Biochem - Mini Exam 1

8/22/2019 Biochem - Mini Exam 1

1/6

_____ is an essential

cofactor in the

conversion of orotate

to ______

A common

mechanism used inallosteric 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?

1. _PRPP_ is an essential cofactor in

the conversion of orotate to _OMP_

2. binding of product to enzymes PRPP

sythetase andGlutamine PRPPamidotransferase raises their Km,

resulting in less enzymatic activity

for a given [substrate]

3. "heritable unit"

4. 8 histone proteins and 146 bp DNA

5. hyperbolic (asymptotic with x-axis)

6. Sigmoidal

7. 5-flurouricil

8. DNA polymerase 3

9. Block xanthine oxidase, thus

inhibiting purine degradation and

reducing [uric acid]

10. 10 base pairs per turn (i.e. 36

degrees separation between each

base pair)

11. Leading strand is continuous

synthesis 5'-->3'

Lagging strand is discontinuous

synthesis 5'-->3' via Okazaki

fragments

12. 5'-->3'

By convention,

RNA is written in

which direction?

Carbamoyl

phosphate

synthetase II isactivated by:

Carbamoyl

phosphate

synthetase II is

inhibited by:

Conversion of

IMP to _______

is accompanied

by hydrolysis on

one ATP.

Conversion ofIMP to _______

is accompanied

by hydrolysis on

one GTP.

Define "missense

mutation"

Define "non-

sense mutation"

Define "reverse

non-sense

mutation"Define "silent

mutation"

Define

"transition

mutation"

Define

"transversion

mutation"

Describe a

common

mutation thatwould be fixed by

base excision

repair.

Describe the

basic sequence of

base excision

repair.

13. 5'-->3'

14. ATP, PRPP

15. UTP, CTP

16. IMP-->GMP with hydrolysis of one ATP

17. IMP-->AMP with hydrolysis of one GTP

18. point mutation that alters one amino

acid

19. point mutation introduces a STOP codon

20. point mutation changes a stop codon to

an amino acid

21. point mutation causes no change in

amino acid sequence

22. purine --> purine, ie. AG-->GA

pyrimidine --> pyrimidine

23. purine --> pyrimidine

pyrimidine --> purine

24. C-->U is a common mutation. It is

corrected by base excision repair.

25. 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.

Biochem - Mini exam 1Study online at quizlet.com/_cb5nq


2/6

Describe the basic

sequence of events in

nucleotide excision

repair.

Describe the basic

sequence of mismatch

repair

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

Free phosphate is

located on which end

of DNA? Which end

contains a free

hydroxyl group?

26. ABC exinuclease recognizes and

removes damaged nucleotides and

surrounding 12-13 nucleotides.

DNA polymerase fills in the gap.

Nick repaired by DNA ligase.

27. 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.

28. dihydrofolate reductase

29. topoisomerase I and topoisomerase

II

30. 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.

31. DNA repair - has 3'-->5'

exonuclease activity AND 5'-->3'

32. thymidine kinase

33. thymadilate synthase

34. Inactive purine analog is

administered. Viral thymidine

kinase activates drug 3000x better

than native thymidine kinase.

35. Polymorphism - differences

between individuals chromosomes

(hair color, skin color, etc.)

Mutation - a polymorphism

resulting in an adversely altered

phenotype

36. 5' end = free phosphate

3' end = free hydroxyl

Gain of function

mutations are generally

inherited in what

fashion? (autosomal

recessive, dominant, sex

linked recessive,

dominant, etc..)

Gout results from:

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 whichstrand needs to be

repaired and which one

is correct?

How is DNA replication

manipulated to target

the AIDS virus?

How many

chromosomes dohumans 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:

37. Autosomal dominant

38. low solubility of uric acid + high

[uric acid] --> uric acid crystals

lodge in joints

39. 6,000-7,000 bp

40. 150-300 bp

41. Virus mutates reverse

transcriptase active site,

excluding AZT.

42. The template strand has

modifications such asmethylation, the new strand does

not.

43. 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

44. 23 - 22 pairs plus sex

chromosome (XX or XY)

45. 2 substrates: one activates and

one inhibits

46. 4 types, 8 protein units (2 of each

type)

47. 3' -OH end (AKA the growing

end)

48. primase

49. DNA polymerase


3/6

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 non-

specific?

In production of nucleotide

triphosphates from nucleotide

monophosphates, the 3nd

phosphate is added by ________.

Is this enzyme specific or non-

specific?

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?

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 ______.

Purine degradation can not occur

in ______ due to a deficiency of

______.

50. DNA ligase

51. nucleoside

monophosphate

kinase; these

enzymes are specific

for a particular base

52. nucleoside

diphosphate kinase;

these enzymes are

NOT specific.

53. Aspartate

transcarbamoylase

54. Carbamoyl

phosphate;

Carbamoyl

phosphate

synthetase II

55. it synthesizes DNA

(the telomere

segment) from an

RNA template

56. Autosomal recessive

57. colon cancer

58. Base, pentose sugar,

phosphate

59. Adenine and guanine

60. Orotate is converted

to OMP, which is

phosphorylated to

become _UTP_, andfinally converted to

_CTP_.

61. Purine degradation

can not occur in

_SCIDs_ due to a

deficiency of

_adenosine

deaminase_.

Purine salvage can not occur

in ______ due to a deficiency

of ______.

Ribonucleotides are converted

to their deoxy form by the

enzyme _______.

T or F: DNA is found in only

one form of helix.

T or F: DNA is the genetic

material in all organisms

T or F: DNA synthesis does not

require a primer.

T or F: excessive pyrimidine

degradation can cause gout.

T or F: from the origin of

replication, DNA synthesis

occurs in a bidirectional

manner.

T or F: once melted, DNA is

permanently denatured

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 transcriptof RNA is usually active and

ready for translation into

protein

Telomeres are added onto

which end of DNA?

The "non-coding" regions of

DNA are called _____.

62. Purine salvage can not

occur in _Lesch-Nyhan

syndrome_ due to a

deficiency of _HPRT_.

(HPRT=HGPRT)

63. Ribonucleotide reductase

64. F: it's found in 3 forms -

A,B,Z. Also, it may be

found in non-helical

forms such as tetraplex

65. F: there are some

exceptions, i.e. RNA

virus and prions

66. F: DNA synthesis require

a primer. DNA or RNA

can serve as the primer

for synthesis of

additional DNA.

67. False: pyrimidine

degradation end-product

is urea, which is highly

soluble.

68. True

69. F: it can anneal or

"hybridize"

spontaneously becausethe double stranded helix

is thermodynamically

favorable

70. True: dependent on

[glutamine] and [PRPP]

71. False: they are important

to the cell

72. F: primary transcriptsmust usually be processed

to become activated

73. 3' end. Synthesized 5'--

>3', so the 3' end is where

you run out of template

and need to add a

telomere

74. Introns


4/6

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?

The pyrimidine biosynthetic

pathways begins with a tri-

enzyme 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?

75. terminal transferase

76. RNAse P

77. Exons

78. cAd - aspartate

transcarbamoylase

79. DNA polymerase 1

80. nucleosome

81. DNA polymerase 1

82. DNA ligase

83. phosphodiester

84. CG base pairs raise Tm

because they have 3

hydrogen bonds

compared to only two H-

bonds between AT

85. CAD - carbamoyl

phosphate synthetase II,

aspartate

transcarbamoylase,

dihydroorotase

86. glutamine-PRPP

amidotransferase

87. 1 meter

88. Helicase

89. long interspersed

elements

90. small interspersed

elements

91. tRNA, mRNA, rRNA

92. They are very basic

(positively charged)

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 terminateRNA 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 thyminedimers?

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?

93. Define 5' and 3' ends of introns

to be spliced

94. De novo synthesis and salvage

95. hairpin turns or rho protein

96. Initiation, elongation,

termination

97. splicing out of introns,

terminal additions (5' cap, 3'

poly-A tail, base and nucleotide

modifications

98. G,C,U,A. U replaces T.

99. UV radiation

100. SCIDs and Lesch-Nyhan

syndrome

101. protects single-stranded DNA

of lagging strand

102. adds 3' poly-A tail to mRNA.

103. a-amanitin; poison of death

cap mushroom

104. RNA polymerase 2

105. PRPP synthetase

106. dihydrofolate reductase

107. Pribnow box - approx. 10 bp

downstream of start site.

108. remnants of reverse

transcriptase

109. a loop of RNA with three

phosphodiester bonds - used in

splicing


5/6

What is AZT? What

does it do?

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

eukaryoticpromoter in RNA

transcription?

What is the function

of topoisomerase I?

What is the function

of topoisomerase

II?

What is the

hyperchromic

effect?

What is thekaryotype?

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?

110. 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

111. [purines]=[pyrimidines]

112. A ribozyme - AKA RNA withcatalytic activity

113. highly repetitive segments, about 10

bp long, that repeat millions of times

114. Purines=dicyclic

Pyrimidines=monocyclic

115. 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.116. DNA lacks a 2' -OH group which is

present on RNA

117. causes a frame shift

118. uric acid

119. TATA box

120. break one strand of DNA - relax

DNA

121. break two strands of DNA - supercoil

DNA

122. Absorbance increases at DNA melts

(due to increased exposure of

absorptive aromatic ring structures)

123. complete chromosomal complimentin the cell (23 chromosomes)

124. No primers are needed for RNA

synthesis

125. Promoters dictate start site for RNA

synthesis

126. Converts PRPP to IMP, which is

converted to either AMP or GMP

What is Tm?

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 toglutamine 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?

When is recombination

repair used?

Where is the function of

histone H1, and where is it

found?

127. Temperature at which half of

the DNA in a sample is

single-stranded

128. DNA from the homologous

chromosome

129. PRPP (an activated sugar),

amino acids (glutamine,

aspartate, glycine), CO2,

tetrahydrofolate, ATP

130. PRPP (an activated sugar),

amino acids (glutamine,

aspartate), HCO3-, ATP

131. Nucleotide excision repair

132. PRPP

133. glutamine

134. addition of 5' guanosine CAP

with a 5'-5' triphosphate

linkage AND a 3' poly-A tail

135. methotrexate and 5-

Fluorouricil

136. H2A, H2B, H3, H4

137. Nucleoside only contains a

base and pentose sugar, but

not a phosphate.

138. After replication

139. Example: O6-methylguanine

is restored to normal guanineby methyltransferase. The

enzyme is deactivated in the

process.

140. When both strands of DNA

are damaged, ie. double

strand break

141. It's a l inker protein found

outside of the coiled

nucleosome


6/6

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 aheadof 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?

142. Adinine, guanine (GAs are pure)

143. Cytosine, urasil, thyamine (CUT)

144. orotate

145. 3 - it attaches many more base pairs to the DNA strand (500000 at a time befo

falling off) compared to DNA polymerase 1, which falls off every 3-200 bp

146. Gyrase (aka Topoisomerase 1)

147. DNA polymerase III

148. Ribonucleotide reductase

149. B form - right handed helix

150. GMP, AMP, IMP

151. tRNA

152. mRNA?

153. rRNA

154. tRNA - extensive methylation and modification of bases occurs

155. Modified G base pairs with T instead of C.

Biochem - Mini Exam 1

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