mol bio

• Enzyme kinetics is the study of the rates at which enzymes catalyze chemical reactions.
• Early Schools of Thought:

  • Vitalism: Intact cells possess a "vital force" and studying life requires looking into intact cells
  • Mechanism: To study life, cells must be dissected like a machine
• Two Roots of Molecular Biology:

  • Biochemistry: Focuses on the structure and properties of biomolecules
  • Microbial Genetics: Provides information on the genetic material, its transmission, and expression, using simple systems like phages and bacteria
• Molecular Biology:

  • Defined by William T. Astbury in 1945 as the study of the physical and chemical structure of biological macromolecules
  • Present-day definition: the study of genes and their products, and how these products function and interact in the organization and perpetuation of living things
• The Scope of Molecular Biology:

  • Genetic Material:
  • Identity
  • Replication
  • Reading stored information
  • Regulation of gene expression
  • Biomolecules:
  • Synthesis
  • Degradation
  • Transport in and out of the cell
  • Cellular structure and functions:
  • Supramolecular/ultracellular structures
  • Functions of specialized cells
  • Molecular Basis of Biological Phenomena:
  • Aging
  • Development
  • Immune response
  • Diseases and their treatment
• Approaches to problems:

  1. Correlation of structure and function:

  • Examples:
  • Collagen (tendon protein): Triple helix for additional strength in structural functions
  • DNA: Double-stranded with specific base pairing for stability and replicability
  • Cell membrane: Non-polar fatty acid chains to prevent free-passing of polar substances

  2. Physical measurements:

  • Ultracentrifugation
  • Electrophoresis
  • Infrared Absorption spectroscopy

  3. In vitro approach:

  • Crude and reconstituted extracts
• The Logic of Molecular Biology:

  • Efficiency: Evolution led to competition and survival as determinants of efficiency, minimizing energy and material waste
  • Development and Evaluation of Models: Models are tentative explanations of how a system works, tested for validity and revised based on new experimental evidence
  • Strong Inferences: All possible explanations for a phenomenon are stated, experimentally eliminated one by one until only one remains - strong inference
• The Transforming Principle:

  • Frederick Griffith (1928) conducted a transformation experiment on Diplococcus pneumoniae (Pneumococcus)
  • In vitro Transformation by M.H. Dawson and J.L. Alloway showed that a transforming agent is responsible for changing avirulent R types to virulent S types
• Chemical Nature of the Transforming Substance:

  • Ostwald T. Avery, Colin M. MacLeod, and Maclin McCarty (1944) identified DNA as the transforming substance through various isolation steps and qualitative chemical tests
• The Blender Experiment:

  • Alfred Hershey and Martha Chase (1952) demonstrated that DNA is the genetic material, not proteins, through labeled phages and cell lysis
• Structural Studies on DNA:

  • Pioneering researchers:
  • Pheobus Levene: DNA is linear and made up of nucleotides with four bases (ATCG)
  • Erwin Chargaff, Ernst Fischer, and R. Hotchkiss: Discovered the base pairing rules (#A = #T, #C = #G)
  • Linus Pauling: Proposed DNA as a triple-stranded molecule
  • Maurice Wilkins and Rosalind Franklin: Provided X-ray diffraction photograph of crystalline DNA
  • DNA Double Helix:
  • James Watson and Francis Crick (1953) credited with discovering the DNA double helix structure
• Nucleic acids are chemical repositories of genetic information
• Located inside the nucleus for eukaryotes or in the nucleoid region for prokaryotes
• Nucleic acids are biopolymers of nucleotides linked together by phosphodiester bonds
• There are two forms of nucleic acids: DNA (2’-deoxyribonucleic acid) and RNA (ribonucleic acid)
• Nitrogenous bases in nucleic acids are flat aromatic rings that are basic and have conjugated double bonds
• Purines include adenine (A) and guanine (G)
• Pyrimidines include cytosine (C), thymine (T), and uracil (U)
• Tautomeric shift in bases can result in anomalous base pairing
• Formation of nucleotides involves the liberation of two moles of water
• Nucleotides are linked by β-N-glycosidic bonds and phosphoester bonds
• Nucleosides consist of sugar + base only
• Examples of nucleosides include adenosine, cytidine, guanosine, thymidine, and uridine
• DNA is a linear sequence of deoxyribonucleotides
• DNA has two complementary strands held together by hydrogen bonds
• The primary structure of DNA consists of alternating sugar and phosphate groups linked by phosphodiester bonds
• DNA molecules have a double helix structure with major and minor grooves
• RNA exists mostly as single-stranded polynucleotides with sugar ribose and bases A, C, G, U
• RNA secondary structures include stem-loop and cloverleaf structures
• RNA-DNA hybrids can form and RNA molecules can fold back on themselves
• DNA packaging in the cell helps compactly pack DNA in a small nucleus in an orderly manner
• Chromosomes are composed of chromatins (DNA + associated proteins)
• Histones and non-histone chromosomal proteins are involved in DNA packaging
• Nucleosomes consist of about 147 bp supercoiled DNA wrapped twice around the histone octamer
• Histone H1 is the linker histone that condenses the "beads on a string" structure
• The 30-nm chromatin fiber can have a solenoid or zigzag model and can form looped domains
• Non-histone protein scaffold is involved in the formation of looped domains
• Metaphase chromosomes from a honey bee show the final packaged DNA structure
• Denaturation is the process of strand separation
• Involves disruption of hydrogen bonds between base pairs