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Transcript
Biochemistry All Matter is composed of Atoms The Structure of the Atom Electrons: Negative electrical charge Protons: Positive electrical charge Neutrons: No net electrical charge Molecules • Two or more atoms held together by Chemical bonds Chemical Bonds • form because of the interactions between the electrons of the atoms The atom’s ELECTRONEGATIVITY (ability to attract electrons) • Determines the type and strength of the Chemical bond Ions • Ions are atoms that have either a positive or negative electrical charge because the electron number is NOT equal to the proton number IONIC BONDS • Form between atoms when electrons are TRANSFERED from one atom to another forming ions of opposite electronic charges • http://www.dac.neu.edu/physics/b.mahe swaran/phy1121/data/ch09/anim/anim09 04.htm Covalent Bonds • Form when atoms share electrons • Occur when the electronegativities between the atoms are similiar • http://www.dac.neu.edu/physics/b.maheswaran/phy1 121/data/ch09/anim/anim0904.htm • Some molecules have Single Covalent Bonds… which means the atoms share one pair (a single pair) of electrons • Some molecules have Double Covalent Bonds… which means the atoms share two pairs of electrons • Some molecules have Triple Covalent Bonds… which means the atoms share Three pairs of electrons Nonpolar Covalent Bonds • Occur when the electronegativities of both atoms are identical and the electrons are shared equally Polar Covalent Bonds • Occur when the electronegativities of both atoms are Different and the electrons are shared unequally Negative Pole Positive Pole Hydrogen Bonds • Hydrogen bonds are weak bonds which form between molecules Hydrogen Bond Bond Strengths • Ionic Bonds are weak and are easily broken in water • Covalent Bonds are generally strong • Hydrogen Bonds are very weak The Properties of Water • 1. Water is the Universal Solvent. • Ionic compounds and Polar covalent molecules readily dissolve in water Hydrophilic Molecules (water-loving) • Are substances that dissolve in water…. Salts, sugars, etc…. Hydrophobic Molecules (water-fearing) • Are substances that do not dissolve in water… oils, waxes, etc… Water Has A High Specific Heat Capacity…. The capacity of a substance to change temperature in response to a gain or loss of heat… water changes temperatures very slowly • Specific Heat - the amount of heat needed to raise 1 g of the substance 1 degree C. • Why? ……… Hydrogen bonding. Water Has A High Heat Of Vaporization • Heat of Vaporization: the quantity of heat a liquid must absorb for 1g of it to convert to a gaseous state. Liquid Water Is Cohesive • Water sticks to water. • Why? Because the polarity of water results in hydrogen bonding. Liquid Water is Adhesive • Water sticks to other molecules. • Why? Hydrogen bonding. Water transport in trees uses Cohesion and Adhesion Water Has A High Surface Tension • The surface of water is difficult to stretch or break. • Why? • Hydrogen bonding. Water Stabilizes Temperature • Water can absorb and store a huge amount of heat from the sun. • Result - climate moderation • Result - organisms are able to survive temperature changes. Evaporative Cooling Result: • Water cools organisms from excessive heat buildup. • Why? As water evaporates it takes the heat with it. Water Expands and becomes less dense when It Freezes….so it floats • The distance between water molecules INCREASES from the liquid to the solid form. • Why? • Hydrogen bonding Water Benzene Floats Sinks Result • Ice floats and forms an blanket of insulation during the winter………. Aquatic life can live under ice. Water is used to make Solutions • A Solution is a Homogeneous mixture of two or more substances. • Solvent + Solute Solution • Sugar water, Saltwater, Pepsi Solvent • The dissolving agent • Present in a greater proportion Examples: • Water • Methane Solute • The substance that is dissolved. • Present in smaller quantity Examples: • Salt in saltwater • Sugar in sugar water Solution Concentration • Usually based on Molarity • Molarity - the number of moles of solute per liter of solution. • A mole is = 6.021x1023 One Mole of each Sugar Copper Sulfate Sulfur Mercury Oxide Sodium Chloride Copper Dissociation of Water • Water can sometimes split into two ions. • In pure water the concentration of each ion is 10-7 M • Adding certain solutes disrupts the balance between the two ions. • The two ions are very reactive and can drastically affect a cell. Acids • Materials that can release H+ Example: HCl HCl H+ + Cl- Hydrochloric acid, vinegar, etc… Effects of Acid Rain Bases • Materials that can absorb H+ • Often reduce H+ by producing OHExample: NaOH NaOH Na+ + OHDrano, Soaps, etc……. pH Scale • A logarithmic scale for showing H+ concentration in a solution. pH = - log [H+] pH Scale Acids: pH < 7 Neutral: pH 7 Bases: pH >7 • Acids: pH <7 etc. • Bases: pH >7 etc. Each pH unit is a 10x change in H+ Buffers • Materials that have both acid and base properties. • Resist pH shifts. • Cells and other biological solutions often contain buffers to prevent damage. Organic Molecules • Contain carbon atoms, exceptions are carbon monoxide and carbon dioxide • Carbon has 4 electrons available to form 4 chemical bonds….therefore large molecules are easily formed using carbon as the backbone. • Large carbon based molecules are usually found as long chains or rings. Macromolecules • Most macromolecules are “polymers” ….molecules that consist of a single unit (monomer) repeated many times. Functional Groups • Many organic molecules share similar properties because they have similar clusters of atoms, called the….. Function Groups • Each Functional Group gives the molecules a particular property, such as acidity or polarity. Functional Groups Four Main Types Of Macromolecules • Carbohydrates • Lipids • Protein • Nucleic acids Carbohydrates • Used for fuel, building materials, and receptors. • Made of C,H,O • General formula is CH2O • C:O ratio is 1:1 Types Of Carbohydrates • Monosaccharides • Disaccharides • Polysaccharides Monosaccharides • • • • Mono - single Saccharide - sugar Simple sugars. Can be in linear or ring forms. • Glucose, Fructose, Galactose…. all with the chemical formula C6H12O6….. Same chemical formula, different shapes. • Most words ending with the letters OSE are carbohydrates. Glucose, Fructose, Galactose Disaccharides • Sugar formed by joining two monosaccharides together thru the process of Dehydration Synthesis….(removing water)…aka…. Condensation Synthesis. • all with the chemical formula C12H22O11 • glucose + fructose = sucrose (table sugar) + H2O • glucose + galactose = lactose ( the sugar in milk) + H2O • glucose + glucose = maltose + H2O Condensation Synthesis or Dehydration Synthesis • The chemical reaction that joins monomers into polymers. • Covalent bonds are formed by the removal of a water molecule between the monomers. Hydrolysis • Reverse of condensation synthesis. • Using water (Hydro), to split (Lysis) • Breaks polymers into monomers by adding water Examples of Disaccharides produced through Dehydration Synthesis • Maltose = glucose + glucose • Lactose = glucose + galactose • Sucrose = glucose + fructose Polysaccharides all with the chemical formula (CH2O)n • Many joined simple sugars. • Used for storage or structure. • Examples: Starch - a polymer of a-glucose molecules, principle energy storage molecules in plants Glycogen - a polymer of a-glucose molecules, principle energy storage molecules in animals, stored in the liver and muscles cells Cellulose - a polymer of b-glucose molecules, principle structural molecules in plant cell walls…. Major component of wood Chitin - a polymer of b-glucose molecules, each modified with a nitrogen group, principle structural molecule in the cell walls of fungi and the exoskeletons of the arthropods. Lipids (Fats) • Diverse hydrophobic molecules which are insoluble in water (and other polar molecules) and soluble in non-polar molecules like ether and chloroform • Made of C,H,O • No general formula. • C:O ratio is very high in C Types of Lipids (Fats) • Triglycerides • Phospholipids • Steroids Triglycerides • Three fatty acids joined to one glycerol. • Joined by an “ester” linkage between the -COOH of the fatty acid and the -OH of the alcohol. • Differ in which fatty acids are used. • Used for energy storage, cushions for organs, insulation. Acid Fat Fats and Oils • Fats - solid at room temperature. • Oils - liquid at room temperature. • Saturated - solid at room temperature. • Unsaturated - liquid at room temperature. Saturated Fats • Saturated - no double bonds. Unsaturated Fats • Unsaturated - one or more C=C bonds. Can accept more Hydrogens. • Double bonds cause “kinks” in the molecule’s shape. Question ? • Which has more energy, a kg of fat or a kg of starch? …. (Hint) in Fats there are more C-H bonds which provide more energy per mass. • Answer… carbohydrates (starch) have 4 calories per gram, lipids have 9 calories per gram Phospholipids • Similar to fats, but have only two fatty acids. • The third -OH of the glycerol is joined to a phosphate group replacing a fatty acid • Major component of the Plasma Membrane of all cells Result • Phospholipids are amphipathic which means they have a nonpolar, hydrophobic tail, but a polar, hydrophilic head. • Self-assembles into bilayers, an important part of cell membranes. Steroids • Characterized by a backbone of four fused carbon rings. • Differ in the functional groups attached to the rings. • Examples: –cholesterol –sex hormones Proteins • Made of C,H,O,N, and sometimes S. • No general formula • Polymers of amino acids Uses Of Proteins • Structural Proteins: used to make skin, hair, muscles, etc… • Enzymes: Control Metabolism • Antibodies: Provide protection against foreign substances • Transport Proteins: Transport molecules across membranes • Storage: such as ovalbumin in eggs Proteins Proteins are Polypeptide chains of Amino Acids linked by peptide bonds. Amino Acids • All have a Carbon with four attachments: -COOH (acid) -NH2 (amine) -R group • 20 different kinds of amino acids because there are 20 different kinds of R groups Amino Group Carboxyl Group AKA: Acid Group Amino Acids Amino Acids R groups The properties of the R groups determine the properties of the protein. Polypeptide Chains • Formed by dehydration synthesis between the carboxyl group of one amino acid and the amino group of the second Amino Acid. Levels Of Protein Structure • Organizing the polypeptide into its 3-D functional shape. – Primary – Secondary – Tertiary – Quaternary Primary Structure • Order of amino acids in the polypeptide chain. • Many different sequences are possible with 20 AAs. Secondary Structure • 3-D structure formed by hydrogen bonding between the R groups. • Two main secondary structures: - a helix - pleated sheets Tertiary • 3D shape as bonding occurs between the R groups. • Examples: – Hydrophobic interactions – Ionic bonding – Disulfide bridges – Hydrogen Bonding Quaternary • When two or more polypeptides unite to form a functional protein. • Example: hemoglobin Is Protein Structure Important? Denaturing Of A Protein • Events that cause a protein to lose structure (and function). • Example: –pH shifts –high salt concentrations –heat Nucleic Acids • • • • • Stores the genetic Information Polymers of nucleotides Made of C,H,O,N and P No general formula Examples: DNA and RNA Nucleotides of DNA and RNA Nucleotides have three parts: – Nitrogenous Base – Pentose sugar (Deoxyribose in DNA and Ribose in RNA) – Phosphate Group Nitrogenous Bases • Rings of C and N • Two types: – Pyrimidines (single ring) Thymine, Cytosine – Purines (double rings) Adenine, Guanine Pentose Sugar • 5-C sugar • Ribose - RNA • Deoxyribose – DNA DNA: Deoxyribonucleic Acid • Double Helix Structure • The two strands of DNA are antiparallel, oriented in opposite directions… one strand is arranged in the 3’ – 5’ direction while the other is arranged in the 5’ – 3’ direction (5’ means the phosphate group is attached to the 5th carbon on the Deoxyribose molecule. • Makes up genes. RNA: Ribonucleic Acid • Important molecule in protein synthesis. • Genetic information for a few viruses only. Differences between DNA and RNA • RNA is a single strand • DNA has Deoxyribose, RNA has ribose • Thymine is replaced by Uracil Chemical Reactions in Metabolic Processes • In order for chemical reactions to occur, the reacting molecules must first collide and then have enough energy (Activation energy) to trigger the formation of new bonds. • Some reactions require catalysts. Catalysts are molecules which trigger or accelerate chemical reactions without being chemically altered themselves. Metabolism • Chemical reactions which occur within living organisms are called Metabolic reactions….. • Two types of Metabolic Reactions: *Anabolic Reactions: Build molecules and store energy *Catabolic Reactions: Breakdown Molecules and release energy Chemical Equilibrium • The net direction of metabolic reactions, forward or reverse, is determined by the concentration of the reactants and the products. Enzymes: Globular proteins which catalyze metabolic reactions. • Enzyme: Catalyzes the Reaction • Substrate: molecule acted upon • Products: Resulting molecules • Enzyme + Substrate • Maltase + Maltose Enzyme – Substrate Complex Maltase + Maltose Complex Active Site Enzyme + Products Maltase + glucose + glucose Enzymes • Most Enzymes end with the letters ASE • Enzymes are substrate specific….. Examples: • Maltase can only breakdown Maltose • Sucrase can only breakdown Sucrose • Amylase can only breakdown Amylose Enzymes The efficiency of Enzymes is affected by: - pH shifts: pepsinogen is only activated when stomach acids lower the pH - Heat: denatures enzymes Cofactors • Are nonprotein molecules that assist enzymes… since they are nonproteins they are used up in the reactions. • A holoenzyme is the union of a cofactor and enzyme. • The enzyme is called an Apoenzyme when it’s part of a holoenzyme Inorganic Cofactors Are usually metals, like Iron (Fe+2), Magnesium (Mg+2) CoEnzymes Are organic molecules which aid in enzyme reactions……. Some vitamins are coenzymes. Since they are nonproteins they are also used up in the reactions. ATP Adenosine TriPhosphate Source of Activation energy for Metabolic Reactions Allosteric Enzymes • Have two types of binding sites…. One for the substrate and one for the allosteric effector. • Two types of Allosteric Effectors: • 1. Allosteric Activator – binds to the enzyme and changes its shape to induces a reaction • 2. Allosteric Inhibitor – binds to the enzyme and induces inactivity Allosteric Enzymes Competitive Inhibition Is when an enzyme mimic occupies the active site preventing a reaction. Noncompetitor Inhibitor Prevents enzyme reactions by binding to the substrate at locations other than the active or allosteric site. Cooperativity • Occurs when an enzyme becomes receptive to additional substrate molecules after one substrate molecule attaches to an active site. • Example: Hemoglobin…… its binding capacity to additional oxygen molecules increases after the first oxygen fills the active site. Cooperativity