Bacterial growth and cell division

Question 1

what is the structure of the bacterial chromosome like ?

Answer 1

Bacterial DNA is not structured its simple and not organised into chromatins or histones

• DNA is supercoiled and not uniformly associated with proteins
• circular DNA, no nuclease
• DNA is organised into domains by scaffold proteins in nucleoid

Question 2

what are scaffold proteins ?

Answer 2

non-uniform proteins

Question 3

what are some of the other proteins that are bound to DNA ?

Answer 3

• RNA polymerase
• transcriptional regulators
• small DNA binding proteins, H-NS, HU, IHF (and others)

Question 4

how is DNA looped into hoops ?

Answer 4

by domain proteins

Question 5

what does supercoiling do to the loops ?

Answer 5

it turns the open loops into wound up compact loops

Question 6

how many kilo bases is the E. coli chromosome?

Answer 6

4.6 x 10^4 kilobases

Question 7

what is the difference between a plasmid and a chromosome ?

Answer 7

• chromosome is covered with protein where as plasmid is not
• plasmids are used as gene carriers where as chromosomes are not

Question 8

for a cell to recognise it has to be replicated, what does every DNA molecule need to have ?

Answer 8

an origin of replication = oriC

Question 9

what is oriC ?

Answer 9

a gene that says this DNA needs to be copied

Question 10

what binds to oriC ?

Answer 10

DnaA

Question 11

what is DnaA ?

Answer 11

it is an initiating protein which then attracts other proteins required for DNA replication

Question 12

what is the origin of replication called in plasmids ?

Answer 12

oriV

Question 13

what is the role of primase in the initiation step of DNA replication ?

Answer 13

synthesises RNA primer

Question 14

what enzyme is DNA replication carried out by ?

Answer 14

DNA polymerase III

Question 15

what happens once DNA is extended from the primer ?

Answer 15

DNA Pol I removes RNA

Question 16

in what direction does DNA replication proceed ?

Answer 16

5’ to 3’ direction on both strands

Question 17

is leading strand DNA synthesis continuous or discontinuous ?

Answer 17

continuous

Question 18

as leading strand DNA synthesis is continuous what enzyme is it carried out by ?

Answer 18

DNA polymerase III

Question 19

is lagging strand continuous or discontinuous ?

Answer 19

it’s discontinuous

Question 20

what enzyme are Okazaki fragments made by ?

Answer 20

DNA Pol III

Question 21

what does DNA polymerase I do ?

Answer 21

• extends ends of Okazaki fragments until adjacent RNA primer reached
• 5’ to 3’ exonuclease activity of DNA pol I removes RNA primer
• DNA pol I fills gaps between Okazaki and uses 3’ - 5’ exonuclease activity (proofreading function) to correct errors

Question 22

what does DNA ligase do in the lagging strand during initiation ?

Answer 22

DNA ligase joins the fragments

Question 23

what is the role of helices in the replication fork ?

Answer 23

helices unwinds the dsDNA ahead of the replication fork

it opens it out to help primases and DNA polymerases to get in

Question 24

what is the role of SSB (single-stranded binding protein) ?

Answer 24

it keeps unwound strands apart

Question 25

DNA replication is bidirectional. what does this mean ?

Answer 25

it moves away from the centre

Question 26

what happens in the elongation step of DNA replication ?

Answer 26

- DNA replication occurs at the centre of the cell by a complex of proteins = replisome - proceeds at a constant rate irrespective of growth conditions - once replication begins, it continues until the end and does not require additional protein synthesis

Question 27

what happens in the termination step of DNA replication ?

Answer 27

- the two replication forks meet at the terminus (terC) - a termination protein (Tus) is bound to terC region - terC is flanked by DNA sequences that form structure that block progression of replication fork

Question 28

how does the ter structure slow the replication forks down ?

Answer 28

Ter has a special DNA sequence either side of it that form structures that slows the replication fork down

Question 29

where does all DNA replication occur ?

Answer 29

All DNA replication occurs at centre of cell = Replisome

Question 30

what is partitioning ?

Answer 30

partitioning separates chromosome into two daughter cells

Question 31

what is the Z-ring ?

Answer 31

it is the first ring of protein that starts the separation of the two cytoplasms

Question 32

what happens to the origin and terminus when DNA replication is initiated ?

Answer 32

the origin and terminus is in the centre

Question 33

what are the 6 protein subunits of the RNA polymerase holoenzyme ?

Answer 33

- core enzyme (5 subunits) | - sigma factor

Question 34

where does the sigma factor bind and what does it do ?

Answer 34

the sigma factor binds to the -10 and -35 sequences in bacterial promoters and identifies the beginning of a gene

Question 35

what are the role of regulatory proteins ?

Answer 35

they control binding RNA Pol to promoters

Question 36

what does -10 refer to ?

Answer 36

-10 refers to 10 bases before transcription starts

Question 37

what are the 3 phases of translation in bacteria ?

Answer 37

- initiation - elongation - termination

Question 38

what happens in initiation ?

Answer 38

binding of ribosome to mRNA

Question 39

what happens in elongation ?

Answer 39

- movement of ribosome along mRNA | - synthesis of polypeptide

Question 40

what happens in termination?

Answer 40

- release of mature polypeptide | - recycling of ribosome

Question 41

what are the two subunits of prokaryotic ribosomes ?

Answer 41

50S and 30S

Question 42

which ribosome subunit binds first ?

Answer 42

30s binds first | - IF3 (initiation factor 3) binds to 30s unit and prevents binding to 50s

Question 43

what is the name of the tRNA that can enter the P site ?

Answer 43

fmet-tRNAmet

Question 44

what does the fmet-tRNAmet do ?

Answer 44

it binds to 30s at p (peptidyl) site | - it requires IF-2 and GTP

Question 45

what is IF-1 (initiation factor 1) required for ?

Answer 45

it binds the 30s + fmet-tRNA stably to mRNA

Question 46

what are the 3 sites on the ribosome ?

Answer 46

exit site peptidyl site amino acyl site

Question 47

when does termination occur in prokaryotic protein synthesis ?

Answer 47

when STOP codon is in A site | - requires specific release factors to cause dissociation of ribosome complex

Question 48

what are the different stop codons recognised by protein RF (release factors) ?

Answer 48

- UAA (ochre) - UAG (amber) - UGA (opal)

Question 49

what is the release factor that recognises UAA ?

Answer 49

RF1/RF2

Question 50

what is the release factor that recognises UAG ?

Answer 50

RF1

Question 51

what is the release factor that recognises UGA ?

Answer 51

RF2

Question 52

what is the strongest stop codon ?

Answer 52

UAA

Question 53

at what site on the ribosome do RFs act at ?

Answer 53

site A

Question 54

what is it called when multiple ribosomes bind to one transcript ?

Answer 54

polyribosome | - result in multiple copies of the new protein being produced from one RNA molecule

Question 55

what happens during cytokinesis ?

Answer 55

the nucleoid and cytoplasmic contents have to be divided between the two daughter cells

Question 56

what happens to FtsZ when GTP is bound to it ?

Answer 56

it forms straight filaments | straight chains fo FtsZ

Question 57

what happens when GTP is hydrolysed to GDP ?

Answer 57

introduces a curvature (curves)

Question 58

how do coccoid bacteria divide in comparison to rod shaped bacteria ?

Answer 58

coccoid bacteria can divide in one plane or many where as rod shaped bacteria can only divide in one plane