Molecular Biology Primer: All About DNA
Introduction
This page is a quick introduction to molecular biology. You will find on this site numerous references to DNA, RNA and proteins. In order to understand those pages, a basic understanding of how these molecules interact is necessary. This description is a very simplified version of what actually happens within a cell. In reality, the system is quite complex, with dozens of accessory molecules and co-factors required at each step.
DNA
DNA (deoxyribonucleic acid) is the information storage molecule for the cell. Each cell contains within the DNA the entire instruction set to produce and run an entire organism (including you). In multicellular organisms, most of the DNA is stored in a central location within the cell, called the nucleus.
Bases
DNA is composed of only four bases, which can be thought of as letters of
the DNA alphabet. The structure of these four letters is shown in the figure
to the right.
There are two purine bases (adenine and guanine) and two pyrimidine bases
(thymine and cytosine). The bases are commonly abbreviated with the first
letter of their names:
Base | Abbrev. |
---|---|
adenine | A |
guanine | G |
thymine | T |
cytosine | C |
Nucleotides
When a base, such as adenine, is linked to a deoxyribose sugar through a
glycosidic bond, the structure is called a nucleoside.
When
the deoxyribose sugar is phosphorylated, on either the 3' or the 5' position
(or both), the structure is a called a nucleotide. The precursors of DNA
synthesis are deoxynucleoside-5'-triphosphates or dNTPs.
DNA structure
DNA is composed of a polynucleotide (multiple nucleotides) chain that is formed by linking nucleotides through 3',5'-phosphodiester bonds. In this way, DNA forms a long chain of sequential nucleotides.
DNA chains are not usually just single strands of nucleotides. Usually,
nucleotides of two polynucleotide strands are base-paired to each
other. The nucleotide base adenine pairs through hydrogen bonds with the
nucleotide thymine forming an
adenine-thymine (A-T) base pair. Guanine binds with cytosine forming a
guanine-cytosine (G-C) base pair. Because of this base pairing,
polynucleotide chains in double-stranded DNA are always complementary to
each other.
DNA Double Helix
The nature of the bonds between nucleotide bases results in the famous "double helix" DNA structure. The hydrogen bonding between strands of DNA holds the strands together until they are separated for DNA replication or RNA transcription.
DNA Replication
DNA is replicated (reproduced) through an extremely complicated process. This
is the simplified version.
The
two strands of DNA are separated and a new complementary strand is
synthesized for each old strand by adding complementary base pairs to the
newly-synthesized strand (see figure at right). The DNA polymerase (the
enzyme that makes new DNA) reads the base on the original strand and adds
the complementary base to the newly synthesized strand. DNA is always
synthesized in a 5’ to 3’ direction. Since one strand runs in the opposite
direction, it must be synthesized in pieces that are later connected with
DNA ligase. In reality, both strands are synthesized in pieces, since the
DNA is unwound at numerous sites simultaneously on each chromosome in order
to produce a complete copy in a short period of time (hours instead of
weeks).
RNA
How does DNA turn in you?
Since DNA just stores information, there needs to be a way to turn the
information into physical bodies.
This feat is accomplished through the synthesis of
an intermediate information-carrying molecule that carries the information
from the nucleus to the cytoplasm, where it is processed into proteins. The
intermediate molecule is called RNA (ribonucleic acid). As you can tell from
the name, it differs from DNA in that part of it (the ribose sugar) has an
extra oxygen compared to DNA (the "deoxy" version). In addition, RNA does
not use thymine as a base, but another nucleotide known as uracil (see figure right). Uracil
forms base pairs with
adenine, as thymine does in DNA. RNA is transcribed from DNA through an
enzyme called RNA polymerase, in a process that is known as transcription.
There are several kinds of RNA, which have different functions. However, the
RNA that eventually codes for proteins is called messenger RNA (mRNA).
Translation
Once mRNA
is synthesized, it is processed (usually through splicing) in the nucleus
before moving to the cytoplasm. In many instances, alternate splicing of an
RNA transcript can produce multiple proteins. It is one of the chief ways
that 25,000 genes in the human genome can make ~100,000 proteins. Proteins
are produced from an mRNA template using a process known as translation.
The translation process is quite complicated and requires numerous molecular
machines and co-factors. This description is a simplified version of what
happens. A large molecular machine, called the ribosome, binds to the
mRNA. Ribosomes are composed of two subunits. The large subunit is composed
of three forms of ribosomal RNA (rRNA) and 49 different proteins. The
smaller subunit is composed of one rRNA and 33 different proteins. A third
kind of RNA, transfer RNA (tRNA), carries amino acids that are used
to make proteins according to the mRNA template. One end of tRNA, consisting
of three bases, called the anti-codon, binds to a series of three
complementary bases, called the codon on the mRNA strand. The other
end of the tRNA binds to a specific amino acid. Specific sequence on the RNA
are translated into proteins according to the genetic code. Each set
of three nucleotide bases codes for one amino acid. This code
is nearly universal for all organisms (with a few exceptions). The code is
reproduced below:
Codon | AA | Codon | AA | Codon | AA | Codon | AA |
---|---|---|---|---|---|---|---|
UUU | Phe | UCU | Ser | UAU | Tyr | UGU | Cys |
UUC | UAC | UGC | UGC | ||||
UUA | Leu | UCA | UAA | Stop | UGA | Stop | |
UUG | UCG | UAG | UGG | Trp | |||
CUU | Leu | CCU | Pro | CAU | His | CGU | Arg |
CUC | CCC | CAC | CGC | ||||
CUA | CCA | CAA | Gln | CGA | |||
CUG | CCG | CAG | CGG | ||||
AUU | Ile | ACU | Thr | AAU | Asn | AGU | Ser |
AUC | ACC | AAC | AGC | ||||
AUA | Met | ACA | AAA | Lys | AGA | Arg | |
AUG | ACG | AAG | AGG | ||||
GUU | Val | GCU | Ala | GAU | Asp | GGU | Gly |
GUC | GCC | GAC | GGC | ||||
GUA | GCA | GAA | Glu | GGA | |||
GUG | GCG | GAG | GGG |
An animated model of how proteins are formed can be watched to the right (Point mouse over thumbnail). The 30s subunit of the ribosome binds to the mRNA. A specific tRNA (usually the first codon codes for methionine) binds to the codon of the mRNA The 50s ribosomal subunit binds to the 30s subunit. The next tRNA binds to the next codon on the mRNA and numerous initiation factors and the enzyme peptidyl transferase link the two amino acids together through a peptide bond. As the ribosomal complex moves along the mRNA, the peptide chain gets longer until the entire protein is formed. Other molecular machines are responsible for making sure that the protein folds into the correct three dimensional shape.
Conclusion 
DNA is made of 4 chemical bases that are linked together sequentially. These 3 billion bases determine what you will look like and how your body will work. In order to express the information stored in the DNA, your cells have a complicated system that moves the DNA out of the cell's nucleus (through mRNA) into the cytoplasm. Once the mRNA is in the cytoplasm it is translated into proteins, which are the building blocks of the cell. Are you ready to use your new knowledge? Check out these articles:
- Is the Chemical Origin of Life (Abiogenesis) a Realistic Scenario?
- Evolution Deception in California State High School Biology Textbook Biology: Principles & Explorations
- Descent of Man Theory: Disproved by Molecular Biology
- Bad Designs in Biology? - Why the "Best" Examples Are Bad
- When Junk DNA Isn't Junk
- Pseudogenes: Argument for Evolution and Against Design?
Related Resources 
Fazale Rana (Ph.D.
in chemistry), vice president of research and apologetics at
Reasons To Believe, has written a
new book,
The Cell's Design: How Chemistry Reveals the Creator's Artistry, that
attempts to show that cellular biochemistry points to the existence of the
Creator who designed it. Whereas most intelligent design books attempt to show
the existence of design by demonstrating the existence of irreducible
complexity, Dr. Rana examines the cell's biochemistry with broad strokes of how
everything works together with such marvelous fidelity. So, even if a single
piece or line of evidence might be dismissed as a statistical outlier, the
weight of evidence makes a powerful case for design by a Creator.
Reasons
To Believe's third in a series of books proposing a testable creation model
takes on the origin and design of the universe. Previous books,
Origins of Life: Biblical and Evolutionary Models Face Off
and Who
Was Adam?: A Creation Model Approach to the Origin of Man, examined the
origin of life on earth and the origin of mankind, respectively.
Creation As Science develops a biblical creation model and compares
the predictions of this model compared to a naturalistic model, young earth
creationism, and theistic evolution. This biblical creation model is divided
into four main areas, the origin of the universe, the origin of the Solar
System, the history of life on earth, and the origin and history of mankind.
The Edge of Evolution: The Search for the Limits of Darwinism by Michael Behe
Darwin's Black Box author Michael Behe takes on the limits of evolution through an examination of specific genetic examples. Behe finds that mutation and natural selection is capable of generating trivial examples of evolutionary change. Although he concludes that descent with modification has occurred throughout biological history, the molecular devices found throughout nature cannot be accounted for through natural selection and mutation. Behe's book claims to develop a framework for testing intelligent design by defining the principles by which Darwinian evolution can be distinguished from design.
Today's New Reason To Believe
[Active Archive Link, Click Above]
- 10/27/2008 12:05 AM
A Dark Galaxy: Finding the “Missing” Dark Stuff
Previously Posted January 28th, 2008 by Hugh Ross Many independent sets of observations confirm that only about six percent of all the ordinary matter (neutrons and protons) in the universe is made up of stars and stellar remnants.1 The other 94 percent is dark. While astronomers have verified ... - 10/24/2008 12:05 AM
From Dust to Planets
Previously Posted on October 26th, 2007 by David H. Rogstad, Ph.D. When the Bible tell us that we have been made from the “dust of the earth,” and will eventually “return to the dust,” it is more true than perhaps the authors realized. Prevailing theory for the formation ... - 10/23/2008 12:05 AM
Flightless Birds Run Down Evolution
Posted by Fazale ‘Fuz’ Rana, Ph.D. Newly Discovered Example of Convergence Challenges Biological Evolution Lately, my wife has had trouble hanging onto cell phones. Within the span of two weeks she lost not one cell phone, but two. But my wife is not the only one who has lost the ... - 10/22/2008 12:05 AM
Antarctica and North America Once Connected
by Jeffrey Zweerink From a biblical perspective, the advent of continents plays a critical role in God’s transformation of Earth from “formless and void” to an environment teeming with diverse life-forms. In fact, the formation of continents warrants mention as one of the ... - 10/21/2008 12:05 AM
The Golden Rule of Apologetics, Part 6 (of 7)
Kenneth Richard Samples What can Christian apologists do to represent the arguments of others with fairness and intellectual integrity? This series has focused upon the need to apply the biblical principle of the Golden Rule to the enterprise of Christian apologetics. In Matthew 7:12, Jesus ... - 10/20/2008 12:05 AM
Rare Solar System Location
by Hugh Ross Many astronomers have noted that the present solar system environment is amazingly benign for advanced life. The solar system’s current position (in between two nearby exceptionally symmetrical and widely separated spiral arms that are devoid of any significant spurs or ... - 10/17/2008 05:51 AM
A Family Breakup Kills the Dinosaurs
Previously posted on Oct. 19th, 2007 by David H. Rogstad, Ph.D. In 1980 Nobel Prize-winning physicist Luis Alvarez and his geologist son Walter Alvarez proposed a provocative theory. They suggested that the Earth had been struck by an asteroid in its past to explain the unusual amount of iridium ...
Last Modified February 14, 2008