BY 123 - Notes for Weeks 1 and 2
BY 123 - Notes for Weeks 1 and 2 BY 123-2F
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This 10 page Class Notes was uploaded by Noah Probst on Sunday January 17, 2016. The Class Notes belongs to BY 123-2F at University of Alabama at Birmingham taught by Samiksha Ashok Raut in Winter 2016. Since its upload, it has received 60 views. For similar materials see General Biology in Art at University of Alabama at Birmingham.
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Date Created: 01/17/16
Introductory Biology I Ch. 1: Evolution, Themes of Biology, and Scientific Inquiry *NOTE: All references to figures are figures in Introductory Biology 1 by Campbell Learning Objectives: Concept of life Biological Organization/Hierarchy Themes in Biology Scientific Method A. Concept of Life 1. Biology – Bio=life; logy=study 2. Biologist – One who studies biology. 3. Branches/specialties of biology – cell, biochemistry, bacteriology, bioinformatics, etc. 4. What is life? What comes to mind when you think of life? Alive. How is something alive? Physiological activities (breathing, eating, energyprocessing), response to a stimuli, process energy, reproduction, ATP. See Fig. 1.2 in book ** Everything in biology has specific order. E.g. energy processing, parts of sunflower, response to the environment, evolutionary adaptation (all things adapted to environment in some way). **See Fig. on p. 2 Theme: New properties emerge at each level in biological organization/hierarchy. Google Earth analogy: Biology is the same in that you must use a reductionist approach. Start with the biosphere and zoom in. Google Earth=earthcountrystatecityyour house. Biology (in decreasing size order) = biosphere ecosystem community population organism organ system organ tissue cell organelle macromolecule molecule. Biological organization/hierarchy Emergent properties – assemble simple things Reductionism – breaks down to simple approach to study final details. Systems Biology Theme: Organisms Interact with Other Organisms and the Physical Environment Organisms constantly are interdependent on one another Theme: Life Requires Energy Transfer and Transformation All organisms need energy to do work; ATP in form of chemical energy In figures 1.6a – energy flow from sunlight to producers to consumers and b – using energy to do work Theme: Structure and Function are correlated at All Levels of Biological Organization E.g. birds bodies are light, bones are hollow – if heavy, birds wouldn’t be able to take off Theme: The cell is organism’s basic unit of structure and function/life Eukaryotic – “Eu”=true; “karyon”=nucleus; DNA bound in nucleus by membrane Prokaryotic – “Pro”=first; “karyon”=nucleus; primitive (old) nucleus; much smaller; no nucleus – DNA suspended in cytoplasm, no organelles, no endoplasmic reticulum **Remember fine distinctions between eukaryotes (can be single or multicellular) and prokaryotes (always unicellular). Theme: Continuation of life based on hereditable info in the form of DNA Any given organism (Fig 1.6) – starts as nuclei containing DNA, ends as offspring with traits from both parents. Fig 1.7 – double helix DNA known as master molecule Fig. 1.8 (parts of eukaryotic and prokaryotic cell – KNOW THEM!) Theme: Feedback Mechanisms Regulate Biological Systems Fig. 1.13a (a) Negative feedback – very good way for cell to shut off processes (like when you turn off lights to save electricity) – reason many processes in cell come to stop (b) Positive feedback – produces more and more – z feeds back into system and keeps the process going. E.g. oxytocin – hormone produced when women go into labor, stops when baby expelled due to negative feedback. Core Theme: Evolution accounts for the unity and diversity of life. Taxonomy – places organisms in specific groups (classify w/ class system) 3 higher levels of classification are the domains of bacteria, archaea, and eukarya. The domain is the highest level of taxonomy. Bacteria – no membranebound nucleus, prokaryotes. Archaea – no membranebound nucleus, prokaryotes. Eukarya – multicellular Dependent on mode of nutrition Kingdoms Plantae, Fungi, and Animalia; unicellular protists. See Fig. 1.15 Scientific Method How do scientists do science? Observations, forming logical hypotheses, testing, data, inference/conclusion. Data, qualitative or quantitative? Qualitative – in form of descriptions. Quantitative – anything you can measure. E.g. Jane Goodall’s study on primates. Questions that cannot be answered by science A hypothesis must be testable and falsifiable E.g. a hypothesis that ghosts are fooled by a flashlight cannot be tested Supernatural and religious explanations outside the bounds of science Experimental group – E.g. taking nucleus out of amoeba to see if it dies Control group – to rule out effects by other factors; make sure microloop in Fig. 117, p 18. Theories in Science In the context of science, a theory is (a) broader in scope than a hypothesis; (b) general, and can lead to new testable hypotheses; and (c) supported by a large body of evidence in comparison to a hypothesis Theory is not immortal; e.g. cell theory KEY TERMS: theory, hypothesis, cell theory, cell, population, taxonomy, domain, kingdom, prokaryote, eukaryote, hypothesis testing, observational study, exponential study, control group. Chapter 2 Learning objectives: Structure of atoms Molecules Bonds KEY TERMS: neutron, electron, proton, element, atomic number, isotope, mass number, valence shell, valence electron, chemical bond, covalent bond, nonpolar covalent bond, polar covalent bond, electronegativity, polarity, ionic bond, ion, cation, anion, single bond, double bond, triple bond Importance of chemistry in biology – we eat and breathe chemicals Review: Matter is anything that takes up space; elements can’t be broken down; atom – nucleus made of protons and neutrons and surrounded by electrons (technically do not orbit) in the form of a negative cloud. Electrons determine chemical behavior. Compound examples – sodium + chlorine = sodium chloride (NaCl). *Fig 2.3 Table 2.1 Elements in the human body: O, C, H, N, Ca, P, K, S, Na, Cl, Mg, and trace elements. *know atomic and mass numbers and isotopes Fig. 2.8 Octet rule Elements tend to lose, gain, or share electrons to obtain complete outer shell with 8 electrons Octet rule and chemical stability? A complete outer shell with eight electrons increases stability. The formation and function of molecules depend on chemical bonding between atoms Atoms with incomplete valence shells can share or transfer electrons The formation and function of molecules depend on chemical bonding between atoms Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms These interactions usually result in atoms staying close together, held by attractions. Covalent bonds The sharing of a pair of valence electrons by 2 atoms In a covalent bond, the shared electrons count as part of each atom’s valence shell. *Fig 2.12 Ionic bonds Formed by complete transfer of electrons Fig 2.16 Hydrogen bonding – not bonds; force of attraction – function as bridges between molecules or parts of same molecule Van der Waals Interactions Electrons shared equally Geckos can climb on walls because of these interactions in their feet Molecular Shape and Function Shape tied with functions (molecular geometry in chemistry) E.g. endorphin effect – natural molecule released by brain that releases pain Chemical reactions make and break chemical bonds 2H +2 22H O 2 Photosynthesis is an important chemical reaction Chapter 3 Key Terms: solution, solvent, solute, hydrogen bond, hydrophilic, hydrophobic, cohesion, adhesion, supreme tension, specific heat, acid, base, acidity, alkalinity, pH, pH scale, buffer Humans can live 4872 hrs without water. For a polar bear water is a necessity in more ways than one. All organisms need water. Whether or not water can be found on Mars is a key factor in whether or not humans can ever inhabit it. Chapter 3, water and life Learning Obj. Polar covalent bonds in water molecules: hydrogen bonding Emergent properties of water Water: Solvent of life Acid and basic conditions affect living organisms Molecule that supports Life Water is the biological medium on Earth All living organisms require water more than any other substance Most cells are surrounded by water, and cells themselves are about 7095% water The abundance of water is the main reason the Earth is habitable E.g. fruits shrink when they are dried because they consist primarily of water Why water is such an efficient solvent (a) Nonpolar covalent bond in H molecule – electrons are halfway between the two atoms, shared equally. (b) Polar covalent bonds in water molecule – electrons are not shared equally (O is more electronegative than H), so partial charges exist on the O and H atoms (a) Water is polar – electrons are pulled towards O. (Figure 2.12) (b) H bonds form between water molecules. The polarity of water molecules results in H bonding Fig 3.2 Water is unique as a solvent: Structure – small size, bent shape, high polarity covalent bonds, overall polarity 4 emergent properties we’re interested in studying: cohesive, adhesive, denser as solid than a liquid, able to absorb large amounts of energy Fig 3.3 Adhesion – attraction b/w “unlike” molecules. Water bonds w/ any glass or plastic like surface. Cohesion – attraction b/w like molecules. E.g. water – water bonds. Helps water move up Hydrogen bonding contributes Happens because of polar nature, and possible because of H bonding Surface tension – a measure of how hard it is to break the surface of a liquid – surface tension related to cohesion Fig 2.15 Adhesion – Water molecules adhere to glass and pull upward at perimeter Cohesion – molecules at top connected to ones on bottom makes dome shape – due to surface tension, resist upward pull of adhesion Belly flopping hurts due to film layer caused by surface tension Most of the time people make things from plastic; plastic is moldable and shrinks – water does not; it expands going from liquid to solid Fig 2.16 Ice – water molecules form crystal lattice Liquid – no crystal lattice forms Liquid water denser than ice Ice floats What would happen if ice would sink? A solid block of ice would be made; animals would die Ice fishing is possible because fish still live underneath Moderation of temperature Water absorbs heat from warmer air and releases stored heat to cooler air Water can absorb or release a large amount of heat w/ only a slight change in its own temperature Fig 35 Water’s high specific heat The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its T by 1 degree C Water’s specific heat is 4.18 J/g Water resists changing its temperature because of its high specific heat Table 2.1 Evaporative cooling Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water In the south, humidity, not temperature, water in atmosphere does not allow easy escape of water Polar covalent bonds are bonds b/w oxygen and hydrogen Water: The Solvent of Life A solution is a liquid that is a homogeneous mixture of substances A solvent is the dissolving agent of a solution A solute is the substance being dissolved An aqueous solution is one in which the water is the solvent Water and hydrogen bonds Hydrophilic – ions and polar molecules that stay in solution – they stay in solution because of their interactions w/ water’s partial charges – H bonding makes it Hydrophobic (Fig 2.13, 2.14, and 3.8) – 2.14 – all hydrophobic bonds are completely separated from water molecules – opposite charges, no H bonds, forming Acids and Bases An acid is any substance that measures the H concentration of a solution of a solution. An acid is a proton donor. E.g. HClH Cl + + A base is any substance that reduces the H concentration of a solution. Bases are proton acceptors. Acids and bases play very key roles in maintaining pH of bodily fluids; they decide whether certain enzymes are functioning or not. pH scale + in any aqueous solution at 25 C, the product of H and OH is constant and can be written as [H ] [OH] = 10 14 The pH of a solution is defined by the negative logarithm of H concentration, + written as pH = log[H ] For a neutral aqueous solution [H ] is 10 = (7) = 7 + [H ] and [OH] are equal at pH=7; 07 = acid and 714 = base (increasing [OH ]) Buffers The internal pH of most living cells must remain close to pH 7 + Buffers are substances that minimize changes in concentrations of H and OH in a solution + Most buffers consist of an acidbase pair that reversibly combines with H Solute Concentrations in Aqueous Solutions Molecular mass is the sum of all masses of all atoms in a molecule Numbers of molecules are usually measured in moles where 1 mole (mol) = 6.02x10 molecules 23 Avogadro’s number and the unit dalton were defined such that 6.02x10 daltons = 1 g. Molarity (M) is the number of moles of solute per liter of solution. Chapter 4 Learning objectives Carbon atomes can form diverse molecules by bonding to 4 other atoms Molecular diversity arising from carbon skeleton variation Isomers Functional groups ATP *all organisms are made of carbon Where does carbon come from? Photosynthesis – light energy plant caterpillar bird decomposer – presence of sunlight allows carbon dioxide to be taken in Carbon/carbon based compounds coming from living organisms. The study of this is organic chemistry. “urea” – Berzelius synthesized this in a lab without needing living organisms – huge break through chemical evolution – “prebiotic soup” – all carbonbased compounds getting formed by simple gases assembled to form the first cells 1953 – Miller’s Lab – MillerUrey Experiment – simulated “prebiotic” soup to show how life formed 2008 – larger scale experiment done to show formation of earth How can carbon atoms form diverse molecules by bonding to four other atoms? Fig 4.4 – valence=outermost shell electrons – helps us decide chemical behavior Fig 4.3 – the above gives rise to more molecular formulas Molecular Diversity Arising from Carbon Skeleton Variation Fig 4.5 – (a) length – gives rise to ethane, propane, 1butene, 2butene, etc. (b) branching butane, 2methylpropane, cyclohexane, benzene Most carbonbased compounds include H (covalent bond) – incomplete without it Form Hydrocarbons HCs are organic molecules consisting of only C and H Many organic molecules (e.g. fats) have HC components HCs can undergo reactions that release a large amount of energy – end up releasing a lot of energy as a result An adipose cell is a fat cell (Fig 4.6) Isomers Isomers are compounds with the same molecular formula but different structures and properties. 3 different kinds of isomers (a) structural – different covalent arrangements of atoms, (b) cistrans – same covalent bonds but differ in spatial arrangements, (c) enantiomers – isomers that are mirror images of each other. Importance of Enantiomers in Pharmaceutical Industry Fig 4.8 Ibuprofen for pain/inflammation. Effective enantiomer: Sibuprofen; ineffective: R Albuterol for asthma. Effective: R, ineffective: Sst Thalidomide – relieves women from nausea 1 period of pregnancy; the bad isomer was not seen, and many kids were born with flipperlike limbs as a result. The Chemical Groups most Important in the Process of Life Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties The seven functional groups that are most important in the chemistry of life: hydroxyl (e.g. acetone), carboxyl (e.g. acetic acid), carbonyl, amino (e.g. glycine), sulfhydryl (e.g. cysteine), phosphate (e.g. glycerol phosphate), methyl (5methyl cytidine) Fig 4.9a – hydroxyl structures and e.g. ATP: An Important Source of Energy for Cellular Processes Fig 4 Adenosine triphosphate (3 P groups) – when it reacts with water (depicted as a circled P), remove 1 P group adenosine diphosphate ATPADPAMP (adenine monophosphate) Chapter 5 Learning Obj. The molecules of life: macromolecules Carbs Lipids Proteins Nucleic Acids The Molecules of Life All living things are made up of 4 classes of organic molecules Macromolecules are polymers, built from monomers Polymer= “many;” meno=”part” Monomer=”one part” 3 of 4 classes of life’s organic molecules are polymers: carbs, proteins (building blocks are amino acids), and nucleic acids *lipids do not meet definition of a true polymer The Synthesis and Breakdown of Polymers Dehydration – dehydrate – removal of water Hydrolysis – “water” “break” Fig. 5.2 (a) Dehydration reaction synthesizing a polymer – condensation – to remove water (b) Hydrolysis: breaking down a polymer (could be made of 4 monomers) – hydrolysis adds a water molecule, breaking a bond Dehydration reactions remove a water molecule, forming a new bond. Short polymer larger polymer Carbohydrates – hydrates of carbon Simple sugars; sugar=(CH O) 2 n Polymers of sugars Glucose (C H O ) 6C atom molecules 6 12 6 Simple sugars Monosaccharides have molecular formulas that are normally multiples of CH O 2
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