DNA and Its Role in Heredity
DNA: The Genetic Material
By the early 1900s, geneticists had associated the presence of genes with chromosomes.
Circumstantial evidence pointed to DNA as the genetic material.
A dye that binds to DNA showed that the amount of DNA in somatic cells was twice that in eggs or sperm, as would be expected from Mendel’s discoveries.
In 1952, Alfred D. Hershey and Martha Chase performed experiments confirming that DNA is the genetic material.
The T2 bacteriophage, a virus that attacks E. coli, consists almost entirely of a DNA core packed in a protein coat.
When a T2 bacteriophage attacks a bacterium, part but not all of the virus enters the bacterial cell.
The Hershey-Chase experiment (1952) determined that DNA was the part of the virus that entered the bacterium, so that it was able to replicate itself.
They used radioactive isotopes to determine this.
The Structure of DNA
Scientists set out to determine the structure of DNA hoping to find the answers to two questions:
How is DNA replicated between nuclear divisions?
How does DNA cause the synthesis of specific proteins?
The structure of DNA was determined after many types of evidence were combined.
By the 1950s it was known that DNA was a polymer of nucleotides.
The four nucleotides that make up DNA differ only in their nitrogenous bases.
There are two purines (adenine and guanine) and two pyrimidines (cytosine and thymine).
In 1950, Erwin Chargaff noted that in DNA from all species tested, the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine.
English physicist Francis Crick and American geneticist James D. Watson established the general structure of DNA.
The English chemists Rosalind Franklin and Maurice Wilkins were able to provide key information about the structure of DNA based on X-ray crystallography.
X-ray crystallography is the positions of different atoms in a crystalline substance shown after X-rays pass through it..
The results of X-ray crystallography convinced them that the DNA molecule was a helix.
X-ray crystallography also provided the values of certain distances within the helix.
Four features summarize the molecular architecture of DNA:
The DNA molecule is a double-stranded helix.
The diameter of the DNA molecule is uniform.
The twist in DNA is right-handed.
The two strands run in different directions (they are antiparallel).
The sugar–phosphate backbones of each strand coil around the outside of the helix.
The nitrogenous bases point toward the center of the helix.
Hydrogen bonds between complementary bases hold the two strands together.
A always pairs with T (two hydrogen bonds).
G always pairs with C (three hydrogen bonds).
The phosphate groups link the 3˘ carbon of one deoxyribose molecule to the 5˘ carbon of the next.
Thus a single strand of DNA has a 5˘ phosphate group at one end (the 5˘ end) and a free 3˘ hydroxyl group at the other end (the 3˘ end).
In a double helix, the 5˘ end of one polypeptide is hydrogen-bonded to the 3˘ end of the other, and vice versa.
The Molecular Mechanisms of DNA Replication
DNA replication during S Phase of Interphase takes place in two steps:
The hydrogen bonds between the two strands are broken, making each strand available for base pairing.
The new nucleotides are covalently bonded to each growing strand at the 3˘ end of the growing strand.
DNA Proofreading and Repair
Although errors in DNA replication (mutations) are essential for evolution, the vast majority of DNA errors are neutral at best and fatal at worst.
To minimize the number of errors, our cells have three DNA repair mechanisms:
Proofreading
Mismatch repair
Excision repair
As they add new bases to a growing strand, DNA polymerases (enzymes putting the new strand together) make a proofreading check.
When a DNA polymerase recognizes an error, it removes the wrong nucleotide and tries again.
The error rate of DNA polymerase on each attempt is only about 1 in 10,000.
This proofreading function reduces the overall error rate to about one base in a billion.
The mismatch repair mechanism scans new DNA for mismatched base pairs.
DNA is subject to damage by chemicals, radiation, and random spontaneous chemical reactions.
Excision repair enzymes "inspect" the cell’s DNA for damage throughout the lifetime of the cell, then cut the damaged strand and remove it.
DNA polymerase and DNA ligase fill in and seal up the resulting gap.
Bioinformatics
Bioinformatics: Analysis of nucleotide or amino acid sequences
Using Gene Prediction Software and Sequence Alignment Software as members of a bioinformatics research company.
Applications:
DNA fingerprinting (Profiling, crime investigation, paternity)
Agriculture (Golden Rice Project: engineering rice to contain carotenoids to increase Vit A consumption)
Pharmacology (Genetic differences in response to medication)
Environmental Science (confirmation of relationships of species, improved captive breeding programs to increase diversity)
Medicine (Classifying cancer by monitoring gene expressions)
Onconomics Corporation
You are an employee of a biotechnology company using bioinformatics to identify DNA sequences associated with a certain cancer as a precursor for development of an anti-cancer drug, OncoX.
Part I (5 points)
Assemble a continuous DNA sequence (also called a contig) form a series of short, overlapping sequences.
Compare same sequences from different individuals (there may be some differences depending on the alleles present in that individual. These are called polymorphisms.)