Biology CH.1 Notes

Chapter 1: Biology and Evolution

  • Biology Only Makes Sense in the Light of Evolution

    • Definition of Evolution:

    • Evolution: Change over time in a population.

    • Historical Context:

    • At the time of Darwin, evolution was not a new concept.

    • Jean-Baptiste Lamarck: Proposed the theory of acquired characteristics.

    • Charles Darwin: Credited with developing the modern theory of evolution.

    • His seminal work, On the Origin of Species, was published in 1859.

    • Two Key Definitions of Evolution from Darwin:

    • Descent with Modification: The idea of a common ancestor, emphasizing the importance of heritable variation.

    • Natural Selection: Defined as differential reproductive success, which requires variation among individuals in a population.

      • Concept: Individuals that possess favorable traits tend to reproduce more successfully, passing traits to their offspring.

Organizing Life - Taxonomy

  • Taxonomy: The branch of biology that names and classifies species.

  • Hierarchical Classification Levels:

    • Domain: Eukarya

    • Kingdom: Animalia

    • Phylum: Chordata

    • Class: Mammalia

    • Order: Carnivora

    • Family: Canidae

    • Genus: Vulpes

    • Species: vulpes

Organizing Life - Phylogeny

  • Phylogeny: The evolutionary history and relationship of an organism and groups of organisms.

    • Questions Phylogeny Seeks to Answer:

    • What species did an organism evolve from?

    • What species is an organism most closely related to?

    • Example Relationships:

    • Most recent common ancestor of badger & otter.

    • Most recent common ancestor of coyote & wolf.

    • Most recent common ancestor of badger & wolf.

    • Most recent common ancestor of all five species.

Organizing Life – Nature’s Order and Emergent Properties

  • Biological Organization: Based on a hierarchy of structural levels.

  • Emergent Properties: Novel properties that develop at each level upward in the biological hierarchy.

Levels of Biological Organization

  • Atom (example: Hydrogen)

  • Molecule (example: Water)

  • Organelle (example: Nucleus)

  • Cell (example: Neuron)

  • Tissue (example: Nervous Tissue)

  • Organ (example: Brain)

  • Organ System (example: Nervous System)

  • Organism (example: Sea Lion)

  • Population (example: Colony)

  • Community (example: Forest)

  • Ecosystem (example: Coast)

  • Biosphere (example: Southern California)

Chemistry's Relevance to Life

  • Small changes in molecules can have BIG effects on organisms.

    • Chemical Example:

    • Estradiol:

      • Molecular Structure: OH, CH3

    • Testosterone:

      • Molecular Structure: OH, CH3.

  • Example of a Chemical Relevant to Biology:

    • Devil's Garden: A flowering tree (Duroia hirsuta).

Fundamentals of Matter

  • Matter: Anything that takes up space and has mass.

  • Element: Substances that cannot be broken down by chemical means into smaller substances.

  • Atom: The smallest unit of an element with its own chemical properties.

  • Determining Factors of an Atom:

    • Protons: Positively charged; determine the element.

    • Neutrons: Neutral; determine isotope.

    • Electrons: Negatively charged; form a negative cloud with negligible mass; determine chemical behavior.

  • Nucleus: Center of the atom, containing protons and neutrons.

Atomic Numbers and Mass

  • Atomic Number: The number of protons in an atom.

  • Atomic Mass: The sum of protons and neutrons in an atom.

  • The Periodic Table represents all known elements on Earth.

Essential Elements for Life

  • 25 of the 92 known elements are essential for life.

  • Elements present at lower levels but still critically important include:

    • Oxygen (O):

    • Life Composition: 65%

    • Atmosphere: 21%

    • Earth's Crust: 46%

    • Carbon (C):

    • Life Composition: 18%

    • Atmosphere: Trace

    • Earth's Crust: Trace

    • Hydrogen (H):

    • Life Composition: 10%

    • Atmosphere: Trace

    • Earth's Crust: 0.1%

    • Nitrogen (N):

    • Life Composition: 3%

    • Atmosphere: 78%

    • Earth's Crust: Trace

Isotopes

  • Isotopes: Multiple forms of an element with different numbers of neutrons.

  • Examples of Isotopes:

    • 1H has 0 neutrons.

    • 2H has 1 neutron.

    • 3H has 2 neutrons.

    • Specific Examples:

    • Carbon-14 (14C): Used in radioactive dating.

    • Tritium (3H): A radioactive isotope with a half-life that can be measured in scientific studies.

Radioactive Decay

  • Radioactive Isotopes: Unstable versions of elements that undergo radioactive decay, emitting energy and converting into another element.

  • Example of Decay Process:

    • Uranium-238 (U-238) decays through emission of high-energy particles into Thorium-234 and eventually to Lead-206.

  • Half-Life: The time it takes for half of a substance to decay.

    • Example:

    • Carbon-14: Half-life is 5730 years.

    • Potassium-40: Half-life is approximately 1.3 billion years.

Applications of Radioisotopes

  • Research Tool: Different isotopes behave identically in reactions. Used for diagnostics (radioactive tracers) and treatment in nuclear medicine.

    • Examples of tracers: Technetium-99 (Tc99), Flourine-18 (FDG).

    • Applications: Cancer treatment and diagnosis.

Chemical Bonds

  • Types of Bonds:

    • Covalent Bonds: Atoms share pairs of valence electrons.

    • Covalent bonds can be single, double, or triple bonds (H2, O2, N2 respectively).

    • Ionic Bonds: Formed through the complete transfer of one or more valence electrons, resulting in charged ions.

    • Example: Sodium chloride (NaCl).

    • Hydrogen Bonds: A weak bond formed between a partially positive hydrogen atom and a partially negative atom.

    • Van der Waals Interactions: Weak attractions that occur when transiently positive and negative regions of molecules attract each other.

Electronegativity and Chemical Behavior

  • Electronegativity: An atom’s ability to attract electrons.

  • Electronegativity influences bond formation:

    • Nonpolar Covalent Bonds: Atoms have similar electronegativities (equal sharing of electrons).

    • Example: H2, O2, C-H bonds.

    • Polar Covalent Bonds: Atoms share electrons unequally.

    • Example: Water (H2O).

  • Bond Polarity: Determined by the difference in electronegativity:

    • Nonpolar: Electronegativity difference ≤ 0.3

    • Polar: Electronegativity difference between 0.3 and 1.7

    • Ionic: Electronegativity difference ≥ 1.7

Organic Chemistry

  • Organic Molecules: Originally defined as those produced exclusively by living organisms; now defined as any molecules containing carbon.

    • The field of organic chemistry studies carbon-containing compounds.

  • Carbon's Versatility:

    • Can make up to 4 bonds, allowing for diverse arrangements and complex molecules essential for life.

  • Hydrocarbons: The simplest organic molecules, consisting only of carbon and hydrogen.

Structural Variations in Hydrocarbons

  • Hydrocarbons can vary in:

    • Length

    • Branching

    • Double bonds

    • Rings (such as benzene, significant in biochemistry).

  • Isomers: Molecules with the same chemical formula but different arrangements of atoms.

    • Types of Isomers:

    • Structural Isomers (different covalent arrangements).

    • Cis-Trans Isomers (differing arrangements around double bonds).

    • Enantiomers (mirror images of each other).

Importance of Enantiomers

  • Specific enantiomers can have vastly different biological effects.

    • Example:

    • Ibuprofen: S-Ibuprofen is effective for pain and inflammation, while R-Ibuprofen is ineffective.

    • Albuterol: R-Albuterol treats asthma, while S-Albuterol is not therapeutically beneficial.

Functional Groups in Biological Molecules

  • Functional Groups: Chemical groups that affect the function of molecules and often participate in chemical reactions.

    • Important functional groups include:

    • Hydroxyl Group (—OH): Present in alcohols, polar, forms hydrogen bonds with water.

    • Carbonyl Group (C=O): Found in sugars; can be a ketone or aldehyde based on its position.

    • Carboxyl Group (—COOH): Acts as an acid and found in amino acids; ionizes to release hydrogen.

    • Amino Group (—NH2): Acts as a base and is also found in amino acids.

    • Sulfhydryl Group (—SH): Important for protein structure through cross-linking.

    • Phosphate Group (—OPO₃²⁻): Important for energy transfer (ATP) and found in nucleic acids.

    • Methyl Group (—CH₃): Affects gene expression and the function of hormones.

Conclusion

  • The study of biology intricately connects chemistry, evolution, and the complex interactions of molecules that govern life. Understanding the underlying structures and functions is crucial to the field of biological sciences.