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Biochem 2 > Exam 2 - DNA Structure > Flashcards

Exam 2 - DNA Structure Flashcards

1
Q

(T/F) More heat energy is required to break the bonds of AT pairs than CG bonds

A

false

G-C = 3 bonds
A-T = 2 bonds
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2
Q

_____ the wavelength used to monitor DNA/detect protein

A

260 nm

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3
Q

______ techniques that widely uses DNA denaturation

A

hybridization probes, PCR

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4
Q

_____ term referring to when Absorbance increases as the bases become unstacked

A

hyperchromicity

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5
Q

____ the temperature at which half the DNA becomes single stranded is called the

A

melting temperature, Tm

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6
Q

*(T/F) Tm shifts to the right as GC

content increases

A

true

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7
Q

which of the ff does not apply to DNA denaturation?

a. When cooled, DNA strands will reanneal
b. Each double stranded DNA has its own specific melting temperature
c. DNA melting temps depend on AT content
d. DNA melting temp depend of strand complementary and length of DNA

A

C

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8
Q

(T/F) SNPs can be detected using melting temperature

A

true

temp is lower than the strand with no mutation

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9
Q

_______ refers
to the complete set of genetic information carried by an
organism or the DNA that carries this information

A

genome

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10
Q

_____ the number of nucleotides that the haploid human genome consists

A

3.2 E9 nucleotides

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11
Q

which of the ff is not true about the genome?

a. genes are the functional units of heredity
b. is haploid in humans
c. the more comples an organism, the larger its genome
d. encodes proteins

A

none of the above :)

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12
Q

(T/F) smaller, simpler organisms have compact genomes with little noncoding segements of DNA

A

true

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13
Q

which of the ff is not true about the genome?

a. humans have plenty of junk DNA with no known function
b. yeasts have smaller genomes
c. 45%of the genome are derived from viruses
d. the human does not contain any mobile elements

A

D

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14
Q

_____ are segments of DNA that can move within or between genomes that accumulate during evolution

A

transposable elements

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15
Q

____ are intervening noncoding DNA sequences that break up the coding sequences

A

introns

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16
Q

____ are the coding sequences in the DNA

A

exons

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17
Q

_____ the average size of a human gene

A

27,000 nucleotides

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18
Q

which of the ff is not true?

a. Approximately 1300 nucleotides encode the average size human protein of about 430 amino acids
b. promoters are considered as coding sequences
c. about ~25,700 nucleotides consist of introns
d. a human gene is about 27,000 nucleotides

A

B

they are non coding!

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19
Q

____ are examples of non coding DNA sequences

A

gene promoters, introns, “junk” DNA, regulatory DNA sequences

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20
Q

(T/F) promoters regulate gene expression

A

true

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21
Q

*(T/F) only 1.5% of the human genome encodes for amino acids

A

true!

exons/amino acids

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22
Q

(T/F) organisms with compact genome have introns like humans

A

false

more compact = no introns, shorter
humans= longer, mostly introns

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23
Q

_____ the smallest human chromosome

A

chromosome 22

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24
Q 
which of the ff is not a mobile genetic element?
a. DNA only transposons
b. LINES
c. SINES
d. retrovirallike
elements
A

all are mobile elements!

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25
Q

____ consist
of short nucleotide sequences (14
nucleotides or less) that exist in multiple copies

A

Simple sequence repeats

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26
Q

____ large stretches of the genome (1000-200,000

nucleotides) present in two or more locations of genome

A

Segmental duplications

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27
Q

_____ are duplicated genes that have become inactive (nonfunctional) over time due to accumulation of mutations

A

pseudogenes

humans have least 20,000

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28
Q

(T/F) DNA must be tightly packaged yet organized (without tangling) to allow binding of enzymes that regulate DNA replication, repair, and transcription

A

true

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29
Q

which of the ff is not true?

a. DNA is compacted 1000 fold in mitotic chromosomes
b. DNA is compacted 1,000 fold in interphase chromosomes
c. a cell can have 2 meters of DNA stretched end to end
d. histone mass almost equal to DNA mass

A

A

10,000 fold in mitotic chromosome

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30
Q

(T/F) histones are are present at very low concentrations in the nucleus

A

false

high conc

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31
Q

______ the complex of histones and nonhistones with DNA

A

chromatin

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32
Q

____ refers to a chromatin that becomes partially unfolded

A

“beads on a string”

beads = nucleosomes (dna around histones)
string = DNA
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33
Q

*(T/F) Nucleosomes represent the first stage of DNA packing in the nucleus

A

true

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34
Q

(T/F) DNA wrapped around the is 146 nucleotides long and can wrap 1.65 times around the histone core while linker DNA ranges from a few nucleotides up to about 80

A

true

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35
Q

______ can refer either to the core particle plus one of its adjacent DNA linkers or just the core particle

A

nucleosome

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36
Q

which of the ff is false?

a. Nucleosomes plus DNA = simplest form of chromatin
b. nucleosome particles repeat at intervals of about 50K nuleotides
c. Nucleosomes condense the length of DNA by about one third
d. Represent the first level of DNA packing in chromosomes

A

B

only 200 nucleotide intervals

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37
Q

which of the ff is false about the core histone structure?
a. its N-terminal tail is subject to chemical modification
b. its three α helices are connected by two loops
c. the N-terminal form the “histone fold”
d. histone fold mediates the histone-histone
binding during assembly of the nucleosome core

A

C

alpha helices form the histone fold

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38
Q

which of the ff histone properties is false?
a. rich in basic amino acids and are negatively charged
b. the aa charges neutralize the charge of DNA backbone
c. histone-DNA binding is thru a combo of electrostatic and
hydrophobic interactions and hydrogen bonding
d. are lysine and arginine rich

A

A

basic aas are POSITIVELY charged

DNA is neg

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39
Q

(T/F) Histones H4 primary aa sequences are not highly conserved

A

false

it is most highly conserved

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40
Q

(T/F) mutations in histone gene sequences can alter gene expression

A

true

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41
Q

_____ a less well-conserved histone that bind both the linker DNA and nucleosome core to pull the nucleosomes together to form the 30 nm fiber

A

histone H1

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42
Q

which of the ff about the histone is false?

a. the amino terminal tails may bind to each other to condense the chromatin
b. Histone H4 is well conserved
c. packing of the nucleosomes form a 30 nm fiber
d. nucleosomes are packed in a smooth pattern

A

D

packed in a zigzag pattern

43
Q

(T/F) cells contain proteins that form chromatin remodeling complexes that use ATP hydrolysis to temporarily alter nucleosome structure and loosen
their interactions with DNA

44
Q

which of the ff is false about nucleosome remodeling?

a. Permits proteins involved in regulating gene expression, DNA replication and repair to access underlying DNA
b. uses GTP hydrolysis
c. Alters the position of nucleosomes along the DNA
d. chromatin remodeling complexes have up to 10 protein subunits

A

B

uses ATP synthesis

45
Q

(T/F) chromatin remodeling complexes include classes that can alter nucleosome structure or re-form nucleosomes

46
Q

which of the ff is not an enzyme mediated modification of the N-terminal tails of histones?

a. Acetylation and methylation of histamines
b. phosphorylation of serines
c. ubiquitination of lysines
c. methylation of lysines

A

A

it should be Acetylation and methylation of LYSINES

47
Q

(T/F) regulation of chromatin structure/remodeling and gene expression involve non-covalent modification of the N-terminal

A

false

COVALENT modification of the N-terminal

48
Q

(T/F) attachment of ubiquitin functions to tag proteins for

degradation by proteasomes

49
Q

(T/F) histone remodeling affects the 30nm chromatin fiber and attract the binding of ubiquitin to chromatins

A

first part is TRUE, last part FALSE

it attracts binding of specific proteins

50
Q

*(T/F) Acetylation of lysine residues destabilizes chromatin structure by eliminating its - charge and diminishing its ability to neutralize + charge on DNA and compact
chromatin

A

false

lysine = +
DNA = -
51
Q

(T/F) specific protiens that bind to chromatin either increase or decrease chromatin compaction (chromatin remodeling)

52
Q

_____ enzyme that catalyzes acetylation of lysine

A

histone acetyltransferases (HATs)

53
Q

(T/F) different combinations of histone tail modifications encode signals that are used by the cell

54
Q

_____ are long, dimeric molecules that are hinged and hydrolyze ATP and are part of larger protein complexes that may bind to loops of chromatin to participate in the condensation of mitotic chromosomes

A

SMC ( Structural Maintenance of Chromosome) proteins

55
Q

______ are larger protein complexes

A

condensins

56
Q

(T/F) Bacterial genes usually occur on a circular DNA molecule while eukaryotes have linear DNA

57
Q

which of the ff does not apply to bacterial DNA?

a. carry genes that encode antibiotic resistance
b. are short, self replicating
c. contain histones
d. are not packaged into nucleosomes
e. can be either positively or negatively supercoiled

A

C

they dont!

58
Q

____ aka bacterial DNA

A

chromosome

different structure from eukaryotes!

59
Q

(T/F) The circular molecule is associated with proteins that condense the DNA but differ from those in eukaryotes

60
Q

________ a group of enzymes that regulate the supercoiling status of DNA

A

topoisomerase

61
Q

_____ a topoisomerase that negative supercoils intoDNA

A

DNA gyrase

62
Q

which of the ff does not apply to bcaterial DNA electrophoresis?

a. Relaxed circular DNA migrates the slowest
b. Supercoiled migrates the fastest
c. Linearized DNA runs in the middle
d. none of the above

63
Q

(T/F) DNA replication is semi conservative

64
Q

(T/F) enzymes that are involved in DNA replication for prokaryotes and eukaryotes are the same

A

false

process is similar

65
Q

______ performed famous experiment that proved DNA

is replicated by a semiconservative mechanism

A

Meselson and Stahl

66
Q

____ the method used by Meselson and Stahl to study extracted DNA

A

density gradient ultracentrifugation

67
Q

(T/F) DNA contains 15N nitrogen isotope

A

false

14-N isotope

68
Q

(T/F) Meselson and Stahl showed that After second generation in normal media, both intermediate and light forms of DNA detected

A

true

must read again and understand this!

69
Q

which of the ff does not apply to DNA replication?

a. replication is bidirectional in pro and eukaryotes
b. new strands grow in 3’-5’ direction
c. prokaryotic DNA has one origin
d. eukaryotic DNA has multiple origins

A

B

grows 5’-3’

70
Q

_____ enzyme that catalyze the ddition of new nucleotides

A

DNA polymerase

71
Q

(T/F) DNA polymerase catalyzes 3’ to 5’ polymerization

A

false

5’-3’

72
Q

____ are transient segments of DNA that are 100200

nucleotides in length

A

Okazaki fragments

73
Q

____ the daughter strand synthesized continuously

A

leading strand

74
Q

____ the daughter strand is synthesized

in a discontinuous manner

A

lagging strand

75
Q

______ enzyme that joins the Okazaki fragments

A

DNA ligase

76
Q

____ the major enzyme involved in synthesis of new

DNA strands in E. coli and has a higher turnover number and processivity

77
Q

______ refers to number of nucleotides added per minute to growing chain

A

turnover number

78
Q

____ number of nucleotides joined before dissociation of the enzyme from the template

A

processivity

79
Q

the E.coli DNA polymerase that consists of single polypeptide

a. Pol I
b. Pol II
c. Pol III
d. Pol V

80
Q

the E.coli DNA polymerase that consists multipltisubunit complexes

a. Pol I
b. Pol II & I
c. Pol III & II
d. Pol V

81
Q

the E.coli DNA polymerase that repair and patches DNA

a. Pol I
b. Pol II
c. Pol III
d. Pol V

82
Q

the E.coli DNA polymerase that function mainly in repairing DNA

a. Pol I, II & III
b. Pol II, IV and V
c. Pol III, V and I
d. Pol V

83
Q

which of the ff is not required in the synthesis of the new DNA strand?

a. primer
b. Mg2+
c. deoxyribonucleotide
d. template

A

C

need deoxyribonucleoSIDE TRIPHOSPHATE

84
Q

(T/F) Pols can only initiate DNA polymerization even without the presence of a nucleotide with 3’ OH group

A

false

a nucleotide with a 3’ OH group
must be already present

85
Q

(T/F) new DNA strand is initially non covalently linked to 3’ OH group of the RNA primer

A

false

COVALENTLY linked

86
Q

(T/F) polymerase undergoes conformational change when it covalently links new nucleotide to growing chain

87
Q

(T/F)Polymerases have exonuclease activities that functions in proofreading and DNA repair

88
Q

_____ enzymes that cleave nucleotides one at a time from the end of a polynucleotide chain

A

EXonucleases

89
Q

_____ are enzymes that cleave cleave bonds within a nucleic acid chain

A

enDOnucleases

90
Q

(T/F) Pols I, II, and III all have 3’ to
5’ exonuclease activity while Only Pol I has 5’ to
3’ exonuclease activity

91
Q

the polymerase that removes RNA primer

a. pol I
b. pol V
c. pol II
d. none of the above

92
Q

____ developed the DNA sequencing (dideoxy) method

A

Coulson and Sanger

93
Q

(T/F) ddNTPs lack 3’ OH and block addition of deoxy ribonucleoside triphosphates

94
Q

(T/F) Histones are synthesized in the nucleus and it is also where modifications that affect chromatin structure/function occur after nucleosome is assembled

A

false

histones are synthesized in the CYTOSOL, modified in the NUCLEUS. the rest are true

95
Q

(T/F) Digestion of chromatin with nuclease cleaves the linker DNA and the DNA attached to the histone protein core

A

false

cleaves linker DNA only

96
Q

(T/F) incubation of nucleosomes with high salt concentrations will separate nucleosome protein core from the DNA

97
Q

(T/F) linker DNA can be a few nucleotides to 80 nucleotides long

98
Q

(T/F) the + charge of histones facilitates DNA compaction bu reducing electrostatic repulsion between the negative charges of DNA backbone

99
Q

(T/F) introns of DNA bind more tightly to the histone core due to their numerous interaction (type of binding) to one another

A

false

any DNA sequence can bind to the core

100
Q

(T/F) in vivo, the proteins bound to DNA affects its binding to the nucleosome

101
Q

which of the ff is not involved in forming the chromatin fiber?

a. N-terminal tails
b. Histone H4
c. Histone H1
d. zigzag packing pattern

A

B

this is a core subunit

102
Q

(T/F) acetylations, ubiquitination & methylation of lysines, phosphorylation of serines are all non covalent modification in the core histone tails

A

false

it is a COVALENT modification

103
Q

_______ enzymes that degrade proteins that are tagged by ubiquitin

A

proteasomes

104
Q

(T/F) combinations or patterns of histone tail modification encodes a signal used by the cell to mark a just replicated region, mark sequences that should not be transcribed or attract binding of proteins for some specific functions

Biochem 2 (13 decks)

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