Chapter 10 Molecular Biology of the Gene

I. DNA: Structure and Function

1. By the 1940s, DNA was proven to be the hereditary material.  Molecular biology is the study of biology at the molecular level.

2. Both DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids, which contain polynucleotides.

3. DNA consists of deoxyribose, phosphoric acid and nitrogenous base (G, guanine; A, adenine; T, thymine; C, cytosine).  RNA consists of ribose, phosphoric acid and nitrogenous base (G, guanine; A, adenine; U, uracil; C, cytosine).

4. The covalent linkages that join nucleotides (monomers) together in polynucleotides (polymers) are phosphodiester bonds and form sugar-phosphate backbone.

5. In 1953, Watson and Crick deduced that the three-dimensional structure of DNA is a double helix.

6. DNA replication requires that each DNA strain serves as a template to guide the synthesis of the other new strain (a semiconservative mode).  DNA polymerase is an enzyme to synthesize new DNA strain from the template DNA strain (DNA-dependent DNA polymerization).

II. The Flow of Genetic Information from DNA to RNA to Protein

1. The central dogma of molecular biology is a molecular “chain of command” from DNA to RNA (in the nucleus ) to protein (in the cytoplasm).

2. An organism's genotype determines its phenotype.

3. Transcription is the synthesis of RNA from the DNA template (i.e., the transfer of genetic information from DNA into an RNA molecule).  Translation is the synthesis of a polypeptide from an mRNA molecule (i.e., the transfer of the genetic information from RNA into a protein).

4. The covalent linkages that join amino acids (monomers; 20 common residues) together in polypeptides (polymers) are peptide bonds.

5. In 1940s, Beadle and Tatum proposed the “one gene-one enzyme” hypothesis.  Their hypothesis was modified as the “one gene-one polypeptide”.

6. Genetic information in DNA is transcribed into RNA and then translated into polypeptides.

7. Codon is a three-nucleotide sequence in mRNA (triplets) that specifies a particular amino acid (i.e., the basic unit of the genetic code).  The genetic code is the set of rules relating nucleotide sequence to amino acid sequence.  The genetic code is nearly universal, shared by organisms from the simplest bacteria (prokaryotes) to the most complex plants and animals (eukaryotes).

8. RNA polymerase is an enzyme to synthesize RNA during transcription (DNA-dependent RNA polymerization).

9. There are 3 phases in transcription: initiation, elongation, and termination.

(1)  Initiation: the attachment of RNA polymerase to the promoter and the start of RNA synthesis.  A promoter is a specific sequence in the DNA at the beginning of the gene, where RNA polymerase binds to.

(2)  Elongation: the RNA grows longer.

(3)  Termination: the RNA polymerase reaches the terminator and the end of RNA synthesis.  A terminator is a specific sequence in the DNA at the end of the gene, where RNA polymerase detaches from.

10. The processing of eukaryotic RNA:

(1)  In eukaryotes, exons are the coding regions representing the parts of a gene that are expressed.  Introns are internal noncoding regions.

(2)  There are 3 events in the processing of eukaryotic RNA: 5' capping, RNA splicing, and 3' polyA tail.  RNA splicing is the removal of introns and joining of exons.

11. There are 3 different kinds of RNA: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

(1)  A tRNA is a molecular interpreter to convert a codon of mRNA to an amino acid of protein.

(2)  A specific amino acid attaches at the 3' end of a tRNA, while the anticodon of tRNA is complementary to a codon on mRNA.

(3)  Ribosomes containing two subunits are the organelles that coordinate the functioning of mRNA and tRNA in protein synthesis in the cytoplasm.  Each subunit is made up of proteins and rRNA.

(4)  A fully assembled ribosome has a mRNA binding site on the small subunit and 2 tRNA binding sites on the large subunit: the P site holds the tRNA carrying the growing polypeptide chain, while the A site holds the tRNA carrying the next amino acid to be added to the chain.

12. There are also 3 phases in translation: initiation, elongation, and termination.

(1)  Initiation: a mRNA molecule binds to a small ribosomal subunit, the initiator tRNA carrying methionine (Met) binds to the start codon (AUG) at the P site and a large ribosomal subunit binds to the small subunit forming a functional ribosome.

(2)  Elongation: codon recognition in the A site, peptide bond formation and translocation from the A site to the P site.

(3)  Termination: translation continues until a stop codon (UAA, UAG or UGA) reaches the A site.  A stop codon does not code for an amino acid but instead stops translation.

13. Mutation is a change in the nucleotide sequence of DNA and is a major source of genetic diversity.

(1)  An A-to-T mutation in the b-subunit of hemoglobin gene with a change of amino acid from Glu to Val causes sickle-cell disease.

(2)  Three types of mutations: nucleotide substitution, deletion and insertion.

(3)  Silent mutation is a base substitution at DNA but no change in the protein product, for example, GAA and GAG code for the same Glu.

(4)  Missense mutation is a base substitution at DNA and does change the amino acid into a different amino acid with a totally different character in the protein product, for example, GGC (Gly) to AGC (Ser).

(5)  Nonsense mutation is a base substitution at DNA and change the amino acid into a stop codon, for example, AGA (Arg) to UGA (stop).

(6)  Mutations involving the deletion or insertion of nucleotides in a gene often have disastrous effects (frameshift mutation; changes in reading frame during translation).

(7)  Mutagen is a chemical or physical agent that interacts with DNA and causes a mutation.

(8)  High-energy radiation, such as X-ray or ultraviolet (UV) light, is a physical mutagen.  The anti-AIDS drug AZT and sodium azide are chemical mutagens.

III. Viruses and Other Noncellular Infectious Agents

1. A virus is a microscopic particle capable of infecting cells of living organisms and contains a bit of nucleic acid (DNA or RNA) wrapped in a protein coat.

2. Bacteriophages (Phages) are viruses that attack bacteria.  Lytic cycle is a viral reproductive cycle resulting in the release of new viruses by lysis of the host cell.  Lysogenic cycle is a viral reproductive cycle in which the viral genome is incorporated into the host chromosome as a prophage.

3. Most known plant viruses have RNA as their genetic material, for example, the tobacco mosaic virus (TMV).

4. Animal viruses have RNA as their genetic material, for example, influenza, measles, mumps, acquired immune-deficiency syndrome (AIDS) and polio viruses.  DNA viruses include hepatitis, chicken pox and herpes infections.

5. AIDS is caused by human immunodeficiency virus (HIV).

(1)  A retrovirus is an RNA virus that reproduces by a DNA molecule.  It reverse-transcribes its RNA into DNA by reverse transcriptase (RT; RNA-dependent DNA polymerization), inserts the DNA into a cellular chromosome and then transcribes more copies of the RNA from the viral DNA.

(2)  HIV infects and kills white blood cells (helper T cells; CD4 T lymphocytes) that are important in the immune system of humans.  Secondary infections cause a collection of symptoms that eventually kill AIDS patients.

(3)  AIDS has no cure yet.  There are 2 categories of anti-HIV drugs: protease inhibitor and reverse transcriptase inhibitor (for example, azidothymidine; AZT).

(4)  The key to AZT's effectiveness is its shape that is similar to T (thymine) to bind to reverse transcriptase.  However, this binding of AZT to RT terminates further incorporation into a growing DNA chain.

(5)  Many HIV-infected patients take a “drug cocktail” that contains both protease and RT inhibitors.

6. Viroids are small circular RNA molecules that infect plants.  Viroids do not encode proteins but can replicate in host plant cells.

7. Prion

(1)  A prion is an infectious protein that may multiply by converting related normal proteins to more prions.

(2)  A prion (scrapie prion protein; PrP^SC) is a misfolded form of a protein (cellular prion protein; PrP^C).

(3)  Prions cause several degenerative brain diseases in different animals, including scrapie in sheep, mad cow disease in cattle and Creutzfeldt-Jakob disease in humans.

IV. Bacterial Plasmids

1. As prokaryotic cells, bacteria are valuable as microbial models in molecular biology research.

2. Most of a bacterium's chromosome is a single, huge, closed, circular dsDNA (double-stranded DNA) with associated proteins.

3. Bacteria can transfer DNA in 3 ways: transformation, transduction (infection), and conjugation.

(1)  Transformation is the incorporation of DNA from the surrounding environment into a prokaryotic cell.

(2)  Transduction is the transfer of bacterial genes from one bacterial cell to another by a phage (by infection).

(3)  Conjugation is the transfer of bacterial genes between two bacterial cells mediated by a special piece of DNA called the F (fertility) factor during sexual mating.

4. Plasmids are small, circular dsDNA molecules that can serve as carriers for gene transfer in bacteria.  Every plasmid has an origin (ori) of replication, where DNA replication starts, required for its replication within the bacterium.