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The Chemistry of Life Unit III What is Biochemistry? Biochemistry is the study of structure, composition (what things are made up of), and chemical reactions that occur in living things. Living things (biotic factors) depend on chemistry for life…so biology and chemistry are closely related! So what makes up these living things? Matter is anything that takes up space Matter is made up of small units called atoms. Atoms are made up of 3 subatomic particles: Protons (which have a + charge) Electrons (which have a – charge) Neutrons (which have no charge ) Elements When atoms of the same type come together they make up units called elements. An element is a pure substance made of only 1 type of atom (it is usually abbreviated by a chemical symbol): Chemical Compounds Remember that elements are made up of small units called atoms. When these elements come in close contact with each other, they often have an “attraction” – like magnets. The attraction of these elements often leads to a bond – the joining of atoms to one another When two or more elements are put together, they form a chemical compound. These compounds are usually represented by a chemical formula – a combination of chemical symbols that represent the joining of these elements Example: NaCl (salt) or H2O (water) Chemical Bonds The atoms in compounds are held together by chemical bonds Bond formation involves the electrons that surround each atomic nucleus Electrons that are available to form bonds are called valence electrons The main types of chemical bonds are ionic bonds and covalent bonds Ionic Bonds An ionic bond is formed when one or more electrons are transferred from one atom to another An atom that loses electrons is no longer neutral, instead it becomes positively charged An atom that gains an electron is no longer neutral, instead it becomes negatively charged These positively and negatively charged atoms are called ions Covalent Bonds Sometimes electrons are shared by atoms instead of being transferred These electrons are located in a region between the atoms A covalent bond forms when electrons are shared between atoms The structure that results when atoms are joined together by covalent bonds is called a molecule (this is the smallest unit of most compounds) Covalent & Ionic Bonds IONIC BONDS: electrons are transferred between atoms COVALENT BONDS: electrons are shared between atoms Properties of Water Water is the most abundant compound in living things Some of water’s properties that facilitate an environment for life are: Cohesive and adhesive behavior Ability to moderate temperature Expansion upon freezing Versatility as a solvent http://www.sumanasinc.com/webcontent/animati ons/content/propertiesofwater/water.html The Polarity of Water The water molecule is a polar molecule: The opposite ends have opposite charges Water is polar because the oxygen atom has a stronger electronegative pull on shared electrons in the molecule than do the hydrogen atoms Polarity allows water molecules to form hydrogen bonds with each other (these are weak covalent bonds) Cohesion & Adhesion Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion the attraction of water molecules to other water molecules as a result of hydrogen bonding cohesion due to hydrogen bonding contributes to the transport of water and dissolved nutrients against gravity in plants Adhesion is the clinging of one substance to another adhesion of water to cell walls by hydrogen bonds helps to counter the downward pull of gravity on the liquids passing through plants Adhesion Water-conducting cells Direction of water movement Cohesion 150 µm Cohesion and adhesion work together to give capillarity – the ability of water to spread through fine pores or to move upward through narrow tubes against the force of gravity. Surface Tension The high surface tension of water, resulting from the collective strength of its hydrogen bonds, allows the water strider to walk on the surface of the pond. Surface tension is directly related to the cohesive property of water – it is a measurement of how difficult it is to stretch or break the surface of a liquid. Moderation of Temperature Water can absorb or release a large amount of heat with only a slight change in its own temperature The ability of water to stabilize temperature stems from its relatively high specific heat This is the amount of heat that must be absorbed or lost for 1g of a substance to change its temperature by 1°C Water’s High Specific Heat Water’s high specific heat can be traced to hydrogen bonding Heat is absorbed when hydrogen bonds break Heat is released when hydrogen bonds form High specific heat of water is due to hydrogen bonding – H-bonds tend to restrict molecular movement, so when we add heat energy to water, it must break bonds first rather than increase molecular motion. A greater input of energy is required to raise the temperature of water than the temperature of air! Minimizes temperature fluctuations to within limits that permit life Evaporative Cooling Evaporation is transformation of a substance from liquid to gas Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas As a liquid evaporates, its remaining surface cools, a process called evaporative cooling The high amount of energy required to vaporize water has a wide range of effects: Helps stabilize temperatures in organisms and bodies of water Evaporation of sweat from human skin dissipates body heat and helps prevent overheating on a hot day or when excess heat is generated by strenuous activity. The Density Anomaly Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense Water reaches its greatest density at 4°C If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth Due to geometry of water molecule, they must move slightly apart to maintain the max number of H bonds in a stable structure. So at Zero degrees Celsius, an open latticework is formed, allowing air in – thus ice becomes less dense than liquid water floats on top of the water. Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds break and re-form The Solvent of Life Water provides living systems with excellent dissolving capabilities A solution is a liquid that is a homogeneous mixture of substances Solvent (dissolving agent) Solute (substance that is dissolved) An aqueous solution is one in which water is the solvent Hydration Shell http://www.sumanasinc.com/webcontent/animations/content/propertiesofwater/water.html • A hydration shell refers to the sphere of water molecules around each dissolved ion in an aqueous solution – Water will work inward from the surface of the solute until it dissolves all of it (provided that the solute is soluble in water) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Acids and Bases An acid is any substance that increases the H+ concentration of a solution A base is any substance that reduces the H+ concentration of a solution pH Scale 0 1 Gastric juice, 2 lemon juice H+ H+ Battery acid + – H H+ OH + OH– H H+ H+ H+ 3 Vinegar, beer, wine, cola 4 Tomato juice Acidic solution 5 Black coffee Rainwater 6 Urine OH– H+ OH– H+ OH– OH– OH– + H+ H+ H Neutral solution Neutral [H+] = [OH–] Saliva 7 Pure water Human blood, tears 8 Seawater 9 10 OH– Milk of magnesia OH– OH– H+ OH– – OH– OH OH– + H Basic solution 11 Household ammonia 12 Household 13 bleach Oven cleaner 14 Buffers The internal pH of most living cells must remain close to pH 7 Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution They do so by accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions when they are depleted Most buffers consist of an acid-base pair that reversibly combines with H+ CO2 + H2O <= H2CO3 => HCO3- + H+ Macromolecules Many of the molecules in living cells are so large that they are known as macromolecules Formed by a process called polymerization (making large compounds by joining smaller compounds together) Smaller unit known as monomer – join together to form polymers Four groups of organic compounds found in living things are Carbohydrates Lipids Nucleic acids Proteins Monomers, Polymers, and Macromolecules Monomers: repeating units that serve as building blocks for polymers Polymers: long molecule consisting of many similar or identical building blocks linked by COVALENT bonds Macromolecules: LARGE groups of polymers covalently bonded – 4 classes of organic macromolecules to be studied: 1. Carbohydrates 3. Proteins 2. Lipids 4. Nucleic Acids Formation of Macromolecules http://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html Monomers are connected by a reaction in which 2 molecules are bonded to each other through a loss of a water molecule (called a condensation reaction or dehydration reaction) because a water molecule is lost. Polymers are disassembled into monomers by hydrolysis, a process that is essentially the reverse of the dehydration reaction. Hydrolysis means to break with water. Bonds between monomers are broken by the addition of water molecules. The Synthesis and Breakdown of Polymers As each monomer is added, a water molecule is removed – DEHYDRATION REACTION. This is the reverse of dehydration is HYDROLYSIS…it breaks bonds between monomers by adding water molecules. Organic Compounds and Building Blocks Carbohydrates – made up of linked monosaccharides Lipids -- CATEGORY DOES NOT INCLUDE POLYMERS (the grouping is based on insolubility) Triglycerides (glycerol and 3 fatty acids) Phospholipids (glycerol and 2 fatty acids) Steroids Proteins – made up of amino acids Nucleic Acids – made up nucleotides Carbohydrates – Fuel and Building Material Carbs include sugars & their polymers Carbs exist as three types: 1. monosaccharides 2. disaccharides 3. polysaccharides (macromolecule stage) Made up of C, H, and O in a 1:2:1 ratio (CnH2nOn) Monosaccharides Are major sources of energy for cells! Ex. Glucose – cellular respiration Are simple enough to serve as raw materials for synthesis of other small organic molecules such as amino and fatty acids. Most common: glucose, fructose, galactose Glucose, Fructose, Galactose Glucose: made during photosynthesis main source of energy for plants and animals Fructose: found naturally in fruits is the sweetest of monosaccarides Galactose: found in milk is usually in association with glucose or fructose All three have SAME MOLECULAR FORMULA but differ structurally so they are ISOMERS! Disaccharides Consists of two monosaccharides joined by a GLYCOSIDIC LINKAGE – a covalent bond resulting from dehydration synthesis. Examples: Maltose – 2 glucoses joined (C12H22O11) Sucrose – glucose and fructose joined (C12H22O11) Lactose – glucose and galactose joined (C12H22O11) Examples of Disaccharide Synthesis Polysaccharides These are the polymers of sugars – the true macromolecules of the carbohydrates. Serve as storage material that is hydrolyzed as needed in the body or as structural units that support bodies of organisms. These are polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Storage & Structural Polysaccharides STARCH AND GLYCOGEN are storage polysaccharides. Starch: storage for plants Glycogen: storage for animals Cellulose and Chitin are structural polysaccharides: Cellulose: found in cell wall of PLANTS Chitin: found in cell wall of FUNGI Lipids http://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html Does not include polymers – only grouped together based on trait of little or no affinity for water: Hydrophobic (water fearing) Hydrophobic nature is based on molecular structure – consist mostly of hydrocarbons! Hydrocarbons are insoluble in water b/c of their non-polar C—H bonds! Lipids: Highly Varied Group Smaller than true polymeric macromolecules Insoluble in water, soluble in organic solvents Serve as energy storage molecules Can act as chemical messengers within and between cells Includes fats, steroids, and waxes “Fats” -- Triglycerides Made of two kinds of smaller molecules – glycerol and fatty acids (one glycerol to three fatty acids) Dehydration synthesis hooks these up – 3 waters produced for every one triglyceride ESTER linkages bond glycerol to the fatty acid tails – bond is between a hydroxyl group and a carboxyl group Glycerol is an alcohol with three carbons, each one with a hydroxyl group Fatty acid has a long carbon skeleton: at one end is a carboxyl group (thus the term fatty “acid”) the rest of the molecule is a long hydrocarbon chain The hydrocarbon chain is not susceptible to bonding, so water H-bonds to another water and excludes the fats Lipids The Synthesis and Structure of a Fat, or Triglycerol • One glycerol & 3 fatty acid molecules • One H2O is removed for each fatty acid joined to glycerol • Result is a fat Saturated vs. Unsaturated “Fats” Refers to the structure of the hydrocarbon chains of the fatty acids: No double bonds between the carbon atoms of the chain means that the max # of hydrogen atoms is bonded to the carbon skeleton (saturated) THESE ARE THE BAD ONES!!! – they can cause atherosclerosis (plaque develop, get less flow of blood, hardening of arteries)! If one or more double bonds is present, then it is unsaturated and these tend to kink up and prevent the fats from packing together Examples of Saturated and Unsaturated Fats and Fatty Acids At room temperature, the molecules of a saturated fat are packed closely together, forming a solid. At room temperature, the molecules of an unsaturated fat cannot pack together closely enough to solidify because of the kinks in their fatty acid tails. Saturated and Unsaturated Fats and Fatty Acids: Butter and Oil UNSATURATED SATURATED Phospholipids Have only two fatty acid tails! Third hydroxyl group of glycerol is joined to a phosphate group (negatively charged) Are ambivalent to water – tails are hydrophobic, heads are hydrophilic. At cell surface, get a double layer arrangement – phospholipid bilayer Hydrophilic head of molecules are on outside of the bilayer, in contact with aqueous solutions inside & outside cell. Hydrophobic tails point toward interior of membrane, away from water. The Structure of a Phospholipid NUCLEIC ACIDS http://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html POLYMERS OF INFORMATION – BUILDING BLOCKS OF DNA & RNA What Determines the Primary Structure of a Protein? Gene – unit of inheritance that determines the sequence of amino acids made of DNA (polymer of nucleic acids) Building blocks of nucleic acids are nucleotides: phosphate group, pentose sugar, nitrogenous base (A,T,C,G,U) Two Categories of Nitrogenous Bases Pyrimidines and Purines: Pyrimidines: smaller, have a six-membered ring of carbon and nitrogen atoms (C , U, T) Purines: larger, have a six- and a five-membered ring fused together (A, G) NUCLEIC ACIDS consist of: phosphate group, pentose sugar, nitrogenous base Nucleic Acids Exist as 2 types : DNA and RNA *DNA -- *double stranded (entire code) *sugar is deoxyribose *never leaves nucleus *bases are A,T,C,G *involved in replication and protein synthesis *RNA -- *single stranded (partial code) *sugar is ribose *mobile – nucleus and cytoplasm *bases are A,U,C,G *involved in Protein Synthesis Nucleic Acids Proteins http://bcs.whfreeman.com/thelifewire/content/chp03/0302002.html Account for over 50% of dry weight of cells Used for: *structural support *storage *transport *signaling *movement *defense *metabolism regulation (enzymes) Are the most structurally sophisticated molecules known Are polymers constructed from 20 different amino acids Hierarchy of Structure in Proteins Amino acids – building blocks of proteins 20 different amino acids in nature Polypeptides – polymers of amino acids Protein – one or more polypeptides folded and coiled into specific conformations • All differ in the R-group (also called side chain) • The physical and chemical properties of the R-group determine the characteristics of the amino acid. • Amino acids possess both a carboxyl and amino group. How Amino Acids Join Carboxyl group of one is adjacent to amino group of another, dehydration synthesis occurs, forms a covalent bond: PEPTIDE BOND When repeated over and over, get a polypeptide On one end is an N-terminus (amino end); On other is a C-terminus (carboxyl end) Making a Polypeptide Chain Note: dehydration synthesis. Note: carboxyl group of one end attaches to amino group of another. Note: peptide bond is formed. Note: repeating this process builds a polypeptide. Protein’s Function Depends on Its Conformation Functional proteins consist of one or more polypeptides twisted, folded, and coiled into a unique shape Amino acid sequence determines shape Function of a protein depends on its ability to recognize and bind to some other molecule. CONFORMATION IS KEY! Four Levels of Protein Structure Primary Structure: unique sequence of amino acids (long chain) 2. Secondary Structure: segments of polypeptide chain that repeatedly coil or fold in patterns that contribute to overall configuration 1. are the result of hydrogen bonds at regular intervals along the polypeptide backbone Tertiary Structure: superimposed on secondary structure; irregular contortions from interactions between side chains 4. Quaternary Structure: the overall protein structure that results from the aggregation of the polypeptide subunits 3. The Primary Structure of a Protein This is the unique amino acid sequence…notice carboxyl end and amino end! These are held together by PEPTIDE bonds!!! The Secondary Structure of a Protein Alpha Helix & Beta Pleated Sheet BOTH PATTERNS HERE DEPEND ON HYDROGEN BONDING BETWEEN C=O and N-H groups along the polypeptide backbone. Alpha Helix – delicate coil held together by H-bonding between every fourth amino acid Beta pleated sheet – two or more regions of the polypeptide chain lie parallel to one another. H-bonds form here, and keep the structure together. NOTE – only atoms of backbone are involved, not the amino acid side chains! Tertiary Structure of a Protein Tertiary structure: superimposed on secondary structure; irregular contortions from interactions between side chains (R-groups) of amino acids: nonpolar side chains end up in clusters at the core of a protein – caused by the action of water molecules which exclude nonpolar substances “hydrophobic interaction” van der Waals interactions, H-bonds, and ionic bonds all add together to stabilize tertiary structure may also have disulfide bridges form …when amino acids with 2 sulfhydryl groups are brought together – these bonds are much stronger than the weaker interactions mentioned above Examples of Interactions Contributing to the Tertiary Structure of a Protein Quaternary Structure Quaternary Structure: the overall protein structure that results from the aggregation of the polypeptide subunits Ex. collagen – structural Ex. hemoglobin – globular The Quaternary Structure of Proteins Review: The Four Levels of Protein Structure https://mywebspace.wisc.edu/jonovic/web/proteins.html What determines Protein configuration? Polypeptide chain of given amino acid sequence can spontaneously arrange into 3D shape Configuration also depends on physical and chemical conditions of protein’s environment if pH, salt [ ], temp, etc. are altered, protein may unravel and lose native conformation – DENATURATION •Denatured proteins are biologically inactive! •Anything that disrupts protein bonding can denature a protein! Denaturation and Renaturation of a Protein Denatured proteins can often renature when environmental conditions improve! Metabolic Pathways Metabolism is the totality of an organisms chemical reactions (all processes that involve building materials or breaking down materials): Catabolic – degradative processes, where complex molecules are broken down into simpler compounds and energy is released. Anabolic – consume energy to build complicated molecules from simpler ones. Ex. Cellular respiration Ex. Protein synthesis These pathways intersect in such a way that the energy released from Catabolic can be used to drive Anabolic This transfer of energy is called Energy Coupling Chemical Reactions Everything that happens in an organism – its growth, its interaction with the environment, its reproduction, and even its movement is based on chemical reactions A chemical reaction is a process that changes one set of chemicals into another set of chemicals Can occur slowly or very quickly The elements that enter into a chemical reaction are known as reactants The elements or compounds produced by a chemical reaction are known as products Chemical reactions always involve the breaking of bonds in reactants and the formation of new bonds in products Energy is released or absorbed whenever chemical bonds form or are broken Energy Changes in Exergonic and Endergonic Reactions Exergonic Reaction: Endergonic Reaction: Reaction proceeds with a net RELEASE of free energy…these reactions occur spontaneously. Reaction proceeds with an ABSORPTION of free energy…these reactions are not spontaneous. Activation Energy Chemists call the energy that is needed to get a reaction started the activation energy Some chemical reactions that make life possible are too slow or have activation energies that are too high to make them practical for living tissue These chemical reactions are made possible by catalysts A catalysts is a substance that speeds up the rate of a chemical reaction Catalysts work by lowering the activation energy needed to make the reaction occur Enzymes http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html Enzymes are proteins that act as biological catalysts Cells use enzymes to speed up chemical reactions Enzymes act by lowering the activation energies required to start these chemical reactions Enzymes are very specific, generally catalyzing only one chemical reaction Enzymes are not changed or used up during chemical reactions Enzymes cannot cause chemical reactions – these reactions would all occur naturally, just at a slower rate! Chemical Reactions and Enzymes Activation energy- energy needed to get a reaction started Enzymes are proteins that act as biological catalysts (speed up a reaction) Enzyme Action For a chemical reaction to take place, the reactants must collide with enough energy so that existing bonds will be broken and new bonds will be formed Enzymes speed up chemical reactions by providing a site where reactants can be brought together to react Such a site reduces the energy needed for the reaction by placing the reactants in a position favorable for the reaction to occur The reactants of enzyme-catalyzed reactions are known as substrates Enzymes can be affected by changes in pH, changes in temperature and can be turned on or off at critical stages in the life of a cell Enzymes The reactant an enzyme acts on is its substrate. Enzymes are substrate specific, and can distinguish its substrate from even closely related isomers! Each enzyme has an active site – the catalytic center of the enzyme! Chemical Reactions and Enzymes Enzymes – VERY IMPORTANT! Changes the rate of a chemical reaction Enable specific molecules, called substrates, to undergo chemical change See “Inside Story” – page 166 Physical and Chemical Environment Affects Enzyme Activity Temperature – too high, denatures protein pH – too high or too low, denatures protein Cofactors – inorganic nonprotein helper bound to active site; must be present for some enzymes to function (zinc, iron, copper) Coenzymes – organic nonprotein helper bound to active site; again, must be present (vitamins) http://www.sumanasinc.com/webcontent/animations/content/proteinstruct ure.html Inhibitors Enzyme Inhibitors – stop enzyme from working! 2 types – competitive and noncompetitive Competitive blocks active site, mimics substrate Noncompetitive bind to another part of enzyme and change shape of enzyme – so can’t work on substrate http://bcs.whfreeman.com/thelifewire/content/chp 06/0602001.html Figure 6.17 Inhibition of Enzyme Activity Mimics the substrate and competes for the active site. Binds to the enzyme at a location away from the active site, but alters the shape of the enzyme so that the active site is no longer fully functional. Feedback inhibition Feedback Inhibition: Switching off of a metabolic pathway by its end product, which acts an inhibitor of an enzyme within the pathway.