Chemistry of Life - Note

Unit 1: Chemistry of Life Chapter 2: The Chemical Context of Life - - - - - - - - Chemicals play a major role in communication, attraction of mates, and defense against predators o Ex: Wood ants that live in colonies of hundreds shoot formic acid to protect themselves Matter: anything that takes up space and has mass Element: a substance that cannot be broken down to other substances by chemical reactions o Make up all matter o 92 elements occurring in nature (gold, copper, carbon, oxygen) o Symbols are generally the first two letters of the element  May be derived from German or Latin sometimes Compound: substance consisting of two or more different element combined in a fixed ration o Ex: NaCl is always in a 1:1 ratio o Chemical properties of elements change when they are put into compounds  Na is metal and Cl is a poisonous gas, but NaCl is table salt Essential Elements: elements that an organism needs to live a healthy life and reproduce o 20 – 25% of the 92 natural elements o Which essential elements are needed for life vary based on the organism Oxygen, carbon, hydrogen, and nitrogen make up 96% of living matter o Calcium, phosphorus, potassium, sulfur, and a few others make the other 4% Trace Elements: elements required by an organism in only minute quantities o Ex: Iron (Fe) Some naturally occurring elements may be toxic to organisms o Ex: Arsenic  May contaminate ground water o Some species are adapted to environments with elements that are toxic to other organisms Atom: smallest unit of matter that still retains the properties of an element o Symbolized by abbreviations for each element o Composed of even smaller parts called subatomic particles  Neutrons, protons, and electrons Atomic Nucleus: the center of an atom containing protons and neutrons Dalton: unit of measurement for atomic mass (same as the atomic mass unit or amu) o Neutrons and protons are close to 1 dalton o Electrons weigh 1/2000 daltons  Weight is negligible that it is ignored when calculating the mass of an atom Atomic Number: the number of protons, unique to each element o Written to the left and bottom of element’s symbol as a subscript Unless otherwise stated, an atom is neutral in its electrical charge (# of protons = # of electrons) Mass Number: sum of protons and neutrons in the nucleus of the atom o Written to the left and top of the element’s symbol as a subscript o # of neutrons can be found by subtracting the atomic number from this Hydrogen is the simplest atom and has no neutrons Atomic Mass: an approximation of the total mass of an atom Isotopes: different atomic forms of the same element o Ex: Carbon  Carbon-12 has 6 neutrons - - - - -  Carbon-13 has 7 neutrons o All isotopes behave identically in chemical reactions even though their atomic mass differs Radioactive Isotope: isotope in which the nucleus decay spontaneously, giving off particles and energy o When this leads to a change in the number of protons, it transforms the atom to a different one  Ex: when carbon-14 decays in become nitrogen o Used as tracers to track atoms during metabolism (chemical processes of an organism) in medicine  May be used in combination with imaging instruments (such as PET scanners) o Pose hazard to life by damaging cellular molecules  Severity of this depends on the amount of radiation absorbed o Measure radioactive decay to date fossils  Half-Life: the time it takes for 50% of the parent isotope to decay and become the daughter isotope  Isn’t affected by environmental factors  Radiometric Dating: measure the ratio of different isotopes and calculate how many halflives (in years) have passed since an organism was fossilized or a rock was formed The majority of an atom is the empty space between electron rings Energy: capacity to cause change o Electrons vary in how much energy they carry Potential Energy: energy that matter possesses because of its location or structure o Matter has a natural tendency to move toward the lower possible state of potential energy o Electrons have potential energy because of their distance from the nucleus  Negative electrons are attracted to positive protons in the nucleus, so the further away an electron is from the nucleus the more potential energy it has Electron Shell: different levels of rings around the nucleus where electrons are found o As the shells get further away from the nucleus, the potential energy increases o An electron can only move shells by absorbing or losing an amount of energy equal to the difference of potential energy between the original and new shell  Ex: Light energy can excite an electron to the next level  Ex: Thermal energy can be transferred and push the electron back a level Valence Electrons: electrons in the outermost electron shell (the valence shell) Molecular vs. Structural formula o Each line in the structural formula represents one bond Covalent Bonds: sharing of a pair of valence electrons by two atoms o Molecule: two or more atoms held together by a covalent bond o Electronegativity: the attraction of a particular atom for the electrons of a covalent bond  Oxygen is more electronegative than hydrogen, that’s why oxygen has a partial negative charge and hydrogen has a partial positive charge in hydrogen o Polar Covalent Bond: the electrons of the bond are not shared equally  C-O, H-O, and N-H o Nonpolar Covalent Bond: the electrons of the bond are shared equally  C-H, and 2 of the same atoms (C-C, N-N, O-O, etc.) Ionic Bonds: when two oppositely charged ions result from transferring electrons o Cations are positive(“paw”sitive) and anions are negative Hydrogen Bonds: a hydrogen atom with a partial positive charge allows it to be attracted to a different electronegative atom nearby o Seen in water - - Van der Waals Interactions: individually weak and occur only when atoms and molecules are very close together o Also known as London Dispersion Reactants (reaction)  Products Chemical Equilibrium: the point at which the reactions offset one another exactly Chapter 3: Water and Life - - - - - - Polar covalent bonds in water make the negative oxygen attracted to positive hydrogens from a different molecule (caused by unequal sharing of electrons due to different electronegativities) 5 water molecules together make a tetrahedral structure (shown on the right) Cohesion: make molecules of the same substance attracted to each other because of the hydrogen bonds holding the substance together o These linkages are stronger in water than in other substances o For polar substances only Adhesion: the clinging of one substance to another o Polarity o Ex: Water moves up through a plant because of this Surface Tension: a measure of how difficult it is to stretch or break the surface of a liquid o Related to cohesion o Ex: Insects walk on water Kinetic Energy: the energy of motion o The faster a molecule mores, the more kinetic energy it has o Thermal energy is often associated with this  Heat: transfer of thermal energy from one body of matter to another  Heat moves from the hotter object to the cooler until they are the same temperature o Temperature is the average kinetic every of molecules in a body of matter, regardless of the volume o Calorie (cal): amount of heat it takes to raise the temperature of 1 gram of water 1 degree Celsius  Kilocalories (kcal): amount of heat required to raise the temperature of 1 kg of water by 1 degree Celsius Specific Heat: amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1 degree Celsius o Water has a higher specific heat, so it resists temperature change more  More heat is required to break the strong hydrogen bonds  Regulate cell temperature o Evaporative cooling is enabled by this as it allows for the hottest molecules to be evaporated and lower the average kinetic energy and thereby temperature  Could not happen if water had a low specific heat as too much water would evaporate, including the cooler molecules, leaving the organism dehydrated  Stabilize ocean temperature (make sure the water doesn’t get too hot in the day or too cold in the night)  Prevents terrestrial organisms from overheating (plants and animals)  - - - - In places with more water rather than less water (if there is less water, than then organisms risk dehydration by evaporating the water) o Heat of Vaporization: quantity of heat a liquid must absorb for 1 gram of it to be converted from the liquid to gaseous state  Related to evaporative cooling o Ice floats on liquid water  Most materials contract and become denser as they solidify, but water does not  Molecules become locked into a crystalline lattice  Hydrogen bonds keep the molecules far apart, lessening the density  Important is sustainability of the environment as it allows life to continue under a layer of ice in bodies of water Solution: a liquid that is completely homogenous mixture of two or more substances Solvent: dissolving agent Solute: substance that is dissolved Water is the solvent of life because it is able to dissolve polar substances due to its own polarity Hydration Shell: sphere of water molecules around each dissolved ion Hydrophilic: any substance with an affinity for water o Some may not dissolve in water because of large size o Polar o Hydrophilic tails in the phospholipid bilayer (towards the outside) Hydrophobic: any substance that repels water o Hydrophobic tails in the phospholipid bilayer (towards the inside) Molecular Mass: sum of the masses of all the atoms in a molecule Molarity: the number of moles of solute per liter of solution Hydrogen Ion: what is transferred when a hydrogen atom leaves its electron behind (H+) o Acidic Hydronium Ion: molecule that is formed when the proton binds to the other water molecule (H3O+) This is a reversible reaction pH scale is from 0 to 14 o 0 to 7 is acidic o 7 is neutral o 7 to 14 is basic Buffer: substance that minimizes changes to the concentrations of hydrogen and hydronium ions in a solution pH = -log (H+) H+ (hydrogen) is 1.0 x 10-pH Ocean acidification is when the extra hydrogen ions combine with carbonate ions to make bicarbonate o Affect coral reefs and animals with shells that need carbonate ions for calcification Chapter 4: Carbon and Molecular Diversity of Life - - - Organic Chemistry: study of compounds containing carbon Major elements of life are carbon (C), hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), phosphorus (P) o Mostly uniform from one organism to another C has the ability to form 4 bonds Organisms are distinguished by the types of organic molecules they make Electron configuration is key to an atom’s chemical characteristics as it determines the kinds and number of bonds an atom will form with other atoms o Valence electrons o C usually has a complete valence shall by sharing 4 electrons with other atoms so that 8 electrons are present o C usually forms single or double covalent bonds o When a C atom forms 4 single covalent bonds, the 4 hybrid orbitals cause the bonds to angle towards the corners of an imaginary tetrahedron Hydrocarbons: organic molecules consisting of only carbon and hydrogen Isomers: variation in the architecture of organic molecules o Cis-trans Isomers: same vs opposite sides o Structural Isomer: different covalent arrangements o Enantiomers: mirror images - - Functional Groups: chemical groups directly involved in chemical reactions o Hydroxyl:  Polar because of electronegative O  Forms hydrogen bonds  Compound Name: alcohol o Carbonyl  Polar  Ketone: locked in  Aldehyde: outside o Carboxyl  Polar  Acts as an acid  Can donate an H+  Compound Name: carboxylic acid / organic acid o Amino  Acts as a base  Can pick up an H+  Polar  Compound Name: amine o Sulfhydryl  Cross link to stabilize protein structure  Polar  Compound Name: thiol o Phosphate  Contributes negative charge  1 in a chain of phosphates  2 at the end of a chain  Give a molecule the ability to react with water  Releases energy  Polar  Compound Name: organic phosphate o Methyl  Affects the expression of genes on DNA  Affects the proteins bound to DNA  Affect shape/function of sex chromosomes  Nonpolar  Compound Name: methylated compound Adenosine Triphosphate (ATP): complicated organic phosphate o 3 phosphate groups Chapter 5: The Structure and Function of Large Biological Molecules - - - - Macromolecules 1. Carbohydrates (C, H, O) 2. Proteins (C, H, O, N, S) 3. Nucleic Acids (C, H, O, N, P) 4. Lipids (C, H, O) Monomer: repeating unites that serve as the building blocks of a polymer Polymer: long molecule consisting of many similar or identical building blocks liked by covalent bonds Enzymes: specialized macromolecules that speed up chemical reactions o Initiate dehydration synthesis and hydrolysis Dehydration Reaction: two molecules are covalently bonded to each other with the loss of a water molecule Hydrolysis: a process that is essentially the reverse of the dehydration reaction o Water breakage Carbohydrates: sugars and polymers of sugars o Carbon, hydrogen, oxygen  C:H:O in a 1:2:1 ratio o Monomer: monosaccharide  Disaccharide o Polymer: polysaccharide o Glycosidic linkages (covalent bonds) join the monomers  Alpha: when the hydroxyl group is placed below the plane  Beta: when the hydroxyl group is placed above the plane o Polar due to H-O bonds o Glucose + glucose = maltose o Glucose + fructose = sucrose o Extract energy from glucose by breaking it down through cellular respiration o Cellulose in plant cell walls (structural support)  Never branched  Some hydroxyl groups on glucose monomers are free to make hydrogen bonds with other hydroxyls of other cellulose molecules lying parallel to it  Beta linkages o Plants store starch, a polymer of glucose monomers  Synthesizing starch enables having a stock of surplus glucose  Alpha linkages o Animals store glycogen, a polymer of glucose monomers that is more extensively branched  Hydrolysis of this releases glucose when the demand for sugar increases o Chitin: the carbohydrate used by arthropods to build their exoskeletons and in fungi for their cell walls  Beta linkages  Monomer has an nitrogen-containing appendage o Glycolipids: carbohydrates covalently bonded to lipids - - o Glycoproteins: carbohydrates covalently bonded to proteins  These assist with identification markers Lipids: mix poorly, if at all, with water (hydrophobic) o Consist mostly of hydrocarbon regions o Fat: constructed from glycerol (alcohol) and three fatty acid chains  Fatty Chain: has a long carbon skeleton, usually 16 or 18 carbon atoms with a carboxyl group at one end  C-H bonds are nonpolar, making these hydrophobic  Triacylglycerol: three fatty acid molecules, each joined to glycerol by an ester linkage  Ester Linkage: bond formed between hydroxyl and carboxyl group through dehydration reaction  Also called triglyceride  Saturated Fatty Acid: has the maximum amount of hydrogens  No double bonds  Solid at room temperature  Ex: lard and butter  Unsaturated Fatty Acid: has one or more double bonds between 2 carbons  Cause a kink  Nearly all are cis double bonds  Healthier than saturated  Liquid at room temperature  The kinks prevent the molecule from packing together closely enough to become solid  Ex: oils  Trans Fats: unsaturated fats with trans double bonds  Super unhealthy and contribute to many health problems (ex: atherosclerosis)  Main function is energy storage o Phospholipids: has only 2 fatty acids attached to glycerol  The third hydroxyl group on glycerol is joined to a phosphate group, giving a small negative charge  Hydrocarbon talks are hydrophobic (towards the inside of the membrane)  Hydrophilic heads o Steroids: lipids characterized by a carbon skeleton consisting of four fused rings  Ex: cholesterol  Common component of cell membranes Amino Acids: an organic molecule with both an amino group and a carboxyl group o Catalysts: chemical agents that selectively speed up chemical reactions without being consumed by the reactions  Includes all enzymes  Can be reused o 20 amino acids o Polypeptide: the polymer of amino acids o Protein: biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific 3-D shape o Center of an amino acid has an alpha carbon that links with an  Amino group  Carboxyl group o o o o o o o o o o o o o o o  Hydrogen atom  R-group The R-group determines the unique characteristics of a particular amino acid and affects its functional role in a polypeptide Classified as nonpolar, polar, or charged (+ or -)  Nonpolar amino acids have van Der Waals bonds  Polar amino acids have hydrogen bonds  Charged amino acids (of opposite charges) have ionic bonds Acidic amino acids have side chains that are generally negatively charged because of the carboxyl groups in side chains which dissociate at cellular pH  Acidic / Basic refers to the side chain as the other parts of an amino acid are the same Basic amino acids have side chains with positive charges Enzymatic proteins, defensive proteins, storage proteins, transport proteins, hormonal proteins (coordinate an organism’s activities), receptor proteins, contractile and motor proteins, and structural proteins Peptide Bond: the covalent bond that is formed when the carboxyl group of one is adjacent to the amino group of another  Joined by dehydration reaction Polypeptide Backbone: repeating sequence of atoms  One end has a free amino group and the other has a free carboxyl group Globular proteins are spherical while fibrous proteins are long fibers Function of a protein depends on its ability to recognize and bind to some other molecule Primary Structure: sequence of amino acids  Dictates secondary and tertiary structures  Peptide bonds Secondary Structure: result of hydrogen bonds between the repeating constituents of the polypeptide backbone  Bonds between the carboxyl O (-) and amine H (+)  Alpha helix or Beta pleated sheet  One polypeptide Tertiary Structures: overall shape of a polypeptide resulting from interactions between the side chains of various amino acids  Hydrophobic Interaction: caused by the exclusion of nonpolar substances from water and have van Der Waals interactions  Disulfide Bridges: form where two cysteine monomers with sulfhydryl groups (-SH) are brought close together  Van Der Waals interactions Quaternary Structure: overall protein structure that results from the aggregation of polypeptide subunits  2 or more polypeptides  Hemoglobin Sickle Cell Disease is caused by the substitution of one amino acid (valine) for the normal one (glutamic acid) Chaperonins: protein molecules that assist in the proper folding of other proteins  - Keep the new polypeptide segregated from disruptive chemical conditions in the cytoplasmic environment while it folds spontaneously o X-Ray Crystallography is used to determine the 3-D structure of many proteins Nucleic Acids: polymers made of monomers called nucleotides o Gene: amino acid sequence of a polypeptide programmed by a discrete unit of inheritance o DNA (deoxyribose nucleic acid) and RNA (ribonucleic acid)  Gene Expression: DNA give directions for its own replication, RNA synthesis, and protein synthesis  Deoxy doesn’t have an O in the 2nd corner but oxy does o Proteins are made in ribosomes o Polynucleotides are made of monomers known as nucleotides  Joined by phosphodiester linkages that has a phosphate group linking the sugars of 2 nucleotides o Nucleotides have a 5-carbon sugar (pentose), phosphate group, and nitrogenous base  Adenine - Thymine in DNA  Adenine – Uracil in RNA  Cytosine – Guanin in DNA  Purines: adenine and guanine have 2 rings  Larger  Pyrimidines: cytosine, thymine, uracil have 1 ring o Nucleosides: the same as nucleotides except don’t have a phosphate group o Double helix structure of DNA  Antiparallel (5’  3’ and 3’  5’)  Complementary nitrogenous bases (listed above) o Genomics: analyzing large sets of genes or even comparing whole genomes of different species o Proteomic: similar analysis of large sets of proteins and their sequences Chapter 8: An Introduction to Metabolism (8.4 & 8.5) - - Catalyst: a chemical agent that speeds up a reaction without being consumed by the reaction Enzyme: a macromolecule that acts as a catalyst o All enzymes are catalysts but not all catalysts are enzymes Every chemical reaction involves breaking and forming bonds o This generally involved contorting the starting molecule into a highly unstable state before the reaction can proceed  To reach this stage, molecules must absorb energy which release as heat when the new bonds of the product form Activation Energy: the initial investment of energy for starting a reaction – the reaction to contort the reactant molecules so bonds can break o Free Energy of Activation o EA o Often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings - - - - - o Agitates atoms within molecules to make the breakage of bonds more likely o Accelerates reactant molecules o Transition State: when the molecules have absorbed enough energy for the bonds to break  Unstable condition for the reactants o Graph of an exergonic reaction (release energy  with a spontaneous reaction)  Downhill curve shows the loss of free energy by molecules (releases energy)  Transition state may not be reached without the enzyme (which lowers the E A ) Heat can increase the rate of reaction by allowing reactants to reach the transition state more easily, but this does not work in biological systems o High temperatures would kill cells and denature proteins o Heat would speed up all reactions, not just the ones that are needed o This is why we use catalysts, including enzymes Enzymes hasten reactions that would happen eventually anyways Substrate: the reactant an enzyme acts on Enzyme-Substrate Complex: when the enzyme binds to substrate (or substrates when there are multiple reactants) o The catalytic action of the enzyme converts the substrate to the product Active Site: the restricted region where the enzyme binds to the substrate o Usually only formed by a few of the enzyme’s amino acids o Specificity of an enzyme is attributed to a complementary fit between the shape of its active site and the shape of the substrate  May not be an exact fit by the enzyme can take on the shape  Known as induced fit Substrate is held in the active site by weak interactions like hydrogen and ionic bonds The R groups that make the active site convert the substrate to the product, which then departs so another reaction can be catalyzed Enzymes emerge from the reaction in their original form Most metabolic reactions are reversible When there are multiple reactants, the active sites give a template to the reactants have proper orientation Active site may provide a microenvironment that is more conducive to a particular type of reaction When there are enough substrates for all of the active sites to be occupied, the enzyme is saturated o When saturated, the only way to increase the rate of the reaction further is to add more enzymes Heating the substance will only increase the reaction by causing more movement and collisions up to a certain point, but after that the reaction drops sharply Extreme pH and temperature cause denaturation o The bonds between polypeptides in secondary and tertiary structures are altered o Each enzyme has an optimal pH and temperature Cofactors: nonprotein helpers for catalytic activities Coenzyme: an organic cofactor Enzyme Inhibitors o Make the reaction less effective o When the inhibitor attaches to the enzyme by covalent bonds, it is irreversible o Competitive inhibitors: the inhibitor binds in the active site and prevents the substrate from going in the active sit - - o Noncompetitive inhibitors: do not directly compete with the substance to bind to the enzyme  Bind to the enzyme at a different site and cause the shape to change so that the substrate cannot fit in the active sit properly Allosteric Regulation: a protein’s function at one site is affected by binding of a regulatory molecule to a separate site o Turns the enzyme on and off o Cooperativity: a substrate molecule binding to one active sit in a multisubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites o Feedback Inhibition: a metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway Anabolic reactions build things up (use energy) Catabolic reactions break things down Chapter 37: Soil and Plant Nutrition *includes only basics from reading guide* - - - - Carbon dioxide enters and oxygen exits plants through stomata (pores in leaves) Water enters the plant through roots and travels up the xylem (cohesion and adhesion) tubes to photosynthetic regions o Leaves the plant from leaves through transpiration 90% of a plant’s biomass (not water mass, but the mass of all its macromolecules in dry tissue) comes from carbon Carbohydrates being converted to amino acids or nucleotides require nitrogen o Nitrogen fixation  Nitrogen fixing bacteria convert N2 to ammonia (NH3) which is converted to nitrate NO3that the plant uses by nitrifying bacteria  Some of the ammonia is converted back to N2 and released in the air by denitrifying bacteria o Compounds are polar so they dissolve in water The only type of organisms that have enzyme pathways to take N2 gas out of the air and convert it into soil nitrogen are certain species of bacteria (cyanobacteria) o The legume family works mutualistically with these nitrogen fixers by inviting them in to their roots  When the plant dies, their remains help the bacteria by fertilizing soil  Nodules: swelling in a legume’s roots composed of plant cells with bacteria Mycorrhizae: the intimate mutualistic associations of roots and fungi o Host plant provides the fungi with a steady supply of sugar o Fungus increases the surface area for water uptake and supplies the plant with phosphate and other minerals absorbed from the soil  Also secrete growth factors that stimulate roots to grow and branch and antibiotics to protect the plant from pathogens o Ectomycorrhizae: from a dense sheath, or mantle of mycelia (hyphae), over the surface of the root  These hyphae don’t penetrate root cells, but form a network to facilitate nutriet exchange  Usually thicker, shorter, and more branched  Not root hairs o Arbuscular Mycorrhizae: do not form a dense mantle ensheating the root  More common  Microscopic hyphae establish contact by growing along the root’s surface