Lecture 3 presented

Lecture 3 presented - Lecture 3: Biomolecules and ...

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Unformatted text preview: Lecture 3: Biomolecules and Origins of Life, How it all began? Chapters 2 and 3; Chapter 4 1 What Kinds of Molecules Characterize Living Things? Isomers: molecules with the same chemical formula, but atoms are arranged differently Structural isomers: differ in how their atoms are joined together 2 Figure 3.2 Optical Isomers Optical isomers result from asymmetrical carbons. 3 4 Cells are made of polymers; polymers are made from monomers Polymers are formed in condensa1on reac1ons. Monomers are joined by covalent bonds. A water is removed; so they are also called dehydra1on reacOons. 5 Figure 3.4 Condensation and Hydrolysis of Polymers (A) dehydra1on reacOons 6 What Kinds of Molecules Characterize Living Things? Polymers are broken down into monomers in hydrolysis reac1ons. (hydro, “water”; lysis, “break”) 7 Figure 3.4 Condensation and Hydrolysis of Polymers (B) 8 Proteins Proteins are polymers of 20 different amino acids. Polypep-de chain: single, unbranched chain of amino acids. The chains are folded into specific three dimensional shapes defined by the sequence of the amino acids. MulOple chains can interact. 9 The Chemical Structures of Proteins Amino acids have carboxyl and amino groups—so they funcOon as both acid and base. 10 10 These hydrophylic amino acids attract ions of opposite charges. 11 11 Hydrophylic amino acids with polar but uncharged side chains form hydrogen bonds. 12 12 Hydrophobic amino acids 13 13 Figure 3.5 A Disulfide Bridge What kind of a reacOon is this? 14 14 Figure 3.6 Formation of Peptide Linkages CondensaOon/dehydraOon The peptide bond is inflexible—no rotation is possible. 15 15 Nomenclature!! A polypepOde chain is like a sentence: • The “capital leder” is the amino group of the first amino acid—the N terminus • The “period” is the carboxyl group of the last amino acid—the C terminus Proteins are read, N ­term to C ­term 16 16 Figure 3.7 The Four Lof a proteinProtein The primary structure evels of is the sequence of amino acids. Structure (Part 1) 17 17 Figure Secondary structure:Protein 3.7 The Four Levels of Structure (Part 2) α helix—right ­handed coil resulOng from hydrogen bonding between N—H groups on one amino acid and C=O groups on another. β pleated sheet—two or more polypepOde chains are aligned; hydrogen bonds from between the chains. 18 18 Figure 3.7 The Four L and folding results Tertiary structure: Bendingevels of Protein in a macromolecule with specific three-dimensional Structure (Part 3) shape. 19 19 Figure 3.7 The Four Levels of Protein Structure (Part 4) Quaternary structure: Each subunit has its own unique tertiary structure. 20 20 The Chemical Structures of Proteins Is the structure embedded in the primary sequence!! Let’s do an experiment 21 21 Figure 3.9 Primary Structure Specifies TerOary Structure (Part 1) 22 22 Figure 3.9 Primary Structure Specifies TerOary Structure (Part 2) 23 23 The Chemical Structures of Proteins? CondiOons that affect secondary and terOary structure: • High temperature • pH changes • High concentraOons of polar molecules • Nonpolar substances 24 24 Clicker QuesOon 1 Imagine that the binding site of a protein looks like the following diagram, in which H indicates a hydrophobic binding pocket on the protein and the + and – indicate relaOve charges of those binding pockets. Which of the molecules below will fit into this binding site? + H a. H + – b. – + H – c. – H + 25 Clicker QuesOon 2 Which of the following is a pepOde linkage? a. The bonds in a molecule of CH4 b. DNA to protein c. Amino acid to amino acid d. Protein to protein e. Carbohydrate to protein 26 Clicker QuesOon 3 Protein denaturaOon can be caused by a. high temperatures. b. increases in pH. c. decreases in pH. d. All of the above 27 Carbohydrates Carbohydrates have the general formula Cn(H2O)n • Source of stored energy • Transport stored energy • Carbon skeletons for many other molecules 28 28 Carbohydrates Monosaccharides: simple sugars Disaccharides: two simple sugars linked by covalent bonds Oligosaccharides: three to 20 monosaccharides Polysaccharides: hundreds or thousands of monosaccharides—starch, glycogen, cellulose 29 29 Chemical Structures of Carbohydrates Glucose (monosaccharide) can be used as an energy source. Exists as a straight chain or ring form. Ring is more common—it is more stable. Ring form exists as α ­ or β ­glucose, which can interconvert. 30 30 …OSE, a sugar Figure 3.13 From One Form of 6 carbon sugar; hexose Glucose to the Other 5 carbon sugar; pentose Etc. 31 31 Figure 3.14 Monosaccharides Are Triose Simple Sugars 32 32 Chemical Structures of Carbohydrates Monosaccharides bind together in condensaOon reacOons to form glycosidic linkages. Glycosidic linkages can be α or β. 33 33 Figure 3.15 Disaccharides Form by Sucrose: Glycosidic Linkages (Part 1) 34 34 Figure 3.15 Disaccharides Form by Maltose: Glycosidic Linkages (Part 2) 35 35 Figure 3.15 Disaccharides Form by Cellibiose Glycosidic Linkages (Part 3) 36 36 Chemical Structures and FuncOons of Carbohydrates Oligosaccharides may include other funcOonal groups. Oqen covalently bonded to proteins and lipids on cell surfaces and act as recogniOon signals. Human blood groups get specificity from oligosaccharide chains. 37 37 FuncOons of Carbohydrates Polysaccharides are giant polymers of monosaccharides. Starch: storage of glucose in plants Glycogen: storage of glucose in animals Cellulose: very stable, good for structural components 38 38 Figure 3.16 RepresentaOve Polysaccharides (Part 1) β ­glycosidic linkage Branching linkages 39 39 Starch and Cellulose 40 Chemical Structures of Carbohydrates Carbohydrates can be modified by the addiOon of funcOonal groups: Sugar phosphate Amino sugars Chi-n 41 41 Figure 3.17 Chemically Modified Carbohydrates (Part 1) 42 42 Figure 3.17 Chemically Modified Carbohydrates (Part 2) Found in carOlage and connecOve Ossue in vertebrates 43 43 Figure 3.17 Chemically Modified Carbohydrates (Part 3) 44 44 Lipids Lipids are nonpolar hydrocarbons. When sufficiently close together, weak but addiOve van der Waals forces hold them together. Not polymers in the strict sense, because they are not covalently bonded. 45 45 FuncOons of Lipids • Fats and oils store energy • Phospholipids—structural role in cell membranes • Carotenoids and chlorophylls—capture light energy in plants • Steroids and modified fady acids—hormones and vitamins 46 46 Chemical Structures of Lipids • Animal fat—thermal insulaOon • Lipid coaOng around nerves provides electrical insulaOon • Oil and wax on skin, fur, and feathers repels water 47 47 Chemical Structures of Lipids Fats and oils are triglycerides (simple lipids): composed of fady acids and glycerol Glycerol: 3 —OH groups (an alcohol) FaDy acid: nonpolar hydrocarbon with a polar carboxyl group Carboxyls bond with hydroxyls of glycerol in an ester linkage. 48 48 Figure 3.18 Synthesis of a Triglyceride 49 49 Chemical Structures of Lipids? Saturated faDy acids: no double bonds between carbons—it is saturated with H atoms. Unsaturated faDy acids: some double bonds in carbon chain. monounsaturated: one double bond polyunsaturated: more than one 50 50 Figure 3.19 Saturated and Unsaturated Fady Acids (Part 1) Saturated Fady Acid 51 51 Figure 3.19 Saturated and Unsaturated Fady Acids (Part 2) Unsaturated Fady Acid 52 52 53 Chemical Structures of Lipids? Animal fats tend to be saturated: packed together Oghtly; solid at room temperature. Plant oils tend to be unsaturated: the “kinks” prevent packing; liquid at room temperature. 54 54 Chemical Structures of Lipids Fady acids are amphipathic: they have opposing chemical properOes. When the carboxyl group ionizes it forms COO– and is strongly hydrophilic; the other end is hydrophobic. 55 55 Chemical Structures of Lipids Phospholipids: fady acids bound to glycerol; a phosphate group replaces one fady acid. • Phosphate group is hydrophilic—the “head” • “Tails” are fady acid chains—hydrophobic • They are amphipathic 56 56 Figure 3.20 Phospholipids (Part 1) 57 57 Chemical Structures of Lipids? In water, phospholipids line up with the hydrophobic “tails” together and the phosphate “heads” facing outward, to form a bilayer. Biological membranes have this kind of phospholipid bilayer structure. 58 58 Figure 3.20 Phospholipids (Part 2) 59 59 Other forms of Lipids 60 Figure 3.21 β-Carotene is the Source of Vitamin A Carotenoids: light-absorbing pigments 61 61 Figure 3.22 All Steroids Have the Same Ring Structure Steroids: multiple rings share carbons 62 62 Chemical Structures and FuncOons of Lipids? Vitamins—small molecules not synthesized by the body and must be acquired in the diet. Waxes—highly nonpolar and impermeable to water. 63 63 Clicker QuesOon 4 Which of the following is classified as a lipid, but has a substanOally different chemical structure than the others? a. Cholesterol b. The phospholipids of a membrane c. Oil from a corn plant d. The “fat” in dairy products 64 Nucleic Acids Nucleic acids are polymers specialized for the storage, transmission, and use of geneOc informaOon. DNA = deoxyribonucleic acid RNA = ribonucleic acid 65 Chemical Structures of Nucleic Acids The monomeric units are nucleo1des. NucleoOdes consist of a pentose sugar, a phosphate group, and a nitrogen ­ containing base. 66 Figure 4.1 NucleoOdes Have Three Components 67 What Are the Chemical Structures and FuncOons of Nucleic Acids? RNA has ribose DNA has deoxyribose 68 Chemical Structures of Nucleic Acids? The “backbone” of DNA and RNA is a chain of sugars and phosphate groups, bonded by phosphodiester linkages. The phosphate groups link carbon 3′ in one sugar to carbon 5′ in another sugar. The two strands of DNA run in opposite direcOons (an-parallel). 69 70 71 Chemical Structures of Nucleic Acids DNA bases: adenine (A), cytosine (C), guanine (G), and thymine (T) Complementary base pairing: A–T (2 H ­bonds) C–G (3 ­Hbonds) Purines pair with pyrimidines by hydrogen bonding. 72 Chemical Structures of Nucleic Acids Instead of thymine, RNA uses the base uracil (U). RNA is single ­stranded, but complementary base pairing occurs in the structure of some types of RNA. 73 74 75 Figure 4.3 Hydrogen Bonding in RNA 76 77 Clicker QuesOon 5 Cytosine (C) on one DNA strand pairs with which base on the other strand? a. Adenine (A) b. Cytosine (C) c. Guanine (G) d. Thymine (T) e. Uracil (U) 78 What Are the Chemical Structures and FuncOons of Nucleic Acids The two strands of a DNA molecule form a double helix. All DNA molecules have the same structure; diversity lies in the sequence of base pairs. DNA is an informa-onal molecule: informaOon is encoded in the sequences of bases. 79 79 80 80 The yellow phosphorus atoms and their adached red oxygen atoms, along with deoxribose sugars form the two helical backbones Figure 4.4 The Double Helix of DNA The paired bases are stacked in the center of the coil (blue nitrogen atoms and the gray carbon atoms) 81 81 Figure 4.1 NucleoOdes Have Three Components 82 The FuncOons of Nucleic Acids? The complete set of DNA in a living organism is called its genome. Not all the informaOon is needed at all Omes; sequences of DNA that encode specific proteins are called genes. 83 83 Building our Tree Protein DNA Concepts RNA Carbohydrates Lipids Molecular bonds Founda1ons EvoluOon ScienOfic Method Molecular InteracOons 84 84 Origins of Life, How it all began? Origins of Life, How it all began? Chapter 4 85 85 How Is All Life on Earth Related? All species on Earth share a common ancestor; they are gene-cally related. The fossil record allows study of evoluOonary relaOonships. 86 86 How Is All Life on Earth Related? Modern molecular methods allow biologists to compare genomes. The greater the distance between genomes, the more distant the common ancestor. 87 87 How Is All Life on Earth Related? Earth formed 4.6 to 4.5 billion years ago but it was 3.8 years when the first Prokaryotes emerged. The history of Earth can be pictured as a 30 ­ day month. Each day being 150 million years 88 88 Figure 1.8 Life’s Calendar Recorded History: ~30 seconds 5 min. 500,000 years ago 89 89 How Is All Life on Earth Related? Life arose by chemical evoluOon. Molecules that could reproduce themselves were criOcal. Biological molecules were then enclosed in membranes, forming cells. 90 90 How Is All Life on Earth Related? For 2 billion years, life consisted of single cells called prokaryotes. Where the basic mechanisms of life evolved. 91 91 How Is All Life on Earth Related? Photosynthesis evolved about 2.5 billion years ago. This process transforms sunlight energy into biological energy. Arose in bacteria, and changed the face of the planet. 92 92 How Is All Life on Earth Related? Consequences of photosynthesis: • O2 accumulated in the atmosphere • Aerobic metabolism began • Ozone layer formed, which allowed organisms to live on land This event changed life on the planet as no other event since! 93 93 How Is All Life on Earth Related? Eukaryo1c cells evolved from prokaryotes. These cells have intracellular compartments called organelles with specialized cellular funcOons. The nucleus contains the geneOc informaOon. 94 94 Building our Tree Eukaryotes Photosynthesis Concepts Foundations Prokaryotes Evolution 95 95 How Is All Life on Earth Related? MulOcellular organisms arose about 1 billion years ago. Cellular specializa1on: Cells became specialized to perform certain funcOons. 96 96 How Is All Life on Earth Related? Some organelles probably originated by endosymbiosis: when cells ingested smaller cells. Mitochondria (generate cell’s energy) and chloroplasts (conduct photosynthesis) could have originated when prokaryotes were ingested by larger eukaryotes. 97 97 How Is All Life on Earth Related? EvoluOon results in specia-on. Each species has a disOnct scienOfic name, a binomial: • Genus name • Species name Example: Homo sapiens 98 98 How Is All Life on Earth Related? An evoluOonary “tree” (phylogene)c tree) illustrates the order in which populaOons split and eventually evolved into new species. Systema)sts study the evoluOon and classificaOon of organisms using the fossil record and molecular evidence. 99 99 Figure 1.10 The Tree of Life 100 100 How Is All Life on Earth Related? The three domains of life are separated by molecular techniques: • Bacteria (prokaryotes) • Archaea (prokaryotes) • Eukarya (eukaryotes) 101 101 A beder Tree Bacteria Archaea The macro world Eucarya 102 102 ...
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