DNA and Molecular Genetics

The physical carrier of inheritance
Friedrich Meischer in 1869 isolated DNA from fish sperm and the pus of open wounds. Since it came from nuclei, Meischer named this new chemical, nuclein. Subsequently the name was changed to nucleic acid and lastly to deoxyribonucleic acid (DNA). Robert Feulgen, in 1914, discovered that fuchsin dye stained DNA. DNA was then found in the nucleus of all eukaryotic cells.
During the 1920s, biochemist P.A. Levene analyzed the components of the DNA molecule. He found it contained four nitrogenous bases: cytosine, thymine, adenine, and guanine; deoxyribose sugar; and a phosphate group. He concluded that the basic unit (nucleotide) was composed of a base attached to a sugar and that the phosphate also attached to the sugar
The Structure of DNA
Watson and Crick gathered all available data in an attempt to develop a model of DNA structure.
DNA is a double helix, with bases to the center (like rungs on a ladder) and sugar. phosphate units along the sides of the helix (like the sides of a nvisted ladder). The strands are complementary (deduced by Watson and Crick from Chargaffs data, A pairs with T and C pairs with G, the pairs held together by hydrogen bonds). Notice that a double-ringed purine is always bonded to a single ring pyrimidine. Purines are Adenine (A) and G.uanine (G). We have encountered Adenosine triphosphate (ATP) befare, although in that case the sugar was ribose, whereas in DNA it is deoxyribose . Pyrimidines are Cytosine (C) and Thymine (T). The bases are complementary, with A on one side of the molecule you only get T on the other side, similarly with G and C. If we know the base sequence of one strand we know its complement
DNA Replication
DNA replication involves a great many building blocks, enzymes and a great deal of ATP energy (remember that after the S phase of the cell cycle cells have a G phase to regenerate energy for cell division). Only occurring in a cell once per (cell) generation, DNA replication in humans occurs at a rate of 50 nucleotides per second, SOO/second in prokaryotes. Nucleotides have to be assembled and available in the nucleus, along with energy to make bonds between nucleotides. DNA polymerases unzip the helix by breaking the H-bonds between bases. Once the polymerases have opened the molecule, an area known as the replication bubble forms (always initiated at a certain set of nucleotides, the origin of replication). New nucleotides are placed in the fork and link to the corresponding parental nucleotide already there (A with T, C with G). Prokaryotes open a single replication bubble, while eukaryotes have multiple bubbles. The entire length of the DNA molecule is replicated as the bubbles meet.
HUMAN GENETICS
The human karyotype
There are 44 autosomes and 2 sex chromosomes in the human genome, for a total of 46
Human chromosomal abnormalities
A common abnormalitjL is caused by nondisjunction, the failure of replicated chromosomes to segregate during Anaphase II. A gamete lacking a chromosome cannot produce a viable embryo. Occasionally a gamete with n+1 chromosomes can produce a viable embryo.
In humans, nondisjunction is most often associated with the 21st chromosome, producing a disease known as Down's syndrome -C also referred to as trisomy 21). Sufferers of Down's syndrome suffer mild to severe mental retardation, short stock body type, large tongue leading to speech difficulties, and (in those who survive into middle-age), a propensity to develop Alzheimer's Disease. Ninety five percent of Down's cases result from nondisjunction of chromosome 21. Occasional cases result from a translocation in the chromosomes of one parent. Remember that a translocation occurs when one chromosome (or a fragment) is transferred to a non-homologous chromosome. The incidence of Down's Syndrome increases with age of the mother. although 25% of the cases result from an extra chromosome from the father..
Sex-chromosome abnormalities may also be caused by nondisjunction of one or more sex chromosomes. Any combination (up to XXXXY) produces maleness. Males with more than one X are usually underdeveloped and sterile. XXX and XO women are known, although in most cases they are sterile.
Prenatal detection of chromosomal abnormalities is accomplished chiefly by amniocentesis. A thin needle is inserted into the amniotic fluid surrounding the fetus (a term applied to an unborn baby after the first trimester). Cells are withdrawn have been sloughed off by the fetus, yet they are still fetal cells and can be used to determine the state of the fetal chromosomes, such as Down's Syndrome and the sex of the baby after a karyotype has been made.
RNA Links the Information in DNA to the Sequence of Amino Acids in Protein:
RNA occurs in the nucleus as well as in the cytoplasm (also remember that it occurs as part of the ribosomes that line the rough endoplasmic reticulum).
Crick's central dogma: Infonnation flow (with the exception of reverse transcription) is from DNA to RNA via the process of transcription, and thence to protein via translation. Transcription is the making of an RNA molecule off a DNA template. Translation'is the construction of an amino acid sequence (polypeptide) from an RNA molecule. Although originally called dogma, this idea has been tested repeatedly with almost no exceptions to the rule being found (save retroviruses).
Messenger RNA (mRNA) is the blueprint for construction of a protein. Ribosomal RNA (rRNA) is the construction site where the protein is made. Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time.
RNA has ribose sugar instead of deoxyribose sugar. The base uracil (D) replaces hymine (T) in RNA. Most RNA is single stranded, although tRNA will form a "cloverleaf" structure due to complementary base pairing.
Transcription: making an RNA copy of a DNA sequence
RNA polymerase opens the part of the DNA to be transcribed. Only one strand of DNA (the template -strand) is transcribed. RNA nucleotides are available in the region of the chromatin (this process only occurs during Interphase) and are linked together similar to the DNA process
The Genetic Code: Translation of RNA code into protein
The code consists of at least three bases, according to astronomer George Gamow To code for the 20 essential amino acids a genetic code must consist of at least a 3-base set (triplet) of the 4 bases. If one considers the possibilities of arranging four things 3 a time (4X4X4), we get 64 possible code words, or codons (a 3-base sequence on the mRNA that codes for either a specific amino acid or a control word).
Protein Synthesis
Prokaryotic gene regulation differs from eukaryotic regulation, but since prokaryotes are much easier to work with, we focus on prokaryotes at this point. Promoters are sequences of DNA that are the start signals for the transcription of mRNA. Terminators are the stop signals. mRNA molecules are long (500-10,000 nucleotides). Ribosomes are the organelle (in all cells) where proteins are synthesized. They consist of two-thirds rRNS and one-third protein. Ribosomes consist of a small (in E. coli, 16S rRNA and 21 different proteins. The 50S subunit consists of 5S and 23S rRNA and 34 different proteins. The smaller subunit has a binding site for the mRNA. The larger subunit has two binding sites for tRNA
Transfer RNA (tRNA) is basically cloverleaf-shaped. tRNA carries the proper amino acid to the ribosome when the codons call for them. At the top of the large loop are three bases, the anticodon, which is the complement of the codon. There are 61 different tRNAs, each having a different binding site for the amino acid and a different anticodon. For the codon UUU, the complementary anticodon is AAA. Amino acid linkage to the proper tRNA is controlled by the aminoacyl-tRNA synthetases. Energy for binding the amino acid to tRNA comes from ATP conversion to adenosine monophosphate (AMP).
Translation is the process of converting the mRNA codon sequences into an amino acid sequence. The initiator codon (AUG) codes for the amino acid N-formylmethionine (f-Met). No transcription occurs without the AUO codon. f-Met is always the first amino acid in a polypeptide chain, although frequently it is removed after translation. The intitator tRNA/mRNA/small ribosomal unit is called the initiation complex. The larger subunit attaches to the initiation complex. After the .initiation phase the message gets longer during the elongation phase.
New tRNAs bring their amino acids to the open binding site on the ribosome/mRNA complex, forming a peptide bond between the amino acids. The complex then shifts along the mRNA to the next triplet. opening the A site. The new tRNA enters at the A site. When the codon in the A site is a termination codon, a releasing factor binds to the site, stopping translation and releasing the ribosomal complex and mRNA.
Mutations
We define mutations as any change in the DNA. We now can refine this definition:a mutation is a change in the DNA base sequence that results in a change of amino acid(s) in the polypeptide coded for by that gene. Alleles are alternate sequences of DNA bases (genes), and thus at the molecular level tha products of alleles differ (often by only a single amino acid, which can have a ripple effect on an organism by changing). Addition, deletion, or addition of nucleotides can alter tha polypeptide. Point mutations are the result of the substitution of a single base. Frame-shift mutations occur when the reding frame of the gene is shifted by addition or deletion of one or more bases. With the exception of mitochondria, all organisms use the same genetic code. Powerful evidence for the common ancestry of all living things.
Genes, Viruses and Cancer
Cancer is a disease in which cells escape the restraints on normal cell growth. Cancer is an inheritable disease (at least form cell to daughter cells). Once a cell has become cancerous, all of its descendant cells are cancerous. Gross chromosomal abnormalities are often visible in cancerous cells. Most carcinogens (cancer-generatiing factors) are also mutagens (mutation-generatiing factors). Oncogenes are genes resembling normal genes but in which something has gone wrong, resulting in a cancer. Fifty oncogenes have thus far been discovered.
Viruses seem able to cause cancer in three ways. Presence of the viral DNA may disrupt normal host gene regulation. Since most cancer-causing viruses are retroviruses, the virus may serve as a vector for oncogene insertion. Transfers of genes between eukaryotic cells will allow doctors, who have historically been limited to phenotypic cures, to attack disease at the genotypic level. SV40 virus has been used to inject the rabbit beta-globin gene into monkeys. Viruses can thus serve as a possible vector to place healthy (non-mutated) alleles into eggs.