The DNA molecule and Protein Synthesis

There are two nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
These two enable living organisms to reproduce their complex systems from
generation to generation. DNA is the genetic material that organisms inherit from
their parents. Each time a cell reproduces itself by dividing, the DNA is copied and
passed along from one generation of cells to the next. Within the structure of DNA are
instructions that program all the cells activities. These instructions are packaged in
genes along the entire length of DNA molecule.
The other type of nucleic acid, RNA, functions in the synthesis of proteins specified by
the DNA. Information flows from DNA to RNA and to proteins. The third nucleic acid is
an energy carrier called adenosine triphosphate (ATP). ATP is responsible for
transferring chemical energy from one molecule to another in cellular processes.
The DNA molecule is a polymer of nucleotides that are linked together by hydrogen
bonds. Each nucleotide is itself composed of three parts: a nitrogenous base, which is
joined to a five-carbon sugar (pentose) which in turn is bonded to a phosphate group.

There are two types of bases: purines (adenine, guanine), having a double ring and
pyrimidines (thymine and cytosine) having a single ring. The nucleotides are called
bases because they have basic properties that raise the pH a solution.
The bases are paired and bound to each other by hydrogen bonds. Adenine (A) is
paired with thymine (T) and guanine (G) is paired with cytosine (C).

How nucleotides are linked in a DNA molecule

Another name for a nucleic acid is a polynucleotide. In a polynucleotide, the bases

are linked by covalent bonds called phosphodiester linkages between the phosphate
of one nucleotide and the sugar of the next nucleotide. This results in a backbone of
repeating pattern of sugar-phosphate-sugar-phosphate with variable appendages of
the four kinds of nitrogenous bases.
Watson and Crick model
Watson and Crick in 1953 proposed a double helix for the structure of DNA, somewhat
like a twisted ladder in which the sugar-phosphate backbone of each polynucleotide
strand makes up the sides of the ladder, with the nitrogenous bases making up the
rungs or steps of the ladder.

DNA structure

Most DNA molecules are very large with thousands or even millions of base pairs. One
long DNA molecule represents a large number of genes, occupying a particular
segment along the double helix. The bases in the double helix occur in pairs: adenine
always pairs with thymine, while guanine always pairs with cytosine. If we were to
read the sequence of the bases along one strand along the length of the double helix,
we would automatically know the sequence of bases along the other strand.
For example, if the sequence of bases along one strand is AGGTCCG, the sequence
along the other strand should be TCCAGGC. This is because the two strands of DNA are
complementary.
DNA replication
An important characteristic of a genetic material is its ability to be copied or
duplicated and thus pass on the genetic material to the next generation. Watson and
Crick proposed the following method for the duplication of the genetic material. DNA
replication begins with an unzipping of the parent molecule, breaking the hydrogen

bonds between the base pairs by the action of an enzyme called polymerase. The two
pairs of the molecule unwind. Once exposed, the sequence of bases on each of the
separated strands serves as a template or mould to guide the insertion of a
complementary set of bases on the strand being assembled.

DNA replication

Thus, each C on the parent template guides the insertion of G on the new strand;
each G on the old strand guides the insertion of C on the new strand. Similarly, each A
on the parent strand guides the insertion of T on the new strand, etc. When the
process is completed, two DNA molecules have been formed, identical to each other
and to the parent molecule.
Protein Synthesis
Every cell in our bodies contains genes that specify every aspect of our heredity, such
as the color of the eyes, the structure of the ears or teeth, height, etc. The genetic
instructions stored in DNA allow the cells to produce particular proteins that will
determine the hereditary characteristics of an individual.

In other words, proteins are the tools of heredity. In synthesizing proteins, cells use
RNA.
The structure of RNA
Ribonucleic acid (RNA) is also a polynucleotide. The chain of nucleotides is formed in
exactly the same way as in DNA, but the molecule has some very important
differences:
1. It is a single stranded molecule.
2. The Thymine is replaced by Uracil.
3. It is much smaller than DNA.
4. It comes in three different forms, ribosomal (rRNA), transfer (tRNA) and
messenger (mRNA).
Ribosomal RNA is 80% of the total RNA in a cell. It is involved with the formation of
ribosomes and is therefore important as the site of protein synthesis in a cell.
Messenger RNA is 3-5% of the total RNA in a cell, depending on the protein synthesis
activity at the time. It forms in the nucleus and it is a go-between for DNA in the
nucleus and ribosomes in the cytoplasm.
Transfer RNA is about 15 % of the total RNA in the cell. It is involved in carrying the
amino acids through the cytoplasm to their correct places in a growing polypeptide
chain.
Table: DNA compared with RNA
DNA
Found only in the nucleus
Double stranded
Thymine nucleotide
The sugar is deoxyribose

RNA
Found in the nucleus and in the cytoplasm
Single stranded
Uracil nucleotide
The sugar is ribose

While DNA is found only in the nucleus of a cell, RNA is present both in the nucleus
and in the cytoplasm. mRNA takes coded messages from DNA to the cytoplasm where
they are decoded and used to guide protein synthesis.
Transcription and Translation
Protein synthesis is a two-stage process. The first process is known as transcription,
which involves the formation of mRNA and the copying of genetic information from
DNA to mRNA. The process begins with the binding of an enzyme called RNA
polymerase to special sites on the DNA molecule, followed by the separation of the
two strands of DNA. The RNA polymerase then copies information from one of the two
strands to mRNA.
Transcription takes place in the nucleus of the cell, after which the newly formed
mRNA moves through pores in the nuclear membrane to the endoplasmic reticulum in
the cytoplasm where translation or protein synthesis takes place.
Translation involves coded messages in which three nucleotides in a row on the mRNA
form a codon, with each codon specifying an amino acid. On the other hand, each
tRNA molecule carries at one end an anticodon of three nucleotides that are
complementary to the mRNA codon and an amino acid at the other end. There is at
least one tRNA for each of the 20 amino acids needed to make protein. Some amino
acids may have more than one tRNA molecules.
Protein synthesis begins when mRNA, with the genetic information copied from the
DNA molecule, moves to the endoplasmic reticulum in the cytoplasm and binds to a
ribosome. The binding occurs at a particular site on the mRNA called the initiation
site.

Next, the tRNA with its anticodon, binds to the codon AUG at a site on the mRNA
designated P that initiates every message. The AUG codon represents the amino acid
methionine (met) and is called the initiation codon. This amino acid is always at the
beginning of every protein chain. The tRNA- amino acid complex remains attached to
the mRNA codon. The ribosome moves along the mRNA strand and exposes a new
codon. Another tRNA, with an anticodon complementary to the next codon on the
mRNA assembly line, moves in and occupies the next site on the mRNA called A. In
this case, the codon on the mRNA is GCC, which codes for alanine. The first amino
acid is then linked to the incoming amino acid by a peptide bond.

Protein synthesis

The ribosome moves one codon to the right. The tRNA at site P is released, and site P
now becomes occupied by the second tRNA, leaving site A for the next incoming tRNA
with an anticodon that can base pair with UGG codon. Each time the ribosome moves
along the mRNA, an additional amino acid is added to the growing peptide. The
process continues until a complete protein of a particular sequence is formed.

Termination of protein synthesis occurs at a specific nucleotide sequence on the

mRNA where the last tRNA and completed polypeptide are detached from the
ribosomal complex.
DNA Repair
As the two strands in a DNA molecule are complementary, the information carried by
one strand is identical to the information carried by the other. Therefore, if a part of
one of the strands breaks and gets lost, the cell will still have a full complement of
information stored in the undamaged strand. The lost piece of the damaged strand
can be regenerated with the undamaged strand acting as a template.
Study Questions
1. Describe the structure of DNA, including the double-helix model.
2. Describe how the processes of transcription and translation occur.
3. Write a few notes on each one of the following: DNA, mRNA, tRNA and rRNA
5. How does DNA replicate? Explain the significance of replication.