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!
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Figure 2.2!
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Atomic number!
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Mass number!
O
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CHONPS, Na, K, Ca! 2!
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Chapter 2 - Chemistry!
Electron Shells"
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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!
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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
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Figure 2.10!
Anions (-) and cations (+) attract each other"
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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 "
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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!
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Chapter 2 - Chemistry!
Double Covalent Bonds "
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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!
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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!
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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+
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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!
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Chapter 2 - Chemistry!
Hydrogen Bonding "
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(Martini 2006)!
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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!
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Chapter 2 - Chemistry!
Properties of Water - 2 "
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(Martini 2006)!
3. Water is a good solvent.! • Solute!
• Solvent! • Forms spheres of ! hydration!
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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.!
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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!
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Chapter 2 - Chemistry!
pH Scale "
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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?!
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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-!
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• Add acid (HCl), reaction moves to left (Why?)! • Add base (NaOH), reaction moves to right (Why?)! • Both prevent large changes in [H+]! 20!
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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
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Figure 2.15a!
Water leaves:! “dehydration”!
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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 "
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Water is used to break this bond: “hydrolysis”!
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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)!
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Chapter 2 - Chemistry!
Carbohydrates - 2 "
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For glucose “n” = 6, so (CH2O)n = C6H12O6! Different ways to represent glucose:!
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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!
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Chapter 2 - Chemistry!
Lipids (Fats)! Not water soluble" Some types:!
• Triglycerides ! (saturated and unsaturated fats)! • Phospholipids! • Steroids!
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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!
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Chapter 2 - Chemistry!
Lipids - Triglycerides
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Figure 2.19!
Glycerol!
Fatty acid!
Unsaturated!
Saturated!
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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!
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Chapter 2 - Chemistry!
Lipids - Phospholipids
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Figure 2.20!
+ Note electrical charges! _
More about this in Ch. 3! 33!
Lipids – Steroids
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Figure 2.21!
General structures:! ! General functions:! • Hormones! • A component of cell membranes!
Cholesterol!
Estrogen! Testosterone!
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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)!
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Amino Acids – 1
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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!
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Chapter 2 - Chemistry!
Protein Structure Summary
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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!
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Chapter 2 - Chemistry!
Nucleotide Structure
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Figure 2.26!
Pentose sugar: "Ribose in RNA and ATP! " " "Deoxyribose in DNA!
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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!
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Chapter 2 - Chemistry!
DNA Structure"
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Figure 2.28!
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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.!
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