Exam 2 - DNA Structure Flashcards Preview

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Flashcards in Exam 2 - DNA Structure Deck (104):
1

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

false

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

2

_____ the wavelength used to monitor DNA/detect protein

260 nm

3

______ techniques that widely uses DNA denaturation

hybridization probes, PCR

4

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

hyperchromicity

5

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

melting temperature, Tm

6

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

true

7

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

C

8

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

true

temp is lower than the strand with no mutation

9

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

genome

10

_____ the number of nucleotides that the haploid human genome consists

3.2 E9 nucleotides

11

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

none of the above :)

12

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

true

13

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

D

14

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

transposable elements

15

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

introns

16

____ are the coding sequences in the DNA

exons

17

_____ the average size of a human gene

27,000 nucleotides

18

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

B

they are non coding!

19

____ are examples of non coding DNA sequences

gene promoters, introns, "junk" DNA, regulatory DNA sequences

20

(T/F) promoters regulate gene expression

true

21

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

true!

exons/amino acids

22

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

false

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

23

_____ the smallest human chromosome

chromosome 22

24

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

all are mobile elements!

25

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

Simple sequence repeats

26

____ large stretches of the genome (1000-200,000
nucleotides) present in two or more locations of genome

Segmental duplications

27

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

pseudogenes


humans have least 20,000

28

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

true

29

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


10,000 fold in mitotic chromosome

30

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

false

high conc

31

______ the complex of histones and nonhistones with DNA

chromatin

32

____ refers to a chromatin that becomes partially unfolded

"beads on a string"

beads = nucleosomes (dna around histones)
string = DNA

33

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

true

34

(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

true

35

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

nucleosome

36

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

B

only 200 nucleotide intervals

37

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

C

alpha helices form the histone fold

38

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

basic aas are POSITIVELY charged

DNA is neg

39

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

false

it is most highly conserved

40

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

true

41

_____ 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

histone H1

42

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

D

packed in a zigzag pattern

43

(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

true

44

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

B

uses ATP synthesis

45

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

true

46

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

it should be Acetylation and methylation of LYSINES

47

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

false

COVALENT modification of the N-terminal

48

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

true

49

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

first part is TRUE, last part FALSE

it attracts binding of specific proteins

50

*(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

false

lysine = +
DNA = -

51

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

true

52

_____ enzyme that catalyzes acetylation of lysine

histone acetyltransferases (HATs)

53

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

true

54

_____ 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

SMC ( Structural Maintenance of Chromosome) proteins

55

______ are larger protein complexes

condensins

56

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

true

57

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

C

they dont!

58

____ aka bacterial DNA

chromosome

different structure from eukaryotes!

59

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

true

60

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

topoisomerase

61

_____ a topoisomerase that negative supercoils intoDNA

DNA gyrase

62

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

D :)

63

(T/F) DNA replication is semi conservative

true

64

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

false

process is similar

65

______ performed famous experiment that proved DNA
is replicated by a semiconservative mechanism

Meselson and Stahl

66

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

density gradient ultracentrifugation

67

(T/F) DNA contains 15N nitrogen isotope

false

14-N isotope

68

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

true

must read again and understand this!

69

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

B

grows 5'-3'

70

_____ enzyme that catalyze the ddition of new nucleotides

DNA polymerase

71

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

false

5'-3'

72

____ are transient segments of DNA that are 100200
nucleotides in length

Okazaki fragments

73

____ the daughter strand synthesized continuously

leading strand

74

____ the daughter strand is synthesized
in a discontinuous manner

lagging strand

75

______ enzyme that joins the Okazaki fragments

DNA ligase

76

____ the major enzyme involved in synthesis of new
DNA strands in E. coli and has a higher turnover number and processivity

Pol III

77

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

turnover number

78

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

processivity

79

the E.coli DNA polymerase that consists of single polypeptide
a. Pol I
b. Pol II
c. Pol III
d. Pol V

A

80

the E.coli DNA polymerase that consists multipltisubunit complexes
a. Pol I
b. Pol II & I
c. Pol III & II
d. Pol V

C

81

the E.coli DNA polymerase that repair and patches DNA
a. Pol I
b. Pol II
c. Pol III
d. Pol V

A

82

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

B

83

which of the ff is not required in the synthesis of the new DNA strand?
a. primer
b. Mg2+
c. deoxyribonucleotide
d. template

C

need deoxyribonucleoSIDE TRIPHOSPHATE

84

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

false

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

85

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

false

COVALENTLY linked

86

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

true

87

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

true

88

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

EXonucleases

89

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

enDOnucleases

90

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

true

91

the polymerase that removes RNA primer
a. pol I
b. pol V
c. pol II
d. none of the above

A

92

____ developed the DNA sequencing (dideoxy) method

Coulson and Sanger

93

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

true

94

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

false

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

95

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

false

cleaves linker DNA only

96

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

true

97

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

true

98

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

true

99

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

false

any DNA sequence can bind to the core

100

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

true

101

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

B

this is a core subunit

102

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

false

it is a COVALENT modification

103

_______ enzymes that degrade proteins that are tagged by ubiquitin

proteasomes

104

(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

true