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BIOL 2107 TEST 1
STUDY GUIDE
CHAPTER 1
Define: The properties of life: o Order o Reproduction of viable offspring o Can regulate itself o Growth and development o Energy processing o Evolutionary adaptations o Response to the environment The 7 themes of biology o New properties emerge at each level in the biological hierarchy. o Organisms react with other organisms and the physical environment. Cycling of chemical nutrients. o Life requires energy transfer and transformation. o Structure and function are correlated. o The cell is an organism’s basic unit of structure and function. o The continuity of life is based on DNA. DNA makes mRNA through transcription, which makes proteins through translation. o Feedback mechanisms regulate biological systems. Reductionism o The approach of reducing complex systems to simpler components that are easier to study. Systems biology o Approach that attempts to model the behavior of the whole system based on a study of the interactions among the system’s parts. Emergent properties o 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. Levels of biological organization o The biosphere: all life on Earth and the places where life exists.
o Ecosystem: all living things in a particular area, along with non-living components of the environment that interact with life. o Community: all organisms inhabiting a particular ecosystem. o Population: all individuals on a species living within the bounds of a specified area. o Organism: individual living things. o Organs and organ systems: a body part that carries out a particular function. o Tissues: a group of cells that work together to perform a specific function. o Cells: the fundamental unit of structure and function. o Organelles: functional components in cells. o Molecules DNA o Double-helix nucleic acid molecule, with bases A,C,G and T. Chromosomes o Contains one long DNA molecule. Genes o Units of inheritance that transmit information. A specific nucleotide sequence in DNA. Genomes o The entire library of genetic information that an organism inherits. Negative feedback o Accumulation of an end product of a process slows that process down. Positive feedback o An end product speeds up its own production. The three domains of life o Bacteria Prokaryotic o Archaea Prokaryotic o Eukarya Plantae: carry out photosynthesis. Fungi: absorb nutrients from surroundings, many decompose dead organisms. Animalia: ingestion.
Compounds o A substance consisting of two or more different elements in a fixed ratio. Essential elements o 20% of the 92 natural elements that are required to live and reproduce. O, N, C and H make up 96% of living matter. Trace elements o Required in only small quantities. Ca, P, K, S, Na, Cl, Mg. Neutron o Neutral charge, in atomic nucleus with protons. Proton o Positive charge, in atomic nucleus with neutrons. Electron o Negative charge, in electron cloud surrounding nucleus. Atomic nucleus o Core at the middle of an atom, has a positive charge due to protons. Mass number o Top number, number of protons and neutrons. Atomic number o Bottom number, number of protons=electrons. Same for every isotope of an element. Atomic mass o 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 o The capacity to cause change. Potential energy o 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 o 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 o 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% of the time. No more than 2 electrons can be in an orbital at the same time. Covalent bond o The sharing of a pair of valence electrons by two atoms. Form molecules. Formed due to proximity. Single bond o A pair of shared electrons. Double bond o Sharing two pairs of valence electrons. Valence o A bonding 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. F,O,N, and Cl have the highest electronegativity. Non-polar covalent bond o Electrons are shared equally because the two atoms have the same electronegativity. (Between to atoms of the same element). Polar covalent bond o When one atom is bonded to a more electronegative atom, the electrons are not shared equally. H2O
Define: Water molecule o Shaped like a wide V, with two H atoms joined to the O atom with single covalent bonds. O is more electronegative than H, so this is a polar covalent bond. O region has a partial negative charge, and H regions have a partial positive charge. Liquid water o Hydrogen bonds are very fragile, and they form, break, and re-form often. 4 emergent properties of water: o Cohesion Hydrogen bonding holds water molecules together. Allows for capillary action in plants. o High specific heat 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 of heat 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. o Solvent powers For salts (NaCl): water molecules surround the individual sodium and chloride ions, separating them. O molecules are negatively charged, attracted to sodium cations while H regions are positively charged, attracted to chloride anions. For sugars: water molecules surround each of the solute molecules, forming H bonds with them. Made up of nonionic polar molecules. o Ice floats Ice is less dense than water, so it floats. If temperature is less than 4 degrees, water begins to freeze because more of the molecules are moving too slowly to break hydrogen bonds. Adhesion o The clinging of one substance to another. Adhesion of water to cell walls by hydrogen bonding helps counter downward pull of gravity. Surface tension o A measure of how difficult it is to stretch or break the surface of a liquid. Water has a higher surface tension than most liquids.
Kinetic energy o The energy of motion. Heat o A measure of the matter’s total kinetic energy due to the motion of its molecules. Depends on volume! Temperature o A measure of heat intensity that represents the average kinetic energy of the molecules, regardless of volume. Calorie o The amount of heat tit takes to raise the temperature of 1g of water by 1 degree C. Also, the amount of heat that 1g of water releases when it cools by 1 degree. Kilocalorie o The quantity of heat required to raise the temperature of 1kg of water by 1 degree C. Specific heat o The amount of energy that must be absorbed or released for 1g of that substance to change its temperature by 1 degree. Evaporative cooling o 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 of a plant helps keep the tissues in the leaves from becoming too warm in the sunlight. Heat of vaporization o The quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state. Result of the strength of the hydrogen bonds. Solution o A liquid that is a completely homogenous mixture of two or more substances. Solvent o The dissolving agent of a solution. Solute o The substance being dissolved.
o A logarithmic scale from 0-14. pH declines (becomes more acidic) as H+ increases. Each pH unit is a tenfold difference in H+ and OH- concentrations. pH o –log [h+]. 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: Organic chemistry o The study of carbon compounds. Most organic compounds have hydrogen atoms also. Mechanism o The view that physical and chemical laws govern all natural phenomena. Vitalism o The belief in life forces outside the jurisdiction of physical and chemical laws. Carbon bonds o 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 o Organic molecules with only carbon and hydrogen. Isomers o Compounds with the same number of atoms of the same elements, but different structures and different properties. Structural isomers o Different covalent arrangements of their atoms. Could differ in the location of double bonds. Cis-trans isomers
o Carbons have covalent bonds to the same atoms, but these atoms have different spatial arrangements due to the inflexibility of double bonds. MUST HAVE DOUBLE BONDS. o Cis: the arrangement with both Xs on the same side of the double bond. o 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 o Hydroxyl -OH. Is polar, can form hydrogen bonds with water. Alcohols. o Carbonyl =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 -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. o Amino -NH2. Acts as a base, found in cells with a charge of 1+. Amines. o Sulfhudryl -SH. Can form covalent bonds with each other, called “cross- linking”. Thiols. o Phosphate -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 of a chain of phosphates). Can react with water, releasing energy. o Methyl -CH3. A carbon bonded to three hydrogen atoms. Non-polar, hydrophobic. ATP o Adenosine molecule attached to a string of three phosphate groups. CHAPTER 5
Starch o A polymer of glucose monomers, a storage polysaccharide. Glucose can be taken by hydrolysis, breaking the bonds between glucose monomers. Has 1-4 linkages in amylose, 1-6 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 o Don’t have true polymers, and aren’t big enough to be considered macromolecules. Are all hydrophobic. Are mostly hydrocarbon regions. Fats o Large molecules assembled by dehydration reactions. Constructed from glycerol and fatty acids. Fatty acid o Has a long carbon skeleton, usually 16 or 18 atoms. The carbon at one end is part of a carboxyl group. Tryiacylglycerol o Three fatty acid molecules are joined to glycerol by an ester linkage. Saturated fatty acid o A fatty acid with no double bonds. Are solid at room temperature. Unsaturated fatty acid o A fatty acid with one or more double bonds. Liquid at room temperature. Trans fats o Unsaturated fats with trans double bonds. Phospholipids o 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 of 4 fused rings. Catalysts o Chemical agents that selectively speed up chemical reactions without being consumed in the reaction. Polypeptides o Polymers of amino acids. Protein o A functional molecule that has one or more polypeptides, each in a 3D structure. Amino acid o An organic molecule with an amino and a carboxyl group, with an asymmetric carbon (alpha carbon) in the center. Peptide bond o 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 o A linked series of amino acids. Secondary structure o 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 o A coil held together by hydrogen bonding on every 4th^ amino acid. Beta pleated sheet o Two or more strands of the polypeptide chain lying side by side, connected by hydrogen bonds. Tertiary structure o The overall shape of a polypeptide resulting from interactions between the side chains. Hydrophobic interactions, disulfide bridges, van der Waals interactions, and ionic bonds.
Pyrimidine o A type of nitrogenous base with one six-membered ring of carbon and nitrogen atoms. Cytosine, thymine, and uracil. Purine o Larger, with a six-membered ring fused to a five-membered ring. Adenine and guanine. Deoxyribose o Lacks an oxygen on the second carbon in the ring. Double helix o DNA molecules have 2 strands (polynucleotides) that spiral around an imaginary axis. Antiparallel o The 2 sugar-phosphate backbones run in opposite (5’-3’) directions from each other.
