Molecular Biology: DNA, RNA, and Protein Synthesis

• Molecular biology is the study of the molecular basis of biological activity.
• This field intersects with genetics and biochemistry.
• Molecular biology seeks to understand the interactions within a cell's systems, including those between DNA, RNA, and protein biosynthesis, and how these interactions are regulated.

Key Concepts

• Central Dogma of Molecular Biology: DNA -> RNA -> Protein.
• Genes: Basic units of heredity, composed of DNA and encoding proteins or functional RNA molecules.
• Genome: The complete set of genetic material in an organism.
• Chromosomes: Structures within cells that contain the genes.
• DNA Replication: The process by which DNA is copied.
• Transcription: The process by which RNA is synthesized from a DNA template.
• Translation: The process by which proteins are synthesized from RNA.

DNA (Deoxyribonucleic Acid)

• DNA carries the genetic instructions for growth, development, functioning, and reproduction in organisms and many viruses.
• DNA is a nucleic acid, one of the three major macromolecules essential for life, along with proteins and carbohydrates.
• DNA consists of two long nucleotide chains twisted into a double helix.
• Nucleotides are made of a deoxyribose sugar, a phosphate group, and a nitrogenous base.
• The four nitrogenous bases are adenine (A), guanine (G), cytosine (C), and thymine (T).
• Adenine pairs with thymine (A-T), and guanine pairs with cytosine (G-C).
• The genetic code is determined by the sequence of these bases.

RNA (Ribonucleic Acid)

• RNA facilitates coding, decoding, regulation, and gene expression.
• RNA is a nucleic acid similar to DNA, but with key differences.
• RNA is typically single-stranded.
• RNA contains ribose instead of deoxyribose.
• RNA uses uracil (U) instead of thymine (T).
• Types of RNA include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).
• mRNA carries genetic information from DNA to ribosomes.
• tRNA carries amino acids to ribosomes during protein synthesis.
• rRNA is a component of ribosomes.

Proteins

• Proteins are large biomolecules comprising amino acid chains.
• They catalyze metabolic reactions, participate in DNA replication, respond to stimuli, and transport molecules.
• The sequence of amino acids, dictated by genes, determines a protein's specific three-dimensional structure and activity.
• A protein's amino acid sequence is determined by the genetic code.
• Proteins fold into specific three-dimensional structures essential for their function.

DNA Replication

• DNA replication copies a DNA molecule to produce two identical DNA molecules.
• DNA replication is vital for cell division and inheritance.
• Enzymes involved include DNA polymerase, helicase, and ligase.
• DNA polymerase adds nucleotides to the 3' end of a DNA strand, using the existing strand as a template.
• Helicase unwinds the DNA double helix.
• Ligase joins Okazaki fragments on the lagging strand.
• Replication begins at origins of replication.
• DNA replication is semi-conservative: each new DNA molecule has one original and one new strand.

Transcription

• Transcription synthesizes RNA from a DNA template.
• RNA polymerase catalyzes transcription.
• Transcription starts at a promoter on the DNA.
• RNA polymerase synthesizes RNA by adding nucleotides complementary to the DNA sequence.
• In eukaryotes, pre-mRNA undergoes capping, splicing, and polyadenylation to produce mature mRNA.
• Transcription factors influence RNA polymerase binding, thus regulating the efficiency of transcription and the resulting RNA abundance.

Translation

• Translation synthesizes proteins from mRNA.
• Translation takes place on ribosomes.
• The mRNA sequence is read in codons (three-nucleotide sequences) that specify amino acids.
• tRNA molecules bring the correct amino acids to the ribosome, matching their anticodons with the mRNA codons.
• The ribosome moves along the mRNA, joining amino acids to form a polypeptide chain.
• Translation starts at a start codon (usually AUG) and ends at a stop codon (UAA, UAG, or UGA).
• A polypeptide chain may undergo folding, glycosylation, or cleavage to become a functional protein.

Gene Regulation

• Gene regulation controls the expression of genes.
• Gene regulation can occur at transcription, translation, and post-translation levels.
• Transcriptional regulation controls the rate of transcription by influencing RNA polymerase binding.
• Regulatory proteins like transcription factors can enhance or inhibit transcription.
• Translational regulation controls the rate of protein synthesis.
• Post-translational regulation modifies the protein after synthesis via phosphorylation or ubiquitination.
• Epigenetics influence gene regulation by altering chromatin structure, affecting transcription factor access to DNA.

Molecular Cloning

• Molecular cloning makes multiple copies of a specific DNA fragment.
• A DNA fragment is inserted into a cloning vector like a plasmid or virus (bacteriophage).
• A vector artificially carries foreign genetic material into a host cell for replication and/or expression.
• The recombinant vector is introduced into a host cell for replication.
• Molecular cloning is used in gene sequencing, protein production, and gene therapy.

Polymerase Chain Reaction (PCR)

• PCR amplifies a specific DNA sequence.
• It involves repeated cycles of denaturation, annealing, and extension.
• Denaturation: Heating DNA to separate strands.
• Annealing: Cooling DNA to allow primers to bind to the target sequence.
• Extension: DNA polymerase extends primers and synthesizes new DNA strands.
• PCR applications include DNA sequencing, gene cloning, and diagnostics.

DNA Sequencing

• DNA sequencing determines the nucleotide sequence of a DNA molecule.
• Sanger sequencing uses dideoxynucleotides to terminate DNA synthesis.
• Next-generation sequencing (NGS) allows high-throughput sequencing of millions of DNA fragments.
• DNA sequencing is used in genome sequencing, gene discovery, and personalized medicine.

Mutations

• Mutations are changes in the DNA sequence.
• Mutations can be spontaneous or induced by mutagens like chemicals or radiation.
• Mutations can be harmful, beneficial, or neutral.
• Point mutations involve single nucleotide changes.
• Frameshift mutations involve insertions or deletions of nucleotides that alter the reading frame.
• Mutations can lead to genetic disorders or contribute to evolution.

Recombinant DNA Technology

• Recombinant DNA technology combines DNA from different sources.
• Restriction enzymes cut DNA, and DNA ligase joins the fragments.
• Recombinant DNA technology is used in gene cloning, protein production, and gene therapy.

Applications of Molecular Biology

• Medicine: Development of new diagnostic tests, therapies, and vaccines.
• Biotechnology: Production of biopharmaceuticals, biofuels, and genetically modified organisms (GMOs).
• Agriculture: Development of crops with improved yield, pest resistance, and nutritional value.
• Forensics: DNA fingerprinting for identification and crime solving.
• Research: Understanding fundamental life processes and developing new technologies.