Molecular Biology Text

DNA

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses.

Base Pairs	Within the DNA molecule, there are four bases from two biochemical classes. The purines are guanine (G) and adenine (A). The pyrimidines are cytosine (C) and thymine (T). Another pyrimidine base is uracil (U) that is only present in RNA.
Base Pairings	The four bases can combine in only two ways. G binds with C through three hydrogen bonds, and A binds with T through two hydrogen bonds. Thus there are only two possible base pairings.
Nucleotides	Nucleotides are the building blocks of DNA and RNA they consist of a base (G, A, C, T [U]), sugar (deoxyribose or ribose) and a phosphate group. Nucleotides bind together to form a long polymer molecule, which will form one half of the DNA molecule. The specific sequence of nucleotides along a strand determines the genetic code carried by the organism.

RNA

Ribonucleic acid (RNA) is a long chain of nucleotides, similar in structure to one strand of DNA. One difference is that in RNA, thymine is replaced by its less-stable, unmethylated form, uracil. RNA molecules are constructed during a process called transcription. Transcription assembles RNA based on the sequence of bases on a DNA molecule.

Codon

Each group of three adjacent nucleotides is called a codon and each codon defines a specific amino acid. The sequence of nucleotides contains the information for creating proteins. Proteins are composed of strings of amino acids. In humans, there are twenty different amino acids that combine into more than 20,000 different proteins.

mRNA

Messenger ribonucleic acid (mRNA) is a molecule of RNA encoding a chemical "blueprint" for a protein product. It is transcribed from the DNA template and carries coding information to the sites of protein synthesis in the ribosomes. In mRNA as in DNA, genetic information is encoded in the sequence of nucleotides arranged into codons consisting of three bases each.

tRNA

Transfer ribonucleic acid (tRNA) is a small RNA molecule that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation.

Enzymes

Polymerase	Enzymes that facilitate the polymerization of new DNA or RNA against an existing DNA or RNA template in the processes of replication and transcription. It "reads" an intact DNA strand as a template and uses it to synthesize the new strand.
Helicase	A "motor protein" that separates strands of a DNA double helix or a self-annealed RNA molecule using the energy from ATP hydrolysis by breaking hydrogen bonds between annealed nucleotide bases.
Ligase	Catalyses the joining of two large molecules by forming a new chemical bond.
DNA primase	Sythesizes a short RNA segment (called a primer) complementary to a DNA template and is of key importance for replication because no known DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA primer.
Topoisomerase	Unwinds and winds the DNA, for protein synthesis and DNA replication. They cut the DNA, and at the end of the process connect it again.

Chromosomal Abnormalities

Chromosome abnormalities can be numerical or structural and usually occur as a result of cell division errors. Fluorescent in situ hybridization utilizes a mixture of multi-colored fluorescent labeled probes to assess cells for chromosome abnormalities.

Anueploidy is defined as the occurrence of one or more extra or missing chromosomes leading to an unbalanced chromosome complement, or, any chromosome number that is not an exact multiple of the haploid number. Abnormal chromosome number is one of the most common features of cancer cells and is caused by many mechanisms.

Nondisjunction is the failure of chromosome pairs to separate properly during anaphase, resulting in a cell with chromosome imbalance. This failure to separate is frequently caused by spindle checkpoint defects. Spindle, or mitotic, checkpoints are mechanisms that control the proper cell division in eukaryotic cells. To achieve proper cell division, the two kinetochores on the sister chromatids must be attached to opposite spindle poles. Spindle checkpoints assess the cell for DNA damage and will delay division or target the cell for destruction if repairs are not accurately completed. A weakened or damaged spindle checkpoint would generate daughter cells either lacking a chromosome copy or possessing too many copies.

Aneuploidy is frequently found in bladder cancer. Bladder cancer is the fourth most common cancer in men and the seventh most common cancer in women in the United States. Bladder cancer recurrence rate is 80%, making it a chronic illness. Diagnosis of low grade and recurrent bladder cancer has been difficult due to the low sensitivity of urine cytology and the cost and invasiveness of cystoscopy . A new FISH assay has been developed that tests for aneuploidy of the chromosomes 3, 7 and 17 frequently associated with bladder cancer.

Deletion is the loss of a part of the chromosome or DNA sequences. Loss of genetic material can range from a single nucleotide base pair to an entire piece of chromosome and can be caused by losses from translocation , unequal crossing over, chromosomal crossovers within a chromosomal inversion and breaking without rejoining. FISH can be used to detect the loss of the 9p21 locus found in more than 60% of bladder cancers.

Duplication is the production of multiple copies of a region of DNA that contains a gene; it may occur as an error in a retrotransposition event, a homologous recombination, or duplication of an entire chromosome. FISH is the gold standard for detecting amplification of the HER2/neu ( Human Epidermal growth factor Receptor 2) gene or its protein product. Overexpression of this receptor is found in 15 to 20 percent of breast cancers and also occurs in ovarian cancer, stomach cancer, and serous endometrial carcinoma.

Chromosomal translocation is an abnormality caused when a portion of one chromosome is transferred to a nonhomologous chromosome . Cancer, infertility and a minority of Down's syndrome cases can be attributed to this event. Chromosomal inversion occurs when a piece of chromosome breaks off and reattaches itself in the reverse direction. Carriers of this defect usually do not experience any abnormalities if the chromosome rearrangement does not result in missing or additional genetic information.

References:

Text - Alberts, Bruce, et al. (2002) The Molecular Biology of the Cell (4th edition). Garland Science
Text - Bruns, David E, et al. (2007) Fundamentals of Molecular Diagnostics. Saunders
Text - Interactive Medical (2009). Molecular Diagnostic Testing: Principles and Practice. CE and CME program. www.hpvinstitute.com.
Image - http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg (DNA strand)
Image - http://images2.clinicaltools.com/images/gene/codon.jpg (RNA strand)
Image - http://www.obgynacademy.com/basicsciences/fetology/genetics/images/codon_GCA.gif
Image - http://www.theodora.com/genetics/glossary_t.html (transcription/translation)

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