Molecular Biology: DNA, RNA, and Protein Synthesis

DNA Replication

Steps:
- Initiation: DNA polymerase binds to origin of replication.
- Elongation: DNA polymerase adds new nucleotides to the growing DNA strand.
- Termination: Replication is complete.
Enzymes:
- DNA polymerase: Synthesizes new DNA strands.
- Helicase: Unwinds the DNA double helix.
- Topoisomerase: Relieves tension in the DNA molecule.
- Primase: Synthesizes RNA primers.
- Ligase: Joins the Okazaki fragments.

Transcription

Steps:
- Initiation: RNA polymerase binds to the promoter and unwinds the DNA.
- Elongation: RNA polymerase synthesizes a complementary RNA strand.
- Termination: RNA polymerase reaches the terminator sequence and releases the RNA transcript.
Enzymes & Factors:
- RNA polymerase: Synthesizes RNA.
- Transcription factors: Proteins that help RNA polymerase bind to the promoter.

Translation

Steps:
- Initiation: mRNA binds to the ribosome.
- Elongation: tRNA brings amino acids to the ribosome, where they are added to the growing polypeptide chain.
- Termination: The ribosome reaches a stop codon, and the polypeptide is released.
Genetic code:
- Codons: Three-nucleotide sequences on mRNA that specify amino acids.
- Anticodons: Three-nucleotide sequences on tRNA that are complementary to codons.
- Wobble: The ability of some tRNA anticodons to pair with more than one codon.
RNA roles:
- mRNA: Messenger RNA, carries genetic information from DNA to ribosomes.
- rRNA: Ribosomal RNA, forms the structure of ribosomes.
- tRNA: Transfer RNA, carries amino acids to ribosomes during translation.

Bacterial Gene Regulation

Operons: Clusters of genes that are transcribed together.
Lac operon: An example of an inducible operon, regulated by the presence of lactose.
- In the absence of lactose: Repressor protein binds to the operator, preventing transcription of the lac genes.
- In the presence of lactose: Lactose binds to the repressor, causing it to detach from the operator, allowing transcription.

Horizontal Gene Transfer

Methods Bacteria Use to Acquire Genetic Material:
- Conjugation: Transfer of genetic material through direct contact between bacteria.
- Transformation: Bacteria acquire DNA from the environment.
- Transduction: Transfer of genetic material via bacteriophages.

Mutations in DNA

Types:
- Point mutations: Changes in a single nucleotide.
- Insertions/Deletions: Adding or removing nucleotides.
Causes:
- Spontaneous mutations: Occur naturally during DNA replication.
- Induced mutations: Caused by mutagens, such as radiation or chemicals.

Chromosomes and Cell Cycle

Chromatin: Loosely packed DNA in the nucleus.
Chromosomes: Tightly packed DNA during cell division.
Sister chromatids: Two identical copies of a chromosome.
Centromere: The region where sister chromatids are joined.
Autosomes: Chromosomes that are not sex chromosomes.
Sex chromosomes: Determine sex (X and Y in humans).
Karyotype: A visual representation of an organism's chromosomes.
Telomeres: The ends of linear chromosomes.
Telomerase: An enzyme that adds telomeres to protect the ends of chromosomes during replication.
Cell cycle checkpoints: Ensure that the cell is ready to proceed to the next stage.
Phases of the cell cycle:
- G1 phase: The cell grows and synthesizes proteins.
- S phase: DNA replication occurs.
- G2 phase: The cell prepares for mitosis.
- M phase: Cell division (mitosis or meiosis).
G0 phase: A quiescent state where cells are not actively dividing.

Mitosis

Phases:
- Prophase: Chromatin condenses into chromosomes, the nuclear envelope breaks down, and the mitotic spindle forms.
- Metaphase: Chromosomes align at the metaphase plate.
- Anaphase: Sister chromatids separate and move to opposite poles of the cell.
- Telophase: Chromosomes decondense, the nuclear envelope reforms, and the cytoplasm divides.
Cell types that undergo mitosis: Somatic cells (non-reproductive cells).

Meiosis

Process: Meiosis reduces the number of chromosomes in a cell by half.
Results: Four haploid gametes (sex cells).
Cell types that undergo meiosis: Germ cells (reproductive cells).

Microbial Nutrition and Growth

Heterotrophs: Obtain carbon from organic sources.
Autotrophs: Obtain carbon from inorganic sources (e.g., CO2).
Macronutrients: Required in large amounts (e.g., carbon, nitrogen, phosphorus).
Micronutrients: Required in small amounts (e.g., trace metals).
Growth factors: Organic compounds that are essential for growth.
Transport methods:
- Passive diffusion: Movement of molecules across the membrane without energy.
- Facilitated diffusion: Movement of molecules across the membrane with the help of transport proteins.
- Active transport: Movement of molecules across the membrane against their concentration gradient, requiring energy.
Environmental factors:
- Temperature:
  - Cardinal temperatures: Minimum, optimum, and maximum temperatures for growth.
  - Groups by temperature range: Psychrophiles, mesophiles, thermophiles, hyperthermophiles.
- pH:
  - Acidophiles: Grow at low pH.
  - Alkaliphiles: Grow at high pH.
- Osmotic effects:
  - Halophiles: Grow in high salt concentrations.
- Oxygen effects:
  - Obligate aerobes: Require oxygen for growth.
  - Facultative anaerobes: Can grow with or without oxygen.
  - Obligate anaerobes: Cannot grow in the presence of oxygen.
  - Aerotolerant anaerobes: Can tolerate oxygen but do not use it.
  - Microaerophiles: Require low oxygen levels.
Binary fission: The process of cell division in bacteria.
- Doubling time/generation time: The time it takes for a population of bacteria to double in size.
Bacterial growth curve:
- Lag phase: Bacteria are adjusting to their environment.
- Exponential (log) phase: Bacteria are dividing rapidly at a constant rate.
- Stationary phase: Growth slows down due to limited resources.
- Death (decline) phase: Bacteria die due to a lack of resources and accumulation of toxic waste products.
Methods of measuring cell growth:
- Direct methods:
  - Microscopic count: Counting bacteria directly under a microscope.
  - Plate count: Counting colonies on an agar plate.
- Indirect methods:
  - Turbidity: Measuring the cloudiness of a bacterial culture.
  - Metabolic activity: Measuring the rate of a metabolic process (e.g., respiration).
Biofilms: Communities of bacteria that attach to surfaces.
- Significance: Biofilms can cause infections and resist antibiotics.
Microbiome: The collection of bacteria living in or on a particular environment (e.g., human gut microbiome).
- Significance: Microbiomes play important roles in human health.

Control of Microbial Growth

Sterilization: Killing all microorganisms.
Disinfection: Reducing the number of pathogens to a safe level.
Decontamination/Sanitization: Removal of microorganisms to a safe level as determined by public health standards.
Antisepsis/Degermation: Killing or inhibiting growth of microorganisms on living tissue.
Microbicide: An agent that kills microorganisms.
Microbistatic: An agent that inhibits the growth of microorganisms.
Sepsis: The presence of pathogens in blood or tissues.
Asepsis: The absence of pathogens.
Antiseptics: Chemicals used to prevent infection by killing or inhibiting microorganisms.
Chemical Agents:
- Moist heat: Boiling, autoclaving.
- Dry heat: Incineration, hot-air ovens.
- UV radiation: Damages DNA.
- Ionizing radiation (gamma and X-rays): Damages DNA and proteins.
- Filtration: Physically removes microorganisms.
- Cold: Slows the growth of most microorganisms.
Types of chemical agents:
- Halogens: Chlorine, iodine.
- Oxidizing agents: Hydrogen peroxide.
- Aldehydes: Glutaraldehyde.
- Gases: Ethylene oxide.
- Phenol: Triclosan.
- Chlorhexidine: Both a halogen and a phenol derivative.
- Alcohol: Ethanol, isopropanol.
- Detergents: Quaternary ammonium compounds (quats), anionic detergents.
- Heavy metal compounds: Silver nitrate.
- Acids and alkali: Can damage the cell membrane.