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Transcript
Lecture 19A. DNA computing
What exactly is DNA (deoxyribonucleic acid)? DNA is the material that contains codes for the
many physical characteristics of every living creature. Your cells use different codes to
determine what functions to carry out, just as you use code to communicate. The cell nuclei of
all eukaryotic organisms contain DNA and each cell contains all the genetic code needed to
assemble the entire organism. The amount of information involved requires the individual DNA
strands to be extremely long. Each cell contains about 3 cm of DNA. The fact that this long
molecule fits into a cell of around a few microns across is because DNA is very thin (2 nm in
diameter).
The building blocks
DNA gets its name from deoxyribonucleic acid which is a type of nucleic acid. Nucleic acids are
made up of polynucleotide chains which are formed by many nucleotides bonded together.
Phosphate, Ribose sugar, and Bases
DNA and RNA
There are two different kinds of sugars in a nucleotide, deoxyribose and ribose. If the
polynucleotide chain forms DNA then the sugars in its nucleotides are deoxyribose while
nucleotides containing ribose as its sugar form RNA.
The Bases
There are five different bases in a nucleotide. These bases are adenine, cytosine, guanine,
thymine, and uracil. Uracil is only found in RNA, while thymine is only found in DNA. Each
base is identified by the first letter in its name.
DNA
RNA
Adenine (A)
Adenine (A)
Cytosine (C)
Cytosine (C)
Guanine (G)
Guanine (G)
Thymine (T)
Uracil (U)
Polynucleotide chain
Nucleotides bond together in a chain to form polynucleotide chains such as the one below. In a
polynucleotide chain, there are open ends. The open phosphate end is called the 5' end while the
open sugar end is called the 3' end.
A section of a polynucleotide chain with each individual
nucleotide bonded together.
The Base Pairing
Chargaff's Rule: A=T, G=C. By using Chargaff's rule Watson and Crick discovered that
Thymine paired with Adenine and Guanine with Cytosine. They also discovered that a hydrogen
bond was obtained when the bases were paired together in this way.
A-T
G-C
In a DNA strand Adenine is always paired with Thymine, and Guanine is always paired with
Cytosine.
Double helical DNA
A DNA strand consists of two polynucleotide chains bonded together by their nitrogenous bases,
thus one looks like this.
Proteins
Proteins are sometimes called Polypeptides, since they contain many Peptide Bonds
The peptide bond is an amide bond
R is one of the 20 amino acids
Amino Acids Grouped Alphabetically
Amino Acid
Abrev. Structure Letter
Letter
Name
Amino
Acid
Name
Abrev. Structure
A
Alanine
Ala
M
Methionine
Met
C
Cysteine
Cys
N
Asparagine
Apn
D
Aspartic Acid
Asp
P
Proline
Pro
E
Glutamic
Acid
Glu
Q
Glutamine
Gln
F
Phenylalanine
Phe
R
Arginine
Arg
G
Glycine
Gly
S
Serine
Ser
H
Histidine
His
T
Threonine
Thr
I
Isoleucine
Ile
V
Valine
Val
K
Lysine
Lys
W
Tryptophan
Trp
L
Leucine
Leu
Y
Tyrosine
Tyr
Grouped by Characteristics
Transcription (reading)
DNA contains the blue print for the chemicals that make up our body. DNA tells the body what
proteins to make and the proteins carry out the functions. How does it work? Proteins are made
of Amino Acids which are bonded together in chains during transcription.
The genetic code
The genetic code consists of 64 triplets of nucleotides. These triplets are called codons. With
three exceptions, each codon encodes one of the 20 amino acids used in the synthesis of proteins.
That produces some redundancy in the code: most of the amino acids being encoded by more
than one codon.
One codon, CAT serves two related functions:
•
•
it signals the start of translation
it codes for the incorporation of the amino acid histidine (Met) into the growing
polypeptide chain .
TTT Phe
TCT Ser TAT Tyr
TGT Cys
TTC Phe
TCC Ser TAC Tyr
TGC Cys
TTA Leu
TCA Ser TAA STOP TGA STOP
TTG Leu
TCG Ser TAG STOP TGG Trp
CTT Leu
CCT Pro CAT His
CGT Arg
CTC Leu
CCC Pro CAC His
CGC Arg
CTA Leu
CCA Pro CAA Gln
CGA Arg
CTG Leu
CCG Pro CAG Gln
CGG Arg
ATT Ile
ACT Thr AAT Asn
AGT
ATC Ile
ACC Thr AAC Asn
AGC Ser
ATA Ile
ACA Thr AAA Lys
AGA Arg
Ser
ATG Met* ACG Thr AAG Lys
AGG Arg
GTT Val
GCT Ala GAT Asp
GGT Gly
GTC Val
GCC Ala GAC Asp
GGC Gly
GTA Val
GCA Ala GAA Glu
GGA Gly
GTG Val
GCG Ala GAG Glu
GGG Gly
The genetic code is almost universal. The same codons are assigned to the same amino acids and
to the same START and STOP signals in the vast majority of genes in animals, plants, and
microorganisms. However, some exceptions have been found.
DNA to RNA
Remember the structure of DNA and chromosomes. There are multiple genes on each DNA
strand that spans the chromosome. When the time comes to make a certain protein from the code
of a certain gene, the cell does not need to read the whole DNA strand. Instead, it only reads that
gene, this being the most sensible thing to do. There are a few enzymes that help this process to
work. The first of which are the Basal Factors which are a set of proteins that mark the promoter
region or the beginning of the gene that is to be read. The end of the gene is marked by the
Enhancer Region with the Activator proteins (transcription factors). From the promoter region
and the enhancer region, transcription will take place. The first step begins with the Bending
protein traveling along the gene to a spot between the enhancer region and the promoter
region. Once at this halfway spot the protein bends the DNA strand so that the activator proteins
at the enhancer region are toughing the basal factors at the promoter region. This combining of
the proteins stimulates RNA polymerase to do its work.
RNA polymerase is an enzyme that more or less does the same thing that DNA helicase and
polymerase do. It begins at the promoter region of the gene and unzips the DNA strand. Next, it
constructs a polynucleotide chain of RNA (ribonucleic acid) that compliments the DNA
bases. This enzyme pairs RNA nucleotides with the original DNA nucleotides with the rule of
C=G and A=U. U being Uracil takes the place of Thymine on the RNA strand that is
forming. As separate RNA nucleotides pair up with the bases of the DNA strand the enzyme
bonds them into a polynucleotide chain of messenger RNA (mRNA). When the RNA
polymerase is finished, it drags the mRNA strand away from the DNA strand outside of the
nucleus of the cell into the cytoplasm while the DNA strand "zips" up to its original form.
Introns
Scientists have determined that up to 70 percent of the RNA that is made through transcription
by copying DNA is unneeded. One term for this unneeded DNA is "Junk DNA". It is not
known why there is so much junk DNA, but it possibly could lower the chances of mutations in
the DNA sequence that could cause a disease, or a deformity. This could be true since the
mutations have a greater chance of happening to the junk DNA since there is more of it. Since
there is so much "Junk DNA" in the mRNA strand, it needs to be removed so the correct protein
can be assembled. As the mRNA is taken into the cytoplasm of the cell, an enzyme called a
splice some runs along the polynucleotide chain to determine what part of the DNA strand
should be cut out and discarded. A string of unnecessary mRNA is called an intron. When the
slice some finds an intron it pulls the RNA together so that the intron loops away from the
strand. Then it cuts out the intron and bonds the two ends together. Once the introns are cut out
of the mRNA it is taken into the cytoplasm to undergo the last stage of transcription, protein
synthesis.
Protein Synthesis
Once the mRNA is outside of the nucleus, the protein is made. A special component of the cell
called a Ribosome runs along the strand to determine which amino acids to bond together to
make a protein. The ribosome reads every base in groups of three (codons). There is a different
kind of RNA called tRNA or transfer RNA. Transfer RNA units are simple because they are
made of RNA which is attached to a certain amino acid. On these units of tRNA a special group
of three bases distinguish what amino acid is attached to it. This special group of three bases is
called an anti-codon because the ribosome pairs up anti-codons with codons. Each anti-codon is
the exact compliment of bases as its codon. For example:
Codons
GAC
UCC
CGG
UAU
Anti-codons
CUG
AGG
GCC
AUA
Transformation of genetic code from DNA to the ribosome for protein synthesis via messenger
RNA.
Ribosome
Back to the ribosome. As the ribosome runs along the mRNA strand, it reads the codons. When
the ribosome comes to the codon, AUG, it places its matching anti-codon next to it and uses the
amino acid, methionine, that accompanies this anti-codon as the first amino acid in the amino
acid chain. Then it reads the next codon and the procedure is repeated, but it now bonds the first
amino acid to the second one. This process of reading the codons, matching them with their anticodons, and bonding the amino acids together is continued until the ribosome reads a triplet of
UAA, UAC, or UGA. These codons tell the ribosome to stop bonding the amino acids
together. Once the Ribosome is finished bonding the amino acids together into what is called a
polypeptide chain (not to be confused with polynucleotide chain), named because of the type of
bond between the amino acids, the protein is finished being made and transcription is complete.
AUG is the start codon which tells the ribosome to begin making the polypeptide chain. UAA,
UAC, and UGA are stop codons which tell the ribosome to stop making the polypeptide chain.
Replication (copying)
During mitosis (cell division) cells make copies of their chromosomes. The chromosomes
duplicate themselves so that the cells that come from the original cell will have the same
DNA. In order for this copy to be made, DNA must go through replication. Replication is the
name given for the act of copying DNA strands.
To begin replication, an enzyme called DNA helicase unwinds the long DNA strand. As the
strand unwinds, another enzyme, DNA polymerase, travels up from the 3' end attaching
complimenting bases to the unzipped strand. Then it travels down toward the 5' end connecting
complimenting bases to this side of the double helix. Another DNA polymerase continues this
process by traveling up the 3' end, reaching the DNA helicase (which is still "unzipping" the the
DNA strand), and then traveling down the 5' end. Eventually, this process results in two strands
of DNA; the cell is ready to divide.
PCR (Polymerase chain reaction)