Nucleic Acids: Structure and Chemistry

These flashcards cover key concepts related to the structure and chemistry of nucleic acids as discussed in the lecture.

What causes the denaturation or melting of the double helix in DNA and RNA?

Denaturation is caused by pH extremes or high temperatures that disrupt hydrogen bonds and base-stacking interactions.

What does the hypochromic effect refer to in relation to UV absorption?

The hypochromic effect refers to the decrease in the absorption of UV light when complementary strands of nucleic acids are paired.

How does the melting temperature (TM) relate to nucleic acids?

The melting temperature (TM) is the temperature at which the transition from double-stranded to single-stranded DNA occurs.

Which base pairs stabilize melting temperature the most?

G•C pairs stabilize the melting temperature more than A•T pairs.

What is gel electrophoresis used for?

Gel electrophoresis is a method for visualizing the size of nucleic acid molecules.

What are some methods to detect nucleic acids?

Methods include using fluorescence with Ethidium Bromide or labeled radiation like 32P or 32S.

What is deamination in nucleic acids?

Deamination is the spontaneous loss of exocyclic amino groups, such as the conversion of cytosine to uracil.

Why is thymine used in DNA instead of uracil?

Thymine is used to distinguish between spontaneous deamination of cytosine, which produces uracil.

What are restriction endonucleases used for?

Restriction endonucleases are enzymes that cut DNA at specific recognition sequences.

What kind of bonds do DNA polymerases break and form during nucleic acid synthesis?

DNA polymerases make and break phosphoester bonds while synthesizing nucleic acids.

How does Sanger sequencing differ from Illumina sequencing?

Sanger sequencing typically reads longer sequences (1000 bp) while Illumina sequencing produces millions of shorter reads (about 100 bp).

What unique property does reversible terminator sequencing offer?

Reversible terminator sequencing allows for parallel sequencing of millions to billions of molecules, with each nucleotide labeled with a specific fluorescent dye.

What is the advantage of single molecule sequencing?

Single molecule sequencing allows for longer read lengths averaging over 10,000 bp, which can be beneficial for various genomic analyses.

What is the role of ligase in nucleic acid reactions?

Ligase joins the 3’ end of one nucleic acid polymer to the 5’ end of another.

What causes the denaturation or melting of the double helix in DNA and RNA?

Denaturation is caused by pH extremes or high temperatures that disrupt hydrogen bonds and base-stacking interactions.

What does the hypochromic effect refer to in relation to UV absorption?

The hypochromic effect refers to the decrease in the absorption of UV light when complementary strands of nucleic acids are paired.

How does the melting temperature (TM) relate to nucleic acids?

The melting temperature (TM) is the temperature at which the transition from double-stranded to single-stranded DNA occurs.

Which base pairs stabilize melting temperature the most?

G•C pairs stabilize the melting temperature more than A•T pairs.

What is gel electrophoresis used for?

Gel electrophoresis is a method for visualizing the size of nucleic acid molecules.

What are some methods to detect nucleic acids?

Methods include using fluorescence with Ethidium Bromide or labeled radiation like 32P or 32S.

What is deamination in nucleic acids?

Deamination is the spontaneous loss of exocyclic amino groups, such as the conversion of cytosine to uracil.

Why is thymine used in DNA instead of uracil?

Thymine is used to distinguish between spontaneous deamination of cytosine, which produces uracil.

What are restriction endonucleases used for?

Restriction endonucleases are enzymes that cut DNA at specific recognition sequences.

What kind of bonds do DNA polymerases break and form during nucleic acid synthesis?

DNA polymerases make and break phosphoester bonds while synthesizing nucleic acids.

How does Sanger sequencing differ from Illumina sequencing?

Sanger sequencing typically reads longer sequences (1000 bp) while Illumina sequencing produces millions of shorter reads (about 100 bp).

What unique property does reversible terminator sequencing offer?

Reversible terminator sequencing allows for parallel sequencing of millions to billions of molecules, with each nucleotide labeled with a specific fluorescent dye.

What is the advantage of single molecule sequencing?

Single molecule sequencing allows for longer read lengths averaging over 10,000 bp, which can be beneficial for various genomic analyses.

What is the role of ligase in nucleic acid reactions?

Ligase joins the 3’ end of one nucleic acid polymer to the 5’ end of another.

What is the biochemical significance of cytosine methylation?

Cytosine is often methylated at the C-5 position to form 5-methylcytosine, a modification used by cells for epigenetic gene regulation.

How do polymerases extend a nucleic acid chain?

Polymerases catalyze the addition of nucleotides to the 3' hydroxyl group of a growing chain, meaning synthesis always occurs in the 5' o 3' direction.

What occurs during a transesterification reaction in nucleic acids?

Transesterification is a reaction where one phosphodiester bond is substituted for another, often involving a nucleophilic attack by a hydroxyl group on a phosphate.

Why is RNA susceptible to self-cleavage compared to DNA?

RNA contains a 2'-OH group that can act as a nucleophile to attack the adjacent phosphodiester bond through internal transesterification, leading to backbone cleavage.

What are the primary classes of enzymes used for DNA manipulation?

1. Nucleases: Degrade or cut DNA.

2. Ligases: Join DNA fragments.

3. Polymerases: Synthesize new DNA strands.

4. Modifying Enzymes: Add or remove chemical groups (e.g., kinases, phosphatases).

How does thymine (5-methyluracil) assist in preserving genetic integrity?

Because cytosine spontaneously deaminates to uracil, using thymine in DNA allows repair machinery to recognize uracil as a mutation that needs to be replaced.