INTRODUCTION TO DNA

You've probably heard the term a million times. You know that DNA is something inside cells; you probably know that DNA has
something to do with who we are and how we get to look the way we do. You know that DNA has something to do with
inheritance (I have my dad's nose and my mom's height). But there's a lot more to know about DNA and it's role as "the
building blocks of life."
Scientists now know that DNA carries genetic information that defines many of an organism’s traits (including behaviours) and
its predisposition for certain diseases.
Before DNA was established as the genetic material in cells, scientists knew:
- there was a connection between chromosomes and inherited traits
- the genetic material had to control the production of enzymes and proteins
- the genetic material had to be able to replicate itself with accuracy and still allow mutations to occur.

Have you ever wondered how the DNA in ONE egg cell and ONE sperm cell can produce a whole human being different from
any other? How does DNA direct a cell's activities? Why do mutations in DNA cause such trouble (or have a positive effect)?
How does a cell in your kidney "know" that it's a kidney cell as opposed to a brain cell or a skin cell or a cell in your eye?
How can all the information needed to regulate the cell's activities be stuffed into a tiny nucleus?
To begin to find the answers to all these questions, you need to learn about the biological molecules called nucleic acids.
An organism (be it bacteria, rosebush, ant or human) has some form of nucleic acid which is the chemical carrier of its genetic
information. There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) which code for all the
information that determines the nature of the organism's cells. As a matter of fact, DNA codes for all the instructions needed for
the cell to perform different functions. Did you know that human DNA contains enough information to produce about 100,000
proteins?

DNA, CHROMOSOMES AND GENES

How do these terms relate to one another?

DNA? Chromosomes? Genes? Aren't these just different terms for the same thing? Well, yes and no. To begin to figure out the
difference between these terms, we'll have to learn a little bit about the life of a cell and it's nucleus.
When a cell is not actively dividing, its nucleus contains chromatin, a tangle of fibers composed of protein and DNA. When the
time comes for the cell to divide into two new cells, the DNA is duplicated so that via mitosis each new cell can receive a
complete copy of all the genetic material in the "parent" cell.
During cell division chromatin organizes itself into chromosomes. Each chromosome contains a DNA molecule, and each DNA
molecule is made up of many genes-individual segments of DNA that contain the instructions needed to direct the synthesis of
a protein with a specific function.
Different organisms differ in their complexity and therefore have different numbers of chromosomes and genes. A frog, for
example, has 26 chromosomes (13 pairs), whereas a human has 46 chromosomes (23 pairs). Why do we make a reference to
there being 23 pairs? Why don't we just say 46 chromosomes? This is because the 46 chromosomes in human somatic cells are
actually 23 matched pairs of homologous chromosomes! Each member of the pair comes from one parent; so they may be the
same size and shape, but they don't carry exactly the same information. The 23 pairs of human chromosomes are estimated to
include about 20,000 - 25,000 genes. Each gene codes for ONE protein.
COMPOSITION OF NUCLEIC ACIDS – It's a long story!

Nucleic acids are one of several macromolecules in the body in addition to fats, proteins and carbohydrates. So it isn't surprising
that nucleic acids are built like these other macromolecules. Nucleic acids and the other macromolecules just mentioned are
polymers made up of individual molecules linked together in long chains.
- Proteins are polypeptides made up of individual aminoacids linked together,
- Carbohydrates are polysaccharides made up of individual monosaccharides linked together, and
- Nucleic acids are polynucleotides made up of individual nucleotides linked together.
If you go even further, a nucleotide can itself be further broken down to yield three components:
- a pentose sugar (with 5 carbon atoms),
- a nitrogenous base, and
- a phosphate group (phosphoric acid).

Maurice Wilkins Rosalind Franklin

James Watson and Francis Crick

Erwin Chargaff discovered the relationships between DNA bases
There is variation in the composition of nucleotides in different species.
Regardless of the species, DNA maintains certain nucleotide proportions. That is, the amount of A and T nucleotides are equal
and the amount of C and G nucleotides are equal. This constant relationship is known as Chargaff’s rule.

Rosalind Franklin discovered the basic structure of DNA by x-ray crystallography

In the early 1950s, Rosalind Franklin and Maurice Wilkins used X-ray diffraction to analyze DNA samples. Franklin captured high-
resolution photographs and, using mathematical theory to interpret them, determined the following:
- DNA has a helical structure;
- The nitrogen bases are on the inside of the DNA helix, and the sugar-phosphate backbone is on the outside.

James Watson and Francis Crick built the first accurate model of a DNA molecule
In the early 1950s, Watson and Crick began working on a description of the structure of DNA using the results and conclusions
of their peers.
In 1953, they published a paper that proposed a structure with the following features:
- a twisted ladder, which they called a double-helix; the sugar-phosphate molecules make up the sides or “handrails” of the
ladder, and the bases make up the “rungs” of the ladder by protruding inwards
- the distance between the sugar-phosphate backbones remains constant over the length of a molecule of DNA: an A nucleotide
on one strand always sits across from a T nucleotide (and C across from G) in order to maintain constant distance. These are
called base pairs.
- different sequences of base pairs can exist, which accounts for the differences between species.

LEARN MORE ABOUT COMPOSITION OF NUCLEIC ACIDS

There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). As a matter of fact, DNA
codes for all the instructions needed for the cell to perform different functions. Did you know that human DNA contains enough
information to produce about 100,000 proteins?
Both DNA and RNA contain nucleotides with similar components. In RNA, the sugar component is ribose, as indicated by the
name "ribonucleic acid". In DNA, or deoxyribonucleic acid, the sugar component is deoxyribose. The prefix deoxy means that an
oxygen atom is missing from one of the ribose Carbon atoms.
When a sugar bonds together with a Nitrogen base, you now have two of the three components of a nucleotide. This structure
is known as a nucleoside.
There are FIVE Nitrogen bases that are found in DNA and RNA (although Uracil is found ONLY in RNA and Thymine only in
DNA!). These five bases are divided into two categories based on their molecular structure.
1-purines (Adenine and Guanine)
2-pyrimidines (Thymine, Cytosine, and Uracil)

You should notice that the purines have two ring structures while pyrimidines have only one ring structure.
The nucleotides that are the building blocks of nucleic acids are formed by adding a phosphate group to a nucleoside.
Nucleotides containing ribose are known as ribonucleotides, and those containing deoxyribose are known as
deoxyribonucleotides.
Structural features of DNA:
• The double helix is composed of two polynucleotide strands that twist around one another. Each strand has a backbone of
alternating phosphate groups and sugars.
• The distance between the sugar-phosphate backbones in each strand is constant.
• The bases of each nucleotide are attached to each sugar and face inward.
• The two strands are complementary due to complementary base pairing of A with T and C with G. The strands are held
together by hydrogen bonds between the nitrogenous bases. In the double helix, adenine and thymine form two hydrogen
bonds to each other but not to cytosine or guanine. Similarly, cytosine and guanine form three hydrogen bonds to each
other in the double helix, but not to adenine or thymine.
You may have noticed that every base pair contains one purine and one pyrimidine. This is related to the structure of each
base and how a proper "fit" (both in base size and chemical makeup) allows the DNA helix to exist in a physically and
chemically stable structure.
This complementary base pairing in the two strands explains why A/T and G/C always occur in equal amounts.
• The two strands are antiparallel, where the 5′ end from one strand is across from the 3′ end of the complementary
strand.
DNA REPLICATION

• A cell replicates its DNA before it divides

• During DNA replication, the double-helix unwinds
• Each strand of the double helix serves as a template for synthesis of a new, complementary strand of DNA
• DNA polymerase (the DNA replication enzyme) uses each strand as a template to assemble new, complementary strands of
DNA from free nucleotides
• DNA ligase seals any gaps to form a continuous strand.
• DNA replication results in two double-stranded DNA molecules identical to the parent. In each new helix, one strand is the
old template and the other is newly synthesized, a result described by saying that the replication is semi-conservative.

1) The two strands of a DNA molecule are

complementary: their nucleotides match up according
to base-pairing rules (G to C, T to A).

2) As replication starts, the two strands of DNA

unwind at many sites along the length of the
molecule.

3) Each parent strand serves as a template for

assembly of a new DNA strand from nucleotides,
according to base-pairing rules.

4) DNA ligase seals any gaps that remain between

bases of the “new” DNA, so a continuous strand
forms. The base sequence of each half-old, half-new
DNA molecule is identical to that of the parent.
nucleotide bases, but there are three main kinds of ribonucleic acid, each of which has a specific job to do.
1- Ribosomal RNAs-exist outside the nucleus in the cytoplasm of a cell in structures called ribosomes. Ribosomes are small,
granular structures where protein synthesis takes place. Each ribosome is a complex consisting of about 60% ribosomal RNA
(rRNA) and 40% protein.
2- Messenger RNAs-are the nucleic acids that "record" information from DNA in the cell nucleus and carry it to the ribosomes
and are known as messenger RNAs (mRNA).
3- Transfer RNAs: the function of transfer RNAs (tRNA) is to deliver amino acids one by one to protein chains growing at
ribosomes.

TRANSCRIPTION

The process of converting the information contained in a DNA segment into proteins begins with the synthesis of mRNA
molecules containing anywhere from several hundred to several thousand ribonucleotides, depending on the size of the protein
to be made. Each of the 100,000 or so proteins in the human body is synthesized from a different mRNA that has been
transcribed from a specific gene on DNA.
"Why do we need mRNA if DNA holds all the genetic information?"
The answer for eukaryotic cells (those cells with a nucleus) is the importance of DNA. If DNA is damaged in any way, then the
coding sequence is changed and a mutation could result which could greatly affect the cell or even the whole organism!
Because of this, the DNA should be protected as much as possible.
If the DNA were into the cytoplasm where the ribosomes are, then it would be more vulnerable to damage from: chemicals, UV
light, or other agents.

How is the DNA supposed to get the information it encodes out to the ribosomes which carry out the instructions in the
cytoplasm?
The answer is that there must be a MESSENGER. This messenger is mRNA!
Messenger RNA is synthesized in the cell nucleus by transcription of DNA, a process similar to DNA replication. As in replication,
a small section of the DNA double helix unwinds, and the bases on the two strands are exposed. RNA nucleotides
(ribonucleotides) line up in the proper order by hydrogen-bonding to their complementary bases on DNA, the nucleotides are
joined together by a RNA polymerase enzyme, and mRNA results.
UNLIKE what happens in DNA replication where both strands are copied, only ONE of the two DNA strands is transcribed into
mRNA (remember that RNA is a single-stranded molecule). The DNA strand that is transcribed is called the template strand,
while its complement is called the informational strand. Since the template strand and the informational strand are
complementary, and since the template strand and the mRNA molecule are also complementary, it follows that the messenger
RNA molecule produced during transcription is a copy of the DNA informational strand!
Now that the mRNA has the DNA's instructions, the molecule must travel OUT of the nucleus to the CYTOPLASM where protein
synthesis takes place.

THE PROTEIN SYNTHESIS: GENETIC CODE AND TRANSLATION

Now that the mRNA has the DNA's instructions, the mRNA molecule must travel OUT of the nucleus to the CYTOPLASM where
protein synthesis takes place.
The genetic code specifies which amino acids will be used to build a protein: a sequence of three bases (triplet) specifies a
particular amino acid.
Even though there are only 20 amino acids that exist, there are actually 64 possible triplets (64 codons, 64 anticodons and 64
tRNA molecules), because 4 X 4 X 4 = 64 possible combinations!
There are four choices of bases for the first space (A, U, G, or C), the same four choices for the second space (you can repeat
the same bases), and the same four bases as a choice for the third spot. So, 4 x 4 x 4 is 64!
61 of the codons code for specific amino acids and 3 code for chain termination, signaling the end of the mRNA message.
Note that each amino acid have more than one codon:
Before we continue with the process of translation, let's examine the "players" in this process. The terms important for this
process are:
- the ribosome: there are many ribosomes in the cytoplasm of a cell, and all the ribosomes are made of a small subunit and a
large subunit. These two subunits open up allowing the mRNA message to slide through. Once the mRNA message is in place
and protein synthesis is ready to begin, the two subunits close again so that the mRNA is now in between the two subunits;
- the A site (in the large subunit of the ribosome): is the site where the incoming tRNA will attach itself;
- the P site (in the large subunit of the ribosome): is the site where the growing peptide (another word for protein) will reside;
- Amino acids: amino acids are the building blocks of proteins;there are only 20 amino acids total, but each one has a
generalized structure: each of the 20 different amino acids shares the amino group, the carboxyl group, the Hydrogen atom,
and the central Carbon atom; the only group which differentiates them is the "R" group (R is simply a symbol for the side
group);
- Codons: a codon (on DNA or mRNA) is a sequence of three bases (triplet); each codon specifies a particular amino acid;
- Anticodons: a set of three nucleotide bases (triplet) on a tRNA molecule is called an anticodon;
- tRNA (transfer RNA): this molecule is responsible for bringing in the proper amino acids to the ribosome; the amino acids are
floating free in the cytoplasm and the tRNA molecule acts as a "taxi" whose job is to read the code from the mRNA and bring
the corresponding amino acid into place. What do I mean by "corresponding" amino acid? Every tRNA molecule has its own set
of three bases which is called an anticodon: this anticodon is complementary to mRNA codons. The other "end" of the tRNA
molecule has an "acceptor" site where the tRNA's specific amino acid will bind;

The protein synthesis - translation: 1) INITIATION

Protein synthesis is initiated when an mRNA, a ribosome, and the first tRNA molecule (carrying its Methionine amino acid) come
together.
The ribosome is inactive when it exists as two subunits (a large one and a small one) before it contacts an mRNA. The small
unit of the ribosome will initiate the process of translation when it encounters an mRNA in the cytoplasm.
The first AUG codon acts as a "start" signal for the translation machinery and codes for the introduction of a methionine amino
acid (this codon and, thus, amino acid will always be the first in any and all mRNA molecules!).
Even though every protein begins with the Methionine amino acid, not all proteins will ultimately have methionine at one end. If
the "start" methionine is not needed, it is removed before the new protein goes to work.

The protein synthesis - translation: 2) ELONGATION

The incoming tRNA will bind to the A site (next to the P site with the Methionine tRNA and amino acid):. ALL available tRNAs
will approach the site and try to attach, but the only tRNA which will successfully attach is the one whose anticodon is
complementary to the codon of the A site on the mRNA.
Let's say for example that the second tRNA that lands next to the methionine-tRNA is for Proline. The two tRNAs (holding
Methionine on the P site and Proline on the A site) are now next to each other. What happens next is crucial for the building of
proteins. In order for a protein chain to form, the amino acids must be attached, linked together. The link between amino acids
is called a peptide bond. Once the bond has formed between the two amino acids, the tRNA on the P site leaves and passes its
amino acid on to the tRNA on the A site.
The tRNA with the two amino acids on it is now sitting on the P site (because it is holding the growing protein!). The ribosome
slides down three bases (1 codon on the mRNA) exposing a new A site. The next appropriate tRNA molecule "lands" bringing its
amino acid right next to the tRNA holding the two amino acids. At this point, the process repeats itself: a peptide bond forms
between the two amino acid molecules already joined together and the newly brought in amino acid; the tRNA on the P site
leaves and the chain of amino acids is passed to the tRNA on the A site (now this site is called the P site because this tRNA now
has the growing protein chains). The ribosome slides down another codon and the procedure repeats itself until the termination
event occurs.
The protein synthesis - translation: 3) TERMINATION
The elongation procedure continues until the proper protein is completed. A "stop" codon (U-A-A, U-G-A, or U-A-G) signals the
end of the process. there is no tRNA that is complementary to the Stop Codon, so the process of building the protein stops. An
enzyme called the releasing factor then frees the newly made polypeptide chain, also known as the PROTEIN, from the last
tRNA. The mRNA molecule is released from the ribosome as the small and large subunits fall apart. The mRNA can then be re-
translated or it may be degraded, depending on how much of that particular protein is needed.