Microbial Gene Expression And The Central Dogma (part 3)

Question 1

Expression of genes is an ________________ intense process (especially for __________________).

Answer 1

Energy
Prokaryotes

Question 2

What is spent during the expression of genes in prokaryotes?

Answer 2

1 nucleotide triphosphate (ATP, GTP, CTP, UTP) spent per nucleotide of RNA during transcription

2 GTP spent per amino acid in a protein during translation (elongation process)

Question 3

Microbes typically have _______________ of genes, but only a ______________ f them need to be expressed at any given moment.

Answer 3

Thousands
Small subset

Question 4

What are used to increase or decrease the rate of transcription or translation? Give an example

Answer 4

Environmental signals.
E.g genes that metabolize the sugar, lactose, are only produced when lactose is present in the environment

Question 5

Certain types of genes are always expressed regardless of the environmental signals. What are they called and and what is their control system called?

Answer 5

Housekeeping genes

Constitutive gene expression

Question 6

Explain inducible and repressible genes. They are a form of _____________________ that controls most genes.

Answer 6

Inducible genes: typically not expressed but their expression can be activated by environmental signals.
Repressible genes: typically expressed but their expression can be inhibited by environmental signals.

Regulated expression

Question 7

What are the 2 types of regulated gene expression systems?

Answer 7

1. Transcriptional controls are systems that induce or repress the rate of transcription of a gene into mRNA
2. Translational controls are systems that induce or repress the rate of translation of an mRNA into a protein.

Question 8

Most types of transcriptional controls depend on the use of proteins called ______________________. Which work by enhancing or disrupting the ______________________ of transcription.

Answer 8

Transcription factors

Initiation

Question 9

Initiation of transcription depends on a complex interaction between what 2 things?

Answer 9

Sigma factor and RNA polymerase at the gene’s promoter.

Question 10

How can transcription factors increase and decrease transcription of a gene?

Answer 10

Increase by enhancing and stabilizing the interaction between the sigma factor and the RNA polymerase. (Transcriptional activators)
Decrease by inhibiting and destabilizing the interaction between the sigma factor and the RNA polymerase. (Transcriptional repressors)

Question 12

How do transcriptional activators stabilize RNA polymerase?

Answer 12

By binding to activator binding sites upstream of the promoter.

Question 13

How do transcriptional repressors destabilize or block RNA polymerase?

Answer 13

By binding to operator sequences that are downstream or overlap with the promoter.

Question 14

What is the trp operon and example of? (2 things)

Answer 14

Transcriptional control and a repressible genes.

Question 15

What is the trp operon partially regulated by?

Answer 15

A protein called the trp repressor, which is made by a separate gene elsewhere on the chromosome.

Question 16

What does the trp repressor bind to when active? What is it downstream of?

Answer 16

The trp operator and the promoter, which is where the sigma factor binds.

Question 17

Under what conditions is the trp operon activated?

Answer 17

When there is little or no tryptophan.

Question 18

What do low levels or tryptophan mean?

Answer 18

None is available to bind to the repressor. Without tryptophan bound to it, the repressor is inactive and unable to bind to the operator. As long as the repressor is inactive, transcription is initiated and trp genes are made into mRNA and proteins.

Question 19

What happens when there is lots of tryptophan in the environment?

Answer 19

The trp operon will be repressed and the amino acid tryptophan will bind to the trp repressor and activate it. As long as tryptophan is attached to the repressor, the repressor can bind to operator and block transcription initiation.

Question 20

Because the binding of tryptophan is required for repression, what is tryptophan itself called?

Answer 20

A co-repressor

Question 21

What is leakage expression?

Answer 21

When some mRNA still gets made after a repressor blocks transcription.

Question 22

The lac operon is an example of what 2 things? What does it encode?

Answer 22

Transcriptional controls and an inducible gene.

Encodes 3 enzymes needed to metabolize lactose as a source of carbon.

Question 23

The lac operon uses a combination of both _____________________ and __________________.

Answer 23

Transcriptional activation and repression.

Question 24

What is the activator binding site on the map labeled for the lac operon?

Answer 24

CAP Site

Question 25

What happens when the lactose levels are low?

Answer 25

The lac operon is repressed.

Question 26

What happens in the absence of lactose from the environment?

Answer 26

Lac repressor is active and binds to the operator sequence which blocks the ability of RNA polymerase to bind to the promoter. When repressed, very little mRNA is made.

Question 27

What happens to the cells of E. Coli in the repression conditions?

Answer 27

The cells only have 3 molecules of each lac operon protein due to leakage expression.

Question 28

What happens when lactose levels are high in the environment?

Answer 28

The lac operon is partially induced.

Question 29

What happens to some lactose in microbial cells?

Answer 29

Some is converted into a similar molecule called Allolactose.

Question 30

What does Allolactose bind to?

Answer 30

It binds to the lac repressor, making the repressor inactive and unable to bind to the operator. As long as the Allolactose is attached to the repressor, RNA polymerase can initiate transcription.

Question 31

What is needed to fully induce transcription of the lac operon? What do heterotrophic cells prefer?

Answer 31

A second protein, catabolite activator protein (CAP) , which is only active when glucose levels in the cell are low. Glucose

Question 34

Operon like lac are only fully induced if the cell does not have enough ________________.

Answer 34

Glucose

Question 35

What happens when glucose levels are low?

Answer 35

CAP becomes a transcriptional activator of the lac operon.

Question 36

What does the binding of CAP to the DNA CAP site do?

Answer 36

Stabilizes RNA polymerase and increases the transcription of lac genes.

Question 37

What is Arabinose? What is the abbreviation/name of the Arabinose operon?

Answer 37

Arabinose is a sugar that can be metabolized by feeding it into the pentose phosphate pathway (PPP). (ara)

Question 38

What is unusual about Arabinose?

Answer 38

It can be both repressed and activated by the same protein called AraC.

Question 39

What does the AraC bind to? (2)

Answer 39

2 DNA sequences: 1. The araO2 sequence is the operator sites 2. The araI sequences are the inducer sites

Question 40

What happens when Arabinose is absent?

Answer 40

The operon is repressed and the AraC proteins will bind together across the operator and inducer. This causes the DNA to physically loop around the gene (steric effects).

Question 41

What does the DNA loop of AraC proteins do?

Answer 41

Interferes with RNA polymerase binding and prevents transcription. It also blocks access to the Arabinose promoter (ParaBAD)

Question 42

What is special about the repression mechanism of the Arabinose operon? What is it often used in?

Answer 42

Has a very low leakage expression. Used in genetically engineered plasmids like pGLO

Question 43

What happens when Arabinose is present?

Answer 43

The operon is partially induced.

Question 44

What does Arabinose bind to?

Answer 44

The AraC proteins which changes the way they interact with each other.

Question 45

Once Arabinose is bound to AraC, what happens?

Answer 45

AraC proteins dimerize and bind only to the inducer sites, which stabilizes RNA polymerase and increases transcription of the operon.

Question 46

What is the ara operon fully induced by?

Answer 46

Activated CAP protein.

Question 47

When is the maximum amount of expression of the ara operon?

Answer 47

When Arabinose levels are high and glucose levels are low.

Question 48

What can interrupt transcription elongation? And what is the mechanism of interruption called?

Answer 48

Some types of transcriptional controls. Transcription attenuation

Question 50

In addition to its repressor that regulates initiation of transcription, the_________________ is also regulated during elongation.

Answer 50

Trp operon

Question 51

What is the regulation of the trp operon during elongation due to?

Answer 51

A special sequence in its leader (labeled trpL) called the attenuator.

Question 52

What can the attenuator do? What does it help?

Answer 52

It can interrupt transcription if tryptophan levels are high. Mechanism is one way to deal with the problem of leak expression.

Question 53

The attenuator consists of 4 ________________ that can base pair with each other to form _____________________.

Answer 53

RNA sequences Stem loop structures

Question 54

What does the first sequence of the four RanA sequences of the attenuator contain?

Answer 54

2 codons for tryptophan

Question 55

What must happen for the transcription of trp? What happens if it doesn’t?

Answer 55

Sequences 2 and 3 of the attenuator must form a stem loop, called the anti-terminator loop. Sequences 3 and 4 will form a stem loop instead called the terminator loop, which terminates transcription.

Question 56

What is a key fact to remember when thinking about the transcription attenuation?

Answer 56

Is that in microbes, mRNA molecules are translated by the ribosome while they are still being transcribed by RNA polymerase. This means that the ribosome can potentially interact with the RNA polymerase.

Question 57

What happens if tryptophan levels are low?

Answer 57

The cell needed to express the trp operon to make tryptophan. In this case, the ribosome that is translating the mRNA becomes stalled at the tryptophan codons in sequence 1.

Question 58

Why does the mRNA become stalled is tryptophan levels are low?

Answer 58

There won’t be enough tryptophan tRNA to quickly translate the leader so the ribosome stops while it waits for tryptophan tRNA.

Question 59

What does stalling of the ribosome allow?

Answer 59

Sequences 2 and 3 to form the anti-terminator loop and the elongation of the mRNA continues and trp proteins get made.

Question 60

What happens if tryptophan levels are high?

Answer 60

The cell needs to repress trp and the ribosome that is translating the mRNA does not stall a the the tryptophan codons in sequence 1.

Question 61

Why does the ribosome that is translating the mRNA not stall?

Answer 61

Because the tryptophan levels are high and there is plenty of tryptophan tRNA, so the ribosome keeps translating the leader. This blocks the formation of the 2-3 loop and we get the 3-4 terminator loop formation instead.

Question 62

What does the terminator loop do?

Answer 62

Will pull the mRNA out of the RNA polymerase exit port and results in transcription terminator.