The ONE (Regulation of Gene expression) 63

As complexity of the organism increase what happens to genome size?

increases via teh addition of DNA sequence that functions in the regulation of the cording region(genes)

Constitutive Gene expression

housekeeping genes

Regulated gene expression

- Inducible genes

- Repressible genes

Promoters

Sites in the DNA sequence at which RNA polymerase bind.

How are sequences of promoters in prokaryotes different from eukaryotes?

Prokaryotes are consistent whereas in eukaryotes, the sequence can vary at a greater rate

RNA mediated regulation

Long, noncoding RNA (lncRNA) are transcribed RNA sections that do not code for any translatable genes. The purpose of lncRNAs have been shown to be involved in a number of transcriptional gene regulation processes.

Protein mediated regulation: Specificity factors.

Proteins that alter the specificity toward a given promoter or series or promoters.

Repressor/Activator

Proteins that impede or enhance (respectively) the interaction of the RNA polymerase and promoter

Repressors

Binds at a site near the promoter (operatory) or blocks movement of polymerase to impede transcription, this is referred to as NEGATIVE REGULATION

(think gene starts ON, then is "turned off")

Enhancers

Bind to a site similar to repressors, but binding is enhanced. Most often enhancers are used to increase affinity between RNApol ad DNA. This is referred to as POSITIVE REGULATION

(think gene is on, then TURNED MORE ON (Overdrive))

Protein Regulation- Specificity factors:

Proteins that alter the specificity to a given promoter or set of promoters.

Protein Regulation- Repressors/Activators:

Proteins that impeded or enhancer (respectively) the RNA polymerase-promoter interactions.

Protein DNA Binding Domains- Helix-turn-Helix domain

Important in binding DNA in bacteria and eukaryotes have a similar motif. Proteins is sequence speocific and interacts with the major groove of the DNA molecule.

(Lac repressor employs this motif)

Protein DNA Binding Domains- Zinc Finger:

Small domain stabilized through coordination of a Zn^2+ ion. This motif is predominately found in eukayotes. Although zinc finger motifs weakly intercat, most proteins utilize multiple Zn finger motifs to increase interactions with DNA.

(think it is to increase interactions with DNA using Zn^2+ ion)

Used in regulation of Myt1L protein.

Protein DNA Binding Domains- Homeodomain:

Domain in transcriptional regulators, especially during eukaryotic development.

(Important in binding DNA)

Hox gene cluster important in vascular remodeling, angiogenesis and disease.

Protein DNA Binding Domains- RNA Recognition Motif

Important in recognition of RNA and have the ability to bind DNA. When binding DNA transcription can be induced whereas when recognition of variable RNA structure the can alter the effect.

Dabble in multiple regulatory processes.

Leucine Zipper

Composed of leucine residues on the hydrophobic face of an a-helix. The hydrophobic faces interact with each other with high concentration of basic (+) residues to interact with the DNA backbone.

Helix-LOOP-Helix

Domain occurs in some eukaryotic regulatory proteins implicated in the control of gene expression during development of multicellular organisms.

(associated with muscle differentiation)

Cereblon E3 ligase modulators

Class of anticancer drugs associated with hematological malignancies

Regulation of Gene Expression in Prokaryotes- Lac operon

the site of regulation and expression of enzymes important in using lactose as a alternative source or energy (as apposed to glucose).

Operon

Site of multiple genes that are expressed together (bacteria) to regulate an environmental modification.

What negatively regulates the lac operon in prokayotes?

repressors protein

What positively regulates the lac operon in Prokaryotes?

cAMP and CAP

High glucose, low cAMP, and if lactose absent?

No gene expression

Glucose low, cAMP high, lactose absent?

No gene expression

Glucose high, cAMP low, lactose present

Low level of gene expression

Glucose low, cAMP high, lactose present

High levels of gene expression

Trp molecule

signal that tells the repressor to either block the RNA Polymerase (OFF) or stay out of the way (ON).

Attenuation

Ability to slow or "fine tune" the translation of the trp operon enzymes due to the varying [trp].

what does [TRP] create?

differences in the transcription vs translation speed differenced that halt the production according to availability.

Regulons

set of genes under the same repressor

RNA (trans)

RNA can bind either as a sRNA to exhibit regulation of another mRNA (Trans)

The requirement of the hfq enzyme to support binding between the RNA & RNA is required

RNA (Cis)

Exhibit regulation of itself via riboswitches (cis).

what are Riboswitches?

A riboswitch is a UTR of the mRNA that has the ability to change conformation upon binding a specific molecule (1:1

Ribosomal proteins

Required components of an active ribosome. In the situations of growth, ribosome activity increases, but in the amount of ribosomes present NOT increase in the activity of present ribosomes.

What happens if we increase the about of ribosomes present?

NOTHING

R-proteins operons are?

Feedback regulated to ensure that the amount of r-protein matches rRNA. The r-protein affinity plays a role in regulation of transcription of their operons.

what is gene recombination?

A means of gene regulation. Moving the promoter region from a given gene will suppress the respective gene.

Gene recombitorial regulation

Ensure they are not continuously recognized by host immune system.

What is the difference between Prokaryotes and eukaryotes in transcriptional regulation?

Result of how the DNA is processed and the biomolecules that can interact with the DNA

What is the difference between Prokaryotes and eukaryotes in Translational?

Translational modifications are more prominent due to localization of transcription in reference to translation

Eukaryotic Gene Regulation- Promoters are restricted by?

Restricted by chromatin structure, activation of transcription is associated with changes in structure.

Eukaryotic Gene Regulation: Positive Regulation

More common in Eukaryotes than Prokaryotes

Eukaryotic Gene Regulation: LncRNA

Plays a large role in transcriptional regulation

Eukaryotic Gene Regulation: machinery?

larger and more complex regulatory machinery

Eukaryotic Gene Regulation: Separation:

Easier translational regulation