Molecular Bio Final Alphabet Soup "Gene Regulation"

Made this to help study those pesky proteins and RNAs that can get confusing with all the acronyms and what they do. I definitely added more than what would be tested, but can never be too careful. Hope it helps.

What do activators tend to do in prokaryotes?

Enhance RNA polymerase binding

What do repressors tend to do in prokaryotes?

Block RNA polymerase binding

What does it mean for regulators to work through allostery?

They work by binding to a site other than the active site on the enzyme

What is an operon?

a unit of genetic material that functions in a coordinated manner by means of an operator, a promoter, and structural genes that are
transcribed together

What is the lac operon

An operon containing the necessary genes for lactose metabolism

What is lacZ and what does it do?

Encodes β-galactosidase, which can metabolize lactose. It is only activated in the presence of lactose.

What is CAP and what does it do?

Catabolite activator protein/cAMP receptor protein is an activator that binds upstream of the lac promoter to facilitate RNA polymerase.

What does the lac repressor do?

It binds to the lac operator within the promoter and blocks RNA polymerase from binding.

What is allolactose and what does it do?

Allolactose is made from lactose and is the actual ligand that binds to lac repressor allosterically to remove it from the operator.

What is cAMP and what does it do in the lac operon?

Cyclic-AMP levels are inverse to glucose levels, and so when glucose is low, there is more cAMP that can allosterically bind to CAP to activate it

What happens in a glucose +, lactose + exactly?

Lacctose is present, so lac repressor is removed, but CAP is not present to enhance transcription due to low levels of cAMP. So expression is not inhibited, but its not enhanced either.

What happens in a glucose +, lactose - exactly?

No lactose is present, lac repressor inhibits RNA polymerase binding, no transcription.

What happens in a glucose -, lactose + exactly?

Lactose is present, so allolactose can bind to repressor to allow transcription, and low glucose means that cAMP is present to activate CAP and enhance transcription.

What is NtrC and what does it do?

Nitrogen Regulatory Protein C is an allosteric activator of RNA Polymerase for genes like glnA in response to nitrogen levels

What is NtrB

Nitrogen Regulatory Protein B in response to low nitrogen levels phosphorylates NtrC causing NtrC to reveal its DNA binding domain and activate RNA polymerase

What is σ54 and what does it do?

Sigma factor 54 binds promoter with RNA polymerase and makes contact with the NtrC activation domain

What activity of the NtrC allows for RNA polymerase activation and how?

ATPase activity provides energy to swap from a closed to open complex, activating the RNA polymerase.

How far away from the promoter can NtrC work?

Up to 2 kb away

What is MerR and what does it do?

Mercury regulatory protein activates transcription of MerT in the presence of mercury (Hg+)

What is MerT and what is unique about its promoter?

MerT encodes the gene responsible for mercury resistance and its promoter has 19 bp between the -10 and -35 sequences.

What happens with MerR and MerT when there is low Mercury?

MerR stays bound to the promoter and blocks transcription of MerT

What happens with MerR and MerT when there is high Mercury?

Binding of Hg+ induces a conformational change in MerR that twists the DNA, bring the promoter into view and moving itself out of the way to allow for transcription.

What is the araC/AraBAD operon and what does it do?

Arabinose protein operon encodes enzymes required for arabinose metabolism.

What are araI and what do they do?

AraI are inhibitory sequences before the promoter that are bound to by araC to determine the activity of the araBAD operon.

What is araC and what does it do?

araC proteins bind at araI sequences to either bend DNA and prevent transcriptions, or straighten it to activate transcription of the araBAD operon

What happens in a glucose-/arabinose+ environment?

AraC proteins bind araI₁ and I₂ together and recruit the RNA polymerase

What happens in an arabinose- environment?

AraC bind araI₁ to another more upstream sequence called araO₂ that causes the DNA to bend and prevent RNA polymerase activation.

What are enhancers in eukaryotes?

groups of binding sites often located far from gene that further increase transcription activity

What are insulators in eukaryotes?

block activation of some promoters by certain enhancers

What are GTF’s and what do they do?

General Transcription Factors provide enough to activate basal transcription in eukaryotes

What do activators do in eukaryotes?

increase transcription

Why are activators important for metabolic enzymes?

Can result in 1,000 fold upregulation of the gene

What is Gal4 and what does it do?

It is an example of an activator that activates sequences for GAL1, which encodes an enzyme for galactosidase to metabolize galactose

What are homeodomains?

DNA binding domains of regulatory proteins in all eukaryotes recognized by a helix-turn-helix pattern

What are examples of a Zinc binding domain?

Zinc finger/cluster, domains with Cys/His amino acids to grab zinc, TFIIIA, and the Glucocorticoid receptor

What are leucine zippers and what do they do?

They are structural motifs of regulatory proteins that help them to dimerize and bind to DNA.

What do the different helices in the helix-loop-helix structural motif of leucine zippers do?

Long helix for DNA binding, shorter helix for dimerization or other structural change for function

What is the HMG Box and what does it do?

It’s a structural motif of 3 helices in a boomerang shape that aids in DNA bending and other structural factors

What is the SRY gene and what does it do?

The Sex-determining region Y is a gene that leads to testosterone production

What binds to the SRY gene upstream to activate testosterone production?

HMG factor

Why does TFIID bind more readily to acetylated nucleosomes?

It contains bromodomains

How do insulators act in transcriptional silencing?

They can modify chromatin, marking boundaries between hetero- and euchromatin. These boundaries can prevent silencing of genes surrounded by heterochromatin

What is synergistic regulation?

Multiple activators working to activate
transcription of a gene via co-recruitment of a single
necessary component, individual recruitment of multiple necessary components, or cooperative binding of activators

What is an example of synergistic regulation?

Regulation of the HO gene

What is the HO gene?

A yeast gene related to budding that requires two activators to initiate transcription

What is SWI5 and what does it do?

It is one of the activators necessary for transcription of the HO gene and binds ~1kb upstream of gene to recruit Histone Acetyltransferases(HAT) and remodeling complexes. This also reveals SBF sites

What is SBF and what does it do?

This is the second activator required for transcription of HO gene and it binds to SBF sites adjacent to the promoter to recruit mediator and RNA polymerase

What is combinatorial control?

Control of gene expression requiring presence or absence of a particular combination of regulatory proteins

True or false? In higher organisms, very few genes are controlled by 1 signal.

True

What are 4 ways that eukaryotic repressors can function?

1. binding near promoter and interfering with activator

2. interfere with activators’ active site

3. inhibit transcription initiator

4. nucleosome modification

What is the most common way eukaryotic repressors function and what enzyme is involved?

Nucleosome modification with histone deacetylases (HDAC)

What is signal transduction?

Any process by which a cell converts one
kind of signal or stimulus into another, often in response to external stimuli.

What is STAT?

Signal transducer and activator of transcription

What is SH2?

Src homology domain 2 is a variable domain of STAT allowing different STATs to target different genes

What is a cytokine?

An intercellular signaling molecule

What is an example of signal transduction?

Ras/MAPK

What is the Ras/MAPK cascade and what happens in it?

Upon a binding of a signal molecule, GDP-GTP exchange induces conformational change in Ras leading to mitogen activated protein kinases (MAPK) to pass phosphoryl groups onto transcription factors that will enter the nucleus and change activate transcription.