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The Chemistry of Life Chapters 2 and 3 Atoms Smallest unit of matter that retains physical properties 3 Basic Parts Proton Neutron Electron Nucleus gives an atom its mass Electrons give an atom is behavior Elements Made up of only 1 type of atom Isotopes have same number of p+, but different numbers of n0, so atomic mass varies Form compounds Chemical Bonds Formula tells the ratio of atoms in a compound 98% of living things are made of CHNOPS Chemical Bonds The valence electrons are involved in the bond Atoms are stable when their valence shell is filled Covalent Bonds- atoms share valence electrons and are held together Non-metal to non-metal Molecule is the smallest part of a compound that retains the properties Polarity Covalent bonds share electrons between atoms Electrons shared equally result in a nonpolar bond Electrons shared unequally between the atoms create regions of positive charge and negative charge, though the molecule is neutral, results in a polar bond Polar molecules can interact with each other and with ions Whole molecules can be polar or select bonds in a molecule can be polar Ionic Bonds are a result of the transfer of valence electrons Atoms that lose electrons have more p+ than e- and are called positive ions (cations) Atoms that gain electrons have more e- than p+ and are called negative ions (anions) Metals form cations and non-metals form anions The positive ion is attracted to the negative ion and they stick together Energy Comes in many forms Kinetic, Potential, Chemical, Thermal, Radiant The ability to do work Can be converted from one form to another When atoms for chemical bonds energy can either be absorbed or released Living Things and Energy All living things require energy 1000s of chemical reactions occur in living organisms a day Energy is either stored in bonds formed during a reaction or it is released by the reaction Living organisms use this energy to carry out life processes Metabolism is all of the chemical reactions that occur in an organism Activation Energy Energy required for a chemical reaction to occur Can be a large amount Catalysts lower the activation energy for a reaction They are not used up and can be used repeatedly Enzymes are proteins or RNA that act as catalysts in living organisms- there are 1000s Enzyme has a specific shape that will interact with a specific substrate Substrate is reactant being catalyzed fits in active site on enzyme Enzyme’s shape is changed when substrate bonds at active site Change in shape causes bonds in substrate to weaken and break Products are released by enzyme Enzyme is unchanged and reacts anew with another substrate Enzymes require very specific temperature and pH ranges Changes can cause the enzyme to denature Enzyme Catalyzed Reaction Oxidation Reduction Reactions AKA- Redox reactions Reactions that involve the transfer of electrons LEO says GER Lose electrons oxidize Gain electrons reduce Oxidation and Reduction are coupled together- something is oxidized because something else is reduced Water and Solutions Cells are mainly water and the water is an arena for the chemical reactions of life to occur Water is polar H is slightly +, O is slightly – Allows water molecules to interact with each other, ions, and other polar molecules Water is universal solvent because of its polarity- it dissolves a lot of stuff Hydrogen bonds form between water molecules allowing them to stick together Hydrogen bonds form between H with a slight + charge and areas of – charge or with anions Can be formed or broken easily and repeatedlyweak independently, strong in great numbers Many occur at one time in water H bonds allow water to experience Cohesion- water molecules stick together Adhesion- water molecules stick to other things When ionic compounds are dissolved in water they ionize- break apart into cations and anions Water is less dense as a solid than as a liquid Ice floats- pond ecosystems are conserved even in winter Water has a high specific heat capacity Water absorbs large amounts of heat with little temperature change Solutions Solutions are homogeneous mixtures All substances are evenly distributed throughout Composed of solute and solvent Solute is what is dissolved (less of this) Solvent does the dissolving (more of this) Can have different concentrations How much solute is dissolved in the solvent Saturated- the max amount of solute is dissolved Aqueous solutions have water as the solvent Essential for life Aqueous solutions are essential for cells Blood is an aqueous solution Many organisms live in aqueous solutions- The ocean! Ponds! Lakes! Rivers! Your gut! Acids and Bases Water can ionize (split into ions) H2O H+ + OH - OH - is the hydroxide ion H+ is a proton Water can also accept a proton (H+), forming hydronium ion (H30+) H+ + H2O H30+ This occurs all of the time in water Acids and bases are determined by the ratio of hydronium ions to hydroxide ions Acids H30+ > OH Bases H30+ < OH Compounds that are acids donate a H+ and it will react with H20 to form H3O+ Bases produce OH- which will increase their concentration pH scale is a way to measure the concentration of H3O+ It is a logarithmic scale- so each number is a ten-fold difference in concentration of H3O+ Buffers are chemical substances that can absorb excess acids or bases to maintain pH Very important job Enzymes (biological catalysts) can only function in specific pH ranges Cells must regulate their pH Biochemistry The study of the chemistry that allows life to exist and flourish Biochemistry is centered around the element Carbon Organic compounds are those that contain carbon Inorganic compounds do not generally contain carbon Carbon Carbon has 4 valence electrons and needs 8 Forms covalent bonds to complete its valence shell Carbon is special because is will bond with up to 4 other carbon atoms Can form rings, straight chains, and branched chains A covalent bond is formed when two atoms share 2 electrons Represented with a straight line Carbon can form single, double, and triple bonds Carbon can form almost endless compounds as a result Functional Groups Organic molecules all contain Carbon- so what makes one compound different from another- Functional Groups Functional Groups are specific clusters of atoms attached to a carbon compound Each functional group has specific properties that it gives the compound Large Carbon Molecules Monomers are small, simple molecules that can be bonded together to form polymers Macromolecules are made from polymers Condensation and Hydrolysis Reactions Monomers are bonded together through condensation reactions With the addition of each monomer a water molecule is lost Polymers can be broken down into polymers through hydrolysis reactions A water molecule must be added in order to split one monomer away from the polymer Energy Currency Remember chemical bonds contain energy Breaking or making a bond can either absorb or release energy Some compounds have a lot of energy stored in their bonds This energy can be used to power cell functions Adenosine Triphosphate (ATP) is a high energy compound Bond between the second and third phosphate is hydrolyzed to release energy for cellular functions, leaving ADP and P ATP + H2O ADP + P + Energy ADP + P + energy ATP + H2O Molecules of Life Carbohydrates, Lipids, Proteins, Nucleic Acids Each type has different properties and responsibilities All have C, H, O; some also have N, P, S Put together in different ratios Carbohydrates Roles include energy source and structural components Made of C, H, O in a 1:2:1 ratio (CH2O)n Monomer- monosaccharide Glucose (simple sugar), galactose (milk), fructose (fruits) Disaccharides are made by a condensation rxn joining 2 monosaccharide Glucose + Fructose Sucrose Polymers are polysaccharides- large molecules made by joining many monosaccharides Animals store excess sugar as Glycogen Plants store excess sugar as Starch Cellulose is a polysaccharide made by plants that gives cell walls strength and rigidity Can be broken down by hydrolysis reactions Proteins Have a diversity of structures, resulting in a wide range of functions Account for ~50% dry mass of cells Act as enzymes, play roles in defense, storage, transport, cell communication, movement, structural support Each protein has a unique 3-D shape Composed of mainly C, H, O, N Monomer is amino acid Amino Acids have same basic structure There are 20 amino acids used to build thousands of proteins Amino group, central C, Carboxyl group, and R group (variable- distinguishes 1 aa from another) Polymer is polypeptide Long chain of amino acids Held together by peptide bonds Covalent bonds formed via condensation rxn 1 or more polypeptide chain(s) fold into complex shapes Shape is essential to function Chains held together via interactions like hydrogen bonds Enzymes are important group of proteins Act as biological catalysts Enzyme has a specific shape that will interact with a specific substrate Substrate is reactant being catalyzed fits in active site on enzyme Lipids Function as long term energy storage, in membranes, water proof coverings, steroids (hormones) as chemical messengers Have C, H, O- higher ratio of C and H to O Long chains of C and H store more energy Fatty Acids Carboxyl Group connected to a long carbon chain Carboxyl group is polar and therefore hydrophilic Hydrocarbon chain is non-polar and hydrophobic Fatty acids that have each C bonded to 4 things are called saturated Fatty acids that have double bonds between some C atoms are called unsaturated Triglycerides have 3 fatty acids joined to a glycerol head Saturated triglycerides have a high melting point and are solid at room temp- butter, fats, red meat Unsaturated triglycerides are usually liquid at room temp- Plant oils (olive, sunflower, etc) Phospholipids- 2 fatty acids bonded to a glycerol head and a phosphate group Form water-tight barriers, such as cell membrane (lipid bilayer) Waxes are long chains of fatty acids bonded to large alcohol groups Help plants retain water and earwax protects ear from invaders Steroids are made of 4 carbon rings and functional groups attached Hormones are steroids that have important roles transmitting chemical messages and roles in the cell membrane (cholesterol) Nucleic Acids Function to store and transfer information in cells, including hereditary material Composed of C, H, O, N, P Monomer- Nucleotide Three parts: 5-C sugar, Nitrogenous base, Phosphate group ATP Polymer- Nucleic Acid DNA, RNA