Purple Pages - Foundations of Biology PDF

Purple Pages Foundations of Biology Foundations of Biology How do we know what we know about cell biology?  1. Scientific Method Science – What is the scientific method? Investigative approach to acquiring knowledge by making observations about the natural...

Purple Pages Foundations of Biology Foundations of Biology How do we know what we know about cell biology?  1. Scientific Method Science – What is the scientific method? Investigative approach to acquiring knowledge by making observations about the natural world, developing explanations and testing those explanations Hypothesis-based Science Observations can lead us to ask questions A hypothesis is a tentative answer/explanation to a well framed question A hypothesis must be testable and falsifiable Often create two or more alternative hypotheses A scientific hypothesis leads to predictions that can be tested by observation or experimentation Failure to falsify a hypothesis does not ____ that hypothesis  Example of Hypothesis-based Science 1. Observation: Our tomatoes Farmer Joe’s tomatoes No Fertilizer added Fertilizer added 2. Hypothesis:  3. Experimentation Compares an experimental group with a control group - controlled experiment Variables - factors within experiment 1. Independent - changed by scientist 2. Dependent - response to changes in independent variable 3. Controlled - remains constant  Experimentation Hypothesis: Fertilizer increases the production of tomatoes. Control Group Experimental Group 100 tomato plants 100 tomato plants 1 L water/day/plant 1L water/day/plant 90 days 90 days 25 ºC 25 ºC No fertilizer Add fertilizer Total # of tomatoes Total # of tomatoes Identify the independent, dependent and control variables. 4. Interpretation of Results Statistics - need large sample size 12,000 9,000 6,000 3,000 Control Experimental  Conclusions Does the data falsify or NOT falsify the hypothesis? Now what??? Peer-reviewed Scientific Research Paper  Scientific Theory Scientifically acceptable and well-substantiated explanation of some aspect of the natural world - takes many years to establish - supported by exhaustive experimentation - established truths that are unlikely to be contradicted by future research  Experimental vs. Observational Science In some cases it’s too difficult to establish controlled experiments Ex. astonomy, ecology, evolution Therefore rely on observational science to infer a pattern and cause for the collected data Relies on sophisticated statistical techniques  Biology Biology is the study of living things Cell is the basic unit of life 2. Scale in Biology Light Microscope Electron Microscope  3. Organization of Matter Matter - has mass and occupies space - consists of pure elements An element - a substance that cannot be broken down to other substances by chemical reactions A compound - a substance consisting of two or more elements in a fixed ratio Element + Element = _________ Elements and Living Organisms Which elements make up 96% of the matter in living organisms? What makes living organisms so different? Atomic Structure No neutrons Atomic Number = # of protons Atomic Mass = protons and neutrons What about the electrons??  Isotopes Atoms with same # protons but different # neutrons  Same atomic number but different atomic mass  Radioisotopes Radioisotopes - unstable isotopes that decay and release energy Rate of Half Life Decay is _______  Radioactive Tracers - a substance containing a radioisotope that is used to measure the speed of chemical processes and/or movement of substance. Nuclear Medicine Radioisotopes in diagnostic testing Why was there a global radioisotope shortage between 2007-2010?  Electrons In an atom, the # of electrons = __________ Move around protons in a specific regions called orbitals Stable orbitals have paired up electrons Orbitals are grouped into shells Valence Electrons Electrons in the outermost (valence shell) – Valence electrons – determines reactivity of atom – full valence shells = _______ Which of these elements are inert? 4. Chemical Bonds Reactive elements combine into molecules by forming ____________ Four main types: a. Ionic b. Covalent c. Hydrogen d. van der Waals Forces Do all elements form chemical bonds? a. Ionic Bonds Transfer of electrons from one atom to another resulting in both atoms have charges  ____ cation anion b. Covalent Bonds sharing of a pair of valence electrons by two atoms  Distinct 3D form Structure is related to _______ In a covalent bond do all atoms share electrons equally? Electronegativity - measure of an atom’s attraction for electrons in a covalent bond The more electronegative an atom, the more strongly it pulls shared electrons toward itself  unequal sharing of electrons = __________________  Polar Molecules Partial negative charge Polar Covalent 3.5 Bond Partial positive 2.1 charge If hydrogen is one of the atoms then can lead to HYDROGEN BONDING  c. Hydrogen Bonding Partial positive charge of H atom are attracted to partial negative charge of nearby atoms  - weaker than covalent and ionic bonds  d. van der Waals Forces Weaker than hydrogen bonds Develop between nonpolar molecules Constant motion of electrons causes them to accumulate by chance on one region of molecule  zones of positive and negative charge  Why is it that we are able to live here? 5. Hydrogen Bonds and Water More dense Less dense Dynamic Stable Water, Lattice Structure and H-bonds High specific heat capacity – Allows water to stay as a liquid at temps between 0 -100 ºC. Attraction between water molecules → cohesion Water, Lattice Structure and H-bonds Water = SOLVENT Dissolved substance = SOLUTE Water molecules surround polar molecules and ions =  Allows for separation of molecules  6. Water Ionization and pH Separation of water = H+ and OH- Acid = proton donor Base = proton acceptor Acidity of a solution = the concentration of H+ versus OH- Measured on a _______  Buffers Controls pH by absorbing or releasing H+ Most are weak acids or weak bases What controls the pH of our blood? H2CO3 → HCO3- + H+  7. Carbon Compounds Living matter are all composed of carbon compounds = How many covalent bonds can carbon form? This tetravalence makes large, complex molecules possible 12 6 C Carbon Compounds Vary in length and shape molecules where carbon is bound only to hydrogen = Carbon Bonding Covalent Bonds Carbon Bonding Functional groups - reactive groups - enter into biological reactions - bind to carbon 1. Hydroxyl (–OH) 2. Carbonyl (–C=O) 3. Carboxyl (–COOH) 4. Amino (–NH2) 5. Phosphate (–PO42-) 6. Sulfhydryl (–SH) Structure is related to _________ Dehydration and Hydrolysis Reactions Synthesis of a Polymer - dehydration reaction - remove water - form a bond Breakdown of a Polymer - hydrolysis reaction - add water - break a bond 7. Carbohydrates Sugars and the polymers of sugars Fuel Building material Monosaccharides Multiples of CH2O (1:2:1) Isomers  Isomers of Monosaccharides Same chemical formula Different molecular structure Different function Mirror imaged isomers - Enantiomers Structural isomers Different position of carbonyl group Disaccharides Two monosaccharides Covalent bond in between - glycosidic linkage Glucose + Glucose = Glucose + Fructose = Glucose + Galactose = Disaccharide Synthesis Dehydration Polysaccharides Many monosaccharides - UNBRANCHED - BRANCHED Polysaccharides Different glycosidic linkages - H-bonds - N-groups 8. Proteins Many structures --> many ________ - Structural support - Storage - Transport - Enzymes in reactions - Cellular communications - Movement How many different human proteins?  Proteins Protein = one or more polypeptides Polypeptides - polymers amino acids How many different types of amino acids? Side group  carbon Amino Carboxyl group group Nonpolar Amino Acids Uncharged Polar Amino Acids Charged Amino Acids  Peptides Covalent bond Dehydration Amino acid added only to carboxyl end ___________  Primary Protein Structure Linear sequence of amino acids What does this tell you about the structure of the protein? H3N+ Phe Ala Trp Leu His Gly Val COO-  Secondary Protein Structure H-bonds between Alpha helix amino acids O and H of backbone  folds - Alpha helix - Beta pleated sheets Beta pleated sheets  Tertiary Protein Structure All types of bonds between R groups  3D shape  Function  Quarternary Protein Structure ≥ 2 polypeptides All types of bonds  Prosthetic Groups Non-protein component Need for function 9. Nucleic Acids Polymers of nucleotides Genetic information - inheritance 1. DNA 2. RNA a. mRNA (messenger) b. tRNA (transfer) c. rRNA (ribosomal)  Nucleotides 3 parts (covalent bonds) 1. Nitrogenous base 2. Pentose sugar 3. 1 to 3 phosphate groups What is the difference between DNA and RNA?  Nucleotides Which nucleotide is only found 1 carbon ring in RNA? Which nucleotide is only found in DNA? 2 carbon rings Which nucleotides are used in energy transfer?  DNA and RNA Structure 2 nucleotide chains Sugar-phosphate backbone Phosphodiester bonds Nitrogenous bases inside H-bonds How do you read DNA?  The DNA Double Helix Antiparallel H-bonds If you know the sequence of one DNA strand can you predict the other strand?  10. Lipids Nonpolar molecule Not a true macromolecules – no defined monomer subunit Hydrocarbon backbone Biological lipids: 1. Fats 2. Phospholipids 3. Steroids Fatty Acids ◼ Saturated fats the maximum number of hydrogen atoms possible and no double bonds e.g. Stearic acid Fatty Acids ◼Unsaturated fats one or more double bonds e.g. Oleic acid double bond - Bending  Fats Dehydration Which has more energy, 1 g of starch or 1 g of fat?  Phospholipids In cell membranes 1. 2. 3. 4. Amphipathic  Steroids 4 carbon rings Dual solubility Non-polar Polar Find the differences between these 2 molecules. Cells Cells are composed of these major macromolecules Structural organization of these major macromolecules will determine the functions of cells  Putting it into perspective 1. What is the scientific method? 2. What are living things made of? 3. Why is water required for life? 4. How do those components interact with each other?