Gene Regulation

Are all genes expressed all the time? What is an example?

No and an example is sporulation genes

What is attenuation?

It is a mechanism to couple transcription to nutrient supply. It is a mechanism that causes premature termination of transcription

Would you make genes for amino acid biosynthesis if you already have amino acids?

No

Is attenuation a common mode of regulation for amino acid synthesis? What was it first worked out in?

Yes and in the trp operon

What does the leader sequence code for?

A peptide that functions as the attenuator

What happens if there is a lot of trp in terms of leader sequence? Low amount of trp?

Lots of trp: Make leader and transcription is halted

Low trp: Do not make leader and transcription goes ahead

What is attenuation similar to?

Transcription termination (information that alters the polymerase is in the mRNA)

What does the secondary structure of the mRNA dictate?

If a ribosome can read the message or if it stalls

Is transcription and translation coupled? Describe what happens. Does attenuation work via coupling?

Yes and this means that as the mRNA is being made a ribosome can jump onto it and start making a protein. Yes

What happens in factor independent termination?

There are inverted repeats that are high in G-C content which causes a hairpin structure to form in the mRNA. The single strands anneal to each other to form this secondary structure

Are there multiple start codons on the trp operon?

Yes

What happens when tryptophan is high in terms of gene regulation?

Region 3 pairs with region 4 and this structure terminates transcription.

What happens when tryptophan is low in terms of gene regulation?

Region 2 pairs with region 3 and this structure does not terminate transcription

What is the leader? Where is it located?

It encodes a short polypeptide and contains an attenuator sequence. It is located between the operator and the first trp gene

Does the attenuator encode a polypeptide? If no, what does it do?

No it does not but when transcribed into mRNA it has self complementarity regions and can form various hairpin structures

What happens once RNA Pol has began transcribing the operon? How many tryptophan residues are within the operon?

A ribosome can attach to the growing transcript and start translating the leader region. 2 tryptophan residues

What happens if there is plenty of tryptophan around?

The ribosome won’t have to wait long for a tRNA carrying tryptophan causing translation to finish quickly. This causes the ribosome to fall off after translating the leader sequence. It also causes the terminator hairpin to form which makes RNA polymerase fall off and transcription is terminated.

What happens if there is low levels of tryptophan?

The ribosome will stall at the trp codons because it is waiting for a trp carrying tRNA. There will be slow translation of the leader sequence. This favours the formation of the anti terminator structure (non-terminating hairpin) which prevents the terminator structure from forming and transcription can continue.

Why are tryptophan codons important?

This is because it ties the availability of tryptophan in the environment to an event

What are repressors?

They are proteins that bind to specific DNA sequences called operators.

What do repressors block? What is this similar to?

Binding of RNA polymerase to the promotor. Similar to steric hinderance.

What is the ability to bind DNA regulated by? What are examples of these?

Cofactors such as sugars or other metabolites

How many genes are encoded in the trp operon? Is it polycistronic?

Four and yes

What is LacZ? What is the function?

B-galactosidase and it cuts disaccharide lactose into glucose and galactose

What is LacY? What is its function?

Permease and it lets lactose into the cell

What is LacA?

B-galatosidase transacetyl

What is LacI?

The repressor

What is P?

The promotor

What is lactose?

The inducer

What is IPTG?

It is an artificial inducer and it is an artificial form of lactose

What is the nomenclature for genes? Proteins?

Genes: Lower case and italicized (lacZ)

Protein: Upper case (LacZ)