Gene vs. Protein

Amp^r vs. Amp^s

WT vs. Mutant

gene is lower case and italicized

Protein is upper case and never italicized

ampicillin resistant and amp sensitive

wt: lacZ⁺

mut: lacZ^-

h determines host specificity (i.e. it is a conditional mutation)

h+: only infects E. coli B, cloudy plaque

h: infect B and B/2, clear plaque

r determines rate of cell lysis (host range independent)

r+: slow lysis (allows for greater number of phage assembled), small plaque

r: fast lysis, large plaque

rII+: produces small, ragged plaques on both B and K12 bacteria

rII: produces large, round plaques on B and no plaques on K12 bacteria

A: right handed, short and wide overall, narrow-deep major, shallow-wide minor, helix axis on major groove

B: right handed, ~10 bp/turn, long and thin overall, wide-intermediate depth major, narrow-intermediate depth minor, helix axis on base pairs

Z: left handed, long and thing overall, flat major, narrow-deep minor, helix axis on minor groove

L= Twist(T) + Writhe(W)

T is the number of helix turns

W is the number of times a dsDNA molecule passes over itself (i.e. the number of supercoils)

Alter the linking numbers of closed, circular DNA

TI 1: cuts one strand and passes dsDNA through the break (alters linking number by 1)

TI 2: cuts both strands and passes dsDNA through the break (alters linking number by 2)

treatment by TI's will form subpopulations of DNA with variable degrees of supercoiling

1) DNA A protein binds to the origin of replication (oriC in E. coli) and denatures the DNA

2) DNA C proteins binds to DNA A protein and delivers Helicase to the DNA molecule

3) Helicase extends the replication fork beyond the oriC

4) SSB protein binds the ssDNA to prevent 2⁰ DNA structures from forming

1) Primase binds to DNA behind helicase and polymerizes a short RNA primer

2) DNA Pol III elongates the primer with dNTP's

3) DNA Pol I removes the primer and replaces it with dNTP's

4) DNA ligase joins the end of the new leading strand sequence to the lagging strand at the opposite end of the replication fork

1) Primase lays down and RNA primer on the DNA (5' to 3')

2) DNA Pol III elongates the RNA primer with new DNA

3)DNA Pol I removes the RNA primer that the DNA Pol III is approaching and replaces it with DNA

4) DNA ligase joins the newly synthesized Okasaki fragment made by DNA Pol III to the previously laid fragment at its 3' end

DNA Pol I activity

DNA Pol III activity

DNA Pol I: 5' to 3' polymerase, 3' to 5' exonuclease (proofread), and 5' to 3' exonuclease (primer removal)

DNA Pol III: 5' to 3' polymerase and 3' to 5' exonuclease (proofread)

Theta replication

Rolling circle replication

Theta: a replication bubble opens in the circular DNA and two replication forks proceed bidirectionally and terminate 180 degrees from the origin

Rolling circle: nick made in circular dsDNA, 5' end is displaced and covered with SSB's, polymerization begins at 3' end in the circle using Okasaki fragments, attachment of the replisome to 5' and beginning of leading strand replication

Initiation

1) RNA Pol binds promoter (closed DNA)

2) RNA pol unwinds DNA helix (open DNA)

3) Nucleotides are incorporated (3⁰ complex)

Elongation

1) Sigma factor dissociatoes from core complex and RNA Pol moves along template adding nucleotides

Termination

1) RNA Pol and mRNA dissociate from DNA template

The core RNA Polymerase + sigma factor

The sigma factor binds to the promoter and localizes the core enzyme to the transcription initiation site

Rho independent transcriptional termination

Rho dependent transcriptional termination

independent: a sequence of DNA has two fold symmetry-two sequences that are palindromes of each other-and is separated by a small piece of DNA (the loop)

dependent: Rho protein binds to RNA sequence known as the "rut" site which is anchored to a ribosome and effectively pulls of the RNA Pol which cannot reattach without a primer

alpha: polymerase activity

beta: processivity

epsilon: proofreading activity