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TUTORIAL: DNA BIOLOGY AND TECHNOLOGY
1. Describe the biochemical composition, structure and replication of DNA.

DNA is a polymer where the monomer units of DNA are nucleotides and the
polymer is known as polynucleotide. DNA molecule consists of two strands of
polynucleotide that wound together into a double helix. In the two polynucleotide strands
is a phosphate group linked together by a phosphodiester bond between the phosphate
group of one nucleotide and the hydroxyl group of carbon 3 of the next nucleotide that is
3\u2019 terminal while at one end of each strand is a phosphate group linked to the carbon 5 of
deoxyribose sugar. This is the 5\u2019 terminal of each strand. The 3\u2019 and 5\u2019 terminals of the
two strands are at opposite ends where the two strands is antiparallel. The two
polynucleotide strands in the double helix DNA molecule are held together by hydrogen
bonds between complementary purine-pyrimidine base pairs. There are four different
types of nucleotides found in DNA, differing only in the nitrogenous which are adenine,
guanine, cytosine and thymine.

The sequence of steps in DNA replication is based on the semiconservative model
that is takes place in the 5\u2019-3\u2019 direction using a DNA template strand. This process is
catalyzed by DNA polymerase III. This process begin with the unwinding of the DNA
double helix to form a replication fork. The unwinding is catalyzed by the enzyme, DNA
helicase. The DNA helicase enzyme unwinds the double-stranded DNA to a replication
fork ready for replication. The antiparallel nature of the strands, that is the 5\u2019-3\u2019
orientation of the top strand and the 3\u2019-5\u2019 orientation of the complementary bottom
strand. Then, the DNA is already partially unwound to form a replication fork. On the
bottom template strand, RNA primase attaches a short RNA primer in the 5\u2019-3\u2019 direction.
After that, the RNA primase is removed, and free DNA nucleosides are added by DNA
poltmerase III to the RM|NA primer in the 5\u2019-3\u2019 direction. This new strand is called the
leading strand because it is made in the same direction as the movement of the replication
fork. On the top template strand, RNA primase synthesizes a short RNA primer in the a
short RNA primer in the 5\u2019-3\u2019 direction. RNA primase is removed, and DNA polymerase
III adds nucleosides to the RNA primer one after another opposite to the replication fork

to form a short length DNA. This new short length is called the lagging strand because it
is made in the direction opposite to the movement of the replication fork. The fragment
produced is also called Okazaki fragment. The process repeat as the DNA continues to
unwind. Then, the RNA primers are removed by a different type of enzyme called DNA
polymerase I. The two Okazaki fragments are then sealed and joined up by the DNA
ligase to produce a continuous chain called lagging strand antiparallel to the leading
strand formed earlier. Two new antiparallel continuous strands which are one leading
strand and one lagging strand, are formed. The new double-stranded daughter DNA
molecules daughter DNA molecules then twist or wind to form double helix DNA
molecules.

2.(a) Describe the steps in the synthesis of the polypeptide.

There are two processes that undergoes by a cell in the synthesis of the polypeptide which are transcription and translation. Transcription is a process where the information in DNA is transcribed to a RNA molecule, called messenger RNA (mRNA). During transcription, one of the DNA strands acts as a template whereby a mRNA is transcribed complementary to the DNA template strand. A specific protein-coding gene consists of a promoter followed by the RNA-coding sequences for a protein and then a terminator. The promoter is a base-sequence that specifies where transcription is begins while the RNA-coding sequences is a base-pair sequence that includes coding information for the polypeptide chain specified by the gene. Besides, the terminator is a sequence that specifies the end of the mRNA transcript. Transcription is catalyzed by an enzyme called RNA polymerase when initiation of the transcription at the promoter site is begins. This involves specific recognition of promoter base sequence by RNA polymerase (in prokaryotes) or a complex of proteins (in eukaryotes). RNA synthesized is initiated with the addition of free RNA nucleotides in the 5\u2019-3\u2019 direction opposite with attachment at -OH end to the uncoiling direction of the DNA segment. The same rule of complementary base pairing are followed as in replication, except that uracil (U) replaces thymine (T) to pair with adenine (A), as RNA does not contain tnymine. After the RNA

synthesis is initiated, the RNA elongation will continue to the direction of 5\u2019-3\u2019 direction with the addition of more free nucleotides by RNA polymerase. Then, transcription will terminate when the terminator base sequence is recognized by RNA polymerase. In eukaryotes, introns and exons formed in the pre-mRNA during transcription are removed to produce mature mRNAs.

While translation is a process where the genetic information transferred to a mRNA from the DNA is translated by ribosomes into amino acid sequence on polypeptides. This process requires the assistance of tRNA including the mRNA, rRNA and ribosome, enzymes and ATP which are initiated with the movement of mRNA from nucleus to ribosome. Ribosomes, the organelles on which the mRNA is translated, consist of two subunits, each of which contains rRNA an ribosomal protein. Ribosomes do not carry genetic information but facilitate the interaction of tRNA with mRNA during protein synthesis. The small subunit of a ribosome, binds to the 5\u2019 end of an mRNA molecule. The small subunit slides along the mRNA until it reaches the start codon, which shows where translation should be initiated. The large subunit then binds to the small subunit to form a complete RNA-ribosome complex. The first tRNA occupies the P site and the A site is available for the next tRNA. At the end of the initiation stage, elongation begins when the vacant A site is bound by another charged tRNA with an anticodon complementary to the codon after the start codon on the mRNA. The ribosome moves three (a codon) nucleotides along the mRNA in a \u20185-3\u2019 direction and detaches the peptide from the tRNA at the P site. The detached peptide is then attached by a peptide linkage to the single amino acid on the A site. In the process during which the ribosome slides across to the next codon of the mRNA, the tRNA at the P site is then displaced and detached from the ribosome. The P site is then adjacent tRNA carrying the polypeptide chain. The vacant A site will the be occupied by the next tRNA. The steps repeat in a cycle called ribosome until translation is terminated. When the ribosome reaches a stop codon, there is no tRNA that has a complementary anticodon. This signals the end of translation. The large subunit advances over the small subunit. The polypeptide is detached from the tRNA, and starts to fold up to form the final shape of the protein. The rRNA disintegrates to release the large subunit, small subunit, tRNA and mRNA.

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