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Biology Scientific Study of Life Properties of Life Order, Adaptation, Response to Environment, Regulations, Energy Process, Reproduction Study of Life Microscopic (Cells) to Global (Planet) Hierarchy of Biological Organization: BECPOOTCOM Biosphere, Ecosystem, Community, Population, Organisms, Organs/Organ Systems, Tissue, Cell, Organelles, Molecules Ecosystem - Each organism interacts with its environment (living and non living); - Both organisms and environment are affected by interactions between each other - The nonliving help the living develop Dynamics of Ecosystem 1. Cycling of Nutrients (materials from plants go back to the soil. 2. The Flow of Energy (Sunlight -> Producers -> Consumers) Energy Conversion - Moving, growing, reproducing, and other activities of life require organisms to perform work, depending on an energy source. - include transfer of energy between organisms and their surroundings - Energy flows through an ecosystem: entering as light and exiting as heat. Cells - The Lowest level of organization that can perform all activities required for life - They contain chromosomes made partly of DNA - all are enclosed by membrane and use DNA as genetic Info. DNA a substance of genes that programs cell's production of proteins and transmits info from parent to offspring. 2 Main forms of Cells - Eukaryotic Cells: Subdivided by internal membranes into various membrane enclosed organelles - Prokaryotic Cells: lack membrane enclosed organelles that are found in eukaryotic cells System combination of components that form a more complex organization (Ex. Cells, Organs, Organisms) The Emergent Properties of Systems - due to the arrangement and interactions of parts as complexity increases; as time moves on, every organism becomes more complex. (the hierarchy of biological order) Reductionism define: reducing complex systems to simpler components making it easier to study. (Animalia -> Reptile -> Snake -> Water Moccasin. Systems Biology - GOAL: seeks to create models of behavior of whole biological systems. - these models help scientists predict how a change in part of a system might affect the whole system Three (3) Key Research Developments - High-Throughput Technology: help scientists understand huge amounts of data quickly - Bioinformatics: Software that helps scientists understand biological products; Ex. Math Models - Interdisciplinary Research Team: A Team of members from different fields necessary to understand the whole research; Ex. engineers, medical scientists, chemists, physicists, biologists all working together. Feedback Regulation in Biological Systems - a supply-and-demand economy applies to some of the dynamics of biological systems. - The output(product) of a process regulates that very process. Negative Feedback - the most common - accumulation of an end product of a process slows that process that produces that product. -Ex. Cell -> Creates ATP -> excessive accumulation of ATP-> ATP "feedback" and holds back an enzyme at the beginning of the pathway -> slows ATP production Positive Feedback - An end product speeds up its production. - Ex. Blood Vessel damage cause platelets to gather -> chemical released by the platelets attracts more platelets -> sealing the vessel with a clot. Cladogram a diagram that is based on patterns of shared, derived traits and that shows the evolutionary relationships between groups of organisms/species Taxonomy - Brainchild of Carrolus Linnaeus - branch of biology that names and classifies species according to a system of broader and broader groups Classifying Life Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species Bacteria - Prokaryotic, Unicellular, Micro - one of three domains of life Archaea - Prokaryotic, Unicellular, Micro - one of three domains of life Eukarya - most complex of the three domains of life - eukaryotic, single to multicellular, small to large - includes various Protist Kingdoms and the Kingdoms Plantae, Fungi, and Animalia. Evolution accounts for life's unity and diversity Charles Darwin - In 1859, he published On the Origin of Species by Natural Selection. - proposed that natural selection could enable ancestral species to 'split' into two or more species resulting in the "tree of life" Main Points of On the Origins of Species by Natural Selection - Descent with modificiations (Overtime organisms change) - Natural Selection (Survival of the Fittest; adapt the best to change) Natural Selection Darwin proposed that it was the mechanism for evolutionary adaptation of population to their environment The Tree of Life - Many organisms are related - similar anatomical features adapted for way of life Ex. Bats wings look like peoples hands - kinship connect lifes unity in diversity to Darwins concept "descent with modification" - natural selection enable ancetral species to 'split' - each species on twig of branching tree of life extends back in time to more remote ancetral species; long evolutionary history Biology's 2 processes of Scientific Inquiry 1. Discovery Science 2. Hypothesis-Based Science Discovery Science describes natural structures and processes as accurately as possible through careful observation an analysis of data Types of Data - Recorded Observations - Quantitative: measurements and numbers (more preferred) -Qualitative: recorded descriptions; colors or features Inductive Reasoning Generalization based on large number of specific observations. Ex. The sun always rises in the east. Deduction Reasoning - The "If...then" logic - the logic flows from the general to the specific Scientific Hypothesis - if correct, we can expect a particular outcome - hust have 2 qualities: * must be testable * must be falsifiable Myth of Scientific Method its an idealized form of experimenting. Scientific Theory -Broad in Scope - Generates new hypotheses - is supported by a large body of evidence Model Building in Science Models of ideas, structures and processes help us understand scientific phenomena and make predictions. Culture of Science -Social Activity: biologists, physicist, chemists work together - COMPETITIVE Technology Applies scientific knowledge for some specific purpose underlying themes provide a framework for understanding biology Matter - anything that takes up space and has mass - consist of chemical elements in pure form and in combinations called compounds elements substances taht can't be broken down to other substance by chemical reactions compound substance of two or more elements combined in a fixed ratio and has characteristics differenct from its elements # of essential elements 92 Carbon, Hydrogen, Oxygen, and Nitrogen Make up 96% of living matter Most abundant Element in Earth's Crust Silicon and Oxygen Effects of essential elements deficiencies - nitrogen deficiency: shorter crops - iodine deficiency: Goiter Trace Elements required by an organism in only minute qualities Element Properties - Depend on structure of atoms - each has a certain kind of atom defferent than other elements Atom smallest unit of matter that still retains properties of an element Subatomic Particles - smaller parts of atoms - Neutrons: No Charge - Protons: Positively Charged - Electrons: Negatively Charged Atomic Nucleus Where protons and neutrons are found Electron Cloud Where electrons are found surrounding the nucleus in a cloud. Atomic Number - Number of Protons, unique to each element Atomic Mass - Number of Protons + Number of Neutrons Isotopes of an Element - differ in number of neutrons in the atomic nucleus - have the same number of protons Radioactive Isotopes - Spontaneously give off particles of energy - can be used in biology to date fossils and trace atoms through metabolism Atoms Electrons Vary... In the amount of energy and potential energy they possess Energy The capacity to cause change Potential Energy Energy that matter possesses because of its location or structure. Energy Levels Represented by electron shells - the closer to the nucleus, the less energy the electron has. Chemical Behavior of Atoms based on its electron configuration and distribution Valence Electrons - Electrons in the outermost electron shell - determines the chemical behavior of an atom Valence Shell Outermost electron shell Orbital 3 Dimensional space where an electon is found 90% of the time Electron Shell consists of a special number of orbitals Formation and function of molecules depend on chemical bonding between atoms Covalent Bond - sharing of a pair of valence electrons - the strongest of all the bonds Ex. Diamond(10) Molecule two or more atoms held together by covalent bonds single bond sharing of one pair of valence electrons Double Bond sharing of two pairs of valence electrons electronegativity - the attraction of a particular kind of atom fo the electrons in a covalent bond. - more electronegativity in an atom, more strongly it pulls shared electrons toward itself. nonpolar covalent bond atoms have similar electronegativity, and they share the electron equally Polar Covalent bond atoms have differeing electronegativity and share electrons unequally. Ions - Electrons transfered between two atoms - atoms with more or fewer electrons than usual are charged atoms - sometimes, atoms slip electrons away from their bonding partners Anion Negatively charged ions Cations Positively charged ions Ionic Bonds attraction between anions and cations Ionic Compounds - Called salts which may form crystals hydrogen Bonds formed when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom Van der Waals Interaction - occurs when transiently postive and negative regions of molecules attract each other - weak bonding in a gecko's feet Weak Chemical Bonds - reinforce the shapes of large molecules and help molecules adhere to each other - Van der Waal, Hydrogen Bonds, Ionic Bonds Precise Shapes of Molecules - important to its function in the living cell - found by position of atoms' valence orbitals Molecular Shape find how biological molecules recognize and respond to one another with specificity. Chemical Reaction - making and breaking of chemical bonds that leads to changes in the composition of matter - convert reactants to products Ex. Photosynthesis Water - required by all living organisms - most cells are surrounded by it and are 70 - 95% water. Determination of organisms in environment Amount of water there Three Phases Water is the only common substance to exist in three phases Water Molecules Polar Molecules = Polar Covalent Bonds - opposite ends have opposite charges - polarity allows them to form bonds with each other. Four Water properties that facilitate an environment for life 1) Cohesive Behavior 2) Moderation of Temperature 3) Expansion upon freezing 4) versatility as a Solvent Cohesion Behavior - collectively, hydrogen bonds hold water molecules together - arrangement of molecules is constantly changing - hydrogen bonds last only a trillionth of a second by they constantly form, break, and reform. Adhesion - Counters gravity - the attraction of different substances Surface Tension measure of how hard it is to break the surface of a liquid. Moderation of Temperature - water absorbs heat from warmer air and releases stored heat to cooler air - H2O can perform this with only a slight change in its own temperture. Kinetic Energy energy of motion Heat - the amount of the total amount of kinetic energy due to molecular motion Temperature measures the intensity of heat due to the average kinetic energy of molecules Faster Movement of atoms and Molecules... - more kinetic energy - higher temperatures Change of State of Water - Boils at 100 Degrees Celcius - Freezes at 0 Degrees Celcius Calorie Amount of energy needed to raise or lower the temperature of 1 gram of water by 1 degree C Kilocalorie - amount of energy needed to raise 1 kg of water by 1Degree C - measurements in food 1Joule 0.239 cal 1 Calorie 4.184 Joules Specific Heat must be absorbed or lost for 1 g of that substance to change its temperature by 1 degree C Water Specific Heat - its HIGH specific heat lessens it changes to within limits that permit life - 1 cal/g/Degree C (HIGH) - Bonds broken - bonds formed - heat absorbed - heat released heat of vaporization - the amount of heat a liquid must absorb for 1 g to be converted to gas - molecules move fast enough to depart and enter the air as a gas Evaporative Cooling - as a liquid evaporates, the surface cools - H20 -> Gas = 580 cal (double that amount is needed to evaporate alcohol) - helps stabilize the temp. in organisms and bodies of water Ice Floating - hydrogen bonds in ice are more 'ordered' making ice less dense. - if it sank, bodies of water would freeze solid and life would be impossible on earth - contributes to fitness of environment Water Freezing - molecules slow too much to break hydrogen bonds - become locked in crystalline lattice about 10% than surrounding liquid Solution liquid that's a homogeneous mixture of substances solvent dissolving agent of a solution - water is a versatile solvent b/c polarity - it readily forms H Bonds solute substance dissolved aqueous solution water is the solvent Hydration Shell - ionic compounds dissolve in water and each ion is surrounded by a sphere of H20 molecules dissolving of ionic compounds -NaCl -> both ions are exposed to H20 - oxygen has negative charge and clings to the sodium cations; hydrogen has positive charge and clings to Cl anion hydrophilic substance substance that has an affinity for water hydrophobic Substance substance that does NOT have an affinity for H20 Colloids - Stable suspension of articles in liquid - does'nt dissolve and remain in suspended in aqueous solution. - Ex. oil, pollutions, whip cream Biochemistry Wet Chemistry Dissociation of Water Molecules - leads to more acidic or more basic conditions - H atom leaves its electron behind and is transferred as a proton or H ion (H+) - The molecule w/ the extra proton is now a hydronium ion (H30+) - The molecule that lost the proton is now a hydroxide ion (H+) - statistically rare, yet has great effects on organisms pH potential hydrogen - ability to attract H+ ions - scale describes how acidic or basic a solution is - determined by the relative concentration of H+. Effects of change in pH - concentrations of H+ and OH- are equal in pure water - adding certain solutes (acids & bases) modifies concentration of H+ and OH- Acid any substance that increases the H+ concentration of a solution (molecules with Hydrogen break down) - solutions with pH value < 7 Base any substance that reduces the H+ concentration of a solution - solutions with pH value > 7 pH levels of Substances - most biological fluids : 6 to 8 - most living cells : 7 Buffers - substances that minimize change in concentration of H+ and OH- in a solution - an acid-base pair that reversibly combines with H+