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Entrance Quiz: Chapters 4 + 5 1. What are the 4 major macromolecules? 2. A short polymer and a monomer are linked, what is the by-product and term for this process? 3. How many molecules of water are needed to completely hydrolyze a polymer that is ten monomers long? 4. Why are human sex hormones considered lipids? 5. Identify the macromolecule A B C D Entrance Quiz: Chapters 4 + 5 1. What are the 4 major macromolecules? LIPIDS, NUCLEIC ACIDS, PROTEIN, CARBOHYDRATES 2. A short polymer and a monomer are linked, what is the by-product and term for this process? WATER AND DEHYDRATION 3. How many molecules of water are needed to completely hydrolyze a polymer that is ten monomers long? 9 4. Why are human sex hormones considered lipids? THEY ARE HYDROPHOBIC AND NONPOLAR 5. Identify the macromolecule A PROTEIN B NUCLEIC ACID C LIPID D CARBO LIPIDS FUNCTION: Lipids help to store energy, protects organs, insulate the body, and form cell membranes. EXAMPLES: Lipids - include fats, phospholipids, cholesterol and steroids. FOOD SOURCE: Butter, cheese, meats, milk, nuts, oils. STRUCTURE: Monomer is a fatty acid and glycerol. Polymer is a triglyceride PROTEIN FUNCTION: Proteins are used for muscle movement, are part of the cell membrane and are enzymes. EXAMPLES: Amylase, Collagen FOOD SOURCES: Dairy, eggs, fish, meat, nuts, beans. STRUCTURE: Monomer is an amino acid; Polymer is protein in a polypeptide chain Its structure is: • There are only 20 amino acids but a million proteins • WHY? 1) Different lengths 2) Different combination Carbohydrates FUNCTION: Energy (for Mitochondria) EXAMPLES: Glucose, Starch, Cellulose, Chitin FOOD SOURCES: Sugar, breads, cereal, fruits, milk, pasta, vegetables, rice STRUCTURE: Glucose (monosaccharide) is the monomer. Polyssacharide is the polymer NUCLEIC ACIDS FUNCTION: Transfers genetic information from one generation to the next. EXAMPLES: DNA and RNA FOOD SOURCES: All foods from animals and plants have DNA STRUCTURE: Monomer is a nucleotide (P, S, and B) Its structure is: http://highered.mcgrawhill.com/sites/0072943696/studen t_view0/chapter2/animation__pro tein_denaturation.html Make a model to show the primary, secondary, tertiary, a quarternary structure of a protein Minimum 10 amino acids—pick from each group You must have the structure of the amino acids 2nd structure of a protein H-bonds R groups are NOT involved in H-bonds Tertiary • Interactions with the aqueous solvent, known as the hydrophobic effect results in residues with non-polar side-chains typically being buried in the interior of a protein. • Conversely, polar amino acid side-chains tend to on the surface of a protein where they are exposed to the aqueous milieu. • http://bcs.whfreeman.com/thelifewire/conte nt/chp03/0302002.html Copy this: “ If I am going to be absent on the day of a test, I will contact Ms. Morris.” TITLE page: Chemistry of Life Chemistry of Life Week 7-8 Overview • Living organisms and the world they live in are subject to the basic laws of physics and chemistry. • Biology is a multidisciplinary science, drawing on insights from other sciences. • Life can be organized into a hierarchy of structural levels. • At each successive level, additional emergent properties appear. 2.1 Matter consists of chemical elements in pure form and in combinations called compounds. • Organisms are composed of matter. – Matter is anything that takes up space and has mass. – Matter is made up of elements. 2.1 Matter consists of chemical elements in pure form and in combinations called compounds. • An element is a pure substance that cannot be broken down into other substances by chemical reactions. • There are 92 naturally occurring elements. • Each element has a unique symbol, usually the first one or two letters of the name. Some of the symbols are derived from Latin or German names. 2.1 Matter consists of chemical elements in pure form and in combinations called compounds. A compound is a pure substance consisting of two or more elements in a fixed ratio. • Table salt (sodium chloride or NaCl) is a compound with equal numbers of atoms of the elements chlorine and sodium. Reflect on • Blue green magnets • White-red magnets Essential Elements of Life • Essential elements – Include carbon, hydrogen, oxygen, and nitrogen – Make up 96% of living matter • A few other elements – Make up the remaining 4% of living matter Trace elements • Are required by an organism in only minute quantities – But the absence of trace element can have deadly effects Figure 2.3 (a) Nitrogen deficiency (b) Iodine deficiency Radioactive Isotopes • Spontaneously give off particles and energy – Alpha, beta, gamma radiation Biological Uses for Radioactive Isotopes APPLICATION Scientists use radioactive isotopes to label certain chemical substances, creating tracers that can be used to follow a metabolic process or locate the substance within an organism. In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA. TECHNIQUE Ingredients including Radioactive tracer (bright blue) Incubators 1 2 3 10°C 15°C 20°C 4 5 6 Human cells 1 2 Ingredients for making DNA are added to human cells. One ingredient is labeled with 3H, a radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3H. The cells are placed in test tubes, their DNA is isolated, and unused ingredients are removed. 25°C 30°C 35°C 7 8 9 40°C 45°C 50°C DNA (old and new) 1 2 3 4 5 6 7 8 9 3 A solution called scintillation fluid is added to the test tubes and they are placed in a scintillation counter. As the 3H in the newly made DNA decays, it emits radiation that excites chemicals in the scintillation fluid, causing them to give off light. Flashes of light are recorded by the scintillation counter. RESULTS The frequency of flashes, which is recorded as counts per minute, is proportional to Counts per minute (x 1,000) the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted against temperature, it is clear that temperature affects the rate of DNA synthesis—the RESULTS most DNA was made at 35°C. 30 20 Optimum temperature for DNA synthesis 10 Figure 2.5 0 10 20 30 40 Temperature (°C) 50 PET (positron-emission tomography) Cancerous throat tissue Figure 2.4 Tagging the Brain Covalent Bonds Covalent bonds can be • Single—sharing one pair of electrons C H • Double—sharing two pairs of electrons C C • Triple—sharing three pairs of electrons N N 2.3 The formation and function of molecules depend on chemical bonding between the atoms. Electronegativity: the attractive force that an atomic nucleus exerts on electrons Electronegativity depends on the number of positive charges (protons) and the distance between the nucleus and electrons. Weak Chemical Bonds Hydrogen bonds: attraction between the δ– end of one molecule and the δ+ hydrogen end of another molecule Hydrogen bonds form between H and O and/or H and N. Important with water DNA Proteins Van der Waals Interactions • Van der Waals interactions – Occur when transiently positive and negative regions of molecules attract each other Structure and Function run from large scale body systems through molecules and atoms. Structure and function are what Enzymes are all about Carbon Nitrogen Hydrogen Sulfur Oxygen Natural endorphin Morphine (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. Natural endorphin Figure 2.17 Brain cell Morphine Endorphin receptors (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Why do medics pump wounded soldiers with morphine on the battlefield? Concept 2.4: Chemical reactions make and break chemical bonds • Chemical reactions – Convert reactants to products + 2 H2 Reactants + O2 Reaction 2 H2O Product Life is the result of Chemical Reactions • Photosynthesis – Is an example of a chemical reaction Figure 2.18 Chemical Equilibrium • Chemical equilibrium – Is reached when the forward and reverse reaction rates are equal Take out Water book • Put notes and Hardy Weinberg lab in the center of the table • Make sure there is a post it at the beginning of the lab • If you want to go to a college talk and/or assembly, you MUST have an A or B and no Mi Water: The Molecule That Supports All of Life • Water is the biological medium here on Earth – All living organisms require water more than any other substance – Three-quarters of the Earth’s surface is submerged in water – The abundance of water is the main reason the Earth is habitable 3.1: The polarity of water molecules results in hydrogen bonding • The polarity of water molecules – Allows them to form hydrogen bonds with each other – Contributes to the various properties water exhibits – Hydrogen bonds + H + – – + H + – 3.2: Four emergent properties of water contribute to Earth’s fitness for life 1. Cohesion 2. Moderation of Temperature 3. Insulation of bodies of water by floating ice 4. The solvent of life (universal solvent) 1. Cohesion • Cohesion – the hydrogen bonds holding a substance together. (water – water) • Adhesion – the hydrogen bonds holding one substance to another. (water – glass) • Capillary Action – water transport in plants. Uses Cohesion and Adhesion – Transpiration • Surface tension – measure of how difficult it is to stretch or break the surface of a liquid. – Water has a greater surface tensions than most liquids 2. Moderation of Temperature • Kinetic Energy – energy of motion • Thermal Energy (heat) – total energy within a substance – Calorie – amount of heat energy to heat 1g water by 1°C – Kcal – 1000c • Temperature – average kinetic energy per molecule (Celsius Scale) 2. Moderation of Temperature • Specific heat – the amount of heat absorbed or loss for 1g of a substance to change its temperature by 1°C – Water has high specific heat capacity compared to other substances – 1 cal/g/°C 2. Moderation of Temperature • Evaporation • Heat of vaporization – the amount of heat 1g of a liquid must absorb to be converted to a gas • Evaporative cooling – as a liquid evaporates the surface of the remaining liquid cools – This occurs because the “hottest” molecules leave 3. Insulation of bodies of water by floating ice Hydrogen bond Ice Liquid water Hydrogen bonds are stable Hydrogen bonds constantly break and re-form 3. Insulation of bodies of water by floating ice 4. Solvent of Life • Water is claimed to be the universal solvent. – Solution – homogeneous mixture of two or more substances in the same phase – Solute – substance which is dissolved (in case of liquids, substance with the least amount – Solvent – substance which is dissolving another – Aqueous solution – solution involving water – Hydration shell – pocket formed by water molecules in order to dissolve a substance 4. Solvent of life • Hydrophilic – attracted to water – Can be dissolved – Unless molecule is too large – Colloid – stable suspension of fine molecules in a liquid. (blood, milk) • Hydrophobic – repel water – Non-ionic, nonpolar, can’t form H-bonds 4. Solvent of Life • Solute concentrations in aqueous solutions – Concentration = g solute / ml solvent – Molarity – moles solute / Liter solution Acidic and Basic conditions affect living organisms • Water can dissociate – Into hydronium ions and hydroxide ions • H+ (hydrogen ion) is used to represent the hydronium ion • Changes in the concentration of these ions – Can have a great affect on living organisms • Only 1 in 554 mil pure water molecules will diss. – + H H H H Figure on p. 53 of water dissociating H H H Hydronium ion (H3O+) + H Hydroxide ion (OH–) Acids and Bases • Acids [H+]>[OH-] • Bases [H+]<[OH-] • When acids dissolve in water, they release hydrogen ions—H+ (protons). – H+ ions can attach to other molecules and change their properties. • Bases reduce H+ concentration by accepting H+ ions and/or release OH- ions Strong Acid HCl H Cl HCl is a strong acid—the dissolution is complete. Weak Acid Organic acids have a carboxyl group: COOH COOH H Weak acids: not all the acid molecules dissociate into ions. Strong Base NaOH is a strong base. NaOH Na OH The OH– absorbs H+ to form water. Weak Bases Weak bases: • Bicarbonate ion HCO3 H H 2CO3 • Ammonia NH3 H NH4 • Compounds with amino groups NH2 H NH3 Acids, Bases, pH pH = negative log of the molar concentration of H+ ions. H+ concentration of pure water is 10–7 M, its pH = 7. Lower pH numbers mean higher H+ concentration, or greater acidity. Acids, Bases, buffers • Living organisms maintain constant internal conditions, including pH. – Buffers help maintain constant pH by accepting or donating H+ ions. – They are kept in excess in systems • A buffer is a weak acid and its corresponding base. HCO3 H H 2CO3 Figure 2.17 Buffers Minimize Changes in pH 2.4 What Properties of Water Make It So Important in Biology? Buffers illustrate the law of mass action: addition of reactant on one side of a reversible equation drives the system in the direction that uses up that compound. 2.4 What Properties of Water Make It So Important in Biology? Life’s chemistry began in water. Water and other chemicals may have come to Earth on comets. Water was an essential condition for life to evolve. FRQ • The unique properties (characteristics) of water make life possible on Earth. Select three properties of water and: a) for each property, identify and define the property and explain it in terms of the physical/chemical nature of water. b) for each property, describe one example of how the property affects the functioning of living organisms. Build a carbohydrate • Carbon (black)=4 bonds • Hydrogen (white)=1 bond • Oxygen (red)= 2bonds Pick up 2 FRQ • Look at the FRQs from 2 sample students • Write advice to each student • Rewrite your FRQs—why did you lose points? Carbon • 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 can 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. 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. Glucose=C6H12O6 Carbon=black, Hydrogen=White, Oxygen=Red • 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 CH2O 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 Demonstrate • Dehydration • All the names for a polymer of glucose + glucose 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 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 • 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