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Protein Expression Quiz

What cellular machinery is responsible for protein synthesis?
a) Mitochondrion
b) Ribosome
c) Golgi apparatus
d) Vacuole
Ribosome.
 
Protein synthesis is carried out by the ribosome. A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein, also known as a ribozyme.
Ribosome.
 
Protein synthesis is carried out by the ribosome. A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein, also known as a ribozyme.
What type of RNA is decoded, or translated, by the ribosome to synthesize proteins?
tRNA (transfer RNA)
snoRNA (small nucleolar RNA)
rRNA (ribosomal RNA)
mRNA (messenger RNA)
mRNA (messenger RNA)
 
mRNA is the intermediary between DNA and protein. mRNA is transcribed from DNA to form a transient blueprint that binds to the ribosome. The ribosome then decodes the mRNA as triplet codons corresponding to specific amino acids to synthesize proteins.
mRNA (messenger RNA)
 
mRNA is the intermediary between DNA and protein. mRNA is transcribed from DNA to form a transient blueprint that binds to the ribosome. The ribosome then decodes the mRNA as triplet codons corresponding to specific amino acids to synthesize proteins.
How does one express a toxic protein in E. coli?
Clone the protein into a silent expression vector with low basal promoter activity when uninduced
Use a T7 vector with a T7 lysozyme host strain such as T7 Express lysY-Iq
Clone the protein with a weak Ribosome Binding Site
Express the protein in a different compartment, such as the periplasm, or secrete it to the extracellular milieu
All of the above
All of the above, in order of importance:
  1. Use a T7 vector with a T7 lysozyme host strain such as T7 Express lysY-Iq
  2. Clone the protein into a silent expression vector with low basal promoter activity when uninduced
  3. Clone the protein with a weak Ribosome Binding Site
  4. Express the protein in a different compartment, such as the periplasm, or secrete it to the extracellular milieu
Expressing the protein to the periplasm is a last resort option. The periplasm is not compatible with many proteins since cysteines will be linked. Many proteins will be misfolded/inactive with disulfides if the protein is not naturally secreted.
 
For more information, see the references:
“Recombinant protein secretion in Escherichia coli.” Biotechnol Adv. 2005 May;23(3):177-202
 
What is the best method for expressing an insoluble protein in E. coli?
Express the target protein as a fusion to MBP
Try various homologs from different phyla
Lower the temperature of expression to 16°C
Lower the inducer conditions, including no inducer
All the above
All the above, in order of importance:
  1. Lower the temperature of expression to 16°C
  2. Lower the inducer conditions, including no inducer
  3. Express the target protein as a fusion to MBP
  4. Try various homologs from different phyla
 
For more information, see the reference:
 
All the above, in order of importance:
  1. Lower the temperature of expression to 16°C
  2. Lower the inducer conditions, including no inducer
  3. Express the target protein as a fusion to MBP
  4. Try various homologs from different phyla
 
For more information, see the reference:
 
I am trying to express a eukaryotic, endoplasmic reticulum resident protein, which requires disulfide bonds for proper folding. What is the easiest method to achieve soluble expression?
Co-express eukaryotic chaperones to promote disulfide bond formation
Clone truncated versions of the protein, looking for soluble domains that lack disulfide bonds
Mutagenize the cysteines to alanines, thereby avoiding the necessity for disulfide bonds
Express the protein in an engineered E. coli strain that can oxidize cysteines in its cytoplasm
Express the gene of interest in the cytoplasm of the E. coli strain SHuffle, which has been demonstrated to promote disulfide bond formation for eukaryotic proteins for proper folding and activity. Delete the gene segment which encodes the signal peptide.
 
For more information, see the references:
“Production of disulfide-bonded proteins in Escherichia coli.” Protein Expr Purif. 2012 Mar;82(1):240-251.
“Use of the SHuffle Strains in Production of Proteins.” Curr Protoc Protein Sci. 2016 Aug 1;85:5.26.
 
Express the gene of interest in the cytoplasm of the E. coli strain SHuffle, which has been demonstrated to promote disulfide bond formation for eukaryotic proteins for proper folding and activity. Delete the gene segment which encodes the signal peptide.
 
For more information, see the references:
“Production of disulfide-bonded proteins in Escherichia coli.” Protein Expr Purif. 2012 Mar;82(1):240-251.
“Use of the SHuffle Strains in Production of Proteins.” Curr Protoc Protein Sci. 2016 Aug 1;85:5.26.
 
What is the historical reason for naming the E. coli strain “K-12”?
a. It was isolated from a patient’s stool in the hospital room K-12
b. It was isotyped using the outer membrane K antigens
c. It was stored as a stab in the shelf K, row 12
d. No one knows
No one knows.
 
Lost in history and sadly no one knows. The strain was used as a genetic model in the labs of Edward Tatum (1909 − 1975) and Joshua Lederberg (1925 − 2008), but no record can be found on the naming of this iconic model organism.
 
For more information, see the reference: “How did E. coli get named K-12 ?”
 
No one knows.
 
Lost in history and sadly no one knows. The strain was used as a genetic model in the labs of Edward Tatum (1909 − 1975) and Joshua Lederberg (1925 − 2008), but no record can be found on the naming of this iconic model organism.
 
For more information, see the reference: “How did E. coli get named K-12 ?”
 
Which mRNA sequence helps the bacterial ribosome initiate protein synthesis by properly aligning the start codon?
The Initiation Consensus Sequence
The Kozak Consensus Sequence
The Shine-Dalgarno Sequence
The Okazaki Fragment
The Shine-Dalgarno Sequence.
 
The Shine-Dalgarno (SD) Sequence is a ribosomal binding site in bacterial and archaeal mRNA located approximately 8 bases upstream of the start codon AUG. The sequence is named after the two Australian scientists, John Shine and Lynn Dalgarno, who proposed the sequence in their 1975 Nature article “Determinant of cistron specificity in bacterial ribosomes.”
The Shine-Dalgarno Sequence.
 
The Shine-Dalgarno (SD) Sequence is a ribosomal binding site in bacterial and archaeal mRNA located approximately 8 bases upstream of the start codon AUG. The sequence is named after the two Australian scientists, John Shine and Lynn Dalgarno, who proposed the sequence in their 1975 Nature article “Determinant of cistron specificity in bacterial ribosomes.”
Which of the following is a rare codon in E. coli?
TAG
CGT
AGG
TGG
AGG.
 
AGG is a rare codon for arginine in E. coli. A codon rarely used in synonymous codons is called a rare codon. Changing rare codons to frequent codons often increases protein synthesis yields both in vitro and in vivo.
AGG.
 
AGG is a rare codon for arginine in E. coli. A codon rarely used in synonymous codons is called a rare codon. Changing rare codons to frequent codons often increases protein synthesis yields both in vitro and in vivo.
What is the distinctive characteristic of all in vitro protein expression systems?
Alternative genetic code
Open system
Post-translational modifications
Simple protein purification
Open system.
 
Cell-free (in vitro) protein synthesis takes place in an environment that is not dependent on cell growth, integrity, or viability. The open nature of the system enables easy manipulation of multiple variables such as sequence (codon optimization, tags, point mutations, etc), reaction time, temperature, co-factors, etc. Therefore, cell-free protein synthesis is well suited for unnatural amino acid incorporation, production of toxic proteins, in situ labelling, protein evolution, and production of protein variants.
Open system.
 
Cell-free (in vitro) protein synthesis takes place in an environment that is not dependent on cell growth, integrity, or viability. The open nature of the system enables easy manipulation of multiple variables such as sequence (codon optimization, tags, point mutations, etc), reaction time, temperature, co-factors, etc. Therefore, cell-free protein synthesis is well suited for unnatural amino acid incorporation, production of toxic proteins, in situ labelling, protein evolution, and production of protein variants.
Which protein is the most abundant in bacterial cells?
EF-TU
Actin
Histone
tRNA synthetase
EF (elongation factor)-TU is responsible for catalyzing the binding of an aminoacyl-tRNA (aa-tRNA) to the ribosome as the first step of protein translation.
EF (elongation factor)-TU is responsible for catalyzing the binding of an aminoacyl-tRNA (aa-tRNA) to the ribosome as the first step of protein translation.
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*NO PURCHASE NECESSARY TO PARTICIPATE. This promotion is open only to eligible life science professionals 18 years and older in the US (excluding Puerto Rico), Canada, the UK, BeNeLux, Bulgaria, Croatia, Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Italy, Norway, Poland, Romania, Russia, Serbia, Slovakia, Slovenia, South Africa, Spain, Sweden and Turkey, who complete the quiz no later than 8:00 pm U.S. Eastern Time on March 31st, 2020. Health care professionals may not participate in this promotion. Government Officials prohibited from receiving a prize valued at $10 USD or over may not participate in this promotion. The term “Government Official” shall mean: (i) any officer or employee of a government or any department, agency or instrument of a government; (ii) any person acting in an official capacity for or on behalf of a government or any department, agency, or instrument of a government; (iii) any officer or employee of a company or business owned in whole or part by a government; (iv) any officer or employee of a public international organization such as the World Bank or United Nations, the European Union or the World Health Organization; (v) any officer or employee of a political party or any person acting in an official capacity on behalf of a political party; and/or (vi) any candidate for political office. Up to 20 winners will be chosen at random at the end of the promotion period, and notified via email by New England Biolabs, Inc. (NEB). The estimated value of the water bottle is $10 USD. This promotion cannot be combined with other discounts or promotions. Offer void where prohibited, licensed, or restricted by federal, state, provincial, or local laws or regulation or agency/institutional policy. By submitting your entry, you warrant that you are not prohibited by employment, contract, or law from accepting a promotional item from NEB. Other restrictions may apply.
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