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Chemistry of Organic Molecules Ch. 3 Essential Knowledge (AP Exam) • Organisms must exchange matter with the environment to grow, reproduce and maintain organization. EK 2.A.3 • Evidence of understanding: – Carbon carbohydrates, proteins, lipids, nucleic acids – Nitrogen proteins, nucleic acids – Phosphorus nucleic acids, some lipids Activity • Draw a simple diagram of how the following is cycled through the environment so that it is exchanged with living organisms. • Pages 876-878 in textbook 3.1 Organic Molecules • Organic molecules contain carbon and hydrogen atoms. • Four classes of organic molecules (biomolecules) exist in living organisms: – Carbohydrates – Lipids – Proteins – Nucleic Acids 4 Carbon: The Atom • Carbon has 4 valence electrons – Therefore, it can form 4 covalent bonds – can bond with up to 4 different atoms – can form double and triple bonds The structure of the carbon atom determines its function! Carbon Skeleton Diversity • Organic molecules are diverse in large part due to the variation in carbon skeletons • Which is more flexible- double or single bonds? The Carbon Skeleton and Functional Groups • The carbon chain of an organic molecule is called its skeleton or backbone. • Hydrogen and Carbon have similar electronegativity = non-polar • Functional groups are clusters of specific atoms bonded to the carbon skeleton – have characteristic structures and functions – determine the polarity of organic molecules and the types of reactions the molecule will undergo • See handout Figure 4.9 7 Isomers • Isomers are organic molecules that have identical molecular formulas but a different arrangement of atoms. • Name the two different functional groups: glyceraldehyde H H H O C C C OH OH H dihydroxyacetone H H O H C C C OH H OH • Will these react differently? Why? 8 Biomolecules • Carbohydrates, lipids, proteins, and nucleic acids are called biomolecules. – Usually consist of many repeating units • Each repeating unit is called a monomer. • A molecule composed of monomers is called a polymer (many parts). 9 Essential Knowledge (AP Exam) • The subcomponents of biological molecules and their sequence determine the properties of that molecule. (EK4.A.1) – The structure and function of polymers are derived from the way their monomers are assembled. Activity • Making Models of Macromolecules Glucose is a monomer • Make a ball and stick glucose model. • C6H O6 12 • Combine your glucose model with another glucose model at the #1 Carbon of one model and the #4 Carbon of the other model. • What must occur? The Synthesis of Polymers • A condensation reaction or dehydration reaction occurs when two monomers bond together through the loss of a water molecule Fig. 5-2a HO 1 2 3 H Short polymer HO Unlinked monomer Dehydration removes a water molecule, forming a new bond HO 1 2 H 3 H2O 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer The Breakdown of Polymers • Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction Fig. 5-2b HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 (b) Hydrolysis of a polymer H H H2O HO H Synthesis and Degradation • Enzymes are required for cells to carry out dehydration synthesis and hydrolysis reactions. – An enzyme is a molecule that speeds up a chemical reaction. • Enzymes are not consumed in the reaction. • Enzymes are not changed by the reaction. 18 3.2 Carbohydrates • Functions: – Immediate energy source – Provide building material (structural role) • Contain carbon, hydrogen and oxygen in a 1:2:1 ratio • Varieties: monosaccharides, disaccharides, and polysaccharides Essential Knowledge (AP Exam) EK4.A.1.a.4 • Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. • You must demonstrate an understanding of the above and the example of cellulose versus starch • You must be able to explain and use models to justify the connection between the structure and function of the polymers. Monosaccharides • A monosaccharide is a single sugar molecule. • Also called simple sugars • Have a backbone of 3 to 7 carbon atoms • Examples: – Glucose (blood), fructose (fruit) and galactose • Hexoses - six carbon atoms – Ribose and deoxyribose (in nucleotides) • Pentoses – five carbon atoms 21 • What 2 functional groups are the trademarks of a sugar molecule? • Functional groups of sugars: – Carbonyl groups – Hydroxyl groups Fig. 5-4a •In aqueous solutions many sugars form rings (a) Linear and ring forms Monosaccharide Function • Monosaccharides serve as a major fuel for cells and as raw material for building molecules Disaccharide Structure • A disaccharide is formed when a dehydration reaction joins two monosaccharides • This covalent bond is called a glycosidic linkage Fig. 5-5 1–4 glycosidic linkage Glucose Glucose Maltose 1–2 glycosidic linkage Glucose Fructose Lactose = glucose + galactose Sucrose Polysaccharides • Polysaccharides – polymers of sugars – Function: energy storage and structural • The structure and function of a polysaccharide are determined by – its sugar monomers – the positions of glycosidic linkages Storage Polysaccharides • Starch – An energy storage polysaccharide in plants – consists entirely of glucose monomers • Plants store surplus starch as granules within chloroplasts and other plastids Storage Polysaccharides • Glycogen – An energy storage polysaccharide in animals • Humans and other vertebrates store glycogen mainly in liver and muscle cells Fig. 5-6 Chloroplast Mitochondria Glycogen granules Starch 0.5 µm 1 µm Glycogen Amylose Amylopectin (a) Starch: a plant polysaccharide (b) Glycogen: an animal polysaccharide What is the difference? How is glucose released? Structural Polysaccharides • Cellulose –major component of the tough wall of plant cells –a polymer of glucose • the glycosidic linkages differ from that of starch • difference is based on two ring forms for glucose: alpha () and beta () Fig. 5-7 (a) and B glucose ring structures Glucose (b) Starch: 1–4 linkage of glucose monomers B Glucose (b) Cellulose: 1–4 linkage of B glucose monomers • Polymers with glucose are helical • Polymers with glucose are straight • The differing glycosidic linkages give the two molecules their distinct shapes. • In Cellulose the straight molecules can form hydrogen bonds with each other greater strength isomers of glucose structure determines function… Fig. 5-8 Cell walls Cellulose microfibrils in a plant cell wall Microfibril 10 µm 0.5 µm Cellulose molecules b Glucose monomer • Enzymes that digest starch can’t hydrolyze cellulose – Cellulose in human food passes through the digestive tract as insoluble fiber • Some microbes use enzymes to digest cellulose – Many herbivores, from cows to termites, have symbiotic relationships with these microbes Helpful bacteria • How can herbivores digest cellulose so well? – BACTERIA live in their digestive systems & help digest cellulose-rich (grass) meals Ruminants • Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods • Chitin also provides structural support for the cell walls of many fungi The structure of the chitin monomer. Chitin forms the exoskeleton of arthropods. Chitin is used to make a strong and flexible surgical thread. It has anti viral and anti fungal Properties. Chitin Essential Knowledge AP Exam • (EK4.A.a.a.3) In general lipids are nonpolar. Phospholipids exhibit structural properties, with polar regions that interact with polar molecules (water) and with nonpolar regions where differences in saturation determine the structure and function of lipids. 3.3 Lipids • Lipids are varied in structure. • Large nonpolar molecules that are insoluble in water • Functions: Long-term energy storage Structural components Cell communication and regulation Protection • Varieties: fats, oils, phospholipids, steroids, waxes Triglycerides: Long-Term Energy Storage – Also called fats and oils – Functions: long-term energy storage and insulation – Consist of one glycerol molecule linked to three fatty acids by dehydration synthesis Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H C C H H H C C C C C H H H H H H H H H H H H C C C C C C C OH H H H H H H H H H H C C C O C HO O C H C OH H glycerol a Formation of a fat . H HO OH + H H O C H H HO H H H C C H H 3 fatty acids H H in What is the process that causes fat to form? Fig. 5-11 Fatty acid (palmitic acid) Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage (b) Fat molecule (triacylglycerol) What is the Difference? Triglycerides: Long-Term Energy Storage • Fatty acids are either unsaturated or saturated. – Unsaturated - one or more double bonds between carbons • Tend to be liquid at room temperature – Example: plant oils – Saturated - no double bonds between carbons • Tend to be solid at room temperature – Examples: butter, lard Why are unsaturated fats liquid at room temperature? 45 Saturated vs Unsaturated Mostly animal products Mostly plant products • A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits • Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen • Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds • These trans fats may contribute more than saturated fats to cardiovascular disease Fat Function • The major function of fats is energy storage • Humans and other mammals store their fat in adipose cells • Adipose tissue also cushions vital organs and insulates the body Phospholipids • Phospholipid – two fatty acids and a phosphate group are attached to glycerol • the two fatty acid tails are hydrophobic • the phosphate group and its attachments form a hydrophilic head • The molecule is amphipathic Hydrophilic head Fig. 5-13 Choline Phosphate Hydrophobic tails Glycerol Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model What causes the tails to be nonpolar? (c) Phospholipid symbol Function of Phospholipids • Phospholipids are the major component of all cell membranes • When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior What causes the phospholipids to arrange this way? Phospholipids Form Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Membranes glycerol O Polar Head 1 O CH2 2 CH2 3 R O P O CH2 O Fig. 3.11 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH CH2 CH2 2 CH2 CH3 CH 2 C fatty acids O C CH2 CH 2 CH2 CH2 CH2 CH2 CH2 CH O Nonpolar Tails phosphate b.. Plasma membrane of a cell outside cell inside cell a. Phospholipid structure Steroids • Steroids are lipids characterized by a carbon skeleton consisting of four fused rings • Cholesterol, an important steroid, is a component in animal cell membranes • Examples: cholesterol, testosterone, estrogen • Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease Steroid Diversity Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. OH CH3 CH3 O b. Testosterone CH3 HC CH3 (CH2)3 HC CH3 OH CH3 CH3 CH3 HO c. Estrogen HO a. Cholesterol © Ernest A. Janes/Bruce Coleman/Photoshot Compare the testosterone and estrogen molecules. Demonstration • Grape demonstration: • Why is this occurring? Waxes • Long-chain fatty acid bonded to a long-chain alcohol • Solid at room temperature • Waterproof • Resistant to degradation • Function: protection • Examples: earwax, plant cuticle, beeswax, fruit covering Essential Knowledge AP Exam • (EK 4.A.1.a.2) In proteins, the specific order of animo acids in a polypeptide interacts with the environment to determine the overall shape of the protein, which also involves secondary and quaternary structure and, thus, its function. 3.4 Proteins • Proteins are polymers of amino acids linked together by peptide bonds. A peptide bond is a covalent bond between amino acids. • Two or more amino acids joined together are called peptides. Long chains of amino acids joined together are called polypeptides. • A protein is a polypeptide that has folded into a particular shape and has function. 58 Functions of Proteins • Metabolism Most enzymes are proteins that act as catalysts to accelerate chemical reactions within cells. • Support Keratin and collagen • Transport Hemoglobin and membrane proteins • Defense Antibodies • Regulation Hormones are regulatory proteins that influence the metabolism of cells. • Motion Muscle proteins and microtubules 59 Amino Acids: Protein Monomers • There are 20 different common amino acids. • Amino acids differ by their R groups. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group H2N H C R R = rest of molecule acidic group COOH (EK4.A.1.2) The R group of an amino acid can be categorized by chemical properties and these R groups determine structure and function of that region of the protein. • Amino acids can be classified according to the properties of their side chains (R groups): – Nonpolar – Polar – electrically charged (acidic or basic) Fig. 5-17a Nonpolar Glycine (Gly or G) Methionine (Met or M) Alanine (Ala or A) Valine (Val or V) Phenylalanine (Phe or F) Leucine (Leu or L) Tryptophan (Trp or W) Isoleucine (Ile or I) Proline (Pro or P) Fig. 5-17b 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) Fig. 5-17c 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) Synthesis and Degradation of a Peptide Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group amino acid Fig. 5-18 Peptide bond What type of reaction is this? (a) Side chains Peptide bond Backbone (b) Amino end (N-terminus) Carboxyl end (C-terminus) Levels of Protein Structure • Proteins cannot function properly unless they fold into their proper shape. – When a protein loses it proper shape, it said to be denatured. • Exposure of proteins to certain chemicals, a change in pH, or high temperature can disrupt protein structure. • Proteins can have up to four levels of structure: – – – – Primary Secondary Tertiary Quaternary 67 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H3N+ Primary Structure This level of structure is determined by the sequence of amino acids coded by a gene that joins to form a polypeptide. amino acid C O C CH R N R H O O C CH N H H O O CH R R hydrogen bond C C C N H O H C R C O H N N C C N R C N CH N R H C hydrogen bond O C O O R H N R H C Hydrogen bonding between amino acids causes the polypeptide to form an alpha helix or a pleated sheet. N CH CH Secondary Structure CH C O COO– peptide bond C R C N H R C O C R C C O H H N N CH R C C O C R N H H O R C C α alpha) helix O N H Β (beta) sheet = pleated sheet disulfide bond Quaternary Structure This level of structure occurs when two or more folded polypeptides interact to perform a biological function. H C O N C C N C O Tertiary Structure Interactions of amino acid side chains with water, covalent bonding between R groups, and other chemical interactions determine the folded three-dimensional shape of a protein. C C N O R Four Levels of Protein Structure 1. Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word – Primary structure is determined by inherited genetic information 2. Secondary structure • coils and folds resulting from hydrogen bonds between repeating constituents of the polypeptide backbone • Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet Fig. 5-21c Secondary Structure B pleated sheet Examples of amino acid subunits helix 3. Tertiary structure – determined by interactions between R groups, rather than interactions between backbone constituents • • • • hydrogen bonds ionic bonds hydrophobic interactions van der Waals interactions – Strong covalent bonds called disulfide bridges may reinforce the protein’s structure Fig. 5-21f Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond Fig. 5-21e Tertiary Structure Quaternary Structure 4.Quaternary structure results when two or more polypeptide chains form one macromolecule • Collagen is a fibrous protein consisting of three polypeptides coiled like a rope • Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Fig. 5-21g Polypeptide chain B Chains Chains Hemoglobin Collagen Fig. 5-22 Normal hemoglobin Primary structure Val His Leu Thr Pro Glu Glu 1 2 3 4 5 6 7 Secondary and tertiary structures B subunit Normal hemoglobin (top view) 1 2 3 Normal red blood cells are full of individual hemoglobin molecules, each carrying oxygen. 6 7 B subunit B Sickle-cell hemoglobin a Function a Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced. 10 µm Red blood cell shape 5 Exposed hydrophobic region B Molecules do not associate with one another; each carries oxygen. 4 a Quaternary structure B Function Secondary and tertiary structures Val His Leu Thr Pro Val Glu B a Quaternary structure Sickle-cell hemoglobin Primary structure 10 µm Red blood cell shape Fibers of abnormal hemoglobin deform red blood cell into sickle shape. Why are these two hemoglobin structures different? Essential Knowledge AP Exam • Alterations in a DNA sequence can lead to changes in the type and amount of the protein produced and the consequent phenotype. • A change in the order of amino acids could lead to different R groups and interactions between those R groups. This could change the shape of the molecule & may change its function. What Can Change Protein Structure? • In addition to primary structure, physical and chemical conditions can affect structure • Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel • This loss of a protein’s native structure is called denaturation • A denatured protein is biologically inactive Fig. 5-23 Denaturation Normal protein Renaturation Denatured protein If the denatured protein remains dissolved it may be able to renature once the environment is returned to normal. Animation of Denaturation • http://www.sumanasinc.com/webcontent/a nimations/content/proteinstructure.html Fig. 5-24 •Chaperonins are protein molecules that assist the proper folding of other proteins Polypeptide Correctly folded protein Cap Hollow cylinder Chaperonin (fully assembled) Steps of Chaperonin 2 Action: 1 An unfolded polypeptide enters the cylinder from one end. The cap attaches, causing the 3 The cap comes cylinder to change shape in off, and the properly such a way that it creates a folded protein is hydrophilic environment for released. the folding of the polypeptide. Defects in chaperone proteins may play a role in several human diseases such as Alzheimer disease and cystic fibrosis. Protein-Folding Diseases • Prions are misfolded proteins that have been implicated in a group of fatal brain diseases known as TSEs. – Mad cow disease is one example of a TSE disease. 83 • Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions • Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Fig. 5-16 Substrate (sucrose) Glucose OH Fructose HO Enzyme (sucrase) H2O Essential Knowledge AP Exam • Alterations in a DNA sequence can lead to changes in the type and amount of the protein produced and the consequent phenotype. • A change in the order of amino acids could lead to different R groups and interactions between those R groups. This could change the shape of the molecule & may change its function. Essential Knowledge AP Exam • (EK3.A.1.a.1) Genetic information is stored in and passed to subsequent generations through DNA molecules and in some cases RNA molecules. 3.5 Nucleic Acids • Nucleic acids are polymers of nucleotides. • Two varieties of nucleic acids: – DNA (deoxyribonucleic acid) • Genetic material that stores information for its own replication and for the sequence of amino acids in proteins. – RNA (ribonucleic acid) • Perform a wide range of functions within cells which include protein synthesis and regulation of gene expression 88 Structure of a Nucleotide • Each nucleotide is composed of three parts: – A phosphate group – A pentose sugar – A nitrogen-containing (nitrogenous) base • There are five types of nucleotides found in nucleic acids. – DNA contains adenine, guanine, cytosine, and thymine. – RNA contains adenine, guanine, cytosine, and uracil. • Nucleotides are joined together by a series of dehydration synthesis reactions to form a linear molecule called a strand. 89 Nucleotides Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. phosphate P C O 5' 4' S 1' 2' 3' pentose sugar nitrogencontaining base Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O –O P O C phosphate P O– O 5' 4' S 1' 2' 3' pentose sugar a. Nucleotide structure nitrogencontaining base Structure of DNA and RNA • The backbone of the nucleic acid strand is composed of alternating sugar-phosphate molecules. – RNA is predominately a single-stranded molecule. – DNA is a double-stranded molecule. • DNA is composed of two strands – held together by hydrogen bonds between the nitrogen-containing bases. – Why Hydrogen Bonds????? – The two strands twist around each other to form a double helix. 93 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. RNA Structure Fig. 3.19 N O N P G N N NH2 S H N O P N S Nitrogen-containing bases O U CH3 Backbone NH2 N P N N S S Ribose C Cytosine A Guanine G Adenine P Phosphate U Uracil A N N O P N S C NH2 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. T A C G T A Adenine hydrogen bonds with thymine G C Cytosine hydrogen bonds with guanine C CCytosine S Sugar Guanine A AAdenine GG P Phosphate T TThymine b. Double helix a. Space-filling model N O H N ― N ― ― N N H O H N N sugar N sugar cytosine (C) H guanine (G) H N N ― The bonding is complementary H CH3 O H C N suga r N H N N N O adenine (A) sugar thymine (T) c. Complementary base pairing © Photodisk Red/Getty RF A Special Nucleotide: ATP • ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates. • ATP is a high-energy molecule due to the presence of the last two unstable phosphate bonds. • Hydrolysis of the terminal phosphate bond yields: – The molecule ADP (adenosine diphosphate) – An inorganic phosphate – Energy to do cellular work • ATP is called the energy currency of the cell. 98 ATP Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. adenosine triphosphate c. NH2 NH2 N N N H2O P N adenosine b. P P triphosphate ATP N N N P N adenosine P diphosphate ADP c: © Jennifer Loomis / Animals Animals / Earth Scenes + P phosphate + ENERGY Can DNA help to demonstrate the Theory of Evolution? • The linear sequences of nucleotides in DNA molecules are passed from parents to offspring • Two closely related species are more similar in DNA than are more distantly related species • Molecular biology can be used to assess evolutionary kinship (DNA Sequencing)