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Chapter 5 The Structure and Function of Large Biological Molecules Overview: The Molecules of Life • Four types: – carbohydrates, lipids, proteins, nucleic acids • Macromolecules: large molecules composed of thousands of covalently connected atoms • Molecular structure closely related to function Macromolecules: polymers built from monomers • Polymer (polys “many”, meros “parts”): molecule composed of many similar building blocks • Monomers (mono “single”): small building block molecules • Three of the four classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids Warm up • Have bozeman notes ready to be stamped In your groups, create the two compounds: • Make C2H6 and a CH3-OH • Black = carbon • White = hydrogen • Red = oxygen Combine the two molecules • C2H6 + CH3-OH C3H8 What molecule is left behind? Synthesis and Breakdown of Polymers • Dehydration synthesis: two monomers bond, loss of a water molecule – “Lose H2O to make” • Hydrolysis: polymers disassemble; reverse of dehydration synthesis, water molecule added – “to break apart by adding H2O (a) Dehydration reaction: synthesizing a polymer 1 2 3 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond. 1 2 3 4 Longer polymer (b) Hydrolysis: breaking down a polymer 1 2 3 Hydrolysis adds a water molecule, breaking a bond. 1 2 3 4 QUICK CHECK HO How many molecules of H2O are needed to completely hydrolyze a polymer that is 10 monomers long? Carbohydrates: fuel & building material • • • • Carbohydrates: sugars, polymers of sugars Monosaccharides: single sugars Disaccharides: double sugars Polysaccharides: macromolecules; polymers composed simple sugar building blocks Monosaccharides: simple sugars • molecular formulas multiples of CH2O • glucose (C6H12O6), galactose, fructose – Isomers • classified – number of carbons in carbon skeleton – location of carbonyl group • aldose or ketose Aldoses (Aldehyde Sugars) Ketoses (Ketone Sugars) Trioses: 3-carbon sugars (C3H6O3) Aldose: carbonyl group at the end Ketose: carbonyl group in the middle Glyceraldehyde Dihydroxyacetone Pentoses: 5-carbon sugars (C5H10O5) Ribose Ribulose Hexoses: 6-carbon sugars (C6H12O6) Glucose Galactose Fructose 1 2 6 6 5 5 3 4 4 5 1 3 2 4 1 3 2 6 (a) Linear and ring forms 6 5 4 1 3 2 (b) Abbreviated ring structure • Simple sugars often drawn as linear skeletons, in aqueous solutions many form rings • Monosaccharides • major fuel for cells • raw material for building molecules Disaccharide • dehydration synthesis reaction joins two monosaccharides – sucrose, maltose, lactose • covalent bond called glycosidic linkage • C12H22O11 1–4 glycosidic 1 linkage 4 Glucose Glucose Maltose (a) Dehydration reaction in the synthesis of maltose 1–2 glycosidic 1 linkage 2 Glucose Fructose (b) Dehydration reaction in the synthesis of sucrose Sucrose Polysaccharides • polymers of sugars – energy storage & structural roles – starch, glycogen, cellulose, chitin • structure & function determined by – sugar monomers – positions of glycosidic linkages Storage Polysaccharides • Starch: storage polysaccharide of plants, consists entirely of glucose monomers – stored as granules w/in chloroplasts & other plastids – Amylose: simplest form of starch, unbranched – Amylopectin: branched form • Glycogen: storage polysaccharide in animals – stored in liver & muscle cells – “Carbo” loading Chloroplast Starch granules Amylopectin Amylose (a) Starch: plant polysaccharide Mitochondria 1 m Glycogen granules Glycogen (b) Glycogen: 0.5 m animal polysaccharide Structural Polysaccharides • Cellulose: major component of plant cell walls • polymer of glucose, but the glycosidic linkages differ – difference is based on two ring forms for glucose: alpha () and beta () (a) and glucose ring structures Glucose Glucose (b) Starch: 1–4 linkage of glucose monomers (c) Cellulose: 1–4 linkage of glucose monomers • Starch: polymers with glucose are helical • Cellulose: polymers with glucose are straight • H atoms on one strand can bond with OH groups on other strands • Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants Cellulose microfibrils in plant cell wall Cell wall Microfibril 10 m 0.5 m Cellulose molecules Glucose monomer • Enzymes that digest starch by hydrolyzing linkages can’t hydrolyze linkages in cellulose • Cellulose in human food passes through the digestive tract as insoluble fiber • Some microbes use enzymes to digest cellulose • Many herbivores, from rabbits to termites, have symbiotic relationships with these microbes Structural Polysaccharides Chitin • provides structural support for cell walls of many fungi • forms exoskeleton of arthropods • used as surgical thread Structure of chitin monomer Chitin forms exoskeleton of arthropods Chitin makes strong & flexible surgical thread that decomposes with healing Lipids: diverse group of hydrophobic molecules • Lipids: do not form polymers – Hydrophobic: hydrocarbons form nonpolar covalent bonds • fats, steroids, phospholipids Fats • glycerol and 3 fatty acids – glycerol: three-carbon alcohol w/ hydroxyl attached to each carbon – fatty acid: carboxyl group attached to long carbon skeleton Fatty acid (palmitic acid) Glycerol One of three dehydration reactions in the synthesis of a fat • Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats • Three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride Ester linkage Fat molecule (triacylglycerol) • Fatty acids vary: length (# C), number & locations of double bonds – saturated fatty acids: have maximum number of hydrogen atoms possible, no double bonds • fat molecules can pack together tightly; solid at room temp • saturated fats may contribute to cardiovascular disease through plaque deposits – unsaturated fatty acids: have one or more double bonds • double bonds cause a kink, can’t pack together; liquid at room temp • Saturated fats: solid at room temperature – most animal fats - lard, butter • Unsaturated fats: liquid at room temperature – plant fats: olive oil, fish fats - cod liver oil (a) Saturated fat (b) Unsaturated fat Structural formula Structural formula Space-filling model of Stearic acid Space-filling Model of oleic acid Cis double bond causes bending. • Hydrogenation: converts unsaturated fats to saturated fats by adding hydrogen – Hydrogenating vegetable oils creates unsaturated fats with trans double bonds – trans fats may contribute more than saturated fats to cardiovascular disease • certain unsaturated fatty acids not synthesized in body, must be supplied in the diet • omega-3 fatty acids: required for normal growth, and thought to provide protection against cardiovascular disease • found in fish, nuts, vegetable oils Functions of Fat • energy storage, insulation, cushions internal organs • humans, other mammals store their fat in adipose cells Phospholipids • two fatty acids & phosphate group attached to glycerol • fatty acid tails “hydrophobic”, the phosphate group forms a “hydrophilic” head Hydrophilic head Hydrophobic tails Choline Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol Phospholipids • in water, self-assemble into a bilayer – hydrophobic tails point toward the interior • major component of all cell membranes Hydrophilic head WATER Hydrophobic tail WATER Double Bubble • Write a double bubble map comparing and contrasting carbohydrates with fats Steroids • Steroids: carbon skeletons four fused rings • Sex hormones: testosterone, estrogen, progesterone • Cholesterol: component in animal cell membranes – cholesterol essential in animals – high levels in blood may contribute to cardiovascular disease cholesterol Compare the structure of a fat (triglyceride) with that of a phospholipid. Both have a glycerol molecule attached to fatty acids. The glycerol of fat has 3 fatty acids attached, whereas the glycerol of a phospholipid is attached to 2 fatty acids and 1 phosphate group. Copy the structure of a SINGLE amino acid: Bozeman Video questions (left side of notebook): • What are the monomers (subunits) of a protein? • What is similar from each amino acid? • What reaction combines one amino acid to the next? What is this bond called? • If you have a positive amino acid and a negative amino acid in the same polypeptide, what is going to happen? Proteins: structural diversity results in a wide range of functions • Types: – enzymes, defensive proteins, storage proteins, transport proteins, hormones, receptor proteins, contractile and motor proteins, structural • Functions: – catalysis, defense against foreign substances, store a.a., transport, homeostasis, cellular communication, movement, structural support • Enzymes: proteins that act as catalysts, speed up chemical reactions • can be reused, since they are not consumed in chemical reaction Enzymatic proteins Defensive proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Function: Protection against disease 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: 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. 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. Transport protein Ovalbumin Amino acids for embryo Cell membrane Hormonal proteins Receptor proteins Function: Coordination of an organism’s activities Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. High blood sugar Insulin secreted Normal blood sugar Receptor protein Signaling molecules Contractile and motor proteins Structural 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. 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. Actin Myosin Collagen Muscle tissue 100 m Connective tissue 60 m Polypeptides • Polypeptides: unbranched polymers built from our 20 amino acids • Protein: biologically functional molecule that consists of one or more polypeptides Amino Acid Monomers • Amino acids: organic molecules w/ carboxyl & amino groups – amino acids have different properties due to varying side chains, called R groups Side chain (R group) carbon Amino group Carboxyl group Nonpolar side chains; hydrophobic Side chain (R group) Glycine (Gly or G) Alanine (Ala or A) Methionine (Met or M) Isoleucine (Ile or I) Leucine (Leu or L) Valine (Val or V) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) Polar side chains; hydrophilic Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Electrically charged side chains; hydrophilic Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Basic (positively charged) Acidic (negatively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Amino Acid Polymers • a.a. linked by peptide bonds • Polypeptide: polymer of amino acids – range in length from a few to more than a thousand monomers • each has unique linear sequence of a. a., with carboxyl end (C-terminus) & amino end (Nterminus) Peptide bond New peptide bond forming Side chains Backbone Amino end (N-terminus) Peptide bond Carboxyl end (C-terminus) Protein Structure & Function • protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape (a) A ribbon model (b) A space-filling model • sequence of amino acids determines protein’s three-dimensional structure • protein’s structure determines its function Antibody protein Protein from flu virus Four Levels of Protein Structure • Primary structure: unique sequence of a. a. • Secondary structure: coils & folds in polypeptide chain • Tertiary structure: determined by interactions among side chains (R groups) • Quaternary structure: protein consists of multiple polypeptide chains Amino acids Primary structure: • sequence of a. a. in protein Amino end – determined by DNA Carboxyl end Tertiary structure Secondary structure Quaternary structure helix Hydrogen bond pleated sheet strand Hydrogen bond Transthyretin polypeptide Transthyretin protein Secondary structure: • H bonds w/in polypeptide backbone Hydrogen bond helix – helix: coil Hydrogen bond • Keratin: hair – pleated sheet: folded structure strand: shown as flat arrow pointing to carboxyl end • Silk, spider web pleated sheet What type of secondary structure forms spider webs? Tertiary structure: R group interactions • H bonds, ionic bonds, hydrophobic & Van der Waals interactions • disulfide bridges (strong covalent bonds) reinforce protein structure a b. c. d. Identify R group interactions Quaternary structure: • two or more polypeptide chains form one macromolecule – collagen: fibrous protein consisting of three polypeptides coiled like a rope – hemoglobin: globular protein consisting of four polypeptides: two alpha and two beta chains Heme Iron subunit subunit subunit subunit Hemoglobin Sickle-Cell Disease: Change in Primary Structure • change in primary structure can affect a protein’s structure & it’s ability to function • Sickle-cell disease: inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin Sickle-cell hemoglobin Normal hemoglobin Primary Structure 1 2 3 4 5 6 7 Secondary and Tertiary Structures Quaternary Structure Function Molecules do not associate with one another; each carries oxygen. Normal hemoglobin subunit Red Blood Cell Shape 10 m 1 2 3 4 5 6 7 Exposed hydrophobic region Sickle-cell hemoglobin subunit Molecules crystallize into a fiber; capacity to carry oxygen is reduced. 10 m Considering the chemical characteristics of the amino acids valine and glutamic acid, propose a possible explanation for the dramatic effect on the protein function that occurs when valine is substituted for glutamic acid. The R group on glutamic acid is acidic and hydrophilic, wheras the R group on valine is nonpolar and hydrophibic. Therefore, it is unlikely that valine can participate in the same intramolecular interactions that glutamic acid can. A change in these interactions causes a disruption of the molecular structure. What Determines Protein Structure? • primary structure, physical & chemical conditions – changes in pH, salt concentration, temperature • denaturation: bonds w/in protein destroyed – denatured protein is biologically inactive Normal protein Denatured protein Protein Folding in the Cell • Chaperonins: protein molecules that assist the proper folding of proteins • Diseases: Alzheimer’s, Parkinson’s, & mad cow disease associated with misfolded proteins Polypeptide Correctly folded protein Cap Hollow cylinder Chaperonin (fully assembled) Steps of Chaperonin Action: 1 An unfolded polypeptide enters the cylinder from one end. 2 The cap attaches, causing 3 The cap comes the cylinder to change off, and the shape in such a way that properly folded it creates a hydrophilic protein is environment for the released. folding of the polypeptide. Why does a denatured protein no longer function? The function of a protein is a consequence of its specific shape, which is lost when a protein becomes denatured. Where would you expect a polypeptide region that is high in the nonpolar amino acids valine, leucine, and isoleucine to be located in the folded polypeptide? These are all nonpolar amino acids, so you would expect this region to be located in the interior of the folded polypeptide, where it would not contact the aqueous environment inside the cell. Nucleic acids: store, transmit, & express hereditary information • a. a. sequence of polypeptide programmed by genes – units of inheritance – composed of DNA The Roles of Nucleic Acids • types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) • DNA provides directions for its own replication • DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis • Protein synthesis occurs on ribosomes DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm Ribosome 3 Synthesis of protein Polypeptide Amino acids Components of Nucleic Acids • polynucleotides: polymers of nucleic acids – made of monomers called nucleotides – Nucleotide: – nitrogenous base, a pentose sugar, and one or more phosphate groups – nucleoside: portion of nucleotide w/out phosphate group Nucleoside Phosphate group Nitrogenous base Sugar (pentose) Nitrogenous bases & Pentose sugars Nitrogenous bases • Pyrimidines (cytosine, thymine, and uracil) single six-membered ring • Purines (adenine and guanine) six-membered ring fused to fivemembered ring Pentose sugars: • DNA: deoxyribose • RNA: ribose 5 end 5C 3C Nucleotide Polymers Sugar-phosphate backbone • nucleotides joined by covalent bonds – Between OH group on 3 carbon of one nucleotide and the phosphate on 5 carbon of the next • backbone of sugarphosphate units 5C 3C 3 end – nitrogenous bases as appendages DNA and RNA • DNA – Nucleus, chromosomes – Double helix – Deoxyribose – Bases: adenine, guanine, cytosine, thymine – Base pairing: A-T, C-G – antiparallel: two backbones run in opposite 5→ 3 • RNA – Cytoplasm; mRNA, tRNA, rRNA – Single strand – Ribose – Bases: adenine, guanine, cytosine, uracil – Base pairing: A-U, C-G 5 3 Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3 5 (a) DNA Base pair joined by hydrogen bonding (b) Transfer RNA 1) One side of a DNA strand has this sequence of nitrogenous bases. Copy this strand, then determine it’s complementary strand. Label 5’ and 3’. ATGCATAAG 2) Use the new DNA strand to transcribe mRNA 5’ ATGCATAAG 3’ 3’ TACGTATTC 5’ mRNA AUGCAUAAG For Lab Test: • No Prelab needed, but read through and make a chart explaining what each test indicates and how to test for it : Biurets, iodine, benedicts • Data: Copy the following data table: Solution # Test 1 Buirets 2 Iodine 3 Benedict’s 4 Brown Paper Original color Final color Type of molecule • Answer Questions from results and conclusion with the following mods: Results: • Skip 3,6,9,10, and 12 2: Draw one amino acid and circle the carboxyl group and amino group 5. Explain the difference between sucrose vs. glucose 7. What is the polysaccharide stored called? 8. Draw diagram and answer 11. What the reactive groups? (don’t draw) Conclusion: 2. Skip Construct a table that organizes the following terms. Determine labels for the columns and rows. • • • • • • Phosphodiester linkages Peptide bonds Glycosidic linkages Ester linkages Polypeptides Triacylglycerols • • • • • • Polyneucleotides Polysaccharides Monosaccharides Nucleotides Amino acids Fatty acids Monomers/ subunits Polymer Type of linkage Carbohydrates Monosaccharides Polysaccharides Glycosidic linkages Lipids Fatty acids glycerol Triacylglycerols Ester linkages Proteins Amino acids Polypeptides Peptide bonds Nucleic acids Nucleotides Polyneucleotides Phosphodiester linkages