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50 Cards in this Set

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Feedback inhibition
occurs primarily in the regulation of entire biosynthetic pathways like in the biosynthesis of amino acids or nucleotides
Three characteristics of Feedback inhibition
1) the end product can regulate its own biosynthesis

2) the end product can inhibit the acitivity of the 1st enzyme in the pathway

3) shuts down entire biosynthetic pathway
Allostery
property that makes possible the process of feedback inhibition
Active site
where the substrate binds in an allosteric enzyme
Allosteric Site
where the inhibitor (effector) reversibly binds in an allosteric enzyme

binding at this site changes the enzyme conformation
Isozymes
different proteins that catalyze the same reaction but are subject to different regulatory controls

example is DAHP isozymes in E. coli
Covalent Modification of Enzymes
a regulatory mechanism for changing the catalytic activity of an enzyme

can be reversibly modified most times

Glutamine Synthetase is example of this
Glutamine Synthetase
example of covalent modification

modified by addition of AMP (adenylation)
Protein Splicing
occurs when amino acid residues are removed from the protein itself

intein is removed (portion of the peptide that is removed)
Intein
portion of the peptide that is removed during protein splicing

are self splicing
In what groups does protein splicing occur?
occurs in Archae, Bacteria and Eukarya
DNA Binding Proteins
bind to DNA because of interactions betweeen specific domains of the proteins and specific regions of the DNA molecule

most interact in a sequence specific manner

major groove of DNA is an important site of protein binding
Protein-DNA interactions
central to the completion and regulation of replication, transcription and translation
How are DNA molecules bound to proteins?
amino acid side chains of the binding protein associates to the bases and sugar phosphate backbone of the DNA
How are DNA binding proteins classified?
they are classified by structure or domains
Protein domains commonly found in DNA binding proteins
1) Zinc Finger

2) Leucine Zipper

3) Helix-turn-helix
How do sequence recognition and binding take place in DNA binding proteins?
through H-bonds and van der Waals interactions
Negative control of transcription
Enzymes taht catalyze the synthesis of a specific product are not synthesized if the product is present in sufficent amounts
Inducer
Substance that initites enzyme induction (ex lactose)
Corepressor
substance that represses enzyme synthesis (ex arginine)

effectively called effectors
Repressor proteins
become active after it is bound by the effector

block transcription
Operator
region of DNA (near the promoter) where the repressor/effector complex binds

single mRNA
Operon
clutster of genes arranged in a linear, consecutive fashion

when a single regulatory protein controls a single operon
Induction
involves the binding of an inducer to the repressor

instead of corepressor uses an inducer
Positive control of transcription
involves a regualtory protein (inducer) that activates the binding of RNA polymerase

example is maltose catabolism in e.coli
Activator proteins
bind to specific DNA sequences called activator binding sites

activates transcription

bind several hundred bases before promoter

may bend the DNA
Regulon
when more than one operon is under control of a single regulatory protein

example is maltose catabolism

can be involved with both poistive and negaitve control of transcription
Global Control System
used by cell to make most efficient use of the available carbon sources

cell always uses glucose first
Global Regulatory Systems
regulate expression of many unrelated genes siumultaneously

brought about by changes in the environment
Catabolite repression
ensures that cells always use glucose first

prevents the expression of all other catabolic operons affected by this control mechanism when cells are grown in a medium containing glucose
Glucose Effect
1) best energy source is chosen

2) cell does not waste energy making enzymes for catabolizing the other sugars

3) if glucose is exhausted, next best sugar taken
Stringent Response
a global translational control in prokaryotes that represses tRNA and rRNA synthesis during amino acid starvation
Alarmones
act as the triggers for the stringent response
What are the two alarmones?
1) guanosine tetraphophate ppGpp

2) Guanosine pentaphosphate (pppGpp)
ReIA
synthesizes alarmones

monitors ribosome activity
How do alarmones inhibit rRNA and tRNA?
the interfere with RNA polymerase initions of transcription of genes
Gene regulation
can be brought about by changing the amount or activity of sigman factors
sigma factors
recognize different promoter sequences

(ex. e. coli has 7 different sigma factors each recognizing a different promoter)
How are sigma factors controlled?
1) transcriptional controls (positive or negative)

2) Degradation by proteases (destroys, lowers concentration)

3) Anti-sigma factors (inactive sigma factors)
Sigma factors can also be used for these three different circumstances
1) Nitrogen assimilation

2) iron transport

3) heat shock
Heat Shock Response
produces heat shock proteins (sigma 32)

under "normal" conditions sigma 32 is normally degraded very quickly following its synthesis and is more rare in the cell
Quorum Sensing
sensing mechanism involving signaling molecules that allows cells to survey their environment for cells of their own species

ensures that sufficient cell numbers of a given species are present before eliciting a particular biolgoical response

widespread in gram (-) bacteria
Acylated Homoserine Lactone (AHL)
bacteria synthesize and secrete this

functions as an inducer that combines with an activator protein and triggers the transcription of specific genes
Three examples of Quorum Sensing bacteria
1) V. Fischeri (bioluminescent ability)

2) P. Aeruginosa (produce a biofilm that can prevent antibioltic penetration)

3) S. Aureus (produce peptides that damange host cells and disrupt immune system)
attenuation
mechanism whereby gene expression is controlled after the intiation of RNA synthesis

only seen in prokaryotes
Why does attenuation occur?
because a portion of the newly formed mRNA folds into a unique stem-loop taht causes cessation of RNA polymerase activity
Signal Transduction
when a cell receives an external signal through a sensor that then transmits the signal to the regulatory proteins
Two components of regulatory systems
1) Specific sensor kinase protein

2) Partner response regulator protein
Sensor Kinase
aka histidine kinases

responsible for self-phosphorylation

receive signal from the environment and phosphorylate one of their specific histdine residues
Response regulator
DNA binding protein that regulates transcription

phosphoryl group from histine kinase is transferred here