CH.2B, Chemistry Comes Alive Lecture Notes PDF

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CH.2B, Chemistry Comes Alive Lecture Notes...

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Chapter 2 – Part B Chemistry Comes Alive

Part 2 – Biochemistry • Biochemistry is the study of chemical composition and reactions of living matter • All chemicals either organic or inorganic • Inorganic compounds • Water, salts, and many acids and bases • Do not contain carbon • Organic compounds • Carbohydrates, fats, proteins, and nucleic acids • Contain carbon, are usually large, and are covalently bonded  Both equally essential for life 2.6 Inorganic Compounds Water  Most abundant inorganic compound • Accounts for 60%–80% of the volume of living cells  Most important inorganic compound because of its properties • High heat capacity • High heat of vaporization • Polar solvent properties • Reactivity • Cushioning Water  High heat capacity • Ability to absorb and release heat with little temperature change • Prevents sudden changes in temperature  High heat of vaporization • Evaporation requires large amounts of heat • Useful cooling mechanism Water (cont.)  Polar solvent properties • Dissolves and dissociates ionic substances • Forms hydration (water) layers around large charged molecules • Example: proteins • Body’s major transport medium

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Water (cont.)  Reactivity • Necessary part of hydrolysis and dehydration synthesis reactions  Cushioning • Protects certain organs from physical trauma • Example: cerebrospinal fluid cushions nervous system organs Salts  Salts are ionic compounds that dissociate into separate ions in water • Separate into cations (positively charged molecules) and anions (negatively charged)  Not including H+ and OH– ions Salts (cont.)  Salts (cont.) • All ions are called electrolytes because they can conduct electrical currents in solution • Ions play specialized roles in body functions  Example: sodium, potassium, calcium, and iron • Ionic balance is vital for homeostasis • Common salts in body  NaCl, CaCO3, KCl, calcium phosphates Clinical – Homeostatic Imbalance 2.1  Ionic balance is vital for homeostasis  Kidneys play a big role in maintaining proper balance of electrolytes  If electrolyte balance is disrupted, virtually all organ systems cease to function Acids and Bases  Acids and bases are both electrolytes • Ionize and dissociate in water  Acids • Are proton donors: they release hydrogen ions (H+), bare protons (have no electrons) in solution • Example: HCl → H+ + Cl– • Important acids  HCl (hydrochloric acid), HC2H3O2 (acetic acid, abbreviated HAc), and H2CO3 (carbonic acid) Acids and Bases (cont.)  Bases • Are proton acceptors: they pick up H+ ions in solution © 2016 Pearson Education, Inc.

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• Example: NaOH → Na+ + OH– When a base dissolves in solution, it releases a hydroxyl ion (OH –) Important bases  Bicarbonate ion (HCO3–) and ammonia (NH3)

Acids and Bases (cont.)  pH: Acid-base concentration • pH scale is measurement of concentration of hydrogen ions [H+] in a solution • The more hydrogen ions in a solution, the more acidic that solution is • pH is negative logarithm of [H+] in moles per liter that ranges from 0–14 • pH scale is logarithmic, so each pH unit represents a 10-fold difference  Example: a pH 5 solution is 10 times more acidic than a pH 6 solution Acids and Bases (cont.)  pH: Acid-base concentration (cont.) • Acidic solutions have high [H+] but low pH  Acidic pH range is 0–6.99 • Neutral solutions have equal numbers of H+ and OH– ions  All neutral solutions are pH 7  Pure water is pH neutral • pH of pure water  pH 7: [H+]  10–7 m • Alkaline (basic) solutions have low [H+] but high pH  Alkaline pH range is 7.01–14 Acids and Bases (cont.)  Neutralization • Neutralization reaction: acids and bases are mixed together  Displacement reactions occur, forming water and a salt NaOH + HCl → NaCl + H2O Acids and Bases (cont.)  Buffers • Acidity involves only free H+ in solution, not H+ bound to anions • Buffers resist abrupt and large swings in pH  Can release hydrogen ions if pH rises  Can bind hydrogen ions if pH falls • Convert strong acids or bases (completely dissociated) into weak ones (slightly dissociated)  Carbonic acid–bicarbonate system (important buffer system of blood): 2.7 Organic Compounds: Synthesis and Hydrolysis © 2016 Pearson Education, Inc.

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Organic molecules contain carbon • Exceptions: CO2 and CO, which are inorganic Carbon is electroneutral • Shares electrons; never gains or loses them • Forms four covalent bonds with other elements • Carbon is unique to living systems Major organic compounds: carbohydrates, lipids, proteins, and nucleic acids

2.7 Organic Compounds: Synthesis and Hydrolysis  Many are polymers • Chains of similar units called monomers (building blocks)  Synthesized by dehydration synthesis  Broken down by hydrolysis reactions 2.8 Carbohydrates  Carbohydrates include sugars and starches  Contain C, H, and O • Hydrogen and oxygen are in 2:1 ratio  Three classes • Monosaccharides: one single sugar  Monomers: smallest unit of carbohydrate • Disaccharides: two sugars • Polysaccharides: many sugars  Polymers are made up of monomers of monosaccharides 2.8 Carbohydrates  Monosaccharides • Simple sugars containing three to seven carbon atoms • (CH2O)n — general formula  n  number of carbon atoms • Monomers of carbohydrates • Important monosaccharides  Pentose sugars • Ribose and deoxyribose  Hexose sugars • Glucose (blood sugar) Carbohydrates (cont.)  Disaccharides • Double sugars • Too large to pass through cell membranes • Important disaccharides  Sucrose, maltose, lactose • Formed by dehydration synthesis of two monosaccharides © 2016 Pearson Education, Inc.

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glucose + fructose → sucrose + water

Carbohydrates (cont.)  Polysaccharides • Polymers of monosaccharides  Formed by dehydration synthesis of many monomers • Important polysaccharides  Starch: carbohydrate storage form used by plants  Glycogen: carbohydrate storage form used by animals • Not very soluble 2.9 Lipids  Contain C, H, O, but less than in carbohydrates, and sometimes contain P  Insoluble in water  Main types: • Triglycerides or neutral fats • Phospholipids • Steroids • Eicosanoids Lipids (cont.)  Triglycerides or neutral fats • Called fats when solid and oils when liquid • Composed of three fatty acids bonded to a glycerol molecule • Main functions  Energy storage  Insulation  Protection Lipids (cont.)  Triglycerides can be constructed of: • Saturated fatty acids  All carbons are linked via single covalent bonds, resulting in a molecule with the maximum number of H atoms (saturated with H)  Solid at room temperature (Example: animal fats, butter) Lipids (cont.) • Unsaturated fatty acids  One or more carbons are linked via double bonds, resulting in reduced H atoms (unsaturated)  Liquid at room temperature (Example: plant oils, such as olive oil)  Trans fats – modified oils; unhealthy © 2016 Pearson Education, Inc.

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Omega-3 fatty acids – “heart healthy”

Lipids (cont.)  Phospholipids • Modified triglycerides  Glycerol and two fatty acids plus a phosphorus-containing group • “Head” and “tail” regions have different properties  Head is a polar region and is attracted to water  Tails are nonpolar and are repelled by water • Important in cell membrane structure Lipids (cont.)  Steroids • Consist of four interlocking ring structures • Common steroids: cholesterol, vitamin D, steroid hormones, and bile salts • Most important steroid is cholesterol  Is building block for vitamin D, steroid synthesis, and bile salt synthesis  Important in cell plasma membrane structure Lipids (cont.)  Eicosanoids • Many different ones • Derived from a fatty acid (arachidonic acid) found in cell membranes • Most important eicosanoids are prostaglandins  Play a role in blood clotting, control of blood pressure, inflammation, and labor contractions 2.10 Proteins  Comprise 20–30% of cell mass  Have most varied functions of any molecules • Structural, chemical (enzymes), contraction (muscles)  Contain C, H, O, N, and sometimes S and P  Polymers of amino acid monomers held together by peptide bonds  Shape and function due to four structural levels Amino Acids and Peptide Bonds  All proteins are made from 20 types of amino acids • Joined by covalent bonds called peptide bonds • Contain both an amine group and acid group • Can act as either acid or base • Differ by which of 20 different “R groups” is present

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Structural Levels of Proteins  Four levels of protein structure determine shape and function 1. Primary: linear sequence of amino acids (order) 2. Secondary: how primary amino acids interact with each other  Alpha ( ) helix coils resemble a spring  Beta ( ) pleated sheets resemble accordion ribbons 3. Tertiary: how secondary structures interact 4. Quaternary: how 2 or more different polypeptides interact with each other Fibrous and Globular Proteins  Shapes of proteins fall into one of two categories: fibrous or globular 1. Fibrous (structural) proteins  Strandlike, water-insoluble, and stable  Most have tertiary or quaternary structure (3-D)  Provide mechanical support and tensile strength  Examples: keratin, elastin, collagen (single most abundant protein in body), and certain contractile fibers Fibrous and Globular Proteins (cont.) 2. Globular (functional) proteins  Compact, spherical, water-soluble, and sensitive to environmental changes  Tertiary or quaternary structure (3-D)  Specific functional regions (active sites)  Examples: antibodies, hormones, molecular chaperones, and enzymes Protein Denaturation  Denaturation: globular proteins unfold and lose their functional 3-D shape – Fibrous proteins are more stable – Active sites become deactivated  Can be caused by decreased pH (increased acidity) or increased temperature  Usually reversible if normal conditions restored  Irreversible if changes are extreme – Example: cannot undo cooking an egg Enzymes and Enzyme Activity  Enzymes: globular proteins that act as biological catalysts – Catalysts regulate and increase speed of chemical reactions without getting used up in the process – Lower the energy needed to initiate a chemical reaction  Leads to an increase in the speed of a reaction  Allows for millions of reactions per minute!

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Enzymes and Enzyme Activity (cont.)  Characteristics of enzymes – Most functional enzymes, referred to as holoenzymes, consist of two parts  Apoenzyme (protein portion)  Cofactor (metal ion) or coenzyme (organic molecule, often a vitamin) – Enzymes are specific  Act on a very specific substrate – Names usually end in –ase and are often named for the reaction they catalyze  Example: hydrolases, oxidases Enzymes and Enzyme Activity (cont.)  Enzyme action – Enzymes lower activation energy, which is the energy needed to initiate a chemical reaction  Enzymes “prime” the reaction – Enzymes allow chemical reactions to proceed quickly at body temperatures – Three steps are involved in enzyme action: 1. Substrate binds to enzyme’s active site, temporarily forming enzymesubstrate complex 2. Complex undergoes rearrangement of substrate, resulting in final product 3. Product is released from enzyme 2.11 Nucleic Acids  Nucleic acids, composed of C, H, O, N, and P, are the largest molecules in the body  Nucleic acid polymers are made up of monomers called nucleotides – Composed of nitrogen base, a pentose sugar, and a phosphate group  Two major classes: – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) 2.11 Nucleic Acids  DNA holds the genetic blueprint for the synthesis of all proteins – Double-stranded helical molecule (double helix) located in cell nucleus – Nucleotides contain a deoxyribose sugar, phosphate group, and one of four nitrogen bases:  Purines: adenine (A), guanine (G)  Pyrimidines: cytosine (C) and thymine (T) 2.11 Nucleic Acids  DNA holds the genetic blueprint for the synthesis of all proteins (cont.) – Bonding of nitrogen base from strand to opposite strand is very specific  Follows complementary base-pairing rules: © 2016 Pearson Education, Inc.

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A always pairs with T G always pairs with C

2.11 Nucleic Acids  RNA links DNA to protein synthesis and is slightly different from DNA – Single-stranded linear molecule is active mostly outside nucleus – Contains a ribose sugar (not deoxyribose) – Thymine is replaced with uracil – Three varieties of RNA carry out the DNA orders for protein synthesis  Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)

2.12 ATP  Chemical energy released when glucose is broken down is captured in ATP (adenosine triphosphate)  ATP directly powers chemical reactions in cells – Offers immediate, usable energy needed by body cells  Structure of ATP – Adenine-containing RNA nucleotide with two additional phosphate groups

2.12 ATP  Terminal phosphate group of ATP can be transferred to other compounds that can use energy stored in phosphate bond to do work – Loss of phosphate group converts ATP to ADP – Loss of second phosphate group converts ADP to AMP

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