CS6325 Introduction to Bioinformatics
Homework Assignment I
Due on Feb. 14th, 2008
NOTE: Please type your answers to the questions 1-6.
1. Describe what central dogma is (10 points).
The main idea is the transcription of DNA to RNA to protein: This dogma forms the backbone of
molecular biology and is represented by four major stages.
1. Replication: The DNA replicates its information in a process that involves many enzymes.
2. Transcription: The DNA codes for the production of messenger RNA (mRNA).
3. Reverse Transcription: does the reverse of the transcription, from mRNA to DNA. (Virus usage)
4. Translation: Messenger RNA carries coded information to ribosomes. The ribosomes "read" this
information and use it for protein synthesis.
Proteins do not code for the production of protein, RNA or DNA.
They are involved in almost all biological activities, structural or enzymatic.
2. Describe the process of DNA replication (10 points).
DNA replication is the process of copying a double-stranded deoxyribonucleic acid (DNA) molecule, a
process essential in all known life forms. The general mechanisms of DNA replication are different in
prokaryotic and eukaryotic organisms.
As each DNA strand holds the same genetic information, both strands can serve as templates for the
reproduction of the opposite strand. The template is then separated into two separate complementary
DNA strands. Then each parent strand now is the template that determines the order of nucleotides
along a new complementary strand. At the end, the nucleotides connect to form the sugar-phosphate
3. Describe the process of DNA transcription and reverse transcription (10 points).
Transcription is the process by which genetic information from DNA is transferred into RNA. DNA
sequence is enzymatically copied by RNA polymerase to produce a complementary nucleotide RNA
strand. One significant difference between RNA and DNA sequence is the presence of U, or uracil in
RNA instead of the T, or thymine of DNA.
There are three main stages for transcriptions:
Initiation: Initiated when RNA polymerase binds to promoter binding site
Elongation: moves along DNA strand and adds corresponding complementary RNA nucleotide
Termination: disengages at stop signal.
In the case of protein-encoding DNA, transcription is the first step that usually leads to the translation
of the genetic code, via the mRNA intermediate, into a functional peptide or protein. The stretch of
DNA that is transcribed into an RNA molecule is called a transcription unit. A transcription unit that is
translated into protein contains sequences that direct and regulate protein synthesis in addition to
coding the sequence that is translated into protein. The regulatory sequence that is before, or 5', of the
coding sequence is called 5' untranslated (5'UTR) sequence, and sequence found following, or 3', of the
coding sequence is called 3' untranslated (3'UTR) sequence. Transcription has some proofreading
mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore,
transcription has a lower copying fidelity than DNA replication.
Reverse transcription, also known as RNA-dependent DNA polymerase, is a DNA polymerase
enzyme that transcribes single-stranded RNA into single-stranded DNA. Normal transcription involves
the synthesis of RNA from DNA; hence, reverse transcription is the reverse of this.
4. Describe the process of translation (10 points).
Translation is the second stage of protein biosynthesis (part of the overall process of gene expression).
Translation occurs in the cytoplasm where the ribosomes are located. Ribosomes are made of a small
and large subunit which surrounds the mRNA. In translation, messenger RNA (mRNA) is decoded to
produce a specific polypeptide according to the rules specified by the genetic code. This uses an
mRNA sequence as a template to guide the synthesis of a chain of amino acids that form a protein.
Translation is necessarily preceded by transcription. Translation proceeds in four phases: activation,
initiation, elongation and termination (all describing the growth of the amino acid chain, or polypeptide
that is the product of translation).
In activation, the correct amino acid (AA) is joined to the correct transfer RNA (tRNA). While this is
not technically a step in translation, it is required for translation to proceed. The AA is joined by its
carboxyl group to the 3' OH of the tRNA by an ester bond. When the tRNA has an amino acid linked to
it, it is termed "charged". Initiation involves the small subunit of the ribosome binding to 5' end of
mRNA with the help of initiation factors (IF), other proteins that assist the process. Elongation occurs
when the next aminoacyl-tRNA (charged tRNA) in line binds to the ribosome along with GTP and an
elongation factor. Termination of the polypeptide happens when the A site of the ribosome faces a stop
codon (UAA, UAG, or UGA). When this happens, no tRNA can recognize it, but releasing factor can
recognize nonsense codons and causes the release of the polypeptide chain.
5. Describe the process of PCR (10 points).
PCR is a process based on the ability of a DNA polymerase enzyme that can synthesize a
complementary strand to a targeted segment of DNA in a test tube mixture of the four DNA bases. In
addition, the mixture must also contain two DNA fragments, each about 20 bases long, called
primers, that have sequences complementary to areas adjacent to each side of the target
sequence. (To do PCR, you need to know the DNA sequence around the region you want to
amplify.) These primers can be constructed in the lab, or purchased from commercial suppliers. If
chosen well, the 20-25 base pair sequence will be unique in the entire human genome so will match
only the place specifically chosen thus limiting and defining the area to be copied.
The mixture is first heated to denature (separate) the sides of the double- stranded DNA and then
cooled to allow (1) the primers to find and bind to their complementary sequences on the separated
strands and (2) the polymerase to extend the primers into new complementary strands. Repeated
heating and cooling cycles multiply the target DNA exponentially, since each new double strand
separates to become two templates for further synthesis. In about 1 hour, 20 PCR cycles can amplify
the target by a millionfold. In 32 cycles at 100% efficiency, 1.07 billion copies of targeted DNA
region are created.
6. Describe the process of cloning (10 points).
Recombinant DNA cloning or gene cloning refers to the process by which a fragment of DNA is transferred
from one organism to a self-replicating genetic element such as a bacterial plasmid or a virus. Plasmids are selfreplicating extra-chromosomal circular DNA molecules, distinct from the normal bacterial genome and can be
used to make many copies of the gene. These genetic elements can then be inserted into a cell of interest and
the function of the gene of interest studied.