Lecture 2. The Chemistry of Life PDF

The Chemistry of Life Bui Hong Thuy, Ph.D. School of Biotechnology, International University Email: [email protected] 1  OUTLINES 1. The Chemical Context of Life 2. Water and the Fitness of the Environment 3. C...

The Chemistry of Life Bui Hong Thuy, Ph.D. School of Biotechnology, International University Email: [email protected] 1  OUTLINES 1. The Chemical Context of Life 2. Water and the Fitness of the Environment 3. Carbon and the Molecular Diversity of Life 4. The Structure and Function of Large Biological Molecules 2  OUTLINE 1. The Chemical Context of Life 1.1. Matter consists of chemical elements in pure form and in combinations called compounds 1.2. An element’s properties depend on the structure of its atoms 1.3. The formation and function of molecules depend on chemical bonding between atoms 1.4. Chemical reactions make and break chemical bonds 3 1.1. Matter consists of chemical elements in pure form and in combinations called compounds Elements and Compounds Organisms are composed of matter  Matter : anything that takes up space and has mass  Element: a substance that cannot be broken down to other substances by chemical reactions  Compound: a substance consisting of two or more elements in a fixed ratio. 4  A compound has characteristics different from those of its elements. Ex: NaCl = Na + Cl: Na is a soft, silver-white, highly reactive metal , Cl is a type of gas, and NaCl is salt Sodium Chlorine Sodium chloride The metal sodium combines with the poisonous gas chlorine, forming the edible compound sodium chloride, or table salt 5  Essential Elements of Life  About 25 of the 92 elements are essential to life  Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter (C, H, O, N)  Most of the remaining 4% consists of calcium, phosphorus, potassium,sulfur… (Ca, P, K, S…) Trace elements are those required by an organism in minute quantities (making up less than 0.01% of human body weight). Minerals such as copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn)... 6 If there is a deficiency of an essential element: disease results *Iodine deficiency (Goiter). *Nitrogen deficiency in plants (yellow leaves, Flowering, fruitings, protein and starch contents are reduced). 7 1.2. An element’s properties depend on the structure of its atoms Each element consists of unique atoms An atom is the smallest unit of matter that still retains the properties of an element Atoms are composed of even smaller parts called subatomic particles – Neutrons (no electrical charge) – Protons (positive charge) – Electrons (negative charge) 8  Subatomic Particles  Neutrons and protons form the atomic nucleus  Electrons form a cloud around the nucleus  Neutron mass and proton mass are almost identical and are measured in daltons Cloud of negative charge (2 electrons) Electrons Nucleus 9  Atomic Number and Atomic Mass Atomic number: The number of protons in the nucleus, unique to each element and is used to arrange atoms on the Periodic table. Atomic mass: The sum of protons plus neutrons in the nucleus. Is the average of the mass of all isotopes of that particular element 10  Isotopes  Different forms of the same element  Have the same number of protons, but different number of neutrons  Applications of radioactive isotopes: date fossils, medical tracers (PET scan) 11  Compounds including Incubators RADIOACTIVE radioactive tracer (bright blue) 1 2 3 TRACERS 10°C 15°C 20°C Human 4 5 6 1 Human cells are cells 25°C 30°C 35°C Incubated with 7 8 9 compounds used to 40°C 45°C 50°C make DNA. One compound is labeled with 3H. The cells are placed in test DNA (old and new) 2 tubes; their DNA is isolated; and unused labeled compounds are removed. Cancerous throat tissue 3 The test tubes are placed in a scintillation counter A PET scan, a medical use for RESULTS Optimum temperature for DNA synthesis radioactive isotopes. PET, an acronym for positron-emission Counts per 30 ( 1,000) minute 20 tomography, detects locations 10 of intense chemical activity in 0 10 20 30 40 50 Temperature (ºC) the body. 12  The Energy Levels of Electrons  Energy is the capacity to cause change  Potential energy is the energy that matter has because of its location or structure  An electron’s state of potential energy is called its energy level, or electron shell Third shell (highest energy level) Electrons further from the nucleus have more Second shell (higher Energy energy energy level) absorbed First shell (lowest energy level) Energy lost Atomic nucleus Energy levels of an atom's electrons 13 Electron Distribution and Chemical Properties  The chemical behavior of an atom is determined by its distribution  The periodic table shows the electron distribution for each element Hydrogen 2 Atomic number Helium 1H He 2He Atomic mass 4.00 Element symbol First shell Electron- distribution diagram Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon 3Li 4Be 5B 6C 7N 8O 9F 10Ne Second shell Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon 11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar Third shell 14  Electron Orbitals  Each electron shell consists of a specific number of orbitals  Valence electrons In the outermost, or valence shell Determine the chemical behavior of an atom (a) Electron-distribution diagram Neon, with two filled shells (10 electrons) (b)Separate electron orbitals First shell Second shell -The three-dimensional shapes represent electron orbitals. -Each orbital holds a maximum of 2 electrons. x y z 1s orbital 2s orbital Three 2p orbitals (c)Superimposed electron orbitals The complete picture of the electron orbitals of neon 1s, 2s, and 2p orbitals 15 1.3. The formation and function of molecules depend on chemical bonding between atoms  These interactions usually result in atoms staying close together, held by attractions called chemical bonds Strong chemical bonds – Covalent bonds – Ionic bonds Weak chemical bonds – Hydrogen bonds – Van der Waals forces 16  Name Electron- Space- Structural Covalent bonding (Molecular Formula) distribution Diagram Formula filling Model in four molecules H2. Two hydrogen (a) Hydrogen atoms can form (H2) O2. Two oxygen atoms share two pairs of electrons to form (b) Oxygen a double bond. (O2) H2O. Two hydrogen atoms and one oxygen atom are joined by (c) Water covalent bonds to produce a (H2O) molecule of water. CH4. Four hydrogen atoms can satisfy the valence of one (d) Methane carbon atom, forming methane. (CH4) 17  Electronegativity is an atom’s attraction for the electrons in a covalent bond. The more electronegative an atom, the more strongly it pulls shared electrons toward itself In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally 18 In a polar covalent bond Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen. – This results in a partial negative charge on the O oxygen and a partial positive H H charge on + + the hydrogens. H2O 19  Ionic Bonds Atoms sometimes strip electrons away from their bonding partners Electron transfer between two atoms creates ions  Ions Are atoms with more or fewer electrons than usual Are charged atoms 20  Covalent Bonds  Sharing of a pair of valence electrons by two atoms Hydrogen atoms (2 H) 1 In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus. 2 When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus. 3 The two electrons become shared in a covalent bond, forming an H2 molecule. Hydrogen molecule (H2)  A single bond: Is the sharing of one pair of valence electrons  A double bond: Is the sharing of two pairs of valence electrons 21 An ionic bond is an attraction between an anion and a cation An anion is a negatively charged A cation is a positively charged The lone valence electron of a Each resulting ion has a sodium atom is transferred to completed valence shell. An join the 7 valence electrons of ionic bond can form between a chlorine atom. the oppositely charged ions. Na Cl Na Cl Na Cl Na+ Cl– Sodium atom Chlorine atom Sodium ion Chloride ion (a cation) (an anion) Sodium chloride (NaCl)22  Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride, are often found in nature as crystals Na+ Cl– 23  Weak Chemical Bonds Several types of weak chemical bonds are important in living systems  Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other 24  Hydrogen Bonds A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is + also attracted to another  Water electronegative atom (H2O) A hydrogen bond results from the attraction between the partial + positive charge on the  hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia. Ammonia (NH3) + + + 25  Van der Waals Interactions  Van der Waals interactions are attractions between molecules that are close together as a result of these charges Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface 26  Molecular Shape and Function A molecule’s shape is usually very important to its function A molecule’s shape is determined by the positions of its atoms’ valence orbitals  A molecule’s shape determines how biological molecules recognize and interact with each other with a specificity 27  Molecules with similar shapes can have similar biological effects Carbon Nitrogen Hydrogen Sulfur Natural endorphin Oxygen 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 Morphine (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Brain cell Endorphin receptors 28  1.4. Chemical reactions make and break chemical bonds Making and breaking of chemical bonds 2 H2 O2 2 H 2O Reactants Reaction Products The starting molecules The final molecules  Chemical reactions: Convert reactants to products 29  Chemical reactions  All chemical reactions are reversible: products of the forward reaction become reactants for the reverse reaction For example, hydrogen and nitrogen molecules can combine to form ammonia, but ammonia can also decompose to regenerate hydrogen and nitrogen: 3H2 + N2 2 NH3  Chemical equilibrium is reached when the forward and reverse reaction rates are equal 30  Chemical reactions  Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO2 + 6 H20 → C6H12O6 + 6 O2 31  OUTLINE 2. Water and the Fitness of the Environment 2.1.The polarity of water molecules results in hydrogen bonding 2.2. Four emergent properties of water contribute to Earth’s fitness for life 2.3. Acidic and basic conditions affect living organisms 32 The Molecule That Supports All of Life All living organisms require water more than any other substance Most cells are surrounded by water, and cells themselves are about 70–95% water Water is the biological medium on Earth  The abundance of water is the main reason the Earth is habitable 33 2.1.The polarity of water molecules results in hydrogen bonding  Polarity allows water molecules to form hydrogen bonds with each other _ + – Hydrogen + bond H – O + + – H + A polar molecule: + – The opposite ends have opposite charges 34 2.2. Four emergent properties of water contribute to Earth’s fitness for life  Four of water’s properties that facilitate an environment for life are: – Cohesive behavior – Ability to moderate temperature – Expansion upon freezing – Versatility as a solvent 35  Cohesion Cohesion: hydrogen bonds hold water molecules together, and helps the transport of water against gravity in plants. Adhesion is an attraction between different substances, for example, between water and plant cell walls. 36  Water transport in plants Adhesion of the water to cell walls by hydrogen bonds helps resist the downward pull of gravity Water-conducting cells Cohesion due to hydrogen Direction bonds between water of water 150 µm molecules helps hold movement together the column of water within the cells 37  Surface tension is a measure of how hard it is to break the surface of a liquid Surface tension is related to cohesion 38  Moderation of Temperature Water can absorb or release a large amount of heat with only a slight change in its own temperature Heat and Temperature Kinetic energy is the energy of motion Heat is a measure of the total amount of kinetic energy due to molecular motion Temperature measures the intensity of heat due to the average kinetic energy of molecules A calorie (cal) is the amount of heat required to raise the temperature of 1 g of water by 1°C 39  Water’s High Specific Heat The specific heat: the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC  Water has a high specific heat which allows it to minimize temperature fluctuations to within limits that permit life Heat is absorbed when hydrogen bonds break Heat is released when hydrogen bonds form 40  Evaporative Cooling  Evaporation is transformation of a substance from liquid to gas  Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas  As a liquid evaporates, its remaining surface cools, a process called evaporative cooling  Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water 41 Insulation of Bodies of Water by Floating Ice Ice floats in liquid water because the hydrogen bonds are more “ordered” (crystal lattice) than in liquid water => ice is less dense than liquid water Life can exist under the frozen surfaces of lakes and polar seas Hydrogen Ice bond Liquid water Hydrogen bonds Hydrogen bonds are stable break and re-form 42  The Solvent of Life A solution is a liquid that is a homogeneous mixture of substances A solvent is the dissolving agent of a solution The solute is the substance that is dissolved An aqueous solution is one in which water is the solvent 43  Water is a versatile solvent due to its polarity Negative oxygen regions of polar water molecules are – attracted to sodium Na+ –+ – + cations (Na+) + – – Positive hydrogen + – Na+ + regions of water molecules cling to Cl– – + Cl– chloride anions (CI-) + – – + – – A sphere of waler molecules, called a hydration shell, surrounds each solute ion. 44  Water can dissolve compounds made of nonionic polar molecules, such as sugars  Water can also interact with polar molecules such as proteins if they have ionic and polar regions A water-soluble protein This oxygen is attracted to a slight positive charge on the lysozyme molecule This hydrogen is attracted to a slight negative charge (a) Lysozyme molecule on the lysozyme molecule in a nonaqueous (b) Lysozyme molecule environment (purple) in an aqueous (c) Ionic and polar regions environment on the protein’s surface attract water molecules 45 Hydrophilic and Hydrophobic Substances  A hydrophilic substance -has an affinity for water -Polar or ionic- Ex: Carbohydrates, salts  A hydrophobic substance: -does not have an affinity for water -Nonpolar-Ex: lipids 46 Solute Concentration in Aqueous Solutions Most biochemical reactions occur in water Chemical reactions depend on collisions of molecules and therefore on the concentration of solutes in an aqueous solution Molecular mass is the sum of all masses of all atoms in a molecule Numbers of molecules are usually measured in moles Molarity (M) is the number of moles of solute per liter of solution 47 2.3. Acidic and basic conditions affect living organisms – The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H+) – The molecule with the extra proton is now a hydronium ion (H3O+), though it is often represented as H+ – The molecule that lost the proton is now a hydroxide ion (OH–) H H O H O O H O H H H H 2H2O Hydronium Hydroxide ion (H3O+) ion (OH–) 48 The pH Scale Biologists use something called the pH scale to describe whether a solution is acidic or basic (the opposite of acidic) P- power H- hydrogen Thus pH as a negative logarithm of the molar concentration of hydrogen ions. pH=-log[H+] For a neutral aqueous solution : [H+] is 10–7 = –(–7) = 7 49  pH Scale 0 1 The pH scale and pH Battery acid Gastric juice, values of some 2 lemon juice H+ H+ aqueous solutions H+ 3 Vinegar, beer, – H+ OH OH– H+ H+ wine, cola H+ H+ Acidic solution 4 Tomato juice Acidic solutions have 5 Black coffee pH values less than 7 Rainwater 6 Urine Basic solutions have OH– OH– H+ OH – Neutral Saliva 7 Pure water pH values greater H+ [H+] = [OH–] OH H+ – OH H+ – H+ Human blood, tears than 7 8 Seawater Neutral solution Most biological fluids 9 have pH values in the 10 range of 6 to 8 Milk of magnesia OH– OH– 11 OH– H+ OH– OH– OH – Household ammonia H+ OH– 12 Basic solution Household 13 bleach Oven cleaner 50 14  Buffers The internal pH of most living cells must remain close to pH 7 Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution Most buffers consist of an acid‐base pair that reversibly combines with H+ 51 Threats to Water Quality on Earth Acid precipitation  Refers to rain, snow, or fog with a pH lower than 5.6  Is caused mainly by the mixing of different pollutants with water in the air 0 More 1 acidic 2 3 Acid 4 rain 5 Normal 6 rain 7 8 9 10 11 12 13 More 14 basic 52  OUTLINE 3. Carbon and the Molecular Diversity of Life 3.1. Organic chemistry is the study of carbon compounds 3.2. Carbon atoms can form diverse molecules by bonding to four other atoms 3.3. A small number of chemical groups are key to the functioning of biological molecules 53  Carbon: The Backbone of Life 3.1. Organic chemistry is the study of carbon compounds  Although cells are 70–95% water, the rest consists mostly of carbon-based compounds  Carbon compounds range from simple molecules to complex ones 54 3.2. Carbon atoms can form diverse molecules by bonding to four other atoms The Formation of Bonds with Carbon  Carbon has four valence electrons and may form single, double, triple, or quadruple bonds many different elements Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) H O N C The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules 55  Molecular Diversity Arising from Carbon Skeleton Variation  Carbon may bond to itself forming carbon chains  Carbon chains form the skeletons of most organic molecules  Carbon chains vary in length and shape Ethane Propane 1-Butene 2-Butene (a) Length (c) Double bonds Butane 2-Methylpropane (commonly called isobutane) Cyclohexane Benzene (b) Branching 56 (d) Rings Hydrocarbons  Hydrocarbons are molecules consisting of only carbon and hydrogen, found in many of a cell’s organic molecules  Hydrocarbons can undergo reactions that release a large amount of energy Fat droplets (stained red) 100 µm (a) Mammalian adipose cells (b) A fat molecule 57 The role of hydrocarbons in fats  Isomers Isomers are compounds with the same molecular formula but different structures and properties H 2-methyl butane  Structural isomers have Pentane H C H different covalent H H H H H H C H H H arrangements of their atoms H C C C C C H H C C C H H H H H H H H H  Geometric isomers have the same covalent arrangements X X H X C C C but differ in spatial C arrangements H H X H cis isomer: The two trans isomer: The two CO2H CO2H Xs are on the same Xs are on opposite L isomer D isomer side. sides. C C H NH2 NH2 H CH3 CH3  Enantiomers are isomers that are mirror images of each other 58 Enantiomers are important in the pharmaceutical industry. Two enantiomers of a drug may have different effects Effective Ineffective Drug Condition Enantiomer Enantiomer Ibuprofen Pain; inflammation S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol Ibuprofen reduces inflammation and pain. Albuterol is used to relax bronchial muscles, improving airflow in asthma patients59 3.3. A small number of chemical groups are key to the functioning of biological molecules The Chemical Groups Most Important in the Processes of Life  Functional groups are the components of organic molecules involved in chemical reactions  The number and arrangement of functional groups give each molecule its unique properties Both estradiol and Estradiol Testosterone are steroid with common carbon skeleton (4 fused rings). Hydroxyl group is replaced by carbonyl group Testosterone 60  The seven functional groups that are most important in the chemistry of life: – Hydroxyl (–OH) – Carbonyl (-CO-), – Carboxyl group (-COOH) – Amino (-NH2) – Sulfhydryl (-SH) – Phosphate (-PO4) – Methyl group (-CH3) 61  OUTLINE 4. The Structure and Function of Large Biological Molecules 4.1. Macromolecules are polymers, built from monomers 4.2. Carbohydrates serve as fuel and building material 4.3. Lipids are a diverse group of hydrophobic molecules 4.4. Proteins have many structures, resulting in a wide range of functions 62  4.1. Macromolecules are polymers, built from monomers  All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids  Macromolecules are large molecules composed of thousands of covalently connected atoms  A polymer is a long molecule consisting of many similar building blocks called monomers 63 The Synthesis and Breakdown of Polymers  A condensation reaction called dehydration reaction occurs when two monomers bond together through the loss of a water molecule HO 1 2 3 H HO H Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond H2 O HO 1 2 3 4 H Longer polymer Dehydration reaction in the synthesis of a polymer64  Polymers are disassembled to monomers by hydrolysis that is essentially the reverse of the dehydration reaction HO 1 2 3 4 H Hydrolysis adds a water molecule, breaking a bond H2O Hydrolysis of a polymer HO 1 2 3 H HO H The Diversity of Polymers  Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers 65 4.2. Carbohydrates serve as fuel and building material Sugars Trioses Pentoses Hexoses (C3H6O3) (C5H10O5) (C6H12O6)  Monosaccharides have molecular formulas that are usually multiples of CH2O Glyceraldehyde  Monosaccharides Ribose classified Glucose Galactose The location of the carbonyl group (as aldose or ketose) The number of Dihydroxyacetone carbons in the carbon skeleton Ribulose Fructose 66  Monosaccharides serve as a major fuel for cells and as raw material for building molecules  Though often drawn as linear skeletons, in aqueous solutions many sugars form rings (b) Abbreviated ring structure (a) Linear and ring forms Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5 67  A disaccharide is formed when a dehydration reaction joins two monosaccharides  This covalent bond is called a glycosidic linkage 1–4 glycosidic linkage a) Dehydration reaction in the synthesis of maltose. Joining the glucose monomers in a different way would result in a different disaccharide. Glucose Glucose Maltose 1–2 glycosidic b) Dehydration reaction in linkage the synthesis of sucrose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. Glucose Fructose Sucrose 68  Polysaccharides  Polysaccharides, the polymers of sugars, have storage and structural roles Storage Polysaccharides  Starch, a storage polysaccharide of plants, consists entirely of glucose monomers  Glycogen is a storage polysaccharide in animals Chloroplast Starch Mitochondria Glycogen granules (a) Starch: a plant polysaccharide; The light ovals are granules of starch within a chloroplast of a plant cell. 0.5 µm (b) Glycogen: an 1 µm animal polysaccharide Part of a liver cell; mitochondria are organelles that help Amylose Glycogen break down sugars (unbranched) Amylopectin (branched) 69 (branched) Structural Polysaccharides  Cellulose is a major component of the tough wall of plant cells  glucose  glucose (a)  and  glucose ring structures  Like starch, cellulose is a polymer of (b) Starch: 1–4 linkage of  glucose monomers glucose, but the glycosidic linkages differ (c) Cellulose: 1–4 linkage of  glucose monomers 70  The arrangement of cellulose in plant cell walls Cell walls Cellulose microfibrils About 80 cellulose in a plant molecules associate cell wall to form a microfibril, the Microfibril main architectural unit of the plant cell wall. 10 µm 0.5 µm Cellulose molecules Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups A cellulose molecule attached to carbon is an unbranched  atoms 3 and 6.  Glucose glucose polymer.71 monomer Cellulose is difficult to digest Enzymes that digest starch by hydrolyzing  linkages can’t hydrolyze  linkages in cellulose Some microbes use enzymes to digest cellulose Cellulose-digesting prokaryotes are found in grazing animals such as this cow. 72  Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods Chitin also provides structural support for the cell walls of many fungi (a) The structure (b) Chitin forms the (c) Chitin is used to make of the chitin exoskeleton of a strong and flexible monomer. arthropods. surgical thread. 73 4.3. Lipids are a diverse group of hydrophobic molecules  Lipids are the one class of large biological molecules that do not form polymers  Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds  The most biologically important lipids are fats, phospholipids, and steroids 74  Fats  In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride  Fatty acids vary in length (number of carbons) and in the number and locations of double bonds Fats separate from water because water molecules Fatty acid form hydrogen bonds Glycerol (palmitic acid) with each other and (a) Dehydration reaction in the synthesis of a fat exclude the fats Ester linkage 75 (b) Fat molecule (triacylglycerol)  Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds  Unsaturated fatty acids have one or more double bonds (a)Saturated fat (b) Unsaturated fat Mainly animal fat Mainly plant and fish fats Structural formula Structural formula Oleic acid, an Unsaturated Stearic acid, a fatty acid saturated fatty acid cis double bond Causes bending At room temp, the molecules are packed together => solid At room temp, the molecules cannot pack together => liquid 76 Phospholipids  Two fatty acids and a phosphate group are attached to glycerol  The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head Hydrophobic tails Hydrophilic head Choline Phosphate Glycerol Fatty acids (c) Phospholipid symbol Hydrophilic head Hydrophobic tails (a) Structural formula (b)Space-filling model 77 Phospholipids  The structure of phospholipids results in a bilayer arrangement found in cell membranes  Phospholipids are the major component of all cell membranes Hydrophilic WATER head Hydrophobic WATER tail 78  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  Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease 79 Cholesterol is the “base steroid” from which your body Cholesterol produces other steroids Estrogen Testosterone Estrogen & testosterone are also steroids 80 4.4. Proteins have many structures, resulting in a wide range of functions 81  Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions  Enzymes can perform their functions repeatedly, that keep cells running by carrying out the processes of life 1 Active site is available for 2 2 Substrate binds to a molecule of substrate, the enzyme. reactant on which the enzyme acts. Substrate (sucrose) Glucose Enzyme OH (sucrase) H2O Fructose HO 3 Substrate is converted 4 Products are released. to products. The enzyme sucrase accelerates hydrolysis of sucrose into glucose and fructose 82  Polypeptides Polypeptides are polymers built from the same set of 20 amino acids A protein consists of one or more polypeptides 83  Amino Acid Monomers Amino acids are organic molecules with carboxyl and amino groups Amino acids differ in their properties due to differing side chains, called R groups  carbon Amino Carboxyl group group 84 The 20 amino acids of proteins Nonpolar Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or ) Methionine Phenylalanine Tryptophan Proline (Met or M) (Phe or F) (Trp or W) (Pro or P) 85  Polar Serine Threonine Cysteine Tyrosine Asparagine Glutamine (Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q) Electrically charged Acidic Basic Aspartic acid Glutamic acid Lysine Arginine Histidine (Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H) 86  Amino Acid Polymers Amino acids are linked by peptide bonds Each polypeptide has a unique linear sequence of amino acids Peptide bond (a) Peptide Side chains bond Backbone Amino end Carboxyl end (b) (N-terminus) (C-terminus) 87  Protein Structure and Function Four Levels of Protein Structure Primary Secondary Tertiary Quaternary Structure Structure Structure Structure pleated sheet +H 3N Amino end amino acid subunits helix 88  The primary structure of a protein is its unique sequence of amino acids Primary Structure 1 +H 5 3N Amino end 10 15 Amino acid subunits 20 25 89 Secondary structure Consists of coils and folds in the polypeptide chain into a repeating configuration Includes a coil called an  helix and a folded structure called a  pleated sheet  pleated sheet Examples of amino acid subunits  helix 90  Tertiary structure Is determined by interactions among various side chains (R groups) Strong covalent bonds called disulfide bridges may reinforce the protein’s structure Hydrophobic interactions and van der Waals Hydrogen interactions bond Polypeptide backbone Disulfide bridge Ionic bond 91  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  Chains Polypeptide chain Iron Heme  Chains Hemoglobin Collagen 92 Sickle-Cell Disease: A Change in Primary Structure  Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin Normal hemoglobin Sickle-cell hemoglobin Val His Leu Thr Pro Glu Glu Primary Primary structure ValHis Leu Thr Pro Val Glu structure 1 2 3 4 5 6 7 1 2 3 4 5 6 7 Secondary Secondary and tertiary subunit and tertiary Exposed subunit structures structures hydrophobic region 10 µm 10 µm Red blood Normal red blood Red blood cell shape cells are full of cell shape individual hemoglobin Fibers of abnormal moledules, each hemoglobin deform carrying oxygen. red blood cell into 93 sickle shape. What Determines Protein Structure? Protein structure affect by physical and chemical conditions : alterations in pH, salt concentration, temperature, or other environmental factors. Denaturation is when a protein unravel and loses its native structure biologically inactive Denaturation Normal protein Renaturation Denatured protein 94 Protein Folding in the Cell  Most proteins probably go through several states on their way to a stable structure  Chaperonins are protein molecules that assist the proper folding of other proteins Correctly folded protein Polypeptide Steps of Chaperonin 2 The cap attaches, causing the 3 The cap comes Action: cylinder to change shape in off, and the properly 1 An unfolded poly- such a way that it creates a folded protein is peptide enters the hydrophilic environment for released. 95 cylinder from one end. the folding of the polypeptide. 4.4. Nucleic acids store and transmit hereditary information The Roles of DNA Nucleic Acids 1 Synthesis of mRNA in the nucleus mRNA There are two types of nucleic acids: NUCLEUS Deoxyribonucleic acid CYTOPLASM (DNA) 2 Ribonucleic acid Movement of mRNA mRNA into cytoplasm (RNA) via nuclear pore Ribosome 3 Synthesis of protein Polypeptide Amino acids 96 The Structure of Nucleic Acids  Nucleotides: monomer of polynucleotides  Nucleotide = Nucleosides (Sugar+nitrogen base)+phosphate 5' end Nitrogenous bases Pyrimidines 5'C 3'C Nucleoside Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Nitrogenous base Purines 5'C Adenine (A) Guanine (G) Phosphate 3'C group Sugars Sugar 5'C (pentose) 3'C (b) Nucleotide 3' end Deoxyribose (in DNA) Ribose (in RNA) 97 (a) Polynucleotide, or nucleic acid (c) Nucleoside components: sugars Nucleotide Polymers 5’ end  Made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next  These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages 3’ end 98  The DNA Double Helix  A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix  The DNA double helix consists of two antiparallel nucleotide strands Nucleotides  Adenine always pairs with Thymine by 2 hydrogen bonds.  Guanine pairs with Cytosine through 3 hydrogen bonds 99  Gene  Are the units of inheritance  Program the amino acid sequence of polypeptides  Are made of nucleotide sequences on DNA 100  DNA and Proteins as Tape Measures 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 101  Knowledge Testing 1 1. Distinguish between the following pairs of terms: neutron and proton, atomic number and mass number, atomic weight and mass number. 2. Distinguish between and discuss the biological importance of the following: nonpolar covalent bonds, polar covalent bonds, ionic bonds, hydrogen bonds, and van der Waals interactions. 102  Knowledge Testing 2 1. List and explain the four properties of water that emerge as a result of its ability to form hydrogen bonds. 2. Distinguish between the following sets of terms: hydrophobic and hydrophilic substances; a solute, a solvent, and a solution. 103  Knowledge Testing 3 1. Explain how carbon’s electron configuration explains its ability to form large, complex, diverse organic molecules 2. Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules 3. Name the major functional groups found in organic molecules; describe the basic structure of each functional group and outline the chemical properties of the organic molecules in which they occur 104  Knowledge Testing 4 1. Describe the formation of a glycosidic linkage and distinguish between monosaccharides, disaccharides, and polysaccharides. 2. Distinguish between saturated and unsaturated fats and between cis and trans fat molecules. 3. Distinguish between the following pairs: pyrimidine and purine, nucleotide and nucleoside, ribose and deoxyribose, the 5 end and 3 end of a nucleotide. 105