Chapter 11

Question 1

DNA: The Hereditary Molecule

Answer 1

Early Beliefs: Proteins were thought to be the hereditary molecules.
Key Discovery: Experiments proved that DNA (not proteins) is the genetic material.

Question 2

Watson and Crick

Answer 2

• 1953 Model: Watson and Crick proposed the double-helix structure of DNA.
• Revolutionized Biology: Their model changed the understanding of genetics.
• DNA’s Role: DNA is the genetic material for all living organisms.

Question 3

Molecular Structure of DNA

Answer 3

• Maurice Wilkins & Rosalind Franklin: Used X-ray diffraction to study DNA.
• Franklin’s Interpretation: Observed an X-shaped pattern, suggesting DNA has a helical structure.

Question 4

Chargaff’s Rules

Answer 4

• Erwin Chargaff: Found that nitrogenous bases in DNA occur in specific ratios.
• Base Pairing Rule:
  
  • Amount of adenine (A) = thymine (T)
  • Amount of guanine (G) = cytosine (C)
• Chargaff’s Rule: A = T and G = C

Question 5

The Polynucleotide Chain

Answer 5

• DNA nucleotides are joined to form a polynucleotide chain.
• Sugar-phosphate backbone: Deoxyribose sugars are linked by phosphate groups in an alternating pattern.
• The phosphate group connects the 3′ carbon of one sugar to the 5′ carbon of the next.
• The linkage between sugars is a phosphodiester bond.

Question 6

Polarity (different at each end)

Answer 6

• At the 5′ end, a phosphate group is bound to the 5′ carbon of a deoxyribose sugar.
• At the 3′ end, a hydroxyl group is bound to the 3′ carbon of a deoxyribose sugar.

Question 7

Four Bases in a Polynucleotide

Answer 7

• Phosphodiester bonds connect deoxyribose sugars in DNA.
• Links the four subunits: adenine, guanine, thymine, cytosine.
• The polynucleotide chain has polarity.

Question 8

Base Pairs

Answer 8

• A purine and a pyrimidine pair together to fill the space between the two DNA chains.
• Base pairs:
  
  • A–T (2 hydrogen bonds)
  • G–C (3 hydrogen bonds)
• A cannot pair with C, and G cannot pair with T due to hydrogen bonding requirements.

Question 9

Complementary Strands

Answer 9

• The two strands of a DNA molecule are complementary.
• Complementary base-pairing:
  
  • A pairs with T
  • G pairs with C
• Each base on one strand is paired with its complementary base on the opposite strand.

Question 10

Complementary and Antiparallel

Answer 10

• The two strands of the DNA double helix run in opposite directions (antiparallel).
• The 3′ end of one strand is opposite the 5′ end of the other strand.

Question 11

Semiconservative Replication

Answer 11

• Product molecules are half old and half new.
• Steps in semiconservative replication:
  
  1. Hydrogen bonds between the two strands break.
  2. The strands unwind and separate.
  3. Each strand acts as a template for synthesizing a new, complementary strand.
  4. Each new double helix consists of one old strand (from the parent DNA) and one new strand.

Question 12

DNA Polymerases

Answer 12

• DNA polymerases assemble complementary polynucleotide chains from individual deoxyribonucleotides.
• Four types of deoxyribonucleoside triphosphates are used:
  
  • dATP (for adenine)
  • dGTP (for guanine)
  • dCTP (for cytosine)
  • dTTP (for thymine)
• DNA polymerase adds nucleotides only to the 3′ end (the exposed hydroxyl group) of an existing nucleotide chain.

Question 13

Antiparallel Strands

Answer 13

• The new DNA strand grows at the 3′ end (where there’s an OH group), and the old end has a 5′ triphosphate.
• DNA polymerase can only add nucleotides in the 5′ to 3′ direction.
• Because the strands are antiparallel, the template strand is read in the 3′ to 5′ direction.

Question 14

Sliding DNA Clamp

Answer 14

• DNA polymerase extends the new DNA strand one nucleotide at a time while moving along the template.
• Sliding DNA clamp:
  
  • A protein that wraps around the DNA.
  • Attaches to the back of DNA polymerase.
  • Tethers DNA polymerase to the template strand, speeding up DNA synthesis.

Question 15

Unwinding and Stabilizing DNA

Answer 15

• In the bacterial chromosome, DNA replication begins at a specific region called the origin of replication (ori).
• DNA helicase unwinds the DNA strands, creating a Y-shaped structure known as the replication fork.
• Single-stranded binding proteins (SSBs) bind to the exposed single-stranded DNA, preventing the strands from re-annealing.
• Topoisomerase relieves the tension that builds up ahead of the replication fork by cutting and rejoining the DNA to prevent supercoiling.

Question 16

RNA Primers

Answer 16

• DNA polymerases can only add nucleotides to an existing strand.
• A short RNA primer is synthesized by primase to start the new strand.
• Once the primer is in place, DNA polymerase extends it by adding DNA nucleotides to form the new DNA strand.
• Later in replication, the RNA primers are replaced with DNA.

Question 17

Continuous and Discontinuous DNA Synthesis

Answer 17

• DNA strands are antiparallel, so only one strand allows continuous copying in the 5′→3′ direction.
• The other strand is copied in short segments called Okazaki fragments, which are made in the opposite direction (discontinuous replication).

Question 18

Leading and Lagging Strands

Answer 18

Leading strand:
- Synthesized continuously in the direction of DNA unwinding.
- Follows the leading strand template.

Lagging strand:
- Synthesized discontinuously in the opposite direction of DNA unwinding.
- Follows the lagging strand template

Question 19

Telomeres

Answer 19

• Noncoding DNA at the ends of chromosomes.
• Consist of short, repeating sequences (telomere repeats).
• Protect genes by acting as a buffer during replication.
• Active in embryonic, germ, and cancerous somatic cells.

Question 20

Enzymes in DNA Replication

Answer 20

DNA helicase: Unwinds DNA.
Primase: Initiates all new strands.
DNA polymerase III: Main enzyme for polymerizing new DNA.
DNA polymerase I: Forms the lagging strand.
DNA ligase: Binds Okazaki fragments together.

Question 21

Telomerase

Answer 21

• Telomere repeats shorten with each replication, but genes remain unaffected.
• When the entire telomere is lost, it can cause issues.
• Telomerase prevents telomere shortening by adding repeats to the chromosome ends.
• It uses an RNA template to add telomere repeats to the DNA.
  Telomerase is active in: Rapidly dividing embryonic cells, Germ cells, Cancerous somatic cells

Question 22

Repair Mechanisms for DNA Damage

Answer 22

• Types of repair mechanisms:
  
  1. Proofreading
  2. Mismatch repair
  3. Excision repair

Question 23

Basic Steps in Repair Process

Answer 23

1. Recognize and remove the DNA error.
2. Replace the removed DNA with new DNA using a repair polymerase.
3. Seal the new DNA to the old DNA using DNA ligase.

Question 24

Repairing DNA Damage

Answer 24

Proofreading: DNA polymerases correct errors (base-pair mismatches) during replication.
Post-replication repair: Remaining mismatches are fixed by a DNA repair mechanism after replication.

Question 25

Proofreading

Answer 25

- Corrects errors made by DNA polymerase during replication. - If a nucleotide is mismatched, DNA polymerase reverses using 3′→5′ exonuclease activity to remove the incorrect nucleotide. - Resumes forward synthesis and inserts the correct nucleotide.

Question 26

Mismatch Repair

Answer 26

- Corrects errors during replication that escape proofreading. - Repair enzymes cut the new DNA strand on each side of the mismatch and remove the incorrect portion. - DNA polymerase fills the gap with new DNA, and DNA ligase seals the chain.

Question 27

Mutation and Evolutionary Processes

Answer 27

- Errors that remain after proofreading and DNA repair are the primary source of mutations (changes in DNA sequence passed on in replication). - Mutations in genes can alter the proteins they encode, potentially affecting the organism's function. - Mutations are the ultimate source of variability in offspring, which is acted upon by natural selection.