STRUCTURE AND FUNCTIONS OF DNA AND RNA

The Genetic Code

The genetic code is the basis of all life on earth, and the structure and function of DNA support the cell's
ability to create proteins and RNA to carry out all cellular functions. Understanding how DNA works is crucial
to understanding life processes.
The specific order of the nucleotide bases, reading from the 5' end to the 3' end, makes up the genetic code,
which directs the production of all components of a cell. Deoxyribonucleic acid (DNA) and Ribonucleic
acid (RNA) is a class of molecules called nucleic acids. Nucleic acids were originally discovered in 1868 by
Friedrich Meischer, a Swiss biologist, who isolated DNA from pus cells on bandages. In 1943 and 1952,
Oswald Avery and colleagues and Alfred Hershey and Martha Chase illustrated the information role of DNA.
In 1953, James D. Watson and Francis Crick discovered the structure of DNA at Cambridge University.
Watson, Crick and Wilkins received the Nobel Prize in Medicine for the discovery of DNA's structure. All
nucleic acids are made up of simple repeating units known as nucleotides, linked together to form chains or
strands, often of great length such as DNA molecule. The strands vary in the sequence of the bases found on
each nucleotide. It is this sequence which provides the genetic code for the cell. The genetic code consists of
61 amino-acid coding codons and three termination codons, which stop the process of translation.

The genetic code

DNA Structure
DNA, along with RNA, is a nucleic acid, a macromolecule made up of a strand of nucleotides. Nucleotide
molecules are made of a nucleotide base, a five-carbon sugar and phosphate groups. DNA, deoxyribonucleic
acid, is made of two long strands of nucleotide bases with a sugar and phosphate backbone. The sugar-
phosphate backbones are on the outside and the nucleotide bases are attached in the middle by hydrogen bonds
and the strands are coiled around each other to create a helical ladder-like form. This double helix is then
coiled and folded many times to fit inside a chromosome, which resides in the nucleus of the cell.
DNA is twisted around bead-like proteins called histones in the case of humans. The histones are also coiled
tightly to form chromosomes, which are located in the nucleus of the cell. The information in DNA:
 guides the cell (along with RNA) in making new proteins that determine all biological traits
 gets passed (copied) from one generation to the next
Watson and Crick discovered that DNA shape had two sides, or strands, and that these strands are twisted
together like a coiled ladder - the double helix, the sides of the "ladder" are made up of alternating subunits
of sugars and phosphates and the "ladder rings" are pairs of nitrogen bases, adenine and thymine, guanine and
cytosine. The phosphate of one nucleotide is covalently bound to the sugar of the next nucleotide. The
hydrogen bonds between phosphates cause the DNA strand to twist. The nitrogenous bases point inward on
the ladder and form pairs with bases on the other side, like rungs. Each base pair is formed from two
complementary nucleotides (purine with pyrimidine) bound together by hydrogen bonds. The base pairs in
DNA are adenine with thymine and cytosine with guanine. Note that the C-G pair has three hydrogen bonds
while the A-T pair has only two, which keeps them from pairing wrongly. The sequence of these bases forms
a code, which controls the production of proteins in the cell.
The Double Helix structure of DNA allows it to replicate easily due to the weak hydrogen bonds that unzip
quickly. DNA is a directional polymer because on one side of the ribose backbone the phosphate is bound to
the 5' position and on the other the phosphate is bound to the 3' position. The specific order of the nucleotide
bases, read from the 5' end to the 3' end. This makes up the genetic code, which directs the production of all
the components of a cell. For example, in the figure below, the strand on the left-hand side would be written
as: CAGT. The strand on the right-hand side would be written as: ACTG. The structure allows storage of
information in small space as the double helix curves.

Structure of DNA Molecules

Building blocks of DNA and RNA

Nucleotides
Nucleotides are the monomers, building blocks, of nucleic acids (DNA and RNA). A nucleotide consists of
three molecules linked together: a pentose sugar (deoxyribose or ribose), phosphoric acid and an organic
(nitrogenous) base.
A pentose sugar has basically the same structure as a hexose sugar such as glucose except that there is one
less carbon atom in the ring (see the diagram below). This five-carbon sugar is ribose and it is found in
ribonucleic acid.
Deoxyribonucleic acid has a different sugar, deoxyribose, which is different from ribose in that the hydroxyl
group at position 2 is replaced by a hydrogen atom. Deoxyribose has one less oxygen atom than ribose hence
the name deoxyribose.
The second construction of a nucleotide is phosphoric acid (H3PO4). The phosphate is bonded to the sugar
through phosphor-diester bonds and makes up the backbone of the molecule.
The third component is the organic or nitrogenous base. DNA contains four different organic bases: adenine,
guanine, cytosine, and thymine, abbreviated respectively as A, G, C, and T. The nitrogenous bases form the
"rungs" of the ladder and are connected through hydrogen bonds.
RNA nucleotides have the same bases except uracil, which replaces thymine.
There are two classes of nitrogen bases called purines (double-ringed structures) and pyrimidines (single-
ringed structures). All these five bases are compounds composed of carbon and nitrogen atoms in ring form.
Altogether, there are two purines (adenine and guanine) and three pyrimidines (thymine, cytosine and uracil).
It is the rule that a specific purine always pairs with a specific pyrimidine as alleles, (i.e. complementary pairs),
e.g. adenine with thymine (A-T) and guanine with cytosine (G-C).

Watson and Crick proposed that the DNA is made up of two strands that are twisted around each other to form
a right-handed helix, called a double helix. Base-pairing takes place between a purine and pyrimidine: namely,
A pairs with T, and G pairs with C. In other words, adenine and thymine are complementary base pairs, and
cytosine and guanine are also complementary base pairs. This is the basis for Chargaff’s rule; because of their
complementarity, there is as much adenine as thymine in a DNA molecule and as much guanine as cytosine.
Adenine and thymine are connected by two hydrogen bonds, and cytosine and guanine are connected by three
hydrogen bonds. The two strands are anti-parallel in nature; that is, one strand will have the 3' carbon of the
sugar in the “upward” position, whereas the other strand will have the 5' carbon in the upward position. The
diameter of the DNA double helix is uniform throughout because a purine (two rings) always pairs with a
pyrimidine (one ring) and their combined lengths are always equal (Diagram below).

DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and cytosine pairs with guanine

Ribonucleic acid (RNA): comprises a single strand of nucleotides linked together.

The four bases in DNA's alphabet are:
 adenine (A) - a purine
 cytosine(C) - a pyrimidine
 guanine (G) - a purine
 thymine (T) - a pyrimidine

The nucleotide is the basic building block of nucleic acids.

 The nitrogenous bases

Ribose Deoxyribose
The Five-carbon (Pentose) Sugars

Structure of RNA (Ribonucleic Acid)

RNA is another nucleic acid. It differs from DNA in three major ways:
 The sugar is ribose instead of deoxyribose
 There is only one strand instead of two
 RNA has uracil (U) instead of thymine. So, the base pairs in RNA are cytosine with guanine and
adenine with uracil.

Structure of RNA Molecules

In a prokaryotic cell, both DNA and RNA are found in the cytoplasm. In a eukaryotic cell, RNA can be
found in the nucleus and cytoplasm, while DNA is only found in the nucleus.

DNA Replication
DNA carries the information for making all the cell's proteins. These proteins implement all the functions of
a living organism and determine their characteristics. When a cell reproduces, it passes all information on to
the daughter cells.
Before a cell can reproduce, it must first replicate, or make a copy of, its DNA. Where DNA replication
occurs depends on whether the cell is a prokaryote or a eukaryote. DNA replication occurs in the cytoplasm
of prokaryotes and in the nucleus of eukaryotes. Wherever DNA replication occurs, the basic process is the
same.
The structure of DNA makes it easily for DNA replication. Each side of the double helix runs in opposite
(anti-parallel) directions. It can unzip down the middle and each side can serve as a pattern or template for
the other side. This type of replication is called semi-conservative replication because each new molecule
has one “old” and one “new” strand of DNA. However, DNA does not unzip entirely. It unzips in a small area
called a replication fork, which then moves down the entire length of the molecule. Another model of
replication proposed was the conservative replication when the DNA would somehow produce an entirely
new DNA strand during replication.

The third model of DNA replication proposed was the dispersive replication which involved the breaking of
the parental strands during replication, and a re-assembly of molecules that were a mix of old and new
fragments on each strand of DNA.

Steps in DNA replication

1. An enzyme called DNA gyrase makes a nick in the double helix and each side separates
2. An enzyme called helicase unwinds the double-stranded DNA
3. Several small proteins called single strand binding proteins (SSB) temporarily bind to each side and
keep them separated
 4. An enzyme complex called DNA polymerase "walks" down the DNA strands and adds new
nucleotides to each strand. The nucleotides pair with the complementary nucleotides on the existing
strand (A with T, G with C).
5. A subunit of the DNA polymerase proofreads the new DNA
6. An enzyme called DNA ligase seals up the fragments into one long continuous strand. Note that the
little fragments formed are called Okazaki fragments.
7. The new copies automatically wind up again
Since the DNA strands are anti-parallel, unzipping of the DNA helix by the enzyme helicase to form the Y-
shaped replication fork, would make the enzyme DNA polymerase to moves in the 3' to 5' direction along
each template strand. The new (complement) strand grows in the opposite (5' to 3') direction. Then replication
proceeds in the 5' to 3' direction on each strand, one strand will form a continuous copy - the leading strand,
while the other will form a series of short fragments called Okazaki fragments. The Okazaki fragments are
connected by DNA ligase, and because this strand takes more time to assemble than the leading strand, it is
called the lagging strand.

DNA Replication (Helicase, unzips the DNA helix and forms a Y-shaped replication fork)

DNA polymerase moves in the 3' to 5' direction along each template strand. The new (complement)
strand grows in the opposite (5' to 3') direction)

Growth of replication forks as DNA is replicated base by base

Different types of cells replicated their DNA at different rates. Some cells constantly divide, e.g those in hair,
fingernails and bone marrow cells. Other cells go through several rounds of cell division and stop e.g. cells in
the brain, muscle and heart. Also, some cells stop dividing, but can be induced to divide to repair injury e.g.
skin cells and liver cells. In cells that do not constantly divide, the signals for DNA replication or cell division
come in the form of chemicals. These chemicals can come from other parts of the body (hormones) or from
the environment.

DNA replication and its significance

The replication of DNA is a necessary preliminary step for cell division (both mitosis and meiosis). This
process creates the two chromatids that are found in chromosomes that are preparing to divide. By this process,
the whole chromosome is essentially duplicated, but is still held together by a common centromere. Enzymes
are responsible for all the key events.

Functions of DNA – Storing the Genetic Code

DNA's function is to provide the code on which all life is based. DNA carries all the information for physical
characteristics, which are determined by RNA and proteins made by the information provided by the DNA.
The genetic functions of a DNA include (i) a tape containing the information store encoding the sequences of
proteins and RNA molecules and (ii) a polymer existing as double-helical string enabling the packaging,
accessibility and replication of the information store. These proteins and RNA molecules carry out all of the
functions in the body. In DNA, each protein is encoded by a gene. Specifically, the order of nucleotides within
a gene specifies the order and types of amino acids that must be put together to make a protein.
A protein is made of a long chain of chemicals called amino acids. Proteins function as:
 Enzymes that carry out chemical reactions (e.g. digestive enzymes)
 Structural proteins that are building materials (e.g. collagen and nail keratin)
 Transport proteins that carry substances (e.g. oxygen-carrying hemoglobin in blood)
 Contraction proteins that cause muscles to compress (e.g. actin and myosin)
 Storage proteins that hold on to substances (e.g. albumin in egg whites and iron-storing ferritin in
spleen)
 Hormones - chemical messengers between cells (including insulin, estrogen, testosterone, cortisol,
e.t.c)
 Protective proteins - antibodies of the immune system, clotting proteins in blood
 Toxins - poisonous substances, (e.g. bee venom and snake venom)
The particular sequence of amino acids in the chain is what makes one protein different from another. This
sequence is encoded in the DNA where one gene encodes for one protein. DNA also functions to pass along
all these important instructions to the next generation.

The genetic code consists of 3-base "words" or codons that specify particular amino acids. The order of the
codons designates the order of the amino acids in the protein

How does DNA encode the information for a protein? There are only four DNA bases, but there are 20 amino
acids that can be used for proteins. So, groups of three nucleotides form a word (codon) that specifies which
of the 20 amino acids goes into the protein (a 3-base codon yields 64 possible patterns (4*4*4), which is more
than enough to specify 20 amino acids. Because there are 64 possible codons and only 20 amino acids, there
is some repetition in the genetic code. Also, the order of codons in the gene specifies the order of amino acids
in the protein. It may require anywhere from 100 to 1,000 codons (300 to 2,000 nucleotides) to specify a given
protein. Each gene also has codons to designate the beginning (start codon) and end (stop codon) of the gene.

RNA (Ribonucleic Acid)

RNA is the other nucleic acid. It differs from DNA in three major ways:
 The sugar is ribose instead of deoxyribose
 There is only one strand instead of two
  RNA has uracil (U) instead of thymine. So, the base pairs in RNA are cytosine with guanine and
adenine with uracil.
In a prokaryotic cell, both DNA and RNA are found in the cytoplasm. In a eukaryotic cell, RNA can be
found in the nucleus and cytoplasm, while DNA is only found in the nucleus.

Building a Protein: Transcription

Building proteins is like building a house:
 The master blueprint is DNA, which contains all of the information to build the new protein.
 The working copy of the master blueprint is called messenger RNA (mRNA), which is copied from
DNA.
 The construction site is either the cytoplasm in a prokaryote or the endoplasmic reticulum (ER) in a
eukaryote.
 The building materials are amino acids.
 The construction workers are ribosomes and transfer RNA molecules.

Steps in protein transcription

In eukaryote, DNA never leaves the nucleus, so its information must be copied. This copying process is called
transcription and the copy is mRNA. The process of copying a DNA gene into mRNA is called
transcription. Transcription takes place in the cytoplasm (prokaryote) or in the nucleus (eukaryote). The
transcription is performed by an enzyme called RNA polymerase. To make mRNA, RNA polymerase:
1. Binds to the DNA strand at a specific sequence of the gene called a promoter
2. Unwinds and unlinks the two strands of DNA
3. Uses one of the DNA strands as a guide or template
4. Matches new nucleotides with their complements on the DNA strand (G with C, A with U)
5. Binds these new RNA nucleotides together to form a complementary RNA molecule of the DNA
strand (mRNA). The copy, a "messenger" RNA molecule, leaves the nucleus and heads to a ribosome.
6. Stops when it encounters a termination sequence of bases (stop codon)
Note that mRNA is single-stranded as opposed to DNA which forms complementary double-stranded helixes.
In prokaryotes, all of the nucleotides in the mRNA are part of codons for the new protein. However, in
eukaryotes only, there are extra sequences in the DNA and mRNA that do not code for proteins called introns.
The mRNA then undergoes further processing as follows:
 Introns are cut out or removed
 The coding sequences are spliced together
 A special nucleotide "cap" gets added to one end
 A long tail consisting of 100 to 200 adenine nucleotides is added to the other end.
Finally, the working copy of the blueprint (mRNA) goes to the construction site where the workers will build
the new protein. If the cell is a prokaryote such as an E. coli bacterium, then the site is the cytoplasm. If the
cell is a eukaryote, such as a human cell, then the mRNA leaves the nucleus through large holes in the nuclear
membrane (nuclear pores) and goes to the endoplasmic reticulum (ER).
An example of a DNA gene for some fictitious protein is given below. Transcribe the DNA code to RNA
code, and then translate the RNA code to an amino acid sequence.

TAC GGA ATC CTT TAG AAG CTG TAT CCT ACT

What would the RNA codons be?

UAC GUU CAA UAA CGG CAC UCU UAG ACU ACU

What would the amino acid sequence be? Use codes “sta” for start and “sto” for stop.
 Table of the genetic code based on mRNA codons. Some tables are based on the DNA codons

Building a Protein: Translation - the assembly process

When the working copy of the blueprint get to the site, the workers must assemble the materials according
to the instructions; this process is called translation. In the case of a protein, the workers are the ribosomes
and special RNA molecules called transfer RNA (tRNA). The construction materials are the amino acids.
Translation is the construction of an amino acid sequence (polypeptide) from an RNA molecule.
Ribosome. The ribosome is made of RNA called ribosomal RNA (rRNA). In prokaryotes, rRNA is made in
the cytoplasm; in eukaryotes, rRNA is made in the nucleolus. The ribosome has two parts, which bind on
either side of the mRNA. Within the large part are two "chambers or rooms" (P and A sites) that will fit two
adjacent codons of the mRNA, two tRNA molecules and two amino acids. At first, the P site holds the first
codon in the mRNA and A site holds the next codon.
The tRNA molecules. In the cytoplasm, each transfer RNA (tRNA) has a binding site for an amino acid.
Because each tRNA is specific for a single amino acid, it must be able to recognize the codon on the mRNA
that codes for that particular amino acid. This requires energy, usually provided by ATP. Therefore, each
tRNA has a specific three-nucleotide sequence called an anti-codon that matches up with the appropriate
mRNA codon, like a lock and key. For example, if a codon on mRNA has the sequence ...-uracil-uracil-
uracil-... (UUU) which codes for the amino acid phenylalanine, then the anti-codon on the phenylalanine
tRNA will be adenine-adenine-adenine (AAA); (note that A always binds with U in RNA). The tRNA
molecules float in the cytoplasm and bind free amino acids. Once bound to amino acids, the tRNAs (also
called amino-acyl tRNAs) then carries its attached amino acid to the ribosome.
 An overview of transcription and translation.
Note that this sequence of amino acids is known by using a table of the genetic code.
Amino acids Corresponding DNA codons Corresponding RNA codons
alanine CGA, CGG, CGT, CGC GCU, GCC, GCA, GCG
arginine GCA, GCG, GCT, GCC, TCT, TCC CGU, CGC, CGA, CGG, AGA, AGG
asparagine TTA, TTG AAU, AAC
aspartic acid CTA, CTG GAU, GAC
cysteine ACA, ACG UGU, UGC
glutamic acid CTT, CTC GAA, GAG
glutamine GTT, GTC CAA, CAG
glycine CCA, CCG, CCT, CCC GGU, GGC, GGA, GGG
histidine GTA, GTG CAU, CAC
isoleucine TAA, TAG, TAT AUU, AUC, AUA
leucine AAT, AAC, GAA, GAG, GAT, GAC UUA, UUG, CUU, CUC, CUA, CUG
lysine TTT, TTC AAA, AAG
methionine (start codon) TAC AUG
phenylalanine AAA, AAG UUU, UUC
proline GGA, GGG, GGT, GGC CCU, CCC, CCA, CCG
serine AGA, AGG, AGT, AGC, TCA, TCG UCU, UCC, UCA, UCG, AGU, AGC
threonine TGA, TGG, TGT, TGC ACU, ACC, ACA, ACG
tryptophan ACC UGG
tyrosine ATA, ATG UAU, UAC
valine CAA, CAG, CAT, CAC GUU, GUC, GUA, GUG
(stop codon) ATT, ATC, ACT UAA, UAG, UGA
Mitochondrial DNA
Mitochondria (and chloroplasts in plants) have their own small loops of DNA and reproduce on their own,
independent of what goes on in the nucleus. This DNA codes for some mitochondrial proteins, but others are
provided from the DNA stored in the nucleus. Mitochondria resemble an early form of bacteria, which is
thought to have been captured into eukaryotic cells early in the history of life on Earth. The bacteria coexisted
with the cell (endosymbiosis) and evolved into mitochondria. Another unique aspect of mitochondrial DNA
is that you inherit it only from your mother (the mitochondria that exist in the egg cell). Although the sperm
cell that fertilizes the egg contains a mitochondrion from the father, it does not get released and passed on.

The Protein Synthesis Process

The processes of synthesis of protein follow the events below:
1. A ribosome binds to mRNA with the AUG codon in the P-site and the UUU codon in the A-site.
2. An amino acyl-tRNA (anti-codon = UAC) with an attached methionine comes into the P-site of the
ribosome
3. An amino acyl-tRNA (anti-codon = AAA) with an attached phenylalanine comes into the A-site of the
ribosome
4. A chemical bond forms between the methionine and phenylalanine (in a protein, this covalent bond is
called a peptide bond).
5. The methionine-specific tRNA leaves the P-site and goes off to gather another methionine
6. The ribosome shifts so that the P-site now contains the UUU codon with the attached phenyl-alanine
tRNA and the next codon (ACA) now occupies the A-site.
7. An amino acyl-tRNA (anti-codon) with an attached threonine comes into the A-site of the ribosome.
8. A peptide bond forms between the phenylalanine and the threonine.
9. The phenylalanine-specific tRNA leaves the P-site and goes off to find another phenylalanine.
10. The ribosome shifts down one codon so that the stop sequence is now in the A-site. Upon encountering
the stop sequence, the ribosome detaches from the mRNA and splits into its two parts, the threonine-
specific tRNA releases its threonine and leaves, and the new protein floats away
Several ribosomes can attach to a molecule of mRNA one after another and begin making proteins.

Role of RNAs in Protein Synthesis

DNA in the nucleus acts as the basis for template for the production of another sort of nucleic acid called
messenger RNA (mRNA). Messenger RNA has the ability to convey the instruction needed for protein
synthesis from the nucleus to the cytoplasm. The idea that DNA makes protein through an intermediated RNA
is known as the central dogma of molecular genetics. When messenger RNA gets out into the cytoplasm it
attaches itself to a ribosome where it causes amino acids to assemble in the right order. This is known as
transfer RNA. The transfer RNA molecules transfer (carry) amino acids to ribosome. The main property of
transfer RNA is their ability to bind to amino acids at one end and to messenger RNA at the other.

The central dogma

DNA Mutation

Variations in the sequence of genes during can have important consequences and cause disease.

As DNA polymerase copies the DNA sequence, some errors or mistakes may occur. For example, one DNA
base in a gene may be substituted for another. This error is called mutation (point mutation) or variation in
the gene. This error may not have much effect on the protein made by the gene if the changed amino acid is
not in a crucial part of the protein. However, if the changed amino acid is in a crucial part of the protein, the
protein may be defective and not work at all; this type of change can lead to disease.
Other types of mutations in DNA can occur when small segments of DNA break off the chromosome. These
segments can get placed back at another spot in the chromosome and interrupt the normal flow of information.
These types of mutations (i.e. deletions, insertions, inversions) usually have severe consequences.
Mutations can therefore be defined as any change in the DNA or more appropriately as a change in the DNA
base sequence that result in a change of amino acid(s) in the polypeptide coded for by that gene.

DNA Sequencing
Basically, to sequence DNA, one needs to place all the enzymes and nucleotides (A, G, C and T) necessary to
copy DNA into a test tube. A small percentage of the nucleotides have a fluorescent dye attached to them (a
different color for each type). You then place the DNA that you want to sequence into the test tube and let it
incubate for a while.
During the incubation process, the sample DNA gets copied over and over again. For any given copy, the
copying process stops when a fluorescent nucleotide gets placed into it. So, at the end of the incubation
process, you have many fragments of the original DNA of varying sizes and ending in one of the fluorescent
nucleotides.

Phenylketonuria
A gene in the DNA codes for an enzyme that allows the breakdown of a specific amino acid called
phenylalanine found in milk. In some individuals, this gene is missing or defective. They do not make the
enzyme and cannot break down phenylalanine. As infants, if these individuals receive regular milk or milk
products, the unbroken phenylalanine will accumulate and cause brain damage (The disease is called
phenylketonuria). Fortunately, a genetic test is conducted at birth that can identify these babies, who can
then be fed milk products lacking phenylalanine (such as soy milk).

Review Questions
1. Describe the general characteristics of nucleic acids.
2. Explain the general functions of nucleic acids.
3. Explain the chemical basis of genetic information.
4. Describe the general structure and components of a DNA molecule.
5. Distinguish between the functions of messenger RNA and transfer RNA.
6. Distinguish between transcription and translation.
 7. Explain two functions of ribosomes in protein synthesis.
8. Distinguish between a codon and an anticodon.
9. Explain how a DNA molecule is replicated.
10. Define mutation, and explain how mutations may originate.