Study Guide biology 1305
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This 10 page Study Guide was uploaded by Lillian Scott on Tuesday September 22, 2015. The Study Guide belongs to biology 1305 at University of Texas at El Paso taught by Apodaca, Jennifer in Summer 2015. Since its upload, it has received 47 views. For similar materials see General Biology in Biological Sciences at University of Texas at El Paso.
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Date Created: 09/22/15
EXAM 1 PROACTIVE REVIEW Take some time to review the outline lling in missing information Use the questions provided to test your knowledge use this guide as a way to irther your understanding Try each question do not simply look up the answers For the vocabulary word see if you can de ne each and group similar ideas together For all of the information present think about forming a study group and quizzing each other or work together to answer the questions just make sure you CAN yourself answer the questions Also remember you can always come to of ce hours Learning Objectives Students should be able to Introduction to Biology Name five fundamental characteristics shared by all living organisms Describe the two components of the cell theory Brie y explain the theory of natural selection and explain under what conditions natural selection will happen e g Must the variation be heritable Read a phylogenetic tree and understand the role of similarities and differences in constructing phylogenetic trees Describe what biologists do that is how they approach problems and why they do experiments The Chemical Basis of Life Explain how and why atoms interact to form molecules Sketch examples of how electrons are shared in nonpolar covalent bonds polar covalent bonds and ionic bonds List the unusual properties of water Explain how these properties relate to the structure of water molecules and how they make water important for life De ne energy and describe the major forms it can take Understand in what way chemical bonds can be considered a form of energy Explain both in mathematical terms and in plain English how changes in entropy and potential energy determine whether or not a reaction is spontaneous Understand under what conditions a nonspontaneous reaction can occur Know why carbon is a key element for life List the six major functional groups their structural formulas and their basic characteristics Protein Structure and Function Explain and give examples of why proteins are essential to cell function Sketch the basic structure of an amino acid and describe why and how the side chains affect the function and structure of each amino acid Describe the four levels of protein structure and give examples of each Explain what an enzyme is understand why enzymes are needed to help chemical reactions proceed in living cells and know the role of the active site Nucleic Acids and the RNA World Sketch a nucleotide label its three basic parts and identify the 239 339 and 539 carbons Make another sketch showing the primary and secondary structures of DNA Describe the primary secondary tertiary and quaternary structures of RNA and explain in what ways RNA differs from DNA Explain why and how the secondary structure of DNA allows organisms to store and copy information Explain why RNA and not DNA was probably the rst selfreplicating molecule and describe at least one piece of experimental evidence that supports this hypothesis Lipids Membranes and the First Cells Sketch a phospholipid39s molecular structure and explain why phospholipids spontaneously form bilayers in water Predict which way a certain substance will diffuse given its concentration on either side of a selectively permeable membrane Predict which way water will move given the overall solute concentration on either side Describe at least three ways in which membrane proteins can help substances cross a cell membrane De ne the difference between passive transport and active transport and give examples of each An Introduction to Carbohydrates List the features shared by all carbohydrates Sketch several representative monosaccharides illustrating three ways in which monosaccharides can differ from one another Describe the type of monomer the type of linkage the branching if any and the major functions of the following polysaccharides starch glycogen cellulose chitin and peptidoglycan Give examples of the four major functions that carbohydrates can perform in cells raw materials structure cell identity and chemical energy storage 339 carbon 539 carbon acetaldehyde acid acid base reaction acidity activation energy active site adaptation adenine A adenosine triphosphate ATP adhesion alcohol aldehyde aldehyde aldose alkalinity allosteric regulation amine amino acids amino group amphipathic amylase amylopectin amylose anion antiparallel arti cial selection atom atomic number autoradiography ballandstick model base binomial buffer carbohydrate carbon carbonyl group carboxyl group carboxylic acid catalysis cation cell cell membrane cell signaling cell theory cell wall cellcell recognition cellulose chemical bond chemical energy chemical equilibrium chemical evolution chemical reaction chitin cholesterol coenzymes cofactors cohesion competitive inhibition complementary base pairing complementary strand complex carbohydrate concentration concentration gradient condensation reaction covalent bond Cterminus cytosine C dalton dehydration reaction denaturation deoxyribonucleic acid DNA deoxyribonucleotide deoxyribose dimer disaccharide disul de bond disul de bonds domain double bond double helix electrically charged electron electron shell electronegativity element endergonic endergonic endothermic energy entropy enzyme equilibrium ester linkage eukaryote evolution exergonic exothermic experimental study fat fatty acid rst law of thermodynamics tness uidmosaic model formaldehyde ee energy ee radicals freezefracture electron microscopy inctional group galactose gel electrophoresis generation genus s genera Gibbs ee energy glucose 0t andB glycerol glycogen glycoprotein glycosidic linkages 0c and B guanine G hairpin heat heritable trait hexose homeostasis hydrocarbon hydrocarbon tail hydrogen hydrogen bond hydrogen ion hydrolysis hydrophilic hydrophobic hydroxide ion hydroxyl group hypertonic hypothesis hypothesis testing hypotonic induced t initiation inorganic molecules integral membrane protein ion ionic bond isotonic isotope ketone ketose kinetic energy kingdom linear form lipid lipid bilayer liposome lockandkey model macromolecule major groove mass number mechanical energy meniscus micelle microscope minor groove modi cation molarity mole molecular chaperone molecular formula molecular weight molecule monomer monosaccharide multienzyme complex N acetylglucosamine NAc natural selection neutron nitrogen nitrogenous base nomenclature nonpolar nonpolar covalent bond nonspontaneous chemical reactions Nterminus nucleic acid nucleotide nucleus null hypothesis observational study oil oligopeptide oligosaccharide OparinHaldane proposal orbital organic molecules organic phosphate osmosis oxygen ozone pentose peptide bond peptidoglycan permeability pH scale phosphate group phosphodiester linkage phospholipid phosphorylase phosphorylation photons photosynthesis phylogenetic tree phylogeny phylum planar bilayer plasma membrane polar polar covalent bond polar head group polarity polymer polymerization polypeptide polysaccharide population potential energy prebiotic soup prediction primary structure prion product prokaryote protein proton purine pyrimidine quaternary structure reactant reaction rate renaturation residue Rgroup ribonucleic acid RNA ribonucleotide ribose ribose problem ribozyme ring form RNA world hypothesis saturated lipid scanning electron microscope SEM scienti c name scienti c theory second law of thermodynamics secondary structure selective permeability side chain simple sugar single bond solute solution solvent sound energy space lling model speciation species speci c heat spontaneous chemical reactions starch stemandloop structure steroid structural formula substrates sugar sugarphosphate backbone sulfhydryl group surface tension system taxon s taxa pl taxonomy temperature template strand termination tertiary structure tetramer theory thermal energy thiol thymine T transition state transitionstate facilitation tree of life triacylglycerol triglyceride triose triple bond unsaturated lipid uracil U valence electron valence shell Van der Waals interactions wax Xray crystallography ochelix Bpleated sheet AG I WHAT DOES IT MEAN TO SAY THAT SOMETHING IS ALIVE A All living organisms share fundamental traits which are II THE CELL THEORY A Statement of the cell theory B Are all organisms made of cells 1 Cells were first described and identified in cork tissue Hooke 1665 and in water and a variety of living tissues van Leeuwenhoek 2 A cell is an organized compartment 3 The components of the cell theory are C Where do cells come from 1 Spontaneous generation hypothesis versus allcellsfromcells hypothesis a Pasteur s experiment supported the allcellsfromcells hypothesis b What problems would have arisen if Pasteur had not kept all variables except the independent variable the same III THE THEORY OF EVOLUTION BY NATURAL SELECTION A What is evolution 1 Species 2 The characteristics of a species can be modified from generation to generation process component a Darwin and Wallace 1858 proposed B What is natural selection 1 Natural selection occurs whenever two conditions are met a b 2 How do these two conditions lead to evolution 3 Natural selection acts on individuals but evolutionary change affects only populations 4 Examples of selection IV THE TREE OF LIFE A Evolution leads to speciation the generation of new species 1 This implies that all species come from preexisting species and that their ancestry can be traced back to a single common ancestor 2 Therefore we should be able to reconstruct the quottree of lifequot a family tree of all organisms B Using molecules to understand the tree of life 1 Evolutionary relatedness should be re ected in molecular 2 Woese and colleagues proposed using to assess the relatedness of all living groups of organisms 3 Surprises of the new tree of life based on molecular data a There are three major lineages in the tree of life b Fungi are more closely related to than to plants 4 The tree of life is continuously being revised to re ect new data C How should we name branches on the tree of life 1 The three major lineages of life Bacteria Archaea and Eukarya are called domains 2 A phylum 3 There is not yet agreement on how to name the sublineages within phyla Many evolutionary biologists no longer use these terms for example Class Mammalia is now simply called Mammalia without the Class Yet still KNO WALL of these levels 4 Each species has a unique V DOING BIOLOGY A The nature of science 1 Biologists test the predictions made by 2 Biologists explore only those types of questions that can be tested b B An introduction to hypothesis testing 1 State the hypothesis as precisely as possible and list the predictions that it makes Remember to search for alternative hypotheses 2 Design an observational or experimental study that can test the predictions 3 Interpret the results a If the predictions are accurate the hypothesis is b If the predictions are not accurate the hypothesis as originall stated is not correct It may need to be modified or discarded altogether in favor of an alternative hypothesis C An introduction to experimental design 1 Experiments allow researchers to test the effect of a single 2 Important features of experimental design a It is critical to include groups to rule out the effect of other factors b Control groups and experimental groups are exposed to exactly the same conditions c Repeating the test is essential THE CHEMICAL BASIS OF LIFE 1 Atoms Ions and Molecules The Building Blocks of Chemical Evolution 96 of every organism is composed of the elements A Basic atomic structure 1 Parts of an atom a Protons l The number of protons gives an atom 2 Number of protons number b Neutrons l The number of neutrons does not affect the atom39s but affects its 2 Number of protons number of neutrons number 3 have different numbers of neutrons c small outside nucleus negative charge d Most of an atom39s volume is empty space 2 Electron orbitals and valence a Electrons occupy b Unpaired electrons are unstable and tend to form bonds c atom s valence B How does covalent bonding hold molecules together 1 A pair of electrons is shared between two atoms with 2 If the electrons are shared equally between the two atoms then the covalent bond is nonpolar Examples H H bonds and bonds 3 If the electrons are pulled closer to one of the atom s nuclei then the covalent bond is a The tendency of an atom to hold electrons tightly is its b Polar covalent bonds result in partial charges on certain parts of the molecule Example water 4 Single bonds share one pair of electrons C Ionic bonding ions and the electronsharing continuum 1 In an ionic bond the 2 The donor atom carries a charge the recipient atom carries a charge 3 Covalent and ionic bonds represent two extremes of an electronsharing continuum D The geometry of simple molecules 1 The orientation of the orbitals E Representing molecules 1 Molecular formula 2 Structural formula 3 Ballandstick model 4 Spacefilling model F Basic concepts in chemical reactions l A chemical reaction is a rearrangement of the bonds between atoms and can result in the breakdown of molecules or the formation of new molecules 2 Quantifying molecules 11 The Early Oceans and the Properties of Water A Why is water such an efficient solvent 1 Polarity and shape a H20 is a polar molecule due to b H20 is bent which allows the partial negative charge on the oxygen to quotstick outquot 2 Hydrogen bonds a Due to water39s polarity and shape hydrogen b Hydrophilic c Hydrophobic d Nonpolar amp Polar B How does water s structure correlate with its properties 1 Cohesion adhesion and surface tension result 2 Water expands as it forms a solid so ice oats How does this properties in uence life in ponds rivers and other waterways 3 Water has a very high specific heat and heat of vaporization C Acid base reactions involve a transfer of protons l Dissociation ofwater H20 H OH 2 Acids donate during a chemical reaction bases take 3 pH is a measure of the concentration of hydrogen ions in solution a pH log H Fig 216 b A pH below 7 is a pH above 7 is a pH of7 is 4 Buffers weak acids protect cells against damaging changes in pH by taking up H ions when they are in excess and releasing them when they are scarce 111 Chemical Reactions Chemical Evolution and Chemical Energy A How do chemical reactions happen 1 In a chemical reaction reactants are converted into products 2 Most reactions are reversible 3 Chemical equilibrium a Rate of forward reaction equals rate of reverse reaction equilibrium is dynamic but stable b Equilibrium can be disturbed by adding more reactant or product or by altering the temperature 4 Reactions that absorb heat are endothermic reactions that release heat are exothermic B What is energy 1 Energy is 2 Examples of different forms of energy a l in chemical bonds is called chemical energy b l of molecular motion is called temperature 3 First law of thermodynamics C Chemical evolution a model system 1 reactions are those that proceed on their own without any added energy a Reactions tend to be spontaneous if either or both of these conditions are met 1 The products have lower potential energy than the reactants negative AH exothermic reaction 2 The product molecules are less ordered than the reactant molecules positive AS increase in entropy 2 The Gibbs freeenergy change AG summarizes the combined effects of changes in heat and disorder a AG AH T AS b If AG is negative the reaction is exergonic and c If AG is positive the reaction is endergonic and d If AG 0 the reaction is at equilibrium 3 The role of temperature and concentration in chemical reactions a A spontaneous reaction may not be fast b Higher concentrations and temperatures tend to speed up chemical reactions D How did chemical energy change during chemical evolution 1 Early Earth was probably bombarded with highenergy photons which can break molecules apart to form highly reactive free radicals a Free radicals are thought to be responsible for some of the key reactions in early chemical evolution 2 Experiments modeling conditions on early 3 Chemical energy and chemical evolution a During chemical evolution the energy in sunlight was converted to chemical energy the potential energy stored in chemical bonds b This allowed for larger more organized molecules to be formed from smaller simpler ones IV The Importance of Carbon A carbon atom can Molecules that contain carbon are called A Linking carbon atoms together 1 The carbon atoms in an organic molecule furnish a skeleton that gives the molecule its overall shape 2 After organic molecules formed heat could drive the formation of more complex organic molecules from simpler ones B Functional groups 1 Functional groups 2 There are six major functional groups function as function as are reactive with one another and can are highly soluble have two negative charges and can affect Large amounts of energy can be released when the bonds between adjacent phosphate groups are broken f can link two PROTEIN STRUCTURE AND FUNCTION 1 Early OriginofLife Experiments A The OparinHaldane proposalstates that 1 Formation of small carboncontaining compounds formaldehyde etc 2 Formation of midsized buildingblock molecules amino acids sugars and nucleotides from the small compounds 3 Formation of large biomolecules proteins nucleic acids and complex carbohydrates from the buildingblock molecules 4 Development of the ability to selfreplicate by one of the large biomolecules B Stanley Miller39s experiment 1953 1 Miller C More recent experiments 11 Amino Acids and Polymerization A The structure of amino acids 1 Most proteins are composed of only 2 All amino acids have a A central carbon with four bonds attached to these four components 1 b A basic amino group NH3 9990 2 c An acidic COO d A hydrogen atom e An Rgroup also called B The nature of side chains 1 The side chain makes each of the 20 amino acids unique 2 Side chains can have functional groups that affect reactivity 3 Polarity affects solubility 4 Side chains containing carboxyl sulfhydryl hydroxyl or amino groups tend to be both 5 Explain why the amino acids with polar side chains are hydrophilic and the amino acids with nonpolar sid chains are hydrophobic C How do amino acids link to form proteins 1 Polymerization is a A protein is a polymer that consists b Polymerization always requires 2 Could polymerization occur in the environment of early Earth a Polymerization occurs via b Hydrolysis c Polymerization can happen spontaneously in some situations such as on clay particles and near undersea volcanoes This may have occurred on ancient Earth 3 The peptide bond a A peptide bond b Peptide bonds are unusually stable and help provide a structural framework or quotbackbonequot for the entire molecule III Proteins Are the Most Versatile Large Molecules in Cells A Catalysis B Defense C Movement D Signaling E Structure F Transport IV What Do Proteins Look Like A Protein structure 1 Proteins differ in size shape and 2 A protein39s structure has basic levels of organization B Primary structure is 1 Every protein has a unique sequence of amino acids 2 The sequence of amino acids dictates all higher levels of protein structure due to the nature of the Rgroups present 3 Even small changes in the amino acid sequence can result in significant changes in overall protein function Example hemoglobin and sicklecell anemia C Secondary structure emerges when parts of the polypeptide backbone interact 1 Each peptide bond is polar because the has a slight positive charge and the carboxyl group has a slight negative charge 2 The carboxyl portion of one peptide bond can form a hydrogen bond with the amino portion of another peptide bond 3 The hydrogen bonding can result in two different structures a b c Which one forms if either is determined by D Tertiary structure is due to sidechain interactions 1 Depending on their identity Rgroups can interact in the following ways a b c d e E Quaternary structure arises when different polypeptides interact 1 Many proteins are actually multiple polypeptide chains subunits folded together 2 The subunits F Folding and function 1 Most elements of protein structure are based 2 Folding happens spontaneously 3 Folding is essential for 4 Folding is often 5 Prions Describe and label elements of the primary secondary tertiary and quaternary structures if any of the proteins in V Enzymes An Introduction to Catalysis See Handout I have started to create an outline for you for the first exam I hope it acts as a pattern to help you create the rest of the study guide as well as future outlines While reading the text you can type into Word the bold words or words you do not know After you create a list you can a Select the text in a bulleted or numbered list b On the Home tab in the Paragraph group click Sort c In the Sort Text dialog box under Sort by click Paragraphs and Text and then click either AscendingDescending Use the main section headers to create major sections and ll in major themes concepts and ideas Keep track how to have divided information make indents and formal sections capital letter number lower case letter roman numeral for example 0 Indentify the main point than record definitions or key words as well as important people that help with shaping the concept 0 Think about how all the information relates what joins concepts together Write out those linkages as well 0 Also include examples or points that help you remember If you are having trouble finding such points Step out and try write a summary of that section using only 5 words at a time What points could you structure with these 5 word sentences Further Questions Harvester ants feed on seeds found in arid landscapes such as deserts in some such landscapes there has been documented many species of these ants Some of the harvester ants are smaller where as some are larger some form larger colonies where as some have small colonies Scientist have noted that species that have the same job in communities compete for resources such as food and only one species wins If this is true how can so many harvester ants live in a small area How would you test if the ants are in competition Create an outline that would demonstrate how would you conduct such an experiment Please included controls experimental design what kind of data would you collect In your own words how did complex molecules form on earth Cite speci c steps and requirements Concluded with the ramifications of C as the base for organic life and why is water so necessary for life If NASA researchers announced they found life on another planet what would they need to demonstrate to convince you they had truly found life Define evolution Compare and contrast evolution and natural selection If populations vary and natural selection is dynamic and changing favoring the fitter does this explain why species go extinct Living fossils are organisms that resemble organisms that existed long ago If similar and related organisms evolved and went extinct how and why are living fossils observed Some organisms look extremely similar to their ancestors many species of sharks are a good example How could you explain such conserved body plans Make an outline for the following questionDo antibacterial soaps really work Discuss how this could be tested What observations may be made andor what experiments might be done to test these hypotheses For an experiment determine the controls they would need to give them confidence in the validity of their results Types of chemical bonds Describing hydrogen covalent and ionic bonds after defining the types of bond give a chemistry example In addition make nonbiological analogies to these types of bonds think comparing the molecules in covalent bonds to partners in a threelegged race The properties of water Describe water s unique properties After describing the properties answer the following questions How a leaf can land on the water s surface but a rock sinks Why is there less variation between day and night temperatures and the beach than there is between day and night temperatures in the desert Why salt dissolves in water but gasoline does not Please make a Bohr model for the following 0 H C N H20 and C2H4 What type of atoms are the first four what type of molecules are the last two What if anything is important about the last two molecules Fill in the following table of water s properties and their biological consequences Property Biological Consequences Solvent High cohesion High adhesion Denser as a liquid than a solid High specific heat High heat of vaporization
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