BIO340 EXAM#2 CH7

Why are they different in the structure and function?

• same genome in nearly all cells

• differentiation without DNA sequence change

• Example: neuron vs. liver vs. muscle

cell type differences reflect gene ______ programs, not genomic differences

expression

de-differentiate

A single plant can form a clone of progeny cells that later give rise to an entire plant

Housekeeping Genes

expressed in most cells (ex actin)

Specialized genes

cell-type specific (ex. liver enzyme)

cell identity

defined by gene expression

transcription regulators bind

CIS- regulatory genes

recognition via major groove of DNA

hydrogen bonds and ionic interactions

position and arrangement of ^(&^(&^(* determine

gene expression patterns

Most significant bindings are in the ___ groves

Major

• different base pairs in DNA can be recognized from their edges without the need to open the double helix

THE TYPES OF HELIX PROTEINs

Dimerization

enchances thier bindings at CIS-reulatory sequences

dimer’s binding is ___

dynamic

can bind and unbind leading to transcription activation/inactivation of specific genes in response to signals

A eukaryotic gene control region includes many ___ sequences

cis-regulatory

Eukaryotic transcription work in___

groups

may be activators or repressors of transcription

Activators

promote the assembly of transcription

repressors

inhibit the assembly of transcription

DNA looping

allows distant enhancers to affect promoters

Coactivators and corepressors

so NOT bound to DNA directly

long noncoding DNA

also found in assemblies, these RNAs act as scaffolds to hold groups of proteins together

transcriptional synergy

greater than additive effect of multiple activators working together.

•Final transcriptional activity of the gene

results from competitions between

_______

activators and repressors

Eukaryotic repressor proteins can act by competitive DNA binding

activator and repressor have overlapping binding sites

Eukaryotic repressor proteins can act by making the activation surface

The binding and repressor site are close by, so the activator connects to the activation surface to the repressor

Eukaryotic repressor proteins can act by direct interaction with the general transcription factor

The repressor binds to the transcription factor, while nothing connects to the activator

Eukaryotic repressor proteins can act by recruiting chromatin remodeling complexes

chromatin remodeling complex surrounds chromatin and messes with the structure

Eukaryotic repressor proteins can act by recruitment of histone deacetylases

histone deacetylase attaches to the repressor and starts acetylation of histones

Eukaryotic repressor proteins can act by recruiting histone methyl transferase

Histone methyltransferase connects to repressor, starts histone methylation, and proteins bind to methylated histones

what controls the expression of the transcription regulators

Extracellular signals such as:

• hormones

• environmental conditions: temperature, pH, nutrient level

regulators act in

combinations

few regulators

combinatons

Cell fate depends on ___

regulatory combination

Transcription regulatory regulators are controlled by protein synthesis

the protein is synthesized only when needed

Transcription regulatory regulators are controlled by Ligand binding

ligand binding activates the protein

Transcription regulatory regulators are controlled by covalent modification

Covalent modification, such as phosphorylation, activates or inactivates it

Transcription regulatory regulators are controlled by addition of a second subunit

A DNA-binding protein forms a complex with a separate activating protein

Transcription regulatory regulators are controlled by unmasking

An inhibitory protein is phosphorylated and released

Transcription regulatory regulators are controlled by stimulation of nuclear entry

Nuclear entry is stimulated by the removal of an inhibitor

Transcription regulatory regulators are controlled by release from membrane

proteolytic cleavage releases a regulator from a membrane

flow od transcription regulators

signal —> regulator activation —> gene expression change

each regulator contains ___ genes

many

master transcription regulator

regulates expression of multiple genes (liver / neutron)

regulatory

cell identify is ___, not genomic

Induced Pluripotent Stem Cells (ips Cells)

• Differentiation is reversible

• 3 master regulators —> fibroblasts to pluripotent

• Oct4, SOX 2, Ktf4

• Transcription networks determine cell identity

resemble embryonic stem cells

iPS cells

differentiated cells

remain stable, and their daughter cells retain same idenity

Cell memory

• Stable transmission of gene expression patterns

• requires continued production of transcription regulators

positive feedback loops

master regulators activated a self-sustaining circuit

regulator passed to daughter cells

maintains identity through cell division

transcriptional attenuation

Premature termination of RNA synthesis

RNA structure determines termination

alternative RNA splicing

one gene —> multiple proteins

• regulated splice site selection

• increases protein diversity

• pos and neg regulators: RNA-binding proteins

mRNA modification

RNA editing can change the meaning of the RNA message

• Nucleotides in mRNA can be covalently modified

• ex. A—> I and C—> U

  • changes codon

  • DNA sequence unchanged

Normal RNA export control

• only processed mRNA exported

• unspliced RNA retained and degraded

• nuclear export is a quality-contorl checkpoint

HIV strategy

• viral DNA integrated into the host genome

• one last RNA transcript —> multiple spliced mRNAs

REC protein mechanism

rev binds rec respond element (RRE)

functional consequences

• early phase: only spliced RNA is replicationexported

• late phase: unspliced RNA exported

• controls timing of viral replicarion

• contributes to viral latency