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Background:
In the 1950s, monumental race in the scientific community was run between to research groups
striving for the same goal, determining the structure of DNA. Dr. Watson and Dr. Crick head a
lab in England while Linus Pauling ran his group at Cal-Tech. Watson and Crick where very
intimidated by Pauling, he had just won the 1954 Nobel Prize in chemistry. They were David
and Pauling was Goliath. Like David, Watson and Crick won. And like Davids slaying of
Goliath, Watson and Crick used a tactic unfamiliar to Pauling. They were not releasing their
findings. While Pauling regularly published his findings, which Watson and Crick led them to
their structure of DNA. They ensured the only people they spoke of about their research would
not be talking to anyone in Paulings group. Yes, scientist are people too and they can play
dirty. If you dont think they played dirty read their book, The Double Helix written by Dr.
James D. Watson.
For all organisms, DNA, deoxyribonucleic acid, is composed of the same components. The
components of DNA are sequenced a specific side-by-side arrangements termed base pairs,
along the DNA strands. This order blueprints the exact instructions required to create a
particular organism with its own unique traits.
A genome is an organisms complete set of DNA. Genomes vary widely in their number of base
pairs. The smallest known genome for an organism, a bacteria, contains about 600,000 base
pairs. The human genome consists of approximately 3 billion base pairs. All the cells in a the
human body contain the genome, except for mature red blood cells.
DNA in the human genome is arranged into 24 distinct chromosomes. 22 of which are found in
all human, the last two are gender specific. Each chromosome is a physically separate
molecule that ranges in length from roughly 50 million to 250 million base pairs. A chromosome
is large enough to be viewed with an electron microscope, the figure on the left in the picture
below is a chromosome.
The chromosomes are divided into sections which determine each specific trait an organism
exhibits. The genes are specific sequences of bases that encode instructions on how to make
proteins. It is estimated that there are 30 40 thousand genes. Oddly, of the 3 billion base
pairs in the genome, the genes comprise only about 2%, or 60 million of the base pairs. The
remaining non-coded regions functions may include structural support and the what-wherewhen and number of proteins made.
DNA and genes seem to get all the publicity, but remember they are the blue prints, they dont
actually do anything other than store information. The proteins that the genes create are
responsible for performing most life functions. The picture below shows an overall view of the
steps from Chromosome to DNA to gene to base pair sequence to amino acid sequence to
protein.
N2
N1
2
N
3
purine
adenine (A)
NH2
N
6
5
5
9
pyrimidine
C4H4N2
purine
guanine (G)
O
N
N
pyrimidine
cytosine (C)
NH2
N
NH
N
pyrimidine
thymine (T)
O
NH2
NH
O
pyrimidine
uracil (U)
O
5'
3'
N
H
-D-2-deoxyribose
OH
O
H
NH
1'
H
2'
OH
OH
found in RNA
HOH2C
4'
5'
OH
O
H
3'
1'
H
2'
OH
found in DNA
Phosphate, PO4-3:
O-
O P O
ONucleotides:
Upon combining these three structural components, a nucleotide is created. The nucleotide
consists of a base and a phosphate bound to the sugar. To create one nucleotide, the base
binds to the carbon 1 and the phosphate binds to carbon 5. The base-sugar bond is an Nglycosidic bond and the phosphate-sugar bond is a phosphoester bond.
Normally the gylcosidic bond is formed between two carbohydrate monomers and is C-O-C,
which is an particular type of ester. This bond replaces the central oxygen with a nitrogen,
hence the N-glycosidic bond nomenclature. These are both dehydration reactions.
The ester functional group consists of a carbonyl group bonded to an oxygen with R-groups
attached to the ends. The phosphoester bond specifies that one of the R-groups be a
phosphate group.
ester
phosphoester
O
O
O
R'
O C R
O P O C R
O
O P O
5'
CH2
N
N
5'
O P O
CH2
OH
deoxyadenosine monophosphate
dAMP
deoxyguansine monophosphate
dGMP
O
NH2
N
O P O
5'
CH2
OO
1'
H
2'
OH
NH 2
1'
2'
2'
OH
O
H
NH
1'
deoxycytidine monophosphate
O P O
NH
5'
CH2
OH
1'
H
2'
deoxythymidine monophosphate
dCMP
dTMP
The nucleotides for RNA are the same except for the nucleotide containing the thymine, a uracil
has replaced this base and the sugar becomes ribose, instead of deoxyribose.
O
NH
O-
5'
O P O
CH2
OH
O
H
1'
H
2'
OH
OH
uridine monophosphate
UMP
The following table should help with the nomenclature of the nucleotides. The red is for RNA
and the blue is for DNA.
RNA base-ribose
DNA
base
base
base-deoxyribose
adenine adenosine A adenine
deoxyadenosine
dA
guanine guanosine G guanine
deoxyguanosine
dG
cytosine
cytidine
C cytosine
deoxycytidine
dC
uracil
uridine
U thymine
deoxythymidine
dT
The MP in the AMP or UMP stands for monophosphate, obviously meaning one phosphate.
This must be specified as we will find in the topic of metabolism ADP and ATP are very
important sources of cellular energy.
NH2
N
O
-
O
O P O
O P
-
5'
CH2
O
H
1'
NH2
N
O
O P
O P
-
O
O P O
5'
CH2
ADP
O
H
2'
OH
1'
H
2'
OH
OH
ATP
OH
Structure of DNA:
DNA is composed of nucleotides. These nucleotides are linked through a phosphate ester
bond, similar to the one which links the phosphate to the sugar. The same sugar bonds to a
phosphate on the other nucleotide, this time at the 3 carbon. Since this same phosphate now
has two ester style bonds the link is called a phosphodiester bond. A four nucleotide sequence
is depicted below.
NH2
N
OO P O
5'
CH2
H
3'
O
O P O
1'
NH2
5'
CH2
H
3'
O
O P O
H
N
H
5'
CH2
NH
NH2
H
3'
O
O P O
NH
H
5'
CH2
OH
O
H
3'
OH
The DNAs is actually composed to two separate strands and its overall structure is similar to
that of a spiral staircase. The sugar and phosphate are considered the backbone of the
molecule and comprise the hand-rails of the stair case, with the bases forming the stairs. The
two strands are held together by hydrogen bonding formed between the bases. The adenine
and thymine bases form a double hydrogen bond and the cytosine and the guanine form a triple
hydrogen bond. The strands actually are antiparallel. Meaning they are laid out in opposite
directions. From the above 4 nucleotide sequence you can see that one of the ends has a free
3 carbon. The ends are numbered as 3 and 5.
The two below diagrams give a visual picture of the hydrogen bonding.
DNA Replication:
Mitosis is the process that takes place in the nucleus of a dividing cell and results in the
formation of two new nuclei each having the same number of chromosomes as the parent
nucleus. This process must occur prior to a parent cell dividing into two daughter cells.
Replication of DNA occurs at this time.
This process is semiconservative. The each of the parent strands becomes one of the strands
in the new double helix. Using the parent strand as a template maintains a low percentage of
copy error. The semiconservative process was verified by the Meselson and Stahls density
labeling experiment. In the experiment they parent DNA was composed of nucleotides
composed of N-15. The resulting daughter DNA strands where composed of half N-15 and half
N-14. When the next generation was allowed to spawn half of the DNA was composed of N-14,
while the other half was composed of N-15 and N-14. At the time of this experiment a
second theory, the conservative model, rivaled the semiconservative model. The follow picture
depicts the predicted out come for each theory.
RNA Structure:
There are three main structural differences between DNA and RNA.
RNA normally consists of a single strand
Uracil replaces thymine
the sugar ribose replaces deoxyribose
Types of RNA:
Protein Synthesis:
Transcription and translation are the two steps whereby DNA encodes for the production of
amino acids into proteins. The following figure gives an overview of the entire process of protein
synthesis.
Transcription
Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA
transcription. A portion of one strand of the DNA double helix is used as a template, this section
is named a gene. The RNA polymerase synthesizes a mRNA from this gene. This mRNA
migrates from the nucleus to the cytoplasm. The gene contains coded sections, exons and is
sectioned with non-coded portions, introns. The mRNA copies all of this information, including
the intron nucleotides. The mRNA will go through a maturation process called splicing where
the non-coding sequences, introns are eliminated, as depicted below.
Translation:
The coding mRNA sequence can be described as a unit of three nucleotides called a codon.
The ribosome binds to the mRNA at the start codon, AUG that is recognized only by the tRNA.
The ribosome proceeds to the elongation phase of protein synthesis. During this stage,
complexes, composed of an amino acid bound to tRNA, sequentially bind to the appropriate
codon in mRNA by forming complementary base pairs with the tRNA anticodon. The ribosome
moves from codon to codon along the mRNA. This process aligns the amino acids and a
peptide bond is formed between these closely positioned amino acids. Amino acids are added
one by one, translated into polypeptidic sequences dictated by DNA and represented by mRNA.
At the end, a release factor binds to the stop codon, terminating translation and releasing the
complete polypeptide from the ribosome.
The amino acids that correspond to each codon are listed in tables. These tables come in two
formats, each is shown below. Each amino acid corresponds with anywhere from one to six
specific codons. In addition, three codons are used for starting and stopping sequences rather
than specifying amino acids to be added to the sequence. Note that the base sequences
shown here are codons, mRNA rather than anti-codons, tRNA.
The 1984 Nobel Prize for Chemistry was awarded to Professor Merrifield of Rockefeller
University for developing an automated version of this technique capable of producing the
hormone insulin (51 -amino acids). The above diagram summarizes the sequence of steps
involved. The protein is engineered by simply dipping starting material into a series of different
beakers.
Simple, elegant, useful and can be FULLY automated.
The following figure gives the primary structure of the two chains in human insulin.
Biochemists can now use a refinement of the genetic modification technique to redesign
proteins. Once they have isolated the gene for a particular protein they can alter its code so that
a change occurs in the proteins primary structure. They then incorporate the modified gene into
a micro-organism where it is decoded as before, but this time a new protein appears.
Swapping one a-amino acid in a protein can have a large effect on how the protein behaves. As
the primary structure dictates secondary and tertiary structure therefore function. Biochemists
have already used this protein engineering to modify human insulin in a way that makes it
become absorbed more quickly after injection. Multiple changes are needed to humanize
antibodies.
Computer modeling techniques allow protein chemists to make predictions about how proposed
-amino acid changes might change the structure and activity of a protein.
Genetic and protein modification have enormous potential. Besides insulin, genetic modification
can produce human growth hormone and the blood clotting Factor VIII. Genetic engineering
may provide an alternative to conventional plant breeding techniques in farming. In addition it is
already possible to introduce into a plant new genes that enable it to produce its own protein
insecticide or that make it resistant to disease. Hepatitis B vaccine, oil-digesting bacteria and
bacteria that produce biodegradable plastic are all recently developed products of genetic
modification techniques.
DNA Fingerprinting:
In DNA ID "chemical scissors" called restriction enzymes are used to cut the extremely long
DNA molecule into fragments. Each restriction enzyme cuts at each point on the DNA molecule
where specific patterns of nitrogen bases occur. Everyone has these patterns in their DNA, but
not at the same places. Because the patterns occur in different places, the length of the
fragment differs from person to person. In very rare instances two people might have the same
pattern of fragment lengths produced by one restriction enzyme. Therefore, in DNA ID samples
are tested with more than one enzyme. The probability that two or more people will produce the
same pattern when their DNA is cut by two or more restriction enzymes is very small.
Statisticians call this the multiplication rule, because the individual probabilities of a mistaken
identity for each pattern are multiplied together to find the overall probability.