Molecular Biology: Gene Expression and Protein Synthesis

Gene Expression and the Central Dogma

• The information content of genes is in the specific sequences of nucleotides.
• DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins.
• Proteins are the links between genotype and phenotype.
• Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation.
• Central dogma: information cannot be transferred from protein to protein or protein to nucleic acid, but can be transferred between nucleic acids and from nucleic acid to protein.

The Genetic Code

• The flow of information from gene to protein is based on a triplet code: a series of three nucleotides.
• The code of a gene is transcribed into a complementary three-nucleotide code of mRNA called a codon.
• 64 possible codons: 3 stop codons, 61 sense codons.
• The genetic code is 'degenerate' but not ambiguous.
• Codons must be read in the correct reading frame in order for the specified polypeptide to be produced.
• The genetic code is nearly universal, shared by the simplest bacteria to the most complex animals.

DNA Structure and Replication

• Watson: DNA was a double helix.
• Watson and Crick: built models of a double helix to conform to the X-rays and chemistry of DNA.
• Franklin: two outer sugar-phosphate backbones, with the nitrogenous bases paired in the molecule's interior.
• Watson: built a model in which the backbones were anti-parallel.
• Watson and Crick reasoned that the pairing was specific, dictated by the base structures.
• Purine + purine = too wide.
• Pyrimidine + pyrimidine = too narrow.
• Purine + pyrimidine = width consistent with X-ray data.
• Parental molecule: separation of parental strands into templates, formation of new strands complementary to template strands.
• Semiconservative replication: DNA replication accomplished by separation of the strands of a parental duplex, each strand then acting as a template for synthesis of a complementary strand.

Transcription

• The stretch of DNA that is transcribed is called a transcription unit: it includes a promoter, an RNA-coding region, and a terminator.
• The DNA sequence where RNA polymerase attaches is called the promoter.
• The three stages of transcription: initiation, elongation, and termination.
• Both strands of DNA can encode genes, but the coding sequence of one gene will always be on one strand.
• RNA splicing removes introns and joins exons, creating an mRNA molecule with continuous coding sequence.
• Some introns contain sequences that may regulate gene expression.
• Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing.

Translation

• Genetic information flows from mRNA to protein through the process of translation.
• Three properties of RNA enable it to function in this role: it can form a three-dimensional structure because of its ability to base-pair with itself, some bases in RNA contain functional groups that may participate in catalysis, RNA may hydrogen-bond with other nucleic acid molecules.
• tRNA molecules are not identical: each carries a specific amino acid on one end and has an anticodon on the other end.
• The anticodon base-pairs with a complementary codon on mRNA.
• Translation is a complex biochemical and mechanical process.
• Accurate translation requires two steps: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase, a correct match between tRNA anticodon and an mRNA codon.
• Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis.
• The two ribosomal subunits are made of proteins and ribosomal RNA.
• P site: holds the tRNA that carries the growing polypeptide chain.
• E site: discharged tRNA leaves.
• A site: holds the tRNA that carries the next amino acid.

Mutations

• Mutations are sustainers of life and can cause problems.
• Source of all genetic variation, which further provides the raw material for evolution, source of many diseases and disorders, useful for probing fundamental biological processes.
• Main types of mutations: base substitutions, insertions, and deletions.
• Loss of function mutations: a mutation that results in reduced/abolished protein function.
• Gain-of-function mutations: a mutation that confers new/enhanced activity to a protein.
• Conditional mutation: a mutant allele causes a mutant phenotype in only a certain environment, but causes a wild-type phenotype in some different environment.