Nucleotides and Nucleic Acids Flashcards
What are the 4 functions of mono- and dinucleotides?
- Oxidation-reduction reactions (NAD/FAD)
- Energy transfer (ATP)
- Intracellular signalling (GTP/ cAMP)
- Biosynthetic Reactions (also ATP)
What are the two functions of polynucleotides?
- Storage and decoding genetic information (dNA/rNA)
What are nucleosides?
A base joined to a five-carbon ribose or deoxyribose.
How does naming change when a pyrimidine becomes a nucleoside?
The ending becomes “-idine”
How does naming change when a purine becomes a nucleoside?
The ending becomes “-osine”.
What are nucleotides?
A nucleoside joined to a phosphate group.
What is a phosphodiester bond?
A bond formed between phosphate and carbons that joins two nucleotides into a chain.
What is a phosphoanhydride bond?
A bond formed between phosphate groups.
What is the net charge of dNA?
Negative.
Is dNA backbone polar or non-polar?
Polar.
What are oligonucleotides?
A chain consisting of 50 or more nucleotides.
What are polynucleotides?
A chain consisting of a large number of nucleotides.
Why is DNA more stable than RNA in alkaline conditions?
The spontaneous hydrolysis of phosphodiester bonds occurs in alkaline (ph>10) conditions but is prevented in DNA due to the absence of a hydroxy group at C2.
What is dideoxyribose? How is it used in modern sequencing?
A ribose sugar without any hydroxy groups at C2 or C3. This prevents the extension of a DNA molecule by DNA polymerase during electrophoresis.
Dideoxyribose is also present at the 3’ end of a nucleic acid to prevent additional phosphodiester bonds.
What is the general solubility of nucleic acid bases?
Because they are mainly hydrophobic, the bases are primarily insoluble in water.
Why do nucleic acids have a ‘sense of direction?’
The free ends of nucleic acid are structurally different from one another, (5’ vs 3’), therefore there should be no 3’OH groups connecting to other 3’OH groups.
What bond interaction causes DNA chains to form a double helix?
Hydrogen bonds through bases.
What did Erwin Chargaff determine about base composition values in DNA?
The amount of adenosine is equal to thymidine; the amount of cytidine is equal to guanosine.
What is a Hydrogen Bond?
A polar interaction in which a hydrogen atom is shared between two electronegative atoms, much weaker than covalent bonds.
Why is adenosine specifically compatible with thymidine? Why can adenosine not pair with cytidine?
The amino and carbonyl functional groups between A and T allow for specific hydrogen-bonding interactions. Because A has only 2 H-bond participants when oriented toward another base, while C has 3, there would be a mismatch in hydrogen bonding and instability would ensue.
What is B-form DNA?
The structure is stabilized by base stacking interactions and hydrogen bonds. The strands are antiparallel and have an overall right-handed twist.
What is base-stacking?
The primary stabilizing force present in B-DNA, occurs due to VDW and hydrophobic forces between bases.
Describe the hydrophobicity of B-form DNA, why is there a difference in hydrophobicity throughout the molecule?
The core of the nucleic acid is hydrophobic, while the exterior is polar. This difference is due to bases being nonpolar whereas the phosphodiester backbones are polar.
Why are bases excluded from water in B-form DNA?
Water interrupts hydrogen bonding between bases, causing instability.
