CHAPTER 9 Flashcards
(177 cards)
1
Q
Levels of structure of nucleic acid
the order of bases on the polynucleotide sequence; the order of bases specifies the genetic code
A
1°structure
2
Q
Levels of structure of nucleic acid
the three-dimensional conformation of the polynucleotide backbone
A
2°structure
3
Q
Levels of structure of nucleic acid
supercoiling
A
3°structure
4
Q
Levels of structure of nucleic acid
interaction between DNA and proteins
A
3°structure
5
Q
a biopolymer containing three types of monomer units
A
Nucleic acid
6
Q
three types of monomer units in Nucleic acid
A
a base derived from purine or pyrimidine (nucleobases)
a monosaccharide, either D-ribose or 2-deoxy-D-ribose
phosphoric acid
7
Q
Pyrimidines
A
Cytosine (DNA, RNA)
Uracil (RNA)
Thymine (DNA)
8
Q
Purines
A
Adenine (DNA, RNA)
Guanine (DNA, RNA)
9
Q
Structure
Two rings, nine-membered molecule
Number of nitrogen atoms
Four
A
Purines
10
Q
Structure
One ring, six-membered molecule
Number of nitrogen atoms
Two
A
Pyrimidines
11
Q
The Properties of Pyrimidines and Purines Can Be Traced to Their ______ Nature
A
Electron-Rich
12
Q
The aromaticity and electron-rich nature of pyrimidines and purines enable them to undergo
A
keto-enol tautomerism
13
Q
The keto tautomers of uracil, thymine, and guanine predominate at pH
A
7
14
Q
is a chemical equilibrium between a keto form (a ketone or aldehyde) and an enol form (an alcohol).
A
keto-enol tautomerism
15
Q
By contrast, the enol form of cytosine predominates at pH
A
7
16
Q
Protonation states of the nitrogens determines whether they can serve as
A
H-bond donors or acceptors
17
Q
a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate
A
Deoxyribonucleic acids, DNA
18
Q
he sequence of bases along the pentose-phosphodiester backbone of a DNA molecule
A
Primary Structure
19
Q
base sequence is read from the
A
5’ end to the 3’ end
20
Q
DNA differs from RNA in what way do they differ?
A
Sugar is 2’-deoxyribose, not ribose.
* Sometimes “d” used to designate “deoxy”
21
Q
the ordered arrangement of nucleic acid strands
A
Secondary structure
22
Q
the double helix model of DNA 2°structure was proposed by
A
James Watson and Francis Crick in 1953
23
Q
a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis
A
Double helix
24
Q
structure based of DNA was based on the
A
X-Ray crystallography
25
The double helix is stabilized by ________ bonds
hydrogen
26
_________ pairs that arise from hydrogen bonds
Base pairs
27
had the pairing data, but didn't understand its implications
Erwin Chargaff
28
whose X-ray fiber diffraction data was so crucial
Rosalind Franklin'
29
showed that DNA was a helix
Francis Crick
30
figured out the H bonds stabilized the DNA structure
James Watson
31
A major factor stabilizing the double helix is base pairing by hydrogen bonding between __________ and between ________
T-A
C-G
32
T-A base pair comprised of _ hydrogen bonds
2
33
G-C base pair comprised of _ hydrogen bonds
3
34
what base pair is stronger
G-C base pair comprised of 3 hydrogen bonds
35
what base pair is weaker
T-A base pair comprised of 2 hydrogen bonds
36
Watson-Crick A:T and G:C base pairs. All H-bonds in both base pairs are
straight
37
The _________ groove is large enough to accommodate an alpha helix from a protein
major
38
The "tops" of the bases (as we draw them) line the "floor" of the _________ groove
major groove
39
What base pairing has a bigger major groove
C-G (cytosine-guanine) base pair will have a larger major groove
40
proteins that can recognize the pattern of bases and the H-bonding possibilities in the major groove
Regulatory proteins (transcription factors)
41
The Structure of DNA
An antiparallel double helix
42
The Structure of DNA
Diameter
Length
Base pairs
Diameter of 2 nm
Length of 1.6 million nm (E. coli)
Base pairs: A-T, G-C
43
Eukaryotic DNA wrapped around histone proteins to form ________
nucleosomes
44
______________ of DNA gives identical progeny molecules because base pairing is the mechanism that determines the nucleotide sequence of each newly synthesized strand.
Replication
45
Other Forms of DNA
B-DNA
A-DNA
Z-DNA
46
Other Forms of DNA
considered the physiological form
a right-handed helix, diameter 11Å
10 base pairs per turn (34Å) of the helix
B-DNA
47
Other Forms of DNA
a right-handed helix, but thicker than B-DNA
11 base pairs per turn of the helix
has not been found in vivo
Is the dehydrated B-DNA
A-DNA
48
Other Forms of DNA
a left-handed double helix
may play a role in gene expression
Z-DNA
49
Comparison of A,B, and Z forms of DNA
has more proteins to be attached
B-DNA
50
Comparison of A,B, and Z forms of DNA
Both A and B-DNA are __________-handed helices
right
51
Comparison of A,B, and Z forms of DNA
occurs in nature, usually consists of alternating purine-pyrimidine bases
Z-DNA
51
Comparison of A,B, and Z forms of DNA
Z-DNA is ______ handed
left
52
Comparison of A,B, and Z forms of DNA
Z-DNA is ______ handed
left
53
Comparison of A,B, and Z forms of DNA
Methylated cytosine found also in
Z-DNA
53
In Base stacking seen in standard B-DNA,
each base rotated by ________ compared to the next and, while this is perfect for maximum base pairing, it is not optimal for maximum overlap of bases; in addition, bases exposed to the minor groove come in contact with water
32°
54
Other Features of DNA
the arrangement of bases in nucleic acids, like DNA, where the bases stack on top of each other in a parallel configuration. This stacking is a key interaction that stabilizes the structure of DNA
Base stacking
54
In Base stacking
bases are hydrophobic and interact by hydrophobic interactions, which are called
Van der waals
54
In Base stacking seen in standard B-DNA,
many bases adopt a __________ in which base pairing distances are less optimal but ____________ is more optimal and water is eliminated from minor groove contacts
propeller-twist
base stacking
55
refers to the angle between the planes of two bases within a base pair, where they are twisted relative to each other like an airplane propeller
propeller twist
56
how is Z-form is derivative of B-form
Produced by flipping one side of the backbone 180˚ without disturbing the backbone covalent bonds or hydrogen bonds
under specific conditions, primarily when there are repeating sequences of cytosine and guanine base pairs, with the key change being a significant alteration in the sugar-phosphate backbone geometry, causing the DNA to "zigzag" into a left-handed helix, unlike the smooth right-handed B-form
56
describes the non-covalent interactions between the aromatic rings of stacked bases along the DNA strand, essentially how well the bases sit on top of each other
base stacking
57
right-handed, short and broad, 2.3 Å, 11 bp per turn
helix on major groove
minor groove is broad but shallow
anti glycosyl bond confirmation
a-DNA
57
right-handed, longer, thinner, 3.32 Å, 10 bp per turn
helix axis through base pairs
minor groove narrow but intermediate depth
helix on minor groove
anti glycosyl bond confirmation
b-DNA
58
left-handed, longest, thinnest, 3.8 Å, 12 bp per turn
lacks a major groove entirely
minor groove narrow but deep
helix on minor groove
anti glycosyl bond confirmation at C, syn at G
Z-DNA
58
refers to the spatial arrangement where the base of a nucleoside (like adenine or cytosine) is rotated away from the sugar ring, meaning it projects "outwards" from the sugar molecule, which is the most common conformation observed in DNA and RNA due to steric factors
anti glycosyl bond confirmation
59
Bases that are exposed to minor groove contact with water
They twist in a “propeller twist” fashion
Helical/Propeller Twists
59
the alternative conformation, where the base is rotated closer to the sugar, is called
syn glycosyl bond confirmation
60
Helical/Propeller Twists results to the
Results in:
* less optimal base pair distance
* More optimal base pair stacking (eliminates presence of water molecules)
*crooked hydrogen bonding due to the bulkiness of the aromatics
61
is essential for normal embryonic development
switches genes off, so that the information they encode is not expressed
Methylation of cytosine residues
61
Methylation of cytosine residues forms
(forming 5-methylcytosine)
62
is the study of heritable changes in the genome that occur without a change in nucleotide sequence (such as cytosine methylation)
changes can influence expression of the information encoded by the genome
Epigenetics
63
a chemical modification of DNA that occurs when a methyl group attaches to the cytosine base. It's a common form of DNA modification in both bacteria and eukaryotes.
epigenetic process that involves adding a methyl group to the fifth carbon of cytosine, which can significantly alter chromatin structure and subsequently impact gene expression by making the DNA more compact and less accessible to transcription factors, usually leading to gene silencing
Cytosine methylation
64
Cytosine methylation is catalyzed by
DNA methyltransferase (DNMT) enzymes.
65
Distort the Double Helix
The double helix is a very dynamic structure
Because it is flexible, aromatic macrocycles – flat hydrophobic molecules composed of fused, heterocyclic rings, can slip between the stacked pairs of bases
Insertion of these agents distorts the DNA double helix, thereby interfering with DNA replication, transcription, and repair
Intercalating Agents
65
Intercalating Agents
Ethidium bromide
Acridine orange
Actinomycin D
65
The structures of ethidium bromide, acridine orange, and actinomycin D, three intercalating agents, and their effects on DNA structure.
mutagenic and carcinogenic
66
the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling
DNA - 3° Structure
67
Circular DNA ends are joined by what bond
phosphodiester bonds
67
Tertiary structure
a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds
Circular DNA
68
Further coiling and twisting of DNA helix.
Supercoiling
69
cut the phosphodiester backbone of one strand, pass the end through, and reseal
what enzyme and what class
Topoisomerases Class I
70
a bacterial topoisomerase
DNA gyrase
71
cut both strands, pass some of the remaining DNA helix between the cut strands, and reseal
what enzyme and what class
Topoisomerases Class II
72
Can DNA Adopt Structures of Higher Complexity?
Yes, DNA can adopt structures of higher complexity beyond the classic double helix, forming secondary and tertiary structures depending on the sequence and environmental conditions, including structures like hairpins, cruciforms, triplexes, and G-quadruplexes, which are considered "non-canonical" DNA structures with potential biological roles in processes like replication and transcription
72
what type of DNA structure where there are ten bp per turn of helix
duplex DNA
73
what type of DNA structure where sometimes DNA has more or less than 10 bp per turn - a supercoiled state
Circular DNA
74
what supercoiling may promote cruciforms
Negative supercoiling
74
what type of DNA structure occur in palindromic regions of DNA
Cruciforms
75
Enzymes called _____________ can introduce or remove supercoils
topoisomerases or gyrases
76
Are One Kind of Structural Complexity in DNA
Double-stranded circular DNA forms _________, if the strands are underwound, or overwound.
Supercoils
77
underwound, or overwound what type of supercoiling
when the strands are underwound; this is referred to as negative supercoiling, while overwinding results in positive supercoiling
78
is a topoisomerase that introduces negative supercoils into DNA
DNA Gyrase
79
___________ supercoils cause a torsional stress on the molecule, so the molecule tends to unwind.
_________ supercoiling makes it easier to separate DNA strands and access the information encoded by the sequence.
Negative supercoils
80
A 400-bp circular DNA molecule in different topological states:
(a) relaxed
(b) negative supercoils distributed over the entire length
(c) negative supercoils creating a localized single-stranded region.
80
how do DNA Gyrase or topoisomerase do the supercoiling
Conformational changes in the enzyme allow an intact region of the DNA duplex to pass between the cut ends. The cut ends are religated (3), and the covalently complete DNA duplex is released from the enzyme. The circular DNA now contains two negative supercoils (4).
81
Negatively Supercoiled DNA Can Arrange into a
a highly condensed, donut-shaped structure where DNA strands are tightly packed together in loops, forming a circular ring-like shape, often observed in viruses and sperm cells, where the DNA needs to be extremely compact
is stabilized by wrapping around proteins that serve as spools for the DNA “ribbon”.
Toroidal State
81
Negative Supercoiling has the Potential to Cause Localized Unwinding in DNA
true
82
Human DNA’s total length is
2 meters
82
This must be packaged into a nucleus that is about 5 micrometers in diameter
It is made possible by wrapping the DNA around protein spools called ___________ and then packing these in helical filaments
nucleosomes
83
helical filaments with nucleosomes are thought to arrange in loops associated with the
nuclear matrix
83
are the two classes of chromatin proteins
Histones and nonhistone chromosomal proteins
84
refers to the three-dimensional structure of DNA where the double helix itself is further coiled into a higher-order structure, creating supercoils, which can be either positively or negatively oriented depending on the direction of the additional twist; this structure is crucial for compacting DNA within the nucleus and facilitating biological processes like replication and transcription.
Super DNA Coiled Topology
85
Five distinct histones are known:
H1, H2A, H2B, H3, and H4.
86
copies of histones per nucleosomes
1 and not in core - H1
by pairs in core H2A, H2B, H3, H4
86
Are the Fundamental Structural Unit in Chromatin
Nucleosomes
87
Pairs of histones H2A, H2B, H3, and H4 aggregate to form octameric core structures; the DNA helix is wound around these core octamers, creating
nucleosomes
88
the nucleoprotein complex, consists of histones and nonhistone chromosomal proteins
Chromatin
88
proteins that are regulators of gene expression
Nonhistone proteins
89
The Structure of the Nucleosome –
a Histone Octamer wrapped with DNA
90
Structural Organization of Chromatin Gives Rise to
Chromosomes
90
The ___________ motif is the “primary” structure of chromatin.
beads-on-a-string motif
91
______________ level of chromatin structure is the 30-nm fiber, formed when an array of nucleosomes in a zig-zag pattern adopts a two-start helical conformation
“secondary”
91
Higher levels of chromatin structural organization are achieved when the 30-nm fiber forms long loops of 60-150,000 bp
true
91
Electron microscopic analysis of human chromosome 4 suggests that 18 such loops are then arranged radially about the circumference of a single turn to form a __________ of the chromosome.
miniband unit
92
Prokaryotic DNA is circular. It can form
supercoils
92
can be considered to a 2-stranded, right handed coiled rope
Double helix
93
In Chromatin, _________ consists of: DNA wrapped around histone core
Nucleosome
93
In Chromatin, Each “Bead” is a
nucleosome
94
Recent research has shown that structure and spacing of nucleosomes is important in chromatin function.
true
94
The rate of mutation surrounding nucleosomes is ___________
not constant
95
a protein, particularly rich in the basic amino acids Lys and Arg; found associated with eukaryotic DNA
Histone
95
In chromatid, Substitution mutations peak in the nucleosomes themselves, and are at a low point in the _____
linker regions
96
Steps in the thermal denaturation and renaturation of DNA.
heat, denaturation, nucleation site, Zippering
96
Single-Stranded DNA Can Renature to Form _________
DNA Duplexes
96
DNA molecules wound around particles of histones in a beadlike structure
Chromatin
97
in DNA denaturation, as strands separate, absorbance at 260 nm increases, which is called
hyperchromicity
97
disruption of 2° structure
most commonly by heat
Denaturation
97
the higher the % [insert base pairing], the higher the Tm
G-C
98
in DNA denaturation, midpoint of transition (melting) curve =
Tm
99
renaturation is possible on slow cooling
true
99
Stacked base pairs in native DNA absorb less light due to __________ electron interactions
pi to pi
100
When DNA is heated to 80°C or more, its UV absorbance __________ by 30-40%
This hyperchromic shift reflects the unwinding of the DNA double helix
increases
100
In renaturatuin, When Temp is lowered, the absorbance drops, reflecting re-establishment of the double helix and base-pair stacking
true
101
consist of long, unbranched chains of nucleotides joined by phosphodiester bonds between the 3’-OH of one pentose and the 5’-OH of the next
the pyrimidine bases are uracil and cytosine
single stranded
RNA
102
the pentose unit of RNA is
Beta-D-ribose
102
Information encoded in the ___________ sequence of DNA is transcribed through RNA synthesis
nucleotide
103
Information encoded in the nucleotide sequence of DNA is transcribed through RNA synthesis
Sequence then dictated by DNA sequence
Central dogma of biology
104
Transcription product of DNA
In prokaryotes and In eukaryotes
In prokaryotes, a single mRNA contains the information for synthesis of many proteins
In eukaryotes, a single mRNA codes for just one protein, but structure is composed of introns and exons
105
The Roles of Different Kinds of RNA
Small
Processes initial mRNA to its mature form in eukaryotes
Small nuclear RNA
105
intervening sequence in mrna
intron
105
DNA is transcribed to produce heterogeneous nuclear RNA (hnRNA)
mixed introns and exons with poly A tail
Splicing produces final mRNA without introns
Eukaryotic mRNA
106
coding sequence in mrna
exon
107
The Roles of Different Kinds of RNA
Small
Transports amino acids to site of protein synthesis
Transfer RNA
107
The Roles of Different Kinds of RNA
variable in size
Combines with proteins to form ribosomes, the site of protein synthesis
Ribosomal RNA
107
The Roles of Different Kinds of RNA
variable in size
Directs amino acid sequence of proteins
Messenger RNA
108
The Roles of Different Kinds of RNA
Small
Affects gene expression; used by scientists to knock out a gene being
studied
Small interfering RNA
108
The Roles of Different Kinds of RNA
Small
Affects gene expression; important in growth and development
Micro RNA
108
The Roles of Different Kinds of RNA
Variable (long)
Still under debate, but appears to affect development and be related to certain disease states
Long noncoding RNA
109
the smallest kind of the three RNAs
a single-stranded polynucleotide chain between 73-94 nucleotide residues
carries an amino acid at its 3’ end
intramolecular hydrogen bonding occurs in tRNA
Transfer RNA, tRNA:
109
only a few types of rRNA exist in cells
true
109
: a ribonucleic acid found in ribosomes, the site of protein synthesis
Ribosomal RNA, rRNA
110
in both prokaryotes and eukaryotes, ribosomes consist of _______ subunits, one larger than the other
two
110
___________ consist of 60 to 65% rRNA and 35 to 40% protein
ribosomes
110
Ribosomal RNA analyzed by
analytical ultracentrifugation
111
Ribosomal RNA particles characterized by sedimentation coefficients, expressed in
Svedberg units (S)
112
serves as a scaffold for ribosomal proteins
rRNA
113
The different species of rRNA are referred to according to their
sedimentation coefficients
113
rRNAs typically contain certain ____________ nucleotides, including pseudouridine and ribothymidylic acid
modified nucleotides
114
the genetic information in the nucleotide sequence of mRNA is translated into the amino acid sequence of a polypeptide chain by ribosomes
true
114
eukaryotic ribosomes have what sedimentation coefficients and subunits
80s
Subunits: 40s and 60s
16s rna for 40s, 21 proteins
23s and 5s rna for 60s, 31 proteins
115
prokayotic ribosomes have what sedimentation coefficients and subunits
70s
Subunits: 30s and 50s
18s rna for 30s, 33 proteins
28s and 5s rna for 50s, 49 proteins
116
a ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins
present in cells in relatively small amounts and very short-lived
single stranded
biosynthesis is directed by information encoded on DNA
Messenger RNA, mRNA:
116
a complementary strand of mRNA is synthesized along one strand of an unwound DNA, starting from the ________ end
3’ end
117
is a recently discovered RNA
Found in nucleus of eukaryotes
Small (100-200 nucleotides long)
Forms complexes with protein and form small nuclear ribonucleoprotein particles
their particles help with processing of initial mRNA transcribed from DNA
3’ end
118
Why is DNA 2'-deoxy and RNA is not?
Vicinal -OH groups (2' and 3') in RNA make it more susceptible to hydrolysis
DNA, lacking 2'-OH is more stable
This makes sense - the genetic material must be more stable
RNA is designed to be used and then broken down
119
resistant to dilute acid
RNA
120
depurinated by dilute acid
DNA
121
Alkaline hydrolysis of RNA steps
Nucleophilic attack by OH- on the P atom leads to 5'-phosphoester cleavage.
Random hydrolysis of the cyclic phosphodiester intermediate gives a mixture of 2'- and 3'-nucleoside monophosphate products.
121
hydrolyzed by dilute base
RNA
121
not susceptible to base
DNA
122
Restriction Enzymes that has No ATP requirement
Recognition sites in dsDNA have a 2-fold axis of symmetry
Cleavage can leave staggered or "sticky" ends or can produce "blunt” ends
Type II Restriction Enzymes
123
Bacteria have learned to "restrict" the possibility of attack from foreign DNA by means of
Restriction Enzymes
124
Type _____ and ___________ restriction enzymes cleave DNA chains at selected site
II and III
124
Restriction Enzymes that Names use 3-letter italicized code:
1st letter - genus; 2nd,3rd - species
Following letter denotes strain
Type II Restriction Enzymes
125
Restriction Enzymes may recognize 4, 6 or more bases in selecting sites for cleavage
true
126
An enzyme that recognizes a 6-base sequence is a
"six-cutter"
126
is the first restriction enzyme isolated from the R strain of E. coli
EcoRI
