Test 2 Practice Questions

1.  Explain three different kinds of RNA that are NOT messenger RNA, and do not get translated by ribosomes.

tRNA (transfer RNA), rRNA (ribosomal RNA forms the core of each subunit), other nuclear RNAs such as those in RNA-protein particles of the spliceosome. Each RNA has its own function, and is not translated to protein. Each RNA makes a stem-loop structure.

2.  Compare and contrast transcription of DNA to RNA in prokaryotes and in eukaryotes.

DNA transcribed in prokaryotes occurs throughout the cell, together with translation of RNA by the ribosome to make proteins. In eukaryotes, transcription occurs in the nucleus. Some translation occurs, mainly to check that the mRNA was transcribed correctly, but most translation occurs outside the nucleus, in the cytoplasm.

Prokaryotes have one RNA polymerase. Eukaryotes have three different RNA polymerases, one of which (RNA Pol II) transcribes the mRNA; the others transcribe tRNA, rRNA and other functional RNAs.

3.  How can a bioinformatics program recognize a gene sequence in a genome?  How would this be different in bacteria and in eukaryotes?  What problems arise?

A bioinformatics program checks for the presence of ATG start codons as well as stop codons, and promoter sequences. In eukaryotes, the program also has to check for intron splice joint sequences. The large number and size of introns increases the chance of mistaking the location of intron splice joints, resulting in incorrect identification of a gene sequence.

4.  Explain how a transfer RNA (tRNA) is matched with an amino acid, and how the correct amino acid is selected to add to a nascent polypeptide.

A tRNA has to be matched to an amino acid by an amino-acid tRNA transferase. Each tRNA needs a specific transferase enzyme.
The correct amino acid is inserted as a result of base pairing between the tRNA anticodon and the mRNA codon, positioned within the A site of the ribosome.

5.  Is the genetic code a three-letter code or a two-letter code?  Explain.

The genetic code is based on three-letter "words," but in most cases the third base does not need to match exactly; either it doesn't matter, or only purine/pyrimidine is what matters. Methionine and Tryptophan however do require an exact three-letter match.

6.  How does translation by the ribosome initiate?  Elongate?  Terminate?

Review here:

7.  Explain the molecular basis of mutations: transitions, transversions, frame-shift, pyrimidine dimers, chromosome backbone breakage, chromosome rearrangements.  Explain physical or chemical events that can cause each mutation.

Transitions are point mutations in which a purine replaces a purine, or a pyrimidine replaces a pyrimidine. They are the most common point mutations. They occur when the DNA polymerase makes an error, or when one base is chemically changed, such as cytosine deamination.
Transversions occur when a purine is exchanged for a pyrimidine. They are rarer, resulting from multiple errors in an enzyme pathway.
Frameshift occurs when the DNA polymerase inserts an extra base or removes a base. They occur by accident when an intercalating agent has inserted between two base pairs.
Pyrimidine dimers occur as a result of a reaction from UV absorption. The DNA polymerase then inserts the wrong bases to pair with them.
Chromosomes can break at the phosphodiester backbone as a result of absorbing X-rays or cosmic rays.
When a chromosome breaks, one arm tends to get stuck onto another chromosome by a repair enzyme.

8.  Explain the informational effect of mutations (each of the above.)  Explain how each molecular kind of mutation can have a major effect, or a minor effect (or none) on phenotype.

A point mutation can have no effect if it does not change the coding specificity of the codon. This is called a silent mutation.
If the mutation makes a codon that specifies a different amino acid, but the protein still works the same, then it is a missense mutation, but its effect is a neutral mutation. Alternativerly, if the amino acid forms part of a critical active site, then it could be a null mutation.
A mutation that causes a premature stop codon is a nonsense mutation. It could result in a null mutation, if no functional product is formed.
Inserting or removing a base pair causes a frameshift. The frameshift usually leads to premature termination at a nonsense codon, and results in a null phenotype.
Chromosome breakage and rearrangement may lead to multiple problems for the individual; or it may have no effect, if all the genes remain present somewhere. However, a rearranged chromosome in the germ cells is very likely to cause problems in the offspring because it will produce gametes with uneven amounts of genes (an extra copy of some genes, or missing others.)

9.  Explain how an intron is spliced out of a cell.  Include the roles of information (base pair sequence), of chemical reactions, and of accessory particles.

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10.  Explain two different ways that differential splicing of exons can regulate development.


11.  Explain how the cell cycle is regulated by gene expression, and how the components of cell cycle regulation are vulnerable to predisposition to cancer.


12.  Explain the difference between orthologs and paralogs.  Illustrate by describing a specific example of a pair of orthologs, and a pair of paralogs.

Orthologs are genes in two different organisms that evolved from a common ancestral gene; for example, the beta globin gene in mice and in humans. They have the exact same function.

Paralogs are genes within an organism that arose from a genome duplication. They have evolved different functions. For example, the genes for different opsins in color vision evolved from duplication of an original opsin gene, followed by accumulation of mutations and altered wavelength sensitivity.

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