01. Molecular Structures — Nucleic Acids

Question 1

What are the three main functions of DNA?

Answer 1

All three functions involve information:

1. Storage of information via base sequence
2. Preservation of information via faithful replication
3. Variability of information via the ability to mutate

Question 2

What is the molecular biology definition of a gene?

Answer 2

The entire DNA sequence needed to produce a functional protein or RNA molecule.

Question 3

What kind of information does DNA store?

Answer 3

1. Coding sequences for products like proteins and RNA
2. Regulatory signals (i.e. binding sites)

Question 4

How does DNA replicate “faithfully”?

Answer 4

• DNA replicates semi-conservatively.
• Each strand of the parental double helix serves as a template (or predictor) of a daughter strand via complementary base pairing.
• Since one strand predicts the other, information is preserved.

Question 5

Describe how Meselson & Stahl demonstrated semi-conservative replication of DNA.

Question 6

Describe the four different kinds of DNA mutations that are possible.

Answer 6

1. Silent — the mutation does not alter the regulatory sequence/protein/RNA product in any way, often because of codon degeneracy.
2. Missense — swapping a base recruits a different amino acid.
3. Nonsense — the mutation causes a premature stop codon; UAA, UAG, UGA.
4. Frameshift — insertion or deletion of bases results in a new transcript/polypeptide.

Question 7

Why are mutations (ones that create new alleles) important?

Answer 7

Mutations can cause several changes:

1. Novel transcripts and proteins can have valuable new or improved functions.
2. No products may be produced, limiting the function of the cell.
3. Expression of a product is altered via regulatory sequence mutation.

Selection for or against these changes results in evolution.

Question 8

Which chemical bonds contribute to the 3D structure of DNA?

Answer 8

Several forces contribute to the double helix (in order of contribution):

1. Rigid phosphate backbone — linked via phosphodiester bonds, gives the molecule a negative charge.
2. Stacking Van der Waals forces — aka London dispersion forces — are the attractive/repulsive forces that occur because of dipoles. Dipoles are formed from random dispersions of electrons around a molecule. Numerous bases will stack these forces.
3. Hydrophobic interactions — non-polar groups will avoid water. Thus the negatively charged backbone faces water while the non-polar bases face the inside.
4. Ionic interactions — cations will stabilize the negatively charged sugar-phosphate backbone. AKA DNA shielding.
5. Hydrogen bonds — a noncovalent bond that creates an attraction between nitrogenous bases of two complementary strands of DNA.

Question 9

Label the following nitrogenous bases:

Question 10

What is the difference between ribose and 2’ deoxyribose?

Answer 10

• Deoxyribose — an H atom on its 2’ carbon. Forms DNA.
• Ribose — a hydroxyl (OH) group on its 2’ carbon. Forms RNA.

Question 11

What is the difference between a nucleotide and a nucleoside?

Answer 11

• Nucleoside — a sugar and a base.
• Nucleotide — a nucleoside with 1 - 3 phosphate groups.
  
  • Mono
  • Di
  • Tri

Question 12

What are the 4 different functions of nucleotides?

Answer 12

1. Information — as in DNA/RNA
2. Energy — power chemical reactions (like ATP/GTP)
3. Coenzymes — cofactors for enzymes (like Coenzyme A, AMP)
4. Regulation — signals and transductors (like cyclic AMP, GTP)

Question 13

Describe the 3D structure of DNA.

(Hint: describe the polymer shape, its components, and the forces holding it together.)

Answer 13

• DNA exists as a right-handed double helix.
  
  • It has a major and minor groove.
• Sugar-phosphate backbone
  
  • Nucleotides are chained together via phosphodiester bonds between the 3’ hydroxyl of one base and the 5’ phosphate of the next.
  • The backbone is negatively charged.
• Nitrogenous bases
  
  • Parallel to each other
  • Perpendicular to the long axis of the molecule
  • Held together by hydrogen bonds
  • A=T, C≡G
• Chains are antiparallel and complementary
  *

Question 14

Compare and contrast the alternative forms of DNA.

Answer 14

• 3 forms of DNA
• A, B, Z (check chart)

Question 15

Describe 3 unusual forms of DNA and how they occur.

Answer 15

1. Slipped — tandem repeats in the same strand bind to each other to form single-stranded loops.
2. Cruciform — inverted repeats on both strands bind to each to form a cruciform four-way junction.
3. Triple helix — when a purine strand and pyrimidine strand are present, a third strand can be accommodated; can occur in a test tube or in vivo.

Question 16

In angstroms, what is the rise/base pair along the helix axis in B-DNA?

Answer 16

3.4 angstroms, or 0.34 nm.

Question 17

What is the pitch/turn of helix in B-DNA?

Answer 17

34 angstroms or 3.4 nm.