Am I cooked?

Negative Numbers ( -100, -1000)

Positions Upstream of the start site

diffeential gene regulation

Cells of different tissues express different sets of genes

Why does transcription initiation in eukaryotes require numberous proteins and allosteric changes?

Assembly of the transcription complex requires multiple proteins (activators, coactivators, RNA Pol II, GTFs) and allosteric changes that allow them to properly bind each other and DNA, ensuring efficient transcription initiation

transcription initiation complex

exists to assemble proteins at the promoter to position RNA polymerase and unwind DNA

Enhancer

DNA sequence that increases transcription when bound by activators.

Where are enhancers found?

Upstream, downstream, or within introns-- or far from gene

"Action at a Distance"

Enhancers affect transcription from far away via DNA looping

"Upstream"

Region before the transcription start site.

"Downstream"

Region after the transcription start site.

+1

transcription start site

Cell Differentiation

Cells becoming specialized for structure & function; occurs during embryonic development and can continue into adulthood

positive feedback loop

Some Transient Signal turns on expression of protein A, making transcription factor activate its own gene. Once its on it continues to be produces even after initial signal is gone. This memory allows cell to remember its identity and maintain differentiated state over time

stem cell

unspecialized cell that can develop into a specialized cell under the right conditions

RNA Polymerase

transcription enzyme

All genes...

have a series of enhancer sequences with specific regulatory proteins

Similarities of prokaryotic and eukaryotic gene regulation

Both regulate gene expression with DNA-Binding proteins & respond to environmental signals

Prokayotic gene regulation

operons, transcription and translation are couples, simpler regulation

Eukaryotic gene regulation

Complex regulation, changes in chromatin structure, transcription occurs in nucleus, many levels of control

RNA Pol I

transcribes rRNA

RNA Poly II

transcribes mRNA and some snRNA

RNA Poly III

transcribes tRNA and 55 rRNa

general transcription factors (GTFs)

Correctly position polymerase at/around start site and help intiate transcription. analogous to Bacteria Sigma Factor

TFIID/TBP

bind to TATA box using TBP, bending DNA and allowing other proteins access

TFIIH

releases Pol II by phosphorylation of the C-Terminal tail of RNA Pol II. Leads to start of transcription

How do activators stimulate transcription through direct association

Activators directly bind RNA Pol II/GTFs to increase transcription

How do repressors inhibit transcroption through direct association

By binding/interfering with transcription machinery

How do activators and repressors regulate transcription by chromatin modification

Activators: reruit chromatin-modifying enzymes to open DNA

Repressors: Promote Chromatin condensation, making DNA less accessible to transcription machinery

How do HATs affect chromatin structure

add acetyl groups to histones that loosen the chromatin --> increasing transcription

How do HDACs affect chromatin structure?

remove acetyl groups, tightening chromatin --> decreasing transcription

How does the glucocorticoid receptor regulate genes

A ligand-activated transcroption factor that binds to glucocortid hormones, enters nucleus, and regulates gene ecpression by binding specific DNA sequences

Why is a skin cell different from a muscle cell?

They're diff because they express different genes, allowing them to produce different proteins and giving each cell a unique structure & function

If DNA is a molecule with Partial and Full charges

then it can form non-covalent bonds w/ proteins with polar and charged amino acids

What is the significance of the phosphorylated tail of RNA Pol II

- start of elongation

- recruits RNA processing proteins (capping, splicing, polyadenylations)

- Coordinates initiation --> elongation transition, integrating transcription with RNA maturation

How do cells control gene expression in a temporal manner?

By controlling the expression of regulatory factors allowing genes to be ecpressed only when needed

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