Biochem - Mini exam 1

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1.

_____ is an essential cofactor in the conversion of orotate to ______ A common mechanism used in allosteric regulation of purine biosynthesis involves: A gene is defined as a _____ _____. A nucleosome contains ____ histone proteins and ____ bp of DNA A plot of [glutamine] against enzyme activity is _______ in shape. A plot of [PRPP] against enzyme activity is _______ in shape. Activity of thymadylate synthase is directly inhibited by ______. All but the last okazaki fragment of the lagging strand is synthesized by: Allopurinol blocks activity of which enzyme? What is it used to treat? Approximately how many base pairs are contained in a single turn of DNA Briefly describe the replication mechanism differences on the leading and lagging strands. By convention, DNA is written in which direction?

_PRPP_ is an essential cofactor in the conversion of orotate to _OMP_

13.

By convention, RNA is written in which direction? Carbamoyl phosphate synthetase II is activated by: Carbamoyl phosphate synthetase II is inhibited by: Conversion of IMP to _______ is accompanied by hydrolysis on one ATP. Conversion of IMP to _______ is accompanied by hydrolysis on one GTP. Define "missense mutation" Define "nonsense mutation" Define "reverse non-sense mutation" Define "silent mutation" Define "transition mutation" Define "transversion mutation" Describe a common mutation that would be fixed by base excision repair. Describe the basic sequence of base excision repair.

5'-->3'

14.

ATP, PRPP

2.

binding of product to enzymes PRPP sythetase andGlutamine PRPP amidotransferase raises their Km, resulting in less enzymatic activity for a given [substrate] "heritable unit"

15.

UTP, CTP

3.

16.

IMP-->GMP with hydrolysis of one ATP

4.

8 histone proteins and 146 bp DNA

5.

hyperbolic (asymptotic with x-axis)

17.

IMP-->AMP with hydrolysis of one GTP

6.

Sigmoidal
18.

point mutation that alters one amino acid point mutation introduces a STOP codon point mutation changes a stop codon to an amino acid point mutation causes no change in amino acid sequence purine --> purine, ie. AG-->GA pyrimidine --> pyrimidine purine --> pyrimidine pyrimidine --> purine C-->U is a common mutation. It is corrected by base excision repair.

19.

7.

5-flurouricil
20.

8.

DNA polymerase 3

21.

22.

9.

Block xanthine oxidase, thus inhibiting purine degradation and reducing [uric acid] 10 base pairs per turn (i.e. 36 degrees separation between each base pair) Leading strand is continuous synthesis 5'-->3' Lagging strand is discontinuous synthesis 5'-->3' via Okazaki fragments 5'-->3'

23.

10.

24.

11.

25.

12.

modified base is removed by DNA glycosylase. Sugar phosphates are removed by AP endonucelase. DNA polymerase fills in missing nucleotides. Nick is sealed by ligase.

26.

Describe the basic sequence of events in nucleotide excision repair. Describe the basic sequence of mismatch repair

ABC exinuclease recognizes and removes damaged nucleotides and surrounding 12-13 nucleotides. DNA polymerase fills in the gap. Nick repaired by DNA ligase. Mismatched bases are identified by MutL and MutS. MutH binds to MutL and the non-methylated strand of DNA is nicked by endonuclease. Exonuclease removes erroneous DNA and DNA polymerase fills in the blank. Ligase closes the nick. dihydrofolate reductase

37.

27.

Gain of function mutations are generally inherited in what fashion? (autosomal recessive, dominant, sex linked recessive, dominant, etc..) Gout results from:

Autosomal dominant

38.

low solubility of uric acid + high [uric acid] --> uric acid crystals lodge in joints 6,000-7,000 bp 150-300 bp Virus mutates reverse transcriptase active site, excluding AZT. The template strand has modifications such as methylation, the new strand does not. Aids virus used reverse transcriptase, so nucleoside analogs (AZT) can be administered that inhibit DNA replication only in AIDS virus. To function, nucleoside must be converted to nucleotide 23 - 22 pairs plus sex chromosome (XX or XY) 2 substrates: one activates and one inhibits 4 types, 8 protein units (2 of each type)

39.

How big are LINES (~size in base pairs) How big are SINES? (~ size in base pairs) How can the AIDS virus avoid inhibition by AZT? How does mismatch repair identify which strand needs to be repaired and which one is correct? How is DNA replication manipulated to target the AIDS virus?

28.

Dihydrofolate is converted to tetrahydrofolate by the enzyme: DNA is supercoiled by two enzymes. They are: DNA polymerase 1 has both 5'-3' and 3'-5' exonuclease activity. DNA polymerase 3 has only 3'-5' exonuclease activity. Which statements are true or false? DNA polymerase 1 is primarily responsible for: dTMP is converted to dTTP by the enzyme _____. dUMP is converted to dTMP by the enzyme _____. Explain how DNA replication is manipulated to treat HERPES virus Explain the difference between polymorphism and mutation

40.

41.

29.

topoisomerase I and topoisomerase II Both are true. It's important that DNA polymerase 3 NOT have a 5'3' exonuclease activity because it is responsible for synthesizing DNA in that direction and it would be counterproductive to also be able to degrade it in that direction. DNA repair - has 3'-->5' exonuclease activity AND 5'-->3'

42.

30.

43.

31.

44.

32.

thymidine kinase
45.

How many chromosomes do humans have? How many substrates bind to glutamine PRPP amidotransferase? How many types of proteins and how many individual protein units are found in a histone? In DNA synthesis, where is dNTP added? In lagging strand DNA synthesis, RNA primers are created by: In lagging strand synthesis, gaps that result from removal of RNA primers are filled in by:

33.

thymadilate synthase
46.

34.

Inactive purine analog is administered. Viral thymidine kinase activates drug 3000x better than native thymidine kinase. Polymorphism - differences between individuals chromosomes (hair color, skin color, etc.) Mutation - a polymorphism resulting in an adversely altered phenotype 5' end = free phosphate 3' end = free hydroxyl

47.

3' -OH end (AKA the growing end) primase

35.

48.

49.

DNA polymerase

36.

Free phosphate is located on which end of DNA? Which end contains a free hydroxyl group?

50.

In lagging strand synthesis, nicks between each fragment are repaired by: In production of nucleotide triphosphates from nucleotide monophosphates, the 2nd phosphate is added by ________. Is this enzyme specific or nonspecific? In production of nucleotide triphosphates from nucleotide monophosphates, the 3nd phosphate is added by ________. Is this enzyme specific or nonspecific? In prokaryotes, the rate-limiting step in pyrimidine biosynthesis is catalyzed by the enzyme _______. In pyrimidine biosynthesis, glutamine, CO2, and ATP are combined to form _______ by the enzyme _______. In what way is telomerase like reverse transcriptase?

DNA ligase

62.

Purine salvage can not occur in ______ due to a deficiency of ______.

51.

nucleoside monophosphate kinase; these enzymes are specific for a particular base nucleoside diphosphate kinase; these enzymes are NOT specific.

Purine salvage can not occur in _Lesch-Nyhan syndrome_ due to a deficiency of _HPRT_. (HPRT=HGPRT) Ribonucleotide reductase

63.

Ribonucleotides are converted to their deoxy form by the enzyme _______. T or F: DNA is found in only one form of helix.

64.

52.

F: it's found in 3 forms A,B,Z. Also, it may be found in non-helical forms such as tetraplex F: there are some exceptions, i.e. RNA virus and prions F: DNA synthesis require a primer. DNA or RNA can serve as the primer for synthesis of additional DNA. False: pyrimidine degradation end-product is urea, which is highly soluble. True

65.

T or F: DNA is the genetic material in all organisms T or F: DNA synthesis does not require a primer.

53.

Aspartate transcarbamoylase Carbamoyl phosphate; Carbamoyl phosphate synthetase II it synthesizes DNA (the telomere segment) from an RNA template Autosomal recessive

66.

54.

67.

T or F: excessive pyrimidine degradation can cause gout.

55.

68.

56.

Loss of function mutations are generally inherited in what fashion? (autosomal recessive, dominant, sex linked recessive, dominant, etc..) Mutations in mismatch repair in humans causes: Name the three main components of a nucleotide. Nucleotide salvage is most important for which bases? Orotate is converted to OMP, which is phosphorylated to become ______, and finally converted to ______.

T or F: from the origin of replication, DNA synthesis occurs in a bidirectional manner. T or F: once melted, DNA is permanently denatured

69.

57.

colon cancer Base, pentose sugar, phosphate Adenine and guanine Orotate is converted to OMP, which is phosphorylated to become _UTP_, and finally converted to _CTP_. Purine degradation can not occur in _SCIDs_ due to a deficiency of _adenosine deaminase_. T or F: regulation of Glutamine PRPP amidotransferase is dependent on two independent substrates with two independent Km's T or F: SINES are generally non-coding segments of DNA T or F: The primary transcript of RNA is usually active and ready for translation into protein Telomeres are added onto which end of DNA?

F: it can anneal or "hybridize" spontaneously because the double stranded helix is thermodynamically favorable True: dependent on [glutamine] and [PRPP]

58.

70.

59.

60.

71.

False: they are important to the cell F: primary transcripts must usually be processed to become activated 3' end. Synthesized 5'->3', so the 3' end is where you run out of template and need to add a telomere Introns

72.

61.

Purine degradation can not occur in ______ due to a deficiency of ______.

73.

74.

The "non-coding" regions of DNA are called _____.

75.

The 3' end of tRNA is cleaved by: The 5' end of tRNA is cleaved by: The coding regions of DNA are called ______. The committed step of pyrimidine biosynthesis is catalyzed by which component of the tri-enzyme complex? The final okazaki fragment of the leading strand is synthesized by: The first "level" of super coiling is the formation of the ______. The first DNA polymerase to be described is called: The last phosphodiester bond of the lagging strand is formed by: The nucleic acid backbone is joined via what type of linkage? The presence of which bases raise Tm for a piece of DNA? Why?

terminal transferase RNAse P

93.

76.

What are the functions of U1 snRNA and U2 snRNA, respectively. What are the major sources of nucleotides in the body? What are the stop signals used to terminate RNA transcription? What are the three major steps in RNA synthesis/transcription? What are the typical modifications involved in the maturation of RNA? What bases are present in RNA? What causes thymine dimers? What diseases result in increased incidence of gout? what does "SSB" do? What does polyadenylate polymerase do? What drug inhibits RNA polymerase 2? Where is it found? What enzyme catalyzes transcription of mRNA, snRNA, and miRNA? What enzyme is critical to both purine and pyrimidine biosynthesis? What enzyme is inhibited by methotrexate? What functions as the promotor in bacterial RNA transcription? What information is encoded in LINES? What is a lariat structure?

Define 5' and 3' ends of introns to be spliced De novo synthesis and salvage

94.

77.

Exons cAd - aspartate transcarbamoylase

95.

78.

hairpin turns or rho protein

96.

79.

DNA polymerase 1
97.

Initiation, elongation, termination splicing out of introns, terminal additions (5' cap, 3' poly-A tail, base and nucleotide modifications G,C,U,A. U replaces T. UV radiation SCIDs and Lesch-Nyhan syndrome protects single-stranded DNA of lagging strand adds 3' poly-A tail to mRNA. a-amanitin; poison of death cap mushroom RNA polymerase 2

80.

nucleosome DNA polymerase 1

98.

81.

82.

DNA ligase
99.

83.

phosphodiester CG base pairs raise Tm because they have 3 hydrogen bonds compared to only two Hbonds between AT CAD - carbamoyl phosphate synthetase II, aspartate transcarbamoylase, dihydroorotase glutamine-PRPP amidotransferase 1 meter

100.

84.

101.

102.

85.

The pyrimidine biosynthetic pathways begins with a trienzyme complex. What are the names of the three enzymes involved? The rate-limiting step of purine biosynthesis is catalyzed by _______. Uncoiled, the DNA in a single cells would be approximately how long? Unwinding of DNA is catalyzed by which enzyme? What are "LINES" What are "SINES" What are the 3 main types of RNA? What are the chemical properties of histone proteins?

103.

104.

86.

105.

PRPP synthetase

87.

106.

dihydrofolate reductase

88.

Helicase long interspersed elements small interspersed elements tRNA, mRNA, rRNA
109.

89.

107.

Pribnow box - approx. 10 bp downstream of start site. remnants of reverse transcriptase a loop of RNA with three phosphodiester bonds - used in splicing

90.

108.

91.

92.

They are very basic (positively charged)

110.

What is AZT? What does it do?

Acts as a purine analog but blocks DNA synthesis once incorporated. Because it's incorporated by reverse transcriptase, it is useful in treatment of HIV [purines]=[pyrimidines] A ribozyme - AKA RNA with catalytic activity highly repetitive segments, about 10 bp long, that repeat millions of times Purines=dicyclic Pyrimidines=monocyclic In prokaryotes, coding regions for a protein are contiguous. In eukaryotes, coding region for a protein may be broken up and separated by non-coding introns. DNA lacks a 2' -OH group which is present on RNA causes a frame shift

127.

What is Tm?

Temperature at which half of the DNA in a sample is single-stranded DNA from the homologous chromosome

128.

111.

What is Chargaff's rule? What is RNAse P? What is satellite DNA? What is the basic structure of purines and pyrimidines? What is the difference between coding regions of DNA in prokaryotes and eukaryotes? What is the difference between DNA and RNA What is the effect of a base insertion or deletion mutation? What is the end product of purine degradation? What is the eukaryotic promoter in RNA transcription? What is the function of topoisomerase I? What is the function of topoisomerase II? What is the hyperchromic effect? What is the karyotype? What is the role of "primers" in RNA synthesis? What is the role of "promoters" in RNA synthesis? What is the role of Glutamine PRPP amidotransferase?

112.

What is used as a template for repair in the case of a double strand break, or when both strands are mutated? What materials are required for purine biosynthesis? What materials are requires for pyrimidine biosynthesis? What mechanism do humans use to correct thymine dimers? What molecule binds to glutamine PRPP amidotransferase to activate its activity? What molecule binds to glutamine PRPP amidotransferase to inhibit its activity? What post-transcriptional modifications are made to RNA? What two inhibitor drugs prevent synthesis of thymadylate? What types of proteins are found within a histone? What's the difference between a nucleotide and a nucleoside? When does mismatch repair occur? When is direct repair used?

129.

113.

PRPP (an activated sugar), amino acids (glutamine, aspartate, glycine), CO2, tetrahydrofolate, ATP PRPP (an activated sugar), amino acids (glutamine, aspartate), HCO3-, ATP Nucleotide excision repair

114.

130.

115.

131.

132.

PRPP

116.

117.

133.

glutamine

118.

uric acid
134.

119.

TATA box
135.

addition of 5' guanosine CAP with a 5'-5' triphosphate linkage AND a 3' poly-A tail methotrexate and 5Fluorouricil H2A, H2B, H3, H4 Nucleoside only contains a base and pentose sugar, but not a phosphate. After replication Example: O6-methylguanine is restored to normal guanine by methyltransferase. The enzyme is deactivated in the process. When both strands of DNA are damaged, ie. double strand break It's a linker protein found outside of the coiled nucleosome

120.

break one strand of DNA - relax DNA break two strands of DNA - supercoil DNA Absorbance increases at DNA melts (due to increased exposure of absorptive aromatic ring structures) complete chromosomal compliment in the cell (23 chromosomes) No primers are needed for RNA synthesis

136.

121.

137.

122.

138.

139.

123.

124.

140.

125.

Promoters dictate start site for RNA synthesis

141.

When is recombination repair used? Where is the function of histone H1, and where is it found?

126.

Converts PRPP to IMP, which is converted to either AMP or GMP

142. 143. 144.

Which bases are purines? Which bases are pyrimidines? Which compound is the common precursor of all pyrimidines? Which DNA polymerase is more "processive," 1 or 3? What does that mean? Which enzyme helps to reduce tension ahead of the replication fork? Which enzyme is primarily responsible for DNA replication? Which enzyme is responsible for the removal of the 2' -OH group from nucleotides? Which form of DNA is most common? Is it left or right-handed helix? Which molecules function as inhibitors in the purine biosynthesis feed-back mechanism? Which RNA is a clover-leaf structure? Which RNA is least abundant? Which RNA is most prevalent? Which type of RNA typically undergoes the greatest amount of "base modification?" Why does the modified G need to be repaired?

Adinine, guanine (GAs are pure) Cytosine, urasil, thyamine (CUT) orotate 3 - it attaches many more base pairs to the DNA strand (500000 at a time before falling off) compared to DNA polymerase 1, which falls off every 3-200 bp Gyrase (aka Topoisomerase 1) DNA polymerase III Ribonucleotide reductase B form - right handed helix GMP, AMP, IMP tRNA mRNA? rRNA tRNA - extensive methylation and modification of bases occurs Modified G base pairs with T instead of C.

145.

146.

147.

148.

149.

150.

151. 152. 153. 154.

155.