Atoms and Basic Chemistry

Structure of Atoms

Atoms are the fundamental units of matter, retaining the properties of their respective elements.

• Protons: Positively charged particles located in the nucleus.

• Neutrons: Neutral particles also found in the nucleus.

• Electrons: Negatively charged particles orbiting outside the nucleus.

Taxonomy and Domains of Life

Three Domains and Taxonomic Hierarchy

All living organisms are classified into three domains, which are further organized by a hierarchical system.

• Bacteria

• Archaea

• Eukarya

Taxonomic Hierarchy: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

Genetics: Genes, Chromosomes, and Genetic Code

Key Definitions

• Gene: A segment of DNA encoding instructions for a specific trait or product.

• Chromosome: A long DNA molecule containing many genes.

• Genetic Code: The set of rules by which information in DNA/RNA is translated into proteins.

Introns vs. Exons

• Introns: Non-coding RNA segments removed before mRNA is finalized.

• Exons: Coding segments retained in mature mRNA and used for protein synthesis.

Mnemonic: INtrons = IN the trash; EXons = EXpressed

Genotype vs. Phenotype

• Genotype: The genetic makeup of an organism.

• Phenotype: Observable traits resulting from genotype and environment.

Example: Genotype = genes for eye color; Phenotype = actual eye color.

Macromolecules and Micromolecules

Types and Functions

• Macromolecules:

  • Carbohydrates: Quick energy source

  • Lipids: Long-term energy, membrane structure

  • Proteins: Enzymes, structure, transport

  • Nucleic acids: DNA and RNA

• Micromolecules: Small molecules such as water, vitamins, minerals, and ions.

Cellular Energy and ATP

ATP and Energy Reactions

• ATP (Adenosine Triphosphate): The primary energy carrier in cells.

• ATP hydrolysis releases energy:

• Activation Energy: Minimum energy required to initiate a chemical reaction.

• Exergonic Reactions: Release energy; products have less energy than reactants.

• Endergonic Reactions: Absorb energy; products have more energy than reactants.

Scientific Method

Steps in Scientific Investigation

1. Observation

2. Question

3. Hypothesis (testable explanation)

4. Experiment

5. Data Collection/Analysis

6. Conclusion

7. Communication of Results

Germ Theory and Koch's Postulates

Establishing Microbial Disease Causation

• Germ Theory: Microorganisms can cause disease.

• Koch's Postulates:

  1. Microorganism found in diseased individuals.

  2. Isolated and grown in pure culture.

  3. Causes disease in healthy host.

  4. Same organism recovered from newly diseased host.

Microscopy

Types and Resolving Power

• Light Microscope: Uses visible light and glass lenses; can view living cells; lower resolution.

• Electron Microscope: Uses electrons; much higher resolution; cannot view living specimens.

• Resolving Power: Ability to distinguish two close objects as separate.

DNA vs. RNA

Base Pairing: DNA: A–T, C–G; RNA: A–U, C–G

Central Dogma: Replication, Transcription, Translation

Key Processes

• DNA Replication: DNA is copied before cell division.

  • Strands separate; complementary nucleotides added; two DNA molecules produced.

• Transcription: DNA information is copied into mRNA (in eukaryotes, occurs in nucleus).

• Translation: Ribosome reads mRNA; tRNA brings amino acids; protein is synthesized.

Summary: Replication = DNA → DNA; Transcription = DNA → RNA; Translation = RNA → Protein

Gram-Positive vs. Gram-Negative Bacteria

Gram Stain Steps

1. Crystal violet (primary stain)

2. Iodine (mordant)

3. Alcohol/acetone (decolorizer)

4. Safranin (counterstain)

Mnemonic: Gram+ = Purple; Gram− = Pink

Prokaryotes vs. Eukaryotes

Major Cell Organelles

Note: Prokaryotes lack nucleus, mitochondria, ER, Golgi, and other membrane-bound organelles.

Cell Transport Mechanisms

Passive vs. Active Transport

• Passive Transport: No ATP required; moves substances down concentration gradient.

  • Simple Diffusion: Direct movement through membrane (e.g., O2).

  • Facilitated Diffusion: Movement via membrane proteins (e.g., ions, glucose).

  • Osmosis: Diffusion of water across a selectively permeable membrane.

• Active Transport: Requires ATP; moves substances against concentration gradient.

  • Endocytosis: Cell engulfs material.

    • Phagocytosis: "Cell eating" (large particles)

    • Pinocytosis: "Cell drinking" (liquids/small substances)

  • Exocytosis: Vesicle releases material outside the cell.

Osmosis: Tonicity

Endosymbiotic Theory

Origin of Eukaryotic Organelles

• Mitochondria and chloroplasts originated as free-living bacteria engulfed by ancestral cells.

• Evidence: Own DNA, ribosomes, division similar to bacteria, double membranes.

Bacterial Structures

Flagella and Motility

• Flagella: Used for movement; arrangements include monotrichous (one), lophotrichous (tuft), amphitrichous (both ends), peritrichous (all around).

• Pili: Hair-like, used for attachment and DNA transfer.

• Fimbriae: Short, numerous, mainly for attachment.

• Capsule: Protective layer aiding in immune evasion, surface attachment, and desiccation resistance.

• Chemotaxis: Movement toward/away from chemicals (positive = toward, negative = away).

Microbial Culture and Media

Types of Media

• Culture: Growing microorganisms in controlled conditions.

• Pure Culture: Contains only one species.

• Agar: Solidifying agent for media.

• Selective Media: Inhibits some organisms, allows others.

• Differential Media: Distinguishes organisms based on appearance or biochemical reactions.

Mnemonic: Selective = who can grow; Differential = how they look/react

Fungi

Types and Structures

• Yeast: Single-celled, reproduce by budding.

• Mold: Multicellular, composed of hyphae forming a mycelium.

• Hyphae: Thread-like structures.

• Spores: Reproductive/dispersal units.

• Dimorphic: Can exist as yeast or mold depending on conditions.

• Budding: New yeast cell grows from parent.

Algae

Characteristics

• Mostly photosynthetic, contain chlorophyll.

• Unicellular or multicellular; aquatic habitats.

• Produce food via photosynthesis.

Comparison: Algae are photosynthetic; fungi are not. Algae vs. protozoa: algae are autotrophic, protozoa are heterotrophic.

Protozoa

Life Cycle and Forms

• Trophozoite: Active, feeding, disease-causing form.

• Cyst: Dormant, protected form for survival and transmission.

• Life Cycle: Cyst → Trophozoite → Cyst

• Transmission: Contaminated food/water, fecal-oral route, vectors.

Helminths

Major Groups and Infection Sites

• Helminths: Parasitic worms.

• Major Groups:

  • Roundworms (nematodes)

  • Tapeworms (cestodes)

  • Flukes (trematodes)

• Can infect intestines, blood, lungs, liver, and other tissues.

Bacterial Endospores

Structure and Function

• Highly resistant structures formed by some bacteria under adverse conditions.

• Survive heat, drying, chemicals, radiation, and nutrient deprivation.

• Note: Endospores are for survival, not reproduction.

Gene Transfer and Mutations

Vertical vs. Horizontal Gene Transfer

• Vertical: Parent to offspring (e.g., cell division).

• Horizontal: Between unrelated cells.

  • Transformation: Uptake of environmental DNA.

  • Transduction: DNA transfer via bacteriophage.

  • Conjugation: Direct transfer via pilus.

Mutations

• Mutation: Change in DNA sequence; source of genetic variation.

• Spontaneous Mutation: Occurs naturally (e.g., replication errors).

• Induced Mutation: Caused by external agents (e.g., UV, chemicals).

Key Concepts to Memorize

• Gram+ = purple, thick peptidoglycan; Gram− = pink, thin peptidoglycan + outer membrane

• DNA → RNA → Protein (Central Dogma)

• Transcription = DNA → mRNA; Translation = mRNA → protein

• Passive transport = no ATP; Active transport = requires ATP

• Hypotonic = water in; Hypertonic = water out

• Phagocytosis = cell eating; Pinocytosis = cell drinking

• Endospore = survival, not reproduction

• Vertical gene transfer = parent to offspring; Horizontal = cell to cell

• Spontaneous mutation = natural; Induced = external cause

• Selective media = inhibits certain organisms; Differential = distinguishes organisms

• Trophozoite = active; Cyst = dormant/protected

• Yeast = budding; Mold = hyphae