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Transcript
Chapter 5 The structure and function of large biological molecus AP minknow •The role of dehydration synthesis in the formation of organic compounds and hydrolysis in the digestion of organic compounds. •How to recognize the four biologically important organic compounds (carbohydrates, lipids, proteins, and nucleic acids) by their structural formulas. •The cellular functions of all four organic compounds. •The four structural levels that protein can go through to reach their final shape (conformation) and the denaturing impact that heat and pH can have on protein structure. Quick on Carbon Chapter 4: Carbon and the molecular diversity of life. • 4.2 – Carbon atoms can form diverse molecules by bonding to four other atoms – Carbon has amazing ability to form molecules because: • • • • • It has 4 valence electrons It can form up to 4 covalent bonds These can be single, double, or triple cov. Bonds It can form large molecules. These molecules and be chains, ring-shaped, or branched – Isomers – are molecules that have the same molecular formula, but different in their arrangement of these atoms. • This can result in different molecules with very different activities. Isomers Quick on Carbon 4.3 Characteristic chemical groups help control how biological molecules function FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O OH (may be written HO C C OH ) STRUCTURE In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) Figure 4.10 O The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is doublebonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (— COOH). Some important functional groups of organic compounds NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) EXAMPLE H H H C C H H Ketones if the carbonyl group is Carboxylic acids, or organic within a carbon skeleton acids Aldehydes if the carbonyl group is at the end of the carbon skeleton H OH H C H C H H Ethanol, the alcohol present in alcoholic beverages H O C H C OH H H Acetone, the simplest ketone H Figure 4.10 C O H H C C H H O C Propanal, an aldehyde H Acetic acid, which gives vinegar its sour tatste Quick on Carbon 4.3 Characteristic chemical groups help control how biological molecules function AMINO SULFHYDRYL H N H Figure 4.10 O SH (may be written HS The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. PHOSPHATE ) O P OH OH The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO32–) is an ionized form of a phosphoric acid group (— OPO3H2; note the two hydrogens). Some important functional groups of organic compounds H O C HO C H H N H H Glycine Figure 4.10 H H C C H H OH OH H SH H C C C H H H O O P O O Ethanethiol Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Glycerol phosphate 5.1 Macromolecules are polymers built from monomers. • Monomer – smaller repeating units of a polymer • Polymer – large molecule consisting of many similar or identical building blocks • Polymers with molecular weights >1000 • Polymerization – process of joining monomers to form polymers The synthesis and breakdown of polymers • Dehydration synthesis (dehydration reaction) – synthesis reaction forming a byproduct of water • Hydrolysis – degradation of a molecule using water to break down bonds – These processes are often aided by enzymes Dehydration Synthesis The Diversity of Polymers • Each cell has thousands of different kinds of macromolecules. – The inherent different between human siblings reflect the variations in polymers: • Especially DNA and proteins • There are four major classes of biological macromolecules – – – – Carbohydrates Lipids Proteins Nucleic Acids 5.2 Carbohydrates serve as fuel and building material • Carbohydrates: molecules in which carbon is flanked by hydrogen and hydroxyl groups. H—C—OH • Main Functions – Energy source – Carbon skeletons for many other molecules Carbohydrates • Monosaccharides: simple sugars • Disaccharides: two simple sugars linked by covalent bonds • Oligosaccharides: three to 20 monosaccharides • Polysaccharides: hundreds or thousands of monosaccharides— starch, glycogen, cellulose Carbohydrates Cells use glucose (monosacchar ide) as an energy source. Exists as a straight chain or ring form. Ring is more common—it is more stable. Carbohydrates Carbohydrates • Monosaccharides have different numbers of carbons. – Trioses: three carbons– structural isomers glyceraldehyde – Hexoses: six carbons—structural isomers – Pentoses: five carbons Carbohydrates • Monosaccharides bind together in condensation reactions to form glycosidic linkages. • Glycosidic linkages can be α or β. Beta – glycosidic linkage Alpha – glycosidic linkage Carbohydrates • Oligosaccharides may include other functional groups. • Often covalently bonded to proteins and lipids on cell surfaces and act as recognition signals. • ABO blood groups Carbohydrates • Starch: storage of glucose in plants – 1-4 glycosydic linkages between alpha glucose • Cellulose: very stable, good for structural components (cell walls of plants – 1-4 glycosydic linkages between beta glucose • Glycogen: storage of glucose in animals – 1-4 glycosydic linkages between alpha glucose • with branching Chitin • Chitin, another important structural polysaccharide – Is found in the exoskeleton of arthropods CH O – Can be used as surgical thread H 2 O OH H OH H OH H H H NH C O CH3 (a) The structure of the (b) Chitin forms the exoskeleton of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging Figure 5.10 A–C in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. 5.3 Lipids are a diverse group of hydrophobic molecules Lipids are nonpolar hydrocarbons: • • • • Fats and oils—energy storage Phospholipids—cell membranes Steroids Carotenoids Fats serve as insulation in animals, lipid nerve coatings act as electrical insulation, oils and waxes repel water, prevent drying. Lipids Fats and oils are triglycerides— simple lipids— made of three fatty acids and 1 glycerol. Glycerol: 3 —OH groups—an alcohol Fatty acid: nonpolar hydrocarbon with a polar carboxyl group—carboxyl bonds with hydroxyls of glycerol in an ester linkage. Lipids • Saturated fatty acids: no double bonds between carbons—it is saturated with hydrogen atoms. • Unsaturated fatty acids: some double bonds in carbon chain. – monounsaturated: one double bond – polyunsaturated: more than one Lipids Animal fats tend to be saturated—packed together tightly—solid at room temperature. Plant oils tend to be unsaturated—the “kinks” prevent packing— liquid at room temperature. Lipids Phospholipids: fatty acids bound to glycerol, a phosphate group replaces one fatty acid. Phosphate group is hydrophilic—the “head” “Tails” are fatty acid chains— hydrophobic Lipid (phospholipid bilayer) Lipid (Steroids) • Steroids – Are lipids characterized by a carbon skeleton consisting of four fused rings – Many hormones, including vertebrate sex hormones, are steroids produced from cholesterol – Steroids play a role in regulating cell activities Lipids (carotenoids) Carotenoids: light-absorbing pigments 5.4 Proteins have many structures, resulting in a wide range of functions Functions of proteins: • Structural support • Protection • Transport • Catalysis • Defense • Regulation • Movement Proteins • Proteins are made from 20 different amino acids (monomeric units) • Polypeptide chain: single, unbranched chain of amino acids – The chains are folded into specific three dimensional shapes. – Proteins can consist of more than one type of polypeptide chain. Protein (polypeptide) The composition of a protein: relative amounts of each amino acid present The sequence of amino acids in the chain determines the protein structure and function. Proteins • Amino acids have carboxyl and amino groups—they function as both acid and base. Functional Group – The α carbon atom is asymmetrical. – Amino acids exist in two isomeric forms: • D-amino acids (dextro, “right”) • L-amino acids (levo, “left”)— this form is found in organisms Proteins (amino acids are grouped by characteristics) CH3 CH3 H H3N+ C CH3 O H3N+ C O– H Glycine (Gly) C H H3N+ C O– CH CH3 CH3 O C H H3N+ C CH2 CH2 O C O– Valine (Val) Alanine (Ala) CH3 CH3 H O H3C H3N+ C C O C O– O– Leucine (Leu) CH H Isoleucine (Ile) Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ C H H3N+ C O– Methionine (Met) Figure 5.17 CH2 O C H CH2 O H3 N+ C C O– Phenylalanine (Phe) H O H2C CH2 H2N C O C O– H C O– Tryptophan (Trp) Proline (Pro) Proteins (amino acids are grouped by characteristics) OH OH Polar CH2 H3N+ C CH O H3N+ C O– H C CH2 O H3N+ C O– H C CH2 O C H Serine (Ser) Threonine (Thr) O– H3N+ C O H3N+ C O– H Electrically charged C CH2 H3N+ C O H H3N+ NH3+ O CH2 C H3N+ – O C C H O C O– H C CH2 CH2 CH2 CH2 CH2 C O CH2 C O– H3N+ C H Glutamic acid (Glu) NH+ NH2 CH2 H Aspartic acid (Asp) O C CH2 C O– CH2 Basic O– O CH2 Asparagine Glutamine (Gln) (Asn) Tyrosine (Tyr) Cysteine (Cys) Acidic –O C NH2 O C SH CH3 OH NH2 O C Lysine (Lys) H3N+ CH2 O O– NH2+ CH2 H3N+ C H NH CH2 O C C O– H O C O– Arginine (Arg) Histidine (His) Proteins • Amino acids bond together covalently by peptide bonds to form the polypeptide chain. – Dehydration synthesis Proteins A polypeptide chain is like a sentence: • The “capital letter” is the amino group of the first amino acid— the N terminus. • The “period” is the carboxyl group of the last amino acid—the C terminus. Proteins The primary structure of a protein is the sequence of amino acids. The sequence determines secondary and tertiary structure—how the protein is folded. The number of different proteins that can be made from 20 amino acids is enormous! • Protein structure –Primary –Secondary –Tertiary –Quartinary Proteins (primary structure) Proteins (secondary structure) Secondary structure: • α helix—right-handed coil resulting from hydrogen bonding; common in fibrous structural proteins • β pleated sheet—two or more polypeptide chains are aligned Proteins (tertiary structure) Tertiary structure: Bending and folding results in a macromolecule with specific three-dimensional shape. The outer surfaces present functional groups that can interact with other molecules. Proteins (tertiary structure) Tertiary structure is determined by interactions of R-groups: • Disulfide bonds • Aggregation of hydrophobic side chains • van der Waals forces • Ionic bonds • Hydrogen bonds • Proteins (Quartinary structure) Quaternary structure results from the interaction of subunits by: – hydrophobic interactions – van der Waals forces – ionic bonds – hydrogen bonds. Proteins (Sickle-cell Disease) – Results from a single amino acid substitution in the protein hemoglobin Hemoglobin structure and sickle-cell disease Primary structure Normal hemoglobin Val His Leu Thr 1 2 3 4 5 6 7 Secondary and tertiary structures Red blood cell shape Figure 5.21 Val His Leu Thr structure 1 2 3 4 Secondary subunit and tertiary structures Quaternary Hemoglobin A structure Function Sickle-cell hemoglobin Pro GlulGlu . . . Primary Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen Quaternary structure ... Val 5 6 7 Pro subunit Function 10 m 10 m Red blood cell shape Exposed hydrophobic region Glu 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. EnzymeSubstrate Complex Proteins (Denaturing) • Conditions that affect secondary and tertiary structure: • High temperature • pH changes • High concentrations of polar molecules • Denaturation: loss of 3dimensional structure and thus function of the protein Proteins (folding) • Proteins can sometimes fold incorrectly and bind to the wrong ligands. • Chaperonins are proteins that help prevent this. Polypeptide Cap Correctly folded protein Hollow cylinder Chaperonin (fully assembled) Figure 5.23 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 shape in off, and the properly such a way that it creates a folded protein is hydrophilic environment for the released. folding of the polypeptide. 5.5 Nucleic acids store and transmit hereditary information Nucleic acids: DNA— (deoxyribonucleic acid) and RNA— (ribonucleic acid) Polymers (polynucleotides) — made of the monomeric units are nucleotides. Nucleotides consist of a pentose sugar, a phosphate group, and a nitrogen-containing base. 5.5 Nucleic acids store and transmit hereditary information DNA—deoxyribose RNA—ribose 5.5 Nucleic acids store and transmit hereditary information The “backbone” of DNA and RNA consists of the sugars and phosphate groups, bonded by phosphodiester linkages. The phosphate groups link carbon 3′ in one sugar to carbon 5′ in another sugar. Antiparallel The two strands of DNA run in opposite directions. 5.5 Nucleic acids store and transmit hereditary information DNA bases: adenine (A), cytosine (C), guanine (G), and thymine (T) Complementary base pairing: A—T C—G Purines pair with pyrimidines by hydrogen bonding. • A particular small polypeptide is nine amino acids long. Using three different enzymes to hydrolyze the polypeptide at various sites, we obtain the following five fragments (N denotes the amino end of the chain): Ala-Leu-Asp-Tyr-Val-Leu Tyr-Val-Leu N-Gly-Pro-Leu Asp-Tyr-Val-Leu N-Gly-Pro-Leu-Ala-Leu Determine the primary structure of this polypeptide. – – – – N-Gly-Pro-Leu-Ala-Leu-Asp-Tyr-Val-Leu Asp-Tyr-Val-Leu-Gly-Pro-Leu-Ala-Leu N-Gly-Pro-Leu-Ala-Leu-Ala-Leu-Asp-Tyr-Val-Leu N-Gly-Pro-Leu-Asp-Tyr-Val-Leu-Tyr-Val-Leu • (a) You are studying a cellular enzyme involved in breaking down fatty acids for energy. Looking at the R groups of the amino acids in the following figures, what amino acids would you predict to occur in the parts of the enzyme that interact with the fatty acids? * – – – – – non-polar polar electrically charged polar and electrically charged all of these The 20 Amino Acids of Proteins The 20 Amino Acids of Proteins (cont.) • (b) You are studying a cellular enzyme involved in breaking down fatty acids for energy. Where would you predict to find the amino acids in the parts of the enzyme that interact with the fatty acids? – On the exterior surface of the enzyme – Sequestered in a pocket in the interior of the enzyme – Randomly dispersed throughout the enzyme • The R group or side chain of the amino acid serine is –CH2 –OH. The R group or side chain of the amino acid alanine is –CH3. Where would you expect to find these amino acids in globular protein in aqueous solution? – Serine would be in the interior, and alanine would be on the exterior of the globular protein. – Alanine would be in the interior, and serine would be on the exterior of the globular protein. – Both serine and alanine would be in the interior of the globular protein. – Both serine and alanine would be on the exterior of the globular protein. – Both serine and alanine would be in the interior and on the exterior of the globular protein. • (a) The sequence of amino acids of the enzyme lysozyme is known. Following is a list of amino acids and the number of each in the lysozyme molecule. Based on this list and the structures of the amino acids how many S-S bonds are possible in lysozyme? – – – – – 0 2 4 6 8 Amino Acids in the Lysozyme Type Number in Type Number in Molecule Lysozyme Lysozyme Alanine Arginine Asparagine Aspartic acid 12 11 13 8 8 2 Leucine Lysine Methionine Phenylalanin e Proline Serine Cysteine Glutamic acid Glutamine Glycine Histidine 8 6 2 3 2 10 3 12 1 Threonine Tryptophan Tyrosine 7 6 3 The 20 Amino Acids of Proteins The 20 Amino Acids of Proteins (cont.) • (b) The sequence of amino acids of the enzyme lysozyme is known. Following is a list of amino acids and the number of each in the lysozyme molecule. Based on this list and the structures of the amino acids is the net charge on lysozyme positive or negative? – positive – negative Amino Acids in the Lysozyme Type Number in Type Number in Molecule Lysozyme Lysozyme Alanine Arginine Asparagine Aspartic acid 12 11 13 8 8 2 Leucine Lysine Methionine Phenylalanin e Proline Serine Cysteine Glutamic acid Glutamine Glycine Histidine 8 6 2 3 2 10 3 12 1 Threonine Tryptophan Tyrosine 7 6 3 The 20 Amino Acids of Proteins The 20 Amino Acids of Proteins (cont.) • Polymers of glucose units are used as temporary food storage in both plant and animal cells. Glucose units are connected to one another by 1, 4-linkages to make a linear polymer and by 1, 6-linkages to make branch points. • (cont.) Polysaccharides of glucose units vary in size. The three most commonly Type of Cell Type Polymer Average encountered are: Starch Size Amylopectin Plant Number of 1,4-Bonds Between Branches 100,000,000 24 to 30 Amylos Glycogen 500,000 3,000,000 Plant Animal Linear 8 to 12 • (cont.) When each polymer bond is made, a water molecule is released and becomes part of the cell water. How many water molecules were released during formation of each of the Glycogen? – – – – – 1,000,000 2,000,000 2,666,666 3,000,000 3,300,000