Prelim Flashcards
(204 cards)
1
Q
- Disovery of DNA
- First person who identified “nuclein” inside the nuclei of our White Blood Cells (WBC)
- discovered DNA and the first person to extract DNA using pus in surgical bandages.
A
Friedrich Miescher
2
Q
- Investigates the Structure of the DNA
- First to discover the order of the three major components of single nucleotide
- First to discover the:
- Carbohydrate component of RNA: Ribose
- Carbohydrate component of DNA - First to correctly identify the way RNA and DNA molecules are put together.
A
Phoebus Levene
3
Q
total amount of purines which is your Adenine plus Guanine would equate or equal to the total amount of your pyrimidines which your Cytosine and Thymine
A
Chargaff’s rule
4
Q
Chargaff’s rule
A
Erwinn Chargaff
5
Q
the same nucleotides do not repeat in the same order which is an idea that was proposed by
A
Levene
6
Q
He noted that the nucleotide composition of DNA varies among species
A
Erwinn Chargaff
7
Q
Proposed the Double Helix Structure
A
James Watsons & Francis Crick
8
Q
Work by English researchers, Rosalind Franklin and Maurice Wilkins
A
X-ray Crystallography Work
9
Q
HUMAN GENOME PROJECT is a project that was proposed in 1987 by
A
Dr. Alvin W. Trivelpiece.
10
Q
how many chemical base pairs that make up human genomic DNA.
A
3 billion chemical base pairs
11
Q
Human Genome Project which operated from
A
1990 up to 2003
12
Q
The Human Genome Project was further intended
A
- To Improve the technologies needed to interpret and analyze genomic sequences.
- To Identify all the genes encoded in human DNA
- To address the ethical, legal, and social implications that may arise from defining the entire human genomic sequence.
13
Q
in a span of –?–, we were already able to map the whole human genome and all of the chromosomes in the human body and identified where these genes came from
A
13 years
14
Q
has enable the identification of a variety of genes that are associated with disease
A
HapMap database
15
Q
the idea that knowledge of patient’s entire genome sequence will give healthcare providers the ability to deliver the most appropriate effective care for that patient
A
personalized medicine
16
Q
DNA Composition
A
Carbon, Hydrogen, Oxygen, Phosphorus, & Nitrogen (CHOPhoN)
17
Q
holds genetic information that is unique to the organism from which it was isolated
A
DNA
18
Q
DNA
A
DEOXYRIBONUCLEIC ACID
19
Q
is based on the order or sequence of nucleotides in the nucleic acid polymer
A
DNA storage system
20
Q
basic structure of DNA is composed of
A
Pentose Sugar, Nitrogenous Base, & Phosphate Group
21
Q
Nucleic acids are macromolecules that exist as polymers
A
polynucleotides
22
Q
polynucleotide is consist of many monomers considered the building blocks of all nucleic acid molecule
A
nucleotide
23
Q
4 Nitrogenous bases that make up the majority of DNA
A
Adenine. Guanine,Cytosine, and Thymine
24
Q
substitution of Thymine in RNA
A
Uracil
25
Nitrogen base is attached to the deoxyribose sugar which forms a polymer with the deoxyribose sugar of the other nucleotides through the
phospodiester bond
26
Nine-member Double rings is also known as
Purines
27
Six-member Single Ring is also known as
Pyrimidines
28
Purines
Adenine & Guanine
29
Pyrimidines
Thymine, Uracil, & Cytosine
30
is called a pentose sugar because it has
5-carbon ring and 1 oxygen.
31
The difference between DNA and RNA lies in the
C-2’ -position of the ribose sugar ring
32
In RNA, the carbon at the C-2 position is attached to a?
hydroxyl (OH) group
33
In DNA, the carbon at the C-2 position is attached to a?
hydrogen (H) atom.
34
pentose ring in DNA is considered a deoxyribose because it is a?
deoxygenated five-carbon sugar ring
35
In the absence of the C-2’ hydroxyl group of DNA the sugar is more specifically named
2- deoxyribose
36
a molecule composed of a purine or pyrimidine (nitrogenous base) and a ribose or deoxyribose sugar
Nucleoside
37
Nitrogenous base + Deoxyribose (sugar) =
NUCLEOSIDE
38
If the base is a purine, the --?-- atom is covalently bonded to the sugar.
N-9 atom
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If the base is a pyrimidine, the --?-- atom bonds to the sugar
N-1 atom
40
When a phosphate group attaches to a nucleoside through a phosphoester bond it is a?
Nucleotide
41
Nucleoside + Phosphate Group =
Nucleotide
42
phosphoester bond is linked between
5’ - hydroxyl group of the sugar and a phosphate group.
43
Nitrogenous base + sugar = ?
NItrogebous base + sugar + phosphate = ?
1. NUCLEOSIDE
2. NUCLEOTIDE
44
numbering of the positions in the nucleotide molecule starts with the
ring positions of the nitrogen base
45
Single units within nucleotides are also called
nucleoside monophosphates.
46
a significant form because it serves as the precursor molecule during nucleic acid synthesis within the cell
triphosphate form
47
In a polynucleotide chain, nucleotides are joined together through phosphodiester bond to form a long chain of nucleotides called as
PHOSPHATE DEOXYRIBOSE BACKBONE
48
formation of a phosphodiester bond involves ? or the removal of a molecule of water
dehydration reaction
49
Such a phosphodiester bond results in a repeating pattern of the sugar-phosphate units called
sugar-phosphate backbone
50
Such a phosphodiester bond results in a repeating pattern of the sugar-phosphate units called a sugar-phosphate backbone, and this provides for the polynucleotide chain with a linkage direction of ?
3’-->5’ phosphodiester linkage direction.
51
T/F: DNA is antiparallel.
T
52
nitrogen bases are oriented towards the --?--where the hydrogen bond with their homologous bases to stabilize the structure.
center
53
two polynucleotide chains in the double helix are held by
hydrogen bonding
54
two polynucleotide chains in the double helix are held by hydrogen bonding between the nitrogenous bases, we call this?
base pairing.
55
Cytosine and guanine has how many hydrogen bonds
3 hydrogen bonds
56
adenine and thymine has ow many hydrogen bonds
2 hydrogen bonds
57
formation of hydrogen bonds between two complementary strands of DNA
Hybridization
58
T/F: Single strands of DNA with identical sequences will not hybridize with each other.
T
59
The bases are positioned such that the sugar phosphate chain that connects them (sugar phosphate backbone) is oriented in a
spiral or helix around the nitrogen bases
60
Two long polynucleotide chains are coiled around a central axis, forming a
right-handed double helix.
61
The two DNA strand are antiparallel, that is, their 5’ --> 3’ orientation runs in what direction
opposite direction
62
base of both chains lie --?-- to the axis, and they are stacked on one another.
Perpendicular
63
result of the formation of a hydrogen bond in DNA.
Nitrogenous bases of opposite chains are paired
64
The double helix model is mainly based on the ?
1. X-ray diffraction data collected by Rosalind Franklin and Maurice Wilkins
2. DNA composition studies observed by Erwin Chargaff.
65
X-ray diffraction data showed that:
1. DNA is a --?-- helix
2. The repeat distance in the helix is --?--, with a diameter of --?--
4. The distance between adjacent nucleotide is --?-
1. regular
2. 34 angstroms (A ̊ )
3. 20 A ̊
4. 3.4 A ̊
66
The discovery of double helical model of DNA relied on the critical data from
Chargaff’s findings
67
Each complete turn of helix is --?--, The double helix has a diameter of 20 A ̊ .
34 A ̊long
68
The twisting of the two strands around one another forms a double helix with a
minor groove and a major groove.
69
In a minor groove, the distance between the two DNA strands is
12 A ̊
70
In a major groove, the distance between the two DNA strands is
22 A ̊
71
The double helix in DNA is normally right-handed, which means the turns run --?-- as viewed along the helical axis
clockwise
72
how many base pairs per turn is an average structure.
10 base pairs
73
If it has more base pairs per turn, it is said to be
overwound.
74
If it has fewer base pairs per turn, then it is
underwound
75
overwound base pairs
> 10 base pairs
76
underwound base pairs
< 10 base pairs
77
The degree of local winding can be affected by
overall conformation of the DNA double helix or the binding of proteins to specific sites on the DNA.
78
Why do we need to emphasize major and minor grooves?
major and minor grooves are sites which we take advantage of on how we can denature our DNA.
79
The double helix is also be penetrated by --?--, molecules that slide transversely into the center of the helix.
intercalating agents
80
can displace your hydrogen bonds and separate the two strands of that double helix.
denaturing agents (formamide or urea)
81
The amount of adenine residues is -?- to the amount of thymine residues in DNA.
proportional
82
the amount of guanine residues is -?- to the amount of cytosine esidues in DNA.
proportional
83
T/F: The sum of the purines equal to the sum of pyrimidine.
T
84
T/F : The percentage of (G+C) is not necessarily equal the percentage of (A+T)
T
85
ALTERNATIVE FORMS OF DNA
B-DNA, A-DNA, Z-DNA
86
An alternative form of DNA, the Watson-Crick DNA molecule represents the DNA molecule in solution, which is the DNA molecule that exists in a very high relative humidity environment
B-DNA
87
B-DNA exists in a very high relative humidity environment with a percentage of
92%)
88
An alternative form of DNA:
1. double helix is said to be right-handed because the turns run as viewed along the helical axis
2. has 10 base pairs in each turn
3. length of one complete turn of the helix
along its axis is 34 A
B-DNA
89
An alternative form of DNA bserved when DNA is dehydrated or under high salt conditions
A-DNA (deydrated version of B-DNA)
90
An alternative form of DNA:
1. right-handed
2. A-DNA is both shorter and thicker than B-DNA.
3. Each repeat double helix in A-DNA is 24.6 A ̊
4. Each turn has about 11 base pairs (bp).
A-DNA (deydrated version of B-DNA)
91
An alternative form of DNA which the backbone formed a zig-zag structure
Z-DNA
92
Z-DNA is formed under conditions of
high salt or in the presence of alcohol
93
An alternative form of DNA:
1. longer and narrower than B-DNA
2. repeat helix is 45.6 A ̊
3. each helical turn has 12 base pair
4. left-handed helix turns counterclockwise away from the viewer when viewed down its axis.
Z-DNA
94
Z-DNA minor groove is (a) and major groove is (b)
(a) very deep and narrow
(b) shallow (non-existent)
95
also known to occur in nature when there is a sequence of alternating purinepyrimidine.
Z-DNA
96
Z-DNA is also known to occur in nature when there is a sequence of alternating purinepyrimidine. Because sequences with (?) at the number 5 position of the pyrimidine ring can also be found in the Z form and is (?), it may play a role in the regulation of gene activation
1. cytosine methylated
2. hypo-postulated
97
B-DNA
Helix:
Base pairs per turn:
Repeat helix (length):
Formation:
Structure: N/A
: Right-handed
:10 bp
: 34 A ̊
: very high relative humidity environment (92%
98
A-DNA
Helix:
Base pairs per turn:
Repeat helix (length):
Formation:
Structure:
: Right-handed
: 11 bp
: 24.6 A ̊
: Dehydrated; under high salt conditions
: Shorter and thicker than B-DNA
99
Z-DNA
Helix:
Base pairs per turn:
Repeat helix (length):
Formation:
Structure:
: Left-handed
: 12 bp
: 45 A ̊
: high salt or in the presence of alcohol.
: Longer and narrower than B-DNA
: Zigzag backbone; hypo-postulated so may play a role in gene activation
100
each of the two new daughter cells that are created then receives one copy of the genome through a process called
cell division.
101
A process to ensure that the DNA is duplicated before cell division so that each offspring cell receives chromosome(s) identical to the parent’s
DNA replication
102
To accomplish this feat in a reasonable period of time, replication initiates throughout --?-- at multiple origins along each chromosome.
S phase
103
DNA replication must also be coordinated with --?-- to ensure that each daughter cell receives a complete and unaltered complement of genetic information.
chromosome segregation
104
In this model, 2 parental strands separate, allowing each separated strand to serve as a template for the synthesis of a complementary strand
semiconservative model
105
In this replication mechanism, each double stranded daughter DNA molecule will have:
1. conserved DNA strand that is derived from the parental DNA
2. a newly synthesized strand
semiconservative model
106
TYPE OF PHASE
1. The DNA double helix is opened at the origin of replication and unwound on both sides of the origin to form two structure called replication forks that unwind the double helix in opposite directions.
2. Replication enzymes and proteins are loaded to the single strand, and these will form the templates for the daughter strands that are to be synthesized
INITIATION
107
TYPE OF PHASE
1. during this phase, the replication machinery moves along the parent DNA strands and forms the daughter strands as it proceeds.
2. this is the time that you add your nucleotides
elongation phase
108
TYPE OF PHASE
In this phase, DNA replication occurs when the two replication forks moving in opposite directions meet, and the replication complexes are disassembled.
Termination
109
The process of DNA replication can be divided into three phases:
initiation, elongation, and termination.
110
DNA replication starts at specialized sites called --?-- and moves away from an origin in both directions, creating a structure known as a -?-
1. origins of replication
2. replication bubble
111
The DNA double helix is opened at the --?-- and unwound on both sides of the origin to form two structure called --?-- that unwind the double helix in -?- directions.
1. origins of replication
2. replication forks
3. opposite
112
the sites at which single-stranded DNA is exposed, and at which DNA synthesis occurs
(5’ ---> 3’ direction)
replication forks
113
recruited to the origin Replication bubble allows both strands to be copied in opposing directions
Helicase (orange rings)
114
helicase recruits --?-- "RNA primers" (green) which synthesize on both strands.
primase
115
functions by synthesizing short RNA sequences that are which serves as its template.
Primase
116
Why Is there primase?
Because your DNA polymerase cannot synthesize nucleotide without a based template.
117
Protein complex that serves as a processivity-promoting factor in DNA replication
Sliding clamp (Beta Clamp)
118
As a critical component of the holoenzyme, the -?-protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand.
clamp protein
119
recruited and interacts with the sliding clamp to
elongate 3'end of primers.
DNA polymerases (blue)
120
Replication of the leading strand is -?-, but replication of the lagging strand is -?-, and produces short fragments
1. continuous
2. discontinuous
121
A major enzyme, one that polymerize the nucleic acid chain and reads the template in the 3 primes to the 5 prime directions.
DNA polymerase
122
Replication is complete:
RNA primers are -?- and DNA polymerases fill in -?-. DNA ligases -?- any gaps that remain.
1. removed
2. nucleotides
3. seal
123
also known as Semidiscontinuous Mechanism
Okazaki
124
In this model, both strands could not replicate continuously.
Okazaki
125
1. DNA polymerase could make one strand which is the strand continuously in the 5’ --> 3’ direction at the replication fork on the exposed 3’ --> 5’ template strand.
2. Its direction of synthesis is the same as the direction in which the replication fork is movingg
leading strand
126
The other strand, which is the -?- strand, would have to be made discontinuously in small fragments—Okazaki fragments.
Lagging strand
127
The discontinuity of synthesis of the lagging strand is because its direction of synthesis is -?- to the moving direction of the replication fork.
opposite
128
The small Okazaki fragments of the lagging strand
are then linked together by an enzyme called?
DNA ligase
129
enzyme that harnesses the chemical energy from the ATP hydrolysis to separate the two DNA strands at the replication fork
Helicase
130
The binding of --?-- can stabilize the single- stranded DNA so they will not anneal to reform the double helix and protect the single-stranded DNA from hydrolysis by nucleases
Single-Strand Binding Protein
131
SSBs allows enzymes to attach to the newly opened single strand and initutate --?-
elongation
132
T/F: In prokaryotes, DNA exists in a negatively supercoiled, closed circle form
T
133
When two DNA strands are separated during replication, -?- are introduced ahead of the replication fork
positive supercoils
134
an essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed- circular DNA
DNA Gyrase
135
DNA gyrase belongs to the class of enzymes known as -?- that are involved in the control of topological transitions of DNA
topoisomerases
136
unusual feature of DNA polymerase
cannot synthesize a new DNA strand from the very start of the parent strand
137
short strand of RNA is termed
primer
138
responsible for copying a short stretch of the DNA template strand to produce the RNA primer sequence
Primase
139
The leading strand requires how many primer
1
140
the primer is --?-- bonded to the template so it can provide a stable framework to which the nascent chain starts to grow.
hydrogen-bonded
141
The eukaryotic primase complex contains four subunits:
1. Two of them function as a primase
2. an αlpha catalytic subunit
3. an accessary subunit
142
T/F: Primases and αlpha catalytic subunit bind in a complex with the DNA polymerase.
T
143
T/F: the polymerase-α subunit-primase complex synthesizes a stretch of 10–30 nucleotides of RNA.
T
144
αlpha catalytic subunit continues to synthesize a short stretch of DNA 6before the DNA polymerase takes over the replication process. This phenomenon is called
polymerase switching.
145
An exonuclease
DNA Polymerase
146
- A broad class of enzymes that cleave off nucleotides one at a time from the three prime or five prime ends of DNA and RNA chains
- it also functions to protect the sequence of nucleotides, which must be faithfully copied
Exonucleases
147
this enzyme will remove a mismatch in the primer sequence before beginning polymerization
DNA Polymerase
148
During DNA synthesis, this exonuclease function gives the enzyme the capacity to --?-- newly synthesized DNA, that is, to remove a misincorporated nucleotide by breaking the phosphodiester bond and replace it with the correct one
proofread
149
First polymerase enzyme to direct during the
initial synthesis
DNA Polymerase III
150
T/F: after RNA removal, DNA polymerase I uses its polymerase activity to fill in the gap left by the RNA with new DNA.
T
151
- can synthesize polynucleotide chains without a template
- This enzyme will add nucleotides to the end of a DNA strand in the absence of hydrogen base pairing with a template.
- used in the laboratory to generate 3 ′ -end labeled DNA specie
Terminal Transferase
152
T/F: Only DNA polymerase I has 5’ --> 3’ exonuclease activity which can remove short stretches of nucleotides during repair.
T
153
also called nick translation.
cut-and-patch process
154
Polymerase I also uses nick translation in the --?-- process
repairing process
155
enzyme responsible for sealing the nick between the new strands and the synthesized by polymerase III and polymeraseI
DNA Ligase
156
often used in vitro as a method to introduce labeled nucleotides into DNA molecules. The resulting labeled products are used for DNA detection in hybridization analyses.
Nick translation
157
1. DNA polymerase III holoenzyme
2. Responsible for the coupling of DNA replication
3. Composed of: DNA polymerase, Sliding clamp, & Clamp loader
Replisome
158
The coupling of DNA replication on the leading and lagging strands is achieved by physically associating the proteins replicating each strand into one large protein called
replication complex, or replisome.
159
play an important role in recruiting DNA polymerase to the appropriate location on the DNA template. They localize specifically at the region where DNA synthesis needs to commence.
clamp loader and sliding clamp
160
responsible for holding catalytic cores onto their template strands.
sliding clamp
161
places the clamp on DNA
clamp loade
162
Polymerases are linked together by a protein called --?-- and is associated with the clamp loader and links this polymerases-clamp loader complex to the helicase.
Tau protein
163
replication pattern of most eukaryotic and bacterial DNAs
Bidirectional replication
164
circular E. coli chromosome has a --?-- because it replicates from a single starting point—the origin of replication.
single replicon
165
replicating DNA begins to take on the -?- shape until both replication fork meet on the other side of the circle
theta (θ)
166
T/F: Eukaryotic chromosomes have many replicons, and the replication in these replicons begins simultaneously.
T
167
end of the chromosome,
telomere
168
The two circular DNA are separated by
topoisomerases
169
- enzymes that in the degree of DNA supercoiling.
- They can also convert one isomer of DNA to another
- has 2 Families: Type I & Type II
topoisomerase
170
topoisomerase family:
enzymes transiently cleave and reseal one strand of duplex DNA in the ABSENCE OF ATP and relax a supercoil by either passing the other strand through an enzyme link.
Type one
171
topoisomerase family:
enzymes will cleave and relegate both strands in the PRESENCE OF ATP; requires ATP
Type two
172
T/F: DNA gyrase belong to the type II
T
172
G-rich stand always at
3' end
173
Eukaryotic chromosomes end in distinctive sequences called -?- that help preserve the integrity and stability of the chromosomes
telemore
173
1. TTGGGG = ?
2. TTAGGG = ?
1. protozoans
2. vertebrates
174
T/F: The telomeres consist of simple sequence repeats
T
175
solves the problem by producing an associated RNA that complements the three prime overhang at the end of the chromosome and the rest of the DNA polymerase continues.
Telomerase binds to 3’ GC rich tail. Repeated TTGGGG sequences are synthesized
176
T/F: Once DNA is polymerized, it is not static.
T
177
T/F: Once DNA is polymerized, it is not static. The information stored in the DNA must be tapped selectively to make RNA and, at the same time, protected from damage.
T
178
An endonucleases that recognize specific base sequences and break or restrict the DNA polymer at the sugar-phosphate backbone
Restriction Enzymes
179
type of restriction enzyme to take note is -?- because this is the one used most frequently in the laboratory
type II
180
type of restriction enzyme that do not have methylation activity.
type II
181
they read the same 5 prime to 3 prime (5’ – 3’)
on both strands of the DNA referred to as the bilateral symmetry.
palindromic
182
cleave the DNA directly at the binding site, producing fragments of predictable size.
Type II restriction enzymes
183
Uses of restriction enzyme
1. Analysis of gene rearrangements
2. Mutation detection
3. DNA recombination in vitro
4. Mapping a DNA fragment
184
catalyzes the formation of a phosphodiester bond between adjacent 3 ′ -hydroxyl and 5 ′ -phosphoryl nucleotide ends
DNA Ligase
185
degrade DNA from free 3 ′ -hydroxyl or 5 ′ - phosphate ends
Nucleases (Exonuclease)
186
use of Nucleases (Exonuclease)
DNA manipulation in vitro
187
1. unwinds dsDNA (breaks hydrogen bonds = ?
2. relieves the tension created by helicase
( breaks the phosphodiester linkages in DNA Backbone= ?
1. Helicase
2. Topoisomerase
188
are the targets for several anticancer drugs
topoisomerase
189
catalyze the addition of methyl groups to nitrogen bases, usually adenineand cytosine in DNA strands
Methyltransferase
190
Most prokaryotic DNA is -?-, or -?-, as a means to differentiate host DNA from non-host and to provide resistance enzymes
1. methylated
2. hemimethylated
191
T/F: eukaryotic DNA is methylated in specific regions
T
192
A process of separating dsDNA into single strands
DNA denaturation
193
opposite of DNA denaturation
renaturation
194
T/F: DNA denaturation is by breakind hydrogen bonds
T
195
Factors of DNA denaturation
1. Temperature :
2. salt concentration :
3. pH :
1. Temperature : High
2. salt concentration : Low
3. pH : High
196
T/F: DNA denaturation is also termed as DNA melting
T
197
T/F: but when you lower the temperature, the hydrogen bond would form and the hydrogen bonds are restored called DNA renaturation
T
198
MELTING TEMPERATURE is the middle point of a temperature range where (?)% of your DNA strands are denatured and the amount of denatured DNA is measured at an absorbance of (?)nanometer.
1. 50%
2. 260 nm
199
Unusual secondary structures of DNA that are SEQUENCE-SPECIFIC
1. slipped structures
2. cruciform,
3. triple-helix DNA
200
T/F: The secondary structure have something to do with super coiling.
F; Tertiary structure
201
tertiary winding of DNA helix axis that occurs when the double helix is under or over wound.
DNA supercoiling
202
defines the DNA super helical structure or we call these DNA tertiary structure
rethink/twist
