Questions and Answers of Biochemistry Concepts And Connections

What is a σ factor? Why is it important in transcription?
What is the difference between σ70 and σ32?
Diagram a termination of transcription showing how inverted repeats can be involved in releasing the RNA transcript.
What is an aptamer?
What is a riboswitch?
What are the products of the reactions of the three eukaryotic RNA polymerases?
List the Pol II general transcription factors.
Describe the function of three eukaryotic response elements.
Diagram a gene that is affected by CRE and CREB, showing which proteins and nucleic acids contact each other.
Defend or attack this statement: “All eukaryotic promoters have TATA boxes.”
Give examples of structural motifs found in transcription factors that interact with other proteins instead of DNA.
What is the difference in how mediator works with activation vs. repression of transcription?
How do nucleosomes add to the complexity of eukaryotic transcription?
What are the two main circumstances necessary for active transcription?
What are the two main components to activation of transcription via epigenetic mechanisms
What are chromatin remodeling complexes?
What are the most well-studied chromatin remodelers?
What enzymes are involved in histone acetylation and deacetylation?
In what processes are non-coding RNAs important?
What is a potential link between prostate cancer and miRNA-101?
What are the guide and passenger strands in production of small RNAs?
What is the principal difference between the binding of siRNA and miRNA with mRNA?
What is the difference between how miRNA stops gene expression and how siRNA does?
List three important structural motifs in DNA-binding proteins.
List several ways in which RNA is processed after transcription.
What do the proteins Tau and troponin have in common?
Why is a trimming process important in converting precursors of tRNA and rRNA to the active forms?
List three molecular changes that take place in the processing of eukaryotic mRNA.
What are snRNPs? What is their role in the processing of eukaryotic mRNAs?
Diagram the formation of a lariat in RNA processing.
Why are proteins more effective catalysts than RNA molecules?
What does “epigenetics” mean
What is an “epimutation”?
What is the link between epigenetics and cancer?
What is the epigenetic change that Peleg studied with respect to aging mice?
How did scientists restore memory in mice? How did this support their theory about epigenetics and cognitive memory?
Prepare a flow chart showing the stages of protein synthesis.
A genetic code in which two bases encode a single amino acid is not adequate for protein synthesis. Give a reason why.
Define degenerate code.
Which nucleotides break the rules of Watson–Crick base pairing when they are found at the wobble position of the anticodon?Which ones do not?
It is possible for the codons for a single amino acid to have the first two bases in common and to differ in the third base. Why is this experimental observation consistent with the concept of wobble?
The nucleoside inosine frequently occurs as the third base in codons. What role does inosine play in wobble base pairing?
How would protein synthesis be affected if a single codon could specify the incorporation of more than one amino acid (an ambiguous code)?
Comment on the evolutionary implications of the differences in the genetic code observed in mitochondria.
What is the role of ATP in amino acid activation?
Can the same enzyme esterify more than one amino acid to its corresponding tRNA?
A friend tells you that she is starting a research project on aminoacyl esters. She asks you to describe the biological role of this class of compounds. What do you tell her?
Is amino acid activation energetically favored? Why or why not?
What is the role of the 50S ribosomal subunit in prokaryotic protein synthesis?
How does puromycin function as an inhibitor of protein synthesis?
Describe the role of the stop signals in protein synthesis.
Does mRNA bind to one or to both ribosomal subunits in the course of protein synthesis?
You are studying with a friend who says that the hydrogen-bonded portions of tRNA play no important role in its function. What is your reply?
E. coli has two tRNAs for methionine. What is the basis for the distinction between the two?
In prokaryotic protein synthesis, Nformylmethionine (fmet) is the first amino acid incorporated, whereas (normal) methionine is incorporated in eukaryotes. The same codon (AUG) serves both. What
Describe the recognition process by which the tRNA for N-formylmethionine interacts with the portion of mRNA that specifies the start of transcription.
The fidelity of protein synthesis is assured twice during protein synthesis. How and when?
In the early days of research on protein synthesis, some scientists observed that their most highly purified ribosome preparations, containing almost exclusively single ribosomes, were less active
Suggest a scenario for the origin and development of peptidyl transferase as an integral part of the ribosome.
Would you expect electron microscopy to give detailed information about ribosomal structure?
How does it improve the efficiency of protein synthesis to have several binding sites for tRNA close to each other on the ribosome?
A virus does not contain ribosomes. How does it manage to ensure the synthesis of its proteins?
What conserved sequences are important to codon recognition in prokaryotic release factors?
What sequence in the prokaryotic release factors is important to the hydrolysis of the peptide bond?
Why do amino acids other than methionine occur in the N-terminal position of proteins from eukaryotes?
Would puromycin be useful for the treatment of a virus infection? Why or why not? Would chloramphenicol be useful?
Why is it advantageous to have a mechanism to override the effect of stop codons in protein synthesis?
What process distinguishes a short term memory from a long-term one?
What transcription factor in the nucleus of a neuron is known to play a role in creating long-term memories?
What is one experiment done to show that protein synthesis is required to make long-term memories?
The amino acid hydroxyproline is found in collagen. There is no codon for hydroxyproline. Explain the occurrence of this amino acid in a common protein.
What types of proteins are known to be translated using an alternate start codon?
What are chaperones?
How would protein synthesis be different if there were no chaperones?
How were chaperones discovered?
Are chaperones the only proteins that aid in correct protein folding?
What role does ubiquitin play in the degradation of proteins?
Consider protein degradation in the absence of ubiquitinylation. Is the process likely to be more or less efficient?
What are exonic splicing enhancers and how are they important?
How can a silent mutation lead to “exon skipping”?
What process in mRNA folding leads to sensitivity to pain due to an effect on the COMT gene?
What diseases are known to be caused by silent mutations?
What transcription factors are important to how we adapt to high altitude?
What advantages does fluorescent labeling offer over radioactive methods of labeling DNA?
What methods are used to visualize radioactively labeled nucleic acids?
How does the use of restriction endonucleases of different specificities aid in the sequencing of DNA?
What is the importance of methylation in the activity of restriction endonucleases?
Why do restriction endonucleases not hydrolyze DNA from the organism that produces it?
Give three examples of DNA palindromes.
What are three differences between the sites recognized by HaeIII and those recognized by BamHI?
Describe the cloning of DNA.
What vectors can be used for cloning?
What are some general “requirements” for recombinant DNA technology?
What are the purposes of genetic engineering in agriculture?
What human proteins have been produced by genetic engineering?
You go for a drive in the country with some friends and pass a cornfield with a sign. They do not understand the cryptic message on the sign, with the letters “Bt” followed by some numbers.You
A friend tells you that she doesn’t want to feed her baby high-production milk because she is afraid that the BST will interfere with the baby’s growth by overstimulation. What do you tell her?
Outline the methods you would use to produce human growth hormone (a substance used in the treatment of dwarfism) in bacteria.
Bacteria and yeast are known not to have prions (Chapter 4). What does this fact have to do with the popularity of expressing mammalian proteins using bacterial vectors?
Why is it a large undertaking to construct a DNA library?

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