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3'-untranslated region (3'-UTR)

answer

is a particular section of mRNA that follows the coding region that is not translated. These are found in both prokaryotes and eukaryotes

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5'-untranslated region (5'-UTR)

answer

also known as the leader sequence, is a particular section of mRNA and the DNA that codes for it. Stats at the +1 position (where transcription begins) and ends one nucleotide before the start codon. Usually contains ribosome binding site-maybe a hundred or more nucleotides long

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attenuation

answer

this is a second mechanism of negative feedback in the trp operon. This is made possible by the fact that in prokaryotes, (which have no nucleus) the ribosomes begin translating the mRNA while RNA polymerase is still transcribing the DNA sequence. This allows the process of translation to directly affect transcription of the operon

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attenuator

answer

plays an important regulatory role in prokaryotic cells because of the absence of the nucleus in prokaryotic organisms. It refers to a specific regulatory sequence that, when transcribed into RNA forms hairpin structures to stop transcription when certain conditions are not met.

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?-galactosidase

answer

is a hydrolase enzyme that catalyzes the hydrolysis of ?-galactosides into monosaccharides.

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cAMP (cyclic AMP)

answer

is a second messenger important in many biological processes. It is used for intracellular signal transduction such as transferring the effects of hormones like glucagon and adrenaline which cannot pass through the cel membrane. It is involved in the activation of protein kinases

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cAMP-CRP complex

answer

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CAP (catabolite activator protein)

answer

is a regulatory protein in bacteria. It binds cAMP, which causes a conformational change that allows the protein to bind tightly to a specific DNA sequence in the promoters of the genes it controls.

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catabolite repression

answer

is an important part of global control system of various bacteria and other micro-organisms. Catabolite repression allows bacteria to adapt quickly to a preferred (fast matabolisable) carbon and energy source first. Can be initiated by glucose.

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codon

answer

tri nucleotide sequences which determine amino acid sequencing (proteins)

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constitutive enzyme

answer

are enzymes that are not controlled by induction or repression (they just keep doing their thing regardless of circumstances)

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CRP (cAMP receptor protein)

answer

s a regulatory protein in bacteria. It binds cAMP, which causes a conformational change that allows the protein to bind tightly to a specific DNA sequence in the promoters of the genes it controls.

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gratuitous inducer

answer

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inducer

answer

is a molecule that starts gene expression. For a gene to be expressed, its DNA sequence must be copied, to make mRNA. Inducers function by disabling repressor proteins

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inducible enzyme

answer

is an enzyme that is expressed only under conditions in which it is clear of adaptive value, as opposed to constitutive enzyme which is produced all the time. Typically used for the breaking down of things in the cell. Inducers cause the gene to turn on (controlled by the amount of reactant which turns the gene on)- can also remove the repressor

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negative regulation

answer

this involves the binding of a repressor to the operator to prevent transcription.

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open reading frame (ORF)

answer

is a DNA sequence that does not contain a stop codon in a given reading frame. These are often used along with other evidence to initially identify candidate protein coding regions in a DNA sequence

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operator

answer

a segment of DNA that a regulator binds to. It is classically defined as a segment between the promoter and the genes of the operon. In the case of a repressor, the repressor protein physically obstructs the RNA polymerase from transcribing the genes.

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partial diploid

answer

question

polynucleotide phosphorylase

answer

is a bifunctional enzyme with a phosphorolytic 3' to 5' exoribonuclease activity and a 3' terminal oligonucleotide polymerase activity. It is involved with mRNA processing and degradation in bacteria, plants and humans.

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positive regulation

answer

Can also regulate positively by an activator protein, which stimulates transcription by binding to DNA
-inducer binds to activator protein and causes a conformation change allowing it to bind to the DNA and begin transcription
-or the activator proteins are normally bound to the DNA, however when a corepressor is bound by the activator it is prevented from binding to the DNA. This stops activation and transcription.

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primary transcript

answer

is a RNA molecule that has not yet undergone any modification after its synthesis. For example a precursor messenger RNA (pre-mRNA) is a primary transcript that becomes a messenger RNA after processing

question

promoter

answer

a nucleotide sequence that enables a gene to be transcribed. The promoter is recognized by RNA polymerase, which then initiates transcription.

question

promoter upstream element (UP element)

answer

question

pulse-chase experiment

answer

is a method for examining a cellular process occurring over time by successively exposing the cells to a labeled compound (pulse) and then to the same compound in an unlabeled form (chase). Radioactivity is a commonly used label.

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repressor

answer

is a DNA binding protein that regulates the expression of one or more genes by binding to the operator and blocking the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes. They are coded for by regulator genes. Inducers can interact with repressors and cause them to detach from the operator.

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ribonuclease (RNase)

answer

is a type of nuclease that catalyzes the degradation of RNA into smaller components. Can be either endoribonucleases or exoribonucleases.

question

What are the methods of regulation

answer

Bacterial transcription can be either constitutive or regulated. Transcription of some operons is subject to repression , or is positively regulated by activation. Attenuation is another mechanism of regulation used for regulation of some operons encoding enzymes for amino acid biosynthesis.

question

What ways can operons be regulated

answer

-repression
-attenuation
-can be positively regulated by activation

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What is catabolite repression?

answer

Glucose is the preferred carbon source, so in the presence of glucose, many operons are turned off. These operons are activated by the CRP-cAMP complex which forms in the absence of Glucose.

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A transcriptive cascade controls regulation of what

answer

Both the lytic and lysogenic pathways in lambda.

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What is the key determinant in the switch between lysis and lysogeny

answer

The binding of repressors at OR

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Bacterial mRNAs may be _____ or ______ meaning they have one or more ORFs.

answer

monocistronic, polycistronic

question

T or F Bacterial mRNA have long half lives and tRNA and rRNAs are much less long lived

answer

False its the reverse case

question

Where does the most regulation in bacteria occur

answer

in Transcription

question

What does the lac operon (lacZYA) encode for?

answer

Lactose Utilization

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How is transcription of the lac operon induced?

answer

By the presence of lactose or IPTG in the medium

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How does the lac repressor repress transcription?

answer

The lac repressor binds to the lac operon. Binding of the inducer to the Lac repressor prevents the repressor from binding to the operator, and transcription can proceed.

question

T or F E.coli uses galactose in preference to lactose or other sugars, and the presences of this inhibits expression of the lac operon

answer

False. Glucose is the preferred sugar, and its presence inhibits the expression of the lac operon

question

What is low in the presence of glucose

answer

Cellular cAMP

question

What is CRP-cAMP complex

answer

It is a transcriptional activator that forms in the absence of glucose.

question

What causes negative regulation and positive regulation in the lac operon?

answer

The lac repressor causes negative regulation, and CRP-cAMP causes positive regulation

question

What binds to an activator site in the lac operon

answer

CRP-cAMP

question

E.coli rRNA primary transcripts contain ____ rRNAs and ____ tRNAs. These must be processed to produce mature ___, _____, and _____ rRNAs

answer

3, several, 16S, 23S, 5S,

question

tRNAs are also processed. Where does processing occur and how?

answer

They occur at both the 5' and 3' end, and they are produced by modification of bases.

question

The trp repressor does what

answer

Acts to repress the transcription of the trp operon.

question

What does tryptophan do?

answer

It acts as a corepressor to allow the Trp repressor to bind to the operator to repress transcription.

question

In attenuation the trp leader region can form what? This region does what?

answer

It can form two mutually exclusive hairpin structures. It encodes a short peptide and has two trp codons.

question

What happens under low tryptophan conditions?

answer

Ribosomes will pause at the Trp codons and allow formation of the antiterminator hairpin structure and transcription proceeds. (2-3 Bind)

question

What happens under high tryptophan levels?

answer

Ribosomes read through the trp codons and the transcription terminator hairpin structure will form. Transcription terminates before RNA polymerase reaches the tryptophan biosynthetic genes

question

What promoters help determine whether lambda undergoes lysis or lysogeny?

answer

PR, PL, PRE, and PRM

question

PR and PL are regulated by what

answer

OR and OL operator regions, each which have three operator sites.

question

The in which ____ binds to ___ and ___ determines whtere lambda enters the lytic or lysogenic state.

answer

CI, OL, OR

question

The lac repressor binds to what site within the lac operon?

answer

lacO

question

Name all the parts of the lac operon

answer

The lacO, LacZ, LacA,LacP

question

The lac repressor is inactivated by binding to which of the following?

answer

allolactose

question

T or F- A polycistronic mRNA is transcribed from the lac operon when lactose is present and glucose is absent in the E. coli cell.

answer

True

question

The lac repressor protein is active in the absence of lactose within the cell

answer

true

question

In the trpL mRNA, the attenuator sequence is located closest to what stem loop region?

answer

Region 1

question

If transcription is proceeding without pausing, what stem loop structures are formed in the trpL mRNA?

answer

1-2 and 3-4

question

T or F-The process of attenuation is the trp operon turns off the operon when it is not needed by the cell?

answer

True

question

If regions 1 and 2, and 3 and 4 of the trpL mRNA form stem loops, the trpE gene will be transcribed.

answer

False

question

The inducer for the lac operon is

answer

allolactose

question

What is the most convincing evidence that lacI is a diffusible protein?

answer

A partial diploid with only one functional lacI gene is able to regulate both copies of the lac operon

question

T or F-Genes within an operon are generally involved in the same biochemical pathway?

answer

true

question

T or F- Catabolite repression requires an inducer and an activator protein.

answer

True

question

What is not a structural gene of the lac operon

answer

LacI

question

What lac operon element, when nonfunctional would lead to a reduction in the total amount of functional lacZ produced by a bacterial cell?

answer

The CAP site

question

Attenuation of the trp operon occurs when

answer

in presence of high levels of tryptophan

question

Why does the ribosome stall on region 1 during attenuation

answer

Translation of this region requires trp-tRNA (trp)

question

Why can it be beneficial for bacterial cells to have multiple cistrons on one mRNA?

answer

Often polycistronic mRNAs encode proteins in a specific metablic pathway. When they are all together, their synthesis is regulated coordinately, and a single signal will cause similar quantities of related proteins to be produced at the same time

question

How can the lac operon ever be induced if the lactose operon inducer ( the protein that binds to the repressor) is allolactose in the cell, a product of the lac operon enzymes

answer

The binding of a repressor is never infinitely strong. Sometimes (meaning approximately once a generation) the protein will come loose and RNA polymerase will be able to transcribe the gene. This is basal level of transcription. This allows permease to bring into the cell and ? galactosidase is available to convert a small amount of lactose into allolactose. The allolactose binds to the repressor, causes it to change conformation so that it falls off the operator. RNA poly, can then freely transcribe the lac genes making the lac enzymes much more readily

question

What does the lac operon encode

answer

The lac operon codes for ? galactosidase, which metabolizes lactose into glucose and galactose, permease, which helps lactose to enter the cell, and ? galactoside transacetylase, which has an unknown function

question

What does the trp operon encode?

answer

The trp operon codes for three enzymes that are essential for tryptophan (an amino acid) synthesis.

question

The attenuation of tryptophan depends on what

answer

the secondary structure of the mRNA (formation of the 3-4 hairpin)

question

What are the DNA sequence components of the trp operon?

answer

Promoter, operator, leader (with attenuator), trpE, trpD, trpC, trpB, trpA

question

Why is it strange to have two adjacent tryptophan codons?

answer

It is rare because normally tryptophan accounts for only 1% of amino acid residues in a protein

question

How does a cell know to metabolize glucose rather than lactose?

answer

Glucose is involved in the inhibition of phosphorylation of adenylate cyclase which prevents cAMP formation. With no cAMP, the cAMP-CRP complex cannot form and therefore cannot bind to its activator site upstream from the promoter to activate synthesis.

question

What is another way that glucose can slow lac operon expression?

answer

It can act through an inducer exclusion mechanism. In this mechanism, a product of glucose (EIIA) binds to lactose permease (the product of the lacY gene) which inactivates it. This prevents lactose from entering the cell and being converted into allolactose. With no allolactose, the repressor protein will remain bound to the operator.

question

The E. coli ____ gene codes for ?-galactosidease

answer

lac Z

question

___ is the a true inducer of the lactose operon.

answer

Allolactose

question

The segment that codes for a polypeptide chain is called

answer

open reading frame

question

The ___ complex binds to an activator site upstream from the lac promoter and activates lac operon transcription

answer

cAMP-CRP

question

Catabolite sensitive operons cannot be induced if what is present

answer

glucose

question

Negative ____ occurs because the gene product regulates tis own synthesis.

answer

autoregulation

question

What does bacteria use to degrade mRNA

answer

RNases

question

What does the lac y gene code for

answer

permease

question

What does the lac a gene code for

answer

transacetylase

question

What does the lac I code for

answer

the repressor (which binds to lac O or the operator when the inducer is absent- Allolactose is the inducer)

question

What binds to the lac P

answer

CAP-cAMP, and RNA polymerase

question

The lac promoter is what

answer

Lac P

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