Chapter 2 - Molecules of Life (Biochemistry)! Periodic Table of Elements " " Figure 2.2!

Chapter 2 - Chemistry! Chapter 2 - Molecules of Life (Biochemistry)! Element = a quantity of matter composed of atoms of the same type! Atoms: net ch...
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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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