Biological Sciences B. CHEM. ENGG. Part 1. Chemicals of life: Water, Amino acids, Carbohydrates, Lipids. Dr. Ratnesh Jain

Transcription

1 Biological Sciences B. CHEM. ENGG. Part 1. Chemicals of life: Water, Amino acids, Carbohydrates, Lipids Dr. Ratnesh Jain

2 The Foundations Content Cellular Foundations Chemical Foundations Physical Foundations Genetic Foundations Water Amino Acid Carbohydrate Lipids

3 Biomolecules The Distinguishing features of living organisms: A high degree of chemical complexity and Microscopic organization. Systems for extracting, transforming, and using energy from the environment A capacity for precise self-replication and self-assembly Mechanisms for sensing and responding to alterations in their surroundings Defined functions for each of their components and regulated interactions among them A history of evolutionary change

4 Cells Are the Structural and Functional Units of All Living Organisms Cellular Foundations Cellular Dimensions Are Limited by Oxygen Diffusion Page 4

5 There Are Three Distinct Domains of Life Page 5

6 Escherichia coli Is the Most-Studied Prokaryotic Cell Page 6

7 Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study 5-30 µm µm Page 7

8 The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic Page 8

9 Cells Build Supramolecular Structures Page 9

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12 Take home message.. All cells are bounded by a plasma membrane; have a cytosol containing metabolites, coenzymes, inorganic ions, and enzymes; and have a set of genes contained within a nucleoid (prokaryotes) or nucleus (eukaryotes). Phototrophs use sunlight to do work; chemotrophs oxidize fuels, passing electrons to good electron acceptors: inorganic compounds, organic compounds, or molecular oxygen. Bacterial cells contain cytosol, a nucleoid, and plasmids. Eukaryotic cells have a nucleus and are multicompartmented, segregating certain processes in specific organelles, which can be separated and studied in isolation. Cytoskeletal proteins assemble into long filaments that give cells shape and rigidity and serve as rails along which cellular organelles move throughout the cell. Supramolecular complexes are held together by noncovalent interactions and form a hierarchy of structures, some visible with the light microscope. When individual molecules are removed from these complexes to be studied in vitro, interactions important in the living cell may be lost. Page 12

13 Page 13 Chemical Foundations

14 Biomolecules Are Compounds of Carbon with a Variety of Functional Groups Page 14

15 Cells Contain a Universal Set of Small Molecules Page 15

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17 Macromolecules Are the Major Constituents of Cells Page 17

18 Three-Dimensional Structure Is Described by Configuration and Conformation Page 18

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20 Page 20 Molecular asymmetry: chiral and achiral molecules

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22 Interactions between Biomolecules Are Stereospecific Page 22

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24 Take home message.. Because of its bonding versatility, carbon can produce a broad array of carbon carbon skeletons with a variety of functional groups; these groups give biomolecules their biological and chemical personalities. A nearly universal set of several hundred small molecules is found in living cells; the interconversions of these molecules in the central metabolic pathways have been conserved in evolution. Proteins and nucleic acids are linear polymers of simple monomeric subunits; their sequences contain the information that gives each molecule its three-dimensional structure and its biological functions. Molecular configuration can be changed only by breaking covalent bonds. For a carbon atom with four different substituents (a chiral carbon), the substituent groups can be arranged in two different ways, generating stereoisomers with distinct properties. Only one stereoisomer is biologically active. Molecular conformation is the position of atoms in space that can be changed by rotation about single bonds, without breaking covalent bonds. Interactions between biological molecules are almost invariably stereospecific: they require a complementary match between the interacting molecules. Page 24

25 Physical Foundations Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings Organisms Transform Energy and Matter from Their Surroundings The Flow of Electrons Provides Energy for Organisms Page 25

26 Creating and Maintaining Order Requires Work and Energy Energy Coupling Links Reactions in Biology Page 26

27 Take home message.. Living cells are open systems, exchanging matter and energy with their surroundings, extracting and channeling energy to maintain themselves in a dynamic steady state distant from equilibrium. Energy is obtained from sunlight or fuels by converting the energy from electron flow into the chemical bonds of ATP. The tendency for a chemical reaction to proceed toward equilibrium can be expressed as the free-energy change, G, which has two components: enthalpy change, H, and entropy change, S. These variables are related by the equation GH T S. When G of a reaction is negative, the reaction is exergonic and tends to go toward completion; when G is positive, the reaction is endergonic and tends to go in the reverse direction. When two reactions can be summed to yield a third reaction, the G for this overall reaction is the sum of the G s of the two separate reactions. This provides a way to couple reactions. Page 27

28 Take home message.. The conversion of ATP to Pi and ADP is highly exergonic (large negative G ), and many endergonic cellular reactions are driven by coupling them, through a common intermediate, cto this reaction. The standard free-energy change for a reaction, G, is a physical constant that is related to the equilibrium constant by the equation G RT ln Keq. Most exergonic cellular reactions proceed at useful rates only because enzymes are present to catalyze them. Enzymes act in part by stabilizing the transition state, reducing the activation energy, G, and increasing the reaction rate by many orders of magnitude. The catalytic activity of enzymes in cells is regulated. Metabolism is the sum of many interconnected reaction sequences that interconvert cellular metabolites. Each sequence is regulated so as to provide what the cell needs at a given time and to expend energy only when necessary. Page 28

29 Page 29 Genetic Foundations

30 Take home message.. Genetic information is encoded in the linear sequence of four deoxyribonucleotides in DNA. The double-helical DNA molecule contains an internal template for its own replication and repair. The linear sequence of amino acids in a protein, which is encoded in the DNA of the gene for that protein, produces a protein s unique three-dimensional structure. Individual macromolecules with specific affinity for other macromolecules self-assemble into supramolecular complexes. Page 30

31 Page 31 Evolutionary Foundations

32 Page 32 Water

33 Water is the most abundant substance in living systems, making up 70% or more of the weight of most organisms. Weak Interactions in Aqueous Systems Hydrogen Bonding Gives Water Its Unusual Properties Page 33

34 Water Forms Hydrogen Bonds with Polar Solutes Page 34

35 Water Interacts Electrostatically with Charged Solutes Page 35

36 Entropy Increases as Crystalline Substances Dissolve Page 36

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38 Page 38 Amphipathic compounds in aqueous solution

39 Weak Interactions Are Crucial to Macromolecular Structure and Function Page 39

40 Solutes Affect the Colligative Properties of Aqueous Solutions Osmosis Page 40

41 Ionization of Water, Weak Acids, and Weak Bases Pure Water Is Slightly Ionized The Ionization of Water Is Expressed by an Equilibrium Constant Page 41

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43 Weak Acids and Bases Have Characteristic Dissociation Constants Page 43

44 Buffering against ph Changes in Biological Systems Hasselbalch equation Page 44

45 Water as a Reactant Water is both the solvent in which metabolic reactions occur and a reactant in many biochemical processes, including hydrolysis, condensation, and oxidation-reduction reactions. Page 45

46 Page 46 Amino Acid

47 Amino Acids Share Common Structural Features Page 47

48 Amino Acids Can Be Classified by R Group Page 48

49 20 Common Amino Acids Page 49

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51 Uncommon Amino Acids Also Have Important Functions Page 51

52 Amino Acids Can Act as Acids and Bases Page 52

53 The 20 amino acids commonly found as residues in proteins contain an carboxyl group, an -amino group, and a distinctive R group substituted on the -carbon atom. The -carbon atom of all amino acids except glycine is asymmetric, and thus amino acids can exist in at least two stereoisomeric forms. Only the L stereoisomers, with a configuration related to the absolute configuration of the reference molecule L-glyceraldehyde, are found in proteins. Other, less common amino acids also occur, either as constituents of proteins (through modification of common amino acid residues after protein synthesis) or as free metabolites. Amino acids are classified into five types on the basis of the polarity and charge (at ph 7) of their R groups. Amino acids vary in their acid-base properties and have characteristic titration curves. Monoamino monocarboxylic amino acids (with nonionizable R groups) are diprotic acids (H3NCH(R)COOH) at low ph and exist in several different ionic forms as the ph is increased. Amino acids with ionizable R groups have additional ionic species, depending on the ph of the medium and the pka of the R group. Page 53

54 Page 54 Carbohydrate

55 Monosaccharides and Disaccharides The Two Families of Monosaccharides Are Aldoses and Ketoses Monosaccharides Have Asymmetric Centers Page 55

56 Page 56 Aldoses

57 Page 57 Ketoses

58 Organisms Contain a Variety of Hexose Derivatives Page 58

59 Disaccharides Contain a Glycosidic Bond Page 59

60 Sugars (also called saccharides) are compounds containing an aldehyde or ketone group and two or more hydroxyl groups. Monosaccharides generally contain several chiral carbons and therefore exist in a variety of stereochemical forms, which may be represented on paper as Fischer projections. Epimers are sugars that differ in configuration at only one carbon atom. Monosaccharides commonly form internal hemiacetals or hemiketals, in which the aldehyde or ketone group joins with a hydroxyl group of the same molecule, creating a cyclic structure; this can be represented as a Haworth perspective formula. The carbon atom originally found in the aldehyde or ketone group (the anomeric carbon) can assume either of two configurations, and, which are interconvertible by mutarotation. In the linear form, which is in equilibrium with the cyclized forms, the anomeric carbon is easily oxidized. A hydroxyl group of one monosaccharide can add to the anomeric carbon of a second monosaccharide to form an acetal. In this disaccharide, the glycosidic bond protects the anomeric carbon from oxidation. Oligosaccharides are short polymers of several monosaccharides joined by glycosidic bonds. At one end of the chain, the reducing end, is a monosaccharide unit whose anomeric carbon is not involved in a glycosidic bond. The common nomenclature for di- or oligosaccharides specifies the order of monosaccharide units, the configuration at each anomeric carbon, and the carbon atoms involved in the glycosidic linkage(s). Page 60

61 Polysaccharides Page 61

62 Page 62 Amylose and amylopectin, the polysaccharides of starch

63 Page 63 The structure of cellulose

64 Bacterial and Algal Cell Walls Contain Structural Heteropolysaccharides Peptidoglycan of the cell wall of Staphylococcus aureus, a gram-positive bacterium. Peptides (strings of colored spheres) covalently link N-acetylmuramic acid residues in neighboring polysaccharide chains. Page 64

65 Glycosaminoglycans Are Heteropolysaccharides of the Extracellular Matrix Page 65

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67 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids Proteoglycans Are Glycosaminoglycan- Containing Macromolecules of the Cell Surface and Extracellular Matrix Page 67

68 Oligosaccharide linkages in glycoproteins Page 68

69 Glycolipids and Lipopolysaccharides Are Membrane Components Page 69

70 Working with Carbohydrates Page 70

71 Page 71 Lipid

72 Storage Lipids Fatty Acids Are Hydrocarbon Derivatives Page 72

73 Triacylglycerols Provide Stored Energy and Insulation Page 73

74 Structural Lipids in Membranes Page 74

75 Glycerophospholipids Are Derivatives of Phosphatidic Acid Page 75

76 Some Phospholipids Have Ether-Linked Fatty Acids Page 76

77 Sphingolipids at Cell Surfaces Are Sites ofbiological Recognition Sterols Have Four Fused Carbon Rings Page 77

78 Lipids as Signals, Cofactors, and Pigments Phosphatidylinositols and Sphingosine Derivatives Act as Intracellular Signals Page 78

79 Steroid Hormones Carry Messages between Tissues Page 79

80 Page 80 Vitamins A and D Are Hormone Precursors

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82 Working with Lipids NaOH/Methanol Page 82

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