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Chapter 3 Biological Molecules http://youtu.be/PYH63o10iTE 1 Carbon Chemistry • Carbon is the Backbone of Biological Molecules (macromolecules) • All living organisms Are made up of chemicals based mostly on the element carbon Video Figure 4.1 2 There are 4 types of Biological Macromolecules Carbohydrates like sugar, starch, chiton, cellulose, potatoes and candy! Lipids like fat, butter, cream and olive oil (all other oils as well including motor oil) Proteins like steak, collagen (jello), hair and the machinery that runs your cellular metabolism Nucleic Acids – these are DNA and RNA which are responsible for storing information about how to build proteins 3 Carbon Chemistry • Organic chemistry is the study of carbon compounds • Carbon atoms can form diverse molecules by bonding to four other atoms or molecules • Carbon compounds range from simple molecules to complex ones • Carbon has four valence electrons and may form single, double, triple, or quadruple bonds 4 How Many? • A single carbon atom can form a maximum of ___covalent bond(s)? 5 • The electron configuration of carbon gives it covalent compatibility with many different elements Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) H O N C Figure 4.4 6 • The bonding versatility of carbon allows it to form many diverse molecules, including carbon skeletons Name and Comments (a) Methane Molecular Structural Formula Formula Ball-andStick Model SpaceFilling Model H CH4 H C H H (b) Ethane C2H 6 (c) Ethene Figure 4.3 A-C (ethylene) C2H4 H H H C C H H H H H C C H H 7 • Carbon may bond to itself forming carbon chains • Carbon chains form the skeletons of most organic molecules • Carbon chains vary in length and shape • The following diagrams show the atoms and their bonds H H H H H C C C C H H H H Butane (b) Branching (c) Double bonds (d) Rings Figure 4.5 A-D H H H H H H C C H H H Ethane (a) Length H H H H H H H H H H C C C C H H 1-Butene H H H C C C H C C H H C Cyclohexane H C C C H H H H Propane H H C H H H H C C C H H H H isobutane H H H H H H C C C C H H H 2-Butene H H C C H C C C Benzene 8 So…. • Carbohydrates look something like this… • CH3-CH2-CH2-CH2 9 Notice that the way the methane is drawn bears no resemblance to the actual shape of the molecule. Methane isn't flat with 90° bond angles. This mismatch between what you draw and what the molecule actually looks like can lead to problems if you aren't careful. 10 Hydrocarbons • Hydrocarbons are molecules consisting of only carbon and hydrogen • Hydrocarbons Are found within many of a cell’s organic molecules Fat droplets (stained red) Figure 4.6 A, B (a) A fat molecule 100 µm (b) Mammalian adipose cells 11 Functional Groups • Functional groups are the parts of molecules involved in chemical reactions • They Are the chemically reactive groups of atoms within an organic molecule • Give organic molecules distinctive chemical properties Estradiol HO Female lion OH CH3 CH3 O Figure 4.9 OH CH3 Testosterone Male lion 12 Macromolecules – Are large molecules composed of smaller molecules – Are complex in their structures Figure 5.1 13 Macromolecules •Most macromolecules are polymers, built from monomers •A monomer is a single unit of a polymer like legos! • Four classes of life’s organic molecules are polymers – Carbohydrates (include sugars, starches etc) – Proteins – Nucleic acids – Lipids (fats) 14 • A polymer – Is a long molecule consisting of many similar building blocks called monomers – Specific monomers make up each macromolecule – E.g. amino acids are the monomers for proteins 15 The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration synthesis • DRAW THIS AND CHECK WITH YOUR GROUP THAT IT IS RIGHT! HO 1 2 3 H Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond HO 1 2 H HO 3 H 2O 4 H Longer polymer Figure 5.2A (a) Dehydration reaction in the synthesis of a polymer 16 Building up and breaking down • When you are building a biochemical, you put monomers together and it’s called “DEHYDRATION SYNTHESIS” • When you break it down to release energy, it is called “hydrolysis” • Hydro=water lysis=to break • If water is a product, then it’s hydrolysis • Ex: galactose+glucose = lactose + water 17 The Synthesis and Breakdown of Polymers • Polymers can disassemble by – Hydrolysis (addition of water molecules) – DRAW THIS AND COMPARE IT WITH YOUR GROUP TO MAKE SURE IT’S RIGHT! HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 H H H 2O HO H Figure 5.2B (b) Hydrolysis of a polymer 18 • Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers • An immense variety of polymers can be built from a small set of monomers 19 Carbohydrates • Serve as fuel and building material • Include both sugars and their polymers (starch, cellulose, etc.) • Carbohydrates are either: • Monosaccharides – a single monomer Disaccharides - two monomers • Polysaccharides – three or more monos 20 Sugars • Monosaccharides – Are the simplest sugars – Can be used for fuel – Can be converted into other organic molecules – Can be combined into polymers 21 Monosaccharides • • • • Glucose Maltose Sucrose Fructose • Note the “ose” 22 • Examples of monosaccharides Triose sugars Pentose sugars (C3H6O3) (C5H10O5) Aldoses H C O H O C H O C H C OH H C OH H C OH H C OH H C OH HO C H C OH H H C OH H Glyceraldehyde H H H H C OH H HO C H C OH HO C H H C OH H C OH H C OH H C OH H H Glucose Galactose H C OH C O H C OH C O O C OH H C OH HO H H C OH H C OH Dihydroxyacetone H C OH H C OH H C OH H H O H H C OH C Ketoses H C Ribose Figure 5.3 Hexose sugars (C6H12O6) Ribulose C H H Fructose 23 • Monosaccharides – May be linear – Can form rings H H HO H H H O 1C 2 6CH C OH C H C OH 3 4 5 C 6 C OH OH 2OH 5C H 4C OH 3 H OH C H 6CH O H 2C OH H 1C H O H 4C OH 2OH 5C H OH 3C H CH2OH O H H 1C 2C OH OH 6 H 5 4 HO H OH 3 H O H 1 2 OH OH H Figure 5.4 (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. 24 • Disaccharides – Consist of two monosaccharides – Are joined by a glycosidic linkage – a glycosidic bond is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate. – To clarify: Disaccharides are formed when two monosaccharides join together by the dehydration synthesis reaction resulting in a glycosidic bond 25 (a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units H forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the HO number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. H (b) Dehydration reaction H in the synthesis of O sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. CH2OH CH2OH O H OH H H H H OH HO H OH H 2O H O H Glucose CH2OH H O H HO H 2O O H H OHOH H HO H O H H OH O H CH2OH H 1–4 1 glycosidic linkage HO OH H Fructose H O H H O H H OH OH Maltose H H 4 O CH2OH O H OH Glucose Glucose CH2O H O H O H H H OH CH2OH CH2OH H HO H O H O H OH H 1–2 H glycosidic 1 linkage O CH2OH O 2 H HO H CH2OH OH H Sucrose Figure 5.5 26 Polysaccharides • Polysaccharides (poly = many) – Are polymers of sugars – Serve many roles in organisms 27 Storage Polysaccharides • Starch Chloroplast Starch – Is a polymer consisting entirely of glucose monomers – Is the major storage form of glucose in plants 1 m Amylose Amylopectin Figure 5.6(a) Starch: a plant polysaccharide 28 • Glycogen – Consists of glucose monomers – Is the major storage form of glucose in animals Mitochondria Giycogen granules 0.5 m Glycogen Figure 5.6(b) Glycogen: an animal polysaccharide 29 Structural Polysaccharides • Cellulose – Is a polymer of glucose and is considered a fiber! It is indigestible by humans – Cows can digest it because they have four stomachs 30 – Has different glycosidic linkages than starch H 4 H O CH2O H O HO H H H O H H H O H glucose O C H H O H C H C H C O H H O H O H O H C C CH2O H O H O H H H 4 H O O H H O H 1 H glucose (a) and glucose ring structures H O CH2O H O O H 1 O 4 CH2O H O O H 1 O 4 CH2O H O O H 1 O 4 CH2O H O O H H O Figure 5.7 A–C O H 1 O 4 O H O CH2O H O O H O O H O O O H H H (b) Starch: 1– 4 linkage of glucose monomers CH2O H O O H 1 O H O O H O O CH2O CH2O O O H H H H (c) Cellulose: 1– 4 linkage of glucose monomers O H 31 The formulae for both glucose and fructose are identical. How do they differ? 32 – Is a major component of the tough walls that enclose plant cells Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0.5 m Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. Figure 5.8 OH CH2OH OH CH2OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH OH CH 2 2OH H CH2OH OH OH CH2OH O O O O OH OH OH O O OH O O O O CH OH OH CH2OH 2 H Glucose monomer Cellulose molecules A cellulose molecule is an unbranched glucose polymer. 33 • Cellulose is difficult to digest – Cows have microbes in their stomachs to facilitate this process Figure 5.9 34 • Chitin, another important structural polysaccharide – Is found in the exoskeleton of arthropods – Can be used as surgical thread CH2O H O OH H H OH H OH H H NH C O CH3 (b) Chitin forms the exoskeleton (a) The structure of the of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging Figure 5.10 A–C in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. 35 Lipids • Lipids are a diverse group of hydrophobic (water fearing) molecules • Lipids – Are the one class of large biological molecules that do not consist of polymers – Share the common trait of being hydrophobic 36 Fats – Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids – Vary in the length and number and locations of double bonds they contain 37 Fats – Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids – Vary in the length and number and locations of double bonds they contain 38 Fats • Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids 39 40 Fats • Vary in the length and number and locations of double bonds they contain 41 • Saturated fatty acids (saturated with hydrogen) – Have the maximum number of hydrogen atoms possible – Have no double bonds Stearic acid (a) Saturated fat and fatty acid Figure 5.12 42 • Unsaturated fatty acids – Have one or more double bonds Oleic acid Figure 5.12 (b) Unsaturated fat and fatty acid cis double bond causes bending 43 • Phospholipids – Have only two fatty acids – Have a phosphate group instead of a third fatty acid 44 • A hydrogenated fat is more solid - butter • An unsaturated fat is liquid - oils 45 • Phospholipid structure – Consists of a hydrophilic “head” and hydrophobic “tails” CH2 CH2 O O P O– + N(CH3)3 Choline Phosphate O CH2 CH O O C O C CH2 Glycerol O Fatty acids Hydrophilic head Hydrophobic tails Figure 5.13 (a) Structural formula (b) Space-filling model (c) Phospholipid symbol 46 • The structure of phospholipids – Results in a bilayer arrangement found in cell membranes WATER Hydrophilic head WATER Hydrophobic tail Figure 5.14 47 Steroids • Steroids – Are lipids characterized by a carbon skeleton consisting of four fused rings – Examples are hormones such as estrogen and testosterone 48 • One steroid, cholesterol – Is found in cell membranes – Is a precursor for some hormones H 3C CH3 CH3 CH3 CH3 Figure 5.15 HO 49 Proteins • Proteins have many structures, resulting in a wide range of functions • Proteins do most of the work in cells and act as enzymes. Enzymes are proteins. • Proteins are made of monomers called amino acids 50 • An overview of protein functions Table 5.1 51 • Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose OH Enzyme (sucrase) H 2O Fructose H O 4 Products are released. Figure 5.16 3 Substrate is converted to products. 52 Polypeptides • Polypeptides – Are polymers (chains) of amino acids • A protein – Consists of one or more polypeptides 53 • Amino acids – Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups – YOU MUST REMEMBER THIS! 54 Twenty Amino Acids • 20 different amino acids make up proteins H H3N+ C C H Glycine (Gly) O O– CH3 CH3 H3N+ C O C H Alanine (Ala) H3N + O– CH CH 3 3 CH3 CH3 C C H Valine (Val) O CH CH H3N 2 C + O– C H Leucine (Leu) CH 3 CH O O– H3C H3N + 2 CH C C O O– H Isoleucine (Ile) Nonpolar CH 3 S CH NH 2 CH H3N+ 2 C O C O– H Methionine (Met) CH H3N+ C 2 C O O– H Phenylalanine (Phe) CH2 H3N+ C C O O– H Tryptophan (Trp) H2 C H2 N CH2 CH 2 C H C O O– Proline (Pro) Figure 5.17 55 OH OH Polar H3N + CH2 C O C H CH H3N O– Serine (Ser) C + O C H3N O– H + CH2 C H O C CH2 H3N O– C + O C H Electrically charged H3N + C + O– O– O NH3+ NH2 C CH2 C CH2 CH2 CH2 CH2 CH2 CH2 O H O– H3N + CH2 C O C H O– H3N + CH2 C H Aspartic acid (Asp) O– + CH2 C O C H O– Glutamine (Gln) Asparagine (Asn) C C C H3N Basic O C CH2 O H Acidic –O CH2 H3N Tyrosine (Tyr) Cysteine (Cys) Threonine (Thr) C NH2 O C SH CH3 OH NH2 O Glutamic acid (Glu) O– Lysine (Lys) NH2+ H3N + CH2 O C NH+ H3N + CH2 C H NH CH2 O C C O– H O C O– Arginine (Arg) Histidine (His) 56 Amino Acid Polymers • Amino acids – Are linked by peptide bonds 57 • Again, building proteins is dehydration synthesis and breaking proteins is hydrolysis • Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state 58 Protein Conformation and Function • A protein’s specific conformation (shape) determines how it functions 59 • Four Levels of Protein Structure Primary structure – Is the unique sequence of amino acids in a polypeptide +H 3N Amino end Amino acid subunits Gly ProThrGly Thr Gly Glu Cys LysSeu LeuPro Met Val Lys Val Leu Asp AlaVal ArgGly Ser Pro Ala Glu Lle Leu Ala Gly Asp Thr Lys Ser Lys TrpTyr lle Ser Pro Phe His Glu AlaThrPhe Val Asn His Ala Glu Val Thr Asp Tyr Arg Ser Arg Gly Pro lle Ala Ala Leu Leu Ser Pro SerTyr Tyr Ser Thr Thr Ala Val Val Glu Thr Pro Lys Asn Figure 5.20 c o o– Carboxyl end 60 • Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the helix and the pleated sheet – Be sure that you can identify what this structure looks like! pleated sheet Amino acid subunits O H H C C N C N H R R C C N O H H C C R N H C H R O C O C N H N H N H O C O C H C R H C R H C R H C R N H O C N H O C O C H C O N H N C C H R R H C R R O H H C C N C C N OH H R R R O O H H C C N O H O H H C C N C C N OH H R O C H H N HC N H C N H C N C H H C O C O R R C R O C H H NH C N C H O C R R C C O R H C N HC N H O C H helix Figure 5.20 61 • Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups Hyrdogen bond CH22 CH O H O H 3C CH CH3 H 3C CH3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+-O C CH2 Ionic bond 62 • Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen Chains Iron Heme Chains Hemoglobin 63 Review of Protein Structure +H 3N Amino end Amino acid subunits helix 64 Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease – Results from a single amino acid substitution in the protein hemoglobin 65 Primary structure Normal hemoglobin Val His Leu Thr Pro Glul Glu 1 2 3 4 5 6 7 Secondary and tertiary structures Red blood cell shape Figure 5.21 Val His Leu Thr Pro Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen Val Glu structure 1 2 3 4 5 6 7 Secondary subunit and tertiary structures Quaternary Hemoglobin A structure Function Sickle-cell hemoglobin . . . Primary Quaternary structure Function 10 m ... Exposed hydrophobic region subunit 10 m Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. Red blood cell shape Fibers of abnormal hemoglobin deform cell into sickle shape. 66 What Determines Protein Conformation? • Protein conformation Depends on the physical and chemical conditions of the protein’s environment • Temperature, pH, etc. affect protein structure 67 •Denaturation is when a protein unravels and loses its native conformation (shape) Denaturation Normal protein Figure 5.22 Denatured protein Renaturation 68 The Protein-Folding Problem • Most proteins – Probably go through several intermediate states on their way to a stable conformation – Denaturated proteins no longer work in their unfolded condition – Proteins may be denaturated by extreme changes in pH or temperature 69 • Chaperonins – Are protein molecules that assist in the proper folding of other proteins Cap Polypeptide Correctly folded protein Hollow cylinder Steps of Chaperonin Chaperonin (fully assembled) Action: An unfolded poly1 peptide enters the cylinder from one Figure 5.23 end. The cap attaches, causing The cap comes 3 the cylinder to change shape off, and the in properly such a way that it creates a folded protein is hydrophilic environment for released. the folding of the polypeptide. 2 70 • X-ray crystallography – Is used to determine a protein’s three-dimensional structure Photographic film Diffracted X- rays X-ray source X-ray diffraction pattern X-ray beam Crystal Nucleic acid Protein Figure 5.24 (b) 3D computer model (a) X-ray diffraction pattern 71 Nucleic Acids • Nucleic acids store and transmit hereditary information • Genes – Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleotide sequences on DNA 72 The Roles of Nucleic Acids • There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) 73 Deoxyribonucleic Acid • DNA – Stores information for the synthesis of specific proteins – Found in the nucleus of cells 74 DNA Functions – Directs RNA synthesis (transcription) – Directs protein synthesis through RNA (translation) DNA 1 Synthesis of mRNA in the nucleus NUCLEUS 2 Movement of mRNA into cytoplasm via nuclear pore mRNA CYTOPLASM mRNA Ribosome 3 Synthesis of protein Figure 5.25 Polypeptide Amino acids 75 The Structure of Nucleic Acids 5’ end • Nucleic acids 5’C – Exist as polymers called polynucleotides – Nucleic acids are polymers of nucleotides O 3’C O O 5’C O 3’C (a) Polynucleotide, or nucleic acid Figure 5.26 OH 3’ end 76 77 • Each polynucleotide – Consists of monomers called nucleotides – Sugar + phosphate + nitrogen base Nucleoside Nitrogenous base O O P 5’C O CH2 O O Phosphate group Figure 5.26 3’C Pentose sugar (b) Nucleotide 78 Nucleotide Monomers • Nucleotide monomers – Are made up of nucleosides (sugar + base) NH and phosphate groups C Nitrogenous bases Pyrimidines O O 2 C C CH3 N CH C CH HN HN CH C CH C C CH N N O N O O H H H Cytosine Thymine (in DNA)Uracil (in RNA) RNA) Uracil (in U C U T Purines O NH2 N C C N C C NH N HC HC C CH N C N NH2 N N H H Adenine Guanine A G 5” Pentose sugars HOCH2 O 4’ OH H H 1’ 5” HOCH2 O OH 4’ H H 1’ H H H 3’ 2’ H 3’ 2’ OH H OH OH Deoxyribose (in DNA) Ribose (in RNA) Figure 5.26 (c) Nucleoside components 79 Nucleotide Polymers • Nucleotide polymers – Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next 80 81 DNA nucleotides 82 Be sure that you can recognize a single strand of DNA 83 Can you do this? • In DNA, A always pairs with T and G always pairs with C • Therefore, can you tell me what the compliment of this is? • AGTACTG 84 • TCATGAC 85 Gene • A specific stretch of DNA that programs the amino acid sequence of a polypeptide is a gene • The sequence of bases along a nucleotide polymer – Is unique for each gene 86 The DNA Double Helix • Cellular DNA molecules – Have two polynucleotides that spiral around an imaginary axis – Form a double helix – Check this out 87 • The DNA double helix – Consists of two antiparallel nucleotide strands 5’ end 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands A 3’ end Nucleotide about to be added to a new strand 5’ end 3’ end Figure 5.27 5’ end New strands 3’ end 88 A,T,C,G • The nitrogenous bases in DNA – Form hydrogen bonds in a complementary fashion (A with T only, and C with G only) – RNA substitutes Uracil for Thymine 89 DNA and Proteins as Tape Measures of Evolution • Molecular comparisons – Help biologists sort out the evolutionary connections among species 90 The Theme of Emergent Properties in the Chemistry of Life: A Review • Higher levels of organization – Result in the emergence of new properties • Organization – Is the key to the chemistry of life 91 Large biological molecules Carbohydrates Functions Components Examples Monosaccharides: glucose, fructose Disaccharides: lactose, sucrose Polysaccharides: starch, cellulose Dietary energy; storage; plant structure Monosaccharide Lipids Long-term energy storage fats; hormones steroids Fatty acid Glycerol Components of a triglyceride Amino group Proteins Enzymes, structure, storage, contraction, transport, and others Fats triglycerides; Steroids testosterone, estrogen Carboxyl group Side group Lactase an enzyme, hemoglobin a transport protein Amino acid Phosphate Base Nucleic acids Information storage DNA, RNA Sugar Nucleotide Figure UN3-2 92