Molecular Biology

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1. The backbone of DNA is this por- ribose + phosphate portion of the nu-
tion of DNA cleotide since it is invariant

2. The nonbackbone of DNA is the aromatic base (adenine or guanine or

uracil or thymine or cytosine)

3. Draw example of DNA structure

4. ATP vs. dATP ATP has an extra OH which is why d

stands for deoxyadenosine

5. Nucleotides in the DNA chain are phosphodiester bonds (between the

covalently linked by these 3'hydroxy group of one deoxyribose
and the 5' phosphate group of the next
deoxyribose)

6. Draw a phosphodiester bond

7. Draw the cytosine

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8. Draw thymine (DNA only)

9. Draw uracil (RNA only)

10. Draw adenine

11. Draw guanine

12. Is DNA right-handed or left-handed right

double helix?

13. What holds the bases together in hydrogen bonds

DNA?

14. A always bonds to T

15. G always bonds to C

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16. DNA in the nucleus is bonded how? double stranded (2) in an antiparallel
orietnation (5' end to 3' end of other)

17. This is the term for binding two annealing or hybridization

complimentary strands of DNA into
a double-stranded structure

18. What is the term for separation of melting or denaturation

strands?

19. What are the pyrimidine bases? C, T, U (c.u.t pyramid cake)

20. What are the purine bases? A, G

21. These type of interactions between hydrophobic

bases in DNA help to stabilize it

22. The sum total of an organism's ge- genome

netic information is called its

23. Each piece of ds-DNA is called a chromosome

24. Prokaryotic (bacterial) genomes singular circular chromosome

are composed of a

25. How is DNA size in number of There is no relation. Amphibians

base pairs related to animal intelli- (dumb) have highest number. Most
gence? base pairs are repetitive DNA with no
known function.

26. Prokaryotes use this enzyme to DNA gyrase

twist the gigantic DNA molecule
into a circle called supercoils

27. What are the globular proteins that histones

help are wrapped with eukaryotic
DNA to help pack it away

28. Partially packed DNA form beads nucleosomes

that are called
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29. Fully packed DNA is called chromatin

30. Are histones mostly basic or Basic since DNA is acidic (compli-
acidic? mentary)

31. Stained chromosomes produce euchromatin (higher transcription

lighter regions called rates since less dense)

32. Stained chromosomes produce heterochromatin

darker regions called

33. Describe a centromere It is the ball in the middle where spin-

dle fibers attach to chromatids during
cell division. These fibers attach via
multiprotein complexes called kineto-
chores.

34. If the centromere isn't perfectly short arms (p)

center, there will be small arms and long arms (q)
long arms. What letter shorthand is
given to both?

35. What is the term given when a cen- metacentric

tromere is perfectly center?

36. The end of linear chromosomes are telomeres

called

37. What type of DNA is found at the single stranded

very end of the chromosome?

38. These are the regions composed of intergenic regions

noncoding DNA

39. Describe SNPs a.k.a single nucleotide polymor-

phisms
These are single nucleotide changes
every 1000 base pairs

40. Describe Copy Number Variation

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These are structural variations in the
genome that lead to different sections
of DNA being copied or deleted

41. Describe Repeated Sequences: Just like it sounds, these are short
Tandem Repeats sequences of nucleotides which are
repeated one after another from any-
where between 3 to 100 times. These
are random across the genome.

42. Describe Repeated Sequences: Mobile genetic elements that can

Transposons jump around the genome. These
transposons can mutate and change
the chromosome through inversions,
deletions, and rearrangements.

43. These are the templates in DNA genes

that produce another nucleic acid
known as RNA

44. This is the subtype of RNA that is mRNA

first read and then used to con-
struct protein

45. This is the term for the synthesis of translation

proteins using RNA

46. This is the term for the synthesis of transcription

RNA from DNA

47. The ribosome is a massive enzyme ribosomal RNA

composed of many proteins and
pieces of RNA known as

48. Describe the central dogma DNA -> RNA -> protein (information is
used to create actual objects)

49. How many nucleotide letters is a 3

codon?

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50. How many codons are there? 64 (= 4^3)

51. How many codons specify amino 61

acids?

52. How many codons specify stop 3

codons

53. Stop codons are also called nonsense codons since they don't
code for any amino acid

54. Name the stop codons UAA, UAG, UGA

55. Two or more codons coding for the synonyms

same amino acid are known as

56. Because it has synonyms, the ge- degenerate

netic code is said to be

57. Each codon specifies how many only one

amino acids?

58. Codons have no ambiguity

59. Cell division requires DNA replication

60. DNA replication occurs during this S (synthesis) phase

phase of the interphase cell cycle

61. Old DNA is called parental DNA

62. New DNA is called daughter DNA

63. Conservative replication means parental ds-DNA remains as is

64. Describe dispersive theory both copies of genomes were com-

posed of new and old DNA.

65. Meselson and Stahl showed DNA is semiconservative. After replication,

replication one strand is parental and one strand
is daughter.
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66. In order for DNA to be replicated, it unwind

first must

67. What enzyme unwinds the double helicase

helix and separates the strands?

68. This is the name for the specific origin of replication

location on the chromosome where
helicase begins the unwinding

69. These enzymes help the chromo- topoisomerases

some to no break and not get tan-
gled when unwinded. It functions to
cut one or both strands and unwrap
the helix releasing tension

70. These help to protect DNA that has Single-strand binding proteins (SS-
been unpackaged in prep for repli- BPs)
cation and helps to keep strands
seperated

71. Seperated DNA strands are re- open complex

ferred to as an

72. This must be synthesized by primo- RNA primer

some to act as a end piece from
which DNA polymerase can add to
the chain

73. How long is RNA primer? 8-12 nucleotides

74. What happens to the RNA primer It is replaced by DNA

after replication is complete?

75. The central component of primo- primase

some is an RNA polymerase called

76. DNA polymerase

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This catalyzes the elongation of the
daughter strand using the parental
template

77. Template strand is read in what di- The template must be read 3' to 5'
rection? since the end result (daughter) must
line up with template 5' to 3'

78. The daughter strand always goes 5' to 3' (DNA is always synthesized 5'
this direction to 3')

79. The strand side where there is no leading strand (continous)

need for more primers is called the

80. The strand side where there needs lagging strands (discontinous)
to be new primers is called the

81. The fragments among the lagging okasaki fragments

strand are known as

82. This is the enzyme that catalyzes RNAse

fragmentation of primers

83. This is the enzyme that facilitates DNA ligase

the joining of DNA strands togeth-
er after being separated. It cat-
alyzes the phosphodiester bonds
between the added okasaki frag-
ments and

84. This is the enzyme that adds the DNA polymerase III
okazaki fragments

85. This is the enzyme that removes DNA polymerase I

RNA primer fragments and adds
nucleotides where the RNA primers
were removed from

86. Describe DNA polymerase III super-fast elongation, proofreading

function (can chop off the nucleotide
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just added if there was an error), but
has no repair function

87. Describe DNA polymerase I can proofread, can do excision repair,

removes primer fragments

88. What is the basic purpose of DNA checkpoint and repair

polymerase II, IV, and V

89. Replication of circular prokaryotes theta replication

chromosomes end up looking like a
theta greek letter. Thus, replication
of prokaryotes is known as

90. These are disposable repeats at Telomeres

the end of the chromosomes that
shorten during cell division

91. This is the number of times a nor- Hayflick limit

mal human cell type can divide un-
til telomere length stops cell divi-
sion

92. This is an enzyme that adds repet- telomerase (cancer cells can express
itive nucleotide sequences to the telomerase)
ends of chromosomes and there-
fore lengthens telomeres

93. Name the seven types of mutations L.A.I.D T.I.P

loss of heterozygosity
amplification
insertion
deletion

translocation/rearrangement
inversion
point mutations

94. Describe point mutations single base pair substitution

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95. Transition is a type of point muta- purine switched for another purine, or
tion where pyr is switched for another pyr

96. Transversion is a type of point mu- purine swtiches for a pyr. Or a pyr
tation where switches for a purine

97. There are three subtypes of point missense, nonsense, and silent
mutations. What are they?

98. Describe a missense mutation This causes one amino acid to be re-
placed by another amino acid

99. Describe nonsense mutation This is where a stop codon replaces a

regular codon and prematurely short-
ens the protein

100. Describe a silent mutation This is where a codon is changed into

a new codon for the same amino acid.
There is no change in the protein's
amino acid sequence.

101. Mutations that cause a change in frameshift mutations

the reading frame are called

102. An inversion is when a segment of a chromosome is re-

versed end to end

103. This is when a segment of a chro- Chromosome amplification

mosome is duplicated.

104. This results when recombination translocations

occurs between nonhomologous
chromosomes.

105. This occurs in a diploid organism Loss of Heterozygosity

when one allele of a certain gene
is lost, either due to deletion or a
recombination event.

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106. These special things can insert in Transposons
any part of the genome, can affect
gene expression, or cause muta-
tions, they can promote or turn off
gene expression.

107. These are repair pathways that rely homology-dependent repair pathways
on the characteristic DNA whereby
DNA has one strand that is undam-
aged, and perfectly complementary

108. Repair that happens before DNA excision repair

replication is called

109. Repair that happens during and af- post-replication repair

ter DNA replication

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