L10: Enzymes allosteric changes, Nucleic Acids - DNA Structure Flashcards
1
Q
What are the three levels of DNA structure?
A
- Primary
- Secondary
- Tertiary
2
Q
What is a nucleoside?
A
- Just the sugar and the base
3
Q
What is a nucleotide?
A
- Building block for nucleic acids
- When a nucleoside has 1-3 phosphate groups attached.
4
Q
What is the difference between DNA and RNA?
A
- RNA has a hydroxyl group attached to the 2’ carbon whereas DNA has a hydrogen attached to the 2’ carbon.
- Sugar is ribose in RNA and deoxyribose in DNA
- Uracil replaces thymine
5
Q
On which end are nucleotides attached to?
A
- 3’ end
6
Q
What is the directionality of each strand?
A
- DNA strands are anti-parallel
- One strand is 3’-5’ and the complementary strand is 5’-3’
7
Q
Describe the polymerization of DNA or RNA.
A
- Requires an enzyme (DNA/RNA Polymerase)
- Requires a form of energy - monomer has tri-phosphates (ATP, CTP, GTP or TTP)
- The 5’ carbon of a new monomer is added to the 3’ carbon of the existing strand (or 1st monomer)
8
Q
Why are monomers shown as triphosphate?
A
- Called an “activated monomer”
- Binding of 3 phosphates creates an unfavorable state
(3 negative ions in close proximity) - Removing the outermost phosphates release energy.
- The energy can be used to link the monomer to the polymer
9
Q
Discuss general geometry of Chargaff’s (watson-crick) base pairs.
A
- Purine-pyramidine is just right
- A-T is held together by 2 H-bonds
- G-C is held together by 3 H-bonds.
- allows to form a uniform structure
10
Q
What holds 2 DNA strands together?
A
- H-bonds
- Stacking interactions
11
Q
What drives the spontaneous formation of the DNA double helix?
A
- The hydrophobic effect
12
Q
What is the deal with the major and minor grooves?
A
- Are regions where proteins bind to the DNA.
- Different proteins recognize the different sequences of bases (i.e. bind to specific regions of the DNA).
