Science: "branch of knowledge or study dealing with a body of facts or truths systematically arranged and showing the operation of general laws"

Acquisition of Data
• Qualitative Data: perceived through senses
• Quantitative Data: often perceived through machines to insure repeatability

Apply logical sequence of study such as the hypothetico-deductive method:

Identify a biological problem or ask a question about the natural world

• 1. Devise an hypothesis (educated guess) to answer question based on the factual data that exists
• 2. Devise alternative explanations (hypotheses)
• 3. Construct a crucial experiment that would have alternative possible outcomes, each that would exclude one or more hypotheses.
• 4. Make predictions of all possible outcomes of the experiment
• 5. Carry out the experiment (cleanly) Use control experiments to validate experimental results; to insure change is due to a single variable
• 6. Repeat experiments, then recycle the procedure to answer new questions that arise from new data.
Experimental Variables
• Independent
• Dependent
• Controlled

 
Replicates
Deductive Reasoning
Inductive Reasoning

What is life?
Introduction. All living organisms have gross similarities.
How do we explain the "UNITY" vs. "DIVERSITY" of life?

Hierarchy of structural complexity

Atoms --> Molecules --> subcellular structures --> cells --> tissues --> organs and organ systems --> organisms --> populations --> communities --> ecosystems --> biosphere

Unity of Life; Common Properties

1. Contain DNA
2. Cell is basic living unit; lowest level of structure
3. Metabolize (extract and use energy)
4. Highly ordered (energy used to maintain order)
5. Reproduction: must reproduce or species dies
6. Growth and Development: multicellular organisms follow similar patterns of development
7. Response to environment
8. Homeostasis
9. Evolutionary adaptation

Principle of Evolution

Evolutionary Time line

• 3.5 BYA: oldest prokaryotic fossils
• 2.5 BYA: oxygen starts accumulating in atmosphere
• 1.5 BYA: oldest eukaryotic fossils
• 700 MYA: complex multicellular organisms arising
Darwin's Theory of Natural Selection

Sources of Genetic Variation

• Sexual Recombination
• Mutation - gives rise to new traits in a population. Must be in reproductive cells to be passed to next generation
Origin of New Species
• Evidence: Volvox syngens
• Deer mouse: subspecies between 4 existing populations
Evidence supporting principle of Evolution by process of natural selection
• Biogeography and plate tectonics
• Fossil Record
• Taxonomy
• Comparative Anatomy
• Homologous structures
• Vestigial organs/ structures
• Comparative embryology
• Molecular biology - DNA sequences


Classification of Organisms:

Binomial system of nomenclature: Linnaeus
Systematics
• Taxonomy: ID of organisms and the assigning of names to them.
• Phylogenetic Reconstruction: gradual levels of change in organization between species; ID evolutionary patterns that unite different organisms
• Classification: Categorizes phylogenetic information into a "retrieval system"
Five Kingdom System of Classification and hierarchy of taxons:
• Prokaryotic Unicells (Monera)
• Eukaryotic Unicells (Protista)
• Eukaryotic Multicellular Organisms
• Plants (Plantae); Autotrophic
• Fungi (Fungi); Heterotrophic with absorptive nutrition
• Animals (Animalia); Heterotrophic with ingestive nutrition
Hierarchy of taxons:
• Kingdom,
• Phylum (Division),
• Class,
• Order,
• Family,
• Genus,
• species
Ecology and interaction of organisms
• Producers (autotrophs),
• consumers (heterotrophs; herbivores and carnivores), and
• decomposers (heterotrophs; detritivores)
• Food Chains and Food Webs
• Energy Flow and trophic levels Inorganic

Historical Perspective leading to:

I. The Cell Theory

• All organisms are composed of one or more cells.
• The cell is the basic living unit of organization for all organisms.
• All cells arise from pre-existing cells.

Structural complexity (simplified):

• Plasma membrane
• Ribosomes
• Cytoplasm
• Cell Walls

Endomembrane System>>

• Plasma membrane
• Fluid-Mosaic model
• Phospholipid structure/bilayer
• Membrane proteins
• peripheral proteins
• integral proteins
• recognition proteins (remember oligosaccharides?)
• receptor proteins (e.g. hormone receptor)
• transport proteins (Facilitated diffusion or Active Transport)
• energy requiring pumps
• channel proteins; gated and ungated
• carrier proteins
• Nucleus
• nuclear envelope
• nuclear pores
• nucleolus
• ribosome assembly
• Chromosomes
• DNA
• Histone protein
• endoplasmic reticulum
• rough - protein processing
• smooth - lipid processing
• golgi bodies (golgi apparatus)
• carbohydrate processing
• transport vesicles

• Microbodies
• lysosomes (digestive organelle); part of endomembrane system
• peroxisomes (remove peroxide H₂O₂; catalase)
• glyoxysomes (plants only; lipid metabolism)
• Mitochondria
• Plastids (plants only)
• Chloroplasts
• leucoplasts or amyloplasts (starch storage)
• chromoplasts (pigment storage)
• Cytoskeleton
• Microfilaments
• Actin (Actin and myosin in muscle // plant cytoplasmic streaming)
• Intermediate Filaments
• Microtubules (Protein = "- and $-tubulin)
• flagella and cilia (9 + 2 array of MT's; 9 "doublets surrounding 2 central MT's)
• mitotic/meiotic spindles
• other structures
• Microtubule-Organizing Centers (MTOC's)/Centrioles / Centrosomes / and basal bodies

(Plants but not animals) (note plastids, lack of centrioles, glyoxysomes, plus....)

• Central Vacuole
• Cellulosic Cell Walls
• Primary walls (stretchable)
• Secondary walls (strength and support/ reinforced)

• Cell communication structures
• plasmodesmata (plants)
• gap junctions (animals)
• desmosomes (animals)
• tight junctions (animals)
• Extracellular matrix
• plants, fungi, some protists, bacteria: CELL WALLS
• animals: Glycocalyx

V. Membrane Structure and Function

• Fluid Mosaic Model of membrane structure; concept of selective permeability
• Phospholipids (phospholipid bilayer)
• Proteins (integral and peripheral positions - see notes above)

• Diffusion
• Simple
• Bulk Flow
• Osmosis
• Tonicity
• Turgor (plants)
• Water potential

Chemistry

Atomic Structure

• Protons - Atomic number - gives elemental characters
• Neutrons - vary #, change elements properties -Isotopes
• Electrons -How you manage electrons describes all bonds
• Electron orbitals and stability
• Electron energy shells and atomic stability
Chemical Bonds
• Ionic Bonding
• Covalent Bonding
• Polar vs. nonpolar covalent bonding
• Hydrogen Bonding
Water - Characteristics which make it important to biological systems- due nearly entirely to H-bonds
• Solvent Properties
• Liquid at physiological temperatures
• Living systems are hydraulic systems; water is not compressible
• High specific heat and High Heat Capacity - resistant to temp. changes
• High Latent Heat of vaporization - Cools surface
• High latent heat of fusion
• Unique density changes with temperature change in liquid phase
• Mixing effects
• insulation effects (ice floats)
• Uniform viscosity at all temperatures
• Adhesive and cohesive properties
• High tensile strength (surface tension)
pH

Measurement:

• [H+]
• pH scale; acidic --> neutral --> basic
Buffers; compounds that resist changes in the [H+]

Basically any carbon-containing molecule with possible exception of some simple molecules (e.g. CO2)

Structure of carbon containing compounds: (differences impart different functions)

• Simple,
• linear,
• branched chains, or
• ring structures -


Condensation synthesis

Hydrolysis

Functional Groups

• methyl,
• hydroxyl,
• aldehyde,
• ketone,
• carboxyl,
• amino,
• phosphate


Carbohydrates: 2 or more hydroxyl groups and either a ketone or aldehyde group

• Monosaccharides (highly reactive; reducing sugars)
• Disaccarharides (reactive groups tied up; more stable)
• Oligosaccharides (signal recognition)
• Polysaccharides
• Storage & (e.g. starch, glycogen)
• Structural Polymers (e.g. cellulose, chitin)


Lipids (long chain hydrocarbons that are nonpolar)

• Fatty acids
• Glycerol function
• Saturated vs. unsaturated fats
• Phospholipids
• Lipids without fatty acids (steroids, cholesterol)


Proteins (things that do the work in a cell)

• Amino acids (properties of different amino acids)
• Peptide Bond
• Polypeptides
• Structure
• primary,
• secondary,
• tertiary,
• quaternary
• Protein conformation and conformation changes
• Protein domains
• Protein chaperones / denaturation and renaturation
• Lipo- and glyco-proteins


Nucleic Acids

• Nucleotides (sugar, phosphate, and nitrogenous base)
• Nitrogenous Bases
• Purines: Adenine, Guanine
• Pyrimidines: Cytosine, Thymine, Uracil
• Ribose vs. Deoxyribose sugar
• Adenosine phosphates (AMP, ADP, ATP)
• Other nucleotide triphosphates (GTP, CTP, TTP, UTP)
• Electron Carriers
• NAD+ / NADH
• NADP+ / NADPH
• FAD+ / FADH2