Occlusion- LacI binds to the operon and cuases inclusion,(promoter is hiden)

RIRPA-

Mediated by GalR
o This mechanism allows RNA polymerase to bind to the promoter, but makes specific
protein-protein interactions between RNA polymerase and GalR.
o The interactions prevent RNA polymerase from catalyzing the open complex formation
and initiating transcription. (It grabs RNA polymerase and doesn’t allow the melting of
the DNA and transcription.)

transcriptional Activators

-Assist RNAP in initiating transcription

Alternative Sigma Factors

After specificity of RNAP for a specific promoter. 

Catabolic Activator Protein

(AKA CRP)

Binds to the Site in the Promoter Region of LaC Operon

Requires a small molecule ligand to bind promoter CAMP (cyclic AMP).  

Cap/Camp---Alpha CTD

six amino acids

helps RNAP bind to the promoter- main reason for existance. 

A- Negetive

B- Positive 

Required to initiate transcription

Bind to specific sites in promoter region

Assist in RNAP binding promoters

Assist RNAP in initiating transcription

binding or activity initiated by ligands 

Pre-recruitment

Recruitment

Post reqruitment

SIGMA 4- binds to

while SIGMA 2 binds to

sigma 4- binds to -34

sigma 2 binds to -10 

Ecoli has

1 Sigma factor

1> Sigma factor(S)

0 Sigma factor 

RNA polymerase with the Sigma 70 recognizes the host DNA and binds to it- transribes a new Sigma

the new sigma replaces the sigma 70 and transcribes  genes of the sigma factor. the new Sigma transcribes genes for another sigma- the latter sigma transcibes the late genes.  

Sigma A is the sigma 70 equivalent of Ecoli

Sigma H is the equivalent of Sigma Stationary. 

Negetive Control- Regulation by a repressor

Positive Control- Regulation by an activator 

Inducible- Genes turn on in response to a stimulus

Repressible- turn off in response to a stimulus 

Lytic Phase- Lyse the cell at the end to reproduce

Lysogenic phas -Enter genome and lay low

(Only lysogeny is reversible) 

icosahedral virus

Linear DNA molecules

Relatively simple tail

binds to the LamB- an Ecoli membrane protein used to take up maltose.  

Alt

Int

Xis

Alpha

Beta

Gamma 

CIII

CII

CI

N

CRO 

DNA synthesis, Late transcription Control, Lysis

genes 

O- DNA Synthesis

P- DNA Synthesis

Q- Late transcription Control

S-Lysis

R-LYSIS

A race between three chemicals-

CII CI and Cro 

CII- is a transcriptional activator of early genes including the cI repressor.

CI is a repressor protein, which represses expression of lysis genes

If cII wins the race, lytic functions are repressed

PR: cro and cII.

PRE: cI.
PRM: cI.

Attentuator mutants are repressed-

While Wild type are repressed- 

Attenuator- 70

Wild Type-700 

Leader attenuator region of the TRP mRNA contains four runs of nuecleotides that can form three hairpin loops.

Under one set of conditions two of the loops can form simultaniously, under another set of conditions, - only one of the loops can form.  

Aconitase

Fumirase

Succinix Dehydrogenase Complex (SDH) 

A protease cuts up specific proteins much like the Proteasae in HIV that makes the proteins for the capsul-

A Proteolysis- destroys Proteins. 

CLP and Lon proteases explain? 

ATP dependent Serine Proteases

Need ATp to work and need Serine at their active site 

First class- recognition at the C terminus

Second Class- Recognition by a Chaperone protein

1st class- Clp or Lon recognize the proteins at the C terminus, the proteases are looking for Particular motifs. 

2nd Class

Recognition by a Chaperone Protein

(special to the CLP protease)

Chaperone carries the protein to the Clp protease

Clp protease hydrolizes and destoys the Protein

ATP Dependent

Multimeric barrel shape (14 subunits)

Each subunit contains a domain

Substrate binding Domain

Atpase Domain

Proteolytic Domain

Segregates Protein for degredation 

LacI represses when not in the presence of Allalactose

Allalactose binds to LacI to cuasing a conformational change  and LacI comes off lifting repression

Isozymes

Transcription

SPLICING

TRANSPORTATION TO THE CYTOPLASM

TRANSLATION 

the initiator  (where the assembly of RNAPII occurs)

TATA box which recuits tata binding proteins

Assembly of the promoter 

Nucleosome Remodeling

and

Recruitment of RNA polymerase

(both typically have to occur and both might work together- but this is not necessary) 

Euchromatin is loose while heterochromatin is tightly compact

Euchromatin is transcriptionally active while Heterochromatin is transcriptionally inactive. 

2nm-Naked DNA

11nm- Beads on a string

 30- Compaction to Chromatin fiber 

300- protein structure upon which loops of chromatin are attached

What Dna is typically found in a cell during interphase?

What type of DNA is needed for transcription? 

300nm is what is usually found in a cell during interphase

You need 2nm Dna for transcription 

HAT- Enzymes used to acetylate histone tails. Alteration of side groups changes histone function.Acetylation loosens up the complex.

HRC 

A Binding Site (Activator) binds an enhancer site and interacts with another factor to promote nucleosome

remodeling 

A specific binding site recuits HATS

Once the HAts are in position we have acelyiation of the tails around the promoter region

The acetylation loosens the promoter up

Nucleosome Remodeling

HAT or HRC will work together, HAT or HRC or both to remodel the histones to release sites for other binding proteins 

We have a 30NM Chromatin fiber

A chromatin remodeling complex is recuited

A binding protein one is included

there is remodeling-

Dna binding protein 2 is recruited

the second protein rercruits Histone acetyl transferase

Acetylation occurs and we have unraveling 

Heterochromatin remodeling

The enhancer reacts with an activator-

the Activator reacts with the appropriate protein

in mediator complex

the mediator complex helps recruit RNAP II to the tata box to which TFID is already bound.  

The GAL ACTIVATION-

WHAT DO YOU KNOW ABOUT IT?

Found in Sacromyaces Cervissae

(utilizes galactose as a Carbon energy source)

Genes controling this process are very tightly regulated

Expression of the Gal gene requires- Gal4

(binds close to the promoter)

DNA binding domain

Leucine Finger and a Zinc finger that fits in the major grove to identify the DNA binding sites. 

Acidic Activation Domain

(in the coiled coil) Domain in the protein that is involved in the recruitment of RNAP II via the mediator 

Acidic amino acids- like

Aspartic and Glutamic amino acids 

used to determine which proteins interact with each other.

Takes advantage of the modularity of the DNA binding domain (DBD) and the acidic activation
domain (AAD).
• The two domains do not need to be part of the same protein for activation to occur at the gal
promoter. However, it is required that the AAD and the DBD contact each other.

Activated by Ligand Binding

Components of hormone response systems:
o The hormone receptor – many of the hormone receptors themselves are the
transcriptional activator.
o DNA binding site – an enhancer element located somewhere in the vicinity of the gene
that acts as a hormone response element.

Hormone activates its receptor in the cytoplasm.
 Once the activator is activated it needs to transmit the message to the nucleus.
 

Hormone activates a receptor directly in the nucleus.
The hormone itself must get into the nucleus

Gene activated by the Glucocorticoid family of hormones.

the metallothionine gene is partially controlled by
glucocorticoid proteins.

A- Outside

B- Inside 

In its absence the GlucoCorticoid receptor is bout to Hsp90 

Activator and

the Hormone Response Element 

1. (a) The binding site for the repressor overlaps with the binding site of the activator,
preventing the activator from binding. Repression via occlusion.
 If the repressor gets there first, no activation. If the activator gets there first, it
wins.
2. (b) Non-overlapping and non-interfering binding sites. The repressor protein has a
domain that interacts with the activator, which prevents it from recruiting the mediator
complex and RNAP-II.
 Specific protein-protein interactions between the repressor and activator when
bound to the enhancer element.
3. (c) The repressor binds to the binding site in the DNA and has a second domain that
interacts with the mediator. (Looks like an activator so far.)
 In this case, however, the interaction is strong enough to hang on to the mediator
after recruitment. Mediator remains associated with the repressor and RNAP-II
cannot get going. It prevents it from forming the open complex and extending
transcription.
 This is a high affinity interaction such that the mediator remains associated with
the repressor.
4. (d) Chromatin remodeling.
 Recall that one type of activator remodels chromatin to loosen the structure to let
other activators and RNAP-II in to start transcription.
Instead of loosening the structure for access to the genes, this type of repressor’s
job is to compact the structure.
 One class of these repressors are histone deacetylases, which are the opposite of
HATs (histone acetyl transferases, from a previous lecture)

By deacetylating the histones, the whole system of DNA gets tighter again, into
the higher level fibers.

Splicing Regulatory proteins.

involved in splice site recognition. 

Decision of which alternative splicing pattern to use

decide which RNA sequence  

A stimulon that controls SOS stimuli

has three domains

a dimerization domain,
a DNA binding domain (HTH),
and an autoproteolytic domain

functions as a homodimer

LEX A

REC A 

Cytokine off state

Monomer

when turned on active- you get a dimer that phosphorylates himself and regions of the autokinase

Stat gets phosphorylated and sent to the nucleus 

activated by phosphorylation-

mediated by brick2

two key interactions- one of the domains interacted with intermediates

all done by allosterism- interactions- gaining and losing abilities to interact with each other. 

Ras GTP

RAS GDP