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SF:Biochemistry > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

Describe the components of a nucleotide.

A

A nucleotide consists of a phosphate group, a sugar ring, and a heterocyclic nitrogenous base.

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2
Q

Define nucleosides and how they differ from nucleotides.

A

Nucleosides are nucleotides without the phosphate group, consisting only of a sugar and a nitrogenous base.

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3
Q

How are nucleotides formed from amino acids and sugars?

A

Nucleotides are created as monophosphates from amino acids and sugars, and then converted to triphosphates for incorporation into DNA.

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4
Q

Explain the significance of the phosphate group in nucleic acids.

A

The phosphate group gives nucleic acids a negative charge and is a strong acid, contributing to the overall stability of the nucleic acid structure.

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5
Q

What sugar is found in DNA and how does it differ from RNA?

A

DNA contains deoxyribose sugar, while RNA contains ribose, which has a hydroxy group that can be hydrolyzed.

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6
Q

How does the sugar ring contribute to nucleic acid stability?

A

The sugar ring provides structural stability to nucleic acids, helping to maintain their integrity.

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7
Q

Describe the role of nitrogenous bases in nucleic acids.

A

Nitrogenous bases are essential components of nucleic acids, providing the genetic code and allowing for base pairing in DNA and RNA.

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8
Q

Describe the main structural difference between DNA and RNA.

A

DNA uses deoxyribose as its sugar, while RNA uses ribose.

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9
Q

Define the bases found in DNA.

A

DNA contains adenine, guanine, cytosine, and thymine.

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10
Q

How does RNA differ from DNA in terms of nitrogenous bases?

A

RNA uses uracil in place of thymine, which is found in DNA.

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11
Q

Identify the smallest molecular weight base in DNA and RNA.

A

Cytosine is the smallest molecular weight base.

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12
Q

Describe the structure of DNA.

A

DNA is a polymer of nucleotides linked via phosphodiester bonds, with a sugar-phosphate backbone, polarity, and base pair arrangements.

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13
Q

How do the strands of DNA interact with each other?

A

Each strand of DNA binds to an antiparallel strand through hydrogen bonding of base pairs.

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14
Q

Define the stability difference between DNA and RNA.

A

RNA is less stable than DNA because it contains a hydroxy group that can be hydrolyzed.

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15
Q

What are the base pairing rules in DNA?

A

Adenine (A) pairs with Thymine (T) and Guanine (G) pairs with Cytosine (C).

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16
Q

Explain the significance of polarity in DNA structure.

A

DNA has polarity with the phosphate group on the 5’ end and the OH group on the 3’ end, which is important for replication and function.

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17
Q

Describe the role of phosphodiester bonds in DNA.

A

Phosphodiester bonds link nucleotide monomers together, forming the backbone of the DNA polymer.

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18
Q

What are major and minor grooves in DNA?

A

Major and minor grooves are the spaces between the two strands of DNA that allow proteins to access the bases for binding.

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19
Q

How does the sugar phosphate backbone affect DNA’s charge?

A

The sugar phosphate backbone creates a negative charge on DNA due to the phosphate groups.

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20
Q

Define the Watson-Crick model of DNA.

A

The Watson-Crick model describes DNA as a double-stranded double helix where the strands run antiparallel and nucleotides are oriented in opposite directions, with hydrogen bonding between bases.

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21
Q

Describe the strength of GC bonds compared to AT bonds in DNA.

A

GC bonds are stronger than AT bonds because GC pairs form three hydrogen bonds, while AT pairs form only two.

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22
Q

How does GC content affect the melting point of DNA?

A

High GC content (greater than 50%) results in a high melting point, while low GC content (less than 50%) leads to a low melting point.

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23
Q

Define Chargaff’s rule in the context of DNA structure.

A

Chargaff’s rule states that the ratio of purine nucleotides (adenine and guanine) to pyrimidine nucleotides (thymine and cytosine) in DNA is 1-to-1.

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24
Q

What can be inferred about a DNA fragment with 30% GC content?

A

If a DNA fragment has 30% GC content, according to Chargaff’s rule, it must contain 15% guanine and 15% cytosine.

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25
Q

How does GC content influence access to polymerases in DNA?

A

If GC content is greater than 50%, it results in poor access to polymerases, while less than 50% allows for easier access.

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26
Q

Explain the significance of hydrogen bonds in DNA structure.

A

Hydrogen bonds between complementary strands of DNA hold the two strands together, with GC pairs forming three bonds and AT pairs forming two.

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27
Q

What is the relationship between GC content and the stability of DNA?

A

DNA with high GC content is more stable and harder to break apart due to the stronger hydrogen bonding.

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28
Q

How does the structure of DNA facilitate the transfer of genetic information?

A

The complementary nature of base pairing allows DNA to transmit genetic information through replication.

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29
Q

What force is responsible for holding DNA strands together?

A

Hydrogen bonding between base pairs keeps DNA strands held together.

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30
Q

How can DNA be denatured?

A

DNA can be denatured by disrupting hydrogen bonding, which can occur at high temperatures.

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31
Q

Can DNA be re-annealed after denaturation? If so, how?

A

Yes, DNA can be re-annealed by returning to the proper conditions, such as the correct temperature.

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32
Q

What is DNA hybridization?

A

DNA hybridization is the process where a single strand of DNA binds to another single strand of DNA when there is a significant amount of base pair matching between their sequences.

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33
Q

Describe the process of DNA methylation in humans.

A

During DNA methylation, methyl groups are added to cytosines on both strands of a CG-GC island.

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34
Q

Describe the role of methylation in human DNA.

A

Methylation in human DNA, which affects about 70% of it, prevents gene expression and helps regulate immune responses by distinguishing self DNA from foreign DNA.

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35
Q

How does unmethylated DNA affect the immune system in humans?

A

Unmethylated DNA triggers an immune response in humans because the body recognizes it as foreign, similar to bacterial DNA.

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36
Q

Define the restriction modification system in bacteria.

A

The restriction modification system in bacteria involves methylation of certain DNA parts to protect against viral infections.

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37
Q

What types of DNA bases are typically methylated in both humans and bacteria?

A

In both humans and bacteria, Cytosine and Adenine are typically methylated.

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38
Q

Explain the consequence of random non-methylated DNA in the cell.

A

Random non-methylated DNA is recognized as foreign and is destroyed by endonucleases.

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39
Q

Describe the structure of DNA packaging in eukaryotic cells.

A

DNA packaging in eukaryotic cells involves the formation of a double helix, which wraps around histones to form nucleosomes, leading to the structure of chromatin and ultimately chromosomes.

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40
Q

What is a nucleosome and its role in DNA structure?

A

A nucleosome consists of 8 histones around which DNA is wrapped, playing a crucial role in the packaging and organization of DNA into chromatin.

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41
Q

How does the structure of chromatin relate to chromosomes?

A

Chromatin is the organized structure of DNA and proteins that condenses to form chromosomes during cell division.

42
Q

Describe the role of histones in DNA structure.

A

Histones are proteins that are rich in lysine and arginine, which are positive amino acids that attract the negatively charged DNA. They are responsible for the compact packing and winding of chromosomal DNA.

43
Q

Define histone acetylation and its effect on gene expression.

A

Histone acetylation involves the addition of acetyl groups to lysine residues on histones, which increases gene expression by loosening the DNA structure and allowing for greater accessibility to transcription machinery.

44
Q

Explain DNA methylation and its impact on gene expression.

A

DNA methylation refers to the addition of a methyl group to cytosine bases in DNA, which suppresses gene expression by making the DNA less accessible for transcription.

45
Q

What are chromosomal proteins and their categories?

A

Chromosomal proteins include histones, which are responsible for DNA packing, and non-histone chromosomal proteins, which perform various roles such as regulatory and enzymatic functions.

46
Q

Describe single-copy DNA and its significance.

A

Single-copy DNA is a DNA sequence that does not repeat and holds most of the organism’s important genetic information. It is transcribed and translated and has a low mutation rate.

47
Q

Define repetitive DNA and its characteristics.

A

Repetitive DNA consists of DNA sequences that repeat and is generally found in non-coding regions. It is often tightly packaged, not transcribed, and has a higher mutation rate.

48
Q

What is super repetitive DNA and where is it found?

A

Super repetitive DNA has no genes, is not transcribed, and is found in telomeres. It is characterized by a super high mutation rate.

49
Q

Explain the concept of supercoiling in DNA.

A

Supercoiling refers to the over- or under-winding of DNA, which affects its structure and can influence processes such as replication and transcription.

50
Q

Describe the structure of DNA and RNA in relation to histones.

A

DNA is organized into nucleosomes that are wrapped into supercoils, with histones playing a key role in this organization.

51
Q

Define heterochromatin.

A

Heterochromatin refers to tightly coiled regions of chromatin that are not available for transcription.

52
Q

Define euchromatin.

A

Euchromatin consists of portions of chromatin that are uncoiled and available to be read by transcription machinery.

53
Q

How do nucleosomes affect transcription?

A

Nucleosomes that are tightly organized generally block transcription of their associated DNA.

54
Q

What role do centromeres play in chromatin structure?

A

Centromeres are specific regions of chromosomes that play a crucial role in the separation of chromosomes during cell division.

55
Q

Describe the role of a centromere in chromosome organization during replication.

A

A centromere is the single point region on a chromosome that aids organization during replication by connecting two sister chromatids, which are the original chromosome and its replicated partner.

56
Q

Define the type of DNA found at telomeres and centromeres.

A

DNA around telomeres and centromeres tends to be more repetitive and non-coding, meaning it is not transcribed.

57
Q

How do drug-induced lupus symptoms differ from classic lupus symptoms?

A

Drug-induced lupus causes symptoms similar to lupus, such as a rash, but is characterized by the presence of anti-histone antibodies rather than anti-dsDNA antibodies.

58
Q

List some drugs that can cause drug-induced lupus.

A

Drugs that can cause drug-induced lupus include Hydralazine, Procainamide, and Isoniazid.

59
Q

What is the effect of histone deacetylase inhibitors (HDACs) on gene expression?

A

Histone deacetylase inhibitors (HDACs) increase gene expression.

60
Q

How are histone deacetylase inhibitors (HDACs) related to cancer?

A

HDACs are commonly present in cancers, suggesting a role in cancer biology.

61
Q

Explain the potential relevance of HDACs to Huntington’s disease.

A

Histone deacetylase inhibitors (HDACs) may be relevant to Huntington’s disease, indicating a possible connection between HDAC activity and the disease.

62
Q

Describe the three steps of DNA replication.

A
  1. Double-stranded DNA is separated. 2. DNA that is complementary to the unwound/separated DNA is made. 3. RNA primers are replaced with DNA by a special DNA polymerase.
63
Q

Define the origin of replication.

A

The origin of replication is a little bubble rich in AT bonds where the DNA separates to create two replication forks.

64
Q

How does the unzipping of DNA progress during replication?

A

The unzipping progresses in both directions away from the origin of replication, allowing replication to occur in both directions and reducing the time needed for the process.

65
Q

What enzymes are involved in separating DNA strands?

A

Topoisomerase unwinds the DNA, helicase unzips the DNA by breaking hydrogen bonds, and single-strand binding proteins (SSB) stabilize the unwound DNA by binding to it.

66
Q

Explain the role of single-strand binding proteins (SSB) in DNA replication.

A

SSBs are responsible for keeping DNA unwound after helicase and stabilize single-stranded DNA by binding to it.

67
Q

Identify the enzyme that unwinds DNA during replication.

A

Topoisomerase is the enzyme that unwinds DNA.

68
Q

What is the function of helicase in DNA replication?

A

Helicase unzips the DNA by breaking the hydrogen bonds between the strands.

69
Q

Describe the stability of single-stranded DNA.

A

Single-stranded DNA is unstable and prone to degradation by DNA nucleases.

70
Q

How does DNA polymerase synthesize new DNA?

A

DNA polymerase synthesizes new DNA in the 5’ to 3’ direction, requiring a template and a primer.

71
Q

Explain the process of creating a new DNA strand from the Leading Strand.

A

An RNA primer is placed on the leading strand by DNA Primase, and DNA Polymerase III expands the strand in the 5’ to 3’ direction.

72
Q

What is the direction of the leading strand during DNA replication?

A

The leading strand goes in the 3’ to 5’ direction.

73
Q

How is a new DNA strand created from the Lagging strand?

A

DNA Primase places an RNA primer near the replication fork, and DNA Polymerase III expands the strand in the 5’ to 3’ direction, creating Okazaki fragments.

74
Q

What are Okazaki fragments?

A

Okazaki fragments are short segments of DNA synthesized on the lagging strand during DNA replication.

75
Q

How are RNA primers replaced during DNA replication?

A

RNA primers are removed and replaced by DNA through the activity of DNA polymerase I.

76
Q

What role does DNA ligase play in DNA replication?

A

DNA ligase seals the nicks that remain after the RNA primers are replaced with DNA.

77
Q

Define specific coupling in DNA replication.

A

Specific coupling ensures that nucleotides are incorporated with correct base-pairing along the separated strands (A with T, G with C).

78
Q

Why is DNA replication considered semi-conservative?

A

DNA replication is considered semi-conservative because it produces two double-stranded DNA molecules, each containing one original strand and one newly synthesized strand.

79
Q

List the enzymes involved in DNA replication.

A

The enzymes involved in DNA replication include Helicase and Primase, among others.

80
Q

Describe the role of DNA Helicase in DNA replication.

A

DNA Helicase uses hydrolysis of ATP to unwind the DNA helix at the replication fork, allowing the resulting single strands to be copied.

81
Q

Define the function of Topoisomerases in DNA replication.

A

Topoisomerases relax the super-coiling that results from unwinding the DNA helix.

82
Q

How does Primase contribute to DNA replication?

A

Primase synthesizes RNA primers that act as templates for future Okazaki fragments to build on.

83
Q

Explain the function of Single-stranded binding proteins (SSBPs).

A

Single-stranded binding proteins bind to the separated strands of DNA to prevent them from re-annealing.

84
Q

What is the role of DNA polymerase I in DNA replication?

A

DNA polymerase I synthesizes nucleotides onto primers on the lagging strand, forming Okazaki fragments, and removes primers from the fragments to replace the gap with relevant nucleotides.

85
Q

Describe the function of DNA polymerase III during DNA replication.

A

DNA polymerase III follows the replication fork, adding new nucleotides in the 5′ to 3′ direction, while proofreading and removing incorrect nucleotides.

86
Q

How does DNA ligase assist in DNA replication?

A

DNA ligase helps to anneal strands by joining Okazaki fragments together.

87
Q

Describe the role of Telomerase in DNA structure.

A

Telomerase lengthens telomeres of linear eukaryotic DNA.

88
Q

Define semi-conservative DNA replication.

A

Semi-conservative DNA replication means that during replication, each strand acts as a template for a new DNA molecule, resulting in each daughter cell containing one original strand and one newly synthesized strand.

89
Q

How many origins of replication do prokaryotes typically have?

A

Prokaryotes usually have a single origin of replication for their single, circular DNA.

90
Q

How many origins of replication are found in eukaryotes?

A

Eukaryotes have multiple origins of replication across their numerous linear chromosomes.

91
Q

Explain the End Replication Problem.

A

The End Replication Problem occurs because Primase lays down primers to help replicate DNA, leading to regions near the 3’ end of the original DNA strand that never get replicated, resulting in the gradual shortening of DNA.

92
Q

Describe the role of telomeres in DNA replication.

A

Telomeres are regions of repetitive DNA segments at the end of the DNA that help solve the End Replication Problem by providing a buffer zone, as the end of DNA that isn’t replicated isn’t useful.

93
Q

How does telomerase contribute to DNA replication?

A

Telomerase is an enzyme that can expand telomeres, thereby addressing the End Replication Problem by maintaining the length of telomeres during DNA replication.

94
Q

Define the End Replication Problem in the context of DNA.

A

The End Replication Problem refers to the difficulty in fully replicating the ends of linear DNA molecules, which can lead to the loss of important genetic information during cell division.

95
Q

What are the two solutions the body has to address the End Replication Problem?

A

The body’s first solution is the presence of telomeres, and the second solution is the enzyme telomerase, which can expand telomeres.

96
Q

Describe the Hayflick limit.

A

The Hayflick limit refers to the number of times a normal somatic human cell can divide before cell division stops, due to the shortening of telomeres.

97
Q

How do telomeres affect DNA replication?

A

Telomeres protect and stabilize the coding regions of DNA, but as DNA replication occurs, telomeres shorten, eventually leading to a limit on cell division.

98
Q

Define telomeres and their function.

A

Telomeres are repetitive nucleotide sequences at the ends of chromosomes that protect and stabilize the coding regions of DNA during replication.

99
Q

What happens to cells when they reach the Hayflick limit?

A

When cells reach the Hayflick limit, they stop replicating due to the telomeres reaching their shortest allowable length.

100
Q

Explain the relationship between DNA replication and telomere length.

A

As DNA replication occurs multiple times, telomeres shorten, which eventually limits the number of times a cell can divide.

SF:Biochemistry (13 decks)

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