BiologyChapter1and3.pdf BIOLOGY 108 - 0001
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AP Biology 20122013 Unit 1 Chapter 1 11 Characteristics of Life Emergent Properties properties that form later as parts39 complexity increases ex leaves and photosynthesis each cell part makes it happen together Cells Eukaryotic large and complex organelles multicellular organisms Prokaryotic small and simple make up single cell organism Biological Organization 1 Ecosystems Communities Population Organism Organs Tissues Cells Organelles DOOQONUIPUJN Biosphere 10 Molecules Growth and Development Central Dogma idea that DNA has instructions to make RNA which makes proteins which allows development Gene Expression Positive Feedback speeds up production by stimulating a step with the end product ex when a blood vessel is damaged positive feedback will instruct the body to produce more platelets to seal a wound via clotting Negative Feedback accumulation of an end product slows the process ex if a cell has excess ATP negative feedback will instruct the body to produce less ATP Scientific Process Control Group normal conditions lack of independent variable baseline Controlled Variables constant in all groups Independent Variable level of treatment what39s being changed in the experiment Dependent Variable what changes because of the independent variable Replication ex 4 groups of plants 10 plants in each group how many replicates Answer 10 Null Hypothesis goes against your hypothesis says that there is no relationship between independent and dependent variables any patters were simply by chance SEXPREF Males Females Both Observed 4 2 3 9 Expected 21 54 15 9 OE 19 34 15 D ClE2 361 1156 225 OEFIE 122 214 15 Observed 3 16 2 21 Expected 49 126 35 21 OE 19 34 15 D ClEE 361 1156 225 OEFIE 24 92 64 7 13 5 30 Chi Squares Proximate Cause a particular mechanism in an organism that allows it to behave in a certain way Ultimate Cause evolutionarily why an organism behaves in a certain way 12 Core Theme Evolution Taxonomy names and classifies species Three Domains of Life Bacteria Prokaryotic Archaea Prokaryotic Eukarya Eukaryotes 3 Kingdoms Kingdom Plantae land plants photosynthesis Kingdom Fungi absorb nutrients outside their bodies Kingdom Animalia ingests other organisms Protists single cell Eukaryotes don39t fit into any kingdom Darwin Evolution quotdecent with modificationquot Natural Selection differentiated structural and behavioral traits that follow quotsurvival of the fittestquot 13 Observations and Hypothesis Inductive Reasoning deriving generalizations from specific data ex from observing the sun rising in the East every day for 100 days we can conclude that the sun always rises in the East Deductive Reasoning logic that ows from a broad generalizations to specific data ex from the generalization that all zebras have black and white stripes one can deduce that the zebra you will see at the zoo will have black and white stripes Chapter 2 Chemistry Ties To Biology 2122 Chemical Context of Life Atom smallest unit of matter maintaining properties of an element Subatomic Particles protons neutrons and electrons Daltons unit of measurement used for atoms Mass Number Atomic Mass protons neutrons Isotope different atomic forms of the same element different number of neutrons Radioactive Isotopes unstable spontaneous nucleus decay gives off protons and becomes a different element Ion unequal number of protons and neutrons has a charge Electron Potential Energy determined by its energy levels electron shells closer to nucleus less potential energy periods rows of periodic table correspond to electron energy level Valance Electrons electrons in outermost shell of an atom atom with completed shell is unreactive 23 Chemical Bonding Covalent Bonding sharing of a pair of valance electrons completing a valance shell Electronegativity attraction of an atom to electrons of a covalent bond pull on shared electrons same element same electronegativity electron pull is equal quotnonpolar bondquot Ionic Bonding one atom strips another atom of an electron Cation Anion lt Attract One Another Ionic Compounds Salts formed by ionic bonds Hydrogen Bonding very weak bond formed between hydrogen atoms van der Waals Interactions everchanging polarity of individual regions of an atom form weak temporary bonds Polar Bond one atom is bonded to a more electronegative atom unequal sharing of electrons ex Water NonPolar Bond electrons are shared equally 24 Chemical Reactions Reaction Properties all matter is conserved reversible chemical equilibrium reactions offset one another exactly reactions continue to occur but there is no net effect Chapter 3 31 Water Molecules Polar Molecule unequal sharing of electrons charge is unevenly distributed Oxygen is more electronegative than hydrogen Oxygen is partly negative Hydrogen is partly positive Hydrophilic substances with an affinity for water Hydrophobic substances with no affinity for water nonionic and nonpolar ex vegetable oil Water Molecule Properties Hydrogen Bonds constantly breaking and reforming in liquid state 32 Emergent Properties of Water 1 Cohesion Hydrogen bonds keep substance structured and held together Allows water to nourish plants against gravity through Capillary Action Extremely high surface tension and adhesion properties Adhesion allows water to cling to other polar molecules 2 Moderation of Temperature Water can absorb and release heat Heat Energy more volume more heat Temperature Average Kinetic Energy volume doesn39t matter High Specific Heat 1 call g X C it takes a LOT of heat to change water39s temperature stabilizes ocean temperature High Heat of Vaporization it takes a LOT of heat to evaporate water as liquid evaporates the liquid remaining cools down moderates Earth39s climate hot molecules evaporate leaving cool ones 3 Ice Density As water freezes it expands and therefore becomes less dense allowing ice to oat in water As temperature nears freezing hydrogen bonds move too slow to break so they become locked into frozen solid Ice is 10 less dense than water 4 Solubility Solution substances completely mixed together one homogenous product Solvent dissolving agent commonly water Solute substance that is dissolved Aqueous Solution solution in which water is the solvent How Dissolving Works water molecules surround individual ions separating them cations of the solute will attract to the oxygen and the anions of the solute will attract the hydrogen Colloid particles that are suspended in a liquid and do not dissolve Hydration shell water molecule sphere around dissolved ion Molecular Mass sum of all of the masses of all atoms in a molecule mole 602 x 1023 Like Dissolves Like Water will only dissolve other polar molecules 33 Acids and Bases Acids increase the hydrogen ion concentration of a solution more H than OH Bases reduce the hydrogen ion concentration of a solution pH Scale measure of how acidic or basic a solution is pH logH Neutral Solution 7 on pH Scale Acidic Solution 06 Basic Solution 814 Buffers a substance that minimizes changes in how acidic or basic a solution is it accepts hydrogen ions from a solution When there are too many and donates them When there aren39t enough usually acidbase pairs AP Biology Chapter 5 Carbon and Macromolecules Carbon Compounds Organic Chemistry the study of carbon compounds organic compounds thought only to arise in living organisms Vitalism the belief in a life force outside the laws of physics and chemistry mechanism the belief that all natural phenomena are governed by the laws of physics and chemistry Diverse Carbon Molecules Carbon Basics 4 valance electrons Usually forms single or double covalent bonds Hydrocarbons molecules consisting of only carbon and hydrogen Major component of petroleum and tails on fats in living organisms Non Polar Bonds petroleum and fat will not dissolve in water Isomers compounds with the same number of atoms of the same elements but different structures exhibiting different properties Structural Isomers differ in covalent arrangements of their atoms H c H H H I r391 I 39T H H H I H II H H Butane Methylpropane Both have C5H12 but differ in arrangement Cis Trans Isomers differ in arrangement about a double bond H H H CH3 CCf CC r x x K H3C CH3 H3C chibutane yumlb utene G39sisomer Transisomer H H R H C I C C I C R R H R Cis Isomer H39s and R39s on same sides Trans Isomer H39s and R39s on opposite sides Enantiomers isomers that are mirror images of each other and differ in shape due to an asymmetric carbon Asymmetric Carbon carbon attached to four different atoms Two different ways they can be arranged in space analogy a quotrightquot molecule won39t fit into the quotleftquot space like a right hand won39t fit a left glove Functioning of Biological Molecules Functional Groups chemical groups that affect molecular function by being involved in chemical reactions 7 Most Important Chemical Groups hydroxyl carbonyl carboxyl amino sulfhydryl phosphate and methyl all hydrophilic increase solubility of organic compounds Adenosine Triphosphate ATP organic molecule adenosine attached to three phosphate groups ADP When one phosphate splits off When reacted With water JIICTDHM HOUI iOKMUlA HAL39E OF COMPOUNDS EXAMPLL H H N JICLII 2 OH Alcohols IN 391 n tra R Tl R 39N H A39mt39m aces I 1 0 nonInquot zeal ionized Glycine 39 Ca boxyi R C Aldehydes an am 113 nod H T H gum um R SH 7 or H p c R I I H H Mon 45mm Fans OH OH II 0 O R c R 39 I I I C b L L 1 Waxmm O P O39 Cmaaqmosuhdih H C C C on o I I I I I howec lowed O H II H GM lml HI mphd39e Polar can form hydrogen bonds With water molecules helps dissolve organic compounds such as sugars Abundant in Carbohydrates Carbonyl CO Ketones if carbonyl group is Within a skeleton Aldehydes if carbonyl group is at the end of a carbon skeleton Found in Carbohydrates Carboxyl COOH Acts as an acid can donate an H because bond between 0 and H is so polar Found in Lipids Amino NH2 Acts as a base can pick up an H from surrounding solution usually water Amino group With Carboxyl group makes an Amino Acid Sul aydryl SH Two sulfhydryl groups can react forming covalent bonds can stabilize a protein Phosphate OPO3 Contributes negative charge to molecule of Which it is a part Usually contained in Nucleic Acid If Nucleic Acid does NOT have a phosphate group gt Nucleoside Chapter 5 Large Biological Molecules 51 Macromolecules 4 Main Classes of Molecules Carbohydrates Lipids Proteins and Nucleic Acids Macromolecules largest molecules classes of Carbohydrates Proteins and Nucleic Acid exhibit unique emergent properties Polymer long molecule consisting of many similar or identical building blocks linked by covalent bonds Monomers repeating units or building blocks of a polymer Enzymes macromolecules that speed up chemical reactions Dehydration Reaction reaction between two monomers with the loss of a water molecule each monomer involved provides part of the water molecule lost one provides the hydroxyl group the other the hydrogen Hydrolysis reverse of dehydration reaction disassembles monomers bond between monomers is broken by addition of a water molecule example digestion breaks down food polymers so it can enter our cells Polymers Diversity any and all diversity comes from the arrangement of common monomers 52 Carbohydrates Fuel and Building Material Carbohydrates sugars and polymers of sugars Monosaccharides simple sugars or monomers from which complex carbs are formed ex Glucose C6H1206 Disaccharides double sugars two monosaccharides joined by a covalent bond Glycosidic Linkage links together the two monosaccharides formed by a dehydration reaction Most common disaccharides sucrose table sugar linkage of glucose and fructose Polysaccharides many sugar building blocks a few hundred thousand joined by glycosidic linkages Serves as storage or building material Storage Polysaccharides Starch plants use starch to stockpile surplus glucose serves as stored energy stored glucose can be withdrawn through hydrolysis Glycogen animal sotrage polysaccharide stockpiled glucose usually in liver and muscles is released through hydrolysis when demand for sugar increases Structural Polysaccharides Cellulose structural polysaccharide used for tough walls that enclose plant cells strong materials not digestible by humans most abundant organic compound on Earth Chitin carbohydrate used by arthropods to build their exoskeletons Alpha and Beta Configuration Alpha a glucose ring with the hydroxyl group positioned below the plane Glucose In Starch Beta a glucose ring with the hydroxyl group positioned above the plane Glucose In Cellulose 53 Lipids Lipids hydrophobic macromolecule not true polymers however are assembled by dehydration reactions Fats constructed from glycerol an alcohol and fatty acids major function energy storage Triaclyglycerol consists of 3 fatty acids linked to one glycerol molecule Saturated Fatty Acid no double bonds between carbon atoms so many possibilites for bonds with hydrogen it39s saturated with hydrogen example animal fats lard and butter solid at room temp Unsaturated Fatty Acid one or more double bonds with fewer hydrogen atoms example plant and fish fats liquid at room temp olive oil Trans Fats saturated fats with trans double bonds Phospholipids make up cell membranes hydrophilic head with hydrophobic tail when added to water creates a bilayer shielding the hydrophobic tails quotperforms similar function in cellsquot a bilayer as a boundary between cell and its external environment Seroids carbon skeleton with four fused rings example cholesterol or vertebrate sex hormones Cholesterol precursor from which other steroids are synthesized 54 Proteins Account for 50 of dry mass of all cells Function of Proteins Accelerate chemical reactions defense storage transport cellular communication movement and structural support Enzymes regulate metabolism made of proteins quotacts as a catalyst speeding up chemical reactions Polypeptide polymers of amino acids Protein macromolecule made of one or more polypeptides Amino Acid molecule possessing an amino group ex NH2 and a carboxyl group 02H center of amino acid is the quotalpha carbonquot Peptide Bond two amino acids become joined by a dehydration reaction through linking their carboxyl groups loss of water molecule Many of these bonds creates a polypeptide Levels of Protein Structure Primary Structure linked series of amino acids with a unique sequence Secondary Structure segments of their polypeptide chains repeatedly coiled and folded result of hydrogen bonds between repeating Alpha Helix delicate coil shape held together by hydrogen bonding between every fourth amino acid Beta Pleated Sheet foldedpaper looking structure two or more strands lie side by side connected by hydrogen bonds between parts of two parallel polypeptide backbones Tertiary Structure overall shape of a polypeptide resulting from interactions between side chains Hydrophobic Interaction hydrophobic side chains cluster in the protein away from water van der Waals interactions hold them together Disulfide Bridges covalent bonds that reinforce shape of a protein Quanternary Structure overall protein structure that results from all polypeptide subunits SickleCell Disease caused by substitution of one amino acid for the normal one Denaturation unraveling of a protein caused by a change in environment example really high fevers change in environment can be fatal to humans Chaperonins protein molecules that assist in the proper folding of other proteins XRay Crystallography method used to determine 3D structure of proteins 55 Nucleic Acids Gene a discrete unit of inheritance consisting of DNA Nucleic Acids polymers made of monomers called nucleotides Deoxyribonucleic Acid DNA Provides directions for its own replication and directs RNA synthesis Genetic material inherited from parents proteins implement that genetic code Resides in the nucleus of a cell Ribonucleic Acid RNA Controls protein synthesis mRNA messenger RNA directs production of polypeptide Flow of genetic information DNA gtRNA gtProtein Polynucleotides polymers that make up nucleic acids Nucleotides made up of a nitrogen base a five carbon sugar pentose and phosphate groups Nucleoside portion of nucleotide without a phosphate group Pyrimidine has one sixmemebered ring of carbon and nitrogen atoms members of family are Cytosine C Thymine T and Uracil U Purine larger sixmembered ring fused to a fivemembered ring members of family are Adenine A and Guanine G Deoxyribose Sugar sugar in DNA Ribose Sugar sugar in RNA Double Helix two strands spiral around an imaginary axis shape of DNA Antiparallel the two strands of DNA run in opposite directions ex like a divided highway DNA A always pairs with T and C always with G RNA A pairs with U T is not present and C with G Transfer RNA tRNA brings amino acids to the ribosome during synthesis of polypeptide Chapter 8 An Introduction to Metabolism 81 Metabolism39s Transformation of Matter and Energy Metabolism all of an organism39s chemical reactions manages the material and energy resources of a cell Metabolic Pathway the path a molecule takes from beginning to after several reactions caused by enzymes Catabolic Pathways release energy by breaking down molecules ex cellular respiration Anabolic Pathways consume energy to build molecules ex synthesis of a protein from amino acids First Law of Thermodynamics the energy of the universe is constant it can be transferred but not created or destroyed Conservation of Energy Entropy a measure of disorder or randomness Second Law of Thermodynamics every energy transfer increases the entropy of the universe Spontaneous Process does not require any input of energy ex an old car rusting For a process to occur spontaneously it must increase the entropy of the universe Universe quotthe systemquot plus quotthe surroundingsquot 82 FreeEnergy Change Free Energy the portion of a system39s energy that can perform work when temperature and pressure are uniform throughout the system AGm AHm TASK Change in Free Energy Change In Total Energy Temperature X Change in Entropy Negative change in G spontaneous reaction Every spontaneous process decreases system39s free energy end product is more stable AG Gfmal Ginitial Free Energy Instability Example a glucose molecule is less stable more likely to break down than the simple molecules into which it can be split Equilibrium Maximum Stability As a reaction proceeds towards equilibrium free energy decreases A process is spontaneous and can do work only when it is moving towards equilibrium not at equilibrium Exergonic Reaction net release of free energy AG is negative moves towards equilibrium Note breaking of bonds doesn39t release energy it is the potential energy of creating new bonds Endergonic Reaction absorbs free energy from surroundings not spontaneous Metabolism never reaches equilibrium defining feature of life Constant ow of materials in and out of cells 83 Powers of ATP Cellular Work Chemical Work pushing of endergonic reactions that would not occur spontaneously ex synthesis of polymers from monomers Transport Work pumping of substances across membranes against direction of spontaneous movement Mechanical Work movement of chromosomes during cellular reproduction Energy Coupling use of an exergonic process to drive an endergonic one ATP contains sugar ribose nitrogenous base adenine and chain of 3 phosphate groups acts as immediate source of energy powering cellular work one nucleoside triphosphate used to make RNA bonds between phosphate groups can be broken by hydrolysis Phosphorylated Intermediate the hydrolysis of ATP usually results in the transfer of a phosphate group from ATP to this intermediate happens through coupling of exer and endogonic reactions ATP can be regenerated by adding phosphate to ADP ariaV V Z Lil EVA Endergonic 39 f Exergonic Energy from Energy for Cellular Respiration Cellular Work ADP i Heat ltATP Cycle endergonic Catabolic exergonic pathways are used to power this endergonic reaction 84 Enzyme Catalysts Enzyme macromolecule usually protein that acts as a catalyst to speed up a reaction Activation Energy energy required to contort a reactant molecule so the bonds can break and the reaction can occur Transition State when reactants have absorbed enough energy for bonds to break and are unstable Energy Barrier reactants must get to that activation energy in order to react creating a barrierenter Enzyme Catalysts Enzymes can lower the Activation Energy required Substrate reactant an enzyme acts on Enzyme Substrate Complex binding of enzyme and substrate analogy lock and key Active Site restricted region of enzyme that binds to substrate Induced Fitchange in shape of enzyme to make the active site fit snugly around substrate substrate is held by weak hydrogen and ionic bonds Ways Enzymes Can Lower Activation Energy 1 Active site provides template for substrates to come together in a way that allows the reaction to occur 2 Enzyme may stretch the substrate toward their transitionstate form 3 Active site provides a microenvironment more conductive to particular reaction 4 Direct participation of the active site in the chemical reaction Environment Effects on Enzymes Higher Temperature to a point Higher Enzymatic Activity Optimal pH 68 Cofactors nonprotein helpers for catalytic activity Coenzyme if the cofactor is an organic molecule ex nutritional vitamins Competitive Inhibitors reduce productivity of enzymes by blocking substrates from entering active sites NonCompetitive Inhibitors do not directly compete with the substrate bind to another part of the enzyme to impede reaction Enzyme Inhibition Examples poisons antibodies etc Selective Inhibition naturally present in cell to regulate enzyme activity 85 Enzyme Regulation Allosteric Regulation protein39s function at one site is affected by binding of a regulatory molecule to a separate site may result in inhibition or stimulation to enzyme activity Activator stabilizes shape that has functional active sites ex ATP Inhibitor stabilizes inactive form of enzyme ex ADP Cooperativity amplifies response of enzymes to substrates Feedback Inhibition metabolic pathway switched off by inhibitory binding of its end product to an enzyme that acts early in the pathway ex when ATP inhibits an enzyme in an ATP generating pathway due to overstock of ATP