Marieb Chapter 2 Part B: Chemistry Comes Alive 12/10/11 Student version

Study of chemical composition and reactions of living matter Biochemistry 12/10/11 Study of chemical composition and reactions of living matter All chemicals are either organic or inorganic © 2013 Pearson Education, Inc.

Both equally essential for life Classes of Compounds 12/10/11 Inorganic compounds Do not contain carbon (exception is CO2) Organic compounds Contain carbon, are usually large, and atoms are covalently bonded Both equally essential for life © 2013 Pearson Education, Inc.

Water in Living Organisms 12/10/11 Most abundant inorganic compound 60%–80% volume of living cells Most important inorganic compound Due to water’s properties Let’s discuss this! © 2013 Pearson Education, Inc.

High heat of vaporization Properties of Water 12/10/11 High heat capacity Absorbs and releases heat with little temperature change Prevents sudden changes in temperature High heat of vaporization Evaporation requires large amounts of heat Useful cooling mechanism © 2013 Pearson Education, Inc.

Properties of Water Acts as a polar solvent 12/10/11 Acts as a polar solvent Dissolves and dissociates ionic substances Forms layers around large charged molecules, e.g., proteins (colloid formation) Body’s major transport medium Most biological molecules are happy in it (uhm, dissolve!) © 2013 Pearson Education, Inc.

Figure 2.12 Dissociation of salt in water. 12/10/11 δ+ δ– δ+ Water molecule Salt crystal Ions in solution © 2013 Pearson Education, Inc.

Formed or used in some chemical reactions Properties of Water 12/10/11 Formed or used in some chemical reactions Necessary part of hydrolysis and dehydration synthesis reactions Used as cushioning Protects certain organs from physical trauma, e.g., cerebrospinal fluid © 2013 Pearson Education, Inc.

What Are Salts? 12/10/11 Ions ( ) conduct electrical currents in solution Ions play specialized roles in body functions Ionic balance vital for homeostasis Contain cations other than H+ and anions other than OH– Common electrolytes found in the body sodium, chloride, carbonate, potassium, calcium, phosphates © 2013 Pearson Education, Inc.

Acids and Bases Both form electrolytes Acids are Bases are 12/10/11 Both form electrolytes Acids are Release H+ (a bare proton) in solution HCl  H+ + Cl– Bases are Take up H+ from solution or release OH- into solution NaOH  Na+ + OH– OH– accepts an available proton (H+) to form water OH– + H+  H2O © 2013 Pearson Education, Inc.

Some Important Acids and Bases in Body 12/10/11 Important acids HCl, HC2H3O2 (acetic acid), and H2CO3 Important bases Bicarbonate ion (HCO3–) and ammonia (NH3) © 2013 Pearson Education, Inc.

pH: Acid-base Concentration 12/10/11 • Relative free [H+] of a solution measured in a special way • As free [H+] increases, acidity increases [OH–] decreases as [H+] increases pH decreases • As free [H+] decreases, alkalinity increases [OH–] increases as [H+] decreases pH increases © 2013 Pearson Education, Inc.

pH: Acid-base Concentration 12/10/11 pH = negative logarithm of [H+] in moles per liter pH scale ranges from 0–14 Because pH scale is logarithmic (like the Richter Scale) A pH 5 solution is 10 times more acidic than a pH 6 solution © 2013 Pearson Education, Inc.

pH: Expression Of Acid-base Concentration 12/10/11 Acidic solutions  [H+],  pH Acidic pH: Neutral solutions Equal numbers of H+ and OH– All neutral solutions are pH Pure water is pH neutral pH of pure water = pH 7: [H+] = 10–7 m Alkaline (basic) solutions  [H+],  pH Alkaline pH: © 2013 Pearson Education, Inc.

Figure 2.13 The pH scale and pH values of representative substances. 12/10/11 Concentration (moles/liter) [OH−] [H+] pH Examples 100 10−14 14 1M Sodium hydroxide (pH=14) 10−1 10−13 13 Oven cleaner, lye (pH=13.5) 10−2 10−12 12 Household ammonia (pH=10.5–11.5) 10−3 10−11 11 Increasingly basic 10−4 10−10 10 Household bleach (pH=9.5) 10−5 10−9 9 Egg white (pH=8) 10−6 10−8 8 Blood (pH=7.4) 10−7 10−7 7 Neutral Milk (pH=6.3–6.6) 10−8 10−6 6 10−9 10−5 5 Black coffee (pH=5) 10−10 10−4 4 Wine (pH=2.5–3.5) Increasingly acidic 10−11 10−3 3 10−12 10−2 2 Lemon juice; gastric juice (pH=2) 10−13 10−1 1 1M Hydrochloric acid (pH=0) 10−14 100 © 2013 Pearson Education, Inc.

12/10/11 pH Paper

Strong and Weak Acids and Bases 12/10/11 Strong and Weak Acids and Bases strong weak

Acid-base Homeostasis 12/10/11 A pH change interferes with cell function and may damage living tissue Even a slight change in pH can be fatal What are the extremes of pH of the blood? Lowest = Highest = pH is regulated by kidneys, lungs, and chemical buffers (observe in Lab Expt. 2) © 2013 Pearson Education, Inc.

Buffers Acidity reflects only free H+ in solution 12/10/11 Acidity reflects only free H+ in solution Buffers resist abrupt and large swings in pH Release hydrogen ions if pH rises Bind hydrogen ions if pH falls Carbonic acid-bicarbonate system (important buffer system of blood): © 2013 Pearson Education, Inc.

• All three present in solution. • What happens if we add H+? - Buffers 12/10/11 • H2CO3 H+ + HCO3- • All three present in solution. • What happens if we add H+? - • What happens if we add OH-?

Where Do We Find Buffers? 12/10/11

Molecules that contain Organic Compounds 12/10/11 Molecules that contain Except CO2 and CO, which are considered inorganic Carbon always shares electrons; never gains or loses them Carbon forms four covalent bonds with other elements Unique to living systems Carbohydrates, lipids, proteins, and nucleic acids © 2013 Pearson Education, Inc.

(ex.= glycogen, DNA, proteins) Organic Compounds 12/10/11 Many are (ex.= glycogen, DNA, proteins) Chains of similar units called (I call them the “building blocks”) Polymers are synthesized by dehydration synthesis ( ) Polymers are broken down by hydrolysis reactions ( ) © 2013 Pearson Education, Inc.

Figure 2.14 Dehydration Synthesis and Hydrolysis. 12/10/11 Dehydration synthesis Monomers are joined by removal of OH from one monomer and removal of H from the other at the site of bond formation. + Monomer 1 Monomer 2 Monomers linked by covalent bond Hydrolysis Monomers are released by the addition of a water molecule, adding OH to one monomer and H to the other. Monomer 1 + Monomer 2 Monomers linked by covalent bond Example reactions Dehydration synthesis of sucrose and its breakdown by hydrolysis Water is released + Water is consumed Glucose Fructose Sucrose © 2013 Pearson Education, Inc.

Come in monomers and polymers Contain C, H, and O [formula =(CH20)n] Carbohydrates 12/10/11 Sugars and starches Come in monomers and polymers Contain C, H, and O [formula =(CH20)n] Three classes Monosaccharides – one sugar Disaccharides – two sugars covalently bonded Polysaccharides – many sugars covalently bonded © 2013 Pearson Education, Inc.

Functions of carbohydrates 12/10/11 Functions of carbohydrates Major source of cellular fuel (e.g., glucose) Structural molecules © 2013 Pearson Education, Inc.

These are the monomers of carbohydrates Important monosaccharides 12/10/11 Simple sugars These are the monomers of carbohydrates Important monosaccharides Pentose sugars Ribose and deoxyribose (in DNA and RNA) Hexose sugars Glucose (blood sugar) © 2013 Pearson Education, Inc.

Simple carbohydrate molecules important to the body. Figure 2.15a Simple carbohydrate molecules important to the body. 12/10/11 Monosaccharides Monomers of carbohydrates Example Hexose sugars (the hexoses shown here are isomers) Example Pentose sugars Glucose Fructose Galactose Deoxyribose Ribose © 2013 Pearson Education, Inc.

Double sugars (two covalently linked monomers) Disaccharides 12/10/11 Double sugars (two covalently linked monomers) Also called simple carbohydrates Too large to pass through cell membranes Important disaccharides Sucrose, maltose, lactose We have enzymes to break these down © 2013 Pearson Education, Inc.

Simple carbohydrate molecules important to the body. Figure 2.15b Simple carbohydrate molecules important to the body. 12/10/11 Disaccharides Consist of two linked monosaccharides Example Sucrose, maltose, and lactose (these disaccharides are isomers) Glucose Fructose Glucose Glucose Galactose Glucose Sucrose Maltose Lactose © 2013 Pearson Education, Inc.

Polymers of monosaccharides Complex sugars Important polysaccharides 12/10/11 Polymers of monosaccharides Complex sugars Important polysaccharides Plant starch Animal starch (glycogen) Cellulose (woody plants) © 2013 Pearson Education, Inc.

Figure 2.15c Carbohydrate molecules important to the body. 12/10/11 Polysaccharides Long chains (polymers) of linked monosaccharides Example This polysaccharide is a simplified representation of glycogen, a polysaccharide formed from glucose units. Glycogen PLAY Animation: Polysaccharides © 2013 Pearson Education, Inc.

Contain C, H, O (less than in carbohydrates), and sometimes P Lipids 12/10/11 Contain C, H, O (less than in carbohydrates), and sometimes P Insoluble in water Main types: PLAY Animation: Fats © 2013 Pearson Education, Inc.

Neutral Fats or Triglycerides 12/10/11 Called fats when solid (lard, butter) Oils when liquid (canola oil) Composed of three fatty acids covalently bonded to a glycerol molecule Main functions Energy storage Insulation Protection © 2013 Pearson Education, Inc.

Dehydration Synthesis Figure 2.16a Lipids. 12/10/11 Dehydration Synthesis Triglyceride formation Three fatty acid chains are bound to glycerol by dehydration synthesis. + + Glycerol 3 fatty acid chains 3 water molecules Triglyceride, or neutral fat © 2013 Pearson Education, Inc.

Saturation of Fatty Acids 12/10/11 Saturated fatty acids Single covalent bonds between C atoms Maximum number of H atoms Solid animal fats, e.g., butter and lard © 2013 Pearson Education, Inc.

Saturation of Fatty Acids Unsaturated fatty acids One or more double bonds between C atoms Reduced number of H atoms Plant oils, e.g., olive oil

Saturation of Fatty Acids

Saturation of Fatty Acids Trans fats – modified oils – Omega-3 fatty acids –

Saturation of Fatty Acids

Types Of Fat

Modified triglycerides: Phospholipids 12/10/11 Modified triglycerides: Glycerol + two fatty acids and a phosphorus (P) - containing group “Head” and “tail” regions have different properties Important in cell membrane structure © 2013 Pearson Education, Inc.

Phosphorus-containing Figure 2.16b Lipids. 12/10/11 “Typical” structure of a phospholipid molecule Two fatty acid chains and a phosphorus-containing group are attached to the glycerol backbone. Example Phosphatidylcholine Polar “head” Nonpolar “tails” (schematic phospholipid) Glycerol backbone Phosphorus-containing group (polar “head”) 2 fatty acid chains (nonpolar “tails”) © 2013 Pearson Education, Inc.

Steroids—interlocking four-ring structure 12/10/11 Steroids—interlocking four-ring structure Cholesterol, vitamin D, steroid hormones, and bile salts Most important steroid Important in cell membranes, vitamin D synthesis, steroid hormones, and bile salts © 2013 Pearson Education, Inc.

Four interlocking hydrocarbon rings Figure 2.16c Lipids. 12/10/11 Simplified structure of a steroid Four interlocking hydrocarbon rings form a steroid. Example Cholesterol (cholesterol is the basis for all steroids formed in the body) © 2013 Pearson Education, Inc.

12/10/11 Anabolic Steroids

Derived from a fatty acid (arachidonic acid) in cell membranes Eicosanoids 12/10/11 Many different ones Derived from a fatty acid (arachidonic acid) in cell membranes Most important eicosanoid Prostaglandins Role in blood clotting, control of blood pressure, inflammation, and labor contractions © 2013 Pearson Education, Inc.

Other Lipids in the Body 12/10/11 Fat-soluble vitamins Vitamins A, D, E, and K Lipoproteins Transport fats in the blood (LDL, HDL) © 2013 Pearson Education, Inc.

Proteins Contain C, H, O, N, and sometimes S and P 12/10/11 Contain C, H, O, N, and sometimes S and P Proteins are polymers Amino acids (20 types) are the monomers in proteins Joined by covalent bonds called peptide bonds Contain amine group and acid group Can act as either acid or base All identical except for “R group” (in green on figure) © 2013 Pearson Education, Inc.

Figure 2.17 Amino acid structures. 12/10/11 Amine group Acid group Generalized structure of all amino acids. Glycine is the simplest amino acid. Aspartic acid (an acidic amino acid) has an acid group (—COOH) in the R group. Lysine (a basic amino acid) has an amine group (—NH2) in the R group. Cysteine (a basic amino acid) has a sulfhydryl (—SH) group in the R group, which suggests that this amino acid is likely to participate in intramolecular bonding. © 2013 Pearson Education, Inc.

Figure 2.18 Amino acids are linked together by peptide bonds. 12/10/11 Dehydration synthesis: The acid group of one amino acid is bonded to the amine group of the next, with loss of a water molecule. Peptide bond + Amino acid Amino acid Dipeptide Hydrolysis: Peptide bonds linking amino acids together are broken when water is added to the bond. © 2013 Pearson Education, Inc.

Figure 2.19a Levels of protein structure. 12/10/11 Amino acid Amino acid Amino acid Amino acid Amino acid Primary structure: The sequence of amino acids forms the polypeptide chain. © 2013 Pearson Education, Inc.

Figure 2.19b Levels of protein structure. 12/10/11 Secondary structure: The primary chain forms spirals (α-helices) and sheets (β-sheets). α-Helix: The primary chain is coiled to form a spiral structure, which is stabilized by hydrogen bonds. β-Sheet: The primary chain “zig-zags” back and forth forming a “pleated” sheet. Adjacent strands are held together by hydrogen bonds. © 2013 Pearson Education, Inc.

Figure 2.19c Levels of protein structure. 12/10/11 Tertiary structure: Superimposed on secondary structure. α-Helices and/or β-sheets are folded up to form a compact globular molecule held together by intramolecular bonds. Tertiary structure of prealbumin (transthyretin), a protein that transports the thyroid hormone thyroxine in blood and cerebrospinal fluid. © 2013 Pearson Education, Inc.

Figure 2.19d Levels of protein structure. 12/10/11 Quaternary structure: Two or more polypeptide chains, each with its own tertiary structure, combine to form a functional protein. Quaternary structure of a functional prealbumin molecule. Two identical prealbumin subunits join head to tail to form the dimer. © 2013 Pearson Education, Inc.

Fibrous and Globular Proteins 12/10/11 (structural) proteins Most have tertiary or quaternary structure (3-D) Provide mechanical support and strength Examples: © 2013 Pearson Education, Inc.

Fibrous and Globular Proteins 12/10/11 (functional) proteins Compact, spherical, water-soluble and sensitive to environmental changes Tertiary or quaternary structure (3-D) Specific functional regions (active sites) Examples: © 2013 Pearson Education, Inc.

Fibrous and Globular Proteins

Usually reversible if normal conditions restored Protein Denaturation 12/10/11 Denaturation Globular proteins unfold and lose functional, 3-D shape activity destroyed Can be cause by decreased pH, increased ions, or increased temperature Usually reversible if normal conditions restored Irreversible if changes are extreme e.g., cooking meat © 2013 Pearson Education, Inc.

Protein Denaturation

Globular proteins that act as biological catalysts Enzymes 12/10/11 Globular proteins that act as biological catalysts Regulate and increase speed of chemical reactions Lower the activation energy, increase the speed of a reaction (millions of reactions per minute!) © 2013 Pearson Education, Inc.

Figure 2.20 Enzymes lower the activation energy required for a reaction. 12/10/11 WITHOUT ENZYME WITH ENZYME Activation energy required Less activation energy required Energy Reactants Energy Reactants Product Product Progress of reaction Progress of reaction © 2013 Pearson Education, Inc.

Characteristics of Enzymes 12/10/11 Some functional enzymes consist of two parts Protein portion Cofactor (metal ion) or coenzyme (organic molecule often a vitamin) Enzymes are specific Act on specific substrate Usually end in the suffix “- ” Often named for the reaction they catalyze Hydrolases, oxidases © 2013 Pearson Education, Inc.

Enzyme Action

Figure 2.21 Mechanism of enzyme action. 12/10/11 Slide 1 Product (P) e.g., dipeptide Substrates (S) e.g., amino acids Energy is absorbed; bond is formed. Water is released. Peptide bond + Active site Enzyme-substrate complex (E-S) Enzyme (E) Substrates bind at active site, temporarily forming an enzyme-substrate complex. 1 The E-S complex undergoes internal rearrangements that form the product. 2 Enzyme (E) The enzyme releases the product of the reaction. 3 © 2013 Pearson Education, Inc.

Enzyme Action

Enzyme Action

Enzyme Action Enzyme Reactants Product Reactants approach enzyme bind to enzyme Enzyme changes shape Products are released

Deoxyribonucleic acid ( ) and ribonucleic acid ( ) Nucleic Acids 12/10/11 Deoxyribonucleic acid ( ) and ribonucleic acid ( ) Largest molecules in the body Contain C, O, H, N, and P Polymers Monomer = nucleotide a © 2013 Pearson Education, Inc.

Nucleotides - The Building Blocks of DNA and RNA Adenine (A) Cytosine (C) Thymine (T) Guanine (G) Phosphate Deoxyribose Figure 2.23

Deoxyribonucleic Acid (DNA) 12/10/11 Utilizes four nitrogen bases: Purines: Adenine (A), Guanine (G) Pyrimidines: Cytosine (C), and Thymine (T) Base-pair rule – each base pairs with its complementary base A always pairs with T; G always pairs with C Double-stranded helical molecule (double helix) in the cell nucleus Pentose sugar is deoxyribose Provides instructions for protein synthesis Replicates before cell division ensuring genetic continuity © 2013 Pearson Education, Inc.

Figure 2.22 Structure of DNA. 12/10/11 Sugar: Deoxyribose Base: Adenine (A) Phosphate Thymine (T) Sugar Phosphate Adenine nucleotide Thymine nucleotide Hydrogen bond Deoxyribose sugar Sugar- phosphate backbone Phosphate Adenine (A) Thymine (T) Cytosine (C) Guanine (G) © 2013 Pearson Education, Inc.

Base pair Phosphate Sugar Nucleotide

Ribonucleic Acid (RNA) 12/10/11 Four bases: Adenine (A), Guanine (G), Cytosine (C), and Uracil (U) Pentose sugar is ribose Single-stranded molecule mostly active outside the nucleus Three varieties of RNA carry out the DNA orders for protein synthesis Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA) © 2013 Pearson Education, Inc.

Phosphate Ribose Uracil

Structure and function of adenosine triphosphate (ATP) ATP Carries Energy 12/10/11 Structure and function of adenosine triphosphate (ATP) Nucleotide – adenosine triphosphate Universal energy source Bonds between phosphate groups contain potential energy Breaking the bonds releases energy ATP → ADP + P + energy © 2013 Pearson Education, Inc.

Figure 2.23 Structure of ATP (adenosine triphosphate). 12/10/11 High-energy phosphate bonds can be hydrolyzed to release energy. Adenine Phosphate groups Ribose Adenosine Adenosine monophosphate (AMP) Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) © 2013 Pearson Education, Inc.

Function of ATP Phosphorylation 12/10/11 Phosphorylation Phosphates are enzymatically transferred to and energize other molecules Such “primed” molecules perform cellular work (life processes) using the phosphate bond energy © 2013 Pearson Education, Inc.

Figure 2.24 Three examples of cellular work driven by energy from ATP. 12/10/11 Solute + Membrane protein Transport work: ATP phosphorylates transport proteins, activating them to transport solutes (ions, for example) across cell membranes. + Relaxed smooth muscle cell Contracted smooth muscle cell Mechanical work: ATP phosphorylates contractile pro- teins in muscle cells so the cells can shorten. + Chemical work: ATP phosphorylates key reactants, providing energy to drive energy-absorbing chemical reactions. © 2013 Pearson Education, Inc.