lecture 06

Question 1

Division Cycle is dependent on

Answer 1

1. Nutrients available
2. Metabolism
3. Cell length and width
4. Environment

Question 2

What is cell division rate impacted by?

Answer 2

The local environment. The amount of available nutrients specifically determine the cell division rate. Each species has it’s own cell division rate

Question 3

Where does chromosomal replication begin?

Answer 3

At the oriC site in bacterial chromosomes. This is a site that contains these basepairs.

Question 4

ATP-DnaA

Answer 4

Recognizes 9 base pairs in the oriC site and unwinds DNA at the AT rich region.

Question 5

DnaA

Answer 5

Helps ATP-DnaA bind to low affinity sites

Question 6

IHF

Answer 6

Binds and bends DNA to facilitate ATP-DnaA binding

Question 7

Step One

Answer 7

ATP-DnaA, DnaA, IHF form an open complex of the DNA to make it ready for replication. This is known as initiation.

Question 8

DnaC

Answer 8

Loader

Question 9

DnaB

Answer 9

Helicase

Question 10

Step 2

Answer 10

DnaC loads DnaB onto the ssDNA region only after the open complex has been formed.

Question 11

DnaG

Answer 11

Binds to the helicase to synthesize primers

Question 12

Step 3

Answer 12

DnaB expands ssDNA and the DnaG will bind to the helicase to synthesize the first primers.

Question 13

DnaN

Answer 13

This is a sliding clamp that helps secure DNA polymerase to the DNA strand.

Question 14

DNA polymerase

Answer 14

Works to synthesize new DNA strands from a template strand

Question 15

Step 4

Answer 15

DnaN is a sliding clamp and Pol III are loaded onto the DNA for the DNA synthesis to begin

Question 16

Control of Initiation

Answer 16

DNA-ATP is the source for controlling DNA replication initiation. Initiation is controlled strategically because it must start at a pint in time that is compatible with septum formation. If initiation begins too late, replication occurs too late and bacterial daughters don’t have DNA (cell death). If it occurs too early there’s too much DNA in the cell.

Question 17

Dam methylase

Answer 17

An enzyme that methylates the entire chromosome on A nucleotide sites within GATC (5’-3’)

Question 18

ATP-DnaA and Dam methylase interaction

Answer 18

When the chromosome is methylated at A sites ATP-DnaA can still bind to DNA at the oriC site to initiate replication

Question 19

Hemi methylation (Seq A and ATP-DnaA)

Answer 19

Initiation begins
OriC GATC sites become hemi methylated
SeqA can bind at these GATC sites and ATP-DnaA can not rebind to begin initiation again.

Question 20

Dam Methylase (part two)

Answer 20

Dam methylase will also compete with SeqA and eventually the GATC sites become fully methylated. ATP-DnaA can rebind to initiate another round of replication. (why?)

Question 21

RIDA (replicative inactivation of DnaA)
Most widely conserved method of controlling initiation

Answer 21

Hda in ADP bound will bind to clamp after replication has begun. It forces ATP hydrolysis via DnA so DnaA is incapable of initiating another round of replication. Only works as ATP-DnaA not ADP-DnaA.

Question 22

Unfinished replication

Answer 22

lethal

Question 23

How are plasmids inherited?

Answer 23

1. No segregation system (plasmid will become lost if there is no selection maintained because they don’t contain essential genes.
2. Segregation system and the plasmid is maintained in the population even without selection

Question 24

Plasma R1 Segregation (salmonella plasmid containing antibiotic resistance)

Answer 24

1. parR binds to DNA on the plasma
2. parC (DNA sequence on the plasma) now we have the ParR-ParC complex
3. parM will attatch to the parR-parC complex and once both ends connect the actin filament will polymerize to push the two plasmids apart.

Question 25

Bacteria cell membrane

Answer 25

Contains the standard bilipid layer with a hydrophilic head and hydrophobic tails. Bacteria also have hopanoids which make the membrane less fluid like.

Question 26

10-20% of total cell protein is in cytoplasmic membrane

Answer 26

True for prokaryotes!

Question 27

Permeable barrier

Answer 27

Allows for transport of water, carbon dioxide, NH3, short/medium chained fatty acids, and small hydrophobic molecules. Site for electron transport chains to generate energy. Maintains a proton motive force!

Question 28

Is H+ concentration higher on the outside or inside?

Answer 28

Outside

Question 29

Active transport systems

Answer 29

Use the energy of an ion gradient or ATP Allow the accumulation of solutes within the cell to concentrations 100-1000x higher than in the surrounding fluid

Question 30

Facilitate Diffusion

Answer 30

A type of passive transport that does not require ATP to move solutes across the cell membrane. Relies on the natural kinetic energy of molecules and their concentration gradients.

Question 31

Example of Facilitated Diffusion

Answer 31

1. Glycerol is higher outside of cell. 2. Entry of glycerol into the cell will occur because the cell will try to maintain an equilibrium of glycerol concentration 3. The cell can use glycerol immediately which keeps concentrations of glycerol low inside the cell to promote glycerol uptake. Occurs through conformational change!

Question 32

What are the three families of energy-dependent transporters?

Answer 32

1. Simple Transport 2. Group Translocation 3. ABC Transporter They use ATP to power transport

Question 33

Simple Transport

Answer 33

Uses energy of the proton motive force or Na+ gradient to drive uptake or expulsion of another solute.

Question 34

Simple Transport (Symport)

Answer 34

The solutes enter the cell in the same direction

Question 35

Simple Transport (Antiport)

Answer 35

One solute enters the cell and another exits the cell.

Question 36

What to know about these porters?

Answer 36

The porters open and close off environments which force the solutes to move either into or out of the cell depending on concentration of the environment they are exposed to by the movement of the porter.