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Carbon & the Molecular diversity of Life The big picture: • The subcomponents of biological molecules and their sequence determine the properties of that molecule. • The electron configuration of carbon gives it covalent compatibility with many different elements. © 2014 Pearson Education, Inc. • The atomic number of carbon is 6 • How many valence electrons does it have? © 2014 Pearson Education, Inc. Carbon atoms • 4 unpaired electrons in valence shell • Can form up to 4 single covalent bonds • Can also form double bonds, most commonly with: – Oxygen CO2 O=C=O – Carbon To create long chains © 2014 Pearson Education, Inc. Organic compounds • A compound containing carbon • Most, but not all, also contain hydrogen • Most common elements in organic compounds – – – – – – Carbon (all) Hydrogen (most) Oxygen Nitrogen Sulfur Phosphorus © 2014 Pearson Education, Inc. Figure 3.3 Hydrogen (valence 1) © 2014 Pearson Education, Inc. Oxygen (valence 2) Nitrogen (valence 3) Carbon (valence 4) Shapes of Simple Organic Molecules • They are 3-dimensional • When 4 single bonds are formed with a single carbon atom – Angles 109.50 – Tetrahedron © 2014 Pearson Education, Inc. Figure 3.2 Name Methane Ethane Ethene (ethylene) © 2014 Pearson Education, Inc. Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model • Carbon chains can vary in 4 ways – – – – Length Branching Double bond position Presence of rings • Complexity and diversity of organic molecules is due to – Variation in carbon chain structure – Other elements bonded to the chain © 2014 Pearson Education, Inc. Figure 3.4 (a) Length Ethane (c) Double bond position Propane (b) Branching Butane © 2014 Pearson Education, Inc. 1-Butene 2-Butene (d) Presence of rings 2-Methylpropane (isobutane) Cyclohexane Benzene • The simplest carbon chain is made of only carbon and hydrogen. • Hydrocarbon=hydrogen +carbon. • Hydrogen molecules are attached to the carbon molecules wherever electrons are available for covalent bonding. © 2014 Pearson Education, Inc. • Chemical groups can replace one or more of the hydrogen atoms on the hydrocarbon skeleton. • They can contribute to the function of the organic molecule by– Affecting its shape – Being directly involved in chemical reactions © 2014 Pearson Education, Inc. Figure 3.5 Chemical Group Hydroxyl group ( Compound Name Examples OH) Alcohol Carbonyl group ( C O) Ethanol Ketone Aldehyde Acetone Carboxyl group ( Propanal COOH) Carboxylic acid, or organic acid Acetic acid Amino group ( NH2) Amine Glycine Sulfhydryl group ( SH) Thiol Phosphate group ( OPO32–) Organic phosphate Methyl group ( Glycerol phosphate CH3) Methylated compound © 2014 Pearson Education, Inc. Cysteine 5-Methyl cytosine Important terms • Polymer – A long molecule consisting of many similar or identical building blocks linked by covalent bonds. • Monomer – The repeating units that serve as the building blocks of a polymer. • How are monomers joined together? © 2014 Pearson Education, Inc. Synthesis and Breakdown of Polymers • Dehydration reaction – Connects monomers – One provides a hydroxyl group (-OH), the other a hydrogen (-H) – Water is lost • Hydrolysis – The reverse – Breakage using water – Water attaches a hydroxyl to one molecule, hydrogen to the other © 2014 Pearson Education, Inc. Figure 3.6a (a) Dehydration reaction: synthesizing a polymer Short polymer Dehydration removes a water molecule, forming a new bond. Longer polymer © 2014 Pearson Education, Inc. Unlinked monomer Figure 3.6b (b) Hydrolysis: breaking down a polymer Hydrolysis adds a water molecule, breaking a bond. © 2014 Pearson Education, Inc. Macromolecules (+ Lipids) • 4 classes of large organic molecules shared by all living things. – – – – Carbohydrates Lipids Proteins Nucleic acids • Some do not consider lipids to be true “macromolecules” because – They are not big enough – They are not true polymers © 2014 Pearson Education, Inc. As we review each macromolecule • • • • • • Monomer Polymer Type of bond that links the monomers together Basic structure Example Function © 2014 Pearson Education, Inc. Carbohydrates • Monomer- simple sugar, monosaccharide • Disaccharide- 2 simple sugars linked together • Polysaccharide- many simple sugars linked together © 2014 Pearson Education, Inc. • Monosaccharides – Contain a carbonyl group (C=O) and multiple hydroxyl groups (-OH) – Vary in the length of the carbon skeleton and position of the carbonyl group – All have chemical formulas that are multiples of CH2O, ex. Glucose is C6H12O6 – Names end in “ose” – Used as fuel © 2014 Pearson Education, Inc. Figure 3.7 Triose: 3-carbon sugar (C3H6O3) Pentose: 5-carbon sugar (C5H10O5) Glyceraldehyde An initial breakdown product of glucose in cells Ribose A component of RNA Hexoses: 6-carbon sugars (C6H12O6) Glucose Fructose Energy sources for organisms © 2014 Pearson Education, Inc. • Sugars can exist in both a linear and ring form • Equilibrium favors the ring form. • Notice the convention for naming the carbon atoms. © 2014 Pearson Education, Inc. Figure 3.8 (a) Linear and ring forms (b) Abbreviated ring structure © 2014 Pearson Education, Inc. • Two monosaccharides are linked by a covalent bond through a dehydration reaction. • The resulting linkage is called a glycosidic linkage. © 2014 Pearson Education, Inc. Figure 3.9-1 Glucose © 2014 Pearson Education, Inc. Fructose Figure 3.9-2 Glucose Fructose 1–2 glycosidic linkage Sucrose © 2014 Pearson Education, Inc. Polysaccharides • 2 functions – Storage- sugars for later use – Structural- building material © 2014 Pearson Education, Inc. Storage • Plants – Starch • Polymer of glucose • Mostly unbranched • Most animals also have enzymes to break it down so it can be a food source © 2014 Pearson Education, Inc. Figure 3.10a Starch granules in a potato tuber cell Starch (amylose) Glucose monomer © 2014 Pearson Education, Inc. • Animals – Glycogen • • • • Also a polymer of glucose Extensive branching Stored in liver and muscles Stores for only 1 day © 2014 Pearson Education, Inc. Figure 3.10b Glycogen granules in muscle tissue © 2014 Pearson Education, Inc. Glycogen Figure 3.10 Starch granules in a potato tuber cell Starch (amylose) Glucose monomer Glycogen granules in muscle tissue Cellulose microfibrils in a plant cell wall Cellulose molecules © 2014 Pearson Education, Inc. Glycogen Cellulose Hydrogen bonds between —OH groups (not shown) attached to carbons 3 and 6 Structural • Cellulose – Plant cell walls – Never branched – Different from starch because of presence of 2 ring forms of glucose • Cellulose α glucose • Starch β glucose © 2014 Pearson Education, Inc. Figure 3.11 (a) and glucose ring structures Glucose Glucose (b) Starch: 1–4 linkage of glucose monomers (c) Cellulose: 1–4 linkage of glucose monomers © 2014 Pearson Education, Inc. • Cellulose polymers lie parallel and can form hydrogen bonds with neighboring polymers • Creates cable-like microfibrils © 2014 Pearson Education, Inc. Figure 3.10c Cellulose microfibrils in a plant cell wall Cellulose molecules © 2014 Pearson Education, Inc. Cellulose Hydrogen bonds between —OH groups on carbons 3 and 6 Figure 3.10ca Cellulose microfibrils in a plant cell wall © 2014 Pearson Education, Inc. Lipids • No true monomers • Not big enough to be considered “macro” • Share one important trait – They are all hydrophobic (due to hydrocarbons) • 3 biologically important lipids – Fats – Phospholipids – Steroids © 2014 Pearson Education, Inc. Fats • Composed of – Glycerol (1) – Fatty acids (3) • Linkage is called an “ester bond” and it is a covalent bond between a hydroxyl group and a carboxyl group • What kind of reaction is used in the synthesis of a fat? © 2014 Pearson Education, Inc. Figure 3.12 Fatty acid (in this case, palmitic acid) Glycerol (a) One of three dehydration reactions in the synthesis of a fat Ester linkage (b) Fat molecule (triacylglycerol) © 2014 Pearson Education, Inc. Saturated vs. Unsaturated • Are there any carbon double bonds within the hydrocarbon chains of the fatty acids? – Yes- unsaturated – No- saturated © 2014 Pearson Education, Inc. Figure 3.13 (a) Saturated fat Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid © 2014 Pearson Education, Inc. (b) Unsaturated fat Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid Double bond causes bending. Phospholipids • Differ from fats in that there are only 2 fatty acids • The third hydroxyl group of the glycerol molecule bonds to a phosphate • The phosphate is negatively charged AND other small polar molecules can be attached to the phosphate. Both of these things make the phosphate end. . . Hydrophilic! © 2014 Pearson Education, Inc. Hydrophobic tails Hydrophilic head Figure 3.14ab Choline Phosphate Glycerol Fatty acids (a) Structural formula © 2014 Pearson Education, Inc. (b) Space-filling model • Where in a cell might you find phospholipids? © 2014 Pearson Education, Inc. Hydrophobic tails Hydrophilic head Figure 3.14 Choline Phosphate Glycerol Fatty acids (a) Structural formula © 2014 Pearson Education, Inc. Hydrophilic head Hydrophobic tails (b) Space-filling model (c) Phospholipid symbol (d) Phospholipid bilayer Steroids • Carbon skeleton of 4 fused carbon rings • Distinguished by the attached chemical groups • Cholesterol is an example – Common component of animal cell membranes – Other important steroids are synthesized from it © 2014 Pearson Education, Inc. Figure 3.15 © 2014 Pearson Education, Inc. Proteins • Proeios- “first” or “primary” • Play a roll in almost everything a cell does • 50% of dry mass of most cells © 2014 Pearson Education, Inc. Protein functions include: – – – – – – – Speeding up chemical reactions (enzymes) Defense Storage Transport Cellular communication Movement Structural support © 2014 Pearson Education, Inc. Figure 3.16a Enzymatic proteins Defensive proteins Function: Selective acceleration of chemical reactions Function: Protection against disease Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Example: Antibodies inactivate and help destroy viruses and bacteria. Antibodies Enzyme Virus Bacterium Storage proteins Transport proteins Function: Storage of amino acids Function: Transport of substances Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Transport protein Ovalbumin © 2014 Pearson Education, Inc. Amino acids for embryo Cell membrane Figure 3.16b Hormonal proteins Receptor proteins Function: Coordination of an organism’s activities Function: Response of cell to chemical stimuli Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration. Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. Receptor protein High blood sugar Insulin secreted Signaling molecules Normal blood sugar Contractile and motor proteins Function: Movement Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles. Actin Structural proteins Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Myosin Collagen Muscle tissue 30 m © 2014 Pearson Education, Inc. Connective tissue 60 m • Monomer- amino acid • Polymer- polypeptide (unbranched) • Linkage- peptide bond, a covalent bond between an amino group and a carboxyl group (What kind of reaction?) • Protein definition= – A biologically functional molecule that consists of one or more polypeptides folded and coiled into a specific 3-dimensional structure. © 2014 Pearson Education, Inc. Amino acids • 20 amino acids • All have a common structure – α carbon in the center – 4 partners • • • • Hydrogen Amino group Carboxyl group R group (Think “R” = “the rest”) © 2014 Pearson Education, Inc. Figure 3.UN04 Side chain (R group) carbon Amino group © 2014 Pearson Education, Inc. Carboxyl group R Groups • Unique to each amino acid • Often ionized at the pH found in cells (=7.2) • Chemical and physical properties determine the characteristics of the amino acid and its role in a polypeptide © 2014 Pearson Education, Inc. R groups (also called side chains) can be: • Nonpolar: hydrophobic • Polar: hydrophilic • Electrically charged: hydrophilic – Acidic – Basic © 2014 Pearson Education, Inc. Figure 3.17a Nonpolar side chains; hydrophobic Side chain (R group) Glycine (Gly or G) Methionine (Met or M) © 2014 Pearson Education, Inc. Alanine (Ala or A) Valine (Val or V) Phenylalanine (Phe or F) Leucine (Leu or L) Tryptophan (Trp or W) Isoleucine (le or ) Proline (Pro or P) Figure 3.17b Polar side chains; hydrophilic © 2014 Pearson Education, Inc. Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Figure 3.17c Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Aspartic acid Glutamic acid (Asp or D) (Glu or E) © 2014 Pearson Education, Inc. Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Polypeptides • Amino acids linked in a non-branching polymer by peptide bonds through a dehydration reaction. • N-terminus: the amino end of a polypeptide • C-terminus: the carboxyl end of a polypeptide © 2014 Pearson Education, Inc. Figure 3.18 Peptide bond New peptide bond forming Side chains Backbone Amino end (N-terminus) © 2014 Pearson Education, Inc. Peptide bond Carboxyl end (C-terminus) To be clear . . . • A polypeptide is NOT a protein • A protein is one or more polypeptides precisely twisted, coiled and folded into a unique shape. • The sequence of amino acids determines this shape • The shape determines how it functions © 2014 Pearson Education, Inc. • Function depends on the protein’s ability to recognize and bind with other molecules. • The binding requires an exact match between the protein and the other molecule. • Like puzzle pieces or a lock and key. © 2014 Pearson Education, Inc. Figure 3.20 Antibody protein © 2014 Pearson Education, Inc. Protein from flu virus 4 Levels of Protein Structure • • • • Primary Secondary Tertiary Quaternary © 2014 Pearson Education, Inc. Primary • The sequence of amino acids • The primary structure then controls the secondary and tertiary structures . © 2014 Pearson Education, Inc. Figure 3.21a Primary structure Amino acids 1 10 5 Amino end 30 35 15 20 25 45 40 50 Primary structure of transthyretin 65 70 55 60 75 80 90 85 95 115 120 110 105 100 125 Carboxyl end © 2014 Pearson Education, Inc. Secondary • Coiled or folded patterns that result from hydrogen bonds between parts of the polypeptide backbone NOT the R-groups. • 2 types – α helix – Β pleated sheet © 2014 Pearson Education, Inc. Figure 3.21ba Secondary structure helix pleated sheet Hydrogen bond strand Hydrogen bond © 2014 Pearson Education, Inc. Tertiary • The overall shape of the polypeptide resulting from interactions between the side chains (Rgroups) © 2014 Pearson Education, Inc. Interactions contributing to tertiary structure – Hydrophobic interactions • Amino acids with nonpolar (hydrophobic) side chains get moved to the inner core away from water, then van der Waals interactions hold them together. – Hydrogen bonds • Between polar side chains – Ionic bonds • Between positively and negatively charged side chains – Disulfide bridges • Covalent bond between the sulfur of 2 cysteine monomers © 2014 Pearson Education, Inc. Figure 3.21d Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Polypeptide backbone © 2014 Pearson Education, Inc. Figure 3.21bb Tertiary structure Transthyretin polypeptide © 2014 Pearson Education, Inc. Quaternary • The overall protein structure that results from the aggregation of polypeptide subunits. © 2014 Pearson Education, Inc. Figure 3.21bc Quaternary structure Transthyretin protein © 2014 Pearson Education, Inc. Figure 3.21b Secondary structure Tertiary structure Quaternary structure Transthyretin polypeptide Transthyretin protein helix pleated sheet © 2014 Pearson Education, Inc. Figure 3.21f Heme Iron subunit subunit subunit subunit Hemoglobin © 2014 Pearson Education, Inc. Figure 3.22a Normal Primary Structure 1 2 3 4 5 6 7 © 2014 Pearson Education, Inc. Secondary and Tertiary Structures Quaternary Structure Normal hemoglobin subunit Function Molecules do not associate with one another; each carries oxygen. Figure 3.22aa 5 m © 2014 Pearson Education, Inc. Figure 3.22b Sickle-cell Primary Structure 1 2 3 4 5 6 7 © 2014 Pearson Education, Inc. Secondary and Tertiary Structures Quaternary Structure Exposed hydrophobic region Sickle-cell hemoglobin subunit Function Molecules crystallized into a fiber; capacity to carry oxygen is reduced. Figure 3.22ba 5 m © 2014 Pearson Education, Inc. Figure 3.22 Sickle-cell Normal Primary Structure 1 2 3 4 5 6 7 1 2 3 4 5 6 7 © 2014 Pearson Education, Inc. Secondary and Tertiary Structures Quaternary Structure Function Normal hemoglobin subunit Molecules do not associate with one another; each carries oxygen. 5 m Exposed hydrophobic region Sickle-cell hemoglobin subunit Red Blood Cell Shape Molecules crystallized into a fiber; capacity to carry oxygen is reduced. 5 m Protein structure depends on: • • • • • • Primary sequence of amino acids AND pH Salt concentration Temperature Other environmental factors © 2014 Pearson Education, Inc. Denaturation • When environmental conditions are changed, the chemical bonds and interactions are destroyed . • The protein unravels. • Without its native shape, it is no longer functional. © 2014 Pearson Education, Inc. Figure 3.23-2 Normal protein © 2014 Pearson Education, Inc. Denatured protein Nucleic Acids • Two types – DNA (deoxyribonucleic acid) – RNA (ribonucleic acid) • Function: Store, transmit, and help express hereditary information. • Monomer: nucleotide © 2014 Pearson Education, Inc. Terms to know • Chromosome: a single long DNA molecule • Gene: A specific nucleotide sequence of DNA that codes for a specific amino acid sequence • A chromosome may be composed of >100 genes. © 2014 Pearson Education, Inc. Structure of Nucleic Acids • Monomer: nucleotide • Polymer: poly nucleotide • Nucleotide = nucleoside (nitrogenous base + 5 carbon sugar) + 1 or more phosphates • Nitrogenous (nitrogen-containing) as in “acid vs. base” not as in “foundation”. The N tends to take up H+ from solution acting as a base. © 2014 Pearson Education, Inc. Figure 3.26b Nucleoside Nitrogenous base Phosphate group (b) Nucleotide © 2014 Pearson Education, Inc. Sugar (pentose) 2 types of nitrogenous bases • Pyrimidine- One 6-member ring of C and N – Cytosine – Thymine (only in DNA) – Uracil (only in RNA) • Purine- 6-member ring fused to a 5-member ring – Adenine – Guanine © 2014 Pearson Education, Inc. Figure 3.26c Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Adenine (A) © 2014 Pearson Education, Inc. Guanine (G) Sugars • Deoxyribose-DNA • Ribose- RNA © 2014 Pearson Education, Inc. Figure 3.26d Sugars Deoxyribose (in DNA) © 2014 Pearson Education, Inc. Ribose (in RNA) • Then a phosphate is added at the 5´ carbon of the sugar. • Note: The “prime” symbol ´ distinguishes the sugar carbon from the nitrogenous base carbon. © 2014 Pearson Education, Inc. Figure 3.26b Nucleoside Nitrogenous base Phosphate group (b) Nucleotide © 2014 Pearson Education, Inc. Sugar (pentose) Polynucleotide • Nucleotides joined by phosphodiester linkage • The sugars of the nucleotides are linked into a sugar phosphate backbone. © 2014 Pearson Education, Inc. Figure 3.26a 5 end Sugar-phosphate backbone (on blue background) 5C 3C Nucleoside Nitrogenous base 5C Phosphate group 3C (b) Nucleotide 3 end (a) Polynucleotide, or nucleic acid © 2014 Pearson Education, Inc. Sugar (pentose) • Note: polynucleotides have directionality much like proteins • Each end is different – 5´end-phosphate attached to 5´C – 3´end- OH attached to 3´C © 2014 Pearson Education, Inc. Figure 3.26 5 end Sugar-phosphate backbone (on blue background) Nitrogenous bases Pyrimidines 5C 3C Nucleoside Nitrogenous base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines 5C Phosphate group 3C Sugar (pentose) Adenine (A) Guanine (G) (b) Nucleotide 3 end Sugars (a) Polynucleotide, or nucleic acid Deoxyribose (in DNA) (c) Nucleoside components © 2014 Pearson Education, Inc. Ribose (in RNA) DNA • 2 polynucleotide strands that run antiparallel • Think of a two way street – One strand 5´to 3´ – One strand 3´to 5´ • The 2 strands are held together by hydrogen bonds. © 2014 Pearson Education, Inc. Figure 3.27a 5 3 3 5 (a) DNA © 2014 Pearson Education, Inc. Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding • • • • • Only certain bases will bond together A-T G-C This allows 2 identical strands to be made Form follows function © 2014 Pearson Education, Inc. RNA • Only a single strand, but it can fold on itself • No thymine so. . . • A-U © 2014 Pearson Education, Inc. Figure 3.27b Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding (b) Transfer RNA © 2014 Pearson Education, Inc. Figure 3.27 5 3 Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3 5 (a) DNA Base pair joined by hydrogen bonding © 2014 Pearson Education, Inc. (b) Transfer RNA Evidence for common ancestry • More common DNA sequences= more closely related © 2014 Pearson Education, Inc. For Monday’s Quiz Macromolecules plus lipids To know: • Monomers • Polymers • Linkages • Basic structure • Function • Examples © 2014 Pearson Education, Inc. Figure 3.UN06 © 2014 Pearson Education, Inc. Figure 3.UN06a © 2014 Pearson Education, Inc. Figure 3.UN06b © 2014 Pearson Education, Inc.