Chemistry Comes Alive

Transcription

1 Chapter 2 Part B Chemistry Comes Alive Annie Leibovitz/Contact Press Images PowerPoint Lecture Slides prepared by Karen Dunbar Kareiva Ivy Tech Community College

2 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

3 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

4 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

5 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

6 Figure 2.12 Dissociation of salt in water. H d + d O H d + Water molecule Na + Na + Cl Cl Salt crystal Ions in solution

7 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

8 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

9 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, CaCO 3, KCl, calcium phosphates

10 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

11 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), HC 2 H 3 O 2 (acetic acid, abbreviated HAc), and H 2 CO 3 (carbonic acid)

12 Acids and Bases (cont.) Bases Are proton acceptors: they pick up H + ions in solution Example: NaOH Na + + OH When a base dissolves in solution, it releases a hydroxyl ion (OH ) Important bases Bicarbonate ion (HCO 3 ) and ammonia (NH 3 )

13 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

14 Acids and Bases (cont.) ph: Acid-base concentration (cont.) Acidic solutions have high [H + ] but low ph Acidic ph range is 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

15 Increasingly acidic Increasingly basic Figure 2.13 The ph scale and ph values of representative substances. Concentration (moles/liter) [OH ] [H + ] ph Examples M Sodium hydroxide (ph=14) Oven cleaner, lye (ph=13.5) Household ammonia (ph= ) Household bleach (ph=9.5) Egg white (ph=8) Neutral Blood (ph=7.4) Milk (ph= ) Black coffee (ph=5) Wine (ph= ) Lemon juice; gastric juice (ph=2) M Hydrochloric acid (ph=0)

16 Acids and Bases (cont.) Neutralization Neutralization reaction: acids and bases are mixed together Displacement reactions occur, forming water and a salt NaOH + HCl NaCl + H 2 O

17 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):

18 2.7 Organic Compounds: Synthesis and Hydrolysis Organic molecules contain carbon Exceptions: CO 2 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

19 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

20 Figure 2.14 Dehydration synthesis and hydrolysis. 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. H 2 O 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. H 2 O Monomer 1 Monomer 2 Monomers linked by covalent bond Example reactions Dehydration synthesis of sucrose and its breakdown by hydrolysis Water is released H 2 O Water is H 2 O consumed Glucose Fructose Sucrose

21 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

22 2.8 Carbohydrates Monosaccharides Simple sugars containing three to seven carbon atoms (CH 2 O) n : general formula n = number of carbon atoms Monomers of carbohydrates Important monosaccharides Pentose sugars Ribose and deoxyribose Hexose sugars Glucose (blood sugar)

23 Figure 2.15a Carbohydrate molecules important to the body. Monosaccharides Monomers of carbohydrates Example Hexose sugars (the hexoses shown here are isomers) Example Pentose sugars Glucose Fructose Galactose Deoxyribose Ribose

24 Carbohydrates (cont.) Disaccharides Double sugars Too large to pass through cell membranes Important disaccharides Sucrose, maltose, lactose Formed by dehydration synthesis of two monosaccharides glucose + fructose sucrose + water

25 Figure 2.15b Carbohydrate molecules important to the body. Disaccharides Consist of two linked monosaccharides Example Sucrose, maltose, and lactose (these disaccharides are isomers) Glucose Fructose Glucose Glucose Galactose Glucose Sucrose Maltose Lactose

26 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

27 Figure 2.15c Carbohydrate molecules important to the body. Polysaccharides Long chains (polymers) of linked monosaccharides Example This polysaccharide is a simplified representation of glycogen, a polysaccharide formed from glucose molecules. Glycogen *Notice that in Figure 2.15 the carbon (C) atoms present at the angles of the carbohydrate ring structures are not illustrated and in Figure 2.15c only the oxygen atoms and one CH 2 group are shown. The illustrations at right give an example of this shorthand style: The full structure of glucose is on the left and the shorthand structure on the right. This style is used for nearly all organic ringlike structures illustrated in this chapter.

28 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

29 Animation Fats

30 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

31 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)

32 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 Omega-3 fatty acids heart healthy

33 Figure 2.16a Lipids. Triglyceride formation Three fatty acid chains are bound to glycerol by dehydration synthesis. 3H 2 O Glycerol 3 fatty acid chains Triglyceride, or neutral fat 3 water molecules

34 Lipids (cont.) Phospholipids Modified triglycerides Glycerol and two fatty acids plus a phosphoruscontaining 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

35 Figure 2.16b Lipids. 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 tail (schematic phospholipid) Phosphorus-containing group (polar head ) Glycerol backbone 2 fatty acid chains (nonpolar tail )

36 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

37 Figure 2.16c Lipids. 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)

38 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

39 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

40 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

41 Unnumbered Figure 2.2_page47 Amine group Acid group

42 Figure 2.17 Amino acids are linked together by peptide bonds. Amine group Acid group 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 H 2 O Amino acid Amino acid H 2 O Dipeptide Hydrolysis: Peptide bonds linking amino acids together are broken when water is added to the bond.

43 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

44 Figure 2.18a Levels of protein structure. Primary structure The sequence of amino acids forms the polypeptide chain. Amino acid Amino acid Amino acid Amino acid Amino acid H O R H O R H O H H H N C C N C C N C C N C C N C C H H R H O R H O R

45 Figure 2.18b Levels of protein structure. Secondary structure The primary chain forms spirals ( -helices) and sheets ( -sheets). -Helix: The primary chain is coiled to form a spiral structure, which is stabilized by hydrogen bonds. -Sheet: The primary chain zig-zags, forming a pleated sheet. Adjacent strands are held together by hydrogen bonds.

46 Figure 2.18c Levels of protein structure. Tertiary structure Superimposed on secondary structure. -Helices and/or -sheets are folded up to form a compact globular molecule held together by intramolecular bonds. Tertiary structure of transthyretin, a protein that transports the thyroid hormone thyroxine in blood and cerebrospinal fluid.

47 Figure 2.18d Levels of protein structure. Quaternary structure Two or more polypeptide chains, each with its own tertiary structure, combine to form a functional protein. Quaternary structure of a functional transthyretin molecule. Four identical transthyretin subunits join to form a complex protein.

48 Animation Introduction to Protein Structure

49 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

50 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

51 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

52 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!

53 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

54 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 enzyme-substrate complex 2. Complex undergoes rearrangement of substrate, resulting in final product 3. Product is released from enzyme

55 Energy Energy Figure 2.19 Enzymes lower the activation energy required for a reaction. WITHOUT ENZYME WITH ENZYME Activation energy required Less activation energy required Reactants Reactants Progress of reaction Product Progress of reaction Product

56 Figure 2.20 Mechanism of enzyme action. Slide 1 Substrates (S) e.g., amino acids Energy is absorbed; bond is formed. Water is released. H 2 O Product (P) e.g., dipeptide Peptide bond Active site Enzyme (E) Enzyme-substrate complex (E-S) 1 Substrates bind at 2 The E-S complex active site, temporarily forming an enzymesubstrate complex. undergoes internal rearrangements that form the product. Enzyme (E) 3 The enzyme releases the product of the reaction.

57 Figure 2.20 Mechanism of enzyme action. Slide 2 Substrates (S) e.g., amino acids Active site Enzyme (E) Enzyme-substrate complex (E-S) 1 Substrates bind at active site, temporarily forming an enzymesubstrate complex.

58 Figure 2.20 Mechanism of enzyme action. Slide 3 Substrates (S) e.g., amino acids Energy is absorbed; bond is formed. Water is released. H 2 O Active site Enzyme (E) Enzyme-substrate complex (E-S) 1 Substrates bind at 2 The E-S complex active site, temporarily forming an enzymesubstrate complex. undergoes internal rearrangements that form the product.

59 Figure 2.20 Mechanism of enzyme action. Slide 4 Substrates (S) e.g., amino acids Energy is absorbed; bond is formed. Water is released. H 2 O Product (P) e.g., dipeptide Peptide bond Active site Enzyme (E) Enzyme-substrate complex (E-S) 1 Substrates bind at 2 The E-S complex active site, temporarily forming an enzymesubstrate complex. undergoes internal rearrangements that form the product. Enzyme (E) 3 The enzyme releases the product of the reaction.

60 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)

61 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)

62 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: A always pairs with T G always pairs with C

63 Figure 2.21 Structure of DNA. Phosphate Sugar: Deoxyribose Base: Adenine (A) Thymine (T) Sugar Phosphate P P Adenine nucleotide Hydrogen bond Thymine nucleotide A T C G A Sugarphosphate backbone Deoxyribose sugar Phosphate G G A T A A Adenine (A) Thymine (T) G G C C Cytosine (C) T A Guanine (G)

64 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)

65 Animation DNA and RNA

66 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

67 Figure 2.22 Structure of ATP (adenosine triphosphate). High-energy phosphate bonds can be hydrolyzed to release energy. Adenine P P P Phosphate groups Ribose Adenosine Adenosine monophosphate (AMP) Adenosine diphosphate (ADP) Adenosine triphosphate (ATP)

68 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

69 Unnumbered Figure 2.3_page55 H 2 O ATP ADP + P + i energy H 2 O

70 Figure 2.23 Three examples of cellular work driven by energy from ATP. Solute ATP ADP + P i Membrane protein P P i Transport work: ATP phosphorylates transport proteins, activating them to transport solutes (ions, for example) across cell membranes. ATP Relaxed smooth muscle cell Contracted smooth muscle cell ADP + P i Mechanical work: ATP phosphorylates contractile proteins in muscle cells so the cells can contract (shorten). P P i ATP A B ADP + P i Chemical work: ATP phosphorylates key reactants, providing energy to drive energy-absorbing chemical reactions.