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+ P 1 The ATP Cycle http://www.youtube.com/watch?v=Ahuq XwvFv2E&feature=related 2 The Structure and Hydrolysis of ATP • ATP (adenosine triphosphate) – Is the cell’s energy shuttle – Provides energy for cellular functions Adenine N O O -O O- O- Phosphate groups Figure 8.8 C HC O O O O C NH2 N CH2 O- O H CH N H H H OH C OH N Ribose • Energy is released from ATP – When the terminal phosphate bond is broken P P P Adenosine triphosphate (ATP) H2 O P i + P P Inorganic phosphate Figure 8.9 Adenosine diphosphate (ADP) Energy Chapter 5 The Structure and Function of Macromolecules 5 The Molecules of Life • Overview: – Another level in the hierarchy of biological organization is reached when small organic molecules are joined together – Atom ---> molecule --- compound 6 Macromolecules – Are large molecules composed of smaller molecules – Are complex in their structures Figure 5.1 7 Macromolecules •Most macromolecules are polymers, built from monomers • Four classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids – Lipids 8 • 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 9 The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration synthesis HO 1 H HO H 3 2 Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond HO 1 2 3 H 2O 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer 10 The Synthesis and Breakdown of Polymers • Polymers can disassemble by – Hydrolysis (addition of water molecules) HO 1 2 3 4 H Hydrolysis adds a water molecule, breaking a bond HO Figure 5.2B 1 2 3 H H 2O HO H (b) Hydrolysis of a polymer 11 • 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 12 Carbohydrates • Serve as fuel and building material • Include both sugars and their polymers (starch, cellulose, etc.) 13 Sugars • Monosaccharides – Are the simplest sugars – Can be used for fuel – Can be converted into other organic molecules – Can be combined into polymers 14 • Examples of monosaccharides Triose sugars (C3H6O3) H O Pentose sugars (C5H10O5) H Aldoses C O Hexose sugars (C6H12O6) H C H O C 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 Ribose 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 H H Ketoses C Figure 5.3 Galactose H C OH H 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 H C OH H O Ribulose C H H Fructose 15 • 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. 16 • Disaccharides – Consist of two monosaccharides – Are joined by a glycosidic linkage 17 (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 18 Polysaccharides • Polysaccharides – Are polymers of sugars – Serve many roles in organisms 19 Storage Polysaccharides Chloroplast Starch • 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 20 • Glycogen – Consists of glucose monomers – Is the major storage form of glucose in animals Mitochondria Glycogen granules 0.5 m Glycogen Figure 5.6(b) Glycogen: an animal polysaccharide 21 Structural Polysaccharides • Cellulose – Is a polymer of glucose 22 – Has different glycosidic linkages than starch H CH2OH H 4 HO H OH H O H O C H OH OH glucose H C OH H HO C H 4 H C OH H C OH H C OH CH2OH H OH HO H O OH H 1 H OH glucose (a) and glucose ring structures CH2OH CH2OH O HO O 1 OH O 4 O 4 1 OH OH OH O O 1 OH CH2OH CH2OH O 4 1 OH O OH OH (b) Starch: 1– 4 linkage of glucose monomers CH2OH O HO OH 1 O 4 OH O OH Figure 5.7 A–C OH CH2OH CH2OH O O OH OH O OH O OH (c) Cellulose: 1– 4 linkage of glucose monomers CH2OH OH 23 – 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. 24 • Cellulose is difficult to digest – Cows have microbes in their stomachs to facilitate this process Figure 5.9 25 • 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 (a) The structure of the chitin monomer. Figure 5.10 A–C (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. 26 Lipids • Lipids are a diverse group of hydrophobic molecules • Lipids – Are the one class of large biological molecules that do not consist of polymers – Share the common trait of being hydrophobic 27 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 28 Fats • Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids 29 • Saturated fatty acids – Have the maximum number of hydrogen atoms possible – Have no double bonds Stearic acid Figure 5.12 (a) Saturated fat and fatty acid 30 • 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 31 Fig. 4-7b cis isomer: The two Xs are on the same side. (b) Geometric isomers trans isomer: The two Xs are on opposite sides. • The FDA has determined that partially hydrogenated oils (which contain trans fats) are not "recognized as safe", which is expected to lead to a ban on trans fats from the American diet. Alternatives are saturated fats such as lard, palm oil or completely hydrogenated fats. Hydrogenated oil is not a synonym for trans fat: complete hydrogenation removes all unsaturated, both cis and trans, fats. 33 • Phospholipids – Have only two fatty acids – Have a phosphate group instead of a third fatty acid 34 • 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 35 • The structure of phospholipids – Results in a bilayer arrangement found in cell membranes WATER Hydrophilic heads Hydrophobic tails WATER Figure 5.14 36 Steroids • Steroids – Are lipids characterized by a carbon skeleton consisting of four fused rings 37 • One steroid, cholesterol – Is found in cell membranes – Is a precursor for some hormones H 3C CH3 CH3 CH3 CH3 Figure 5.15 HO 38 Proteins • Proteins have many structures, resulting in a wide range of functions • Proteins do most of the work in cells and act as enzymes • Proteins are made of monomers called amino acids 39 • An overview of protein functions 40 • 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. 41 Polypeptides • Polypeptides – Are polymers (chains) of amino acids • A protein – Consists of one or more polypeptides 42 • Amino acids – Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups 43 Twenty Amino Acids • 20 different amino acids make up proteins CH3 CH3 H H3N+ C CH3 O H3N+ C H Glycine (Gly) O– C H3N C H + O– C CH2 O H 3N C H Valine (Val) Alanine (Ala) CH CH3 CH3 O CH3 CH3 C + O– CH2 O C H Leucine (Leu) H3C H3N + O– CH C O C H Isoleucine (Ile) O– Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ C H H3N+ C O– Methionine (Met) Figure 5.17 CH2 O C H CH2 O C O– Phenylalanine (Phe) H3N+ C H O C H2C CH2 H2 N C O C H O– Tryptophan (Trp) Proline (Pro) 44 O– 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) 45 Amino Acid Polymers • Amino acids – Are linked by peptide bonds 46 Protein Conformation and Function • A protein’s specific conformation (shape) determines how it functions 47 Four Levels of Protein Structure • Primary structure +H – Is the unique sequence of amino acids in a polypeptide 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 48 • Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the helix and the pleated sheet 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 Figure 5.20 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 49 • 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 50 • 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 51 Review of Protein Structure +H 3N Amino end Amino acid subunits helix 52 Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease – Results from a single amino acid substitution in the protein hemoglobin 53 Primary structure Normal hemoglobin Val His Leu Figure 5.21 Glul Glu . . . Primary Val His Leu Thr Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen Pro Val Glu structure 1 2 3 4 5 6 7 Secondary subunit and tertiary structures Quaternary Hemoglobin A structure Red blood cell shape Pro 1 2 3 4 5 6 7 Secondary and tertiary structures Function Thr Sickle-cell hemoglobin Quaternary structure 10 m Red blood cell shape Exposed hydrophobic region subunit Function 10 m ... Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. Fibers of abnormal hemoglobin deform cell into sickle shape. 54 What Determines Protein Conformation? • Protein conformation Depends on the physical and chemical conditions of the protein’s environment • Temperature, pH, etc. affect protein structure 55 •Denaturation is when a protein unravels and loses its native conformation (shape) Denaturation Normal protein Figure 5.22 Denatured protein Renaturation 56 The Protein-Folding Problem • Most proteins – Probably go through several intermediate states on their way to a stable conformation – Denatured proteins no longer work in their unfolded condition – Proteins may be denatured by extreme changes in pH or temperature 57 • 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. 2 The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. 3 The cap comes off, and the properly folded protein is released. 58 • X-ray crystallography – Is used to determine a protein’s threedimensional structure X-ray Photographic film Diffracted Xrays diffraction pattern X-ray source X-ray beam Nucleic acid Protein Crystal Figure 5.24 (a) X-ray diffraction pattern (b) 3D computer model 59 Nucleic Acids • Nucleic acids store and transmit hereditary information • Genes – Are the units of inheritance – determine the amino acid sequence of polypeptides – Are made of nucleotide sequences on DNA 60 The Roles of Nucleic Acids • There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) 61 Deoxyribonucleic Acid • DNA – Stores information for the synthesis of specific proteins – Found in the nucleus of cells 62 DNA Functions – Directs RNA synthesis (transcription) – Directs protein synthesis through RNA DNA (translation) 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 63 64 The Structure of Nucleic Acids 5’ end • Nucleic acids – Exist as polymers of nucleotides 5’C O 3’C O O 5’C (a) Polynucleotide, or nucleic acid Figure 5.26 O 3’C OH 3’ end 65 • Each nucleotide – Consists of 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 66 Nucleotide Monomers • Nucleotide monomers Nitrogenous bases Pyrimidines NH2 O O C C CH C 3 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 – Are made up of nucleosides (sugar + base) and phosphate groups 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 67 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 68 Gene • The sequence of bases along a nucleotide polymer – Is unique for each gene 69 The DNA Double Helix • Cellular DNA molecules – Have two polynucleotides that spiral around an imaginary axis – Form a double helix 70 • 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 71 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) 72 DNA and Proteins as Tape Measures of Evolution • Molecular comparisons – Help biologists sort out the evolutionary connections among species 73 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 74