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Chapter 02 Molecules of Life *See separate FlexArt PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes and animations. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 Why Study Chemistry? The science that deals with the basic properties of matter Chemical substances undergo changes and interact with one another in chemical reactions Metabolism is the use of nutrients for energy or for making substances of cells Understanding the basic principles of chemistry is essential to understanding metabolic processes in living things Understanding microbial metabolism aids understanding human metabolism A Glimpse of History Louis Pasteur (1822–1895) often considered father of bacteriology Started career as chemist for French wine industry Studied tartaric and paratartaric acids • • • • Form thick crusts within wine barrels Identical chemical composition Affect polarized light differently Observed paratartaric acid crystals had two different structures • Realized paratartaric acid composed of mixture of stereoisomers Atoms and Elements Atoms • Basic unit of all matter • Made up of three major components • Protons – Positively charged • Electrons – Negatively charged • Neutrons – Uncharged Atoms and Elements Atom • Protons and neutrons are found in the nucleus • Account for the “weight” of the atom – Atomic mass • Electrons orbit the nucleus = # of Protons + # of Neutrons • Have relatively little mass – Do not contribute to the mass of the atom » Approximately 2,000 electrons = 1 proton • Protons and electrons are equal in a uncharged atom i.e.,complete atom 2.1. Atoms and Elements Atoms distinguished by atomic number • Number of protons in nucleus Also atomic mass Protons ONLY PROTONS + NEUTRONS • Sum of protons and neutrons (electrons too light) • E.g., hydrogen (one proton, no neutrons) has atomic number and mass of 1 2.1. Atoms and Elements Elements consist of only one type of atom • Cannot be chemically separated into simpler parts • Living matter primarily composed of four • Hydrogen, carbon, oxygen, nitrogen • Atoms of an element can have different mass numbers • Same # of protons, different # of neutrons • Termed isotopes 2.1. Atoms and Elements Electrons are arranged in shells around nucleus • First shell can hold up to 2 • Next and subsequent shells can hold up to 8 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Inner shells (closer to nucleus) fill first 6e– 6p+ 6n0 (a) • Biological molecules follow “octet rule” Mass number • Most stable with full outer shell • Electrons farther from nucleus have higher energy level • Valence electrons are those in outer shell Atomic number 12 6 C (b) C • Important in bond formation (c) Element symbol Structure of Four Biologically Important Atoms Chemical Bonds and the Formation of Molecules Atoms are most stable when the outer orbital contains the maximum number of electrons • 2, 8, 8 etc. To fill outer orbitals atoms form bonds with other atoms to fill outer orbitals • Bonds are formed with the sharing or the gain or loss of electrons • Molecules are formed when atoms bond together Chemical Bonds and the Formation of Molecules There are several types of chemical bonds • They also vary in strength Chemical bonds include • Covalent bonds • Ionic bonds • Hydrogen bonds Covalent Bonds Covalent bonds form when atoms share electrons • One pair of shared electrons = one covalent bond • Carbon bonds with hydrogen to form organic molecules • Other compounds are inorganic • Covalent bonds are strong • Difficult to break at biological temperatures Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H 4 H + Each hydrogen atom needs one electron to fill its valence. C Carbon needs four electrons to fill its valence. H C H H Methane (a) H • Requires enzymes H C CH4 H H Each line represents a shared pair of electrons. (b) Ball-and-stick model Space-filling model Chemical formula Covalent Bonds Achieve stability through the sharing of electrons between atoms • Creates a strong bond • Difficult to break • Requires significant energy usually in the form of heat • Never break spontaneously at physiological temperatures – Enzyme required to break at lower temperature • Bonds can be polar or non-polar Covalent Bonds Non-polar and Polar • Covalent bonds may have an equal or unequal attraction for the shared electrons • Non-polar covalent • Bonds formed between identical atoms or between atoms that have similar attraction – H-H or C-H Covalent Bonds • Polar covalent bond • One atom has a greater attraction to the electrons than the other – Produces a slight charge within the molecule » One part of the molecule with be slightly negatively charged and one molecule with by slightly positively charged • Electrons are unequally shared Covalent Bonds Covalent bonds can be non-polar or polar • Non-polar: equal sharing of electrons • Polar: unequal sharing of electrons • One atom more electronegative than other • Important in biological systems – Result in hydrogen bonds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. – O H H (a) + (b) + Increasing electron density Decreasing electron density Ionic Bonds Formed by atoms gaining or losing electrons to obtain stability • Electrons completely leave first atoms and become part of outer orbital of second atom • Loss and gain of electrons leads to charged atoms (ions) – Atom that loses electrons becomes positively charged – Atom that gains electron becomes negatively charged Charged atoms are attracted to each other and form a bond between ions (opposites attract) • Ionic bond Ionic Bonds Ionic bonds formed by atoms gaining or losing electrons • Produces charged atoms, or ions • Cations (positive charge) • Anions (negative charge) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. e– Na Ionic bonds form because Na+ of strong attraction between negative and + Na positive charges • Relatively weak bonds Cl Cl Cl – – (a) (b) Na Cl Na+ Cl– Ionic Bonds Ionic bonds are weaker than covalent bonds • Bonds dissociate in water • Easily broken at room temperature • Approximately 100 time weaker than covalent bonds Important among weak forces holding biological molecules together Hydrogen Bonds Weak bonds formed from the attraction of positively charged hydrogen atoms • Hydrogen atoms in polar molecules are attracted to negatively charged atoms or molecules • Most commonly oxygen or nitrogen • Hydrogen bonds occur between molecules such as water and DNA • Covalent bonds are formed within the molecules – Hydrogen bonds hold molecules together – Covalent bonds hold atoms together Molarity A mole is 6.022 x 1023 particles • A mole of one compound has the same # of molecules as a mole of any other • E.g., 1 mole NaCl = 58.4 g; 1 mole KCl = 74.55 g • Each example has a different mass, but the same number of molecules! Molarity (M) of solution is # moles dissolved in 1 liter H2O • E.g., a 1 M solution of NaCl is 58.4 g dissolved in 1 liter H2O To calculate one mole of NaCl: ∑ Na = 22.9 + Cl= 35.5 = 58.4 g Hydrogen bonds Hydrogen bonds • Form between hydrogen and other electronegative elements (O or N) • Increased number provides stability to molecules Water: a polar molecule Hydrogen Bonding Polar Compounds and Hydrogen Bonding Chemical Compounds of the Cell Most important molecule is water • Importance of water depends on its unusual bonding properties 2.3. Chemical Components of the Cell Water • Makes up over 70% of all living organisms by weight • Polar molecule • Hydrogen bonding explains properties • Ice: each water molecule forms 4 hydrogen bonds • Liquid: hydrogen bonds continually form and break Water molecule – + + Ice Liquid water Water as a Biological Solvent Polarity • Cytoplasm is aqueous and contains polar molecules • Promotes hydrogen bonding (stability) • Promotes interaction within biomolecules • Forces nonpolar molecules (lipids) to aggregate Cohesiveness • H bonds are dynamic: forming, breaking, re-forming • Responsible for water’s important properties: 1. High surface tension, 2. High specific heat 3. Surface ice insulates underlying water – prevents freezing (aquatic organisms can survive) Water Polar nature makes water an excellent solvent • Dissolves polar compounds and those with +/– charge • These compounds are hydrophillic • “Water loving” Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. – – Na+ – – – Water molecules • Non-polar molecules are hydrophobic Na+ • “Water fearing” Cl– • Water with dissolved substances freezes at lower temperatures + + + Salt crystal (NaCl) Cl– + + Polarity and Water Molecules Positive polar end of water surrounds the negative ions Negative polar end of water surrounds the positive ions Hydrogen Bonding Between Water Molecules 2D surface hydrogen bonds are stronger than the 3D in the middle of the volume Strong Surface Tension of Water Acids, Bases, and pH Acid: A hydrogen ion (H+) or proton donor Base: A proton acceptor, or a hydroxyl ion (OH-) donor pH scale: relates proton concentration to pH (logarithmic scale) pH= log (1/[H+ ] The molar concentration of H+ pH of Aqueous Solutions Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Ten-fold increase in [H+] decreases [OH–] by factor of ten 10–14 14 1MNaOH Drain cleaner 13 More basic (higher pH) • Water tends to split into (acidic) and OH– (basic) • Pure water has equal concentrations (each 10–7 M) • Product of [H+] and [OH–] is always 10–14 M H+ pH H+ ion concentration (molarity) 10–7 More acidic (lower pH) pH is measure of [H+] in m/l • Each log unit represents tenfold change in [H+] • Buffers stabilize pH of solutions 12 Lye Household ammonia 11 Milk of magnesia 10 Detergent solution 9 8 Seawater 7 Blood NEUTRAL 6 Milk Urine Unpolluted rainwater 5 Black coffee Beer 4 Vinegar 3 Cola Lemon juice 2 Stomach acid 1 100 0 Battery acid pH Values of Some Common Substances Elements and Small Molecules in Cell ~1% dry weight is inorganic ions • • • • • • • • Na+ (sodium) K+ (potassium) Mg2+ (magnesium) Ca2+ (calcium) Fe2+ (iron) Cl– (chloride) PO43– (phosphate) SO42– (sulfate) Organic compounds • Have important functional groups Elements and Small Molecules in Cell Adenosine triphosphate (ATP) • Energy currency of cell • Three negatively charged phosphate groups repel • • • • Bonds inherently unstable, easily broken Releases energy to drive cellular processes High energy phosphate bonds denoted by ~ ATP ADP + Pi Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Adenosine NH2 N Phosphate groups N O O– P O– O O P O– High-energy bonds O O P O– O CH2 N O OH OH Ribose N Adenine Macromolecules and Their Component Parts Macromolecules are very large • Macro = large Biological macromolecules are divided into four classes • • • • Proteins Polysaccharides (carbohydrates) Lipids Nucleic acids Macromolecules and Their Component Parts All macromolecules are polymers • Poly = many • Large molecules formed by joining smaller subunits together • Joining subunits together involves dehydration reaction – H2O is removed during chemical reaction » Reaction termed dehydration synthesis Macromolecules and Their Component Parts Macromolecules are broken down into smaller subunits • Instead of removing H2O, a molecule of H2O is added • Reaction termed hydrolytic reaction or hydrolysis Dehydration Synthesis A new molecule is synthesized H OH H OH Dehydration Synthesis OH H H2O OH H 2 Separate molecules to be joined Water comes out = Dehydration 2.4. Proteins Proteins More than half of dry weight of cell Versatile, many important roles • • • • • • Catalyze reactions Transport molecules Move cells Provide cellular framework Sense and respond to conditions outside cell Regulate gene expression Amino Acids Proteins made up of amino acids • • • • Infinite possible combinations of 20 amino acids Protein characteristics depend mainly on shape Shape determined by amino acid sequence Amino acids share common structure • Side chain (R group) differs • All except glycine exist as stereoisomers Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. D-Amino acid L-Amino acid X W W C C Y Y X Side chain— “R” is the general designation for a side chain R H Amino group— positively charged at neutral pH Mirror H O N+ C H H C O– Carboxyl group— negatively charged at neutral pH Amino Acid Subunits All amino acids have the following shared features • A carboxyl group (COO-) • An amino group (NH2+) • A central carbon • A side chain • The side chain differentiates the amino acids • Amino acids are subdivided based on similarities of the side chain Peptide Bonds and Their Synthesis The amino acids that form proteins are held together by peptide bonds • Unique type of covalent bond • Formed between the interaction of the carboxyl group of one amino acid and the amino group of the following amino acid – Reaction causes the release of water and the formation of a peptide bond Hydrolysis (lysis, i.e. break apart with water) End with separate amino acids Starting with peptide bonded amino acids O | | || N- C - C - H H | | H R1 H H | | N - C | | | R2 O || -C | OH Water has been used to break (lyse) a bond This is called Hydrolysis break peptide bond and add water parts HOH H2O Break water bonds Bring in water Protein Structure Primary Structure R Determinants: Hydrogen bonding Secondary Structure Polar groups Non-polar groups Covalent Tertiary Structure bonds C C H O H H O N C C R R N C C H H O H H N C R The primary structure can fold into a pleated sheet, or turn into a helix. (a) Secondary Structure -pleated sheet -helix (b) (c) Quaternary Structure (d) Protein Structure Proteins have four structures • • • • Primary Secondary Tertiary Quaternary Protein Structure Primary structure • Sequence of amino acids • In large part determines other protein features Protein Structure Secondary structure • Primary structure folds into new configuration • Helical structure – Alpha (α) helix • Pleated structure – Beta (β) sheet • New configuration results from weak bonds formed between amino acids Protein Structure Tertiary structure • 3 dimensional structure • 2 major shapes • Globular • Fibrous • Becomes functional protein Protein Denaturation Proteins must have specific shape to have proper function • Environmental conditions can break bonds within the protein • Causes shape change – Shape change causes protein to stop functioning » Called denaturation Denaturation can be reversible or irreversible • Environment determines reversibility Carbohydrates Carbohydrates are diverse group of molecules with various sizes Play important roles in all organisms including • Common source of food and energy • Form part of nucleic acids • Form part of bacterial cell wall Carbohydrates Carbohydrates contain carbon, hydrogen and oxygen in 1:2:1 ratio • Each carbon atom is bound to two hydrogen atoms and one oxygen atom • CH2O Polysaccharide • large molecules made of carbohydrate molecules Oligosaccharide • short chains of carbohydrates Monosaccharide • Single carbohydrate molecule Carbohydrates Monosaccharide • Classified by number of carbons in molecule • Most common monosaccharides • 5 and 6 carbon sugars – 5 carbon sugars = pentose » Ribose and deoxyribose – 6 carbon sugars = hexose » Glucose, fructose and galactose Carbohydrates Disaccharides • Produced by joining two monosaccharides through dehydration synthesis • Lactose and sucrose most common in nature • Glucose + galactose = lactose • Glucose + fructose = sucrose • Maltose less common • Glucose + glucose = maltose 2.5. Carbohydrates Monosaccharides have single unit • 5-carbon include ribose, deoxyribose • 6-carbon include glucose, galactose, fructose, mannose • Structural isomers: distinct properties, names • Can exist in alpha (α) or beta (β) form depending on location of hydroxyl group Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 6 CH2OH O 5 H OH H 1 OH HO 4 H H 3 OH H H 1 2 OH OH α form 5 CH2OH O 4 H H 3 OH H 1 2 H OH OH β form 6 OH H Galactose 2 OH CH2OH O H 1 H H 3 H Mannose O OH 2 H OH HO H 4 OH 3 CH2OH 6 5 OH H 1 OH Glucose 5 CH2OH O O H 2 3 Ribose H 4 H HO CH2OH 5 H H 4 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 6 5 H OH OH H 3 4 OH H Fructose 2 1 CH2OH Carbohydrates Polysaccharides • Serve different function • Cellulose most abundant organic molecule on earth • Polymer of glucose molecules • Principle constituent in plant cell wall • Glycogen is carbohydrate storage molecule of animals and some bacteria • Polymer of glucose subunits • Dextran storage molecule for carbon and energy for some bacteria • Polymer of glucose subunits Cellulose Starch Nucleic Acids Two types of nucleic acid • DNA • Carry genetic code in all cells • RNA • Decodes sequence of amino acids to produce proteins • Sub units of nucleic acids are nucleotides DNA Master molecule • Determines specific properties of the cell Nucleotides are composed of three units • Nitrogen containing ring compound • Nitrogenous base – Purine » Adenine and guanine – Pyrimidine » Thymine and cytosine • Five carbon sugar molecule • Deoxyribose • Phosphate molecule DNA Nucleotides are joined through covalent bonding • Bond created between phosphate of one nucleotide and sugar of the adjacent through dehydration synthesis • Phosphate molecule acts as a bridge between the number 3 (3’) carbon of one sugar and the number 5 (5’) carbon of the adjacent – Results in a sugar phosphate backbone 2.6. Nucleic Acids Nucleotides include nucleobase • Purines adenine (A), guanine (G) • Two fused rings Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Pyrimidines cytosine (C), thymine (T) • Single ring structure • Uracil (U) is found only in RNA Purines (double ring) Pyrimidines (single ring) O NH2 N H CH3 N N H H N H N H Adenine (A) (both DNA and RNA) H H Thymine (T) (DNA only) NH2 O N O N H H NH2 H N N H N N H Guanine (G) (both DNA and RNA) N O H Cytosine (C) (both DNA and RNA) H H Uracil (U) (RNA only) H DNA DNA in living organisms is a double stranded helical molecule • Strands are held together by hydrogen bonding between the nitrogen bases • Specific pairing between bases – Adenine binds to thymine » A-T or T-A – Guanine binds to cytosine » G-C or C-G • Bases are complementary RNA Involved in decoding DNA Structure is similar to DNA • Differs in a number of ways • Thymine is replaced by uracil – There is no thymine base in RNA • The sugar is ribose in place deoxyribose • RNA is generally shorter • Exists as a single stranded molecule not double stranded 2.7. Lipids Lipids are non-polar, hydrophobic molecules • Diverse group defined by this physical property • Highly soluble in organic solvents • E.g., ether, benzene, chloroform • Not composed of similar subunits Simple lipids contain carbon, hydrogen, oxygen • Fats most common • Glycerol linked to fatty acids via dehydration synthesis • Fatty acids are long chains of bonded C, H atoms with carboxyl group at one end Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H O H C OH HO C R 3 H2O H O H C O C O H C OH + HO C O R HO C R H Glycerol (b) H C O Dehydration synthesis O H C OH R C R O H C O C R H + 3 fatty acids Triglyceride (fat) Lipids Critical component of the cell membrane • Membranes act a gatekeepers to the cell • Often determines what enters or leaves the cell Heterogeneous group of molecules • Made up of different subunits Defining feature • Insoluble in water Smallest of the four macromolecules Can be divided into two general classes • Simple lipids • Compound lipids Simple Lipids Contain only carbon, hydrogen and oxygen Most common are called fats • Solid at room temperature • Made of glycerol and fatty acids • Fatty acids are long hydrocarbon chains plus an acid group (COOH) at the end • Glycerol is carbon hydrogen chain with three hydroxyl (OH) groups attached – Allows for the binding of three fatty acids to one glycerol » Triglyceride • Fatty acids bond to glycerol covalently through dehydration synthesis 2.7. Lipids Fatty acids: two groups • Saturated: no double bonds • Tails pack tightly so solid at room temperature (fats) • Unsaturated: double bonds • Kinks prevent tight packing so liquid at room temperature (oils) • Monounsaturated: 1 double bond • Polyunsaturated: >1 double bond Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Saturated fatty acid (palmitic acid) HO O H H H H H H H H H H H H H H H C C C C C C C C C C C C C C C C H H H H H H H H H H H H H H H H Unsaturated fatty acid (oleic acid) Double bond (a) • Most natural fatty acids are cis: hydrogens attached to same side of double bond • Trans have hydrogens on opposite sides of double bond Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2.7. Lipids Watery exterior of cell Phospholipid bilayer Compound lipids include other elements Phospholipids important • Phosphate group linked to polar molecule • Yields hydrophilic head group • Hydrophobic fatty acid tails • Form lipid bilayer with polar heads oriented outward toward aqueous environments • Essential component of cytoplasmic membranes Lipoproteins, lipopolysaccharides also compound lipids Watery interior of cell Phospholipid R Polar head group O P O– O Hydrophilic head Hydrophobic tail Phosphate group O CH2 CH CH2 O O C O C CH2 Glycerol O CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH CH2 CH2 CH2 CH CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 Saturated fatty acid CH2 CH2 CH2 CH2 CH2 CH3 Unsaturated fatty acid Simple Lipids Steroids are also considered simple lipids Differ from fats in structure and function • Structure consists of fourmembered ring Classified as lipid because steroids are insoluble in water If one of the rings has a hydroxyl (OH) group attached it is classified as a sterol • Example: cholesterol