Principles of Biology I
Principles of Biology I BIOL 2107
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BIOL 2107 TEST 1 STUDY GUIDE CHAPTER 1 Define o The properties oflife 0 Order 0 Reproduction of viable offspring 0 Can regulate itself 0 Growth and development 0 Energy processing 0 Evolutionary adaptations 0 Response to the environment 0 The 7 themes of biology New properties emerge at each level in the biological hierarchy o Organisms react with other organisms and the physical environment I Cycling of chemical nutrients Life requires energy transfer and transformation Structure and function are correlated The cell is an organism s basic unit of structure and function The continuity oflife is based on DNA I DNA makes mRNA through transcription which makes proteins through translation 0 Feedback mechanisms regulate biological systems 0 o Reductionism o The approach of reducing compleX systems to simpler components that are easier to study 0 Systems biology 0 Approach that attempts to model the behavior ofthe whole system based on a study of the interactions among the system s parts 0 Emergent properties 0 Properties that emerge at each step that were not present at the preceding level Due to the arrangement and interactions of parts as complexity increases 0 Levels of biological organization 0 The biosphere all life on Earth and the places where life exists 0 Ecosystem all living things in a particular area along with nonliving components of the environment that interact with life 0 Community all organisms inhabiting a particular ecosystem Population all individuals on a species living within the bounds ofa specified area 0 Organism individual living things 0 o Organs and organ systems a body part that carries out a particular function 0 Tissues a group of cells that work together to perform a specific function 0 Cells the fundamental unit of structure and function 0 Organelles functional components in cells 0 Molecules 0 DNA 0 Doublehelix nucleic acid molecule with bases ACG and T o Chromosomes 0 Contains one long DNA molecule 0 Genes 0 Units of inheritance that transmit information A specific nucleotide sequence in DNA 0 Genomes o The entire library of genetic information that an organism inherits 0 Negative feedback 0 Accumulation of an end product ofa process slows that process down 0 Positive feedback 0 An end product speeds up its own production 0 The three domains of life 0 Bacteria I Prokaryotic o Archaea I Prokaryotic o Eukarya I Plantae carry out photosynthesis I Fungi absorb nutrients from surroundings many decompose dead organisms I Animalia ingestion o Prokaryotic cells 0 Simpler and smaller don t have any membrane bound organelles Eukaryotic cells 0 Divided into membraneenclosed organelles Has a nucleus Descent with modification 0 Darwin contemporary species arose from a succession of ancestors Natural selection 0 Darwin the natural environment quotselectsquot for the propagation of certain traits among naturally occurring variant traits in the population Inductive reasoning o Deriving generalizations from a large number of specific observations Deductive reasoning 0 Used after the hypothesis has been developed Involves logic that goes from general to specific Hypothesis 0 Atentative answer to a wellframed question Must be testable falsifiable Can t answer supernatural questions Theory 0 Broader than a hypothesis Is general enough to spin off new hypotheses and is generally supported by a much greater body of evidence Controlled experiment 0 Designed to compare an experimental group with a control group Technology 0 Applies scientific knowledge for some specific purpose Science 0 A way of knowing CHAPTER 2 Elements 0 A substance that can t be broken down to other substances by chemical reactions Compounds o A substance consisting of two or more different elements in a fixed ratio Essential elements 0 20 of the 92 natural elements that are required to live and reproduce O N C and H make up 96 ofliving matter Trace elements 0 Required in only small quantities Ca P K S Na Cl Mg Neutron 0 Neutral charge in atomic nucleus with protons Proton 0 Positive charge in atomic nucleus with neutrons Electron 0 Negative charge in electron cloud surrounding nucleus Atomic nucleus 0 Core at the middle of an atom has a positive charge due to protons Mass number 0 Top number number ofprotons and neutrons Atomic numb er 0 Bottom number number ofprotonselectrons Same for every isotope of an element Atomic mass 0 Total mass of an atom Isotopes o Atoms which have the same number of protons but more neutrons and a larger mass Behave the same in a chemical reaction Energy 0 The capacity to cause change Potential energy 0 The energy that matter possesses because of its location or structure Matter has a natural tendency to move to the lowest possible state of potential energy water runs downhill Electron shells 0 Energy levels surrounding the atomic nucleus As the shells get farther from the nucleus potential energy increases When an electron absorbs energy it moves to a shell farther from the nucleus Valence shell 0 The outermost electron shell Atoms with the same number of electrons in their valence shells have similar behavior Valence electrons o The electrons in the outermost shell An atom with 8 valence electrons is unreactive Orbital o The 3D space where an electron is found 90 ofthe time No more than 2 electrons can be in an orbital at the same time Covalent bond 0 The sharing ofa pair ofvalence electrons by two atoms Form molecules Formed due to proximity Single bond 0 A pair of shared electrons Double bond 0 Sharing two pairs ofvalence electrons Valence o Abonding capacity The number of unpaired electrons required to complete the atom s valence shell Electronegativity o The attraction of a particular atom for the electrons of a covalent bond The more electronegative an atom is the more strongly it pulls shared electrons toward itself FON and Cl have the highest electronegativity Nonpolar covalent bond 0 Electrons are shared equally because the two atoms have the same electronegativity Between to atoms of the same element Polar covalent bond 0 When one atom is bonded to a more electronegative atom the electrons are not shared equally H20 Ionic bond 0 When two atoms are so unequal in attraction for valence electrons the more electronegative atom strips an electron away from its partner NaCl The bond between an anion and a cation Ion o A charged atom or molecule Cation o A positively charged ion has fewer electrons Anion o A negatively charged ion has eXtra electrons Ionic compounds 0 Compounds formed from ionic bonds also known as salts Arranged in a 3D lattice and does not consist ofmolecules Hydrogen bond 0 The noncovalent attraction between a hydrogen and an electronegative atom usually 0 or N The partial positive charge on the H atom allows the H to be attracted to a different electronegative atom nearby van der Waals interaction 0 Between nonpolar molecules Changing regions ofpositive and negative charge allow atoms and molecules to stick to each other Occur only when atoms and molecules are very close to each other Weak bonds 0 Hydrogen and van der Waals Reinforce the 3D shape of the molecule Chemical reactions 0 The making and breaking of chemical bonds leading to changes in the composition of matter Chemical equilibrium 0 When the forward and reverse reactions occur at the same rate and the relative concentrations ofproducts and reactants stop changing The point where the reactions offset one another exactly Does NOT mean that productsreactants but that they are stable at a particular ratio CHAPTER 3 Define Water molecule o Shaped like a wide V with two H atoms joined to the O atom with single covalent bonds 0 is more electronegative than H so this is a polar covalent bond 0 region has a partial negative charge and H regions have a partial positive charge 0 Liquid water 0 Hydrogen bonds are very fragile and they form break and reform often 0 4 emergent properties ofwater o Cohesion I Hydrogen bonding holds water molecules together Allows for capillary action in plants 0 High specific heat I Specific heat is the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 degree Water changes its temperature less than other substances when exposed to the same amount ofheat absorption or loss Heat must be absorbed to break the hydrogen bonds meaning that there is a relatively small change in temperature because most of the heat was sued to break the bonds 0 Solvent powers I For salts NaCl water molecules surround the individual sodium and chloride ions separating them 0 molecules are negatively charged attracted to sodium cations while H regions are positively charged attracted to chloride anions I For sugars water molecules surround each of the solute molecules forming H bonds with them Made up of nonionic polar molecules 0 Ice oats I Ice is less dense than water so it oats If temperature is less than 4 degrees water begins to freeze because more of the molecules are moving too slowly to break hydrogen bonds 0 Adhesion o The clinging of one substance to another Adhesion ofwater to cell walls by hydrogen bonding helps counter downward pull of gravity 0 Surface tension 0 A measure ofhow difficult it is to stretch or break the surface of a liquid Water has a higher surface tension than most liquids 0 Kinetic energy 0 The energy ofmotion Heat 0 A measure of the matter s total kinetic energy due to the motion of its molecules Depends on volume Temperature 0 A measure ofheat intensity that represents the average kinetic energy of the molecules regardless ofvolume Calorie o The amount of heat tit takes to raise the temperature of 1g ofwater by 1 degree C Also the amount of heat that 1g ofwater releases when it cools by 1 degree Kilocalorie o The quantity ofheat required to raise the temperature of 1kg of water by 1 degree C Specific heat 0 The amount of energy that must be absorbed or released for 1g of that substance to change its temperature by 1 degree Evaporative cooling 0 As a liquid evaporates the surface of the remaining liquid cools down because the hottest molecules with the mist kinetic energy are most likely to leave as a gas Evaporation of water from the leaves ofa plant helps keep the tissues in the leaves from becoming too warm in the sunlight Heat ofvaporization o The quantity ofheat a liquid must absorb for lg ofit to be converted from the liquid to the gaseous state Result of the strength of the hydrogen bonds Solution 0 A liquid that is a completely homogenous miXture of two or more substances Solvent 0 The dissolving agent of a solution Solute o The substance being dissolved Aqueous solution o A solution in which water is the solvent Hydration shell 0 The sphere of water molecules around each dissolved ion Hydrophilic 0 Water loving Molecules with polar regions salts Hydrophobic 0 Water hating Nonionic nonpolar substances that can t form hydrogen bonds Oil nonpolar covalent bonds share electrons almost equally Colloid o A stable suspension of fine particles in a liquid Molecular mass 0 The sum of all the masses of all the atoms in a molecule Molarity o The number ofmoles of solute per liter of solution Hydrogen ion 0 A single proton with a charge of 1 Occurs when a hydrogen atom in a hydrogen bond between two water molecules shifts and leaves an electron behind Hydroxide ion 0 Has a charge of 1 Is the result of the water molecule that lost a proton OH Hydronium ion 0 The proton binds to the other water molecule H3 0 Acid 0 A substance that increases the hydrogen ion concentration ofa solution When dissolved in water they donate H Base 0 A substance that reduces the H concentration ofa solution Some directly accept H ions some dissociate to form OH ions which combine with hydrogen ions and form water The pH scale o A logarithmic scale from 014 pH declines becomes more acidic as H increases Each pH unit is a tenfold difference in H and OH concentrations pH 0 logh o Buffer o A substance that minimizes changes in the concentrations of H and OH in a solution Does so by accepting hydrogen ions from the solution when there are too many and donating H ions when they have been depleted Carbonic acid H2CO3 CHAPTER 4 Define 0 Organic chemistry 0 The study of carbon compounds Most organic compounds have hydrogen atoms also Mechanism 0 The View that physical and chemical laws govern all natural phenomena Vitalism o The beliefin life forces outside the jurisdiction ofphysical and chemical laws Carbon bonds 0 Has 4 valence electrons acts as an intersection point from which a molecule can branch off in as many as 4 different directions Makes large complex molecules possible Hydrocarbons 0 Organic molecules with only carbon and hydrogen Isomers 0 Compounds with the same number of atoms of the same elements but different structures and different properties Structural isomers 0 Different covalent arrangements of their atoms Could differ in the location of double bonds Cistrans isomers o Carbons have covalent bonds to the same atoms but these atoms have different spatial arrangements due to the in exibility of double bonds MUST HAVE DOUBLE BONDS o Cis the arrangement with both Xs on the same side of the double bond 0 Trans the arrangement with both Xs on opposite sides of the double bond Enamtiomers o Isomers that are mirror images of each other and have a different shape due to the presence of an asymmetric carbon attached to 4 different atoms or groups of atoms Functional group 0 Hydroxyl I OH Is polar can form hydrogen bonds with water Alcohols o Carbonyl I CO Is polar Ketones and aldehydes are structural isomers Found in sugars can form hydrogen bonds Ketone carbonyl group is present within a carbon skeleton Alehyde carbonyl group is present at the end of the carbon skeleton o Carboxyl I COOH an oxygen is double bonded to a carbon atom which is bonded to an OH group Acts as an acid can form hydrogen bonds is polar Ionized form has a charge of 1 is called a carboxylate ion 0 Amino I NH2 Acts as a base found in cells with a charge of1 Amines o Sulfhudryl I SH Can form covalent bonds with each other called quotcross linking Thiols o Phosphate I OPO3 2 Phosphorous atom bonded to 4 oxygen atoms one has double bond 2 have negative charges Negatively charged 2 at the end 1 when in the middle ofa chain ofphosphates Can react with water releasing energy 0 Methyl I CH3 A carbon bonded to three hydrogen atoms Nonpolar hydrophobic ATP 0 Adenosine molecule attached to a string of three phosphate groups CHAPTER 5 Define o Macromolecules 0 Huge molecules carbohydrates proteins and nucleic acids 0 Polymer o A long molecule consisting of many similar building blocks linked by covalent bonds 0 Monomer o The building blocks of polymers 0 Enzyme o Specialized macromolecules that speed up chemical reactions 0 Dehydration reaction 0 Monomers are connected by a reaction where two molecules are covalently bonded to each other with the loss ofa water molecule One monomer donates the OH and another the H Making ofa polymer 0 Hydrolysis o The reverse of the dehydration reaction The bond between monomers is broken by the addition ofa water molecule Disassembles polymers to monomers o Carbohydrates 0 Includes sugars and polymers of sugars Contain carbonyl hydroxyl groups 0 Monosaccharides 0 Have molecular formulas in the multiple of CHZO Has a carbonyl multiple hydroxyl groups Sugars with 6 carbons are called hexoses In aqueous solutions glucose and other 5 or 6 carbon sugars form rings 0 Disaccharide 0 Two monosaccharides joined by a glycosidic linkage o Glycosidic linkage o A covalent bond formed between two monosaccharides by a dehydration reaction 0 Polysaccharides 0 Polymers with several hundred to a few thousand monosaccharides joined by a glycosidic linkage Storage or structural Starch o A polymer of glucose monomers a storage polysaccharide Glucose can be taken by hydrolysis breaking the bonds between glucose monomers Has 14 linkages in amylose 16 in amylopectin In the alpha configuration Glycogen o A polymer of glucose that is like amylopectin but more branched Cellulose o A structural polysaccharide makes up plant walls All glucose monomers are in the beta configuration Mostly straight unlike starch Lipids 0 Don t have true polymers and aren t big enough to be considered macromolecules Are all hydrophobic Are mostly hydrocarbon regions Fats 0 Large molecules assembled by dehydration reactions Constructed from glycerol and fatty acids Fatty acid 0 Has a long carbon skeleton usually 16 or 18 atoms The carbon at one end is part ofa carboxyl group Tryiacylglycerol 0 Three fatty acid molecules are joined to glycerol by an ester linkage Saturated fatty acid 0 A fatty acid with no double bonds Are solid at room temperature Unsaturated fatty acid 0 Afatty acid with one or more double bonds Liquid at room temperature Trans fats o Unsaturated fats with trans double bonds Phospholipids 0 Has only two fatty acids attached to a glycerol The third hydroxyl group is joined to a phosphate group which has a negative charge Hydrocarbon tails are hydrophobic phosphate group heads are hydrophilic Steroids o Lipids with a carbon skeleton of4 fused rings Catalysts 0 Chemical agents that selectively speed up chemical reactions without being consumed in the reaction Polypeptides 0 Polymers of amino acids Protein 0 Afunctional molecule that has one or more polypeptides each in a 3D structure Amino acid 0 An organic molecule with an amino and a carboxyl group with an asymmetric carbon alpha carbon in the center Peptide bond 0 The covalent bond that happens when 2 amino acids are positioned so the carboxyl group of one is neXt to the amino group of the other and they are joined by a dehydration reaction Yields a polypeptide Primary structure 0 Alinked series of amino acids Secondary structure 0 The coils and folds that a protein undergoes The result of hydrogen bonds between the polypeptide backbones The oxygen atoms have a partial negative charge and the nitrogens have a partial positive charge Alpha helix 0 A coil held together by hydrogen bonding on every 4th amino acid Beta pleated sheet 0 Two or more strands of the polypeptide chain lying side by side connected by hydrogen bonds Tertiary structure 0 The overall shape ofa polypeptide resulting from interactions between the side chains Hydrophobic interactions disulfide bridges van der Waals interactions and ionic bonds Hydrophobic interactions 0 As a polypeptide folds into its functional shape amino acids with hydrophobic side chains usually end up in clusters at the core of the protein Disulfide bridges o Covalent bonds that form where 2 cysteine monomers with sulfhydryl groups on their side chains are brought close together by the folding of the protein Quaternary structure 0 Two or more polypeptide chains aggregated into one functional macromolecule Denaturation 0 Chemical bonds and interactions within a protein may be destroyed causing the protein to unravel and lose its native shape Chaperonins 0 Protein molecules that assist in the proper folding of other proteins They keep the new poplypeptide segregated in the cytoplasmic environment while it folds spontaneously Nucleic acids 0 Polymers made ofmonomers called nucleotides DNA 0 Provides directions for its own replication and directs RNA synthesis Has AGC and T AT and CG RNA 0 Directions production ofa polypeptide which folds into all or part of a protein Has AGC and U AU and CG Polynucleotides 0 Nucleic acids that eXist as polymers Consists of nucleotides Each monomer has only one phosphate group Nucleotides 0 Has 3 parts a nitrogenous base a 5carbon sugar and one or more phosphate group Nucleoside o The portion ofa nucleotide without any phosphate groups Pyrimidine o Atype of nitrogenous base with one sixmembered ring of carbon and nitrogen atoms Cytosine thymine and uracil Purine 0 Larger with a siXmembered ring fused to a fivemembered ring Adenine and guanine Deoxyribose o Lacks an oxygen on the second carbon in the ring Double helix 0 DNA molecules have 2 strands polynucleotides that spiral around an imaginary aXis Antiparallel o The 2 sugarphosphate backbones run in opposite 5 3 directions from each other