L10: Enzymes allosteric changes, Nucleic Acids - DNA Structure

Question 1

What are the three levels of DNA structure?

Answer 1

• Primary
• Secondary
• Tertiary

Question 2

What is a nucleoside?

Answer 2

• Just the sugar and the base

Question 3

What is a nucleotide?

Answer 3

• Building block for nucleic acids

- When a nucleoside has 1-3 phosphate groups attached.

Question 4

What is the difference between DNA and RNA?

Answer 4

• 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

Question 5

On which end are nucleotides attached to?

Answer 5

• 3’ end

Question 6

What is the directionality of each strand?

Answer 6

• DNA strands are anti-parallel

- One strand is 3’-5’ and the complementary strand is 5’-3’

Question 7

Describe the polymerization of DNA or RNA.

Answer 7

• 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)

Question 8

Why are monomers shown as triphosphate?

Answer 8

• 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

Question 9

Discuss general geometry of Chargaff’s (watson-crick) base pairs.

Answer 9

• 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

Question 10

What holds 2 DNA strands together?

Answer 10

• H-bonds

- Stacking interactions

Question 11

What drives the spontaneous formation of the DNA double helix?

Answer 11

• The hydrophobic effect

Question 12

What is the deal with the major and minor grooves?

Answer 12

• 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).