DNA and RNA Structure

Question 1

Nucleic Acids consist of

Answer 1

Bases linked to a sugar-phosphate backbone

• Form of linear information
• Each monomeric unit contains a sugar, base, and phosphate

Question 2

The Sugar

Answer 2

DNA has deoxyribose sugar (H on 2’C)
RNA has ribose sugar (OH on 2’C)
- 3’OH and 5’OH are involved in formation of nucleic acid backbone

Question 3

The Backbone

Answer 3

Identical in both RNA and DNA

• Sugars are linked by phosphodiester bridges between the 3’OH of one sugar and the 5’OH of an adjacent sugar
• 3’ to 5’ phosphodiester linkage
• Directionality (polarity): read 5’OH to 3’OH

Question 4

The Bases

Answer 4

Purines: Adenine and Guanine
Pyrimidines: Cytosine, Thymine (DNA only), Uracil (RNA only)

Question 5

What is the structure of nucleotides?

Answer 5

A base, pentose sugar, one or more phosphates (nucleoside joined to phosphoryl group by ester linkage)

Question 6

What is the structure of nucleosides?

Answer 6

Only the base and pentose sugar

Question 7

The Double Helix of DNA

Answer 7

1) Two DNA chains of opposite directionality (antiparallel) intertwine to form a right-handed double helix
2) The sugar-phosphate backbones are on the exterior, bases are interior
3) The bases are nearly perpendicular to the axis of the helix with adjacent bases separated by 3.4A
4) The helix is approx 20A wide

Question 8

DNA base pairing:

Answer 8

G-C: 3 H-bonds (require more energy to break than AT)

A-T: 2 H-bonds

Question 9

DNA Base Pairs Contribute to the Stability of the Helix via:

Answer 9

1) Hydrophobic effect: hydrophobic interactions drive bases inside of the helix, and more polar residues outside
2) Base-stacking: stacked bases attract each other through van der Waals forces

Question 10

The Major and Minor Grooves of DNA

Answer 10

• Major groove is wide, and the minor groove is narrow
• Exist because glycosidic bonds of each base in a pair are not diametrically opposite to each other
• Lined by H-bond donors and acceptors

Proteins read H-bond donor/acceptors on surface of grooves, very specific pattern for which base-pair there is

Question 11

How do prokaryotes package their DNA?

Answer 11

Supercoiled structures or relaxed circle

Question 12

Packaging of Eukaryotic DNA

Answer 12

• 3.6m of DNA/cell packaged into 46 chromosomes contained in a nucleus with a 5uM diameter
• Nucleosomes are: complexes of ~200bp of DNA wrapped around a histone octamer

Question 13

Nucleosomes and Chromatin

Answer 13

• DNA is wrapped around basic histone octamers (Lys and Arg on histone protein surfaces (+) charge to interact with (-) DNA)
• Nucleosomes are compacted into chromatin

Question 14

RNA Folds into Elaborate Structures

Answer 14

• Can have bulges, stemloop, etc.
  RNA can fold more because they have less specificity
• Complex 3D RNA structure allows some RNA to act as catalysts (ribozymes)