Glossary of Microbiolgy- Organization and expression of Genetic Material

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Amber Codon
Ocher Codon
Opal Codon
Stop Codons
Usually the first amino acid in a polypeptide
Site of codon-Anticodon recognition
30s subunit (small subunit) of prokaryote rRNA
Binding site for tRNA and enzymis involved in polypeptide chain elongation
50s subunit (large subunit) of prokaryotic rRNA
Direction of Translation of mRNA
5'->3', which makes the polypeptide NH2->COOH
3 Stages of Translation
1. Polypeptide Chain Initiation
2. Polypeptide chain elongation
3. Polypeptide chain termination
Shine-Delgarno Sequence
Initiation region of mRNA that the ribosomal small subunit binds to to initiate translation of the mRNA
Initiation factor involved in binding of mRNA to the 30s ribosomal subunit to initiat translation
Involved in the attachment of the f-Met-tRNA to the mRNA-30s complex

**GTP is hydrolyzed in this process**
Site of ribosome that has the peptide chain
P site
Site of ribosome that accepts the new tRNA
A site
Charged elongation factor that causes peptide bond formation between the amino acid in the A and P site of the growing peptide chain
Accesory protein in translation that helps translocation (moving of peptide from A site to P site)
Energy used by each peptide bond formed
mRNA with multible ribosomes engaged in protein synthesis
Release Factors
Coded for by nonesense codons
Bound to GTP and cause release of polypeptide from the P-site
Types of postranslational
-Removal of formyl groups on F-met
-Removal of some N terminal AA
-Cleavage of porteins to activate them
-Chemical modification of AA
--adding carbohydrate or hydroxylating AA
-Oxidation of sulfhydryl groups to make disulfide bonds
bacterial genes that are fuctionally related and linked together in transcriptional units
Regulation of enzymes in bacteria
-regulation of enzymatic activity
-Regulation of synthesis of enzymes themselves
Ligands or metabolites that determine the function state (whether repressors/activators can bind to operator/initiator) of the operon
allosteric proteins
mediators of metabolic change

proteins that have a conformational change when bound by effectors and thus mediate metabolic activity of the cell
2 characteristics of feedback inhibition
Usually first enzyme in path is regulated

End products act as effectors
Constituitive Genes
Genes not regulated by induction and repression

The gene products are relatively constant in the cell, regardless of changes in metabolism
Causes of difference in concentration of Constituitive Genes
-Difference in strengths of promoters
-Lifetime of mRNA's
-Efficiency of translation (rib binding)
Regulatory elements
Parts of an operon that can be controlled
-Operater/initiator sites
-Regulatory proteins (and effectors)
The Promoter
-RNA polymerase binding site and initiation of transcription

-Site of the majority of transcriptional regulation
The Operator site
Where the repressor binds to inhibit initition of transcription of the operon
The Initiator Site
(activator site)
Where an activator binds to enhance transcription of the operon
Regulatory proteins that bind to operater and prevent transcription of the operon
Bind to initiator sites to increase transcription of the operon
An opron goes from inactive to active state

-Effector is ussualy the substrate for the pathway
-An Operon goes from active to inactive state

-Effector is usually end product of the pathway
Positive Control
The action of the regulatory protein in it's active state to turn up transcription
Negative Control
The action of the regulatory protein in it's active state to turn down transcription
An effector causing negative control

Remember! Negative control is what happens when transcription is turned down
Effector binds to the active for of an activator, converting it to an inactive form
Repression under positive control
Effector binds to an inactive form of a repressor and activates it, converting it to an active form
Repression under negative control
Effector binds to the active form of a repressor and inactivates it
Induction under negative control
Effector binds to the inactive form of an activator to activate it
Induction under positive control
A group of genes controlling physiologically related functions that ar eregulated by the same regulatory protein, but not grouped together in an operon (more than one promoter)
Products of the structural genes regulate the expression of the operon in which they exist`
Transcriptional termination within operons
-Rho dependent, factors can block the rho binding site to all transcription pass the termination site
A way to regulate operons by premature termination of transcription of the mRNA (before translation can begin)-The mRNA has a leader sequence that can fold up on itself and abort transcription

(trp operon example)
trp operon and attenuation
RNA polymerase pauses at a pause site. If trp is low, it can't be added to the sequence, and the rna pauses, forms a structure that allows it to skip the termination site and transcription continues to make the proteins that make tryptophan. If trp is present in excess, the rnap doesn't stall and the ribosome moves right on to the stop codon and stops--no proteins to make trp
Anti-sense RNA

Example-ompF, ompC regulation
rna that is complementary to a strand of mRNA

Binding of anti-sense RNA to sense RNA prevents translation of the mRNA
Epigenetic control
Regulation of the folding of newly synthesized proteins and it's association with other subunits
Global Regulons
Allows cell to control many operons at once
Examples of global regulons
Catabolite Repression
SOS response
Heat Shock response
Catabolite Repression
-how a bacteria selects it's diet from the menu
Mechanism of catabolite repression in E. coli
CRP/CAP is a repressor under posiitve control. When bound to cAMP, CRP/CAP undergouse a conformational change that allows it to bind to different promoters of different sugar sources. Without cAMP, these mRNA's aren't transcribed, and with glucose, there's no cAMP. Only when glucose is low does the cAMP build up and allow the transcription
The decrease in growth of bacteria when faced with AA starvation

d/t decreased synthesis of translational machinery(rRNA, tRNA, ribosomes)
Amino acids that mediate the down regulation of translational machinery seen in stringency
ppGpp (guanosine tetraphosphate)
pppGpp (guanosine pentaphosphate)
These are made when a ribosome stalls out because there's no AA to fill the A site.
Heat shock proteins
Produced in response to high tempatures
Sensory protein that detects the heat insult and joins up with rpoH (instead of sigma factor) to allow promotion of a heat shock genes
SOS response
-respones in E. coli to extensive DNA damage
-blocks cell division
-Usually blocked by LexA
Mechanism of SOS response
DNA damage->ssDNA interacts with RecA->RecA converted to protease->cleaves LexA repressor->DErepresses DNA repair genes->allows for DNA repair
After repair, RecA is no longer a protease and LexA represses SOS genes again

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