A Way to Think and a Body of Knowledge

Chapter one: Science: a way to think and a body of knowledge. Scientific method Questions: • How is Science different from others ways of looking at the Universe It is different from philosophy because philosophy is based on acceptance vs. proven facts like science is. It is different from religion because they explain the past and the beginning of time by different means. Evolution vs. god. It is different from technology because technology wouldn’t be possible without science, and it takes the scientific processes and knowledge away It is different than art, because art is expressive and science is technical. There is only one way to interpret science while art can be interpreted in many ways. • What are the properties of Life? Evolution, common ancestry, hierarchical classification, natural selection, adaptation, Life’s three domains; bacteria, archea, and eukarya, Order, energy and matter, unity and diversity of life, reproduction and development, cells; the fundamental unit of life, DNA, RNA, and Protein. • Explain How Science Works as a process Scientific method • Compare the approach taken by reductionist and system-level modes of scientific analysis. Reductionist: complex to simple. Each level of organization emerges from the interactions of the components of the level beneath. The Whole picture is lost. Is a thing just the sum of its parts? A generalized system is influenced by its surroundings; it has an input that undergoes system processes, which produces an output, which gives either positive or negative feedback. Models are needed but limited. Positive feedback: the output increases the process- the more you make, the more you get. Negative feedback: the output decreases the process- more gets you less. • Why is biology science: is a natural science concerned with the study of life and living organisms, including their structure, function, growth, evolution, distribution, and taxonomy. • Explain how life is organized across several domains of space and time, and why this organization is necessary. Chapter two: Questions:  The subatomic particles, and their significance. Particles that are smaller than an atom: proton, neutron and electron  The types of chemical bonds, how they form and their relative strengths  Be able to balance chemical equations. Element: substances that cannot be broken down to simpler substances through chemical reactions Atomic number = the number of protons or electrons. Atomic mass= the number of protons and neutrons Matter: Matter has mass and takes up space, Elements are made of matter There are 118 elements, 92 are naturally occurring. O,C,H,N make up 94% Ca, K, S, P make up 4% Trace elements Compound: two or more elements combined in a fixed ratio Three main components of an atom and their charges: atoms are the smallest unit of an element that retains the properties of that element. Protons – positive, neutrons- neutral, and electrons- negative. Protons and neutrons are found in the nucleus. Isotopes are atoms of elements with a different number of neutrons. Valence Shell: is the outermost e- shell in an atom. Elements react to fill their valence shells. If the valence shell is filled the element is stable. It will not react. Needs 8 Electrons are found at different energy levels outside the nucleus. The particular energy levels that electrons spend most of their time are described as energy shells. Electrons are attracted to the nucleus. The electrons farthest away have the most potential energy. Orbitals: are within shells, and can hold two electrons Covalent Bonds: atoms share electrons: the strongest bond. Two types: Non Polar- electrons shared equally between atoms in the bond (H2) Polar bonds- electrons are attracted more strongly to one atom in the bond than the other. (H2O) Ionic Bonds electrons move completely to one atom resulting in a positively charges ion and a negatively charged ion. (Na+Cl-)  and How can you tell if a bond will be non polar covalent, polar covalent or ionic? You have to determine their difference in electronegativity. Subtract the smaller from the larger. If it is > 1.7 its ionic because they have different electronegativity’s and one will steal the electrons from another- one will become positive one will become negative. If it is between 1.7 and .5 the bond is polar covalent. If it is < .5 the bond is non polar covalent this is because they are similar in electronegativity and will share their electrons. Weak Bonds: hydrogen bonds. Hydrogen bond – is formed when a hydrogen is covalently bonded to an electronegative atom is also attracted to another electronegative atom. Van der Waals bonds fleeting attraction between molecules Molecular shape and function: elements properties depend on the structure of it’s atoms. Molecules have specificity/function based on shape Similar shapes can have similar biological effects Chemical Reactions: Molecules under go reactions by forming or breaking covalent bonds. The initial substances are called the reactants, the set of substances resulting from the reaction are products. Chemical reactions are reversible. Chemical equilibrium is achieved when forward and reverse reaction rates are equal Chapter three: Questions: • The importance of hydrogen bonding to the properties of water. • The unique properties of water, and how each contributes to life on Earth. • How to interpret the pH scale: 0-7 is acidic, 7-14 is considered a base. • The importance of buffers in biological systems. Buffers: minimize changes in concentration of H+ and OH- in a solution (weak acids and bases) Buffers keep blood at pH ~7.4 If blood drops to 7 or up to 7.8, then death Carbonic Acid – Bicarbonate System: important buffers in blood plasma Adhesion: bonding between unlike molecules Cohesion: H-bonding between like molecules Surface Tension: Allows water striders to walk on water. Measure of how difficult it is to break or stretch surface of liquid Transpiration: The movement of water up plants: H2O clings to each other by cohesion; cling to xylem tubes by adhesion Heat = Total amount of KE in system Temperature = measure intensity of heat due to average KE of molecules A swimmer in a body of water has a higher temperature, the body of water has more heat. Moderation of Temperature Water’s high specific heat • Change temp less when absorbs/loses heat • Large bodies of water absorb and store more heat à warmer coastal areas • Create stable marine/land environment • Humans ~65% H2O à stable temp, resist temperature change. • • • • • • Evaporative Cooling Water has high heat of vaporization Molecules with greatest KE leave as gas Stable temp in lakes & ponds Cool plants Human sweat Floating of Ice: Ice acts as an insulator. It is less dense as a solid than it is as a liquid.  Life exists under frozen surface (ponds, lakes, oceans)  Ice = solid habitat (polar bears) Water is the solvent of life • Solution = liquid, homogeneous mixture of 2+ substances • Solvent = dissolving agent (liquid) • Solute = dissolved substance • Water = versatile solvent 1mole = 6.022 x 1023 particles 1mole = molecular mass (grams) Molarity = moles per liter of solvent ( water) • Acid = increases H+ concentration (HCl) 0-7 • Base = reduces H+ concentration (NaOH) 7-14 • Most biological fluids are pH 6-8 • Neutral = 7 Ocean acidification Acid Rain Hydrophilic: a substance that is attracted to water Hydrophobic: a substance that repels water and cannot for hydrogen bonds. Chapter Four: Organic Chemistry: the study of carbon compounds. Questions: • The properties of carbon that make it so important. Carbon’s electron configuration allows for it to form large, complex, and diverse organic molecules. It can branch into as many as four directions when forming bonds. Diversity of Carbon: 4 classes of macromolecules: carbohydrates, proteins, lipids, and nucleic acids They can be ring-shaped, chains, or branched • The types of isomers that carbon molecules can form: Isomers: Molecules have same molecular formula, but differ in atom arrangement Structural: branched or straight: different covalent arrangement Geometric (cis-trans): different spatial arrangements Enantiomers: mirror images, different shape due to a asymmetric carbon Pharmacological importance • The functional groups that can bond to carbon and their properties. Functional group: the chemical group that affects molecular function by being directly involved with chemical reactions. Behavior of organic molecules depends on functional groups Most common functional groups: 1. Hydroxyl: OH 2. Carbonyl: C=O 3. Carboxyl: C=O –OH 4. Amino: NH2 5. Sulfhydryl: SH 6. Phosphate:OPO3 7. Methyl: CH3 • Describe the basic structure of a hydrocarbon and explain why these molecules are hydrophobic. Consist of hydrogen and carbon. Since carbon atoms all have the same electronegativity, and the electronegativity of hydrogen is only slightly different than that of carbon, the bonds in hydrocarbons are all non-polar. Thus, hydrocarbons tend to be hydrophobic, especially if they are more than a few carbons in size. • Carbon Skeletons: How can they vary? They vary by attaching the functional groups to a hydrocarbon skeleton ATP: Energy for Cellular Processes