Molecular Neuroscience Study Questions:
Molecular neuroscience is the youngest of the major neuroscience subdisciplines, having been born a mere 15 years ago. Teaching the subject at the graduate level poses a special challenge. A strength of neuroscience is that it draws students from a wide range of undergraduate majors; the molecular biology background of entering students varies widely. Molecular neuroscience is itself rather eclectic. To understand molecular neurobiology, it is essential to have mastered a core of material in the fields of genetics, molecular biology, cell biolgy and protein chemistry. The following is a list of questions on the indispensible core background ideas. We encourage you to go through this list of questions and consult introductory texts in Biochemistry or Molecular Cell Biology to become familiar with this material.
1- Review the structures of adenine, guanine, cytosine, thymidine and uridine
2- What is the difference between ribose and deoxyribose?
3- In DNA, deoxyribose is conjugated at the 1', 3' and 5' positions. What are the substituents on each?
4- Why is A paired with T and C with G?
5- The DNA double helix is described as having "anti-parallel" chains. What is meant by this?
6- How many base pairs are there in a turn of the DNA double helix?
7- Histones are proteins that "coat" DNA in chromosomes. Histones are very enriched in lysine and arginine. Explain. What is a nucleosome?
8- A sample of DNA containing molecules of different sizes is put in an electrophoresis apparatus to separate them basis of size. The idea is that electric charge will provide the "pull" and friction of the gel medium the "drag". What polarity should the electrode you want DNA to migrate to have? Why?
9- Name 2 types of chemical forces that tend to make the 2 strands of a DNA molecule associate in a double helix. Name one that tends to prevent association. Consider DNA in solution. What can be added to the solution to counteract the associative forces? To counteract the dissociative forces?
10- We can separate DNA strands in a test tube and also re-anneal them. This is central to many technical manipulations with DNA. Why? Name 3 techniques that depend on selective annealing of DNA molecules.
11- Name 3 fundamental ways in which the structure of RNA is different from that of DNA.
12- How long are DNA molecules in living cells?
1-What is meant by the genetic code?
2- Why is it called a triplet code?
3- What is a codon?
4- What is an anticodon?
5- What can codons code for other than amino acids?
6-What is codon redundancy?
7- What is wobble?
8- What is meant by codon usage?
1- What is the functional definition of an mRNA?
2- State the "central dogma" of molecular biology
3- The 4 domains of an mRNA are the 5' UTR, the coding portion, the 3'UTR and the poly A tract. Describe the 5' and the 3' border structure of each.
4- Define an open reading frame (ORF). Are all ORFs coding portions? Are all coding portions ORFs?
5- Drawing on your knowledge of protein structure, predict the minimal size of a typical mRNA. Can you predict the maximal size? What are some actual sizes for mRNA?
6- Name 4 widely used methods for discovering the abundance and tissue distribution of mRNA.
7- Name a function that has been proposed for 3'UTRs.
1- Succinctly describe the function of a ribosome.
2- How many subunits does a ribosome have?
3-Describe the RNA components of the ribosome.
4-Describe the protein components of the ribosome.
5- Where are ribosomes located?
6- What is a polysome?
7-Define a transfer RNA (tRNA)
8- Name the 2 key functional parts of a t-RNA
9- Describe the "architecture" of a t-RNA.
10-Describe the ribosome assembly cycle that accompanies synthesis of a protein.
11-What is a Kozak sequence and why is it important?
1- What is a the primary gene transcript?
2-What is an exon? An intron?
3-How are introns removed from the primary gene transcript? Where in the cell
does this happen?
4-What is a promoter?
5-What is an enhancer?
6- What enzyme synthesizes the primary transcript?
7- How and when is the Poly A tract added?
The enzymatic synthesis of DNA is basic to life and to biotechnology. E.coli DNA polymerase is the best studied type.
1- DNA polymerase will synthesize DNA in a test tube. Aside from buffers and salts, what components are necessary for this synthesis?
2- What is the direction of chain elongation?
3- Other than new DNA, what product is generated?
4- Name a common practical use for this reaction in the molecular biology lab.
5- What is the difference between a primer and a template?
1- What is a plasmid? What are its crucial functional domains?
2- What is a bacteriophage? Draw a basic map of bacteriophage lambda
3- What is meant by a "vector" in molecular biology? Why are plasmids and bacteriophage lambda good vectors?
4- What is a restriction endonuclease? Why did these enzymes revolutionize molecular biology?
5- Describe the recognition and cutting sites for typical restriction endonucleases.
6- When we say "a DNA segment was cloned", what exactly do we mean?
7- Cloning is both "amplifying" and "resolving". Explain?
8- Define a genomic library; a genomic phage library.
9- What is a YAC? A BAC? What special uses do they have?
10- Describe the biochemical reaction catalyzed by reverse transcriptase. Define a cDNA.
11- What is a cDNA library?