts ribonucleotides to deoxyribonucleotides? What molecule does the reducing power come from originally?

Back 37

Ribonucleotide reductase. thioredoxin or glucoredoxin (????)

Front 38

38) What class of enzyme breaks nucleic acids into nucleotides? What class of enzymes removes phosphates from nucleotides (converting them to nucleosides)? What class of enzymes breaks them down into bases and sugars?

Back 38

Nucleases, phosphorylases, nucleotidases???

Front 39

39) What muscular enzyme deaminates adenine nucleotide? What enzyme in other tissues deaminates adenosine nucleoside? What is the difference in terms of the order in which the phosphate group and amino group are removed?

Back 39

Adenosine deaminase. In muscle it gets deaminated first, in everywhere else it gets dephosphorylated first.

Front 40

40) What is the enzyme that is defective in most patients with SCID? What are the 2 enzymes of purine degradation that may be defective in SCID?

Back 40

Most common is ADA deficiency. May also be from PNP deficiency. IL2 gamma receptor defect is the most prevalent cause

Front 41

41) What is the common treatment for SCID? Why does it work? What is the drawback? What is an alternative treatment? Why isn’t this available for people with the other form of the defect? Why does enzyme replacement therapy for SCID utilize the enzyme conjugated to PEG rather than the enzyme alone?

Back 41

Enzyme replacement. PEG causes it to increase during lifetime in the blood. Because it is so rare. Bone marrow transplant for others.

Front 42

42) There was an attempt made to replace what enzyme in the first gene therapy trial designed to partially cure or cure a patient in 1990? Was a cure achieved? Why is SCID a “good” disease for early attempts at gene therapy?

Back 42

ADA. No. It’s an awful disease, its monogenic and its on an accessible organ.

Front 43

43) What is the name of the heterogenous base attached to IMP?

Back 43

Hypoxanthine

Front 44

44) What is the nitrogenous product of purine degradation that is excreted? What is it converted from? By what enzyme?

Back 44

Uric acid, xanthine, xanthine oxidase

Front 45

45) What is gout? What are some underlying causes of gout? What are the symptoms and what explains them?

Back 45

Too much uric acid that precipitates in joints and stuff. Under excretion of the kidney, defect with purine metabolism. Pain, renal failure due to the precipitation of uric acid.

Front 46

46) What do allopurinol and rasburicase do? In what way is rasburicase superior? What are the drawbacks of rasburicase and what is it about the drug that leads to these drawbacks? How do the drawbacks explain why allopurinol is preferred and rasburicase is used for people with cancer?

Back 46

allopurinol inhibits xanthine oxidase, rasburicase breaks down uric acid. Rasburicase is better because its more efficient? It is expensive and needs to be given as an IV. Allopurinol is cheap and can be given as a pill but since people with rasburicase already have IVs and stuff, they give them that.

Front 47

47) The degeneration of cytosine, uracil, and thymine have what 2 degradation products in common? What else for cytosine and uracil? Thymine?

Back 47

CO2 and ammonium. C and U have B-alanine too. Thymine gives B-aminoisobutyrate

Front 48

Tetrahydrobiopterin synthesis involves what nucleotide? NAD+ synthesis involves what 2 nucleotides? FMN synthesis involves what vitamin? FAD+ synthesis involves what 2 nucleotides? Coenzyme A synthesis involves what vitamin? Amino acid? Nucleotide?

Back 48

Tetrahydrobiopterin comes from GTP. NAD needs ATP and nicotinamide. FAD needs riboflavin and ATP?? Acetyl CoA needs ATP, pantothenate, and cysteine.

Front 49

49) What is the effect of AZT on a cell? Does it require a salvage pathway to become active?

Back 49

It inhibits DNA elongation. No.

Front 50

1. What does semiconservative replication mean?

Back 50

The two daughter strands of DNA each contain one strand of the parent DNA.

Front 51

2. What three observations have been made of all DNA polymerases?

Back 51

Incoming bases are selected by complementary base pairings by hydrogen bonding with a template strand. Chain growth is in a 5’ to 3’ direction and anti-parallel to the direction of the template strand. All DNA polymerases require a primer strand to add bases to.

Front 52

3. What is the function of DNA polymerase I? What is a Klenow fragment?

Back 52

DNA polymerase I is a 5’ to 3’ polymerase, a 3’ to 5’ exonuclease (proof reading) and a 5’ to 3’ exonuclease ( repair and removal).
A Klenow fragment is the segment of the DNA polymerase that contains the exonuclease activity.

Front 53

4. What is the function of DNA polymerase III?

Back 53

It is the major DNA polymerase in prokaryotes

Front 54

5. What is the function of a topisomerase? Helicase?

Back 54

A topisomerase relieves supercoiling and a helicase unwinds double stranded DNA.

Front 55

6. In replication, which strand is the leading strand and which is the lagging strand?

Back 55

The leading strand is the strand being continuously synthesized and the lagging strand is the strand undergoing discontinuous synthesis.

Front 56

7. How is RNA used in DNA replication? What are Okazaki fragments?

Back 56

RNA acts as the primer for the discontinuous replication of DNA on the 3’-5’ (lagging) strand. Okazaki fragments are the pieces of DNA that are replicated on the 3’-5’ (lagging) strand that will eventually be joined by ligases to make a complete DNA replicate strand.

Front 57

8. Where is e-coli DNA replication initiated and where is it terminated?

Back 57

Initiated at OriC when Dria A (an initiation factor) binds to it. Terminated at ter site.

Front 58

9. What are the processivities of DNA polymerases I and III?

Back 58

DNA polymerase I has a low processivity (20 bases before it disassociates)
DNA polymerase III has a high processivity (5 million bases before it disassociates)

Front 59

1) Name three types of sphingolipids and describe them.

Back 59

Cerebrosides – ceramide monosaccharides are attached to the sphingolipid (ex. Myelin)
Sulfatides – cerebromonosaccharides sulfates
Gangliosides – acidic ceramide oligosaccharides which contain N-acetyl neuraminic acid. Also known as sialic acid. In cell membranes.
Phosphosphosphingolipid – ceramide and CDP-choline or ceramide and phosphatidyl Choline. Sphingomyelin is the best.

Front 60

2) What compounds are the precursors for sphingosine?

Back 60

Sphinganine, which comes from 3-ketosphinganine, which comes from Palmitoyl CoA and Serine.

Front 61

3) How is ceramide formed?

Back 61

Ceramide and COASH are formed from sphingosine and Acyl CoA via an acyl CoA transferase reaction.

Front 62

4) How is sphingomyelin synthesized?

Back 62

Ceramide and CDP-choline to sphingomyelin and CMP (most likely)
Ceramide and phosphatidyl choline to sphingomyelin and DAG (possibly, but probably not)

Front 63

5) What are the four types of glycosphingolipids?

Back 63

Cerebrosides – ceramide monosaccharides are attached to the sphingolipid (ex. Myelin)
Sulfatides – cerebromonosaccharides sulfates
Gangliosides – acidic ceramide oligosaccharides which contain N-acetyl neuraminic acid. Also known as sialic acid. In cell membranes.
Globisides – neutral cerebroside oligosaccharides

Front 64

6) How are cerebrosides synthesized?

Back 64

Ceramide and a UDP-Sugar goes to cerebroside and UDP

Front 65

7) What is PAPS and what is it used for?

Back 65

3-phosphoadenosine-5-phosphosulfate and it is used in the synthesis of sulfatide from galactocerebroside.

Front 66

8) What defect exists in Gaucher’s disease?

Back 66

Glucocerebrosidase is deficient so glucocerebroside builds up because it can’t get converted to ceramide.

Front 67

9) What defect exists in Tay-Sachs disease?

Back 67

Hexosaminidase A is deficient

Front 68

10) What are the general structural features of gangliosides?

Back 68

Acidic ceramide oligosaccharides that contain N-acetyl neuraminic acid

Front 69

1) Where is DNA found in eukaryotes? How is DNA packaged?

Back 69

Nuclei, some in the mitochondria. It is packed by wrapping dsDNA around octomers of histones, the histone groups are connected by linker DNA and then get coiled and supercoiled into chromatin.

Front 70

2) What are some contrasts between features of prokaryotic and eukaryotic DNA replication?

Back 70

More DNA in eukaryotes than prokaryotes. Slower movement of replication forks in eukaryotes. Prokaryotes continuously synthesize DNA, eukaryotes only do during S-phase. Eukaryotes use more DNA polymerase molecules, have more than 1 origin and replication is bidirectional.

Front 71

3) Which DNA polymerase is believed to be responsible for leading-strand synthesis and which for lagging strand synthesis in eukaryotes?

Back 71

Leading strand = DNA polymerase delta
Lagging strand = DNA polymerase alpha

Front 72

4) What proteins are in nucleosomes and why do they bind to DNA?

Back 72

2 molecules of H2A, H2B, H3 and H4 on the inside and H1 on the outside. Because they’re positively charged and DNA has a negative charge.

Front 73

5) What is PCNA and what role does it play?

Back 73

PCNA = proliferating cell nuclear antigen (aka cyclin). Forms a clamp around the template DNA and increases the processivity of DNA polymerase delta (activates).

Front 74

6) What is the arrangement of nucleosomes after DNA replication?

Back 74

New histones are created at the same time and end up along 1 daughter strand near each replication fork and old histones are on the other new strand. May explain why replication fork movement is slow and the shortness of the Okazaki fragments.

Front 75

7) What is the model used to describe DNA replication in mitochondria?

Back 75

Displacement loop mechanism

Front 76

1) What is the definition of biopharmaceutical? What is the definition of recombinant DNA?

Back 76

A biopharmaceutical is a drug produced in living cells. Recombinant DNA is DNA that is made by splicing the DNA of 2 different organisms together.

Front 77

2) Describe how one “recombines” DNA including cutting, hybridizing and ligating it? What enzymes are used for the cutting of DNA?

Back 77

Restriction enzymes are used to “cut” DNA. The restriction enzymes are chosen based on the desired DNA sequence. The DNA is then hybridized by binding with complementary base pairs of a matching strand in the desired organism. Ligation is the binding of the 2 strands of DNA using a lygase.

Front 78

3) What is a plasmid? Give an example of a gene found on a plasmid that is naturally occurring.

Back 78

A plasmid is circular DNA in bacteria. Anthrax toxin occurs naturally on a plasmid.

Front 79

4) What about insulin causes difficulty in producing it by recombinant DNA (two things)?

Back 79

Insulin is not a simple polypeptide chain A and B chain and it has 3’ disulfide linkages.

Front 80

5) What are the advantages of producing insulin in bacteria? What are the advantages of producing it in yeast?

Back 80

Bacteria secretes product more often are easy to maintain and manipulate, yeast can secrete it as a folded protein and is more mammalian like.

Front 81

6) What do we mean by calling enebrel (etanercept) a fusion protein? Why does it involve fusing 2 proteins i.e. what properties are due to each part? What do we mean by calling Enebrel a decoy?

Back 81

Its is fused to IgG1. TNFR is insoluble and degrades quickly. Have the gene for the TNF receptor and IgG1 is soluble and can dimerize. It looks like a TNF receptor (?) so it lures TNF-alpha (a tumor promoter) away from the cell.

Front 82

7) It might be quicker to go from the idea of inhibiting TNF to a drug by making the drug as a biopharmaceutical than it would be to go from the idea of making a conventional drug, Why? What might be an advantage of a small molecule conventional drug?

Back 82

You can use the body’s own mechanisms instead of making a drug in a factory.

Front 83

8) What are the advantages of producing Enebrel in Chinese hamster ovary cells?

Back 83

Its more like production in humans, the folds of the proteins are more humanlike too.

Front 84

9) Are drugs on the market more likely to be polyclonal antibodies or monoclonal antibodies or recombinant DNA molecules based on monoclonal antibody sequence information? Why? What is meant by a humanized antibody?

Back 84

Recombinant DNA based on monoclonal antibody sequence information? Because it’s the easiest to make. A humanized antibody is one people have had an immunogenic response to so they make it in the rat plasmid and then they replace it with human sequence in the plasmid.

Front 85

10) It might be quicker to go from the idea of inhibiting HER2 to a drug by making the drug as an antibody than it would be to go from the idea of making a conventional drug. Why?

Back 85

Because its easier and cheaper and it lets the body heal itself? You don’t have to use effort designing stuff.

Front 86

11) What is the oft-fatal adverse effect of Herceptin? What cancer drugs enhance the chances of this adverse effect?

Back 86

Blocks recovery of heart leading to Heart failure. Anthrocyclines, Herceptin.

Front 87

12) What are the reasons biopharmaceuticals all have to be horrendously expensive?

Back 87

They don’t and they aren’t (insulin). But if this were true it would be because they are complicated to make and research.

Front 88

13) What would be one avenue to offering a less expensive drug that is often taken for small molecule drugs but is not yet available for biopharmaceuticals under today’s laws and regulations? Why might it be a while before that route is available to biopharmaceuticals?

Back 88

Biogenerics. Because bioequivalence is hard to prove, that it’s the same

Front 89

What does PCR (polymerase chain reaction) accomplish?

Back 89

PCR amplifies a fragment of DNA for things like sequencing and cloning.

Front 90

15) What does the making of transgenic animals accomplish? What do knockout animals help determine? What are key differences between the procedures to make transgenic and knockouts?

Back 90

Transgenic animals are for studying gene function. Knock outs are for studying gene transport. ??????????