Microbiology Block B Lecture 1

Front 1

What is the half life of bacterial mRNA?

Back 1

About 2 minutes

Front 2

What is the half life of eukaryotes mrna?

Back 2

4-24 hours

Front 3

When are bacterial genes usually translated?

Back 3

Usually translated as mrna is being synthesised

Front 4

What is the general structure of bacterial gene?

Back 4

Back (Definition)

Front 5

What strand of DNA are genes on?

Back 5

Both but bias towards leading as it has continuous replication

Front 6

How are genes distributed on the chromosome?

Back 6

Generally evenly distributed

Front 7

Are introns rare in bacteria

Back 7

Yes

Front 8

What is an operon

Back 8

Cluster of protein coding open reading frames transcribed as a single mRNA

Front 9

How many bases are there usually between coding regions

Back 9

4-50 bp

Front 10

What does the control of a operon control?

Back 10

Expression of the entire function eg. Pathway

Front 11

What is transcription catalysed by?

Back 11

RNA polymerase

Front 12

What is transcription

Back 12

The copying of genetic information from its DNA repository (genome) in the functional RNA molecules, is catalysed by RNA polymerase (RNAP)

Front 13

What does bacterial RNAP do?

Back 13

Unwinds DNA tk for a transcription bubble containing ss non template DNA and the 8-9 No template DNA/ RNA hybrids

Front 14

What does RNAP do after forming transcription bubble

Back 14

Moves along the DNA while maintaining the transcription bubble until the end of RNA synthesis

Front 15

What replaces thymine in RNA

Back 15

Uracil

Front 16

Why is uracil not used in DNA

Back 16

It is easily degraded to cytosine

Front 17

What forms the main catalytic centre

Back 17

Beta and beta’ crab craw structure

Front 18

What do alpha^2 have a primary role in

Back 18

RNAP assembly

Front 19

What is the role of the sigma factor

Back 19

Determines promoter specificity

Housekeeping/ group 1 contain 2 domains one recognising -10 region and second -35 region

Front 20

What is -10 region

Back 20

Interact with an alpha helix in the protein

Front 21

What is -35 region

Back 21

Interacts with DNA via HTH motif, forming H bonds with DNA bases

Front 22

What does the housekeeping sigma factor help do

Back 22

Helps catalyse the opening of the DNA strands near the transcription start point initiation

Front 23

What are the three major phases of transcription

Back 23

Intimation

Elongation

Termination

Front 24

How does imitation occur

Back 24

Sigma factor interact with RNAP core forming holoenzyme

RNAP holoenzyme binds promoter and opens DNA duplex

Often synthesises short abortive transcription before correct promoter escape

Sigmas factor usually released and core RNAP continues to elongation

Front 25

What is RNAP role in elongation

Back 25

It moves akin the DNA maintaining transcription bubble until end of RNA synthesis

Front 26

What do elongation factors control

Back 26

Control the speed of RNAP by modulating pausing

Front 27

What is the error rate of elongation

Back 27

~10^-4 - 10^-6 error rate

Front 28

Where does mRNA synthesis terminate

Back 28

At the specific sequence at the end of genes

Front 29

What are anti terminator factors and what do they allow

Back 29

Allow RNAP to read through terminators

Front 30

What are the two types of anti termination factors

Back 30

Intrinsic terminators and Rho-dependent terminators

Front 31

What are intrinsic terminators

Back 31

Palindrome followed by poly u tract

Stem loop causes pause leading to dissociation of RNAP

Front 32

What are Rho-dependent terminators

Back 32

Require Rho protein

Front 33

What does Rho-dependent terminator do

Back 33

Rho binds specific sequences in the mRNA, moves down transcript until it contact the eloping RNAP

RNAL pauses at rho dependent terminator= termination

Front 34

How is gene expression is regulated at post translation

Back 34

Protein stability

Front 35

How is gene expression is regulated at translation regulation

Back 35

Translation initiation

Front 36

How is gene expression is regulated at post transcription

Back 36

mRNA stability

Front 37

How is gene expression is regulated at transcription regulation

Back 37

Transcription initiation

Front 38

What is a regulon

Back 38

The set of all genes regulated by a particular factor sigma or tf

Front 39

What is global regulation

Back 39

Genes in a regulon distributed throughout the genome

Front 40

What is the E.Coli Maria’s regulon

Back 40

A. Umber if operon involved in transport and utilisation of malting

Front 41

What is local regulation

Back 41

Bacteria often need to regulate just a few specific genes

Front 42

What do sigma factors do to RNA polymerase wh

Back 42

Give it its specificity

Front 43

What are the two major groups of sigma factor

Back 43

70 and 54

Front 44

What do transcription factors do

Back 44

Bind specific DNA sequences usually close to the promoter and modulate transcription

Front 45

What can tf allow for

Back 45

Positive control and negative control

Front 46

General principle for making gene deletions

Back 46

Remove or replace most or all of the coding sequence of a gene

Delete putative regulatory proteins and determine the effect in the phenotypes or gene expression

Front 47

How do you directly measure gene expression in bacteria

Back 47

Northern blots

Reverse transcriptase

(RT)-PCR

Microassays

RNA- seq

Front 48

What is the general principle for reporter gene fusion

Back 48

Expression of a protein with an easy to assay activity is used as a proxy for the expression kf a gene of interest

Front 49

Can you use lacZ as a selectable marker

Back 49

Yes

Front 50

General principle of reporter fusions lacZ

Back 50

Transcriptional or translation reports

LacZ can cleave chromogenic substrates

Front 51

How do you measure protein DNA interactions

Back 51

Vitro assay

Kinetics

Structure function studies