Principles of Biology I
Principles of Biology I BIO 111
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BIO 111 Ch 1 Notes 1212010 31900 PM Science the knowledge derived from observation and experimentation Hypothesis an educated guess tentative explanation for a scientific phenomenon Characteristics of a good hypothesis can be rejected or refused but not proven must be testable Good science is hypothesisdriven o Come from observations natures questions o Testable statements o Observed occurrence of behavior Prediction explanation of what will arise during experiment o Based on prior experience or observation Controlled experiment o Independent variable whatever factor the scientist is manipulated or changed in the experiment o Dependent variable what is being measured in the experiment o The control the condition held constant for comparison Minnesota tree frogs o Pieter Johnson o Hypotheses 0 Pesticides 0 Heavy metal contamination 0 Infection by parasitic Ribeiroia may cause abnormalities in the limb development of Pacific tree frogs o Hypothesis Infection of the Pacific tree frog tadpoles by the parasite Ribeiroia causes developmental limb abnormalities 0 Conclusion Ribeiroia causes developmental limb abnormalities in Pacific tree frogs Sample size how many test subjects are in the group the larger the sample the more reliable the conclusions Sampling error the accidental selection of a nonrepresentative sample from some larger population Primary literature published article written on the experiment 1212010 31900 PM 1212010 31900 PM Introductory Bio Notes 8242010 21100 PM What is biology o Properties of life 0 1 or more cells 0 Genetic information 0 Use above to reproduce o Geneticallyrelated have evolved o Converts molecules 0 Extract energy to do biological work 0 Regulate internal environment o Viruses have many of the characteristics of life Are viruses alive 0 They cannot reproduce on their own o Biological organization 0 The biospheree ecosystemse communitiesepopulation59 organismse organsorgan systems9 tissuese cells organellese molecules 0 Ecology study of species interactions with each other and their environment 0 We will study the makeup and functions of cellular components 0 httppeertamueducurriculum modulesCell Biologymodu le 1levels200f200rqanizationipq o Cells 0 1665 Robert Hooke observed and named the first cells from a slice of cork 0 Cell theory Matthias Shleiden and Theodor Schwann formulated the cell theory Cells are the basic unit of all living organisms Are distinct from one another Are the building blocks of complex organisms o Spontaneous generation See Fig 47 o MODERN cell theory Adds that cells n Come from preexisting cells a Are chemically similar a Carry out most reactions intracellularly n Replicate and pass on complete genes n Viruses are acellular Unicellular versus multicellular Evolution 0 O 0 Defined as change in the genetic makeup of biological populations over time Unifying principle of biology Charles Darwin 0n the Origin of Species 1859 Common ancestors Concept of species Natural selection 9 adaptations Fig 13 from book shows adaptations CELLS 8242010 21100 PM Heritable information is stored in DNA o Genome DNA deoxyribonucleic acid DNA structure o Double helix model o Nucleotides 9 strands 9 double helix o Sections of DNA are GENES o Genes encode proteins Proteins do work of cells DNA 9 RNA 9 Protein dogma of molecular biology o DNA transcribes to make RNA o RNA translates to make protein o Human DNA has about 3 billion base pairs o Mutations altered proteins NUTRIENTS amp METABOLISM Metabolism sum of all work done in and out of the cells Cells take in nutrients from their environment for energy and to build new structures Breaking down molecules releases energy o For movement o For synthesis o For electrical impulses HOW IS ALL LIFE RELATED All are geneticallyrelated o If they have similar genomes they share a recent common ancestor o If they have dissimilar genomes they share a more distant common ancestor Biologists have used fossil record in order to establish a relationship between organisms9 now we use molecular record HOW DID LIFE ARISE Earth is 4546 billion years old Life arose about 4 billion years ago Random interactions of molecules reproduced and yielded more complex molecules o Formed the first genomes When these molecules could reproduce themselves life arose o Next step of life was the formation of cells o Molecules genomes became enclosed by membranes 0 Created intracellular environment o For 2 billion years all life was unicellular o Prokaryotes o Lived in oceans 0 Little oxygen in the atmosphere PHOTOSYNTHESIS CHANGED THE COURSE OF LIFE All early prokaryotes took in molecules to break them down for energy About 27 billion years some cells became photosynthetic o Take in sunlight and C02 to make sugars 02 is a byproduct o Use of sunlight to generate energy to synthesize sugars oxygen o Oxygenated environment caused Organisms to move onto land 0 Evolution to use aerobic metabolism more efficient than anaerobic metabolism 0 Ozone layer formation 0 PROKARYOTIC vs EUKARYOTIC Prokaryotes started to evolve into eukaryotes about 15 billion years ago o Endosymbiosis organism living inside another symbiosis in which one organism lives inside the body of another o Multicellular organisms arose about 1 billion years ago HOW DO WE STUDY LIFE Science method of learning new information Based on inquiry or observation o Search for informationexplanation Scientific inquiry o Discovery science 0 To describe 0 Descriptive via careful observations 0 Observationse data 0 Data can be quantitative or qualitative 0 Conclusions made via inductive reasoning o Hypothesisbased science 0 To explain 0 What causes o What explains o Hypothesis a possible answer educated guess 0 Must be able to test this 0 Design experiments to test 0 Hypothesisprediction method Make observation Ask question Form hypothesis Make prediction Test prediction 0 Requires DEDUCTION o Deductive reasoning use general information to come up with a specific conclusion 0 Ifthen logic 0 Hypotheses must be testable AND falsifiable If results support it becomes a theory 0 The Scientific Method The steps of hypothesisbased science make up the Scientific Method 0 Controlled experiments Experimental vs control groups have 1 variable difference What if controls are not used Allows others to repeat investigation o Science is powerful 0 Must be repeatable may be rejected PROPERTIES OF WATER 8242010 21100 PM Ice floats Water modulates heat absorption Not all water evaporates Water adheres in droplets Water is the solvent of life o Everything biological is dependent on water o Can dissolve substances in water o Polar c When water is the solvent the solution is called an aqueous solution The solvent of life o Water dissolves polar solutes o Ionic 0 Sugars o Proteinse if polar or ionic o Due to charge attractions o A substance that has an affinity for water is hydrophilic o A substance that repels water fats or oils is hydrophobic Solute concentrations c To make solutions we want to add specific amounts of solute to water How 0 Can add solute to a certain ex 10 NaCl solution 0 Can add solute to a certain concentration ex 100 gL 0 Can add solute to a certain molarity A mole is the number of grams to the molecular weight of a substance Ex Sucrose is 342 gmol o More Solute contrations o Sucrose structure C12H22011 o Sucrose mass 12x12 22x1 11x16 342 d or 342 grams 0 To make a molar solution 1M Add 1 mol of sucrose 342 g water to 1L 0 To make a 5M solution Add 5 mol of sucrose 17109 water to 1L 0 To make a 029 M solution Add 029 mol of sucrose 100 g water to 1L ACIDS and BASES H20 H OH In pure H20 H and OH each present at 1x107 molL Acidic or basic solutions occur when there is more H or OH ions Acid gives up H so H concentration rises Example HCl9 H Cl 9 acidic solution HCI is a STRONG acid Weak acids will not give off all their protons CH3COOH 9e CH3COO H acetic acid o Base reduces H concentration 0 May soak up H NH3 N NH4 0 May release OH which soaks up H NaOH9 Na OH OH H 9 H20 o More OH than H basic solution pH scale o In any solution H OH 1x1014M Neutral solution H 1x107M and OH 1x107M In an acidic solution H may 1x105M This means OH 1x109 In a basic solution OH may 1x104M This means H 1x1010M pH scale is logarithmic pH logH In neutral solution pH log1x107 BUFFERS What is the normal pH inside cells How does pH remain constant Buffers minimize changes of pH By minimizing changes of H OH How o Accepts excess H or donates H when depleted o Buffer made up of either a weak acid or a weak base o If pH increases reaction goes to right o If pH decreases reaction goes to the left MACROMOLECULES Polymers o Monomersepolymers Amino acidse proteins Monosaccharidese polysaccharides Nucleotidese nucleic acids Lipids do NOT form polymers Carbon bonds to Hydrogen Oxygen Nitrogen Carbon o Can form single bonds double bonds or a combination of both Amino acid has an amino group a carboxyl group ATP adenosine triphosphate o Stores and releases energy 0 Via bonds between phosphate groups Isomer o Same of same atoms different arrangements o Function differently o Structural isomer different covalent arrangements o Optical isomer mirror image arrangements Macromolecules o Each has important functions o Functions related to sequences and shapes of macromolecules POLYMERS 8242010 21100 PM Monomers connected together to make polymer via condensation reactions dehydration reaction Polymers can be broken down to monomers via hydrolysis POLYMERS and DIVERSITY We all have the same monomers Diversity comes when the monomers are arranged differently o Example DNA with different sequences proteins with different sequences different phenotypes PROTEINS 10 000 in cell Very important molecules Make up 50 percent of dry mass of cells Function as enzymes hormones receptors structural transport defense movement Common protein enzymes What does an enzyme do o Acts as a catalyst Polymers Made up of amino acids monomers Long polymers are also called polypeptides Short ones are called peptides Amino acidse 20 of these L form AMINO ACIDS ASPECTS 1 Asymmetric C o Alpha carbon 2 Amino group 3 Carboxyl group C00 4 Hydrogen group 5 Variable group side chains o Makes each amino acid different Amino acid groups charged side chains hydrophilic attract ions polar uncharged hydrophilic form hydrogen bonds nonpolar hydrophobic special side chains o Cysteinee forms disulfide bridge o Glycine small o Prolinee contains rings found in loops FWNquot CATEGORIES Electrically charged hydrophilic side chains o Arginine o Histidine o Lysine o Aspartic acid o Glutamic acid Amino acids with polar but uncharged side chains o Serine o Threonine o Aspargine o Glutamine o Tyrosine Special cases o Cysteine o Glycine o Proline Amino acids with nonpolar hydrophobic side chains o Alanine o Isoleucine o Leucine o Methionine o Phenylalanine o Tryptophan o Valine PROTEINS To make polymers carboxyl group of 1 AA links to amino group of next AA via condensation reaction peptide bond Resulting peptide has a beginning and an end o Beginning amino N terminus o End carboxyl C terminus Polymer folds into a 3D shape Folding dependent upon AA sequence Folding determines function PROTEIN STRUCTURE 4 levels 1 Primary o Linear sequence of amino acids 2 Secondary o First degree of folding o Hydrogen bonding o Creates alphahelix betasheets Uturns and random coils 3 Tertiary o Overall 3D shape of protein o Secondary structures fold into this o Created by hydrogen bonds hydrophobic interactions van der Waals forces ionic bonds disulfide bridges o DISULFIDE BRIDGES one cysteine forms a bridge with another cysteine of the protein 4 Quaternary c When two or more polypeptide chains interact o Held together by WEAK bonds o Describes and location of chains o Sickle cell disease example How do proteins interact with other molecules o Shape fit together like a lock and key o Chemistrye amino acid side chains interact Protein folding o What determines the overall shape of a protein 0 Primary structure AA sequence 0 Folds spontaneously o 1 native conformation o Can we unfold proteins 0 Yes 0 pH salt temp chemicalsedenaturation 0 Removal of agenterenaturation Chapter 4 continued 8242010 21100 PM Protein folding Proteins can fold spontaneously but do they always o In a cell many need help o Chaperones proteins that aid folding 0 Also called heat shock proteins HSPs CARBO HYD RATES Roles o Store energy in transportable form o Carbon skeleton Categories o Monosaccharides one 0 Major nutrients for cells glucose 0 Glucose can be in straight chain or ring forms 0 Pentoses 5C sugars Ribose deoxyribose o Hexoses 6C sugars Glucose 0 3C sugars Glyceraldehyde o Disaccharides two 0 2 monomers joined by glycosidic linkage o Glycosidic linkage is a dehydration or condensation reaction H20 is thrown out o Oligosaccharides 320 monomers o Often found on the surface of cells proteins o Polysaccharides longer polymers 0 More monomers joined by glycosidic linkages 0 Can have branching o For storage building material support o Storage polysaccharides 0 Starch made of glucose monomers Joined by alpha 1C4C linkages Found in plants ex potatoes and grains 0 Animals store sugar as glycogen Glucose monomers alpha 1C4C linkage LIPIDS Similar to starch but no branching o Mainly in liver muscle cells Structural polysaccharides o Cellulose Found in plant cell walls Gives strength Most abundant organic compound Made of glucose monomers Beta 1C4C linkages 0 Most organisms cannot digest cellulose Enzyme that digests starch cannot digest cellulose Does provide insoluble fiber Cows and termites can digest cellulose due to microbes Chitin makes up exoskeletons of arthropods also cell walls of many fungi Structurally similar to cellulose with Ncontaining group Nacetyl group O O O O O 0 Not polymerse not covalently linked together Hydrophobic Mostly hydrocarbons Include fats phospholipids steroids include hormones Fatse provide efficient storage insulation cushioning Made from 2 smaller molecules linked together fatty acids and glycerol 0 Glycerol alcohol 0 Fatty acid 16 or 19C long carboxyl group Hydrocarbons are nonpolar Dehydration reaction brings 2 together 3 Fatty acidsefat Via ester linkage OH COOH 0 Can be same or different FAs Called triglyceride FAs vary in length FAs vary in numberlocations of double bonds o No double bonds saturated with H 0 Animal fats 0 One or more double bonds unsaturated o Gives a kink to chain 0 Plants and fishes Phospholipids o Made up of o 2 FA chains Phosphate group additional small molecule o Phospholipids have hydrophobic AND hydrophilic ends amphipathic o Exhibit selfassembly in water o Form phospholipidbilayer o Hydrophobic tails o Hydrophilic heads Steroids o Lipids containing 4 fused rings o Functional groups off rings vary o Cholesterol is precursor for other steroids 0 Hormones 0 Also a component of cell membranes Carotenoids and vitamins o Carotenoidse lightabsorbing pigments o Betacarotene helps trap light energy in plants 0 In humans beta carotene 2 vitamin A molecules Waxes o Hair feathers leaves have waxy coating to repel water o Long molecule with 4060 CH2 groups Nucleic acids o Store transmit use genetic information o DNAe deoxyribonucleic acid 0 Genetic blueprint 0 Can be replicated Prior to cell division 0 Can be transcribed into RNA Translated into protein Structure 0 Polymers of nucleotides 0 Nucleotide has three parts 1 Pentose sugar differs between RNA DNA 2 Nitrogenous base 1 of 5 different ones 3 Phosphate group Difference between DNA and RNA 0 Pentose sugar 0 DNA has H 2 C position 0 RNA has OH at 2 C position What about the different bases 0 2 classes purines pyrimidines 0 RNA has GACU 0 DNA has GACT o Complementary base pairing How are nucleotides linked o 3 OH 69 PO45 o Phosphodiester bonds 0 Have 5 and 3 ends Cell Membranes 8242010 21100 PM Cell Membranes 8242010 21100 PM Cell membranes made up of phospholipids proteins cholesterol Phospholipids hydrophilic head hydrophobic tails c When they are placed in an aqueous solution they will automatically form a bilayer for stability Fluid mosaic model shows the structure of the membrane o All components are fluid meaning they can move Membrane components are held together by hydrophobic interactions o Weak bonds o Components are able to move laterally within this model o Phospholipids can change place 1x10A7 times per second o Main componentphospholipids Membranes can remain fluid even when cold How o 1 Increase in of phospholipids with unsaturated tails o 2 Cholesterol prevents packing of phospholipids o 3 Increase in of lipids with shorter chains Membrane Proteins o Many types of proteins in cell membranes o Proteins present determine function o Different membranes have different proteins Two types of membrane proteins o Integral span the membrane 0 Transmembrane has hydrophobic AA s o Peripheral bound to surface Membrane proteins may be attached Protein functions transport enzymatic activity signal transduction cellcell recognition intercellularjoining attachment to cytoskeleton or ECM o Often have carbohydrate chains added 0 Called glycoprotein s 0 Can also have glycolipids Different carb groups mark each cell or tissue as different Cell adhesion cells connect together Cell recognition cells of the same tissue type bind together o These mediated by the plasma membrane 0 Specifically by integral glycoprotein s Connections between cells o Cell junctions structures that attach seal or allow communication between two cells o Cell of a tissue have orientation 0 Apical top 0 Basal bottom 0 Lateral side o Tight junctions link adjacent cells and seal the space inbetween cells prevent substances from passing between cells also define apical vs basal regions of cell 0 Example intestinal lining o Gap junctions channels that allow water small molecules and ions to pass from cell to cell c Desmosomes connect cells together 0 Uses intermediate filaments 0 Strong stable attachments Plasma membrane attaches to ECM o Stabilizes tissues o Integrin proteins mediate attachment 0 Bind to ECM on one end microfilaments on other end 0 Attachment to ECM is reversible Transport across membranes o Membranes are selectively permeable 0 Some things cross easily some not o What easily crosses the bilayer 0 Carbon dioxide Oxygen Nitrogen and ethanol o What does NOT cross easily 0 Ions polar molecules water glucose o Substances may cross membrane via 0 Passive transporte no energy needed 0 Active transporte energy input required Passive Transport also called diffusion o 1 Simple diffusion substance just crosses the bilayer o 2 Facilitated diffusion requires proteins channels or carriers Solute will move from area of higher concentration to lower concentration 0 Diffuses down its concentration gradient Movement of water Osmosis Regulation of water transport is important Water balance depends upon solute on both sides of the membrane Certain solute concentrations can cause cells to lose or gain water called tonicity o Isotonic solution same solute concentration as a cell A cell placed in isotonic solution will remain the same 0 Hypertonic solution has a higher solution concentration than a cell Lower solute concentration than in the cell THERMODYNAMICS 8242010 21100 PM Loss of usable energye entropy Entropy measure of disorderrandomness 2nd law of thermodynamics says that energy transfertransformation increases entropy Also says that for a reaction to occur spontaneously without energy input it must increase entropy Example food broken down without energy input yet this increases entropy via heat Freeenergy change To understand our chemical reactions we want to which reactions occur spontaneously but how J Willard Gibbs in 1878 defined the Gibbs free energy function Free energy energy that can do work given constant temperature and pressure Look at AG and AH and AS reactions in BOOK o Used to determine which reactions will occur without energy input o Initial state reactants must have more energy than the final state products o Final state has less energy and greater stability less likely to change o Most stable state of a reaction is EQUILIBRIUM Free energy and metabolism Chemical reactions can be exergonic o Release of free energy products have less o Negative AG o The greater the decrease of AG the more work can be done Can also be endergonic o Absorbs free energy o Stores free energy o Positive AG o Cannot occur without energy input Equilibrium Balance between forward and reverse reactions o A state of no net change AG 0 Catabolic reaction series of reactions Products never accumulate and are used in next reaction o Equilibrium never reached for these reactions A cell s work o What kinds of work do cells do 0 Mechanical work example is muscle contraction 0 Transport work pumps ionsmolecules across the membranes 0 Chemical work endergonic reactions ATP Adenosine triphosphate o A nucleotide that can be hydrolyzedbroken down o ATP H20 9 ADP Pi free energy Energy coupling o Can use ATP s hydrolysis favorable to make unfavorable reactions go forward o Transfer of phosphate group occurs o Protein x becomes phosphorylated which is just the addition of a phosphate group o Becomes less stable more reactive can do more work o Loses phosphate group during work December 2nd Notes 8242010 21100 PM LAW OF INDEPENDENT ASSORTMENT When Mendel crossed SS to 55 to get Fls that were Ss he made MONOHYBRIDS o Heterozygous for 1 trait Crossing Fls Ss x Ss monohybrid cross Mendel then worked with 3 different traits Added seed color yellow Y dominant to green y Cross yellowsmooth to greenwrinkled YYSS x yysseYySs F1 0 These are DIHYBRIDS heterozygous for 2 traits o In these plants will YampS be inherited together Or can they be separated If Y amp S were inherited together 4 types of progeny would result as for monohybrid cross 31 ratio 0 This is NOT the case 0 Each trait must be considered separately resulting in 16 types 9331 ratio Mendel s data supported this The alleles segregate independently O O PROBABILITY The laws of probability govern laws of segregation amp independent assortment RULE OF ADDITION 0 Use for probability than any 1 of 2 or more independent events will occut 0 Coin example heads vs tails 12 12 1 8242010 21100 PM 8242010 21100 PM Key terms from lecture chapter 2 Acidia substance that can release a proton in a solution Anioninegatively charged ion atomic nucleusinucleus around an atom atomic numberinumber of protons in the nucleus of an atom also equals the number of electrons around the neutral atom atomic weight atomsiall matter is composed of atoms baseisubstance that can accept a hydrogen ion in a solution bufferisubstance that releases or accepts hydrogen ions and can therefore resist changes in pH cationipositively charged ion chemical bonds covalentibond that arises from the sharing of electrons between to atoms usually a strong bond hydrogen bondiweak bond that arises from attraction between hydrogen atom and a nearby oxygen or nitrogen atom ionic bondibetween positively and negatively charged atoms usually a strong bond vander Waals forcesiweak attractions between atoms usually result in interactions of one atom with the nucleus of another about 1A as strong as a hydrogen bond cohesionitendency of molecules to stick together compoundisubstance made up of atoms of more than one atom electron shellsiregion surrounding the atomic nucleus at a fixed level in which the electrons orbit electronegativityitendency of an atom to attract electrons when it occurs as part of a compound electroninegatively charged atoms outside the nucleus elementisubstance that cannot be converted to simpler substances by ordinary chemical means energyicapacity to do work or move matter against an opposing force capacity to accomplish change heat of vaporizationienergy that must be provided to convert a molecule from a liquid to a gas hydrophiliciworks with water hydrophobicifear of water ioniatom or group of atoms with electrons removed or added isotopesisame number of protons with different number of protons in the same element moleiquantity of compounds whose weight in grams numerically equals its molecular weight AVOGADRO S NUMBER is 6023x10A23 molecular weightisum of atomic weights of the atoms in a molecule moleculeiparticle made up of two or more atoms joined by covalent bonds or ionic attractions neutronino electric charge particle of matter with mass approximately 1 amu pHimeasure of the acidity of a solution polarimolecule in which the electric charge is not distributed equally in the covalent bondsi likes water nonpolarimolecule whose electric charge is evenly balanced from one end to anotheridoes not like water protonipositively charged particle a hydrogen H molecule soluteisubstance that is dissolved in a liquid solutioniliquid that dissolves the substance solvent speci c heat