BIO 101 Textbook Notes PDF

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Notes on the textbook assigned for BIO 101...

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Biology 101 Textbook Notes Macromolecules and the chemistry of biology: 2.1-2.3, 3.1-3.2, 4.3, 5.1, 5.2, 5.5 Proteins – structure: 5.1, 5.4 Proteins – enzymes: 8.4, 8.5 Lipids and bilayers: 5.3, 7.1-3 Cell structure: dynamic membranes and functions: 7.3-7.5 Metabolism: glycolysis: 9.1-9.3, 8.1-8.3 Metabolism: TCA cycle and photosynthesis: 6.5, 9.4, 9.5, 10 Chapter 2: 2.1: Matter consists of chemical elements in pure form and in combinations called compounds  Matter is made up of elements; substances that cannot be broken down to other substances by chemical reactions  Compound: substance consisting of 2+ different elements combined in a fixed ratio (e.g. table salt, H2O)  Essential elements: needed for organism to live a healthy life and reproduce  Oxygen, carbon, hydrogen, and nitrogen: make up most of living matter  Trace elements: required by an organism in only minute quantities 2.2: An element’s properties depend on the structure of its atoms  Atom: smallest unit of matter that still retains properties of an element  Subatomic particles: neutrons, protons, electrons o Protons and neutrons are packed together tightly in the atomic nucleus; attracted to negatively charged electrons o Dalton: unit of measurement for atoms and subatomic particles  Atomic number: number of protons in nuclei of an element (written as subscript to left of symbol for element); atom is usually neutral in electrical charge, meaning proton and electron number is same  Mass number: sum of protons plus neutrons in nucleus (written at top left of element)  Number of neutrons determined by subtracting atomic number from mass number  Mass number is an approximation of the total mass of an atom  Isotopes: different atomic forms of same element (have more neutrons and therefore have greater mass) o Stable isotope: nuclei do not have a tendency to lose subatomic particles (decay) o Radioactive isotope: nucleus decays spontaneously, giving off particles and energy  Radioactive tracers: used in biological research but radiation from decaying isotopes is also dangerous  Parent isotope decays into daughter isotope at fixed rate, expressed as half-life of isotope – time it takes for 50% of the parent isotope to decay o Using radiometric dating scientists measure ratio of different isotopes and calculate how many half-lives passed since an organism was fossilized or a rock was formed  Energy levels of electrons: capacity to cause change

o Potential energy: energy that matter possesses because of its location or structure o Electrons of an atom have potential energy due to distance from the nucleus; the negatively charged electrons are attracted to the positively charged nucleus. The more distant an electron from the nucleus, the greater its potential energy. Electron can only exist at certain energy levels, not between them. o Electrons are found in different electron shells, each with characteristic average distance and energy level. First shell is closest to the nucleus, and electrons in this shell have the lowest potential energy. Electron can move from one shell to another by absorbing/losing amount of energy equal to difference in potential energy between position in old and new shell  electron absorbs energy = moves to a shell farther out; electron loses energy = falls back to a shell closer to the nucleus and lost energy is released as heat  Chemical properties of atom determined by distribution of electrons in atom’s shells; mostly depends on the number of electrons in its outermost shell (“valence electrons” and “valence shell”). If the valence shells are incomplete, the atom is chemically reactive  Orbital: 3D space where an electron is found 90% of the time. No more than 2 electrons can occupy a single orbital. o First electron shell has only one spherical s orbital (1s) o Second electron shell has four orbitals (one large spherical s orbital (2s) and three dumbbell-shaped p orbitals (2p) 2.3: The formation and function of molecules depend on chemical bonding between atoms  Covalent bond: sharing of a pair of valence electrons by two atoms  Molecule: two or more atoms held together by covalent bonds  Single bond: pair of shared electrons  Double bond: atoms are joined by sharing pairs of valence electrons  Valence: bonding capacity of an atom corresponding to number of covalent bonds the atom can form; usually equals number of unpaired electrons required to complete the atom’s outermost (valence) shell – essentially valence is the amount of electrons needed to fill the outermost shell (so for Carbon 4 more are needed to reach 8, for Nitrogen 3 more are needed to reach 8 because it already has 5, etc.)  Electronegativity: attraction of particular atom for electrons of a covalent bond; more electronegative atom pulls shared electrons more strongly toward itself  Nonpolar covalent bond: covalent bond between two atoms of same element; electrons are shared equally because the two atoms have the same electronegativity  Polar covalent bond: atom bonded to a more electronegative atom; electrons of bond are not shared equally  Oxygen is one of the most electronegative elements, attracting shared electrons more strongly than hydrogen  Ionic bond: two ions of opposite charge  Ion: the oppositely charged atoms resulting from the more electronegative atom stripping an electron from its partner o Cation: positively charged ion

o Anion: negatively charged ion o E.g. sodium and chlorine – valence electron of sodium (becomes cation) transferred to chlorine (becomes anion) = both atoms end up with complete valence shells  Ionic compounds or salts: compounds formed by ionic bonds; aggregate of cations and anions bonded by electrical attraction (not all salts have equal numbers of cations and anions) Weak chemical bonds:  Ionic bonds  Hydrogen bonds: hydrogen atom is covalently bonded to an electronegative atom, so hydrogen atom has partial positive charge allowing it to be attracted to different electronegative atom nearby  Van der Waals interactions: electrons may accumulate in one part of molecule; not evenly distributed; interactions are individually weak and occur only when atoms and molecules are very close together. When many interactions occur simultaneously they can be very powerful (e.g. gecko lizard can walk up wall) Molecular shape and function:  Molecule shapes are determined by positions of atoms’ orbitals which undergo rearrangement when atom forms covalent bonds  For atoms with valence electrons in both s and p orbitals, the single s and three p orbitals form four new hybrid orbitals shaped like identical teardrops extending from region of atomic nucleus  tetrahedron pyramid  Molecular shape determines how biological molecules recognize and respond to another with specificity o E.g. opiates: relieve pain and alter mood by weakly binding to specific receptor molecules on surfaces of brain cells, because they have similar shapes to endorphins and mimic them by binding to endorphin receptors Chapter 3: 3.1: Polar covalent bonds in water molecules result in hydrogen bonding  Water molecule: two hydrogen atoms joined to oxygen atom by single covalent bonds; oxygen is more electronegative than hydrogen so electrons are closer to oxygen than hydrogen – these are polar covalent bonds. Unequal sharing of electrons and water shape make it a polar molecule, meaning its overall charge is unevenly distributed o Oxygen region has partial negative charge, hydrogen has partial positive charge o Properties of water arise from attractions between oppositely charged atoms of different water molecules: positive hydrogen attracted to slightly negative oxygen of nearby molecule, forming hydrogen bond 3.2: Four emergent properties of water contribute to Earth’s suitability for life  Cohesion of water molecules: hydrogen bonds hold water molecules close together o Cohesion contributes to transport of water and dissolved nutrients against gravity in plants o Water travels from roots to leaves through network of water-conducting cells

o As water evaporates from leaf, hydrogen bonds cause water molecules leaving to tug on molecules farther down; upward pull is transmitted through waterconducting cells to roots  Adhesion: clinging of one substance to another o Adhesion of water by hydrogen bonds to molecules of cell walls helps counter pull of gravity  Surface tension: measure of how difficult it is to stretch/break surface of a liquid o Water has high surface tension due to collective strength of hydrogen bonds Moderation of temperature by water:  Temperature is moderated as water absorbs heat from air that is warmer and releases stored heat to air that is cooler  Anything that moves (atoms, molecules) has kinetic energy (the energy of motion); the faster a molecule moves, the greater its kinetic energy  Thermal energy: kinetic energy associated with the random movement of atom or molecules  Temperature: measure of energy that represents average kinetic energy of molecules in a body of matter, regardless of volume, whereas the total thermal energy depends in part on matter’s volume  Thermal energy passes from warmer to cooler object until two are same temperature; molecules in cooler object speed up at expense of thermal energy of warmer object  Heat: thermal energy in transfer from one body of matter to another  Calorie: amount of heat it takes to raise temperature of 1g of water by 1 degree Celsius  Kilocalorie: 1000 calories; quantity of heat required to raise temperature of 1 kg of water by 1 degree Celsius  Joule: 1 joule = 0.239 calories  Water’s high specific heat: the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 degree Celsius – specific heat of water is 1 calorie per gram and per degree Celsius (unusually high) o Because of high specific heat, water will change its temperature less than other liquids when it absorbs/loses given amount of heat  water resists changing its temperature o High specific heat is due to hydrogen bonding; heat must be absorbed in order to break hydrogen bonds and released when hydrogen bonds form o Large body of water can absorb and store huge amount of heat from sun but only warms up a few degrees, and cooling is also gradual  high specific heat of water stabilizes ocean temperatures, creating favorable environment for marine life; also allows organisms to resist changes in own temperature  Evaporative cooling: molecules moving fast enough to overcome attraction to one another depart the liquid and enter air as gas (vapor) = evaporation o Heat of vaporization: quantity of heat liquid must absorb for 1g of it to be converted from liquid to gaseous state o Water’s high heat of vaporization results from strength of hydrogen bonds, which must be broken before molecules can evaporate

o High heat of vaporization helps moderate Earth’s climate o As liquid evaporates, the surface of the liquid that remains behind cools down – this evaporative cooling occurs because the “hottest” molecules (greatest kinetic energy) are most likely to leave as gas o Evaporative cooling of water prevents overheating of organisms (e.g. sweat from skin cools body down)  Floating of ice on liquid water: o Water is less dense as solid than liquid = ice floats on liquid water o Water expands when it solidifies, due to hydrogen bonding – as temperature falls from 4 to 0 degrees Celsius water begins to freeze because more and more of its molecules are moving too slowly to break hydrogen bonds; at 0 degrees Celsius, molecules become locked into crystalline lattice, each water molecule hydrogenbonded to four partners o Ability of ice to float due to lower density means only upper inches of ocean freeze, insulating water below and allowing life to exist under frozen surface Water as the solvent of life:  Solution: liquid that is homogeneous mixture of 2 or more substances  Solvent: dissolving agent of a solution; substance being dissolved is the solute (e.g. water is solvent and sugar is the solute – aqueous solution is when solute is dissolved in water)  Water is very versatile as a solvent due to the polarity of water; e.g. oxygen regions of water are negatively charged and attracted to sodium cations; hydrogen regions positively charged and attracted to chloride anions = water molecules surround individual sodium and chloride ions and separate them o Hydration shell: sphere of water molecules around each dissolved ion o Compound does not need to be ionic to dissolve in water; they can dissolve when water molecules surround each solute molecule, forming hydrogen bonds with them  Hydrophilic: substance with affinity for water; some substances can be hydrophilic and not dissolve  Hydrophobic: substances that are nonionic and nonpolar; do not have affinity for water and repel it (e.g. cell membranes made of oils therefore do not dissolve)  Solute concentration in aqueous solutions: o Molecular mass: sum of masses of all atoms in a molecule o Mole: represents exact number of objects o Molarity: number of moles of solute per liter of solution Chapter 4: 4.3: A few chemical groups are key to molecular function The chemical groups most important in the processes of life:  Functional groups: chemical groups that are directly involved in chemical reactions; each has certain properties such as shape and charge that cause it to participate in chemical reactions in certain way

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Seven chemical groups most important in biological processes: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups o All except sulfhydryl are hydrophilic and thus increase solubility of organic compounds in water o Study figure 4.9; page 63 ATP: important source of energy for cellular processes  Adenosine triphosphate (ATP) consists of organic molecule called adenosine attached to string of three phosphate groups  One phosphate may be split off due to reaction with water = ATP becomes diphosphate (ADP)  Stores potential to react with water; reaction releases energy that can be used by cell Chapter 5: 5.1: Macromolecules are polymers, built from monomers  Polymer: long molecule consisting of many building blocks linked by covalent bonds  Monomers: the repeating units that serve as building blocks of a polymer Synthesis and breakdown of polymers:  Enzymes: specialized macromolecules that speed up chemical reactions to facilitate polymer processes  Dehydration reaction: monomers are connected by covalent bonds, with the loss of a water molecule. One monomer provides hydroxyl group (-OH) and the other provides a hydrogen (-H), making a polymer  Hydrolysis: reverse of dehydration; bond between monomers is broken by addition of a water molecule, with a hydrogen from water attaching to one monomer and hydroxyl group attaching to the other (e.g. digestion) The diversity of polymers:  Diversity results from different arrangements of monomers in chain 5.2: Carbohydrates serve as fuel and building material  Carbohydrates: sugars and polymers of sugars; monomers are called monosaccharides  Monosaccharides: have molecular formulas that are some multiple of the unit CH2O  Glucose: most common monosaccharide (C6H12O6); aldose  Monosaccharides are major nutrients for cells; e.g. provide energy in cellular respiration  Disaccharide: two monosaccharides joined by glycosidic linkage, a covalent bond formed by a dehydration reaction o Glucose + glucose = maltose o Glucose + fructose = sucrose o Glucose + galactose = lactose  Polysaccharides: monosaccharides joined by glycosidic linkages; serve as storage material, hydrolyzed to provide sugar for cells; or serve as building material Storage polysaccharides:  Plants store starch: polymer of glucose monomers, synthesizing starch enables plant to store glucose so starch represents stored energy (later withdrawn by hydrolysis) o Amylose is unbranched with 1-4 monomer linkages

o Amylopectin is branched with 1-6 linkages o Glycogen is more branched than amylopectin, stored in animals Structural polysaccharides:  Cellulose: makes up tough walls of plant cells; polymer of glucose with beta configuration (mostly straight structure, never branched, grouped into microfibrils)  Starch: polymer of glucose with alpha configuration (making it largely helical); enzymes that digest starch cannot hydrolyze the beta linkages of cellulose  Chitin: carbohydrate used by arthropods to build their exoskeletons 5.5: Nucleic acids store, transmit, and help express hereditary information  Genes consist of DNA which belongs to class of compounds called nucleic acids: polymers made of monomers called nucleotides  Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) enable living organisms to reproduce; DNA provides instructions and directs RNA synthesis and through RNA controls protein synthesis; this process is called gene expression (flow of genetic information from DNA to proteins)  Each chromosome contains one DNA with genetic material, but proteins carry out actual processes  Messenger RNA (mRNA) directs production of a polypeptide (DNA  RNA  protein)  Nucleic acids form polynucleotides; one nucleotide is composed of a five-carbon sugar (pentose), nitrogenous base, and one or more phosphate groups; portion of nucleotide without any phosphate groups is called a nucleoside o Two families of nitrogenous bases: pyrimidines (one 6 ring of carbon and nitrogen atoms; members are cytosine C, thymine T, uracil U) and purines (larger, 6 ring fused to 5 ring; include adenine A and guanine G). Thymine only found in DNA and uracil only in RNA. o DNA sugar is deoxyribose; RNA sugar is ribose (deoxyribose lacks oxygen atom on second carbon ring) o Phosphate group attached to the 5’ carbon of the sugar  Linkage of nucleotides into polynucleotide involves dehydration reaction (phosphate group links sugars of 2 nucleotides = sugar-phosphate backbone pattern  One end of polymer has a phosphate attached to 5’ carbon, the other end has a hydroxyl group on a 3’ carbon  Sequence of bases along a DNA is unique for each gene and specifies the amino acid sequence (primary structure) of a protein  DNA has two polynucleotides “strands” forming a double helix; the two sugar-phosphate backbones run in opposite 5’-3’ directions = antiparallel; two strands are held together by hydrogen bonds between the paired bases  Adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C); makes the strands that run in opposite directions complementary, making it possible to generate two identical DNA copies in a cell preparing to divide  RNA are single strand, but complementary base pairing can occur between two stretches of nucleotides in the same RNA

o tRNA which brings amino acids to ribosome during polypeptide synthesis has a shape that results from base pairing between nucleotides where complementary stretches run antiparallel to each other o Adenine pairs with uracil instead of thymine 5.4: Proteins include a diversity of structures, resulting in a wide range of functions  Most enzymes are proteins that regulate metabolism by acting as catalysts, chemical agents that selectively speed up chemical reactions (without being consumed by reaction) – carries out processes of life  All proteins are made from same set of 20 amino acids, linked in unbranched polymers through peptide bonds (polymer is called a polypeptide); proteins made up of one or more polypeptides, folded and coiled into specific 3D structure  Amino acid: organic molecule with both amino group and carboxyl group; at center is an alpha carbon, partnered with an amino group, carboxyl group, hydrogen atom, and variable group R (which differs with each amino acid and determines unique characteristics of particular amino acid) o Nonpolar side chains (R groups); hydrophobic o Polar side chains; hydrophilic o Electrically charged side chains; hydrophilic  Acidic (negatively charged)  Basic (positively charged)  Amino acids join by dehydration reactions with the removal of a water molecule to form a peptide bond; repeating sequence is called polypeptide backbone with R groups extending from the backbone; one end of polypeptide has free amino group, opposite end has free carboxyl group  Protein functions: o Enzymatic proteins o Defensive proteins o St...