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
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
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
A tRNA has to be matched to an amino
acid by an amino-acid tRNA transferase. Each tRNA needs a specific
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?
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
6. How does translation by the ribosome initiate? Elongate?
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
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.
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
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
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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