pET Expression Vector Components

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The ______ gene provides resistance to the antibiotic ampicillin.

Ampicillin resistance

The ______ terminator signals the end of transcription for T7 RNA polymerase.

T7

The ______ ori is the origin of replication from the pBR322 plasmid.

pBR322

The Rop gene codes for proteins involved in the ______ of the plasmid.

replication

The LacI protein represses transcription of the gene of interest from the ______ promoter.

T7lac

E. coli is particularly popular when the aim of the cloning experiment is to study the basic features of ______ biology.

molecular

Cloning vectors for ______ are used when the aim of the experiment is to study gene structure and function.

E. coli

The pET expression vector is approximately ______ KB in size.

5.4

In Gateway cloning, a ______ is moved into a vector through a two-step recombination process.

insert

Lambda phage utilizes recombination machinery to integrate its genome into the host bacterial ______ during the lysogenic cycle.

chromosome

The integration reactions in Gateway cloning are mediated by a site-specific ______ system derived from bacteriophage lambda.

recombination

The recombination of attP and attB sites creates ______ and attR sites.

attL

The Gateway system involves two key ______ sites: attB and attP.

recombination

The BP reaction is involved in the creation of ______ clones.

entry

The LR reaction takes place between the attL sites of the generated ______ clone and the attR sites of the destination vector.

entry

Gateway vectors contain modified versions of the att sites so that scientists can easily clone in their desired ______ sequences.

DNA

Hydrogen bonding and ______ interactions occur between proteins and DNA.

Electrostatic

Open chromatin regions have ______ accessibility to transcription initiation complex.

Increased

The stable promotor sequence is characterized by a ______ rich sequence.

GC

Transcription factors bind to specific ______ in the DNA known as a consensus site.

sequence

The rate of peptide chain elongation increases with respect to an increase in ______.

temperatures

Strong promoters have high affinity for ______ polymerase, leading to efficient recruitment and initiation of transcription.

RNA

Epigenetic modifications include ______ methylation and histone acetylation.

DNA

At higher ______, the rate of cHSPA6 synthesis was faster due to an increase in plasmid copy number, transcription rate, and peptide chain elongation rate.

temperatures

Every protein folds differently depending upon its characteristics such as ______, hydrophobicity, post-translational modifications, isoelectric points, etc.

size

Thermus thermophilus, an extremophile, has a ______ rich genome to tolerate high environmental temperatures.

GC

The presence and affinity of transcription factor ______ sites influence the recruitment of RNA polymerase and the efficiency of transcription initiation.

binding

The final growth varied due to different ______ rates under each media.

growth

TB medium showed the highest ______ rate under uninduced conditions.

growth

The induced culture in the TB medium expressing cHSPA6 showed the lowest ______ yield.

volumetric

The LB media showed relatively higher ______ rate under induced culture conditions resulting in higher volumetric yield.

growth

If the rate of protein synthesis supersedes ______ machinery, the recombinant protein will not fold correctly.

protein folding

Promoters may contain additional regulatory elements such as ______ and silencers, which modulate gene expression in response to cellular signals or environmental cues.

enhancers

The presence and activity of these elements can influence ______ strength by affecting the rate of transcription initiation.

promoter

Consult published literature and databases to identify ______ with proven performance in specific host systems.

promoters

Experiment with different ______ to determine their suitability for driving protein expression in your specific application.

promoters

Use bioinformatics tools to predict ______ strength, specificity, and other relevant properties based on sequence analysis.

promoter

Conduct a comprehensive review of published literature and databases to identify ______ with documented performance in specific host systems or for similar protein expression applications.

promoters

Evaluate protein expression levels using quantitative assays such as Western blotting or ______ microscopy.

fluorescence

Utilize resources such as PubMed, ______ databases and scientific journals to gather relevant information.

promoter

Study Notes

Cloning Vectors

  • pET expression vector: a type of cloning vector used for protein expression in E. coli
    • Contains a T7 terminator sequence, which signals the end of transcription for T7 RNA polymerase
    • Has an ampicillin resistance gene, which provides resistance to the antibiotic ampicillin and allows for selection of bacteria that have been successfully transformed with the vector
    • Origin of replication from the pBR322 plasmid, which allows the plasmid to replicate within the host bacteria
    • Rop (Repressor of primer) gene, which regulates plasmid copy number
    • LacI (The gene coding for the lac repressor protein), which can bind to the LacO site and inhibit transcription until IPTG is added

Cloning Vectors for Eukaryotes

  • Most cloning experiments are carried out with E. coli as the host, and the widest variety of cloning vectors are available for this organism
  • E. coli is particularly popular when the aim of the cloning experiment is to study the basic features of molecular biology, such as gene structure and function

Gateway Cloning

  • Based on the principles of recombination reactions similar to those that occur during lambda phage infection in bacteria
    • Lambda phage integration and excision reactions involve recombination of attP and attB sites, creating attL and attR sites
    • Gateway cloning uses a site-specific recombination system derived from bacteriophage lambda
  • Two key recombination sites: attB (bacterial attachment site) and attP (phage attachment site)
  • Recombination of two DNA fragments, like in the Gateway system, requires specific sequences (att) within insert and vector, which are recognized by the recombinase enzyme mixtures (Clonase)

Gateway Cloning Reactions

  • Creation of entry clones: BP Reaction
  • Creation of expression clones: LR Reaction
    • LR Reaction takes place between the attL sites of the generated entry clone and the attR sites of the destination vector

Transcription Initiation Complex

  • Open chromatin regions: increases accessibility and transcription initiation complex
  • Stable promoter sequence (GC rich sequence): enhances affinity and longer residence time between promoter, TFs, and RNA pol
  • Thermus thermophilus: an extremophile with a GC-rich genome, tolerating high environmental temperatures

Transcription Factor Binding Sites

  • Promoters contain transcription factors binding sites
  • Transcription factors: proteins that control gene expression by binding to nearby DNA
  • Presence and affinity of these binding sites influence recruitment of RNA polymerase and efficiency of transcription initiation

RNA Polymerase Binding

  • Promoters interact with RNA polymerase, leading to efficient recruitment and initiation of transcription
  • Strong promoters have high affinity for RNA polymerase

Epigenetic Modifications and Chromatin Structure

  • DNA methylation
  • Histone acetylation

Regulatory Elements

  • Enhancers and silencers: modulate gene expression in response to cellular signals or environmental cues
  • Presence and activity of these elements can influence promoter strength by affecting the rate of transcription initiation

Promoter Selection Strategies

  • Literature Review: conduct a comprehensive review of published literature and databases to identify promoters with proven performance in specific host systems
  • Empirical Testing: clone the promoters into expression vectors and evaluate protein expression levels using quantitative assays
  • Bioinformatics Analysis: use bioinformatics tools to predict promoter strength, specificity, and other relevant properties based on sequence analysis

This quiz covers the components of a pET expression vector, including the T7 terminator, ampicillin resistance gene, and pBR322 origin of replication. Learn about the functions of these elements in molecular biology.

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