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The Chemistry of Life Chapter 2 Section 2-3 and 2-4.

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2 The Chemistry of Life Chapter 2 Section 2-3 and 2-4

3 Carbon Compounds Section 2-3

4 Learning Objectives 1.List characteristics of carbohydrates, lipids, nucleic acids and proteins 2.Describe basic nucleotide structure 3.Explain the special role of nucleic acids in heredity and cellular control 4.Explain why molecular structure and shape is crucial to life – it determines how most molecules recognize and respond to each other

5 Assignments Read Section 2-3 Complete Chapter 2 Chapter Notes through Section 2-3 Read Section 2-4

6 Protein – Green atoms are carbon The Chemistry of Carbon

7 Cells are 70-95% water, the rest consists mostly of carbon-based compounds Cells are 70-95% water, the rest consists mostly of carbon-based compounds Proteins, DNA, carbohydrates, and others Proteins, DNA, carbohydrates, and others All composed of carbon atoms bonded to each other and to atoms of other elements All composed of carbon atoms bonded to each other and to atoms of other elements These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P) These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P) The Chemistry of Carbon

8 Carbon is a girls best friendCarbon is a girls best friend Depression is a mental illness that is sometimes treated with lithium. Carbon is recycled naturally on Earth in a cycle called the carbon cycle. A substrate is something that forms a base for something else to be put on. Allotrope is any of the forms that an element may come in.

9 Organic chemistry Organic chemistry The study of carbon compounds, focuses on any compound with carbon (organic compounds). The study of carbon compounds, focuses on any compound with carbon (organic compounds). The term organic is archaic The term organic is archaic Though organic compounds implies that these compounds can only come from biological processes, they can be synthesized by non-living reactions Though organic compounds implies that these compounds can only come from biological processes, they can be synthesized by non-living reactions The Chemistry of Carbon

10 Organic compounds Organic compounds Any compound with carbon is said to be organic Any compound with carbon is said to be organic CO 2 to CH 4 to proteins and nucleic acids CO 2 to CH 4 to proteins and nucleic acids The Chemistry of Carbon

11 History of Organic Chemistry Began with attempts to purify and improve the yield of products from other organisms. Began with attempts to purify and improve the yield of products from other organisms. First learned to synthesize simple compounds in the laboratory, but First learned to synthesize simple compounds in the laboratory, but they had no success with more complex compounds. they had no success with more complex compounds. The Chemistry of Carbon

12 Swedish chemist Berzelius made a distinction between organic compounds that seemed to arise only in living organisms and inorganic compounds from the nonliving world. Swedish chemist Berzelius made a distinction between organic compounds that seemed to arise only in living organisms and inorganic compounds from the nonliving world. This led early organic chemists to propose vitalism, This led early organic chemists to propose vitalism, the belief in a life outside the limits of physical and chemical laws. the belief in a life outside the limits of physical and chemical laws. The Chemistry of Carbon

13 Support for vitalism began to sink as chemists synthesized more complex organic compounds in the laboratory. Support for vitalism began to sink as chemists synthesized more complex organic compounds in the laboratory. Early 1800s, German chemist Friedrich Wöhler synthesized urea in lab from totally inorganic starting materials. Early 1800s, German chemist Friedrich Wöhler synthesized urea in lab from totally inorganic starting materials. The Chemistry of Carbon

14 Herr Doktor Frederich Wöhler The Chemistry of Carbon

15 Milestones in organic chemistry 1856 – an attempt to manufacture anti-malarial drug quinine led to accidental discovery of a carbon-based dye, Perkins mauve 1856 – an attempt to manufacture anti-malarial drug quinine led to accidental discovery of a carbon-based dye, Perkins mauve 1874 – DDT Dichloro-Diphenyl-Trichloroethane (insecticide properties not discovered until later) 1874 – DDT Dichloro-Diphenyl-Trichloroethane (insecticide properties not discovered until later) 1890s – Aspirin (acetylsalicylic acid) by Bayer AG of Germany 1890s – Aspirin (acetylsalicylic acid) by Bayer AG of Germany The Chemistry of Carbon

16 1953, Stanley Miller at the University of Chicago was able to simulate chemical conditions on the primitive Earth to demonstrate the spontaneous synthesis of organic compounds. 1953, Stanley Miller at the University of Chicago was able to simulate chemical conditions on the primitive Earth to demonstrate the spontaneous synthesis of organic compounds. The Chemistry of Carbon

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18 Organic chemists finally rejected vitalism and embraced mechanism. Organic chemists finally rejected vitalism and embraced mechanism. all natural phenomena, including the processes of life, are governed by the same physical and chemical laws. all natural phenomena, including the processes of life, are governed by the same physical and chemical laws. The Chemistry of Carbon

19 Organic chemistry was redefined as the study of carbon compounds regardless of origin. Organic chemistry was redefined as the study of carbon compounds regardless of origin. Still, organisms produce most organic compounds in an amazing diversity and complexity. Still, organisms produce most organic compounds in an amazing diversity and complexity. However, the same rules apply to inorganic and organic compounds alike. However, the same rules apply to inorganic and organic compounds alike. The Chemistry of Carbon

20 Organic chemistry Organic chemistry The term organic is an archaic or obsolete term held over from the old days when all chemical compounds were divided into two classes: The term organic is an archaic or obsolete term held over from the old days when all chemical compounds were divided into two classes: Inorganic – derived from the nonliving Inorganic – derived from the nonliving Organic – derived from living Organic – derived from living For convenience sake, the terms are still used today. For convenience sake, the terms are still used today. The Chemistry of Carbon

21 Organic chemistry Organic chemistry Organic chemistry is the chemistry of carbon compounds. Biochemistry is the study of carbon compounds that crawl. Organic chemistry is the chemistry of carbon compounds. Biochemistry is the study of carbon compounds that crawl. Mike Adams Mike Adams The Chemistry of Carbon

22 What is the structure of the carbon atom? What is the structure of the carbon atom? With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell. With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell. The Chemistry of Carbon

23 How does carbon s structure relate to its chemical behavior? How does carbon s structure relate to its chemical behavior? Like any atom, carbon will tend to form chemical bonds with other atoms to fill up its valence shell Like any atom, carbon will tend to form chemical bonds with other atoms to fill up its valence shell Like any atom, carbon valence shell has a maximum capacity of eight electrons Like any atom, carbon valence shell has a maximum capacity of eight electrons Therefore, carbon will tend to form chemical bonds with other atoms to share their electrons to fill up its valence shell. Therefore, carbon will tend to form chemical bonds with other atoms to share their electrons to fill up its valence shell. The Chemistry of Carbon

24 How does carbon s structure relate to its chemical behavior? How does carbon s structure relate to its chemical behavior? Carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds. Carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds. This tetravalence by carbon makes large, complex molecules possible. This tetravalence by carbon makes large, complex molecules possible. Carbon has little tendency to form ionic bonds by loosing or gaining 4 electrons. Carbon has little tendency to form ionic bonds by loosing or gaining 4 electrons. The Chemistry of Carbon

25 Carbon s structure makes it themost versatile building blocks of molecules. Carbon s structure makes it themost versatile building blocks of molecules. C The Chemistry of Carbon

26 The electron configuration of carbon The electron configuration of carbon Gives it covalent compatibility with many different elements Gives it covalent compatibility with many different elements H O NC Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) The Chemistry of Carbon

27 Inorganic compounds are not based on carbon: Inorganic compounds are not based on carbon: A C will not be part of their molecular formula A C will not be part of their molecular formula Salts, water, phosphates, sulfates, etc. Salts, water, phosphates, sulfates, etc. NaCl, H 2 SO 4, HCl, etc NaCl, H 2 SO 4, HCl, etc Yet organic living things get needed elements in the form of inorganic compounds. Yet organic living things get needed elements in the form of inorganic compounds. The Chemistry of Carbon

28 From one organism to the next From one organism to the next No real difference in the overall percentages of the major elements of life (C, H, O, N, P, and S). No real difference in the overall percentages of the major elements of life (C, H, O, N, P, and S). Yet because of carbon, the diversity of molecules is not limited Yet because of carbon, the diversity of molecules is not limited The Chemistry of Carbon

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30 Key part of carbon compound diversity is the formation of carbon chains Key part of carbon compound diversity is the formation of carbon chains Carbon atom covalently bonding to carbon atom covalently bonding to carbon atom… Carbon atom covalently bonding to carbon atom covalently bonding to carbon atom… Carbon chains form the carbon skeletons of most organic molecules. Carbon chains form the carbon skeletons of most organic molecules. Vary in length and may be straight, branched, or arranged in closed rings. Vary in length and may be straight, branched, or arranged in closed rings. May also include double bonds. May also include double bonds. The Chemistry of Carbon

31 Carbon skeletons Double bond Ring Structure The Chemistry of Carbon

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33 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings The Chemistry of Carbon

34 Naming carbon ring structures (just kidding!) Naming carbon ring structures (just kidding!) The Chemistry of Carbon

35 Cells join smaller organic molecules together to form larger molecules, known as Cells join smaller organic molecules together to form larger molecules, known as Macromolecules, may be composed of thousands of atoms and weigh over 100,000 daltons Macromolecules, may be composed of thousands of atoms and weigh over 100,000 daltons Macromolecules

36 Daltons Daltons Dalton is unit of measurement equivalent to atomic mass units Dalton is unit of measurement equivalent to atomic mass units One dalton = one atomic mass unit (amu) One dalton = one atomic mass unit (amu) Periodic table displays the atomic mass of the atoms of the elements in amu Periodic table displays the atomic mass of the atoms of the elements in amu Macromolecules

37 Three of the four classes of macromolecules form chainlike molecules called polymers. Three of the four classes of macromolecules form chainlike molecules called polymers. Polymers consist of many similar or identical building blocks linked by covalent bonds. Polymers consist of many similar or identical building blocks linked by covalent bonds. The repeated units are small molecules called monomers. The repeated units are small molecules called monomers. Some monomers have other functions of their own. Some monomers have other functions of their own. Macromolecules

38 How are links in a chain like monomers?

39 Figure 2-13 When small molecules called monomers join together, they form polymers, or large molecules. Macromolecules

40 We shall explore the structure and function of the four major classes of macromolecules which are: We shall explore the structure and function of the four major classes of macromolecules which are: Carbohydrates Carbohydrates Lipids Lipids Proteins Proteins Nucleic acids Nucleic acids Macromolecules

41 Carbohydrates Carbon, hydrogen and oxygen atoms in a 1:2:1 ratio Carbon, hydrogen and oxygen atoms in a 1:2:1 ratio Food molecule – source of energy Food molecule – source of energy Energy is stored when chemical bonds are formed – some bonds store more than others Energy is stored when chemical bonds are formed – some bonds store more than others Energy released when chemical bonds break Energy released when chemical bonds break Digestion of carbohydrates, such as pasta and bread, break these bonds are release the energy Digestion of carbohydrates, such as pasta and bread, break these bonds are release the energy Also used as a structural molecule Also used as a structural molecule

42 Each six sided shape is a glucose molecule. Each six sided shape is a glucose molecule. Glucose is the monomer - monosaccharide in a starch polymer - polysaccharide Glucose is the monomer - monosaccharide in a starch polymer - polysaccharide Carbohydrates

43 Hydrogen bonds between OH groups of carbons 3 and 6 Carbohydrates

44 Cellulose is difficult to digest Cellulose is difficult to digest Cows have microbes in their stomachs to facilitate this process Cows have microbes in their stomachs to facilitate this process Carbohydrates

45 Chitin – important structural polysaccharide Chitin – important structural polysaccharide used in the exoskeletons of arthropods (including insects, spiders, and crustaceans). used in the exoskeletons of arthropods (including insects, spiders, and crustaceans). similar to cellulose, except that it contains a nitrogen-containing appendage on each glucose. similar to cellulose, except that it contains a nitrogen-containing appendage on each glucose. Pure chitin is leathery, but the addition of calcium carbonate hardens the chitin. Pure chitin is leathery, but the addition of calcium carbonate hardens the chitin. Used to make strong, flexible surgical thread that decomposes after the wound heals. Used to make strong, flexible surgical thread that decomposes after the wound heals. Chitin also forms the structural support for the cell walls of many fungi. Chitin also forms the structural support for the cell walls of many fungi.

46 Lipids Not generally soluble in water Not generally soluble in water Mostly carbon and hydrogen atoms; also oxygen Mostly carbon and hydrogen atoms; also oxygen Fats, oils and waxes, plus some steroids (hormones) Fats, oils and waxes, plus some steroids (hormones) The job of a lipid is to: The job of a lipid is to: Store energy Store energy Give structure to cell membranes Give structure to cell membranes As steroids, function as a chemical messenger As steroids, function as a chemical messenger

47 Glycerol Fatty Acid Lipids

48 The three fatty acids in a fat can be the same or different. The three fatty acids in a fat can be the same or different. Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds. Fatty acids may vary in length (number of carbons) and in the number and locations of double bonds. If there are no carbon-carbon double bonds, then the molecule is a saturated fatty acid - a hydrogen at every possible position. If there are no carbon-carbon double bonds, then the molecule is a saturated fatty acid - a hydrogen at every possible position.

49 If there are one or more carbon-carbon double bonds, then the molecule is an unsaturated fatty acid - formed by the removal of hydrogen atoms from the carbon skeleton. If there are one or more carbon-carbon double bonds, then the molecule is an unsaturated fatty acid - formed by the removal of hydrogen atoms from the carbon skeleton. Saturated fatty acids are straight chains, but unsaturated fatty acids have a kink wherever there is a double bond. Saturated fatty acids are straight chains, but unsaturated fatty acids have a kink wherever there is a double bond. Fig. 5.11b

50 Fats with saturated fatty acids are saturated fats. Fats with saturated fatty acids are saturated fats. Most animal fats are saturated. Most animal fats are saturated. Saturated fats are solid at room temperature. Saturated fats are solid at room temperature. A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis) through plaque deposits. A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis) through plaque deposits. Lipids

51 Fats with unsaturated fatty acids are unsaturated fats. Fats with unsaturated fatty acids are unsaturated fats. Plant and fish fats, known as oils, are liquid are room temperature. Plant and fish fats, known as oils, are liquid are room temperature. The kinks provided by the double bonds prevent the molecules from packing tightly together. The kinks provided by the double bonds prevent the molecules from packing tightly together. Lipids

52 Major function of fats is energy storage. Major function of fats is energy storage. One gram of fat stores more than twice as much energy as a gram of a polysaccharide. One gram of fat stores more than twice as much energy as a gram of a polysaccharide. Humans and other mammals store fats as long- term energy reserves in adipose cells. Humans and other mammals store fats as long- term energy reserves in adipose cells. Plants use starch for energy storage when mobility is not a concern but use oils when dispersal and packing is important, as in seeds. Plants use starch for energy storage when mobility is not a concern but use oils when dispersal and packing is important, as in seeds. Lipids

53 Fat also functions to: Fat also functions to: Cushion vital organs. Cushion vital organs. Insulate the organism against the environment. Insulate the organism against the environment. This subcutaneous layer is especially thick in whales, seals, and most other marine mammals This subcutaneous layer is especially thick in whales, seals, and most other marine mammals Lipids

54 Nucleic Acids Contain carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and phosphorus (P) Contain carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and phosphorus (P) Function as the hereditary molecule Function as the hereditary molecule Two forms Two forms RNA – ribonucleic acid RNA – ribonucleic acid DNA – deoxyribonucleic acid DNA – deoxyribonucleic acid Individual monomers are called nucleotides Individual monomers are called nucleotides

55 Five carbon sugar molecule (gray) Five carbon sugar molecule (gray) Nitrogenous base (green) Nitrogenous base (green) Phosphate group (blue) Phosphate group (blue) Thousands of these monomers may be linked by covalent bonds to create DNA or RNA Thousands of these monomers may be linked by covalent bonds to create DNA or RNA Nucleic Acids

56 RNA vs DNA Key difference in structure Key difference in structure RNA contains the sugar ribose RNA contains the sugar ribose DNA contains the sugar deoxyribose DNA contains the sugar deoxyribose Do you see the difference?

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59 How nucleic acids function to store and transmit heredity information will be covered later in the year. How nucleic acids function to store and transmit heredity information will be covered later in the year. Nucleic Acids

60 Activity Building Model of DNA Double Helix Activity Building Model of DNA Double Helix Students will build a model of the DNA double helix using the Kinex model system Students will build a model of the DNA double helix using the Kinex model system STUDENT

61 Proteins may Proteins may Control the rate of chemical reactions Control the rate of chemical reactions Form muscles and bone Form muscles and bone Others transport materials in and out of cells Others transport materials in and out of cells Still others fight disease Still others fight disease Proteins

62 Structural proteins – support Structural proteins – support Storage proteins – storage of amino acids Storage proteins – storage of amino acids Transport proteins – transport of other substances Transport proteins – transport of other substances Hormonal proteins – coordination of activities Hormonal proteins – coordination of activities Receptor proteins – response of cell to chemical stimuli Receptor proteins – response of cell to chemical stimuli Proteins

63 Contractile proteins – movement Contractile proteins – movement Defensive proteins – immune response (antibodies) Defensive proteins – immune response (antibodies) Enzymatic proteins – selective acceleration of chemical reactions Enzymatic proteins – selective acceleration of chemical reactions Proteins

64 Proteins

65 Polypeptides Polypeptides Are polymers of amino acids Are polymers of amino acids A protein A protein Consists of one or more polypeptides Consists of one or more polypeptides An amino acid An amino acid Is only a monomer; a single molecule Is only a monomer; a single molecule It is not protein It is not protein Proteins

66 Amino acids Amino acids Are organic molecules possessing both carboxyl and amino groups Are organic molecules possessing both carboxyl and amino groups Differ in their chemical properties due to differing side chains, called R groups Differ in their chemical properties due to differing side chains, called R groups Proteins

67 Proteins

68 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 20 different amino acids make up proteins O O–O– H H3N+H3N+ C C O O–O– H CH 3 H3N+H3N+ C H C O O–O– C C O O–O– H H3N+H3N+ CH CH 3 CH 2 C H H3N+H3N+ CH 3 CH 2 CH C H H3N+H3N+ C CH 3 CH 2 C H3N+H3N+ H C O O–O– C H3N+H3N+ H C O O–O– NH H C O O–O– H3N+H3N+ C CH 2 H2CH2C H2NH2N C H C Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val)Leucine (Leu)Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) C O O–O– Tryptophan (Trp) Proline (Pro) H3CH3C S O O–O– Amino Acid Monomers

69 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Amino Acid Monomers

70 There are 20 amino acid monomers that put together polypeptides. There are 20 amino acid monomers that put together polypeptides. Because the amino acids have different R groups, they can have different chemical properties. Because the amino acids have different R groups, they can have different chemical properties. Polar vs. nonpolar Polar vs. nonpolar Proteins

71 R groups, assembled in a polypeptide, will interact with each other – attracted or repelled. R groups, assembled in a polypeptide, will interact with each other – attracted or repelled. R group interactions determine the polypeptide 3D shape. R group interactions determine the polypeptide 3D shape. Protein shape makes protein function possible Protein shape makes protein function possible Shape follows function! Shape follows function! Proteins

72 Just 20 amino acid building blocks? Even that few can create incredible diversity. Just do the math. Just 20 amino acid building blocks? Even that few can create incredible diversity. Just do the math. How many polypeptides 4 amino acids long can be made from 20 amino acids? How many polypeptides 4 amino acids long can be made from 20 amino acids? 20 4 or 20 x 20 x 20 x 20 = 160, or 20 x 20 x 20 x 20 = 160,000 Proteins

73 Proteins Amino acids Amino acids Are linked by covalent peptide bonds Are linked by covalent peptide bonds OH DESMOSOMES OH CH 2 C N H C H O HOH Peptide bond OH H H HH H H H H H H H H N N N N N SH Side chains SH OO OO O H2OH2O CH 2 C C C CCC C C C C Peptide bond Amino end (N-terminus) Backbone (a) (b) Carboxyl end (C-terminus)

74 Animation – Protein Synthesis

75 Proteins have four levels of organization Proteins have four levels of organization Primary – the linear sequence of amino acids Primary – the linear sequence of amino acids Secondary – the amino acid chain twists and folds upon itself Secondary – the amino acid chain twists and folds upon itself Tertiary – two or more protein chains link to each other by van der Waals weak bonds Tertiary – two or more protein chains link to each other by van der Waals weak bonds Quaternary – highest level; two or more tertiary units form weak bonds with each other Quaternary – highest level; two or more tertiary units form weak bonds with each other Proteins

76 Four Levels of Protein Structure Primary structure Primary structure Is the unique sequence of amino acids in a polypeptide Is the unique sequence of amino acids in a polypeptide – Amino acid subunits + H 3 N Amino end o Carboxyl end o c Gly ProThr Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Val Arg Gly Ser Pro Ala Gly lle Ser Pro Phe His Glu His Ala Glu Val Phe Thr Ala Asn Asp Ser Gly Pro Arg Tyr Thr lle Ala Leu Ser Pro Tyr Ser Tyr Ser Thr Ala Val Thr Asn Pro Lys Glu Thr Lys Ser Tyr Trp Lys Ala Leu Glu Lle Asp

77 Four Levels of Protein Structure Secondary structure Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Is the folding or coiling of the polypeptide into a repeating configuration Relies on hydrogen bonds Relies on hydrogen bonds

78 Four Levels of Protein Structure Tertiary structure Tertiary structure Overall 3-D shape of a polypeptide Overall 3-D shape of a polypeptide Results from interactions between amino acids and R groups Results from interactions between amino acids and R groups CH 2 CH OHOH O C HO CH 2 NH 3 + C -O-O CH 2 O SS CH CH 3 H3CH3C H3CH3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond CH 2 Disulfide bridge

79 Four Levels of Protein Structure Quaternary structure Quaternary structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen Chains Hemoglobin Iron Heme

80 Summation of the four levels of protein structure. Summation of the four levels of protein structure.

81 Why is understanding these four levels of organization important? Why is understanding these four levels of organization important? Shape is critical to protein functions! Shape is critical to protein functions! Lose the quaternary level means losing their shape – conformation – which means losing function Lose the quaternary level means losing their shape – conformation – which means losing function Now think of bee sting venom and powered meat tenderizer… Now think of bee sting venom and powered meat tenderizer… Proteins

82 You will now work together to learn what they are, what they do and how they are built. You will now work together to learn what they are, what they do and how they are built. Macromolecules

83 Instructions 1.Divide class into 4 person teams with one person for each macromolecule. 2.Position teams in room corners. 3.Each macromolecule will complete the worksheet column for their macromolecule. 4.Macromolecules will then meet together; proteins with proteins, nucleic acids with nucleic acids, … 5.These macromolecule groups share information to improve their work. 6.Macromolecule groups will break up and return to original groups. 7.Now all four will share their facts so that everyone completes the worksheet. 8.Completed worksheets are collected (or completed at home).

84 Summation 1.List characteristics of carbohydrates, lipids, nucleic acids and proteins 2.Describe basic nucleotide structure 3.Explain the special role of nucleic acids in heredity and cellular control 4.Explain why molecular structure and shape is crucial to life – it determines how most molecules recognize and respond to each other

85 Assignments Read Section 2-3 Complete Chapter 2 Chapter Notes through Section 2-3. Complete the Worksheet Section 2-3 / Due next class Read Section 2-4

86 Cornell Notes Using your Cornell Notes, you will now: –compare notes with a partner for one minute. –write reflection in bottom space. –possible open-notes quiz. Cornell Notes must be turned in on day of chapter test; they will be graded.

87 Cornell Notes Tonight –Reread your Cornell Notes in the right column. –Review the ideas in the left column. –Study your summary/reflection.

88 Chemical Reactions and Enzymes Section 2-4

89 Learning Objectives 1.Given a chemical reaction, identify the reactants and products, and the coefficients. 2.Distinguish between energy absorbing and energy releasing chemical reactions. 3.Explain the concept of activation energy.

90 Learning Objectives 4.Explain why molecular structure and shape is crucial to life – it determines how most molecules recognize and respond to each other. 5.Explain why chemical reactions do not create new matter. 6.Explain the relationship between concentration and the rate of reaction. 7.Explain the importance of enzymes to biochemical reactions.

91 Assignments Complete Chapter 2 Chapter Notes through Section 2-4. Complete the Worksheet Section 2-4 / Due next class

92 Chemical property – ability of a substance to undergo a specific chemical change Chemical property – ability of a substance to undergo a specific chemical change Example – rust is a chemical reaction between iron and oxygen to create iron oxide Example – rust is a chemical reaction between iron and oxygen to create iron oxide Composition of matter always changes Composition of matter always changes Chemical Reactions

93 No new matter is created or destroyed during a chemical reaction No new matter is created or destroyed during a chemical reaction If you weighed all the matter of the reactants, and did the same for the products, their masses would be the same If you weighed all the matter of the reactants, and did the same for the products, their masses would be the same The number of atoms on both sides would be exactly the same The number of atoms on both sides would be exactly the same The reactions must be balanced. The reactions must be balanced. Chemical Reactions

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95 Some chemical reactions go to completion; that is, all the reactants are converted to products Some chemical reactions go to completion; that is, all the reactants are converted to products Most chemical reactions are reversible, Most chemical reactions are reversible, the products in the forward reaction becoming the reactants for the reverse reaction the products in the forward reaction becoming the reactants for the reverse reaction Chemical Reactions

96 Example: 3H 2 + N 2 2NH 3 Example: 3H 2 + N 2 2NH 3 Hydrogen and nitrogen molecules combine to form ammonia, but ammonia can decompose to hydrogen and nitrogen molecules Hydrogen and nitrogen molecules combine to form ammonia, but ammonia can decompose to hydrogen and nitrogen molecules Initially, when reactant concentrations are high, they frequently collide to create products Initially, when reactant concentrations are high, they frequently collide to create products As products accumulate, they collide to reform reactants As products accumulate, they collide to reform reactants Chemical Reactions

97 How do we know a chemical reaction happened? How do we know a chemical reaction happened? Clues one can sense Clues one can sense Change in color Change in color Change in temperature / heat energy Change in temperature / heat energy Gas production Gas production Formation of a precipitate Formation of a precipitate Chemical Reactions

98 Demonstration: Chemical Reactions Demonstration: Chemical Reactions Polyurethane Foam Polyurethane Foam Rainbow colors Rainbow colors Mystery nylon polymer Mystery nylon polymer TEACHER

99 Chemical reactions always require the breaking and forming of chemical bonds. Break bonds of reactants. Form new bonds in products. Chemical Reactions

100 Rust is a chemical reaction – Iron and oxygen reactants combine to form iron oxide product.

101 Photosynthesis: a solar-powered rearrangement of matter – Light energy 6CO 2 + 6H 2 O -> C 6 H 12 O6 + 6O 2

102 Energy in Reactions Energy involved in any chemical reactions. Energy involved in any chemical reactions. Break bonds, release energy. Break bonds, release energy. Form bonds, absorb energy. Form bonds, absorb energy.

103 Energy Capacity of a physical system to do work. Capacity of a physical system to do work. A system can have energy in a variety of forms, for example: A system can have energy in a variety of forms, for example: kinetic energy due to its motion, kinetic energy due to its motion, potential energy due to the positions of the components, potential energy due to the positions of the components, chemical energy stored in chemicals that can undergo a reaction. chemical energy stored in chemicals that can undergo a reaction. Energy in Reactions

104 Energy in biochemistry is: Energy in biochemistry is: stored when chemical bonds are formed. stored when chemical bonds are formed. Released when chemical bonds are broken. Released when chemical bonds are broken. Though biochemical systems always lost some energy as heat. Though biochemical systems always lost some energy as heat. The trick in biology is to set up systems that recapture, store and release energy in controlled circumstances. The trick in biology is to set up systems that recapture, store and release energy in controlled circumstances. Energy in Reactions

105 Certain biochemical processes Certain biochemical processes unleash the energy stored in sugar molecules, unleash the energy stored in sugar molecules, recapture it with other molecules, and then use it to (re)build yet more molecules needed by the cell. recapture it with other molecules, and then use it to (re)build yet more molecules needed by the cell. Organisms take in energy from their surrounding – light energy or chemical energy from food molecules – and then release energy as heat or in waste molecules, such as carbon dioxide. Organisms take in energy from their surrounding – light energy or chemical energy from food molecules – and then release energy as heat or in waste molecules, such as carbon dioxide. Energy in Reactions

106 Energy Changes Chemical reactions either release energy or absorb energy Chemical reactions either release energy or absorb energy Reactions releasing energy often occur spontaneously. Reactions releasing energy often occur spontaneously. Reactions absorbing energy do not go until provided with source of energy. Reactions absorbing energy do not go until provided with source of energy. Energy Changes

107 The relationship of energy to stability, work capacity, and spontaneous change There is a tendency of all things to seek their lowest state of energy. The molecule at far right has high-energy chemical bonds that are not stable, so it has a tendency to split apart and release that energy.

108 Energy-releasing chemical reaction between hydrogen and oxygen The amount of energy on the reactant side will equal the amount of energy on the products side (remember some energy always lost as heat energy Ignite with a flame or spark, inputting energy.

109 Energy changes in energy-releasing and energy- absorbing reactions Energy Changes

110 Energy is stored in chemical bonds of molecules. Energy is stored in chemical bonds of molecules. Energy Sources

111 Activation energy – The peak in the curve is the amount of energy required to get the reaction going. Activation energy – The peak in the curve is the amount of energy required to get the reaction going. Strike at match and youll see an example of activation energy. Strike at match and youll see an example of activation energy. The match starts burning only because another chemical reaction provided the activation energy. The match starts burning only because another chemical reaction provided the activation energy. Activation Energy

112 Essential controlling feature of biochemical systems. Essential controlling feature of biochemical systems. Life could not exist by relying on spontaneous reactions. Life could not exist by relying on spontaneous reactions. Activation energy functions as a control or brake on reactions. Activation energy functions as a control or brake on reactions. Biology links energy-releasing reactions to get the activation energy for energy- absorbing reactions. Biology links energy-releasing reactions to get the activation energy for energy- absorbing reactions. Activation Energy

113 Demonstration: Decomposition of Sugar Demonstration: Decomposition of Sugar Students will observe the decomposition of sugar by a strong acid – a chemical reaction Students will observe the decomposition of sugar by a strong acid – a chemical reaction Dehydration of water – removal of water from sucrose which is also an exothermic reaction. Dehydration of water – removal of water from sucrose which is also an exothermic reaction. &feature=related &feature=related &feature=related &feature=related TEACHER

114 Demonstration: Energy Held in Bonds of a Carbohydrate Demonstration: Energy Held in Bonds of a Carbohydrate Students will observe the decomposition of sugar by a strong oxidizer – potassium chlorate – a chemical reaction Students will observe the decomposition of sugar by a strong oxidizer – potassium chlorate – a chemical reaction Highly exothermic requiring we go outside. Highly exothermic requiring we go outside. Chemical bond energy turned into heat energy and light energy. Chemical bond energy turned into heat energy and light energy. U&feature=related U&feature=related TEACHER

115 Some biochemical reactions just will not work well, or at all, without help. Some biochemical reactions just will not work well, or at all, without help. Perhaps their activation energy is too high. Perhaps their activation energy is too high. Perhaps the reactant concentration is always too low. Perhaps the reactant concentration is always too low. Enzymes

116 The help comes in the form of a catalyst: The help comes in the form of a catalyst: Substance that speeds up the rate of a chemical reaction. Substance that speeds up the rate of a chemical reaction. Are not changed due to the chemical reaction. Are not changed due to the chemical reaction. Catalysts lower a reactions activation energy. Catalysts lower a reactions activation energy. Enzymes

117 Enzymes lower a reactions activation energy Easier to get the red line reaction going, isnt it?

118

119 So what is an enzyme exactly? So what is an enzyme exactly? Protein molecules of a very specific shape (conformation). Protein molecules of a very specific shape (conformation). Shape is specific for the reactant(s). Shape is specific for the reactant(s). Reactant is now called a Reactant is now called a substrate. Enzymes

120 Enzymes may put two reactants together to form a new molecule, or Enzymes may put two reactants together to form a new molecule, or Enzymes may take a large molecule and break it into smaller molecules. Enzymes capture the reactants, thereby bringing them close together. Enzymes may take a large molecule and break it into smaller molecules. Enzymes capture the reactants, thereby bringing them close together. Enzymes work only when they are at their highest level of organization – quanternary structure. Enzymes work only when they are at their highest level of organization – quanternary structure. Enzymes

121 Breaking up isnt hard to do… Enzyme hexokinase converts the reactants (substates) glucose and ATP into glucose-6-phosphate and ADP

122 Enzyme sucrase breaks down sucrose into two smaller sugars, fructose and glucose

123 Generally speaking… One enzyme for one chemical reaction. One enzyme for one chemical reaction. So enzyme names come from the reaction is catalyzes. So enzyme names come from the reaction is catalyzes. Look for the –ase suffix to recognize an enzymes name. Look for the –ase suffix to recognize an enzymes name. Carbonic anhydrase catalyzes reaction that removes water from carbonic acid. Carbonic anhydrase catalyzes reaction that removes water from carbonic acid.

124 Its all about breaking existing bonds and forming new bonds. Its all about breaking existing bonds and forming new bonds. Enzymes provide a site where reactants can be brought together, thereby reducing activation energy. Enzymes provide a site where reactants can be brought together, thereby reducing activation energy. Enzymes

125 Enzymes are built for specific substrates Enzymes are built for specific substrates Specificity comes from ability to form weak bonds between active site and substrate Specificity comes from ability to form weak bonds between active site and substrate Wrong substrate may not be able to form these bonds Wrong substrate may not be able to form these bonds Weak bonds hold the substrate to the active site Weak bonds hold the substrate to the active site Enzymes

126 The reactant binds to the enzymes active site

127 Metaphor for the enzyme- substrate complex Enzymes are very specific for substrates, much like a lock is very specific for a key.

128 Enzymes work if the conditions are right. Enzymes work if the conditions are right. Enzymes will not work if temperature, pH or other factors disrupt the shape of the enzyme molecule. Enzymes will not work if temperature, pH or other factors disrupt the shape of the enzyme molecule. Denaturation – weak bonds that hold an enzyme together break; loss of shape and function. Denaturation – weak bonds that hold an enzyme together break; loss of shape and function. Regulation of Enzyme Activity

129 Cells also regulate enzymes by using protein messengers that bind to enzymes to turn them off or turn them on. Cells also regulate enzymes by using protein messengers that bind to enzymes to turn them off or turn them on. Regulation of Enzyme Activity

130 Demonstration: Denaturation Demonstration: Denaturation Fry an egg in class. Fry an egg in class. TEACHER

131 Analyzing Data Read the chart. What do you see?

132 Summation 1.Given a chemical reaction, identify the reactants and products, and the coefficients. 2.Distinguish between energy absorbing and energy releasing chemical reactions. 3.Explain the concept of activation energy.

133 Summation 4.Explain why molecular structure and shape is crucial to life – it determines how most molecules recognize and respond to each other. 5.Explain why chemical reactions do not create new matter. 6.Explain the relationship between concentration and the rate of reaction. 7.Explain the importance of enzymes to biochemical reactions.

134 Assignments Complete Chapter 2 Chapter Notes through Section 2-4. Complete Chapter 2 Chapter Review Problems (graded) Complete the Chapter 2 Chapter Notes to end Check FirstClass for test dates

135 Cornell Notes Using your Cornell Notes, you will now: –compare notes with a partner for one minute. –write reflection in bottom space. –possible open-notes quiz. Cornell Notes must be turned in on day of chapter test; they will be graded.

136 Cornell Notes Tonight –Reread your Cornell Notes in the right column. –Review the ideas in the left column. –Study your summary/reflection.

137 Lab Effect of Temperature on Enzyme Activity Lab Effect of Temperature on Enzyme Activity Distribute lab instructions, Tootpick-ase: An Introduction to Enzymes Simulation of how substrate concentration and temperature affect enzyme function. STUDENT

138 Lab Effect of Temperature on Enzyme Activity Lab Effect of Temperature on Enzyme Activity Distribute lab instructions, Effect of Temperature on Enzyme (Catalase) Activity Conduct lab, Effect of Temperature on Enzyme (Catalase) Activity Students must read and complete the Pre-Lab activity STUDENT

139 Lab Conduct lab, Effect of Temperature on Enzyme (Catalase) Activity Students must have read and completed the Pre-Lab activity

140 Test, Chapter 2 Following the acid/base lab. Following the acid/base lab. Tentative date: Tentative date:


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