Unit 3--Lecture 13 (Molecular Information Flow: Replication)

Question 1

Biological Information

Answer 1

Information is independent of the medium upon which it is stored or encoded

Question 2

Nature of the Genetic Material

Answer 2

Miescher (1869): Nuclein

Griffith (1928): Transformation

Avery, MacLeod, McCarty (1944): Transformation

Hershey and Chase (1944): Blender experiment

Chargaff (1948): The “rules”

Question 3

Monomers

Answer 3

Bases (A, C, G, T)

Nucleosides
—-base
—-sugar

Nucleotides
—-base
—-sugar
—-phosphate

Question 4

Purines

Answer 4

A and G

Two ring structure

Larger

Question 5

Pyrimidines

Answer 5

C, T, and U

One ring structure

Smaller

Question 6

Chargaff’s Rules

Answer 6

Purines match with pyrimidines

Two purines would be too large and bulge

Two pyrimidines would be too short to pair effectively

Hydrogen bonds formed

Question 7

Meselson and Stahl

Answer 7

Conservative, semi-conservative, or dispersive?

1st Gen: Heavy/Heavy

2nd Gen: Intermediate

3rd Gen: Light/Intermediate

4th Gen: More Light/Intermediate

Semi-conservative replication

Question 8

The Genome

Answer 8

Genome: complete cell DNA sequence

Genotype: specific DNA sequence

Phenotype: appearance and/or behavior
—-genotype + environment = phenotype

Large molecules

Prokaryotes are circular and haploid

Question 9

DNA is Packed to Fit the Cell

Answer 9

Nucleoid of E. coli

Circle of dsDNA

Multiple loops held by anchoring proteins

Each loop has supercoiled DNA

Question 10

Supercoiling

Answer 10

Un-supercoiled DNA = 1 wind for 10 bases

Positive supercoils: over winding

Negative supercoils: Under winding

Supercoils twist DNA

Question 11

Topoisomerases

Answer 11

Type I Topoisomerases: relieve torsional stress caused by supercoils

Type II Topoisomerases: Introduce negative supercoils

Archaea Topoisomerases: Introduce positive supercoils

Question 12

DNA Replication

Answer 12

Semi-conservative

Copies information from complementary strand

Question 13

Replication Begins at oriC

Answer 13

DNA opened at oriC

Polymerization follows bi-directionally around the chromosome

Question 14

DNA Helicase Melts DNA

Answer 14

Loader places helices at each end of origin

One helices moves in each direction to copy genome

Question 15

Helicase Recruits Primase

Answer 15

DNA polymerase needs a free 3’ OH

Primase begins replication

RNA primer forms 3’ OH for DNA to attach

Question 16

Primer Recruits Clamp Loader to Each Strand

Answer 16

Clamp binds DNA polymerase III to strand

Question 17

Polymerase Proceeds 5’ –> 3’ on Each Strand

Answer 17

Energy for polymerization comes from phosphate groups

Question 18

Each Fork has Two Strands

Answer 18

Steady growth of new “leading” strand

Leading strand follows helicase

Question 19

Lagging Strand Growth

Answer 19

Okazaki fragments

Question 20

RNase H Removes Primers

Answer 20

One primer for each leading strand

Many primers on lagging strands
—-one per Okazaki fragment

Gaps filled in by DNA polymerase I

Ligase seals nicks

Question 21

Both Forks Move to ter Sites

Answer 21

Movement is simultaneous in opposite directions until both meet again at terminus

Replisomes are actually stationary

DNA is threaded through the replisomes

Question 22

Plasmids

Answer 22

Extrachromosomal pieces of DNA

Low-copy-number plasmids
—-one or two copies per cell

High-copy-number plasmids
—-up to 500 copies per cell
—-divide continuously
—-randomly segregate

Question 23

Plasmid Replication

Answer 23

Bi-directional replication
—-similar to chromosomal replication

Uni-directional (“rolling circle”) replication
—-stars at nick bound by RepA protein
—-helicase moves around plasmid repeatedly
—-used by many bacteriophage viruses

Question 24

Plasmid Genes

Answer 24

Advantageous under special conditions:
—-antibiotic-resistance genes
—-genes encoding proteins to metabolize rare food sources
—-virulence genes to allow pathogenesis
—-genes to allow symbiosis