control of gene expression in prokaryotes ch16

Ribozymes

- riboswitches can function as ribozymes -mRNA molecules with catalytic activity - when bound with small regulatory molecules, can induce the cleavage and degradation of mRNA. 1. transcription & translation of the glmS gene produce an enzyme 2. that helps synthesize the sugar GlcN6P 3. GlcN6P binds to ribozyme & induces self cleavage of the mRNA

when tryptophan level is high

1. RNA polymerase begins transcribing DNA producing region 1 of the 5' UTR 2. ribosome binds to 5' end of 5' UTR & translates region 1 while region 2 is being transcribed 3. RNA polymerase transcribes region 3. ribosome doesn't stall at Trp codons, cuz tryptophan is abundant 4. ribosome covers part of region 2, preventing it from pairing w region 3. region 4 is transcribed & pairs w region 3, producing the attenuator that terminates transcription

when tryptophan level is low

1. RNA polymerase begins transcribing the DNA, producing region 1 of the 5' UTR 2. a ribosome attaches to 5' end of the 5' UTR & translates region 1 while region 2 is being transcribed 3. ribosome stalls at the Trp codons in region 1 cuz tryptophan is low. cuz ribosome is stalled, region 2 isn't covered by ribosome when region 3 is transcribed 4. when region 3 is transcribed it pairs w region 2. when region 4 is transcribed it cannot pair w region 3, cuz region 3 is already paired w region 2. the attenuator never forms, & transcription continues (anti terminator)

when glucose is low

1. levels of cAMP are high, cAMP readily binds CAP, & the CAP-cAMP complex binds DNA (CAP binds to promoter of lac operon & stimulate transcription) - level of cAMP inversely proportional to level of available glucose 2. increasing the efficiency of polymerase (need cap) binding 3. the results are high rates of transcription & translation of structural genes 4. & production of glucose from lactose

when glucose is high

1. levels of cAMP low, & cAMP is less likely to bind to CAP 2. RNA polymerase cannot bind to DNA as efficiently 3. so transcription is at low rate -catabolite repression

when tryptophan is low

1. the trp repressor is normally inactive 2. it cannot bind to operator 3. and transcription takes place

when tryptophan is high

1. tryptophan binds to repressor & makes it active 2. trp repressor then binds to operator & shut transcription off - tryptophan functions as core repressor here - ex of feedback negative regulation.

lac Operon in E coli

A negative inducible operon -Lactose metabolism -Regulation of the lac operon -Inducer: allolactose -lacI: repressor encoding gene (trans) -lacP: operon promoter -lacO: operon operator (cis) 1. permease (encoded by LacY) actively transports lactose into cell 2. where enzyme B-galactosidase breaks it into galactose & glucose 3. B-galactosidase also converts lactose into related compound allolactose (an inducer) 4. and converts allolactose into galactose & glucose

trp Operon of E. coli

A negative repressible operon -Five structural genes - trpE, trpD, trpC, trpB, and trpA—five enzymes together convert chorismate to typtophane (ordered by which is closer to 5' end) - 5'UTR encodes (exception) short proteins which is unstable; only function is to regulate attenuation

Regulator gene

DNA sequence encoding products that affect the operon function are not part of the operon 1. a separate regulator gene w its own promoter encodes a regulator protein - negative control: reg. protein is a repressor (repressor binds to operator & suppresses operon function - gene expression) - positive: " an activator 2. that my bind to the operator site (within operon) to regulate the transcription of mRNA 3. the products of mRNA catalyze rxns in a biochemical pathway

Regulatory Elements

DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences - can enhance or inhibit expression

Attenuation in the trp Operon of E. coli

Four regions of the long 5′ UTR (leader) region of trpE mRNA -When tryptophan is high, region 1 binds to region 2, which leads to the binding of region 3 and region 4 (2 & 3 don't pair), terminating transcription prematurely. - when low, region 2 pairs w 3 & doesn't terminate transcription

single promoter

Many bacterial genes with related functions are clustered and are under the control of single promoter - transcribed together into a single mRNA which is polycistronic - in euk: each gene has own promoter transcribed separately

Gene regulation

Only a subset of genetic information is expressed at any time depending on signals - Bacteria: responds to environmental changes by rapidly altering its biochemistry thru regulation of operons - Eukaryotes: Multicultural specialization - individual cells are specialized for particular task Response to environmental changes

Negative inducible operons

The control at the operator site is negative. -Regulatory protein is synthesized active, binds to the operator and inhibits transcription. No inducer present: 1. the regulator protein is a repressor that binds to the operator & prevents transcription of the structural genes. inducer present: 2. when inducer present, binds to regulator (conformational change shape), thereby making the regulator unable to bind to the operator. transcription takes place - substrate makes the repressor inactive

negative repressible operon

The control at the operator site is negative. Transcription is usually on and needs to be turned off, so the transcription is repressible. - usually controls synthesis of proteins that carry out the biosynthesis of molecules, such as amino acids - Coreprocessor: a small molecule that binds to the repressor and makes it capable of binding to the operator to turn off transcription (conformational change) no product U present: 1. regulator protein is an inactive repressor unable to bind to operator 2. transcription of structural genes therefore takes place product U present: 3. levels of product U build up 4. product U binds to regulator protein (coreprocessor) 5. making it active & able to bind to operator 6. and thus preventing transcription

Repressible operons

Transcription is normally on and needs to be turned off. - involved in synthetic pathways (amino acids) economic to keep on; when enough accumulation can turn off - functions thru feedback of terminal product of operon - neg: product makes repressor active pos: makes activator inactive

inducible operons

Transcription is usually off and needs to be turned on. - breakdown of metabolic pathways (economic to turn on when needed) - neg: substrate makes repressor inactive pos: makes activator active - inducible/repressible depends on if regulator protein is in active or inactive stage

Attenuation

affects the continuation of transcription, not its initiation. This action terminates the transcription prematurely before it reaches the structural genes by forming Attenuator - trp operon only one regulated by both attenuation & repressor -Antiterminator - never shut down completely

Antisense RNA

complementary to targeted partial sequence of mRNA - not siRNAs when extracellular osmolarity is low 1. the ompF mRNA is translated to produce OmpF protein when high: 1. the micF gene is activated and micF RNA is produced 2. micF RNA pairs w 5' end of ompF RNA, blocking the ribosome-binding site. no OmpF protein is produced

Constitutive expression

continuously expressed under normal cellular conditions -Housekeeping genes- encode proteins for important for maintenance of cells (actin, ubiquitin) - dont undergo gene expression regulation

helix-turn-helix

dna binding protein - 2 alpha helices connected by a turn - bacteria & euk.

leucine zipper

dna binding protein - helix of leucine residues & zipper arm - euk transcription factors

zinc fingers

dna binding protein - loop of amino acids containing a zinc ion - euk proteins

Regulatory genes

encoding products that interact with other sequences and affect the transcription and translation of these sequences (many of them are DNA-binding proteins) - regulate expressions of other genes - control transcription of structural genes

Structural genes

encoding proteins used in biosynthesis, metabolism, or have structural role in the cell

DNA-Binding Proteins

have usually functional parts called domains: 60 ~ 90 amino acids, responsible for binding to DNA, forming hydrogen bonds with DNA - Their attachment to DNA affects the expression of genes - bind dynamically (on or off). can activator or inhibit dna. - Distinctive types of DNA-binding proteins based on the motif found within the binding domain - a simple structure that fits into the major groove of the DNA (purpose: to interact w dna either turn off or on gene expression) can form H bonding w bases or non covalent interaction w sugar phosphate backbone of dna.

Negative control

inhibit gene expression - most genes in prok.

lac operon structural genes

lacZ: encoding β-galactosidases lacY: encoding permease lacA: encoding transacetylase -The repression of the lac operon never completely shuts down transcription absence of lactose: 1. regulator protein (a repressor) binds to the operator & inhibits transcription Presence of lactose: 2. some of it is converted into allolactose 3. which then binds to the regulator protein making the protein inactive 4. regulator protein cannot bind to operator 5. and the structural genes are transcribed & translated

Riboswitches

molecules influence the formation of secondary structures in mRNA when regulatory protein present: 1. regulatory protein binds to the riboswitch & stabilizes a secondary structure 2. that masks a ribosome-binding site 3. no translation takes place regulatory protein absent 1. w/o regulatory protein, the riboswitch assumes an alternative secondary structure 2. that makes the ribosome-binding site available 3. translation takes place

inducible and repressible controls

negative: " is repressor positive: regulatory protein an activator

Operon

promoter + additional sequences that control transcription (operator) + structure genes - controlled by regulatory proteins - regulatory sequence upstream operon - operator: DNA sequence that binds to the lacI repressor protein

Inducer

small molecule that turns on the transcription (often an allosteric protein)

Positive control

stimulate gene expression - most genes in euk.

Catabolite repression

using glucose when available, and repressing the metabolite of other sugars - if there is glucose & lactose, lac operon not properly functioned - This is a positive control mechanism. The positive effect is activated by catabolite activator protein (CAP). cAMP is binded to CAP, together CAP-cAMP complex binds to a site slightly upstream from the lac gene promoter