Nucleotides and Nucleic Acids Flashcards
Nucleic Acid
The polymer of nucleotides, sugar + base + phosphate, DNA/RNA
DNA
Double helix containing genetic information
RNA
Responsible for protein synthesis
Nucleotide
Base + sugar + phosphate
Nucleoside
Base + sugar
Deoxynucleoside
Nucleotide with a deoxyribose sugar
Base
Adenine, Guanine, Cytosine, Thymine, Uracil
Purines
Adenine, Guanine
Pyrimidines
Thymine, Cytosine, Uracil
Anti-Parallel
2 biopolymers that run parallel to each other but with opposite directionality
Kb
Kilobase - the unit of measurement equal to 1000 base pairs of DNA or nucleotides in RNA
Oligonucleotide
Short DNA or RNA molecules (<50)
B-DNA
Right-handed double helix (most common)
Stacking Interactions
The primary stabilizing force of DNA
- Van der Waals
- Hydrophobic forces
Melting Temperature (DNA)
The temperature at which half of the DNA strands are in the random coil or single-stranded state
Denaturation
Destroy the characteristic properties of a macromolecule by heat, acidity, etc
Renaturation
Reconstruction of protein/nucleic acid that has been denatured such that molecules resume normal function
Anneal
Recombine DNA in double-stranded form following separation from heat
Draw Uracil
Check Structures Sheet
Draw Thymine
Check Structures Sheet
Draw Cytosine
Check Structures Sheet
Draw Adenine
Check Structures Sheet
Draw Guanine
Check Structures Sheet
Draw Ribose
Check Structures Sheet
Draw Deoxyribose
Check Structures Sheet
Where is N Located on a Base?
Odd numbers (1,3,7,9)
Where Do Bases Link to Sugar?
Pyrimidines = link to sugar C1' from N1 Purines = link to sugar C1' from N9
Naming Nucleosides
Pyrimidines = end in idine
Purines = -ine -> -osine
If the sugar is deoxyribose, put deoxy in front
Phosphoester
Link carbon to a phosphate group
Phosphodiester
Link two different carbons to one phosphate group
Phosphoanhydrides
Link two phosphates to each other
Properties of the Backbone in DNA/RNA
Consistent negative charge
Polar
Is the DNA or RNA Backbone more Polar?
The RNA backbone is more polar because of the 2’OH group on the ribose sugar
Why is RNA More Susceptible to Alkaline Hydrolysis?
Because of the 2’OH group on the ribose sugar
Is DNA or RNA more Stable?
DNA
What are the Forces Involved in Stacking Interactions?
Hydrophobic effect
Van der Waals Forces
Ionic interactions
Chargaff’s Rule
A=T and G=C
Helps to deduce base composition
Maintains the diameter in DNA double helix
How is B-form DNA stabilized?
Primarily base stacking (Van der Waals and hydrophobic forces)
Hydrogen bonding
-AT = 2 H-bonds
-GC = 3 H-bonds
Why is it Important for DNA to be Stabilized by Non-Covalent Forces?
Covalent bonds are rigid and would not allow DNA to function
Non-covalent bonds are strong enough to hold DNA together but attractive forces can be weakened to adapt to environmental changes
B-form DNA Structure
Strands are anti-parallel with an overall right-handed twist
Hydrophobic core and polar exterior
Bases largely excluded from H2O = stabilizes H-bonds
Sugar and phosphate exposed to H2O
H-bonds in pairing interactions
Base pairs are complements of each other
Has grooves
Function of Grooves
There are functional groups on the edge of base pairs that are exposed to water
- important for proteins that must bind to dsDNA and read a sequence
- major grooves have enough space for an alpha protein to bind
RNA vs DNA sequence
RNA is single-stranded, DNA is double-stranded
RNA contains uracil, DNA contains thymine
RNA contains ribose, DNA contains deoxyribose
What Causes the Denaturation of dsDNA
Disruption of non-covalent forces
-separates two paired strands
DNA Melting
Goes from double-stranded to denatured single-stranded
Absorbance changes as DNA melts = base stacking changes
-ssDNA has a higher absorbance than dsDNA
What is Tm?
The midpoint of melting and is a characteristic of the base composition and solvent conditions
Hyperchromicity
High absorbance (ssDNA)
Hypochromicity
Low absorbance (dsDNA)
Renaturation
Reformation of dsDNA so it regains its native conformation
- proper base pairing
- nucleation and zippering
Why do GC pairs have stronger base stacking interactions than AT pairs?
GC pairs are bigger and wider
Therefore, AT pairs denature more readily
Higher GC content results in elevated Tm
How does Changing pH Affect Tm?
Affects the protonation state of DNA
Draw a pH-Tm Graph
See Cheat Sheet
How does Changing [Salt] Affect Tm?
Ions shield negative charges on phosphate backbone
Low salt decreases Tm = destabilizes double helix
High salt elevates Tm = stabilizes double helix
RNA Melting
2x the H-bonds = higher Tm than DNA
ss + ds mixture
