Chapter 19 - Viruses

Characteristics of Life

Living organisms share several fundamental characteristics that distinguish them from non-living matter.

• Reproduction: Ability to produce offspring.

• Evolution: Capacity to change genetically over generations.

• Response to Stimuli: Reacting to environmental changes.

• Cellular Organization: Composed of one or more cells.

• Creation and Use of Energy: Metabolism for growth and maintenance.

• Homeostasis: Regulation of internal conditions.

General Characteristics of Viruses

Viruses are non-cellular pathogens that infect living organisms. They are much smaller than cells and lack many features of life.

• Structure: Consist of a capsid (protein coat), sometimes an envelope (lipid layer), and in some cases, a tail sheath and tail fibers.

• Capsomers: Protein subunits forming the capsid.

• Envelope: Surrounds the capsid in some viruses, derived from host cell membranes.

Tobacco Mosaic Virus

The Tobacco Mosaic Virus infects tobacco plants, causing discoloration and stunted growth. It was the first virus discovered.

Capsid Shapes and Envelopes

The capsid protects viral genetic material and determines the virus's shape.

• Helical Capsids: Rod-shaped, e.g., TMV.

• Polyhedral Capsids: Many-sided, e.g., adenovirus.

• Complex Polyhedral Capsids: Found in bacteriophages.

• Envelope Capsids: Surrounded by a lipid envelope.

Bacteriophages

Bacteriophages are viruses that infect bacteria. Their DNA can integrate into the host genome.

• Phage DNA: May become part of bacterial DNA (prophage).

Viral Replicative Cycles

Viruses reproduce by hijacking host cell machinery.

1. Attachment to host cell.

2. Entry and uncoating (removal of capsid).

3. Replication of viral genome using host resources.

4. Assembly of new viral particles.

5. Release from host cell.

Lytic vs. Lysogenic Cycles

Phages can reproduce via two main cycles:

• Lytic Cycle: Destroys host cell, releases new viruses.

• Lysogenic Cycle: Viral DNA integrates into host genome, replicates without killing cell.

Virulent Phage, Temperate Phage, Prophage

• Virulent Phage: Only uses lytic cycle.

• Temperate Phage: Can switch between lytic and lysogenic cycles.

• Prophage: Viral DNA integrated into host DNA.

Restriction Enzymes, Methylation, CRISPR-Cas Proteins

Bacteria defend against viruses using several mechanisms:

• Restriction Enzymes: Cut foreign DNA at specific sequences.

• Methylation: Addition of methyl groups to protect host DNA from restriction enzymes.

• CRISPR-Cas Proteins: Use RNA guides to target and cut specific DNA/RNA sequences.

Retroviruses and HIV

Retroviruses use reverse transcriptase to convert RNA into DNA.

• HIV: Infects T cells, uses reverse transcriptase to integrate into host genome.

Prions

Prions are infectious proteins that cause neurodegenerative diseases by inducing abnormal folding of normal proteins.

Chapter 20 - DNA Tools and Biotechnology

DNA Cloning

DNA cloning is the process of making identical copies of a DNA segment.

1. Isolate DNA of interest.

2. Insert DNA into a vector (e.g., plasmid).

3. Introduce vector into host cells.

4. Host cells replicate DNA.

5. Harvest cloned DNA or protein product.

Plasmids and Recombinant DNA

• Plasmids: Small, circular DNA molecules in bacteria, replicate independently.

• Recombinant DNA: DNA from two sources combined, often inserted into plasmids.

Cloning Vector

A cloning vector is a DNA molecule (often a plasmid) used to carry foreign DNA into a host cell for cloning.

Restriction Enzymes and Sticky Ends

• Restriction Enzymes: Cut DNA at specific sequences.

• Sticky Ends: Single-stranded overhangs created by staggered cuts, facilitate DNA ligation.

PCR (Polymerase Chain Reaction)

PCR amplifies specific DNA segments using a three-step cycle:

1. Denaturation: Heat to 90°C to separate DNA strands.

2. Annealing: Cool to 50°C to allow primers to bind.

3. Extension: Heat to 72°C for DNA polymerase to synthesize new strands.

Formula:

(where N = number of DNA copies, n = number of cycles)

Nucleic Probes

Nucleic acid probes are complementary DNA or RNA molecules used to detect specific genetic sequences via hybridization.

Complementary DNA (cDNA)

cDNA is synthesized from mRNA using reverse transcriptase, representing only expressed genes.

Stem Cells

• Embryonic Stem Cells: Can differentiate into any cell type (pluripotent).

• Adult Stem Cells: Unspecialized cells found in tissues, limited differentiation.

• Stem Cells: Can self-renew and differentiate into specialized cells.

Pluripotent Cells

Pluripotent cells can become almost any cell type in the body.

Chapter 22 - Descent with Modification: A Darwinian View of Life

On the Origin of Species by Darwin

Published in 1859, Darwin's book introduced the concept of natural selection as the mechanism of evolution.

Evolution and Descent with Modification

• Evolution: Change in allele frequencies in a population over time.

• Descent with Modification: Traits are passed to offspring and change over generations; all species share a common ancestor.

Historical Figures in Evolution

Darwin and Natural Selection

Natural selection is the process where individuals with advantageous traits survive and reproduce more.

• Example: Finches with different beak shapes adapted to food sources on Galapagos Islands.

Adaptations

Inherited traits that improve survival and reproduction in specific environments.

Artificial Selection

Humans selectively breed organisms for desired traits.

Populations Evolve, Not Individuals

Natural selection acts on individuals, but populations evolve over time.

Homology and Homologous Structures

• Homology: Similarity due to shared ancestry.

• Homologous Structures: Similar structure, different function (e.g., human arm, whale flipper).

Vestigial Structures

Remnants of features that served a function in ancestors but are no longer useful.

Convergent Evolution and Analogous Structures

• Convergent Evolution: Independent evolution of similar traits in unrelated groups.

• Analogous Structures: Similar function, different origin (e.g., bat wing, bird wing).

Chapter 23 - The Evolution of Populations

Hardy-Weinberg Equilibrium

Describes a population where allele frequencies remain constant; no evolution occurs.

• Formula:

Conditions for Hardy-Weinberg Equilibrium

• No mutations

• Random mating

• No natural selection

• Large population size

• No gene flow

Genetic Drift, Founder Effect, Bottleneck Effect

• Genetic Drift: Random changes in allele frequencies.

• Founder Effect: Small group forms new population.

• Bottleneck Effect: Sudden reduction in population size.

Gene Flow

Movement of alleles between populations.

Types of Selection

Chapter 24 - The Origin of Species

Macroevolution vs. Microevolution

• Microevolution: Changes in allele frequencies within a population.

• Macroevolution: Broad patterns of change above the species level.

Biological Species Concept

A species is a group of populations whose members can interbreed and produce viable, fertile offspring.

Reproductive Isolation

Biological barriers prevent interbreeding between species.

Prezygotic Barriers

Postzygotic Barriers

Allopatric and Sympatric Speciation

• Allopatric Speciation: Geographic isolation leads to new species.

• Sympatric Speciation: New species arise in same geographic area.

Polyploidy

Condition where cells have more than two sets of chromosomes; important in plant speciation.

Chapter 25 - The History of Life on Earth

Origin of Simple Cells

Simple cells may have arisen through four stages:

1. Abiotic Synthesis: Formation of small organic molecules.

2. Joining into Macromolecules: Dehydration synthesis links monomers.

3. Packaging into Protocells: Membrane-bound droplets with internal chemistry.

4. Origin of Self-Replicating Molecules: RNA polymers with catalytic activity.

Miller and Urey Experiment

Demonstrated abiotic synthesis of organic molecules in a reducing atmosphere (1953).

Hydrothermal and Alkaline Vents

• Hydrothermal Vents: Hot, mineral-rich water from Earth's crust.

• Alkaline Vents: High pH, warm water (40-90°C).

Ribozymes

RNA molecules that catalyze reactions, supporting the RNA world hypothesis.

Stromatolites

Layered structures formed by microbial communities; oldest known fossils (3.5 billion years).

Chapter 26 - Phylogeny and the Tree of Life

Phylogeny and Systematics

• Phylogeny: Evolutionary history of a species or group.

• Systematics: Classification and determination of evolutionary relationships.

Linnaeus, Taxons, Taxonomic Order

Scientific Name

Binomial nomenclature: Genus (capitalized) + specific epithet (lowercase), both italicized. Example: Homo sapiens

Phylogenetic Tree and Branch Point

• Phylogenetic Tree: Diagram showing evolutionary relationships.

• Branch Point: Divergence of two lineages from a common ancestor.

Chapter 27 - Bacteria and Archaea (Prokaryotes)

General Characteristics of Prokaryotes

• Single-celled

• Smaller than eukaryotes (10-100x)

• No nucleus

• No membrane-bound organelles

Cell Wall of Bacteria – Peptidoglycan

Bacterial cell walls contain peptidoglycan, a polysaccharide providing structural support.

Gram Stain: Gram Positive vs. Gram Negative

Capsules, Endospores, Fimbriae, Pili, Flagella

• Capsules: Sticky layer for adherence.

• Endospores: Dormant, resistant cells (e.g., Bacillus, Clostridium).

• Fimbriae: Short, for attachment to surfaces.

• Pili: Longer, for DNA exchange.

• Flagella: Motility structures.

Prokaryotic DNA, Nucleoid Region, Plasmids, Binary Fission

• Nucleoid Region: Non-membrane bound area with DNA.

• Plasmids: Small, circular DNA.

• Binary Fission: Asexual reproduction; exponential growth (1-2-4-8...)

Genetic Recombination: Conjugation, Transformation, Transduction

• Transformation: Uptake of foreign DNA from environment.

• Transduction: DNA transfer via bacteriophages.

• Conjugation: DNA transfer between cells via pili.

Horizontal Gene Transfer

Genes move between different species, increasing genetic diversity.

F Plasmid (F+ Cells, F- Cells), Hfr Cells

• F+ Cells: Have F plasmid, act as DNA donors.

• F- Cells: Lack F plasmid, act as recipients.

• Hfr Cells: F factor integrated into chromosome, high recombination frequency.

R Plasmids

Carry genes for antibiotic resistance.

Prokaryotic Metabolic Types

Obligate Aerobes, Obligate Anaerobes, Facultative Anaerobes

• Obligate Aerobes: Require O2 for respiration.

• Obligate Anaerobes: Poisoned by O2.

• Facultative Anaerobes: Can use O2 or perform fermentation/anaerobic respiration.

Nitrogen Fixation

Conversion of atmospheric nitrogen (N2) to ammonia (NH3).

Biofilms

Surface-coating colonies of cells; can cause dental plaque and corrosion.

Archaea and Extremophiles

• Archaea: Share traits with bacteria and eukaryotes; unique features.

• Extremophiles: Live in extreme environments.

• Extreme Halophiles: Tolerate or require high salt.

• Extreme Thermophiles: Stable at high temperatures.

• Methanogens: Produce methane, obligate anaerobes.