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Chapter 2 Flashcards

1
Q

What is the primary structure of DNA?

A

Nucleic Acid – Long chain or polymer of repeating subunits

DNA is composed of nucleotides that form a long chain.

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2
Q

What are the components of a nucleotide?

A

Composed of:
* Five-carbon sugar
* Phosphate group
* Nitrogen-containing, heterocyclic base

Nucleotides are the building blocks of nucleic acids.

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3
Q

What is the role of the ribose ring in nucleic acid strands?

A

Imparts direction to a DNA/RNA nucleic acid strand

The directionality is crucial for processes like replication and transcription.

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4
Q

What is the main difference between RNA and DNA?

A

The presence of a 2’ hydroxyl group in RNA

This hydroxyl group makes RNA more reactive and less stable than DNA.

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5
Q

What are Edwin Chargaff’s rules?

A
  1. [A] = [T]
  2. [G] = [C]
  3. [A] + [G] = [T] + [C]

These rules describe the base pairing in DNA and are fundamental to the structure of DNA.

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6
Q

How does GC content vary among species?

A

%G+C differs among species but is constant in all cells of an organism within a species

GC content can range from 22% to 73% among different species.

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7
Q

Fill in the blank: The percentage of G+C in DNA varies from ______ among species.

A

22 to 73%

This variation is a characteristic feature of different organisms.

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8
Q

What does the phosphate functional group give?

A

Gives DNA acidic properties

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9
Q

What are the steps to assemble the components?

A
  1. Nitrogenous base is covalently linked to one
    molecule of sugar at the 1’ carbon of the sugar -
    Nucleoside
  2. A nucleoside with one or more phosphates
    attached is a nucleotide.
  3. Nucleotides are linked by 5 to 3′ ′
    phosphodiester bonds between adjacent
    nucleotides to form a DNA or RNA chain
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10
Q

What are the distinct ends of a DNA or RNA chain?

A

5 -PO′ and 3 -OH ends

These ends have different properties.

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11
Q

How is a DNA sequence conventionally written?

A

With the 5 end to the left and the 3 end to the right

This is a standard notation in molecular biology.

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12
Q

What unit is used to measure the length of RNA?

A

Number of nucleotides (nt) or bases

This quantifies the RNA length.

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13
Q

What unit is used to measure the length of double-stranded DNA?

A

Number of base pairs (bp)

Each base pair corresponds to two nucleotides.

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14
Q

How many base pairs are in 1 kilobase pair (kb or kbp)?

A

1000 bp

Kilobase is a common unit in genetics.

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15
Q

How many base pairs are in 1 megabase pair (Mb or Mbp)?

A

1,000,000 bp

Megabase is often used to describe large DNA sequences.

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16
Q

What are oligonucleotides?

A

Short chains of single-stranded DNA (< 50 bases)

Oligonucleotides are often used in PCR and other molecular techniques.

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17
Q

What type of bonds join successive deoxyribose residues in a polynucleotide chain?

A

Phosphodiester bonds

These bonds form the backbone of DNA and RNA.

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18
Q

Where is the free 5 end located in a polynucleotide chain?

A

At one end of the chain (conventionally the left)

This end has a phosphate group.

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19
Q

Where is the free 3 end located in a polynucleotide chain?

A

At the other end of the chain

This end has a hydroxyl group.

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20
Q

What structure do two complementary strands of DNA form?

A

Double helix

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21
Q

What stabilizes the two strands of DNA together?

A

Base pair hydrogen bonding and base stacking

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22
Q

How many hydrogen bonds form between adenine (A) and thymine (T)?

A

Two hydrogen bonds

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23
Q

How many hydrogen bonds form between guanine (G) and cytosine (C)?

A

Three hydrogen bonds

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24
Q

What are the two common ‘Watson-Crick’ base pairs in DNA?

A
  • Adenine (A) with Thymine (T)
  • Guanine (G) with Cytosine (C)
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25
Why are there no other stable base pairs present in DNA?
* May not form two or more hydrogen bonds * Pairing of G with T produces a shape similar to Watson-Crick pairs
26
What mechanisms ensure fidelity of DNA replication?
Proofreading and DNA repair mechanisms
27
True or False: RNA more readily uses alternative base pairing than DNA.
True
28
Fill in the blank: A-T base pairs can form _______ hydrogen bonds.
two
29
Fill in the blank: C-G pairs form _______ hydrogen bonds.
three
30
What is the core structure of double stranded DNA?
A hydrophobic core ## Footnote This hydrophobic core is crucial for the stability of the DNA structure.
31
What are the characteristics of the heterocyclic bases within DNA?
Nonpolar, hydrophobic, and relatively flat rings ## Footnote These characteristics contribute to base stacking.
32
How does base stacking contribute to DNA structure?
By excluding water from the core of the double helix ## Footnote This exclusion enhances the chemical stability of DNA.
33
What provides chemical stability to the DNA double helix?
Base stacking ## Footnote The stacking occurs through the flat, hydrophobic nitrogenous bases.
34
Describe the arrangement of nitrogenous bases in DNA.
Stack onto each other without a gap by means of a helical twist ## Footnote This arrangement is critical for the structural integrity of the DNA.
35
What are the two types of grooves formed in the DNA double helix?
Major groove and minor groove ## Footnote The major groove is wider and more exposed than the minor groove.
36
Which groove of DNA is typically more exposed and readable?
Major groove ## Footnote The sequence in the major groove can be recognized by proteins and other molecules.
37
In which form is DNA schematically represented?
B form ## Footnote This is the most common form of DNA in cells.
38
What are some alternative structures to the B form of DNA?
A form, Z form, B’, C, C’ ## Footnote These structures vary in helical width, handedness, and groove shapes.
39
What is the polarity direction of each DNA strand?
5′ to 3′ ## Footnote This polarity is crucial for DNA replication and function.
40
How are the two strands of DNA oriented in relation to each other?
Antiparallel ## Footnote This orientation is essential for the base pairing mechanism.
41
What are the two key features of the Watson-Crick DNA double helix?
Complementary base pairs and base stacking ## Footnote These features are fundamental for the stability and replication of DNA.
42
What are the two features that make DNA a useful molecule for the transmission of hereditary information?
1. The sequence of nucleotides can be exceptionally complex. 2. It can be replicated by unwinding the two strands of DNA.
43
What is the significance of a sequence of 10 nucleotides in DNA?
It could exhibit 410 (or about a million) different combinations of nucleotide bases.
44
What type of bonds hold each single strand of DNA together?
Covalent bonds.
45
What type of bonds hold the two strands of DNA together?
Weaker bonds, including base stacking and hydrogen bonds.
46
What is DNA denaturation?
Unwinding and separation of DNA strands.
47
How can DNA denaturation be monitored in vitro?
By absorbance spectroscopy.
48
What is Tm in the context of DNA?
The temperature at which half of the bases in a dsDNA sample have denatured.
49
What phenomenon occurs as DNA melts and absorbs UV light?
Hyperchromicity.
50
What are two factors that can change the way DNA denatures?
* G/C content within a strand of DNA * Salt concentrations.
51
What is renaturation or reannealing of DNA?
The process by which denatured DNA can anneal, allowing for hybridization.
52
What is hybridization in the context of DNA?
The complementary base pairing of strands from two different sources.
53
What factors affect the rate at which DNA reanneals?
* Length of the DNA * Initial concentration in the sample.
54
What are some examples of unusual DNA secondary structures?
* Slipped structures * Cruciform structures * Triple helix DNA * G-quadruplex.
55
True or False: The extent of unusual DNA secondary structures occurring in vivo is well understood.
False.
56
What are slipped structures?
Structures that occur in sequences of short tandem repeats ## Footnote Slipped structures can lead to mutations and are associated with certain genetic disorders.
57
What is required for loops to form in DNA?
Loops need to form in both strands of DNA
58
Which diseases are associated with trinucleotide expansions?
Huntington’s disease and Myotonic dystrophy
59
What are cruciforms?
Structures that occur at DNA sequence palindromes or inverted repeats ## Footnote Cruciforms result from the formation of stem-loop structures.
60
What is the structure of a cruciform?
Formed due to the formation of a stem loop structure in the strands of DNA
61
What are triple helices in DNA?
A more complex structure facilitated by mirror repeats ## Footnote A third single strand associates with a double-stranded DNA molecule.
62
What happens to the strands of DNA in a triple helix?
Wraps into the major groove, leaving one strand single stranded
63
What are the symptoms of Friedreich’s ataxia?
Loss of voluntary muscular coordination and heart enlargement
64
What trinucleotide repeat is expanded in Friedreich’s ataxia?
5 -GAA-3′ ′ trinucleotide repeat expansion
65
What is the normal range of GAA repeats in individuals?
6-34 repeats
66
What is the range of GAA repeats in Friedreich’s Ataxia?
66-1700 repeats
67
What structure is formed by expanded GAA repeats?
Triple helix DNA
68
What is a G-quadruplex?
A four-stranded DNA structure in a stretch of tandem guanines
69
What is formed within a G-quadruplex?
G-tetrad
70
What roles do G-quadruplexes play in the genome?
Gene regulation and genomic instability
71
Where are G-quadruplexes commonly found?
In telomeres and promoter regions
72
What is supercoiling of DNA?
Supercoiling conserves cellular space and can store energy ## Footnote Supercoiling can be negative or positive, affecting the stability and functionality of DNA.
73
Is relaxed DNA supercoiled?
No ## Footnote Relaxed DNA does not have supercoils.
74
What is a negative supercoil?
Results from underwound DNA ## Footnote Negative supercoiling is common in cellular DNA.
75
What does a positive supercoil result from?
Results from overwound DNA ## Footnote Positive supercoiling is associated with processes like DNA replication.
76
What is the linking number (L) in DNA?
Number of times two hydrogen bonded strands of DNA cross each other ## Footnote L remains constant despite changes in supercoiling.
77
What does 'twists' (T) refer to in DNA?
Number of twists/turns in a segment of DNA ## Footnote T changes with supercoiling.
78
What are two reasons for negative supercoiling in DNA?
* Space saving * Puts energy into the DNA molecule ## Footnote Negative supercoiling facilitates unwinding of DNA for replication and transcription.
79
What is the typical state of DNA in prokaryotes and eukaryotes?
Virtually all DNA is negatively supercoiled ## Footnote This state is crucial for various cellular processes.
80
What happens to the linking number (L) when transitioning from a supercoiled state to a relaxed state?
The change is negative ## Footnote Example: 9 – 10 = -1.
81
When does positive supercoiling occur in vivo?
* During DNA replication * During transcription ## Footnote Positive supercoiling must be released for these processes to succeed.
82
What role do topoisomerases play in DNA supercoiling?
Catalyze the release of supercoiling by producing breaks in the DNA ## Footnote This allows turns to be added or subtracted from the helix.
83
How does negative supercoiling facilitate DNA processes?
Makes it easier to separate DNA strands during replication and transcription ## Footnote It also puts energy into DNA and aids in packaging.
84
What state does the DNA of thermophilic Archaea exist in?
Positive supercoiled state ## Footnote This protects DNA from denaturation at high temperatures.
85
DNA structure overview: | Primary, secondary, and tertiary
Primary: Nucleotide structure, nucleotides joined by phosphodiester bonds Secondary: Double helix, B-DNA, Unusual structure Tertiary: Supercoiling

Molecular Genetics (8 decks)

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