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
2
Q
_____ the wavelength used to monitor DNA/detect protein
A
260 nm
3
Q
______ techniques that widely uses DNA denaturation
A
hybridization probes, PCR
4
Q
_____ term referring to when Absorbance increases as the bases become unstacked
A
hyperchromicity
5
Q
____ the temperature at which half the DNA becomes single stranded is called the
A
melting temperature, Tm
6
Q
*(T/F) Tm shifts to the right as GC
content increases
A
true
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
8
Q
(T/F) SNPs can be detected using melting temperature
A
true
temp is lower than the strand with no mutation
9
Q
_______ refers
to the complete set of genetic information carried by an
organism or the DNA that carries this information
A
genome
10
Q
_____ the number of nucleotides that the haploid human genome consists
A
3.2 E9 nucleotides
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 :)
12
Q
(T/F) smaller, simpler organisms have compact genomes with little noncoding segements of DNA
A
true
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
14
Q
_____ are segments of DNA that can move within or between genomes that accumulate during evolution
A
transposable elements
15
Q
____ are intervening noncoding DNA sequences that break up the coding sequences
A
introns
16
Q
____ are the coding sequences in the DNA
A
exons
17
Q
_____ the average size of a human gene
A
27,000 nucleotides
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!
19
Q
____ are examples of non coding DNA sequences
A
gene promoters, introns, “junk” DNA, regulatory DNA sequences
20
Q
(T/F) promoters regulate gene expression
A
true
21
Q
*(T/F) only 1.5% of the human genome encodes for amino acids
A
true!
exons/amino acids
22
Q
(T/F) organisms with compact genome have introns like humans
A
false
more compact = no introns, shorter
humans= longer, mostly introns
23
Q
_____ the smallest human chromosome
A
chromosome 22
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!
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
