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CHAPTER 3 THE CHEMICAL BASIS OF LIFE II:ORGANIC MOLECULES The Carbon Atom and the Study of Organic Molecules Formation of Organic Molecules and Macromolecules Four types of Biological Molecules Carbohydrates Lipids Proteins Nucleic Acids Learning Outcome 3.1 The Carbon Atom and the Study of Organic Molecules Explain the properties of carbon that make it the focal point of organic compounds. Compare and contrast different types of isomeric compounds. 3.2 Formation of Organic Molecules and Macromolecules List the four major classes of biological macromolecules. Describe each biological macromolecule, and how monomers of each class are brought together to form the macromolecules. Describe the relationship between functional groups and macromolecules. Appreciate the variety and chemical characteristics of common functional groups of organic compounds. 3.3 Carbohydrates Name the different forms of carbohydrate molecules. Relate the structure of polysaccharides to their functions. 3.4 Lipids Understand the structure of triglycerides. Explain how fats function as energy-storage molecules. Apply knowledge of the structure of phospholipids to the formation of membranes. 3.5 Proteins Describe the possible levels of protein structure. Understand the relationship between amino acid sequence and their three-dimensional structure. Give examples of several different proteins and the general types of functions they carry out in a cell. 3.6 Nucleic Acids Describe the structure of nucleotides. Compare and contrast the structures of DNA and RNA. Explain the functions of DNA and RNA. 2 Nucleus First shell is filled with 2 electrons – Spherical s orbital of second shell is filled with 2 electrons – – – – Other energy orbitals of second shell contain 1 or 0 electrons – (a) Orbitals – – – – + + + + + + – – (b) Simplified depiction of energy shells 3 4 5 6 Isomers Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (b) Two types of stereoisomers 2-methyl butane H H C H H C C H Pentane H H OH H Isopropyl alcohol H H C C H C OH H H H Propyl alcohol (a) Structural isomers (a) Structural isomers (b) having the same covalent arrangements but differ in spatial arrangements H H H H H H H cis isomer: The two Xs areH trans isomer: TheHtwo Xs H C C C C H C C C C on the same side. are on opposite sides. H H cis-butene Cis–trans isomers Molecule H H H trans-butene Mirror image (b) Enantiomers Enantiomers 7 Dehydration (minus water) Synthesis and Hydrolysis (water-split) Water Removed H2O Monomers HO H + H HO H2O HO H2O H HO HO H HO H HO H H (a) Polymer formation by dehydration reactions HO HO H H2O H HO HO H H HO H2O H HO H + HO H H2 O Water Added (b) Breakdown of a polymer by hydrolysis reactions 8 Four major types of organic molecules and macromolecules 1. 2. 3. 4. Carbohydrates Lipids Proteins Nucleic acids 9 Carbohydrates Monosaccharides Composed of carbon, hydrogen, and oxygen atoms Cn(H2O)n Most of the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group 10 6 5 HO H H HO H H H 1 2 3 4 5 6 H C C OH C H C 6 OH C OH OH H D-glucose (linear) 3 H 1 H H 2 OH -D-galactose H C O OH H OH 4 O CH2OH 6 CH2OH 5 O H H OH 4 HO 3 H 1 H OH 2 OH β-D-glucose (ring) H 6 CH2OH 5 O OH H OH 4 HO 3 H 1 H H H 2 H OH -D-glucose 5 HO O 1 2 OH CH2OH H OH H 4 HO 3 H -L-glucose Enantiomers •Linear and ring structures of -D-glucose (b) Isomers of glucose 11 Disaccharides Carbohydrates composed of two monosaccharides Joined by dehydration or condensation reaction to form Glycosidic bond Broken apart by hydrolysis Examples − sucrose, maltose, lactose Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH O H H H OH H HO + H H OH O HO OH H OH Glucose OH CH2OH H Fructose 12 CH2OH CH2OH O H H H OH H HO + H H OH O HO CH2OH Glucose + Fructose OH H OH OH Glucose H Fructose CH2OH O H H H OH H H OH Glycosidic bond HO O CH2OH H H OH + H2O Sucrose + Water O HO H Sucrose CH2OH 13 14 Lipids Fats Composed predominantly of hydrogen and carbon atoms Defining feature of lipids is that they are nonpolar and therefore very insoluble in water Also known as triglycerides or triacylglycerols Formed by bonding glycerol to three fatty acids Joined by dehydration or condensation reaction Broken apart by hydrolysis 15 Fats: saturated vs. unsaturated fatty acid Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O HO C CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 Saturated fatty acid (Stearic acid) O HO C CH2 CH2 CH2 CH CH CH2 CH CH CH2 CH3 Unsaturated fatty acid (Linoleic acid) 16 Phospholipids Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Charged nitrogencontaining region CH3 N+ CH3 CH3 Hydrophilic P head CH2 CH2 Hydrophobic FA tails O O Phosphate Glycerol backbone Ends of fatty acids Polar head (hydrophilic) O– P O H2 C H C O O C O C H2 C CH2 H2 C CH 2 O CH2 H2 C H2 C CH 2 H2C CH 2 H2C CH 2 H2C CH 2 H2C CH 2 H2C H3 C Polar heads Schematic drawing of a phospholipid CH 2 Nonpolar tails Membrane bilayer CH2 H2 C CH2 H2 C CH2 Nonpolar tail (hydrophobic) H2 C Polar heads CH2 H2 C Nonpolar fatty acid tails CH2 H2 C CH2 H3 C Chemical structure Space-filling model (a) Structure and model of a phospholipid Polar heads (b) Arrangement of phospholipids in a bilayer 17 Steroids Four interconnected rings of carbon atoms Usually not very water soluble Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH3 H3 C CH3 CH2 CH CH2 CH2 H CH3 CH CH3 3 HO H H Cholesterol All steroids come from a common precursor cholesterol Tiny differences in chemical structure can lead to profoundly different biological properties: Estrogen vs. testosterone 18 CH3 H3C CH3 CH2 CH CH2 CH3 CH CH2 H CH3 H 3 H Cholesterol HO H3C OH H3C OH H CH3 H H H H HO H O Estrogen Female cardinal Testosterone Male cardinal b: © Adam Jones/Photo Researchers; c: © Adam Jones/Photo Researchers 19 Fig. 4-9 Functional groups are particular groupings of atoms That give organic molecules unique properties A-roid Estradiol Testosterone Proteins : polymers of amino acids Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. R H H N+ H O C C H O– -carbon A typical amino acid 21 3.12 Proteins are made from amino acids linked by peptide bonds • Protein diversity is based on different arrangements of a common set of 20 amino acid monomers • Each amino acid contains A carboxyl group and an amino group An R (variable) group, which distinguishes each of the 20 different amino acids H O H N C H C OH R Amino -carbon group Figure 3.12A Carboxyl (acid) group Nonpolar Glycine (Gly or G) Alanine (Ala or A) Methionine (Met or M) Leucine (Leu or L) Valine (Val or V) Trypotphan (Trp or W) Phenylalanine (Phe or F) Isoleucine (Ile or I) Proline (Pro or P) Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine Glutamine (Asn or N) (Gln or Q) Electrically charged Acidic Aspartic acid Glutamic acid (Glu or E) (Asp or D) Basic Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Peptide bond Side chains (a) Peptide bond Backbone Amino end (N-terminus) (b) Carboxyl end (C-terminus) Final Protein Product Protein Structure Primary Secondary Tertiary Quaternary 25 Primary structure Amino acid sequence Determined by genes Sequence alignment Consensus key * fully conserved residue : conservation of strong groups . conservation of weak groups no consensus (blank) INS_BOVIN MAL--WTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREV INS_SHEEP MAL--WTRLVPLLALLALWAPAPAHAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREV INS_PIG MAL--WTRLLPLLALLALWAPAPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREA INS_PANTR MAL--WMRLLPLLVLLALWGPDPASAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREA INS_HUMAN MAL--WMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREA INS_CHICK MAL--WIRSLPLLALLVFSGPGTSYAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDV :***..**:***:.** :**** *. : INS_BOVIN EGPQVGALELAGGPG-----AGGL---EGPPQKRGIVEQCCASVCSLYQLENYCN INS_SHEEP EGPQVGALELAGGPG-----AGGL---EGPPQKRGIVEQCCAGVCSLYQLENYCN INS_PIG ENPQAGAVELGGGLGG--LQALAL---EGPPQKRGIVEQCCTSICSLYQLENYCN INS_PANTR EDLQVGQVELGGGPGAGSLQPLAL---EGSLQKRGIVEQCCTSICSLYQLENYCN INS_HUMAN EDLQVGQVELGGGPGAGSLQPLAL---EGSLQKRGIVEQCCTSICSLYQLENYCN INS_CHICK EQPLVSS-PLRGEAG--VLPFQQE---EYEKVKRGIVEQCCHNTCSLYQLENYCN ****** *.: :*:.*** 26 Secondary & Tertiary Structure Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. NH3+ Chemical and physical interactions cause folding O CH2 C O– + NH3 CH2 CH2 CH2 CH2 Repeating patterns HC COO– CH3 CH2 CH3 CH2 OH CH2 O NH2 C CH2 CH2 CH2 α helices and β pleated sheets Key determinants of a protein’s characteristics S S CH2 “Random coiled regions” Not α helix or β pleated sheet Shape is specific and important to function 27 Tertiary structure Folding gives complex three-dimensional shape Final level of structure for single polypeptide chain Green fluorescent protein (GFP) Quaternary structure Made up of 2 or more polypeptides subunits – individual polypeptides Multimeric proteins – proteins with multiple parts Protein 28 Fig. 5-22 Normal hemoglobin Primary structure Sickle-cell hemoglobin Primary structure Val His Leu Thr Pro Glu Glu 1 2 3 Secondary and tertiary structures 4 5 6 7 subunit Secondary and tertiary structures Val His Leu Thr Pro Val Glu 1 2 3 Exposed hydrophobic region Quaternary structure Normal hemoglobin (top view) Quaternary structure Sickle-cell hemoglobin Function Molecules do not associate with one another; each carries oxygen. Function Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced. 10 µm Red blood cell shape Normal red blood cells are full of individual hemoglobin moledules, each carrying oxygen. 4 5 6 7 subunit 10 µm Red blood cell shape Fibers of abnormal hemoglobin deform red blood cell into sickle shape. 5 factors promoting protein folding and stability 1. 2. 3. 4. 5. Hydrogen bonds Ionic bonds and other polar interactions Hydrophobic effects Van der Waals forces Disulfide bridges 30 Please note that due to differing operating systems, some animations will not appear until the presentation is viewed in Presentation Mode (Slide Show view). You may see blank slides in the “Normal” or “Slide Sorter” views. All animations will appear after viewing in Presentation Mode and playing each animation. Most animations will require the latest version of the Flash Player, which is available at http://get.adobe.com/flashplayer. 31 Protein-protein interactions 32 Anfinsen Showed That the Primary Structure of Ribonuclease Determines Its Three-Dimensional Structure Prior to the 1960s, the mechanisms by which proteins assume their three-dimensional structures were not understood. Christian Anfinsen, however, postulated that proteins contain all the information necessary to fold into their proper conformation without the need for organelles or cellular factors He hypothesized that proteins spontaneously assume their most stable conformation based on the laws of chemistry and physics HYPOTHESIS Within their amino acid sequence, proteins contain all the information needed to fold into their correct, 3-dimensional shapes. KEY MATERIALS Purified ribonuclease, RNA, denaturing chemicals, size-exclusion columns. Experimental level 1 Conceptual level Incubate purified ribonuclease in test tube with RNA, and measure its ability to degrade RNA. Numerous H bonds (not shown) and 4 S—S bonds. Protein is properly folded. S S S Purified ribonuclease S S S S S 2 -mercaptoethanol + Urea Denature ribonuclease by adding -mercaptoethanol (breaks S—S bonds) and urea (breaks H bonds and ionic bonds). Measure its ability to degrade RNA. No more H bonds, ionic bonds, or S—S bonds. Protein is unfolded. SH SH SH SH SH SH Denatured ribonuclease SH 3 -mercaptoethanol Mixture from step 2 containing denatured ribonuclease, -mercaptoethanol, and urea Layer mixture from step 2 atop a chromatography column. Beads in the column allow ribonuclease to escape, while -mercaptoethanol and urea are retained. Collect ribonuclease in a test tube and measure its ability to degrade RNA. Column containing beads suspended in a watery solution Urea Beads have microscopic pores that trap -mercaptoethanol and urea, but not ribonuclease. Denatured ribonuclease Collection port with filter to prevent beads from escaping Solution of ribonuclease Renatured ribonuclease 4 THE D ATA 5 100 Ribonuclease function (%) Activity restored 6 50 0 Purified ribonuclease (step 1) Denatured Ribonuclease ribonuclease after column (step 2) chromatography (step 3) CONCLUSION Certain proteins, like ribonuclease, can spontaneously fold into their final, functional shapes without assistance from other cellular structures or factors. (Howeve r , as described in your text, this is not true of many other proteins.) SOURCE Habe r , E., and Anfinsen, C.B. 1961. Regeneration of enzyme activity by air oxidation of reduced subtilisin-modified ribonuclease. Journal of Biological Chemistry 236:422–424. Proteins Contain Functional Domains Within Their Structures STAT protein HN3+ COO– Nucleic Acids Responsible for the storage, expression, and transmission of genetic information Two classes Deoxyribonucleic acid (DNA) Store genetic information coded in the sequence of their monomer building blocks Ribonucleic acid (RNA) Involved in decoding this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain 36 Mononucleotide Monomers linked into polymer with a sugarphosphate backbone Monomer is a nucleotide Made up of phosphate group, a five-carbon sugar (either ribose or deoxyribose), and a single or double ring of carbon and nitrogen atoms known as a base 37 Bases Backbone Adenine NH2 N O P O– N H O– O 5 CH2 N O 1 4 Phosphate H H H 3 N Guanine Sugar O H P O– ATP has 3 phosphate groups N H N O O H N 2• H 5 O CH 2 NH2 N O Cytosine 4 H H 3 1 H H NH2 2 H N N O O P O– O 5 CH2 O 4 H H 3 1 H 2 H CH3 Cyclic AMP Has only one phosphate which is linked to ribose in a cyclic form. Thymine H N O O P O– O 5 CH2 4 H H 3 OH N O H 1 H 2 H 38 DNA vs. RNA DNA RNA Deoxyribonucleic acid Ribonucleic acid Deoxyribose Ribose Thymine (T) Uracil (U) Adenine (A), guanine (G), cytosine (C) used in both 2 strands- double helix Single strand Large Small Location to be found? Location to be found? 39 40 ETYMOLOGY OF KEY TERMS enantioopposite; mirror image (from the Greek enantios- in opposition) -gen that which produces (from the Greek genes- born or produced) glycoof, or relating to, sugar (from the Greek glykys- sweet) hydroof, or pertaining to, water (from the Greek hydor- water) isoequal; same (from the Greek isos- equal) macro- large; large enough to be seen with the naked eye (from the Greek makros- long) peptide compound containing two or more amino acids (modern derivative of peptic and pepsin, which is from the Greek peptikos- conducive to digestion) phobic fear or aversion to (from the Greek phobos- fear or panic) polymany (from the Greek polys- many) stereoin three dimensions (from the Greek stereos- solid) 41 Biomolecules Enzymes _______ Structural ________ Transport ________ Functions Sub-unit Bond between monomers ________ Protein ________ Structure Primary ______ Place the letter in the appropriate blank a. Valine b. Pro-Val-Ser-Thr c. α-helix d. DNA polymerase e. Keratin f. Hemoglobin g. Peptide h. Disulfide bonds i. R-groups interactions j. Hydrophobic exclusion Secondary ________ Tertiary Polar & non-polar ________ Cysteine _______ _________