Biology1010, Michael T. Stevens Invitation to Biology Chapter 1 What is Science? The Scientific World View 1) By working together over time, people can figure out how the world works. 2) The universe is a unified system and knowledge gained from studying one part of it can often be applied to other parts. 3) Knowledge is both stable and subject to change. from Benchmarks for Science Literacy Why am I taking this class? When people know how scientists work and reach scientific conclusions, and what the limitations of such conclusions are, they are more likely to react thoughtfully to scientific claims and less likely to reject them out of hand or accept them uncritically from Benchmarks for Science Literacy Why am I taking this class? Once people gain a good sense of how science operates—along with a basic inventory of key science concepts as a basis for learning more later—they can follow the science adventure story as it plays out during their lifetimes. from Benchmarks for Science Literacy 1.5 &1.6 How science operates: The nature of scientific Inquiry More flexible than a rigid set of steps “the scientific method.” Can involve: Making observations Asking questions Gathering information Hypothesizing Experimenting Collecting and analyzing data Making conclusions and sharing results Scientific Theory A widely accepted hypothesis that has been repeatedly tested and never refuted Theories have wide-ranging explanatory power Examples of Scientific Theories Theory of Evolution by Natural Selection The Cell Theory Atomic Theory The Theory of Continental Drift The Heliocentric Theory Limits of Science Scientific inquiry does not address: subjective questions the supernatural 1.7 Role of Experiments Procedures used to study a phenomenon under known conditions Allows you to test a hypothesis Hypotheses are supported or refuted with evidence, they are not proved true or false. Experimental Design Experimental group A group exposed to the variable of interest Control group A standard for comparison Identical to experimental group except for variable being studied Things to consider: Sampling error Non-representative sample skews results Minimize by: Using large sample sizes Replicating Bias More biased Privately-funded research Work done by one individual Less biased Government-funded research (NSF) Interdisciplinary or Collaborative Work Scientists make observations Scientists ask questions Why do certain aspen trees get eaten by caterpillars while others do not? Do the aspen trees that get eaten grow less than the aspen that don’t get eaten? Scientists gather information about the things they plan to study Quaking aspen (Populus tremuloides) Herbivores—animals that eat plants -forest tent caterpillar -large aspen tortrix -gypsy moth caterpillar Chemicals in aspen leaves Phenolic glycosides A caterpillar’s taste test Scientists predict what will happen in their experiments Different aspen trees have different amounts of chemicals that taste bad to caterpillars. Aspen trees that don’t get eaten by caterpillars grow more than aspen that do get eaten. Scientists do experiments Variables in the experiment Genotype—each aspen tree has different genes Defoliation—some trees had their leaves removed, others didn’t Scientists collect data Measured chemicals Measured tree growth Scientists analyze data Leaf chemicals Growth Scientists draw conclusions Aspen trees have different amounts of leaf chemicals. (Genetic variation in leaf chemistry) The amount of leaf chemicals are affected by whether or not the tree got eaten. (Induction) Trees that get eaten grow less. (Negative effects of defoliation) Conclusions Over time, trees with more leaf chemicals will grow faster and make more seeds than their neighbors These seeds grow into new trees So, the next generation of trees will have more leaf chemicals Aspen Population Green = taste good (few chemicals) Red = taste bad (many chemicals) Evolution Changes in populations over time Ecology How species (like trees and caterpillars) work together in their environment Scientists share their results 1.1 Life’s Levels of Organization The cell is the basic unit of life Living things show levels of organization, from the simple to the complex Cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, the biosphere Cells are composed of the molecules of life Nucleic acids (DNA and RNA) Proteins (muscles) Carbohydrates (sugars and starch) Lipids (fats) 1.2 Life’s Unity DNA (deoxyribonucleic acid) The signature molecule of life Molecule of inheritance Directs assembly of amino acids into proteins Heritability of DNA DNA is transmitted from parent to offspring via reproduction DNA codes for traits and directs the development of an organism Energy Is the Basis of Metabolism Energy = Capacity to do work Metabolism = Reactions by which cells acquire and use energy to grow, survive, and reproduce Interdependencies among Organisms AUTOTROPHS Producers Make their own food HETEROTROPHS Consumers Depend on energy stored in tissues of producers or other consumers Energy Flow Usually starts with energy from sun Transferred from one organism to another Energy flows in one direction Eventually all energy dissipates as heat Life responds to change Organisms sense changes in their environment and make responses to them Receptors detect specific forms of energy The form of energy detected by a receptor is a stimulus Homeostasis Maintenance of internal environment within range suitable for cell activities Unity of Life Overview All organisms: Are composed of the same substances Engage in metabolism Sense and respond to the environment Have the capacity to reproduce based on instructions in DNA 1.3 Diversity of Life Millions of living species Additional millions of species now extinct Classification scheme attempts to organize this diversity Prokaryotes No nucleus No organelles Unicellular Ex: bacteria Eukaryotes DNA is inside a nucleus Have organelles Most are larger and more complex than the prokaryotes Can be unicellular or multicellular Three-Domain Classification Bacteria Archaea Eukarya (Eukaryotes)—protists, plants, fungi, and animals Protists Some unicellular, some multicellular Can be producers or consumers Challenging group to classify Ex: paramecia, amoebas, algae Plants Almost all are multicellular Most are photosynthetic producers Make up the food base for communities Ex: aspen, pines, wheat Fungi Most are multicellular Consumers and decomposers Extracellular digestion and absorption Ex: mushrooms, yeasts, molds Animals Multicellular consumers Herbivores Carnivores Parasites Scavengers Move about during at least some stage of their life Taxonomy Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species Scientific Names Two-part naming system devised by Carolus Linnaeus First name is genus (plural, genera) Second name is species Homo sapiens Populus tremuloides Chapter 2: Life’s chemical basis 2.1 Atom—smallest unit that retains the properties of an element. Proton—positive charge, in nucleus Neutron—no charge, in nucleus Electron—negative charge, orbits nucleus Periodic Table If you know the number of protons, neutrons, and electrons, you can predict the behavior of an element. Atomic number = number of protons, unique for each element Mass number = number of protons + number of neutrons Elements in the same column of the table have the same number of electrons available for interaction. 2.2 Radioisotopes Isotope—two or more forms of an element that differ in neutron number. Ex: Hydrogen isotopes: protium, deuterium and tritium Ex: Carbon isotopes: 12C,13C, and 14C Isotopes with too many or too few neutrons are often unstable and are radioactive. Radioisotopes of Carbon Living things produce different forms of carbon. Once an organism dies, 14C starts to decay. Half of the 14C decays in 5,700 years. Used to estimate the age of fossils. Radioisotopes Used as tracers in experiments Used medicinally 2.3 Electrons and energy levels Electrons occupy orbitals. Orbitals closest to the nucleus have the lowest levels of energy. Electrons fill the lower levels first. The lowest level can hold two electrons, higher levels hold eight. Chemical bonding Atoms give up, acquire, and share electrons with other atoms. Chemical bonding results in: Molecules—two or more atoms of the same or different elements joined in a chemical bond 2.4 Atomic Interactions 1) Ionic Bonding Ion: An atom with a positive or negative charge. Ions form when an atom gains or loses electrons. Ionic Bond: The close association of charged atoms 2) Covalent Bonding Covalent Bond: When atoms share one or more electrons. One pair shared (single bond) H-H Two pairs shared (double bond) O=O Three pairs shared (triple bond) Covalent bonds are more stable and stronger than ionic bonds. 3) Hydrogen bonding: a result of polarity Nonpolar: electrons shared equally, no poles Ex: H2, O2, N2 Polar: One atom has a stronger pull on the electrons so the molecule has positive and negative poles. Ex: H2O Hydrogen Bonding An interaction involving hydrogen (+) and some other part of a molecule (-). Bonds that can form and break easily. Crucial biological roles in DNA and water. 2.5 Water’s life-giving properties 1) Polarity of water—no net charge, but has a positive (H) and negative (O) end. Attracts other polar molecules such as sugars and salts (hydrophilic) Repels oil and other nonpolar molecules (hydrophobic) Hydrophilic/phobic interactions important for the formation of cell membranes 2) Water is temperature stabilizing Compared with other fluids, water can absorb a lot of heat energy before increasing in temperature. (High specific heat) Why?—hydrogen bonding Evaporation of Water As water molecules break free, they carry away heat energy Evaporative water loss is used by mammals to lower body temperature Why Ice Floats In ice, hydrogen bonds lock molecules in a lattice Water molecules in lattice are spaced farther apart then those in liquid water Ice is less dense than water Water Is a Good Solvent Ions and polar molecules dissolve easily in water When solute dissolves, water molecules cluster around solute molecules and keep them separated Water Cohesion Hydrogen bonding holds water molecules together Creates surface tension Allows water to move as continuous column upward through stems of plants 2.6 Acids and Bases H2O splits into ions of hydrogen (H+) and hydroxide (OH-) in equal amounts. Water is neutral. Acids have more H+ ions. Bases have fewer H+ ions, they have more OH- ions. The pH Scale Measures H+ concentration Change of 1 on scale means 10X change in H+ concentration Highest H+ Lowest H+ 0---------------------7-------------------14 Acidic Neutral Basic Examples of pH Pure water is neutral with pH of 7.0 Acidic Stomach acid: pH 1.0 - 3.0 Lemon juice: pH 2.3 Basic Baking soda: pH 9.0 Household ammonia: pH 11.0 Molecules of Life Chapter 3 3.1 Organic Compounds Contain carbon and at least one hydrogen atom. Carbohydrates Lipids Proteins Nucleic Acids Carbon’s Bonding Behavior Outer shell of carbon has 4 electrons; can hold 8 Each carbon atom can form covalent bonds with up to four atoms Bonding Arrangements Carbon atoms can form chains or rings Atoms can project from the carbon backbone Functional Groups Atoms or clusters of atoms that are covalently bonded to carbon backbone Give organic compounds their different properties Examples of Functional Groups Hydroxyl group - OH Methyl group -CH3 Carboxyl group - COOH Amino group - NH3+ Phosphate group - PO3- How do cells build organic compounds? With the help of enzymes, cells build polymers from monomers. Enzyme—a protein that accelerates a reaction Monomer—small organic compound Polymer—a molecule that contains repeating monomers Types of Reactions Functional group transfer Electron transfer Rearrangement Condensation Cleavage (Hydrolysis) Condensation Reactions Form polymers from subunits Enzymes remove -OH from one molecule, H from another, form bond between two molecules The removed –OH and H can join to form water Hydrolysis A type of cleavage reaction Breaks polymers into smaller units Enzymes split molecules into two or more parts An -OH group and an H atom derived from water are attached at exposed sites 3.2 Carbohydrates The most abundant biological molecules in nature. Consist of C, H, O in a 1:2:1 ratio. 1) Monosaccharides (simple sugars, one sugar unit) 2) Oligosaccharides (short-chain carbohydrates) 3) Polysaccharides (complex carbohydrates) Monosaccharides Simplest carbohydrates Most are sweet-tasting, water-soluble Most have 5- or 6-carbon backbone Examples: glucose, fructose, ribose, deoxyribose Two Monosaccharides Oligosaccharides Disaccharide = 2 monosaccharides covalently bonded Formed by condensation reaction Polysaccharides Straight or branched chains of many sugar monomers Most common are composed entirely of glucose Cellulose Starch Glycogen Cellulose & Starch Differ in bonding patterns between monomers Cellulose - tough, indigestible, structural material in plants Starch - easily digested, storage form in plants Glycogen Sugar storage form in animals Large stores in muscle and liver cells When blood sugar decreases, liver cells degrade glycogen, release glucose 3.3 Lipids Nonpolar hydrocarbons Most include fatty acids Glycerides (fats and oils) Phospholipids (cell membranes) Waxes Fatty Acids Carboxyl group (-COOH) at one end Carbon backbone (up to 36 C atoms) Saturated - Single bonds between carbons Unsaturated - One or more double bonds Three Fatty Acids Glycerides (fats and oils) Glycerol and 3 fatty acids Butter, lard, vegetable oil. Yield more than 2X energy/gram than carbs. Important for storage. Phospholipids Main components of cell membranes Hydrophilic heads (polar), hydrophobic tails (nonpolar). Waxes Fatty acids linked to alcohols or carbon rings Firm consistency, protect, lubricate Repel water (bird feathers) Prevent water loss (cuticle on plant leaves) Sterols No fatty acids Rigid backbone of four fused carbon rings Cholesterol, Estrogen, Testosterone 3.4 Proteins Very diverse Important for structure, nutrition, enzymatic reactions, cell communication. Made from amino acids Amino Acids Amino group Carboxyl group R group—20 R groups, one for each different amino acid Protein Synthesis Protein is a chain of amino acids l Biology1010 3.4 Proteins Very diverse Important for structure, nutrition, enzymatic reactions, cell communication. Made from amino acids Amino Acids Amino group Carboxyl group R group—20 R groups, one for each different amino acid Protein Synthesis Protein is a chain of amino acids linked by peptide bonds Peptide bond Type of covalent bond Forms through condensation reaction Primary Structure Sequence of amino acids Unique for each protein Two linked amino acids = dipeptide Three or more = polypeptide Primary Structure & Protein Shape Primary structure influences protein shape: H bonding between different amino acids R group interaction Secondary Structure Hydrogen bonds form between different parts of polypeptide chain These bonds give rise to coils (helices) or pleated sheets Examples of Secondary Structure Tertiary Structure Folding and coiling as a result of interactions between R groups Quaternary Structure Some proteins are made up of more than one polypeptide chain Polypeptides With Attached Organic Compounds Lipoproteins Proteins combined with fats Glycoproteins Proteins combined with sugars 3.5 Importance of Protein Structure The substitution of one amino acid (valine for glutamate) changes the shape of red blood cells and results in sickle-cell anemia. Denaturation Disruption of three-dimensional shape Breakage of weak bonds Causes of denaturation: pH Temperature Destroying protein shape disrupts function Ex: Cooking an egg 3.6 Nucleotides make up Nucleic Acids Nucleotide—a small organic compound with: sugar (deoxyribose or ribose) phosphate base (contains nitrogen) Nucleic Acid—single- or double-stranded molecule composed of nucleotides (e.g., DNA and RNA). DNA Double-stranded Consists of four types of nucleotides: Adenine Thymine Guanine Cytosine A pairs with T G pairs with C RNA Usually single strands Four types of nucleotides Adenine pairs with Uracil Guanine pairs with Cytosine RNA is a key player in protein synthesis Nucleotides also function as energy carriers—ATP (adenosine triphosphate) Cell Structure and Function Chapter 4 4.1 The Cell Smallest unit of life Metabolically active Senses and responds to environment Has potential to grow and reproduce Cell Structure All have: Plasma membrane Region where DNA is stored Cytoplasm Why Are Cells Small? Surface-to-volume ratio The bigger a cell is, the less surface area there is per unit volume Above a certain size, material cannot be moved in or out of cell fast enough Surface-to-Volume Ratio 4.2 How we see cells EARLY DISCOVERIES Mid 1600s - Robert Hooke—cork cells Late 1600s - Antony van Leeuwenhoek—protists, bacteria, sperm cells 1820s - Robert Brown—plant cell nucleus Developing Cell Theory (mid 1800s) Matthias Schleiden—plant tissue is composed of cells Theodor Schwann—animal tissue is composed of cells Rudolf Virchow—all cells come from other cells Cell Theory 1) All life is composed of cells 2) Cell is smallest unit having properties of life 3) New cells come from previously existing cells Microscopes Light microscopes Simple Compound Electron microscopes Transmission EM Scanning EM Light Microscopes + Living samples Natural color - Can resolve objects down to about 200 nm Electron Microscopy Uses streams of accelerated electrons rather than lightElectrons are focused by magnets rather than glass lenses + Can resolve structures down to 0.5 nm - Samples are dead Black-and-white images Transmission vs. Scanning Electron Microscopes 4.3 Cell Membranes Main component: a lipid bilayer Gives the membrane its fluid properties Two layers of phospholipids Fluid Mosaic Model Membrane is a mosaic of Phospholipids Glycolipids Sterols Proteins 4.4 Prokaryotic Cells Small and simple, metabolically diverse DNA is not enclosed in nucleus No organelles Ex: Archaea and Eubacteria Prokaryotic Structure 4.6 Eukaryotic Cells Larger and more complex cells DNA is enclosed in a nucleus Have organelles Ex: Plants, Animals, Protists, Fungi 4.7 Functions of the Nucleus Keeps DNA separated from the metabolic machinery of the cytoplasm Makes it easier to organize and copy DNA before cell divison Components of the Nucleus 4.8 Components of Endomembrane System Endoplasmic reticulum Golgi bodies Vesicles Endoplasmic Reticulum System of membranous channels extending throughout cytoplasm Lipid synthesis, initial modification of proteins Two types: smooth and rough Smooth ER No ribosomes on surface Lipid assembly Rough ER Ribosomes give it a rough appearance Initial modification of polypeptides Golgi Bodies Consists of slightly curved sacs Final modification of proteins and lipids Packaging and sorting for cell use and export Material arrives and leaves in vesicles Vesicles Membranous sacs that move through the cytoplasm, cellular recycling centers Lysosomes—contain digestive enzymes Peroxisomes—breakdown hydrogen peroxide and alcohol Central Vacuole Only in plants Many fused vesicles Fluid-filled organelle Stores amino acids, sugars, pigments, toxins Can take up 50-90 percent of cell interior 4.9 Mitochondria Double-membrane bound organelles Inner membranes (Cristae) are folded Sites of respiration—where organic compounds are converted to energy using oxygen. ATP-producing powerhouses In plants and animals 4.9 Chloroplasts Double membrane bound organelles with inner thylakoid membranes Thylakoids contain chlorophyll Important for photosynthesis—using light energy to make carbohydrates Only in plants and protists—not in animals Endosymbiont Theory Both mitochondria and chloroplasts resemble prokaryotes in size and structure Have own DNA, RNA, and ribosomes Evidence shows that they were free-living and then moved inside larger cells 4.10 Plant Cell Features Animal Cell Features 4.12 Cytoskeleton Present in all eukaryotic cells Basis for cell shape and internal organization Allows organelle movement within cells and cell motility Cytoskeletal Elements Microtubules vs. Microfilaments Microtubules found in cilia and flagella Microfilaments are found in pseudopods Cilia and Flagella Cilia—short, usually numerous hair-like projections that undulate Ex: Paramecium, human respiratory tract Flagella—longer, usually fewer whip-like projections Ex: Euglena, sperm cells All eukaryotic cilia and flagella have the same 9 + 2 structure of microtubules—evidence for evolution Pseudopods Temporary, irregular lobes that project from the cell and function in locomotion and prey capture Have microfilaments Ex: Amoeba How Cells Work Chapter 5 5.1 What Is Energy? Capacity to do work Forms of energy Motion, chemical energy, heat, electricity, sound, nuclear forces, gravity First Law of Thermodynamics The total amount of energy in the universe remains constant Energy can be converted from one form to another, but it cannot be created or destroyed Second Law of Thermodynamics No energy conversion is ever 100 percent efficient Entropy—a measure of a system’s disorder Disorder always increases. One-Way Flow of Energy Organisms maintain order by being resupplied with energy The sun is life’s primary energy source Energy flows in one direction from more usuable to less usable forms Heat is the least usuable form of energy Endergonic Reactions Energy input required Product has more energy than starting substances Ex: CO2 + H20 = glucose + O2 (Photosynthesis) Exergonic Reactions Energy is released Products have less energy than starting substance Ex: glucose + O2 = CO2 + H2O (Respiration) The role of ATP Cells use ATP in endergonic reactions Cells gain ATP in exergonic reactions Cells couple these two types of reactions ATP/ADP Cycle When ATP gives up a phosphate, ADP forms ATP can re-form when ADP gains a phosphate group (phosphorylation) This cycle helps drive most metabolic reactions 5.2 & 5.5 Participants in Metabolic Reactions Reactants—starting substances Intermediates—substances formed during a reaction sequence Products—substances left at the end Chemical Equilibrium Redox Reactions Cells release energy through electron transfers Oxidation-reduction (redox) reactions One molecule gives up electrons (is oxidized) and another gains them (is reduced) H+ ions are transferred at the same time OILRIG Electron Transfer Chains Arrangement of enzymes and coenzymes at a cell membrane As one molecule is oxidized, next is reduced Important in photosynthesis and aerobic respiration Uncontrolled vs. Controlled Energy Release Metabolic Pathways Enzyme-mediated sequences of reactions in cells Biosynthetic (anabolic) – ex: photosynthesis Degradative (catabolic) – ex: aerobic respiration 5.3 Enzymes Generally proteins Speed up reactions Not altered or used up in reactions Work in forward and reverse reactions Specific--each type of enzyme recognizes and binds to only certain substrates Activation Energy For a reaction to occur, an energy barrier must be surmounted Enzymes make the energy barrier smaller 5.4 How Enzymes Work 1) Concentrate substrates at the active site 2) Orient the substrates in positions favoring reactions 3) Shut out competing reactions Factors Influencing Enzyme Activity Temperature pH Cofactors Allosteric regulators Effect of Temperature Effect of pH Enzyme Helpers Cofactors—assist enzymatic reactions by accepting and receiving electrons 1) Metal ions 2) Coenzymes Derived from vitamins Antioxidants (neutralize free radicals) Allosteric Activation Allosteric Inhibition Feedback Inhibition 5.6 Cell Membranes Show Selective Permeability Concentration Gradient In the absence of other forces, a substance moves from a region where it is highly concentrated to a region where it is less concentrated “Down” the gradient from high to low Diffusion The net movement of a substance down a concentration gradient Factors Affecting Diffusion Rate Steepness of concentration gradient Steeper gradient, faster diffusion Molecular size Smaller molecules, faster diffusion Temperature Higher temperature, faster diffusion 5.6 Passive vs. Active Transport BOTH USE TRANSPORT PROTEINS Span the lipid bilayer Can open to both sides Change shape when they interact with solutes Passive Transport Flow of solutes through transport proteins down gradient Does not require any energy input Active Transport Movement of solutes through transport proteinsup gradient Transport protein must be activated Uses ATP energy Helps maintain membrane gradients (Ca+, Na+, K+) that are essential for: Muscle contraction Neuron function Membrane Crossing: Overview 5.8 Movement of Water OSMOSIS—diffusion of water molecules across a selectively permeable membrane Osmosis Effects of Tonicity Hypertonic - having more solutes (low water conc.) Isotonic—having the same amount of solutes (same water conc.) Hypotonic – having fewer solutes (high water conc.) Tonicity and Osmosis Where It Starts – Photosynthesis Chapter 6 6.1 Sunlight as an Energy Source Photosynthesis uses a fraction of the electromagnetic spectrum Visible light (380-750 nm) Photons Individual packets of light energy Each type of photon has fixed amount of energy Pigments Light-absorbing molecules Absorb photons with particular wavelengths and transmit others Color you see are the wavelengths not absorbed (reflected) Variety of Pigments Chlorophylls (green) Carotenes (orange) Xanthophylls (yellow) Anthocyanins (purple) Phycobilins (red or blue-green) 6.2 T.E. Englemann’s Experiment (1882) Background Photosynthesis produces oxygen Certain bacterial cells will move toward places where oxygen concentration is high Hypothesis Movement of bacteria can be used to determine optimal light wavelengths for photosynthesis Method Algal strand placed on microscope slide and illuminated by light of varying wavelengths Oxygen-requiring bacteria placed on same slide Results Bacteria congregated where red and violet wavelengths illuminated alga Conclusion Bacteria moved to where algal cells released more oxygen – areas illuminated by the most effective light for photosynthesis Chlorophylls Main pigments in most photoautotrophs 6.3 Photosynthesis A two stage process 1)Light-dependent reactions Occurs in the thylakoid membranes 2) Light-independent reactions Occurs in the stroma Photosynthesis Equation Photoautotrophs Capture sunlight energy and use it to carry out photosynthesis Plants Some bacteria Many protistans Pigments in Photosynthesis Bacteria in plasma membranes Plants in thylakoid membranes of chloroplasts associated with electron transfer chains 6.4 Light-Dependent Reactions Converts light energy to chemical bond energy Pigments absorb light energy, give up electrons that enter electron transfer chains Water molecules are split, oxygen is released, ATP and NADPH are formed ATP and NADPH Formation 6.6 Light-Independent Reactions Energy from ATP and NADPH used to synthesize glucose from CO2 and H20 Light not required Calvin-Benson Cycle Overall reactants Carbon dioxide ATP NADPH Overall products Glucose ADP NADP+ Using the Products of Photosynthesis Glucose is the building block for: Sucrose The most easily transported plant carbohydrate Starch The most common storage form Linked Processes Photosynthesis Energy-storing pathway Releases oxygen Requires carbon dioxide Aerobic Respiration Energy-releasing pathway Requires oxygen Releases carbon dioxide How Cells Release Chemical Energy Chapter 7 7.1 Energy-Releasing Pathways Anaerobic pathways Evolved first Don’t require oxygen Start with glycolysis in cytoplasm Completed in cytoplasm Less efficient (2 ATPs / glucose) Energy-Releasing Pathways Aerobic pathways Evolved later Require oxygen Start with glycolysis in cytoplasm Completed in mitochondria More efficient (36 ATPs / glucose) 7.2 Anaerobic and Aerobic Respiration Both Start with Glycolysis Glycolysis occurs in cytoplasm Catalyzed by enzymes Glucose 2 Pyruvate (6C) (3C) Net Energy Yield from Glycolysis Energy requiring steps: 2 ATP invested Energy releasing steps: 2 NADH formed 4 ATP formed Net yield is 2 ATP and 2 NADH 7.3 If oxygen is present Pyruvate enters a mitochondrion and is modified to become Acetyl-CoA Kreb’s Cycle in a Mitochondrion 7.4 Electron Transfer Chain (ETC) Occurs in the mitochondria Coenzymes deliver electrons to electron transfer chains Electron transfer sets up H+ ion gradients Flow of H+ down gradient powers ATP formation Oxygen is the final electron acceptor Importance of Oxygen ETC requires oxygen Oxygen withdraws Biology1010 Oxygen withdraws spent electrons from the ETC, then combines with H+ to form water Summary of Transfers ATP Accounting Glycolysis 2 ATP formed Krebs cycle 2 ATP formed Electron transfer phosphorylation 32 ATP formed Overview of Aerobic Respiration Efficiency of Aerobic Respiration 39% of the energy in glucose is conserved in the ATP formed Most energy is lost as heat. For comparison, most engines are less than 10% efficient 7.5 & 7.6 Anaerobic Pathways Do not use oxygen Produce less ATP than aerobic pathways (2 % efficient) Two types of fermentation pathways Alcoholic fermentation Lactate fermentation Alcoholic Fermentation Begins with glycolysis Does not break glucose down completely Yields only the 2 ATP in glycosis Steps that follow regenerate NAD+, produce CO2, and produce ethanol as a waste product, toxic above 10% Alcoholic Fermentation Yeasts Single-celled fungi Carry out alcoholic fermentation Used to make bread, beer, and wine. Lactate Fermentation Begins with glycolysis Does not break glucose down completely Yields only the 2 ATP in glycolysis Steps that follow regenerate NAD+ and produce lactate as a waste product Bacteria and fast-twitch muscles Lactobacillus used to make cheeses, yogurt, buttermilk, sour cream, sauerkraut When demands for energy are immediate and intense and cells run out of oxygen, animal muscle cells use lactate fermentation Lactic acid makes muscles sore Chapter 8 How cells reproduce 8.1 Cell Division Eukaryotes: nuclear division cytoplasmic division Prokaryotes: fission Mitosis Nuclear division that occurs in somatic (body) cells Asexual reproduction Growth Replacement/repair Produces two cells that are identical to each other and to the original cell. Chromosome—a molecule of DNA and its proteins Chromosomes must be duplicated before nuclear division 8. 2 Cell Cycle Cell cycle—a cycle starts when a new cell forms. Includes Interphase Includes Mitosis (prophase, metaphase, anaphase, telophase) Interphase The longest portion of the cell cycle Three stages G1—cell growth S—DNA replication G2—preparations for division 8.3--A closer look at mitosis Prophase Chromosomes condense Microtubules form a bipolar spindle Nuclear envelope breaks up Metaphase All chromosomes are aligned midway between the spindle poles (at the cell’s equator) Anaphase Anaphase—Microtubules move sister chromatids of each chromosome apart, to opposite poles Telophase A new nuclear envelope forms around each of two groups of chromosomes as they decondense. Things to remember about mitosis Mitosis produces two cells from one cell All cells are exactly the same They have the same number of chromosomes 8.4 Cytoplasm Division Animals Cleavage—cytoplasm pinches in two. Occurs after mitosis is over. Microfilaments attach to the plasma membrane and contract. Cleavage Plants Cell plate formation Occurs after mitosis is over. Vesicles fuse at the former equator Cellulose accumulates Plasma membrane forms 8.5 When Control Is Lost Growth and reproduction depend on controls over cell division Checkpoint proteins: Mitosis inhibitors—tumor suppressors Mitosis stimulators—oncogenes When checkpoints fail, unregulated growth occurs Ex: Neoplasms Neoplasms Abnormal masses of cells Benign – grow slowly and retain surface recognition proteins that keep them in a home tissue (noncancerous) Malignant – grow and divide abnormally, disrupting surrounding tissues physically and metabolically (cancerous) Metastasis The process of abnormal cell migration and tissue invasion The way cancer cells spread HeLa Cells Line of human cancer cells that can be grown in culture Descendents of tumor cells from a woman named Henrietta Lacks Lacks died at 31, but her cells continue to live and divide in labs around the world Culturing Cells Growing cells in culture allows researchers to investigate processes and test treatments without danger to patients Taxol—anticancer drug derived from Pacific Yew Meiosis and Sexual Reproduction Chapter 9 9.1 Asexual vs. Sexual Reproduction ASEXUAL: One parent produces offspring via mitosis All offspring are genetically identical to one another and to parent (clones) No genetic variation SEXUAL REPRODUCTION: Involves: Meiosis Gamete production Fertilization Produces genetic variation among offspring Genes and alleles Gene—a section of DNA in a chromosome that codes for a heritable trait. Allele—one of two or more forms of a gene that specify different versions of the same trait. Sexual Reproduction Through sexual reproduction, offspring inherit new combinations of alleles, which leads to variations in traits This variation in traits is the basis for evolutionary change Chromosome number Humans have 46 (23 pairs) Diploid vs. Haploid Diploid (2n)—having two of each type of chromosome Haploid (n)—having only one of each type of chromosome 9.2 Homologous Chromosomes Carry Different Alleles Diploid cell has two of each chromosome One chromosome in each pair from mother, other from father Paternal and maternal chromosomes carry different alleles Chromosome Number Sum total of chromosomes in a cell Germ cells are diploid (2n) Gametes are haploid (n) Meiosis halves chromosome number Gamete Formation Gametes are sex cells (egg and sperm) Arise from germ cells Animals produce gametes directly Gamete Formation Plants produce gametes indirectly Plants produce spores that mature into gametophytes Gametophytes give rise to gametes 9.3 Meiosis: Two Divisions Two consecutive nuclear divisions Meiosis I Meiosis II DNA is not duplicated between divisions Four haploid nuclei are formed The two sister chromatids of each duplicated chromosome are separated from each other Stages of Meiosis Meiosis I Prophase I, Metaphase I, Anaphase I, Telophase I Meiosis II Prophase II, Metaphase II, Anaphase II, Telophase II Meiosis I - Stages Prophase I Each duplicated chromosome pairs with its homologue Homologues swap segments (crossing over) Microtubules attach to chromosomes as spindles form. Metaphase I Chromosomes line up in the middle of cell The spindle is now fully formed Anaphase I Homologous chromosomes are separated The sister chromatids of each chromosome remain together Telophase I The chromosomes arrive at opposite poles The cytoplasm divides There are now two haploid cells This completes Meiosis I Meiosis II - Stages Prophase II Microtubules attach to the kinetochores of the duplicated chromosomes Chromosomes move toward the spindle’s equator Metaphase II All of the duplicated chromosomes are lined up at the spindle equator, midway between the poles Anaphase II Sister chromatids separate to become independent chromosomes Separated chromosomes move to opposite poles Telophase II The chromosomes arrive at opposite ends of the cell A nuclear envelope forms around each set of chromosomes The cytoplasm divides There are now four haploid cells 9.4 Crossing Over Effect of Crossing Over After crossing over, each chromosome contains both maternal and parental segments Creates new allele combinations in offspring Random Alignment Initial contacts between microtubules and chromosomes are random Either the maternal or paternal member of a homologous pair can end up at either pole The chromosomes in a gamete are a mix of chromosomes from the two parents Possible Chromosome Combinations As a result of random alignment, the number of possible combinations of chromosomes in a gamete is: 2n (n is number of chromosome types) 23 = 8 246 = 7.04 X 1013 (70 trillion) Fertilization Male and female gametes unite and nuclei fuse Fusion of two haploid nuclei produces diploid nucleus in the zygote Which two gametes unite is random Adds to variation among offspring Factors Contributing to Variation among Offspring Crossing over during prophase I Random alignment of chromosomes at metaphase I Random combination of gametes at fertilization Prophase I (Meiosis) Homologous pairs interact and crossing over occurs Prophase (Mitosis) and Prophase II (Meiosis) Homologous pairs do not interact Anaphase I (Meiosis) Homologous chromosomes are separated Anaphase (Mitosis) and Anaphase II (Meiosis) Sister chromatids of a chromosome are separated Results of Mitosis and Meiosis Mitosis 1 diploid cell to 2 diploid cells 1 haploid to 2 haploid cells Each identical to parent Meiosis 1 diploid cell to 4 haploid cells Each different from parent and different from one another Mitosis & Meiosis Compared Mitosis Functions Asexual reproduction Growth, repair Occurs in somatic cells Produces clones Meiosis Function Sexual reproduction Occurs in germ cells Produces variable offspring 9.5 Life Cycles Animal vs. Plant Life Cycle Biology1010 Observing Patterns in Inherited Traits Chapter 10 10.1Early Ideas about Heredity People knew that sperm and eggs transmitted information about traits Blending theory Problem: Would expect variation to disappear Variation in traits persists Gregor Mendel Strong background in plant breeding and mathematics Using pea plants, he found indirect evidence of how parents transmit genes to offspring The Garden Pea Plant Self-pollinating True breeding Can be experimentally cross-pollinated Genetic Terms Genes Units of information about specific traits Passed from parents to offspring Each has a specific location (locus) on a chromosome Alleles Different forms of a gene--Arise by mutation Dominant allele masks a recessive allele that is paired with it Allele Combinations Homozygous having two identical alleles at a locus AA or aa Heterozygous having two different alleles at a locus Aa Genotype & Phenotype Genotype refers to particular genes an individual carries (AA, Aa, aa) Phenotype refers to an individual’s observable traits (red, pink, white) Cannot always determine genotype by observing phenotype Tracking Generations Parental generation P mates to produce First-generation offspring F1 mate to produce Second-generation offspring F2 10.2Monohybrid Crosses Use F1 offspring of parents that breed true for different forms of a trait:(AA x aa = Aa) A cross between two F1 heterozygotes, which are the “monohybrids” (Aa x Aa) Monohybrid Crosses F1 Results of One Monohybrid Cross F2 Results of Monohybrid Cross Probability The chance that each outcome of a given event will occur is proportional to the number of ways that event can be reached Punnett Square of a Monohybrid Cross Mendel’s Monohybrid Results Testcross Individual that shows dominant phenotype is crossed with individual with recessive phenotype (AA X aa) or (Aa X aa) Examining offspring allows you to determine the genotype of the dominant individual Mendel’s Theory of Segregation Diploid cells have pairs of alleles The two alleles are separated during meiosis They end up in different gametes “For a given trait, alleles separate” 10.3 Dihybrid Cross Experimental cross between individuals that are homozygous for different versions of two traits Dihybrid Crosses Independent Assortment Mendel’sTheory of Independent Assortment A given pair of alleles is sorted into one gamete or another independently of alleles on other chromosomes. 10.4 CODOMINANCE--A pair of non-identical alleles affecting two phenotypes are expressed at the same time Ex: ABO blood groups Genetics of ABO Blood Types: Three Alleles Gene that controls ABO type codes for enzyme that dictates structure of a glycolipid on blood cells Two alleles (IA and IB) are codominant when paired Third allele (i) is recessive to others ABO and Transfusions Recipient’s immune system will attack blood cells that have an unfamiliar glycolipid on surface Type O is universal donor because it has neither type A nor type B glycolipid Type AB is the universal recipient 10.5 Linkage Groups All the genes on one chromosome are called a linkage group. If no crossing over occurs, genes on the same chromosome will be inherited together Crossover Frequency 10.6 Genes and the Environment Environmental conditions affect the expression of genes Phenotypic plasticity Examples: Yarrow, Aspen Himalayan rabbits Leaf chemicals Genes and the Environment Himalayan rabbits are white, but are homozygous for an allele that produces melanin in cool areas of the body 10.7 Complex Variations in Traits Continuous Variation A more or less continuous range of small differences in a given trait among individuals The greater the number of genes and environmental factors that affect a trait, the more continuous the variation in versions of that trait Human Variation Some human traits occur as a few discrete types Attached or detached earlobes Many genetic disorders Other traits show continuous variation Height Weight Eye color Describing Continuous Variation Chromosomes and Human Genetics Chapter 11 11.1 Autosomes vs. Sex chromosomes Autosomes—chromosomes that are the same in both sexes Sex chromosomes—determine gender, different in females and males Sex Chromosomes In mammals and fruit flies: XX is female, XY is male In birds, butterflies, moths, some fish: XY is female, XX is male Human X and Y chromosomes function as homologues during meiosis Sex Determination The Y Chromosome Fewer than two dozen genes identified One is the gene for male sex determination SRY gene (sex-determining region of Y) SRY present, testes form SRY absent, ovaries form Effect of Y Chromosome The X Chromosome--Carries more than 2,062 genes Most genes deal with traits expressed both in females and males Karyotyping A preparation of an individual’s chromosomes The cell cycle is stopped during metaphase Chromosomes are stained and photographed 11.2 & 11.7 Human Genetic Analysis Geneticists gather information from several generations If a trait follows a simple Mendelian inheritance pattern they can predict the probability of the trait showing up again Pedigree Chart that shows genetic connections among individuals Standardized symbols Genetic Abnormality A rare or uncommon version of a trait Example: Polydactyly Unusual number of toes or fingers Does not cause any health problems Genetic Disorder Inherited condition that causes mild to severe medical problems Why don’t they disappear? Mutation introduces new rare alleles In heterozygotes, the harmful allele may not be expressed, but still be passed on to offspring Disorder may not be expressed until after reproduction Patterns of InheritanceAutosomal Dominant Inheritance Trait typically appears in every generation Examples of autosomal dominant disorders Achondroplasia—dwarfism Huntington’s disease—nervous system degeneration Machado-Joseph disease—loss of muscle control Familial hypercholestorolemia—very high cholestorol levels Autosomal Recessive Inheritance Patterns Carriers possible Two carriers have a 25% of having an affected child. Examples of autosomal recessive disorders Albinism—absence of pigments Cystic fibrosis—Causes progressive disability and early death, may require lung transplants. Characterized by shortness of breath, frequent lung and sinus infections, failure to thrive, diarrhea, and infertility. Most common among Caucasians and Ashkenazi Jews 11.4 X-Linked Inheritance Males show disorder more than females Son cannot inherit disorder from his father Examples of X-Linked Traits Color blindness Inability to distinguish among some of all colors Hemophilia Blood-clotting disorder Common in European royal families Hemophilia Biology1010 11.5 Altered Chromosomes Inversion A linear stretch of DNA is reversed within the chromosome Deletion Loss of some segment of a chromosome Most are lethal or cause serious disorder Translocation A piece of one chromosome becomes attached to another nonhomologous chromosome Most are reciprocal Translocation Philadelphia Chromosome Philadelphia chromosome arose from a reciprocal translocation between chromosomes 9 and 22 First chromosomal abnormality to be associated with a cancer (leukemia) Does Chromosome Structure Evolve? Alterations in the structure of chromosomes generally are not good and tend to be selected against Over evolutionary time, however, many alterations with neutral effects became built into the DNA of all species 11.6 Changes in Chromosome Number--Aneuploidy Individuals have one extra or less chromosome (2n + 1 or 2n - 1) Major cause of miscarriages in humans Nondisjunction Autosomal Aneuploidy Down Syndrome (Trisomy of chromosome 21) Mental impairment Can be detected before birth Risk of Down syndrome increases dramatically in mothers over age 35 Aneuploidy involving sex chromosomes Turner Syndrome (XO) Klinefelter Sydrome (XXY) XYY Polyploidy Individuals have three or more of each type of chromosome (3n, 4n) Common in flowering plants Lethal for humans 99% die before birth Newborns die soon after birth 11.8 Genetic Screening Large-scale screening programs detect affected persons Newborns in United States routinely tested for PKU Early detection allows dietary intervention and prevents brain impairment Phenotypic Treatments Symptoms of many genetic disorders can be minimized or suppressed by Dietary controls Adjustments to environmental conditions Surgery or hormonal treatments Genetic Counseling Genetic counseling is available to help parents-to-be make informed decisions. DNA Structure and Function Chapter 12 12.2 DNA is made of nucleotides Each nucleotide consists of Deoxyribose (5-carbon sugar) Phosphate group A nitrogen-containing base Four bases Adenine, Guanine, Thymine, Cytosine Composition of DNA Amount of adenine relative to guanine differs among species Amount of adenine always equals amount of thymine and amount of guanine always equals amount of cytosine A=T and G=C Patterns of Base Pairing 12.4 DNA Replication DNA is two nucleotide strands held together by hydrogen bonds H bonds are easily broken Each single strand then serves as template for new strand Semiconservative Replication Base Pairing during Replication Enzymes in Replication Enzymes unwind the two strands DNA polymerase attaches complementary nucleotides DNA ligase fills in gaps Enzymes wind two strands together DNA Repair Mistakes can occur during replication DNA polymerase and DNA ligase can repair mistakes on the new strand 12.5 Cloning What is a key functional difference between plant and animal cells? Plant cells are generally totipotent while animal cells generally are not. Totipotency—”total potential” The ability of one cell to produce all the different types of a cell in an organism Totipotency of plant cells Animals cell are more limited Most animal cells can’t de-differentiate and become other types of cells once they’ve specialized and matured into skin cells, liver cells, etc. Exceptions Embryonic stem cells--totipotent Blastocyst embryonic stem cells--totipotent Over 100 million Americans suffer from diseases that are prime candidates for stem cell research heart disease, cancer, diabetes, Parkinson''s disease, Alzheimer''s disease, autoimmune diseases Embryos are donated by couples using in vitro fertilization 1) Are these frozen embryos human life, and therefore, something precious to be protected? 2) Shouldn''t they be used for a greater good, for research that has the potential to save and improve other lives if they’re going to be discarded or destroyed otherwise? Stem cells can also be derived from certain mature animal cells Umbilical cord stem cells—multipotent Adult stem cells—multipotent Unfertilized eggs—somatic cell nuclear transfer Remove genetic material from an egg (its 23 chromosomes) Transplant 46 chromosomes from one specialized adult cell Stem cell technology and somatic nuclear transfer can both be used to make new individuals or simply new cells. Cloning Making a genetically identical copy of an individual Researchers have been creating clones for decades These clones were created by embryo splitting Dolly: Cloned from an adult cell--Somatic nuclear transfer Showed that differentiated cells could be used to create clones Sheep udder cell was combined with enucleated egg cell Dolly is genetically identical to the sheep that donated the udder cell More Clones Mice, Cows, Pigs, Goats, Cats, Guar Major problem with cloning No genetic variation Plant cells clone more easily than do animal cells WHY? Late blight of potato The people of Ireland relied heavily on one variety of potatoes called “lumpers” The vegetatively propagated potatoes were all clones--no genetic variation Late blight of potato A water mold, Phytophthora infestans, infected the island and decimated the entire crop for multiple years 1 million people died from starvation At least 1 million left the island Crops with genetic variation are less vulnerable to changing conditions From DNA to Proteins Chapter 13 13.1From DNA to Proteins Two steps produce all proteins: 1) DNA is transcribed to form RNA Occurs in the nucleus 2) RNA is translated to form polypeptide chains, which fold to form proteins Occurs in the cytoplasm Three Classes of RNAs Messenger RNA (mRNA) Carries protein-building instructions Ribosomal RNA (rRNA) Major component of ribosomes Transfer RNA (tRNA) Delivers amino acids to ribosomes A Nucleotide Subunit of RNA RNA Base Pairing during Transcription As in DNA, Cytosine (C) pairs with Guanine (G) But Adenine (A) pairs with Uracil (U) RNA contains no Thymine (T) Promoter A base sequence in the DNA that signals the start of a gene For transcription to occur an enzyme (RNA polymerase) must bind to a promoter Transcription Adding Nucleotides Transcript Modification 13.2 & 13.3 Genetic Code Codons Nucleotide bases read in blocks of three Code Is Redundant Twenty kinds of amino acids are specified by 64 codons Most amino acids can be specified by more than one codon Six codons specify leucine UUA, UUG, CUU, CUC, CUA, CUG tRNA Structure Ribosomes made of rRNA 13.4 Three Stages of Translation Initiation, Elongation, Termination Initiation Initiator tRNA binds to small ribosomal subunit The complex attaches to mRNA and moves along it to an AUG “start” codon Large ribosomal subunit joins complex Binding Sites on Large Subunit Elongation mRNA passes through ribosomal subunits tRNAs deliver amino acids to the ribosomal binding site in the order specificied by mRNA Peptide bonds form between the amino acids and the polypeptide chain grows Elongation Termination In response to a STOP codon: --mRNA is released from the ribosome --new polypeptide is released --the two ribosomal subunits separate Overview What Happens to the New Polypeptides? Some are used the cytoplasm Others enter the endoplasmic reticulum and are modified 13.5 Gene Mutations Small-scale changes in the nucleotide sequence of a DNA molecule --Base-Pair Substitutions --Insertions --Deletions Frameshift Mutations Insertion Extra base added into gene region Deletion Base removed from gene region Both shift the reading frame Result in many wrong amino acids Mutations in Genes Spontaneous Mutation Rates Average rate for eukaryotes is between 10-4 and 10-6 per gene per generation Only mutations that arise in germ cells can be passed on to next generation Factors that increase rates of mutations Ionizing radiation X-rays Nonionizing radiation UV radiation Alkylating agents Cigarette smoke Mutations Harmful, Neutral, Beneficial Depending on the organism’s environment Studying and Manipulating Genomes Chapter 15 15.5 Genetic Changes Humans have been indirectly modifying the genetics of other species for thousands of years Artificial selection (breeding) of plants and animals Genomics The direct study and manipulationof genes and gene function in humans and other organisms. 15.6-15.8 Genetic Engineering Genes are isolated, modified, and inserted into an organism Made possible by recombinant technology GMO = genetically modified organism Engineered Plants Cotton plants that display resistance to herbicide Aspen plants that produce less lignin and more cellulose Tobacco plants that produce human proteins Mustard plant cells that produce biodegradable plastic Engineered Animals Human genes are inserted into mice to study molecular basis of genetic disorders, such as Alzheimer’s disease Reverse dwarfism in mice Produce fluorescent mice Goats that produce human anti-clotting factors Xenotransplantation Transferring an organ from one species into another Researchers have altered a gene in pigs so that pig organs may not be rejected by the human immune system What about the transfer of viruses across species? Avian flu, swine flu, etc. 15.9 Where Do We Go Now? Can we bring about beneficial changes without harming ourselves or the environment? GMOs as crops Many crops (cotton, soybean, corn) are genetically modified GMOs as crops PROS and CONS Superweeds What if engineered genes escape into other species in natural populations? 15.10 Eugenic Engineering--Human Gene Therapy Selecting “desirable” human traits Who decides what is desirable? Evidence of Evolution Chapter 16 Why study evolution? "Nothing in biology makes sense except in the light of evolution." T. Dobzhansky A unifying principle that explains so many of the “whys” in biology : 1) Why new species originate. 2) Why there is such diversity among living things. 3) Why different species share key characteristics. 4) Why species are adapted their environment. What is evolution? “Descent with modification” 16.1 Early Beliefs, Confounding Discoveries Early Europeans (14th Century) held the Aristotelian belief that each species was perfect and immutable. Discoveries Biogeography Comparative morphology Fossils Biogeography Size of the known world expanded tremendously in the 15th century Discovery of new organisms in previously unknown places could not be explained by accepted beliefs Comparative Morphology Study of similarities and differences in body plans of major groups Puzzling patterns: Animals as different as dolphins and bats have similar bones in forelimbs Some parts seem to have no function How do you explain a snake pelvis, the ankle bones of a whale, or your own tailbone? Fossils Similar rock layers throughout world Certain layers contain fossils Deeper layers contain simpler fossils than shallow layers Some fossils seem to be related to living species 16.2 19th Century - New Theories Scientists attempt to reconcile evidence of change with traditional belief that species are perfect and immutable. Two examples Georges Cuvier - multiple catastrophes Jean Lamarck - inheritance of acquired characteristics Charles Darwin At age 22, Charles Darwin began a five-year, round-the-world voyage aboard the Beagle As the ship’s naturalist he collected and examined the species that inhabited the regions the ship visited Voyage of the Beagle 16.3 Darwin’s Theory Takes Form GALAPAGOS Volcanic islands far off coast of Ecuador Darwin found many new species there that had evolved from continental ancestors Galapagos Finches Darwin observed 13 new species of finches with a variety of lifestyles and body forms He attempted to correlate variations in their traits with the environmental challenges they faced Descent with modification In Argentina, Darwin observed fossils of extinct glyptodonts Glyptodonts resembled living armadillos The Theory of Uniformity Principles of Geology by Charles Lyell Theory of Uniformity--gradual, repetitive processes have shaped the Earth more than rare catastrophes Challenged the view that Earth was only 6,000 years old Malthus - Struggle to Survive Thomas Malthus, a clergyman and economist, wrote an essay that Darwin read on his return to England Argued that as population size increases, resources dwindle, and the struggle to live intensifies Darwin’s Theory of Evolution by Natural Selection A population can change over time when individuals differ in heritable traits that affect the ability to survive and reproduce Alfred Wallace Naturalist who worked in Madagascar Arrived at the same conclusions Darwin did Wrote to Darwin describing his views Prompted Darwin to formally present his work On the Origin of Species Darwin’s book Published in 1859 Detailed evidence supporting evolution and speciation by natural selection 16.4 Fossils Recognizable, physical evidence of organisms that lived in the distant past Direct or indirect evidence Fossilization Organism becomes buried in ash or sediments Rapid burial and a lack of oxygen aid in preservation The organic remains become infused with metal and mineral ions Stratification Fossils are found in sedimentary rock This type of rock is formed in layers In general, layers closest to the top were formed most recently Evidence of Past Life 1700s Excavations unearthed similar fossil sequences in distant places Scholars began to see connections between the Earth’s history and the history of life Fossil record is incomplete Species that had large bodies, hard bodies or parts, dense populations, wide distributions, or persisted for a long time period are over-represented in the fossil record. 16.5 Determining the age of fossils Relative dating—fossils from lower rock layers are older than fossils from higher layers. Absolute dating—using radiometric dating to assign an actual age to a fossil Radiometric Dating Radioisotopes Carbon 14 Uranium 238 Half-life The time it takes for half of a quantity of a radioisotope to decay C-14 = 5,730 years U-238 = 4.5 billion years Radiometric Dating Geologic Time Scale Phanerozoic eon Cenozoic era—primates, horses Mesozoic era—dinosaurs, birds, higher plants Paleozoic era—insects, fish, algae, ferns Proterozoic eon—eukaryotes, oxygen accumulates Archean eon--prokaryotes 16.6 Evidence from Biogeography CONTINENTAL DRIFT Idea that the continents were once joined and have “drifted” apart Initially based on the shapes Pangea: supercontinent Evidence of Movement Glacial deposits Fos Biology1010 16.6 Evidence from Biogeography CONTINENTAL DRIFT Idea that the continents were once joined and have “drifted” apart Initially based on the shapes Pangea: supercontinent Evidence of Movement Glacial deposits Fossils and mineral deposits Magnetic orientation of rocks Discovery of seafloor spreading provided a possible mechanism Plate Tectonics Earth’s crust is fractured into plates Movement of plates is driven by upwelling of molten rock at mid-oceanic ridges As seafloor spreads, older rock is forced down into trenches Forces of Change Gondwana Supercontinent preceding Pangea Same series of glacial deposits, coal seams, basalt, and fossils (seed ferns and land reptiles) are found in distantly separated continents Changing Land Masses 16.7 Evidence from Comparative Morphology Comparing body forms and structures of major lineages Morphological Divergence Change from the body form of a common ancestor Homologous structure—similar body part that occurs in different species as a result of descent from a common ancestor (may serve different functions) Morphological Divergence Morphological Convergence Individuals of different lineages evolve in similar ways under similar environmental pressures Analogous structures—may serve similar functions but are not derived from a recent common ancestor 16.8 Comparative Development Each animal or plant proceeds through a series of changes in form as it develops Similarities in these stages may be clues to evolutionary relationships Mutations that disrupt a key stage of development are selected against Developmental Similarities Proportional Changes in Skull 16.9 Comparative Biochemistry—Best Evidence for Evolution Kinds and numbers of biochemical traits that species share is a clue to how closely they are related Can compare DNA, RNA, or proteins More similarity means species are more closely related Comparing Proteins Compare amino acid sequence of proteins produced by the same gene Human cytochrome c Identical amino acids in chimpanzee protein Chicken protein differs by 18 amino acids Yeast protein differs by 56 Sequence Conservation Cytochrome c functions in electron transport Deficits in this vital protein would be lethal Long sequences are identical in yeast, wheat, and primates Sequence Conservation Nucleic Acid Comparison Use single-stranded DNA or RNA Hybrid molecules are created, then heated The more heat required to break hybrid, the more closely related the species 16.10 Taxonomy Field of biology concerned with identifying, naming, and classifying species Binomial system of nomenclature Devised by Carolus Linnaeus Each species has a two-part Latin name First part is generic (genus) Second part is specific name (species) Higher Taxa Kingdom, Phylum, Class, Order, Family, Genus, Species Phylogenetics The scientific study of evolutionary relationships among species We can learn more about a species by studying its close relatives Six-Kingdom Scheme is Problematic Three-Domain Classification 16.12 Evolutionary Tree of Life Processes of Evolution Chapter 17 17.1 Populations Evolve Biological evolution does not change individuals, it changes a population Heritable traits in a population vary among individuals Individuals better-suited to their environment pass more of their alleles on to the next generation Evolution is the change in allele (gene) frequencies of a population Population and Species Population— A group of individuals of the same species occupying a given area Species— A group of organisms that can interbreed to produce fertile offspring What Determines Alleles in New Individual? Mutation produces new alleles Crossing over at meiosis I Independent assortment Fertilization reshuffle alleles present in a gene pool The Gene Pool All of the genes in the population A genetic resource shared by all members of population Fitness—not just aerobics anymore “Success” in the biological world = FITNESS Passing relatively more genes on to the next generation Well-suited to your environment 17.2 Genetic Equilibrium When allele frequencies are not changing Population is not evolving Genetic equilibrium requires all 5 No mutation No natural selection No sexual selection (random mating) No immigration/emigration No genetic drift No Change through Generations Hardy-Weinberg Rule At genetic equilibrium, proportions of genotypes at a locus with two alleles are given by the equation: p + q = 1 p2 + 2pq + q2 = 1 Frequency of allele A = p Frequency of allele a = q Punnett Square Frequencies in Gametes 17.3 Microevolutionary Processes Drive a population away from genetic equilibrium Small-scale changes in allele frequencies brought about by: Mutation Natural selection Sexual selection (non-random mating) Immigration or Emigration Genetic drift 17.4 Directional Selection Allele frequencies shift in one direction Pesticide Resistance Pesticides kill susceptible insects Resistant insects survive and reproduce If resistance has heritable basis, it becomes more common with each generation Antibiotic Resistance Overuse of antibiotics has led to an increase in resistant forms Most susceptible bacteria die out and are replaced by resistant forms DON’T TAKE AN ANTIBIOTIC IF YOU HAVE A VIRUS (cold or flu) 17.5 Stabilizing Selection Intermediate forms are favored and extremes are eliminated Stabilizing Selection: An Example Disruptive Selection Forms at both ends of the range of variation are favored Intermediate forms are selected against Ex: Black-bellied seedcracker 17.6 Sexual Selection Selection favors certain secondary sexual characteristics Through nonrandom mating, alleles for preferred traits increase Leads to increased sexual dimorphism Balanced Polymorphism Polymorphism - “having many forms” Occurs when two or more alleles are maintained at high frequencies Sickle-Cell Trait: Heterozygote Advantage Heterozygotes develop a more mild form of sickle-cell anemia than do homozygotes (AA) Heterozygotes are more resistant to malaria than homozygotes (aa) 17.7 Genetic Drift Random change in allele frequencies brought about by chance Effect is most pronounced in small populations Computer Simulation Computer Simulation Bottleneck A severe reduction in population size Causes pronounced drift Examples: Elephant seals, Cheetah, Many endangered species, Florida Panther Populations recover faster than genetic variation Founder Effect Effect of drift when a small number of individuals start a new population By chance, allele frequencies of founders may not be same as those in original population Inbreeding Nonrandom mating between related individuals Leads to increased homozygosity Can lower fitness when deleterious recessive alleles are expressed 17.8 Gene Flow Physical flow of alleles in a population Tends to keep the gene pools of populations similar Counters the differences that result from mutation, natural selection, and genetic drift 17.9 Speciation & Species Natural selection can lead to speciation Speciation can also occur as a result of other microevolutionary processes Genetic drift Mutation Morphology & Species Morphological traits may not be useful in distinguishing species Members of same species may appear different because of environmental conditions Morphology can vary with age and gender Different species can appear identical Variable Morphology Biological Species Concept “Species are groups of interbreeding natural populations that are reproductively isolated from other such groups.” - Ernst Mayr If gene flow ends, genetic divergence begins Gene flow keeps two populations from diverging If gene flow stops, differences between gene pools gradually accumulate Natural selection, genetic drift, and mutation can contribute to divergence Reproductive Isolation Cornerstone of the biological species concept Speciation is the attainment of reproductive isolation Reproductive isolation arises as a by-product of genetic change Mechanisms of Reproductive Isolation Pre-zygotic isolation Mating or zygote formation is prevented Post-zygotic isolation Takes effect after hybrid zygotes form Zygotes may die early, be weak, or be sterile Prezygotic Isolation Mechanical Isolation Behavioral Isolation Temporal Isolation Ecological Isolation Gamete Mortality Postzygotic Mechanisms Zygotic mortality Hybrid inviability Hybrid sterility 17.10 Mechanisms of Speciation Allopatric speciation Sympatric speciation Parapatric speciation Allopatric Speciation Speciation in geographically isolated populations Probably most common mechanism of speciation Some sort of barrier arises and prevents gene flow Extensive Divergence Prevents Interbreeding Species separated by geographic barriers will diverge genetically If divergence is great enough it will prevent interbreeding even if the barrier later disappears Allopatric Speciation in Archipelagos Island chains some distance from continents Galapagos Islands (Darwin’s finches) Hawaiian Islands Colonization of islands followed by genetic divergence sets the stage for speciation Volcanic origins, variety of habitats Adaptive radiations: Honeycreepers - In absence of other bird species, they radiated to fill numerous niches Fruit flies (Drosophila) - 40% of fruit fly species are found in Hawaii 17.11 Speciation without a Barrier Sympatric speciation ancestral and derived species share the same range Examples: polyploidy and Cichlids Sympatric Speciation by Polyploidy Change in chromosome number (3n, 4n, etc.) Offspring with altered chromosome number cannot breed with parent population Common mechanism of speciation in flowering plants Sympatric Speciation in African Cichlids Multiple species of African Cichlids evolved in the same lake Parapatric speciation Adjacent populations evolve into distinct species while maintaining contact along a common border Parapatric Speciation Examples: Tasmanian velvet worms, Cottonwoods 17.12 Macroevolution We’re All Related All species are related by descent Share genetic connections that extend back to the origin of life Evolutionary Tree (Phylogeny) A phylogeny is a tree, not a ladder Gradual Model Speciation model in which species emerge through many small morphological changes that accumulate over a long time period Punctuation Model Speciation model in which most changes in morphology are compressed into brief period near onset of divergence Adaptive Radiation Burst of divergence Single lineage gives rise to many new species New species fill vacant adaptive zone Adaptive zone is “way of life” or niche Success may hinge on a “key innovation” Extinction Irrevocable loss of a species Mass extinctions have played a major role in evolutionary history Fossil record shows 20 or more large-scale extinctions Reduced diversity is followed by adaptive radiation Who Survived? Species survival was to some extent random Asteroids have repeatedly struck Earth destroying many lineages Changes in global temperature favored lineages that are widely distributed Human-caused extinctions Since extinction is natural, is there anything wrong with letting endangered species go extinct today? 17.14 Adaptation & the Environment An adaptation is any heritable aspect of form, function, behavior, or development that improves the odds of surviving and reproducing in a given environment Biology1010 The Origin and Early Evolution of Life Chapter 18 18.1 The Big Bang 12-15 billion years ago all matter was compressed into a space the size of our sun Sudden instantaneous distribution of matter and energy throughout the known universe Temperatures dropped billions of degrees Gaseous particles condensed into the first stars The star of our solar system—the sun—formed 5 billion years ago. Earth Forms About 4.6 and 4.5 billion years ago Minerals and ice orbiting the sun started clumping together Heavy metals moved to Earth’s interior, lighter ones floated to surface Produced outer crust and inner mantle First Atmosphere Hydrogen gas Nitrogen Carbon monoxide Carbon dioxide No gaseous oxygen Earth Is Suitable for Life Large enough in diameter to hold onto an atmosphere Close enough to the sun that water is not permanently frozen Far enough from the sun that water doesn’t evaporate entirely Stanley Miller’s Experiment Mixed methane, hydrogen, ammonia, and water Simulated lightning Amino acids and other small molecules formed spontaneously 18.2 Where Did Cells Originate? In areas where spontaneously assembled enzymes, ATP, and organic compounds were in close association Clay flats—contain mineral ions that attract amino acids and nucleotides Hydrothermal vents—oxygen-poor areas with iron-sulfide chambers that favor membrane formation Proto-cells—simple membrane-bound sacs that enclosed metabolic machinery and were self-replicating Have been formed experimentally Possible Model RNA World RNA may have been the first genetic material RNA is more simple than DNA so it likely assembled first However, DNA is more stable and can carry more information so DNA was favored by natural selection. 18.3 First Cells Originated in Archaean Eon (3.8 bya) Were prokaryotic heterotrophs Anaerobic respiration No oxygen present Early Proterozoic Eon Origin of photosynthetic bacteria Oxygen accumulates in atmosphere Origin of aerobic respiration Stromatolites Mats of cyanobacteria (photosynthetic prokaryotes) Abundant 2.7 bya Eukaryotes 2.1 bya 18.4 Eukaryotes have organelles ADVANTAGES: Nuclear envelope may have helped to protect genes from competition with foreign DNA ER may have similarly protected and channeled vital proteins Origin of the nucleus and ER Origin of Mitochondria and Chloroplasts--Theory of Endosymbiosis Mitochondria and chloroplasts are the descendents of free-living prokaryotic organisms Prokaryotes were engulfed by early eukaryotes and became permanent internal symbionts 18.5 Evolutionary Tree Population Ecology Chapter 26 26.1 & 26.2 Population -- A group of individuals of the same species occupying a given area Populations can be described in terms of: Age structure, density, distribution, size These vital statistics are called demographics Population Age Structure Populations divided into age categories Pre-reproductive Reproductive Post-reproductive The reproductive base of a population includes first two categories Density & Distribution Density--number of individuals in some specified area of habitat Distribution—pattern in which the individuals are dispersed Determining Population Size Direct counts are most accurate but seldom feasible Can sample an area, then extrapolate Capture-recapture method is used for mobile species 26.3Changes in Population Size Immigration adds individuals Emigration subtracts individuals Births add individuals Deaths subtract individuals Per Capita Rates Rates per individual Total number of events in a time interval divided by the number of individuals Per capita birth rate per month = Number of births per month / Population size Zero Population Growth When number of births is balanced by number of deaths Population size remains stable r Net reproduction per individual per unit time Variable combines per capita birth and death rates Used to calculate rate of growth of a population Exponential Growth Equation G = rN G = population growth r = net reproduction per individual N = population size Exponential Growth The larger the population gets, the faster it grows J-shaped curve Exponential Growth in Field Mice Effect of Deaths Population will grow exponentially as long as per capita death rates are lower than per capita birth rates Biotic Potential Maximum rate of increase per individual under ideal conditions Varies between species (2% to 5% per year for large mammals) In nature, biotic potential is rarely reached 26.4 Limiting Factors Any essential resource that is in short supply All limiting factors acting on a population dictate sustainable population size Carrying Capacity (K) Maximum number of individuals that can be sustained in a particular habitat Logistic growth occurs when population size is limited by carrying capacity S-shaped curve Logistic Growth As the size of the population reaches carrying capacity, rate of reproduction decreases When the population reaches carrying capacity, population growth ceases Overshooting Capacity Population may temporarily increase above carrying capacity Overshoot is usually followed by a crash; dramatic increase in deaths Density-Dependent Controls Limiting factors become more intense as population size increases Disease, competition, parasites, toxic effects of waste products Density-Independent Controls Factors unaffected by population density Natural disasters affect large and small populations alike 26.5 Life History Patterns Patterns of timing of reproduction and survivorship Vary among species Summarized in life tables and survivorship curves Life Table Tracks age-specific patterns Population is divided into age categories Birth rates and mortality risks are calculated for each age category Life Table for Humans Survivorship Curves Graph of age-specific survivorship Type I large mammals Type II birds, lizards, small mammals Type III invertebrates, fishes, plants, fungi Read 26.6 Excellent example of directional selection 26.7 Human Population Growth Population now 6.5 billion Rates of increase vary among countries Average annual increase is 1.3 % Population continues to increase exponentially Side-Stepping Controls Expanded into new habitats Agriculture increased carrying capacity; use of fossil fuels aided increase Hygiene and medicine lessened effects of density-dependent controls Future Growth Exponential growth cannot continue forever Breakthroughs in technology may further increase carrying capacity Eventually, density-dependent factors will slow growth Population Growth Curve Population growth affects quality of life Resource depletion Competition for services Increased pollution Traffic 26.8 Fertility Rates and Age Structure Total fertility rate (TFR) is average number of children born to a woman Highest in developing countries, lowest in developed countries Fertility Rates Compared Age Structure Diagrams Show age distribution of a population Age Structure Diagrams: 1997 Population Momentum Lowering fertility rates cannot immediately slow population growth rate Why? There are already many future parents alive If every couple had only two children, a population would take 60 years to reach ZPG Slowing Growth in China World’s most extensive family planning program Government rewards small family size, penalizes larger families, provides free birth control, abortion, sterilization Since 1972, TFR down to 1.8 from 5.7 Effects of Economics When individuals are economically secure, they are under less pressure to have large families 26.9 Demographic Transition Model Postulates that as countries become industrialized, first death rates drop, then birth rates drop Demographic Transition Model Resource Consumption United States has 5 % of the world’s population Uses 25 % of the world’s minerals and energy Per capita, Americans consume more resources and create more pollution than citizens of less developed nations Projecting Human Population Size Community Structure and Biodiversity Chapter 27 27.1 Community All the populations of species that live together in a habitat Habitat is the type of place where a species normally lives Habitat type shapes a community’s structure Factors Shaping Community Structure Climate and topography Types of foods and resources available Adaptations of species in community Species interactions Arrival and disappearance of species Physical disturbances Niche—way of life Sum of activities and interactions in which a species engages to secure and use resources necessary for survival and reproduction Fundamental vs. Realized Niches Fundamental niche Theoretical niche occupied in the absence of any competing species Realized niche Niche a species actually occupies Realized niche is some fraction of the fundamental niche Species Interactions Most interactions are neutral; have no effect on either species (0/0) Commensalism helps one species and has no effect on the other (+/0) Mutualism helps both species (+/+) Species Interactions Interspecific competition has a negative effect on both species (-/-) Predation and parasitism both benefit one species at a cost to another (+/-) Symbiosis Close association of two or more species during part or all of the life cycle Commensalism, mutualism, competition, predation, and parasitism are all forms of symbiosis 27.2 Mutualism (+/+) Both species benefit Many examples in nature Some mutualisms are obligatory; partners depend upon each other Lichen Obligatory mutualism between fungi and algae Fungus supplies anchorage and water retention Alga supplies photosynthate Mycorrhizae Obligatory mutualism between fungus and plant root Fungus supplies mineral ions to root Root supplies sugars to fungus Yucca and Yucca Moth Obligatory mutualism Each species of yucca is pollinated by only one species of moth Moth larvae can grow only in that one species of yucca 27.3 Competition (-/-) Interspecific - between species Intraspecific - between members of the same species Intraspecific competition is most intense Competitive Exclusion When two species compete for identical resources, one will be more successful and will eventually eliminate the other Competitive Exclusion Expt Resource Partitioning Apparent competitors may actually have slightly different niches Species may use resources in a different way or time Minimizes competition and allows coexistence 27.4 Predation (+/-) Predators are animals that feed on other living organisms Predators are free-living; they do not take up residence on their prey Coevolution Natural selection promotes traits that help prey escape predation It also promotes traits that make predators more successful “Arms race” between predators and prey Predator and Prey Populations are related Multi-level interactions Carnivore-Herbivore-Plants 27.5 Evolutionary Arms Race PREY DEFENSES Camouflage Warning coloration Mimicry Chemistry Predator Responses Any adaptation that protects prey may select for predators that can overcome that adaptation Predator adaptations include stealth, camouflage, and ways to avoid chemical repellents 27.6 Parasitism (+/-) Parasites drain nutrients from their hosts and live on or in their bodies Natural selection favors parasites that do not kill their host too quickly Biological Controls Parasites are commercially raised and released in target areas as biological controls An alternative to pesticides Must be carefully managed to avoid upsetting natural balances 27.7 Skip 27.8 & 27.9 Succession Change in the composition of species over time Pioneer Species Species that colonize barren habitats Lichens Annual plants Grow well in sunny and dry conditions Have many offspring, opportunistic, “weedy” Improve conditions for other species that replace them (N-fixing) Climax Community Stable array of species that persists relatively unchanged over time Succession does not always move predictably toward a specific climax community; multiple stable communities are possible Keystone Species A species that can dictate community structure Removal of a keystone species can cause drastic changes in a community; can increase or decrease diversity Wolf-Elk-Aspen 27.10 Exotic Species Species that has become established outside of its natural home range Becomes part of a new community Exotic Species Introductions Introduction of a non-indigenous (non-native) species can be accidental or intentional EXOTIC SPECIES: Have no natural enemies or controls Can outcompete native species Kudzu in SE United States Tree-of-heaven in Turlock 27.11 Biodiversity The sum of all species occupying a specified area during a specified interval Patterns of Diversity:Latitude Diversity of most groups is greatest in tropics; declines toward poles a) ants b) birds Why are the Tropicsspecies rich? More sunshine, more rain, longer growing season--resources are plentiful and reliable Tropical species have been evolving for a longer period of time than temperate species Species diversity is self-reinforcing 27.12 Endangered Species A species that is extremely vulnerable to extinction Habitat loss is the major cause of species endangerment and extinction Endangered Species Recovery Program at CSU Stanislaus http://esrp.csustan.edu/ San Joaquin kit fox, Riparian brush rabbit, California jewelweed, Kern mallow Indicator Species Types of species that may warn of impending loss of biodiversity Birds, amphibians 27.13Conservation Biology Study of biological diversity Methods of preserving biodiversity Ways to utilize biodiversity sustainably 27.13 Preserving Biodiversity Requires identifying and protecting regions that support the highest levels of biodiversity It is possible to protect a habitat and still withdraw resources in a sustainable way Areas at Risk Ecosystems Biology1010 Chapter 28 28.1 Ecosystem An association of organisms and their physical environment, interconnected by a flow of energy and a cycling of raw materials Modes of Nutrition Autotrophs Capture sunlight or chemical energy Producers Heterotrophs Extract energy from other organisms or organic wastes Consumers Simple Ecosystem Model Trophic Levels Food Chain A straight line sequence of who eats whom Simple food chains are rare in nature Food Web 28.2 & 28.4 Energy Losses Energy transfers are never 100 percent efficient Some energy is lost at each step Limits the number of trophic levels in an ecosystem Biomass Pyramid Energy Pyramid Primary producers trap about 1% of the solar energy that enters an ecosystem Only ~10% is passed on to next level All Heat in the End At each trophic level, the bulk of the energy received from the previous level is used in metabolism This energy is released as heat energy and lost to the ecosystem 28.3 Biological Magnification A nondegradable or slowly degradable substance becomes more and more concentrated in the tissues of organisms at higher trophic levels of a food web Ex: DDT and Mercury DDT in Food Webs Synthetic pesticide used in the US before the 1970s Birds that were top carnivores accumulated DDT in their tissues A side effect of DDT is brittle egg shells Rachel Carson Author of “Silent Spring” (1962) Awakened public interest in limiting the use of pesticides 28.5 Biogeochemical Cycles The movement of an element from the environment to living organisms and back to the environment Main reservoir for the element is in the environment 28.6 Water Cycle Watershed Any region where precipitation flows into a single stream or river. Ex: Mississippi, Amazon, San Joaquin Aquifer Underground layer of rock that contains water (groundwater) Aquifer Depletion Salinization A build up of salt in the soil as irrigation water evaporates Can stunt plant growth and decrease crop yields 28.7 Carbon Cycle Carbon moves through the atmosphere and food webs on its way to and from the ocean, sediments, and rocks Sediments and rocks are the main reservoir Carbon Cycle Carbon in Atmosphere Carbon dioxide is added to atmosphere Aerobic respiration, volcanic action, burning fossil fuels Removed by photosynthesis—plant a tree. 28.8 Greenhouse Effect Greenhouse gases impede the escape of heat from Earth’s surface Ex: Carbon dioxide, CFCs, methane, nitrous oxide Carbon Dioxide Increase Carbon dioxide levels fluctuate seasonally The average level is steadily increasing Burning of fossil fuels and deforestation are contributing to the increase Other Greenhouse Gases CFCs - synthetic gases used in plastics and in refrigeration Methane - produced by termites, bacteria, and livestock Nitrous oxide - released by bacteria, fertilizers, and animal wastes Greenhouse Gases Global Warming Long-term increase in the temperature of Earth’s lower atmosphere Effects of Global Warming As polar ice and glaciers melt, sea levels rise Effects of hurricanes and storms worsen Evaporation rates increase causing climate change (floods and droughts) 28.9 Nitrogen Cycle Nitrogen important to form amino acids and nucleotides Main reservoir is nitrogen gas in the atmosphere (N2) N2 can’t be used directly by plants Nitrogen must first be fixed into useable forms Nitrogen Fixation Volcanic action, lightning, and nitrogen-fixing bacteria convert nitrogen gas into ammonia (NH3) N2 NH3 Nitrogen Cycle Human Effects Humans increase rate of nitrogen loss by clearing forests and grasslands Humans increase nitrogen in water and air by using fertilizers and by burning fossil fuels Resulting nitrogen oxides are air pollutants that cause acid rain. 28.10 Phosphorus Cycle Phosphorus is part of phospholipids and all nucleotides Often a limiting factor in ecosystems Main reservoir is Earth’s crust; no gaseous phase Phosphorus Cycle Human Effects In tropical countries, clearing lands for agriculture may deplete phosphorus-poor soils In developed countries, phosphorus runoff is causing eutrophication (nutrient-enrichment) of waterways 29.2 Air pollution in the San Joaquin Valley Air pollution POLLUTANT substance that has accumulated in harmful or distruptive amounts Air Pollutants Carbon oxides Sulfur oxides Nitrogen oxides (NOx) Volatile organic compounds (VOCs) Particulate Matter (PM) Ozone Particulate Matter (PM) PM2.5 and PM10 based on the particle diameter (µm) May be directly emitted as dust or soot May form in the atmosphere from other compounds Particulate Matter Problematic in winter Worst at night or in early mornings Woodburning stoves and fireplaces In the winter up to 30% of the PM in the valley comes from woodburning. A natural gas fireplace is 300x less polluting than wood. Ozone Not directly emitted Forms when industrial and vehicular emissions (especially NOx and VOCs) react in sunlight Problematic in the summer Worst in the afternoon and evening Carpool, bus, or bike to work/school Use electric lawn mowers and tools Use gas grills instead of briquettes Choose non-motorized recreation Health impacts of PM and Ozone in one year 460 premature deaths 260 hospital admissions 23,300 asthma attacks 325 new cases of chronic bronchitis 3,230 cases of acute bronchitis in children 17,000+ days of respiratory symptoms in children 188,400 days of reduced activity in adults Economic Impacts Air pollution costs the valley $3 billion/yr. ($1,000/person/yr.) In addition to health impacts 188,000 days of school absences 3,000 lost work days Jane V. Hall et al. (2006) CSU Fullerton Valley’s poor air quality Many factors contribute: How bad is it? www.airnow.gov www.valleyair.org Air Quality Index Which cities have the worst air in CA? www.epa.gov/air/data/ Compared to the SJ Valley: Los Angeles area produces 10x the air pollution per square mile. LA’s air is only slightly worse than ours. Compared to the SJ Valley: Bay area produces 6x the air pollution per square mile. Bay area’s air quality is much better than ours. Good news (1990-2005) Attainment of federal standards for PM10 Reduced by 13% Improvement in PM2.5 levels Reduced by 10% Improvement in ozone levels 82% reduction in the number of days violating the standard 21% reduction in the peak concentration So what can we do? Biology1010:Origin and Early Evolution of Life on Earth Some key words, phrases, and ideas : science vs pseudoscience vs not science natural forces vs supernatural forces species--definitions and Latin bionomials Lamarckian evolution vs Darwinian evolution Oparin-Haldane model; Urey-Miller experiment RNA/protein-based metabolism Eubacteria vs Archaea vs proto-Eucarya chemoheterotrophy vs chemoautotrophy vs photoautotrophy fermentation vs anaerobic respiration vs aerobic respiration; membrane-bound electron transport chains anoxygenic photosynthesis vs oxygenic photosynthesis Introduction basic questions for the course What is a species? How many species are there? Where did they all come from? How do they interact with each other and with the environment? early approaches Plato and Aristotle--ideals, the scalae naturae, and special creation Linnaeus--Latin binomials, heirarchy based on structural relationships New questions: What do these relationships mean? What are fossils and what does the fossil record mean de Buffon--centers of creation; still not scientific and does not explain fossil scientific approaches What is science? How is the scientific approach different from other approaches? Hutton and Lyell and the age of the Earth Lamarck and the theory of evolution by acquired characteristics based on the changes seen in the fossil record of a certain group of snails basic mechanism: individuals develop needed traits, lose unnecessary or unused traits changes made in parents are passed along to offspring rejected at first because the idea of evolution was not accepted, later because no known force to account for the development of needed structures in a way that can be inherited by offspring (note: many educated people believe in Lamarckism without realizing it) Darwin used his own observations of relatedness, plus Hutton''s and Lyell''s interpretation of the geologic record, plus Malthus''s ideas concerning the growth of populations to develop a theory of evolution by means of natural selection basic mechanism more offspring are born than will reached maturity--losses caused either by limited resources or by predation (superfecundity and the struggle for existence) while on average offspring are the same as their parents, there is a great deal of genetic variability within a family or species (individual variation and heredity) some of that genetic variability gives organisms a better chance to reproduce (better competitors or better at avoiding predators or something along those lines) a greater proportion of the next generation is born of parents with the "good'' variation, with a better chance at surviving and reproducing so that adaptive traits tend to accumulate within a population tests of the theory the fossil record supports the idea of evolutionary change comparative anatomy (homologous structures) indicates relationships among existing organisms comparative embryology indicates relationships among organisms comparative mlecular biology indicates relationships among organisms Haldane and others provided the means to test evolution on the microscale new problem: What is the source of genetic variation? initially much confusion between genetic and acquired variability and about how the variability is passed on Mendel''s work with pea plants helped, but was ahead of its time; needed evidence from microscopy to support his views Griffith discovered that traits could be passed from bacterium to bacterium (even if dead), implying that traits are carried by particular chemicals; Avery demonstrated that the chemical involved was DNA; Watson and Crick showed how DNA could work as genetic material; we are now able to manipulate DNA to create new variants Earth''s earliest biosphere sources of information structure of the solar system, composition of meteorites geologic history of Earth (times based on layering in sedimentary rocks and radioisotope dating of the rock material) Hadean (4,500 mya to 3,800 mya) -- formation of the Earth, solidification of the crust Archean (3,800 mya to 2,400 mya) -- beginnings of life on Earth Proterozoic (2,400 mya to 550 mya) -- rise of oxygen in the atmosphere, advanced unicellular life on Earth Paleozoic (550 mya to 245 mya) -- early development of multicellular life Cambrian (to about 500 mya) Ordovician (to about 440 mya) Silurian (to about 410 mya) Devonian (to about 360 mya) Carboniferous (to about 290 mya) Permian (to about 245 mya) Mesozoic (245 mya to 65 mya) Triassic (to about 210 mya) Jurassic (to about 140 mya) Cretaceous (to about 65 mya) Cenozoic (65 mya to present) Tertiary (to about 2 mya) Quaternary (to recent times) the biological record: fossils, comparative anatomy and development, comparative molecular biology DNA-DNA hydridization gene sequencing origins origin of the Earth (Hadean period) orgins of life on Earth What constitutes life on Earth? basic features of all life: organization, series of chemical reactions (metabolism), reproduction and growth (genetic machinery), responsiveness and homeostasis features of life on Earth: cellular structure, genetic material consisting of double-stranded DNA, metabolic machinery involving proteins and RNA How did life begin on Earth? early conditions: atmosphere of CO2, N2, H2O, some NH3 and CH4, no O2; the lack of free oxygen may have been crucial build-up of organic molecules led to the formation of a fiarly concentrated primordial soup according to the Oparin-Haldane model, chemical reactions in the atmosphere caused the formation of the more complex molecules (sugars, amino acids); Urey-Miller experiment demonstrated the possibility of forming such molecules in simple systems others, citing problems with the gas mixtures in the Urey-Miller experiment, suggest that precursors molecules were made in deep-sea systems similar to vents in existence today still others contend that the precursors were formed in deep space and came to Earth in comets and meteorites molecules in the primordial soup spontaneously formed more complex structures (proteinoids?, coacervate droplets?) self-replicating structures formed nucleic acids? a quick review of nucleic acids an RNA world? can self-replicate in test-tube can function as organic catalyst somehow became the template for protein production (message, ribosomes, transfer system for amino acids) clay? somehow, the complex structures and the self-regulating structures formed a living structure boundary (this is where proteinoids and droplets come in) metabolic machinery involving enzymes whose formation is directed by RNA energy storage in ATP genetic system to pass information along to the next generation Could this process have been repeated (started) elsewhere in the Solar System? Venus -- probably too hot now and before, closer to the Sun and with a thick CO2 atmosphere Mars -- now too cold and dry, lacking an atmosphere; in the past more similar to Earth so possible; some claim structures found in a meteorite (AH 84001) thought to have originated on Mars are fossils Jupiter, Saturn, and the other gas giants -- no surface, no liquid water moons of the gas giants Europa (Jupiter) Titan (Saturn) life in the Archean hypothesized structure of early cells cell membrane of phospholipids and proteins DNA-based genetics protein synthesis using ribosomes, tRNA (genetic code) chemoheterotrophic metabolism (fermentation) anaerobic division into distinct lineages (domains of life) Eubacteria Archaea proto-Eukaryotes features and evolution of life in the Archean using Eubacteria as an example cell structure genetic material packaged into a nucleoid (bundled DNA) metabolic machinery based on proteins and RNA (more or less standard; slight differences between eubacterial systems and systems in other domains are the basis of selective antibiotics ) cell membrane of phospholipids and proteins (more or less standard) some have complex internal membrane systems to help compartmentalize photosynthesis most have an outer wall containing the peptidoglycan (rigid material of sugar and small proteins) Gram-positive vs Gram-negative walls functions of walls important metabolic features (in the context of the evolution of life) anaerobic vs aerobic chemoheterotroph vs chemoautotroph vs photoautotroph electron-transport chains fermentative vs respiratory heterotrophs non-oxygenic vs oxygenic photoautotrophs nitrogen fixation importance of bacteria in human affairs decomposition sewage treatment primary treatment secondary treatment: sludge digestors/bioreactors; BOD reduction tertiary treatment toxic waste clean-up oil-spills nutrient cycling bacteria-induced redox reactions change solubility of metal ions iron and manganese nodules gold? nitrogen-fixation chemical and food production disease agents types of disease infectious vs non-infectious; contagious viral vs bacterial vs eukaryotic symptoms vs disease Koch''s postulates if the putative pathogen is present in all hosts with the disease; and if it can be isolated and cultured; and if it causes the disease when introduced into a healthy host; and it can be reisolated from the now infected host after the disease develeps then the organism is probably the cause of the disease evolution of bacteria sources of variation mutations conjugation transduction transformation hypothesized pattern of evolution anaerobic respiration (electron-transport chains) chemoautotrophy anoxygenic photoautotrophy -- purple-sulfur bacteria and others nitrogen-fixation oxygenic photoautotrophy (chlorophyll-based photosynthesis) -- cyanobacteria evolution of oxygenic photosynthesis -- the end of the Archean Experimental Biology BSC 3402L Table of Contents Chapter 1 Introduction to Experimental Biology 4 Chapter 2 What is Science? 5 Chapter 3 Plant Reproductive Biology 9 Chapter 4 Pollen Vectors and Pollination Syndromes 16 Chapter 5 Foraging Ecology of Pollinators 26 Chapter 6 Experimental Design and Data 31 Chapter 7 Statistics--Distributions and Differences Between Means 37 Chapter 8 Statistics--Measures of Association 44 Chapter 9 Using the Library and Biological Literature 51 Chapter 10 Scientific Communication Proposals 55 Chapter 11 Scientific Communication Papers and Presentations 60 Chapter 12 Lab Exercise - Floral Morphology and Pollination Systems 65 Chapter 13 Lab Exercise - Costs and Benefits of Foraging 71 Chapter 14 Selected References on Pollination Ecology 77 Appendix 1 Hazards of the Wild 81 Appendix 2 Statement of Voluntary Consent http://educationally.narod.ru/linksexbio.html