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Transcript
Chapter 2 - Chemistry! Chapter 2 - Molecules of Life (Biochemistry)! Element = a quantity of matter composed of atoms of the same type! Atoms: net charge = zero! • Protons (+, mass ≈ 1)! • Neutrons (0, mass ≈ 1)! • Electrons (-, mass negligible)! ! Atom has same # of protons and electrons so charge = 0" Atomic number = # protons! Mass number = "# protons + # neutrons! Periodic Table of Elements 11! Na! Element! 23! " " Figure 2.2! 8 Atomic number! 16 Mass number! O 1! CHONPS, Na, K, Ca! 2! 1! Chapter 2 - Chemistry! Electron Shells" " " " Figure 2.8! What is the charge on an atom of oxygen?! Draw a diagram like the ones above for Na11 and Cl17.! 3! Ions - The Octet Rule (Rule of Eight)! Atoms can gain or lose electrons! Except for the first electron shell, the outermost (valence) shell can hold 8 electrons (This applies to all atoms that you need to know about.)! E.g. Sodium atom (Na1123) loses one electron → Na+! • Giving something away is a “positive” thing to do! • Positively charge ion = cation (ca+ion)! E.g. Chlorine (Cl1735) atom gains one electron → Cl-! • Negatively charged ion = anion! 4! 2! Chapter 2 - Chemistry! Chemical Bonds! Contain energy that is released when the bond is broken ! ! glucose (a sugar) → CO2 + H2O+ energy! ! Energy is required to form chemical bonds! ! CO2 + H2O + energy → glucose! ! Catabolic? Anabolic?! 5! Ionic Bonds " " " " " Figure 2.10! Anions (-) and cations (+) attract each other" 6! 3! Chapter 2 - Chemistry! Covalent Bonds! Do not involve ions - Atoms share electrons! • Strong - hard to break (requires enzymes)! • Most of the energy we get from food involves breaking covalent bonds! A–B ↔ A + B + Energy! ! glucose + oxygen ↔ carbon dioxide + water+ Energy! C6H12O6 + 6 O2 ↔ 6 CO2 + 6 H2O + Energy! ! Single Covalent Bonds " 7! " Figure 2.11! How many electrons are in each atom’s outermost shell?! (Charges on H2O are misleading. i.e., WRONG. See slide 11, 12.)! Shorthand notation: a single line connecting two atoms indicates a pair of covalently shared electrons.! O! ! H H! 8! 4! Chapter 2 - Chemistry! Double Covalent Bonds " " Figure 2.9b! How many electrons are in each atom’s outermost shell?! Carbon dioxide: CO2! Chemical notation: O=C=O, the double lines (=) indicate two pairs of shared electrons in CO2! 9! Covalent Bonds - 2! Nonpolar covalent bonds! • Electrons shared equally between atoms! • Previous slide for CO2 showed nonpolar covalent bonds! ! Polar covalent bonds! • Electrons not shared equally! • One atom “hogs” the electrons! • This leads to the formation of hydrogen bonds.! 10! 5! Chapter 2 - Chemistry! Hydrogen Bonds (H-bonds) " Figure 2.11a! • Relatively weak bonds, but lots of them together can be strong. ! • Result from unequal sharing of electrons in polar covalent molecules.! • Partial positive and negative charges on different molecules attract each other.! Water is a polar covalent molecule. ! • Electrons are shared unequally between atoms.! • Figure 2.10a is! misleading.! 2δ-! δ+ δ+ 11! Correction to Figure 2.11a! 2δ-! δ+! The charges are not “full charges” like those on a sodium or chloride ion.! δ+! They are partial charges, represented by a δ (delta).! 12! 6! Chapter 2 - Chemistry! Hydrogen Bonding " " " (Martini 2006)! 13! Properties of Water! A polar molecule - will form hydrogen bonds with itself! 1. Water has a high heat capacity - hydrogen bonds again.! • Absorbs heat! • Stabilizes temperature! • Evaporation removes heat! 2. Water is a good lubricant - little friction between individual water molecules.! 14! 7! Chapter 2 - Chemistry! Properties of Water - 2 " " (Martini 2006)! 3. Water is a good solvent.! • Solute! • Solvent! • Forms spheres of ! hydration! 15! Properties of Water - 3! 4. Ice floats! (Learn something new every day.) ! • Freezing stabilizes H-bonds - makes ice less dense than water.! 5. Water is cohesive. ! • Water molecules stick together. H-bonds again.! 6. Water has surface tension. H-bonds again.! 16! 8! Chapter 2 - Chemistry! Acids and Bases - pH (not Ph, ph, or PH!!!!!)! Acids give up H+ (hydrogen ions)! "Strong acids completely dissociate (fall apart):! E.g. HCl → H+ + Cl-! "Weak acids do not completely dissociate:! E.g. H2CO3 ↔ H+ + HCO3-! Bases take up H+ or lose OH-! E.g. NaOH → Na+ + OH-! 17! pH is a Measure of Hydrogen Ion Concentration! pH = -log[H+] ! ! "Examples of log:! • log(100) = log(102) = 2! • log(0.01) = log(10-2) =- 2! ! Pure water at 25 °C has [H+] of 10-7 moles/liter! " " "pH = -log[10-7] ! " " " = -(-7)! " " " = 7! pH of 7 is said to be neutral! 18! 9! Chapter 2 - Chemistry! pH Scale " " " "! Blood: 7.35 - 7.45! ! • Gastric juice: 1.2 - 3.0! • Vaginal fluids: 3.5 - 4.5! • Semen: 7.2 - 7.6! • Urine: 4.5 - 8.0! ! Why does it make sense that all pH values listed above aren’t the same as that of blood?! 19! Buffers! Buffers help maintain pH within desirable limits." Composed of a weak acid and a weak base! ! "Carbonic acid <----> Hydrogen ion + bicarbonate ion! " (a weak acid) " " " (a weak base)! Chemically:! " "H2CO3 <---------> H+ + HCO3-! ! • Add acid (HCl), reaction moves to left (Why?)! • Add base (NaOH), reaction moves to right (Why?)! • Both prevent large changes in [H+]! 20! ! 10! Chapter 2 - Chemistry! Types of Chemical Reactions! 1. Dehydration synthesis! • Make more complex molecules from simpler ones! • Require input of energy! • A.K.A. endergonic or anabolic reactions! • Water is formed (dehydration occurs)! ! A-OH + B-H + energy ----------> A-B + H2O! e.g. synthesis of glycogen from glucose! 21! 1. Dehydration Synthesis " Figure 2.15a! Water leaves:! “dehydration”! 22! 11! Chapter 2 - Chemistry! 2. Hydrolysis Reaction! A.K.A. decomposition reaction! • Break larger molecule into smaller parts! • Water is added (hydrolysis means “to break with water”)! • Energy is released (exergonic or catabolic)! ! A-B + H2O ---------> A-H + B-OH + energy! ! e.g. hydrolysis of glycogen to glucose! 23! 2. Hydrolysis Reaction " " " Figure 2.15b ! Water is used to break this bond: “hydrolysis”! 24! 12! Chapter 2 - Chemistry! Many (most) Biological Reactions are Reversible! 3. Reversible reactions! • Substrates and products often exist in equilibrium! ! Generically: AB ↔ A + B! If the concentration of B goes up, which way does the reaction go?! ! e.g. H2CO3 ↔ H+ + HCO3-! ! 25! Organic Molecules - Carbohydrates! General formula = (CH2O)n! • I.e. carbon and water (carbo- + hydro-)! ! General functions:! • Energy source and energy reserve! " " "Glucose and glycogen! • Structural molecules! " " "Deoxyribose in DNA backbone! e.g. "Monosaccharides (e.g. glucose, fructose)! " "Disaccharides (e.g. sucrose, maltose)! " "Polysaccharides (e.g. glycogen)! 26! 13! Chapter 2 - Chemistry! Carbohydrates - 2 " " " " Figure 2.16! For glucose “n” = 6, so (CH2O)n = C6H12O6! Different ways to represent glucose:! 27! Carbohydrates - Polysaccharides! Glycogen! • A string of glucose units! • Stored for energy in animal cells! Starch! • A string of glucose units! • Stored for energy in plant cells! Cellulose! • A string of glucose units! • A structural molecule in plants! Why can’t we digest cellulose in trees?! 28! 14! Chapter 2 - Chemistry! Lipids (Fats)! Not water soluble" Some types:! • Triglycerides ! (saturated and unsaturated fats)! • Phospholipids! • Steroids! 29! Lipids - Triglycerides! General formula:! • Glycerol + 3 fatty acids! Functions:! • Energy storage (twice as much energy per gram as carbohydrates)! • Energy source (fatty acids)! Types:! • Saturated fats (solids at room temp.)! • Unsaturated fats (liquids at room temp.)! 30! 15! Chapter 2 - Chemistry! Lipids - Triglycerides " " " Figure 2.19! Glycerol! Fatty acid! Unsaturated! Saturated! 31! Lipids - Phospholipids! General formula:! • Two fatty acid “tails” + phosphatecontaining “head”! General functions:! • Important component of cell membranes! Are polar molecules! • Hydrophilic head! • Hydrophobic tail! 32! 16! Chapter 2 - Chemistry! Lipids - Phospholipids " " " Figure 2.20! + Note electrical charges! _ More about this in Ch. 3! 33! Lipids – Steroids " " " " Figure 2.21! General structures:! ! General functions:! • Hormones! • A component of cell membranes! Cholesterol! Estrogen! Testosterone! 34! 17! Chapter 2 - Chemistry! Proteins! General formula:! • Chain of amino acids joined by peptide (covalent) bonds" General functions:! • Structural function - Muscle, bone, hair! • Enzymes - Chemical catalysts! • Oxygen carriers (e.g. hemoglobin, myoglobin)! • Hormones (e.g. insulin, growth hormone)! 35! Amino Acids – 1 " " " " Figure 2.22! “R group” or “side chain” determines the amino acid’s properties.! • Hydrophilic?! • Hydrophobic?! • What do you think! “R” stands for?! (Acid)! 36! 18! Chapter 2 - Chemistry! Protein Structure Summary " " Figure 2.24! Primary: ! Linear sequence of amino acids! Secondary:! Local folding into helices, sheets! Tertiary:! Overall 3-D shape of a polypeptide! Quaternary:! Interactions between two or more polypeptides! 37! Nucleic Acids! General formula:! • Composed of nucleotides" Sugar! Nitrogen-containing base! Phosphate! DNA - double stranded! RNA - single stranded! ATP! 38! 19! Chapter 2 - Chemistry! Nucleotide Structure " " " Figure 2.26! Pentose sugar: "Ribose in RNA and ATP! " " "Deoxyribose in DNA! 39! Nitrogenous Bases! A = Adenine! T = Thymine! C = Cytosine! G = Guanine! ! DNA base pairing rules:! A is complementary to T! G is complementary to C! RNA base pairing rules: ! A is complementary to U! G is complementary to C! ! Why are DNA and RNA different? Because nature does it this way.! ! Pretty simple, eh?! 40! 20! Chapter 2 - Chemistry! DNA Structure" " " " " Figure 2.28! 41! To Be Covered Later…! More about Nucleic acids will be covered in Chapter 3 and 21.! ! We will cover Enzyme Function (pp. 31 - 32) with Chapter 3 material.! 42! 21!
