PCB3020 Final Part II

Fall 2026 Dr. Daughdril

How do Transcription factors control gene expression?

By promoting or inhiiting RNA polymerase binding

What is an operon?

An operon is a cluster of genes that get transcribed by one promoter to create one long mRNA strand

Describe the Trp repressor

When the Trp repressor has bound Trp, indicates high Trp levels, Trp repressor binds to operator, RNA polymerase blocked, NO Transcription

When the Trp repressor has no bound Trp, indicates low Trp levels, Trp repressor not bound to operator, RNA polymerase not blocked, Transcription occurs

The Trp repressor can only bind to DNA if it also has Trp bound

Describe the CAP activator

cAMP not bound to CAP, CAP is not bound to DNA at CAP binding site, NO Transcription

cAMP bound to CAP, CAP is bound to DNA at CAP binding site, Transcription occurs

Describe the Lac operon

Low glucose, Creates cAMP, cAMP activates CAP, CAP binds to DNA, Trnascription occurs

High Lactose, Creates allolactose, allolactose binds to Lac repressor, Lac repressor dettaches from DNA, Transcription occurs

What are enhancers in eukaryotic cells and why are they special?

They are DNA sites that eukaryotic gene activators bind to so they can enhance the ratre of Transcription

They are special because they can affect the DNA from thousands of nucleotides away

What are the two chromatin modifying proteins and what do they do? What do they have in common?

Histone Acetyltransferases: Promotes attachment of acetyl groups to Lys residues on the tail of histone proteins, which in turn, attract proteins that promote transcription

Chromatin Remodeling Complexes: Makes DNA more accessible

Both work to enhance the efficiency of Transcription initiation

Define combinatorial control

Describes how groups of Transcription regulators work together to regulate the expression of a single gene. For example: Lac operon

Losing essential proteins may not be disastrous, but it will usually reduce efficiency

What 3 Transcription factors can make a fibroblast into a pluripotent stem cell? What is the significance of a pluripotent stem cell?

Oct4, Sox2, and Klf4

Pluripotent stem cells are able to become any type of cell

What do micro RNA’s do? How do they form?

mRNA’s direct the destruction of target mRNA’s

They do this by first being transcribed and then released into the cytoplasm as a double stranded intermediate

It forms a the RISC complex with a RISC protein

the RISC complex searches for a segment of mRNA with a match to the miRNA to degrade it

Describe the process of GCPR’s

The GCPR is a transmembrane receptor made up of 7 alpha helices. When an extracellular ligand binds to it, the GCPR binds to the G protein

When the GCPR binds, it causes a conformational change in the G protein. This change decreases the affinity for GDP and exchanges it for GTP on the Alpha subunit.

When GTP is bound the Alpha subunit seperates from the Beta Gamma subunits and each is now activated

Describe the process of Adenylyl cyclase

GCPR cascade

Alpha subunit activates Adenylyl cyclase

Adenylyl cyclase converts ATP to cAMP

cAMP activates a protein kinase

Protein kinase phosphorylates CREB

CREB activatse Transcription

Describe the process of Inositol Triphosphate and Diacylglycerol

GCPR cascade

Alpha subunit activates Phospholipase C

Phospholipase C cleaves a Inositol Phospholipid into Inosital Triphosphate (IP3) and Diacylglycerol

IP3 opens a Ca2+ channel in the ER

Ca2+ and Diacylglycerol bind to Protein Kinase C (PKC)

(PKC) activates targets downstream

Describe the process of RTK’s

RTK’s are single pass transmembrane proteins. When an extracellular dimer binds to the RTK’s, the RTK’s phosphorylsate each other which activates them

The activation of hte RTK’s recuits other intracellular proteins to bind to form a signaling complex

Describe the process of Ras

RTK cascade

One of the Intracellular proteins that binds is called Grb2

Grb2 has two SH3 domains that bind to Ras GEF which promotes the exchange of GDP for GTP on the Ras protein, activating it

Activated Ras activates downstream targets

Describe the process of MAP

RTK cascade and Ras cascade

Ras activates MAP Raf

MAP Raf activates MAP Mek

MAP Mek activates MAP Erk

MAP Erk activates other transcriptional regulators downstream

What do Mitogen Activated Protein Kinases do?

Stimulate cell division

Describe the process of Mitogen Stimulation of Cell Cycle Entry

Mitogen binds to a Mitogen Receptor

Mitogen Receptor activates Ras

MAP cascade to cause transcription of the gene that encodes the Myc protein

Myc Protein amplifies the genes that activates G1 - CDK’s, more specifically, the Cyclin D - CDK4

Cyclin D - CDK4 phosphorylates the Rb protein family

This causes a E2F protein to be activated

E2F activates transcription of Cyclin E and Cyclin A, also leads to S - phase gene transcription

Cyclin E and Cyclin A enhance Rb protein phosphorylation which causes a positive feedback loop

Describe the process of PI3

RTK cascade

An intracellular proteins that binds to the signaling complex is the PI3 Kinase

PI3 Kinase phosphorylates Phospho Inisotides

Phospho Inisotides serve as docking sites for PDK1 and Akt

PDK1 gets activated by binding to the Phospho Inisotides, Akt gets activated by PDK1 and mTOR

Activated Akt disassociates from the plasma membrane and phosphorylates Bad protein

Bad protein releases an apoptosis inhibitory protein which inhibtis apoptosis