Energy: Life requires energy transfer and transformation. Work requires a source of energy.

Energy can be stored in different forms, like light, chem, kinetic, or thermal. Energy flows through an ecosystem. Structure and Function: The form always fits the function. Biological structure can provide clues to the function. Knowing the function can provide insight into the biological structure. Cell: Basic unit of life. All cells are enclosed by a membrane, use DNA as their genetic info, and use ATP to do cellular work. Ability of cells to divide is the basis of all repro, growth, and repair of multicellular organisms. Inheritance of DNA: Chromosomes: Contain most of a cells genetic material in the form of DNA Genes: smaller portion of chromosome actually holds the info in it. 6billion base pairs of DDNA, about 25000 genes, about 75000 proteins. Feedback regulation mechanisms: Many biological processes have self regulation feedback mechanisms. There is negative and positive feedback. Evolution: Vast diversity of past and present organisms, but living things shares certain features. Common ancestor? I think so! Descent with modification.

Biology Notes Themes

September 11, 2012 Scientific Method and Experimental Design: What is the Scientific Method? Observation: Question: Hypothesis: Experiment: Collect/Analyze Data: 1, or 2 1) Reject or Refine Hypothesis: Faulty Experiment 2) Hypothesis could be right

Qualitative: Recorded Descriptions Quantitative: Recorded numbers Inductive Reasoning: uses specific observations to construct general scientific principles (hypothesis formation) Deductive reasoning: applies general principles to predict specific results (hypothesis testing) Hypothesis: Proposed explanation Must be both testable and falsifiable. Cannot address supernatural events. Scientific Theory A model, which has been born out of a hypothesis or group of hypotheses that have been supported by repeated testing. Broader in scope than a hypothesis allowing for other more specific hypotheses to be developed Ex: H. Pylori and the bacterial theory of ulcers. Experiments: sets of actions or observations designed to test specific hypotheses Variables: factions that can change in value under different conditions Independent Variables: can be manipulated by the scientist Dependent Variable: cannot be manipulated by scientist Experimental Design is important. Are there proper controls? Are the experiments repeatable? Were there enough subjects studied to make meaningful conclusions. Clinical Trials Random Assignment: Individuals are randomly assigned to experimental and control groups. Blind Experiment: Subjects are not aware of their assigned treatment in order to avoid subject expectation. Double Blind: Neither person who is administrating nor the patient who is receiving knows who is receiving what treatment. Cant prove hypothesis but can give reasons and examples to support it. Independent Variable: Talking to them. Dependent Variable: How much they grow. Variables: water, sunlight, fertilizer, type of plant. Experiment: used a lot of plants. A well-designed experiment must have Independent variable

Dependent variable Appropriate controls Same conditions Accurately reflects the population Random assignment Be repeatable Eliminate bias Be ethical

Ethics in Science Honesty Do not fabricate, falsify, or misrepresent the data, the science is the science. Objectivity Avoid bias in experimental design, data analysis, and data interpretation and peer review Carefulness Carefully and critically examine your own work and work of peers. Animal Care Show proper respect and care for animals when using them in research. Do not conduct unnecessary or poorly designed animal experiments. Human Subjects Protection Minimize harms and risks and maximize benefits; respect human dignity, privacy, and autonomy Responsible publication

Science and Worldviews What is Worldview? Worldview: A set of presuppositions (assumptions which may be true, partially true or entirely false), which we hold (consciously or subconsciously) about the basic makeup of our world. May or may not be consistent We may or may not act consistently on them. We interpret what we see, evaluate events, and use it to guide making choices. What are the general domains of a worldview? 1. God 2. Ultimate Reality 3. Knowledge 4. Ethics 5. Humankind

9/13/12 Evolution Controversy It is controversial because it causes questions to arise about who created the world and how it came to be. Bio evolution: Change in the characteristics of a population. o Due to inheritance genes o This is heritable, not environmental. Occurs over the course of generations. Result of natural selection. Natural Selection Process by which individuals with certain traits have greater survival and repro than individuals who lack these traits Results in an increase of successful traits and decrease in harmful ones. Based upon Individuals within a population vary Some of the variation among individuals can be passed on to their offspring Population of organisms produce more offspring than will survive. Survival and reproduction are not random. The four elements of Natural Selection are; 1. All populations have genetic variation. 2. The environment presents challenges to successful reproduction. 3. Individuals that are better able to cope with the challenges presented by their environment tend to leave more offspring than those individuals less suited to the environment. 4. Individuals tend to produce more offspring than the environment can support. Survival and repro are not random Fitness o The relative survival and reproduction of 1 variant compared to others in the same population. Adaptations o Traits that increase and individuals fitness in a particular environment These are selected for Individuals that possess theses survive and contribute. Adaptations become more common to a population. Natural selection results in a change in the traits of individuals of a population. Individuals do not evolve. The population evolves.

Two words that are not involved in natural selection are want and need. The trait that it has either provides success or it dies off. Artificial Selection We figured out how to do artificial selection before we knew what it scientifically was. Natural Selection in the Human Population: CCR5 delta32 Gene that provides resistance against the plague Also provides resistance to HIV infection. Microevolution vs. Macroevolution Microevolution: Changes within a species Macroevolution: Changes resulting in a new species Both are related to natural selection. Principle to understand how species originate. All species present on Earth today are descendants of a single common ancestor, and all species represent the product of millions of years of accumulated micro evolutionary changes. Charles Darwin Darwin served as the Naturalist on the HMS Beagle from 1831-1836. Duties involved collecting plants, animals, and fossils and making observations and comparisons from place to place. His books shifted ruling paradigm in bio from Natural Theology to Evolution. Descent with modification. Evidence: Anatomical Similarities Between species. Vestigial Traits in Modern species. Shared developmental pathways DNA Similarities o All forms of life use DNA and RNA as the genetic language o All forms of life use protein to enact the function Distribution of Organisms on earth (biogeography) The fossil record. Young Earth Creationists Historical-literal interpretation of Genesis Say that earth is young Accept microevolution Reject stuff Progressive Science and bible live in harmony Reject evolution

 Accept microevolution Accept fossil record Evolutionary Creationists The books complement each other Say earth is old Accept microevolution Accept fossil record Accept common ancestry Accept the theory of evolution. Biochemistry: Cellular Organization. Cell is the basic unit of life. Elements: a substance that cant be broken down by chemical reactions. Atom: smallest amount of an element you can have while still maintain the properties of that element. Atomic # = number of protons Mass # = protons + neutrons Isotopes (of an element): same # of protons, different # of neutrons. Molecule = two or more atoms bonded together Compound = a molecule of two or more different elements together. Number of valence electrons in an atom gives atom its ability to react with other atoms to form molecules. 1st shell 2 electrons 2nd shell 8 electrons 3rd shell 8 electrons Atoms with filled valence shells do not like to make compounds Unreactive Halogens Atoms may share electrons in order to completely fill valence shells. Atoms may donate or receive. Receiving them makes them reduced Getting makes them oxidized If one element is more electronegative then the other, results in polar covalent bonds. If electrons are equally distributed, then it is nonpolar. Ions: a charged (non-neutral) atom Water is excellent solute due to its polarity. Noncovalent attraction between hydrogen and an electronegative atom Permanent dipole Van der Waals interactions: interaction of temporary and induced dipoles caused by movement of electrons. Temporarily happening

September 18, 2012 Review: A population of head lice is resistant to lice shampoo. Why? 1) Individuals vary (resistance v nonresistance) 2) Trait resistance can be passed down 3) Some offspring will die. 4) Only those with the resistant trait survive and reproduce. Chemical Reactions Matter is not created or destroyed, but rearranged. Breaking a bond releases energy. Forming a bond requires energy. Chemical Reactions are reversible. Hydrophilic Water loving Substance has an affinity for water Polar and Ionic Can be hydrophilic with out dissolving Very large molecules Hydrophobic Water fearing Repel water Substance does not have and affinity for water Nonpolar and nonionic Vegetable oil. Oxygen is prevalent because cells are 70-95% water. Carbon is unique because its valence shell, which can make four different types of bonds. It can create several types of bonds. Length Double bonds Branching Presence of Rings Hydrocarbon: just carbons and hydrogens. Isomers Same molecular formula bud different structures and properties. Structural: differences in covalent arrangements of atoms. The longer that they are, the more you can have. Cis-trans: Differ in arrangement about a double bond. Cis: they are on the same side Trans: they are on opposite sides (Geometric isomers)

Enantiomers: differ in spatial arrangement and are mirror images of each other. Usually one enantiomer is biologically active. Carbon: The backbone of life Proteins, carbohydrates, nucleic acids, lipids, are all molecules that distinguished living matter is all composed of carbon Hydrocarbon Functional groups Impacts molecular shape Component involved in chemical reactions Gives molecule its functional properties Denoted by R P.64-65 The Molecules of Life Carbohydrates: water-soluble sugars that are used for energy and structure. Simple sugars (monosaccharaides) have a ration of one C to two H to one O. They are water soluble because of their polarity. Types include disaccharides and polysaccharides Functions: Energy: Simple sugar glucose fuels cellular respirations. Storage: Polysaccharide starch can be broken down by saliva to glucose. Storage in plants The polysaccharide glycogen is used by humans to store as glucose Structure: The polysaccharide cellulose is the structural molecule of plant cell walls. The polysaccharide chitin is the structural molecule of the external skeletons of insects, spiders, and lobsters Nucleic Acid: Hereditary information that is inherited from parents blue prints of the cell. It is made up of nucleotides. Nucleotide: sugar, phosphate, and nitrogen-containing base. Deoxyribonucleic acid (DNA) primary storage of genetic information Ribonucleic acid (RNA) helps to synthesize proteins. A and G are Purines. T and C are pyrimidine DNA is double stranded and forms a double helix. Complementary base paring Antiparallel strands (going in opposite directions of 3-5) DNA -> RNA -> Protein Differences between DNA and RNA DNA: Double Stranded, Uses thymine RNA: Single Stranded, uses Uracil DNA codes for proteins, Transcriptions and translation Protein: Large molecules made of monomer subunits called amino acids. There are 20 amino acids. Polymers of amino acids can be joined together in polypeptides (joined

through covalent bond called a peptide bond). Precisely folded polypeptides produce proteins (affected by the amino acid side group) Acid can donate H+, and basic can accept H+. Particular sequence of amino acids determines: Shape of protein Specialized chemical properties. Four levels of protein folding -Primary Structure Amino acid sequence -Secondary Structure Regions stabilized by hydrogen bonding. Forms alpha helix (coiled) or beta pleated sheets. -Tertiary Structure 3D shape stabilized by interactions between side chains. -Quaternary Structure Multiple polypeptides associate to form the functional protein. Protein Folding Denaturation: the unfolding of a protein so it no longer works Renaturation: folding to a normal folding protein. Environment is also key to folding pH, salt, temperature, solvent, etc. A denatured protein is inactive. Chaperonins: helps with folding of protein, by allowing for a suitable environmental environment for the protein to fold. Protein Function: Enzymatic proteins: speeding up reactions Defensive proteins: specific to different targets, anti bodies Storage proteins: store amino acids, etc. Transport Proteins: cell membrane transport Hormonal proteins: nuff said Receptor proteins: pick up chemical stimuli Contractile and motor proteins: allows for muscles to work Structural proteins: provides structure. Can one Amino acid make much of a difference? Yes. An example is sickle cell anemia. One nucleotide change in the DNA sequence leads to the change in amino acid. Lipids: Not true polymers. Composed mostly of hydrocarbons (hydrophobic) Functions include insulation, padding, energy storage, hormones, and cell membranes. Three types: Fats and oils, steroids, and phospholipids. Fats: a glycerol molecule and three long fatty acid tails. Function in energy storage. Saturated fats have only single bonds. Unsaturated fats have double bonds. SF: raises LDL lipoprotein, raise HDL lipoprotein. USF: improves blood cholesterol. Hydrogenation: performed by manufacturers. Increases saturation, longer. Partially Hydrogenated fats: Raises bad LDL cholesterol, lowers good HDL cholesterol.

Phospholipids: similar to fats, only two fatty acids, phosphate group. Important component of cell membranes. The head of the molecule is hydrophilic, and the tail is hydrophobic. Creates plasma membrane with lipid bilayer. Steroids: Composed of 4 fused carbon containing rings. Cholesterol. Monomer: smallest unit of molecule Polymer: a bunch of monomers. Dehydration (condensation reactions): dehydrations remove a water molecule, forming a new bond. Hydrolysis: add water to a molecule to break a bond. BOTH REQUIRE ENZYMES! SUMMARY AT THE END OF CHAPTER 5, LOOK IT OVER!

9/20/12 ENZYMES! Larger macromolecules may be torn down into smaller molecules through chemical reactions Releases energy These reactions are spontaneous and exergonic Building macromolecules necessary for cell function involves lots of chemical reactions Anabolic reactions-builds things Biosynthetic pathways It also takes a lot of energy These reactions are nonspontaneous and endergonic. Energy The capacity to cause change. Exits in various forms a can be converted from one to another. Laws of Energy Transformation THERMODYNAMICS 1) Energy can be transferred and transformed but cannot be destroyed 2) Energy energy transfer or transformation increases the entropy of the universe. Spontaneous no input of energy, and increases entropy If final energy is lower than initial energy, it will have a negative change in energy. Less free energy is a more stable product. G<0 DeltaG = final state initial state DeltaG = DeltaH TdeltaS ATP Powers Cellular Work Uses energy coupling Uses an exergonic process to drive and endergonic process

Metabolism All of an organisms chemical reactions Emergent property: results from interaction of all cells. Metabolic pathways Catabolic Anabolic Spontaneous chemical reactions may occur so slowly as to be imperceptible Enzymes: macromolecules that act as a catalysts, speed up the rate of a reaction with out being consumed by the reaction. Lower the activation energy required. Proteins (ase) Speed up (catalyze) the rate of reactions Lower the amount of activation energy needed for reaction Function in both catabolic and anabolic reactions. Substrate specificity of enzymes Each enzyme has a specific substrate on which it acts. Induced fit: as a substrate binds, the enzyme tightens around it for a better fit. When the enzyme is saturated with substrate then it will not be able to work any faster. Cofactors Non-protein enzyme helpers Cofactors may be inorganic or organic An organic cofactor is called a coenzyme Coenzymes include vitamins With presence of cofactor, it is now called a holoenzyme Inhibitors Competitive Inhibition: a competitive inhibitor mimics the substrate competing for the active site. Non-competitive: it distorts the shape of the enzyme. FEEDBACK INHIBITION: the end product of a metabolic pathway shuts down the pathway. Feedback inhibition prevents a cell from wasting chemical resources. Digestive Enzymes Metabolic Dna replication Gene Expression Cellular respiration. What happens when enzymes dont function properly? Lactose Intolerance: inability to digest lactose because lacking the enzyme lactase. Metabolism.

Sickle cell anemia incidences General Population 8 in 100,000 has it. As an evolutionary adaptation Two copies of the mutation are required for sickle cell disease Individuals that are carriers have only one copy of the disease. Cell Theory Developed as a result of the microscope First invented in 1590-1595, refined through out the 17th cent Robert Hooke 1665 (dead cells) Leeuwenhoek 1674 (living cells) Schwann (& Schleiden) Proposed 2 of 3 tenets of modern cell theory 1) Cell is the unit of structure, physiology, and organization in living things. 2) The cell retains a dual existence as a distinct entity and a building block of the construction of organisms Rudolph Virchow 3) New cells are produced from pre-existing cells. 2 Kinds of Cells Prokaryotes: No nuclei, no membrane bound organelles, smaller then eukaryotic cells, unicellular, has a cell wall, bacteria Eukaryotes: Nucleus, Membrane bound cells, bigger, unicellular or multicellular, may have a cell wall, all other organisms. Both: cytoplasm, plasma membrane, DNA/ RNA, use ATP to do cellular work. Plasma Membrane: Membrane is fluid structure with mosaic of various proteins embedded in it. Fluid Mosaic Model: Phospholipid bilayer. Also contains proteins. Amphipathic: Hydrophobic portions, hydrophilic portions. *Freeze fracture: freeze the cell, cut through and split off. Anchors: maintain and stabilize cell shape Identifiers: allow cell to be recognized by membrane proteins of other cells Receptors: changes the junction of a cell Joiners Forms junctions with others Enzymes: facilitates metabolic pathway Transporters: allows passage or shuttle of particular molecules. Fluidity of the Membrane Phospholipids in the plasma membrane can move with in the bilayer. Most lipids, and some proteins, drift laterally

September 25, 2012

Rarely does a molecule flip-flop transversely across the membrane. Selective Permeability of the Membrane Hydrophobic core of the membrane impedes the movement of ions and polar molecules. Transport Proteins Allow passage of hydrophilic substances across the membrane Specific for the transport of a particular molecule Channel proteins have a hydrophilic channel that certain molecules are able to use as a tunnel Carrier proteins bind to molecules and change shape to transport them through Passive Transport Movement across a membrane with now energy investment 3 Types: Diffusion: A tendency for molecules to move out evenly into the available space. Occurs down a concentration gradient (no work required) Facilitated Diffusion: Diffusion aided by transport proteins, no energy required because movement is down the concentration gradient. Osmosis: Diffusion of water across a selectively permeable membrane, from regions of lower solute to higher solute. Osmosis Hypotonic: more solutes inside of the cell then in the environment (good for plant cells, bad for animal cells [they lyse]) Hypertonic: more solutes outside of cell then in the environment (animal cell can survive, plant cell gets plasmoylized) Active Transport Move substances against their concentration gradient. Requires energy, usually in the form of ATP Performed by specific proteins embedded in the membranes Bulk Transport Transport of large molecules Requires packaging in vesicles Exocytosis: transport out Endocytosis: transport in ALL THIS ABOVE WILL BE ON TEST 1

Eukaryotic Cells A eukaryotic cell has internal membranes that partition the cell into organelles Plant and animal cells have most of the same organelles Cell Fractionation Technique to study cell structure and function Centrifugation -High speed gets smaller components pellet Cytoplasm Lawns and parks Cytosol Watery matrix containing water salts, and organic compounds Cytoskeleton steel griders Functions: Mechanical support Maintenances of cell shape Anchorage and movement for gorgannelles Cell motility Cell division Muscle contraction Components Microtubules: hallow tubes; protein called tubulin, maintenance of cell shape, cell motility, chromosome movements in cell division, organelle movements Microfilaments: Actin filaments, maintenance of cell shape, changes in cell shape, muscle contraction, cytoplasmic streaming, cell motility/division Intermediate Filaments Keratin, maintains of shape, anchorage, formation of nuclear lamina.