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Biochemistry > Week 3 > Flashcards

Week 3 Flashcards

1
Q

In Eukaryotic cells , DNA is bound to proteins, forming a complex called ______.

A

Chromatin

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2
Q

What phase do the Sister chromatids condense into discrete visible chromosomes ?

A

Metaphase

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3
Q

What are the 4 free bases of DNA?

A

Adenine
Guanine
Cytosine
Thymine

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4
Q

What is the name for the sugar in DNA?

A

Deoxyribose (missing the hydroxyl group on carbon 2 that is found on ribose)

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5
Q

What are Nucleotides composed of?

A

Base + Sugar+ phosphate

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6
Q

What are Nucleosides composed of ?

A

Base+ Sugar (no phosphate)

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7
Q

If the sugar is a deoxyribose rather than ribose, the nucleoside has a “ _____ “ as a prefix , example for Adenine to Adenosine is ?

A

Deoxy

DeoxyAdenosine

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8
Q

What is the monomer unit of nucleic acids?

A

Nucleotides

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9
Q

What is the inorganic phosphate attached to in Nucleotides ?

A

5’-hydroxyl group of the sugar in ester linkage

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10
Q

In Nucleosides, the nitrogenous base is linked by a ________ bond to the anomeric carbon of the sugar.

A

N-glycosidic

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11
Q

What type of bond connects the Nucleotide chains to form DNA backbone?

A

Phosphate backbone - linked by phosphodiester bonds

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12
Q

What is a phosphodiester bond ?

A

linkage of 3’Carbon of one sugar and the 5’ Carbon of the next sugar with Oxygen from a phosphate group

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13
Q

What type of bond exists between bases that holds them together ?

A

Hydrogen bond

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14
Q

How many bonds does Thymine and Adenine have ?

A

2 bonds - Hydrogen bonds (weaker than covalent and allow for seperation )

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15
Q

How many bonds does Guanine and Cytosine have ?

A

3 bonds- Hydrogen bonds

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16
Q

What is the Nucleoside name for Adenine ?

A

Adenosine

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17
Q

What is the Nucleoside name for Guanine ?

A

Guanosine

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18
Q

What is the nucleoside name for Thymine?

A

Thymidine

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19
Q

What is the nucleoside name for Uracil ?

A

Uridine

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20
Q

What is the nucleoside name for Hypoxanthine ?

A

Inosine

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21
Q

What forces stabilize the double helix?

A

Stacked bases have Van Der Waals forces and hydrophobic effects on interior of helix
-additionally the hydrogen bonds between bases

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22
Q

What allows for the negative charge and binding of proteins to the outside of DNA ?

A

the Phosphate group has an exposed -OH on outside that will lose the H ion at physiological pH- negative charge, facilitates binding specific proteins

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23
Q

What forces cause DNA to separate ?

A

Alkali (increased -OH) and heat cause denaturing (strands separate)

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24
Q

What is the different effect of Alkalki on DNA vs RNA?

A

RNA- phosphodiester bonds are broken

DNA- strands separate

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25
Q

What is hybridization ?

A

DNA is combined with RNA strand

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26
Q

How is DNA packaged in Prokaryotes ?

A

Circular DNA is supercoiled and attached to an RNA-protein core

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27
Q

What do topoisomerases do?

A

Relieve stress of DNA strand in supercoils so unwinding can occur

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28
Q

Eukaryotic DNA binds to equal weight of _____.

A

Histones

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29
Q

What are Histones made of ?

A

Large amounts of Arginine and Lysine (both are Positively charged pKa)

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30
Q

What is a nucleosome core made of ?

A 
DNA wrapped around 2  molecules of each of the 4 classes of histones 
H2A
H2B
H3
H4
(8 histones per nucleosome core)
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31
Q

What does H1 Histone do?

A

Joins the Nucleosomes into strands

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32
Q

What are the helical, tubular coils that Nucleosomes are wound into called?

A

Solenoid structures

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33
Q

What is total number of chromosomes per Diploid cell?

A

46 (23 pairs) - 22 are autosomal

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34
Q

What is the difference between Uracil and Thymine with relation to RNA where RNA uses Uracil instead?

A

Thymine has a methyl group at the position 5 of the ring, Uracil does not

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35
Q

What does PRPP stand for ?

A

Phosphoribosyl pyrophosphate - 5-Sugar in DNA and RNA (pentosphosphate)

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36
Q

What does THF stand for ?

A

Tetrahydrofolate

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37
Q

What does GPRT stand for ?

A

Glutamine-phosphoribosyl Transferase

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38
Q

What does CPS II stand for

A

Carbamoyl phosphate synthase II

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39
Q

What substrates are needed to start Purine synthesis ?

A 
PRPP
Glycine
Glutamine
Asparate
Tetrahydrofolate
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40
Q

What substrates are needed to start Pyrimidine synthesis ?

A

PRPP
Glutamine
CO2
Aspartate

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41
Q

Where does Pyrimidine and Purine synthesis normally occur ?

A

Cytosol in Liver cells

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42
Q

What is the main regulated enzyme in Purine synthesis ?

A

GPRT (Glutamine -phosphoribosyl transferase )

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43
Q

What is Glutamine phosphoribosyl transferase inhibited and activated by ?

A

Activated by presence of PRPP

Inhibited by presence of AMP and GMP

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44
Q

What is the main regulated enzyme in Pyrimidine synthesis ?

A

CPS II (Carbamoyl phosphate synthase II )

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45
Q

What will inhibit Carbamoyl phosphate synthase II in the Pyrimidine synthesis cycle?

A

Presence of UMP (Uridine monophosphate)

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46
Q

What form are bases always synthesized in ?

A

Ribose form with the OH group (hydroxyl) attached still to 2’ Carbon

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47
Q

What enzyme will convert Ribose sugars to Deoxyribose sugars and remove the Hydroxyl group?

A

Ribonucleotide reductase (RR)

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48
Q

What level will the conversion of Ribose sugars to Deoxyribose sugars occur?

A 
Diphosphate level (2 phosphates attached to nucleotide)
Ex: CDP, ADP, UDP, GDP are the substrates required
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49
Q

What is the cofactor of RR (Ribonucleotide reductase) needed for the conversion of Ribose sugars to Deoxyribose sugars at the Diphosphate level?

A

Thioredoxin - Holds the two Hydrogen groups onto its 2 Sulfurs that will donate the Hydrogen with the O from the OH on Ribose sugar to release H2O using the RR

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50
Q

Who does the resupplying of Thioredoxin with Hydrogen on its sulfate groups to then be ready use again as a cofactor with Ribonucleotide reductase (RR)?

A

NADPH will be oxidized and its H will go to the Sulfur on Thioredoxin (has 2 Sulfurs)

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51
Q

What enzyme is used to oxidize the NADPH and reduce the Thioredoxin ?

A

Thioredoxin reductase

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52
Q

Ribonucleotide reductase is regulated with allosteric proteins in what two sites ?

A
  1. Enzyme Activity site - (ATP will turn on, dATP will turn off)
  2. Substrate specificity site (any nucleotide, ATP, dATP, dTTP, and dGTP can all go here)
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53
Q

Where is the Ribonucleotide reductase found in the synthesis pathways ?

A

Near the end when the nucleotide will either be made into DNA or RNA

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54
Q

What needs to be in the two allosteric effector sites of RR for CDP to be changed into dCDP (pyrimidine synthesis) ?

A

Activity site - ATP

Substrate specificity site - ATP or dATP

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55
Q

What needs to be in the two allosteric effector sites of Ribonucleotide reductase for UDP to be changed into dUDP (dUDP is necessary for Pyrimidine synthesis of dTDP to make Thymine base pair)

A
  1. Activity site - ATP
  2. Substrate specificity site -ATP or dATP
    (adenosine or Deoxyadenosine triphosphate)
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56
Q

What needs to be in the two allosteric effector sites of Ribonucleotide reductase for GDP to be changed into dGDP (Purine synthesis) ?

A
  1. Activity site - ATP

2. Substrate specificity site - dTTP (Deoxythimidine triphosphate)

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57
Q

What needs to be in the two allosteric effector sites of Ribonucleotide reductase (RR) for ADP to be changed into dADP (purine synthesis) ?

A
  1. Activity site - ATP

2. Substrate specificity site - dGTP (deoxyguanosine triphosphate)

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58
Q

What is synthesis of Phosphoribosyl pyrophosphate (PRPP) activated by ?

A

Free Phosphate group (Pi)

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59
Q

What does synthesis of Phosphoribosyl pyrophosphate (PRPP) require as a cofactor ?

A

Magnesium (2+) or Mg2+ as cofactor

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60
Q

In the synthesis of Phosphoribosyl pyrophosphate, what is the enzyme used to take 2 phosphate groups from ATP (changes to AMP) and adds them toe the 5’ sugar?

A

PRPP synthetase (requires Mg2+ as cofactor)

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61
Q

Where does the PRPP get the sugar from originally ?

A

Hexos monophosphate pathway - gets it from Glucose

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62
Q

Deacetalyation of the histone proteins ________ the positive charge on lysine residues.

A

Increases (so DNA and Histone binds tighter)

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63
Q

Activation of ribonucleotide reductase by ATP will result int he synthesis of dGDP if ______ is bound to the substrate specificity site.

A

dTTP

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64
Q

What synthesis is needed prior to Purine synthesis to start ?

A

PRPP synthesis

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65
Q

What is the first step in Purine synthesis after PRPP is present ?

A

PRPP is combined with Glutamine through condensation reaction

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66
Q

After the second 6’ ring is added onto 5’ ring of PRPP during Purine synthesis , what is the major converging point ?

A

IMP - Inosine monophosphate

-the IMP is attached to the 6’5’ ring combo that was made in the previous pathway

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67
Q

What is the base found in Inosine monophosphate ?

A

Hypoxanthine (not found in DNA)

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68
Q

One of two options after IMP, is for ADP and GDP to go directly to ____ synthesis after conversion to Triphosphate form in the Purine pathway.

A

RNA

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69
Q

Second of the two options after IMP (purine pathway), is for ADP and GDP to go to the _______ _________ to be converted into their deoxy forms for DNA snythesis.

A

Ribonucleotide reductase

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70
Q

What enzyme is used in the first main step of Purine synthesis where PRPP is combined with Glutamine to make 5’-Phosphoribosyl 1-amine

A

GPRT (Glutamine phosphoribosyl amidotransferase)

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71
Q

What does GPRT (Glutamine phosphoribosyl amidotransferase) do ?

A

enzyme that Aminates (adds NH3 to Carbon) the PRPP and takes of the 2 extra phosphate groups leaving only one on PRPP

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72
Q

What does amination add?

A

NH3 to a carbon on PRPP

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73
Q

What does Glutamine get changed into once it is used with Glutamine Phosphoribosyl amidotransferase enzyme and PRPP to animate PRPP ?

A

Glutamate (Glutamic acid) - missing an amide group (NH3)

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74
Q

What can the Glutamine + PRPP step in Purine synthesis be inhibited by ?

A

High levels of BOTH GMP and AMP

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75
Q

What can the step in Purine synthesis where Ribose-5 phosphate is converted to PRPP be inhibited by (negative feedback) ?

A

BOTH GDP and ADP (purine bases) - negative feedback

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76
Q

What can the step where IMP gets converted to XMP (leads to GMP) be inhibited by ?

A

GMP (its direct product)

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77
Q

What can the step where IMP gets converted to Adenylosuccinate (leads to AMP) be inhibited by ?

A

AMP (its direct product)

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78
Q

What can Glutamine phophoribosyl ammidotransferase (GPRT) be inhibited by ?

A

NEEDS BOTH - (GMP,GDP,GTP) with a (AMP,ADP,ATP)

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79
Q

What is a location that Hypoxanthine is found ?

A

tRNA anticodon and in Inosine Monophosphate (converging point for Purine pathway)

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80
Q

In Purine salvage pathway , what does HGPRT stand for ?

A

Hypoxanthine-Guanine Phosphoribosyltransferase

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81
Q

What does HGPRT function to do in the Purine salvage pathway?

A

It will act to convert hypoxanthine back to IMP and Guanine back to GMP (attaches a phosphate group from PRPP)

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82
Q

How does Adenine get recycles in the Purine salvage pathway if it is a Nucleoside (adenosine) and is not going to go the route of Adenosine kinase back to its AMP (nucleotide form) ?

A
  1. Adenosine is deaminated and converted to Inosine
  2. Inosine converted to Hypoxanthine
  3. Hypoxanthine is acted on by HGPRT back to IMP which can then be changed into AMP again
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83
Q

How does GMP get recycled in the Purine pathway ?

A
  1. GMP goes to Guanosine (nucleoside)
  2. Guanosine is changed into free base Guanine
  3. Guanine is acted on by HGPRT back into GMP
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84
Q

In the recycle pathway , once HGPRT gets you back to IMP, where can the pathway lead to ?

A

Either AMP or GMP production

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85
Q

What do phosphorylase enzymes do in the Recycle pathway for Purines to GMP and IMP ?

A

GMP is cleaved to free base from Guanosine to Guanine

IMP is cleaved to fee base from Inosine to Hypoxanthine

86
Q

What doe Phosphoribosyl transferase enzymes do in the Purine pathway (like HGPRT) ?

A

will transfer a ribose 5-Phosphate to a free base - makes it back into nucleotide

87
Q

Adenosine is the only nucleoside base to be _______ _______ in the Purine pathway

A

Directly phosphorylated - (to reconstruct full nucleotide)

- by way of Adenosine kinase

88
Q

If Adenosine is not directly phosphorylated back into a Nucleotide, what will act on it in the Purine recycle pathway?

A

Adenosine deaminase

-changes it into Inosine - then leads to Hypoxanthine and then IMP which can take it back to AMP or GMP

89
Q

If Hypoxanthine is not recycled with HGPRT , then what will act on Hypoxanthine in the degragation of Purine pathway ?

A

Xanthine oxidase

90
Q

What will Xanthine oxidase do ?

A

turns Hypoxanthine into Xanthine, then acts on Xanthine again to turn it into Uric Acid

91
Q

Is Uric Acid soluble ?

A

No - must be excreted in urine, or it can build up in body and cause disease (like Gout and inflammation)

92
Q

What will inhibit the actions of Xanthine oxidase from creating Uric acid ?

A

Allopurinol (drug for Gout)

93
Q

How does Guanine get changed into Xanthine if it is not recycled by HGPRT ?

A

A NH (amine)group is removed - then will be acted on by Xanthine oxidase only once time (as compared to two times) to make Uric Acid

94
Q

What is the most common cause of Gout ?

Least common ?

A 
Most = poor excretion of Uric Acid through urine
Least = decreased activity of HGPRT
95
Q

What does decreased activity of HGPRT do ?

A

causes increased hypoxanthine and xanthine production in the Purine degragation pathway (cant be recycled normally and more Uric acid is made)

96
Q

HGPRT is responsible for the conversion of Guanine to ____ as wel as hypoxanthine to ______.

A

GMP

Inosine-MP

97
Q

SEVERE loss of HGPRT activity causes what syndrome and what symptoms ?

A

Lesch-Nyhan syndrome = mental retardation, compulsive self-mutilation, gout

98
Q

Partial defects of HGPRT enzyme causes ?

A

no severe Lesch-Nyhan syndrom but some premature Gout

99
Q

Gout can be caused by elevated levels of Uric acid. with respect to a possible HGPRT defect, a mutation leading to ________ _____ of this enzyme is likely to produce gout.

A

Decreased activity

100
Q

What is the Important enzyme at the beginning of the Pyrimidine synthesis pathway?

A

Carbamoyl Phosphate Synthase II

101
Q

What does Carbamoyl Phosphate Synthase II produce and which pathway?

A

Carbamoyl phosphate

-Pyrimidine synthesis pathway

102
Q

What inhibits Carbamoyl phosphate synthase II (pyrimidine pathway)?
What is combined to start pathway with CPSII?

A

UTP inhibits

PRPP is combined to continue pathway

103
Q

Name the First 4 major steps in the pyrimidine pathway?

A
  1. Glutamate +CO2+2ATP
  2. CPS II and PRPP interact to make Carbamoyl phosphate
  3. Aspartate is combined- makes Orortate
  4. PRPP added and CO2 removed makes UMP then UDP
104
Q

What is the diverging molecule for the Pyrimidine pathway?

A

UDP

  • can be acted on to become UTP for direct RNA use
  • OR can be acted on by RR to make dUDP
105
Q

How do you get CTP to use for RNA in Pyrimidine pathway?

A
  1. Carbamoyl phosphate
  2. Orotate
  3. UMP
  4. UDP
  5. UTP
  6. Glutamine added to make CTP (used in RNA)
    - Cytosine Triphosphate
106
Q

How do you get dCTP for use in DNA pyrimidine pathway?

A
  1. after Glutamine is added to UTP to make CTP
  2. changed to CDP
  3. RR acts on CDP to make dCDP
  4. dCDP phosphorylated to dCTP for DNA usage
107
Q

Unlike Purine synthesis, the assembly of the _____ group is completed before the addition of the sugar ______ in pyrimidine synthesis De novo.

A

Ring

PRPP

108
Q

What is the rate limiting step for DNA synthesis that is found in the Pyrimidine synthesis pathway?

A

Changing dUMP to dTMP using Folate and the enzyme:

Thymidylate synthase

109
Q

What is the first major intermediate in the pyrimidine pathway that comes after Carbamoyl phosphate ?

A
  1. Aspartate is added to make Carbamoyl phosphate into Carbamoyl Aspartate
  2. converted into Orotic acid (Orate)
110
Q

How can Orotic acid be diagnostic ?

A

Elevated levels in urine can be suggestive of :

  1. Hereditary orotic aciduria (disease)
  2. Defects in Urea cycle
111
Q

What is the enzyme responsible for the addition of PRPP to Orotic acid or Orotate?

A

Orotate phosphoribosyl transferase (adds sugar phosphate group PRPP)

112
Q

What enzyme is responsible for the changing of OMP to UMP?

A

Orotidine 5-P decarboxylase

113
Q

How do you get dUMP for usage to make dTMP?

A

You must get UMP to UDP so the RR can change it into dUDP, then a phosphate is removed to make dUMP which can be acted on by Thymidylate synthase

114
Q

How does Thymidylate synthase change dUMP to dTMP?

A

it adds a methyl group (CH3) to the top right Carbon ring

115
Q

Who is the Methyl donor for the pyrimidine synthesis in dUMP to dTMP with Thymidylate synthase ?

A

Folate (Methylene FH4)

116
Q

What is the inhibitor for Thymidylate synthase ?

A

5-Florouracil

used to block dUMP converting to dTMP

117
Q

What is the inhibitor for the Dihydrofolate FH2 molecule that is left over after Methylene FH4 donates a methyl group to make dTMP?

A

Methotrexate

118
Q

What is the enzyme that Methotrexate inhibits from acting on FH2 Dihydrofolate ?

A

Dihydrofolate reductase (NADPH is stopped from donating its Electron to reduce it back to FH4)

119
Q

What can block more generally folic acid cycles for creating of folic acid needed for DNA syntheses ?

A

Methotrexate

(blocks Dihydrofolate reductase from using NADPH from reducing it back to FH4

120
Q

When is Folate used in Adenine and Guanine Purine synthesis de novo?

A

2 Locations in creation of double ring before you reach IMP molecule , in cascade cycle between Glutamine + PRPP and IMP

121
Q

When is Folate needed in Pyrimidine cycle ?

A

only when converting dUMP to dTMP

122
Q

Folate derivatives are required for the synthesis of which DNA bases?

A

Adenine
Guanine
Thymine (most critical- most direct impact if inhibited)

123
Q

What is the enzyme responsible for salvage of Thymine ?

A

Deoxyribose 1-phosphate

converts free base Thymine to Nucleoside Thymidine

124
Q

What is the enzyme responsible for salvage of Uracil and Cytosine?

A

Ribose 1-phosphate
(converts free bases to Nucleosides
-Uracil to Uridine
-Cytosine to Cytidine

125
Q

What defect will cause hereditary orotic aciduria?

A

UMP synthase is blocked

enzyme Orotidine 5’P deoxcarbylase is blocked

126
Q

What happens if UMP synthase is blocked?

A

Orotic acid will accumulate in body -cause growth retardation

127
Q

What gene defect causes Lesch-Nyhan syndrome?

A

Hypoxanthine-Guanine Phosphoribosyl-transferase SEVERE deficiency or absence

128
Q

What is the metabolite that accumulates if HGPRT is deficient?

A

Purines, Uric Acid accumulates in body

129
Q

What are the effects of Uric Acid accumulating in the body

A

Mental Retardation

-Self-mutilation

130
Q

What gene defect will cause Immunodieficiency disease ?

A

Purine nucleoside phosphorylase

131
Q

If Purine Nucleoside phosphorylase is abscent what happens?

A

Inosine and Guanosine can not be recycled back to free base form- major loss of DNA synthesis ability

132
Q

What causes Severe combined immunodeficiency disease (SCID)?

A

Adenosine Deaminase defect

in purine salvage pathway- Adenosine can not be converted to Inosine for recycling

133
Q

What are the clinical symptoms of Severe combined immunodeficiency disease (SCID) caused by Adenosine Deaminase defect ?

A

Loss of immune system function

-NO B or T cells (bubble boy)

134
Q

What is the major regulatory enzyme for Pyrimidine synthesis ?

A

Carbamoyl Phosphate Synthetase II (CPS II)

135
Q

What does CPS II do ?

A

regulating step synthesizing cabamoyl phosphate from glutamine+CO2+ATP

136
Q

What are the Allosteric effectors that inhibit or activate the activity of Carbamoyl Phosphate Synthetase II ?

A

PRPP - activate

UTP - inhibits

137
Q

What are the major Regulatory enzymes in the Purine synthesis pathway?

A

PRPP synthetase

Glutamine phosphoribosyl amidotransferase (GPRT)

138
Q

What does the regulatory enzyme PRPP synthetase do in Purine pathway ?

A

Conversion of Ribose 5-P to 5-Phosphoribosyl 1-pyrophosphate (PRPP)

139
Q

What does the regulatory enzyme Glutamine phosophoribosyl amidotransferase (GPRT) do ?

A

PRPP is combined with Glutamine by GPRT (first committed step in Purine synthesis)

140
Q

What are the Allosteric effectors of PRPP Synthetase?

A

GDP and ADP presence will both inhibit the production of PRPP (negative feedback)

141
Q

What are the Allosteric effectors of Glutamine phosphoribosyl amidotransferase (GPRT) ?

A

PRPP - activates

IMP, AMP, GMP - inhibit activity (negative feedback)

142
Q

What is the primer for Prokaryotic DNA replication synthesized by ?

A

Primase

143
Q

What is the primer for Eukaryotic DNA replication synthesized by ?

A

Subunits of DNA Polymerase Alpha

144
Q

What is the processing enzyme for DNA replication in Prokaryotes vs Eukaryotes ?

A 
Prokaryotes = DNA polymerase III
Eukaryotes = DNA Polymerase E (epsilon) and D (Delta)
145
Q

What is DNA polymerase Epsilon (E) used for ?

A

Eukaryotic DNA replication on leading strand

146
Q

What is DNA polymerase Delta used for ?

A

Eukaryotic DNA replication of lagging strand

147
Q

What removes the DNA primer in prokaryotic vs. eukaryotic DNA replication?

A 
Prokaryotic = DNA Polymerase I
Eukaryotic = RNaseH (by hydrolysis )
148
Q

What is the problem with linear DNA ?

A

chromosome ends have extra 3’ section (Telomerase is needed to make Telomere)

149
Q

What phase is DNA replicated in

A

S phase

150
Q

What phase is prep for cell division after DNA replication?

A

G2 phase (line up DNA)

151
Q

What are the 5 phases of cell life?

A 
G0 (resting)
G1 (growth and metabolism)
S (DNA replication)
G2 (prep for cell division)
M (Mitosis)
152
Q

What is the only direction DNA can be synthesized in ?

A

5’ to 3’ direction

153
Q

If DNA is synthesized in 5’ to 3’ direction only, what direction is it “copied” in?

A

3’ to 5’

154
Q

DNA polymerases add nucleotides in a strand growing 5’ to 3’ direction and copy a DNA templete in the ____ to ____ direction.

A

3’ to 5’

155
Q

What does Primase do ?

A

Synthesizes RNA primers for DNA replication starts

156
Q

What does Helicase do?

A

Seperates DNA parent strand (breaks hydrogen bonds)

157
Q

What does Topoisomerase do ?

A

Relieves torsional strain on parental duplex caused by unwinding (prior to action of Helicase)

158
Q

What do single-strand binding proteins do ?

A

prevents ssDNA from re-associating during replication

159
Q

What 3 enzymes are used in the lagging strand?

A
  1. primase
  2. DNA polymerase alpha
  3. DNA polymerase delta (helps cleave the primase to next section to make Okazaki fragment)
160
Q

What does the DNA ligase do ?

A

Joins by forming phosphodiester bonds , two adjacent DNA strands that are bound to same template at end of Replication

161
Q

What does Proliferating cell nuclear antigen (PCNA) do ?

A

Enhances processivity of the DNA polymerases, bind to many proteins present at the replication fork by the

162
Q

What is required for DNA ligation by DNA ligase ?

A

Hydroxyl group (-OH ) on the free 3’ side of DNA fragment

  • reason only synthesis in 5’ to 3’ direction
  • phosphodiester bond with next nucleotide on Carbon 2 (lower left corner of 5 carbon sugar)
163
Q

What two features pose a problem at the end of linear chromosomes ?

A
  1. DNA polymerases can only synthesize in 5’ to 3’ direction

2. Can not initiate DNA synthesis on their own

164
Q

True or false, on linear DNA, replication can occur in both directions at the same time when parent strand is split ?

A

True - because the 5’ to 3’ direction will be occurring on both parent strands at the same time so “copying in opposite directions”

165
Q

What is the DNA sequence at the end of a chromosome called?

A

Telomeres (small repeated sequence of 100 to 1000’s of base pairs)

166
Q

What enzyme catalyzes the creation of Telomeres?

A

Telomerase - has protein and RNA sequence

167
Q

How does Telomerase work to make a telomere?

A

has RNA that functions as Template to extra 3’ end

Complement to the DNA found on 3’ extra end so it can bind to prime DNA syntheses of Telomere by DNA Polymerase

168
Q

What are the 3 major types of DNA repair

A
  1. Nucleotide excision repair
  2. Base excision repair
  3. Mismatch repair
169
Q

What is the difference between Nucleotide excision repair and Base excision repair?

A

Nucleotide = large torsional changes (thymine dimers, ring addition by Benzopyrene rings to guanine (smoking)
Base excision repair = single incorrect base repair

170
Q

What is used to remove the base error in base excision repair ?

A

Specific Glycosylase

171
Q

How is the parent strand of DNA retained in DNA replication ?

A

Parent strand is Methylated (CH3 group added)

-useful in Mismatch repair

172
Q

Primase is not required for DNA repair because ?

A

There will be 3’ OH remaining on the adjacent nucleotides to be used for repair

173
Q

True or false:

DNA repair enzymes have endogenous priming abilities

A

False

174
Q

What are the 3 types of DNA rearrangements ?

A
  1. Homologous recombination
  2. Translocations
  3. Transposable elements (retrotransposons)
175
Q

Which DNA rearrangement is considered often deleterious and pathogenic?

A

Translocations

  • breaks in Chromosomes caused by damaging agents
  • whole sections of one chromosome moved to another chromosome entirely
176
Q

What is a transposable element ?

A

“Jumping genes” - corn
Segments of DNA that can move from their original position to a new location without causing damage - just phenotypic changes

177
Q

What do most transposons in Human DNA invlove?

A

RNA intermediate (Alu) - reverse transducer

178
Q

What are the features of Mitochondrial DNA ?

A
  • Exclusively from the mother
  • Extra chromosomal
  • Replicated randomly and separate from Nuclear DNA
  • Heteroplasmy - no cell has identical copies of mtDNA leads to phenotypic variability
179
Q

Reverse transcriptase differs from DNA polymerase in what way ?

A

DNA polymerase has 3’ to 5’ exonuclease activity and Reverse transcriptase does not (lacks proof reading ability)

180
Q

Name the steps that RNA is turned into DNA

A
  1. RNA is copied to make cDNA

2. cDNA is used after RNA is degraded to synthesize double strand DNA

181
Q

What are the Pyrimidines ?

A

Thymine (T)
Cytosine (C)
Uracil (U- RNA only for binding with A)

182
Q

What are the purines ?

A

Guanine (G)

Adenine (A)

183
Q

Purines are composed of a _____ structure.

A

Bicyclic (double ring)

184
Q

Inosine monophosphate can be used to generate what ?

A

AMP or GMP

185
Q

High levels of GMP will inhibit the conversion of ____ to ____.

A

IMP to GMP

186
Q

High levels of AMP will inhibit the conversion of ____ to _____.

A

IMP to AMP

187
Q

Degradation of purines creates _____ ______ , which is insoluble and accumulation can cause gout.

A

Uric acid

188
Q

Hypoxanthine-Guanine phosphoribosyltransferase (HGPRT) can be used to convert hypoxanthine to _____ or Guanine to ______.

A

Hypoxanthine (free base) to IMP(nucleotide)

Guanine (free base) to GMP (nucleotide)

189
Q

Treatment for gout includes inhibition of ______ ______ by allopurinol .

A

Xanthine oxidase (enzyme that converts Hypoxanthine to Xanthine then acts on Xanthine to make Uric acid again)

190
Q

What 3 things are added together and acted on by Carbamoyl phosphate synthetase II (CPS II) to make carbamoyl phosphate in first step of Pyrimidine pathway ?

A

Glutamine + CO2+ ATP

191
Q

Defects in pyrimidine synthesis primarily lead to the generation of _____ ___.

A

Orotic acid

192
Q

What does 5-fluorouracil do ?

A

inhibits thymidylate synthase by reducing dTMP avaliable for DNA replication (blocks conversion of dUMP to dTMP)

193
Q

What does Methotrexate do ?

A

inhibits the folate cycle more generally - Folate is a carbon donor for the synthesis of both purines and pyrimidines (CH3- methyl group)

194
Q

DNA replication occurs in S phase of cell cycle in contrast to ____ and _____ that can occur at all phases.

A

Transcription and Translation

195
Q

How does Topoisomerase work?

A

Causes single or double stranded nicks in the DNA to relieve torsional strain before Helicase breaks hydrogen bonds

196
Q

What is the committed step of purine synthesis ?

A

Formation of 5-Phosphoribosyl-1-Amine by Glutamine Phosphoribosyl amidotransferase

197
Q

What is the commited step of purine synthesis (formation of 5-phosphoribosyl-1-amine by Glutamine phsophoribosyl amidotransferse) inhibited by ?

A

AMP and GMP (mostly but can also be Di and Triphosphate versions)
(ADP and GDP will inhibit the prior step in creation of PRPP which is not ‘commited’ step for Purine pathway as it is used in both purines and pyrimidine synthesis)

198
Q

Cellular concentrations of PRPP and _____ are usually below their Km for glutamine ________ _________. Thus any situation that leads to an increase in their concentration, can lead to an increase in de novo purine biosynthesis.

A

Glutamine

phosphoribosyl amidotransferase

199
Q 
Oxypurine = \_\_\_\_\_\_
Aminopurine = \_\_\_\_\_\_
A

GDP

ADP

200
Q

What enzyme is used to change IMP to XMP and is inhibited by its own product later on of GMP ?

A

IMP dehyrodrogenase

201
Q

What enzyme is used to change IMP to Adenylosuccinate and is inhibited by its own product later on of AMP ?

A

Adenylosuccinate synthetase

202
Q

Which base is the only nucleoside that can be directly phosphorylated to the nucleotide form ?

A

Adenosine is phosphorylated to AMP (Nucleotide) by Adenosine kinase

203
Q

Where does PRPP come into play in the Pyrimidine cycle ?

A

After Orotate is formed (Orotic Acid) - PRPP is added to make UMP then UMP is turned into UDP which is where the path splits

204
Q

Which nucleoside is almost never made in vivo?

A

Thymine - the pyrimidine phosphorylase has a very very low affinity for it - (has highest affinity for Uracil in salvage pathway ) - Thymine has its own “thymidine phosphorylase” that adds a deoxyribose residue in recycling

205
Q

What is the significance of Thymidine kinase above the other kinases ?

A

Allosterically inhibited by dTTP
-Activity in TK is closely related to cell cycle stage, dramatic rise as cell enters S phase - can be radiolabled for use to estimate DNA synthesis

206
Q

What are two ways to make dUMP ?

A
  1. dUDP can be dephosphorylated to form dUMP

2. dCMP can be deaminated to form dUMP (release of NH4 group)

207
Q

AMP is first deaminated to produce _____ using AMP deaminase.

A

IMP

208
Q

After AMP is deaminated to form IMP, then IMP and ___ are dephosphorylated by ________ and the ribose is cleaved from the base by purine nucleoside phosphorylase.

A

GMP

5’nucleotidase

209
Q

What base is produced by IMP cleavage?

A

Hypoxanthine (free base)

210
Q

How is guanine turned into xanthine ?

A

deaminated by enzyme guanase to produce xanthine

211
Q

What is the incentive for the body to recycle purines ?

A

Cost a lot of energy to produce Purine rings, and not much energy is obtained in return from them in salvage process

212
Q

Uric acid has a pK of ____. It is _____ in the body to form Urate. Urate is not very soluble in an aqueous enviornment.

A

5.4

Ionized (Uric acid loses electrons to make Urate)

Biochemistry (20 decks)

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