Chapter 2 Chemical Level of Organization Chapter 3 DNA and RNA Diffusion and Osmosis Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table • Human body is composed of matter – Three forms: • solid (e.g., bone) • liquid (e.g., blood) • gas (e.g., oxygen) • Matter is composed of atoms – Atom, smallest particle that exhibits the chemical properties of an element – arranged in the periodic chart Figure 2.1a Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. IIA IIIA 1 IVA VA VIA VIIA Increasing electronegativity H 2 He 1.008 3 4 Li Be 6.941 9.012 11 12 Na Mg 22.99 24.31 19 VIIIA 5 1 Atomic number H Element symbol B 20 K Ca 39.10 40.08 22 23 24 25 Fe 27 Si 17 S Cl 30.97 2.07 35.45 33 34 35 36 Br Kr 79.90 83.80 53 54 28.09 Zn Ga 63.55 65.38 69.72 46 47 48 49 50 51 52 41 42 43 44 45 Ge As 72.64 18 Ar 39.95 Cu 54.94 32 Ne 20.18 16 Ni Mn 52.00 F 19.00 10 P 58.69 Cr 31 9 15 58.93 V 50.94 30 O 15.99 Co Ti 47.87 40 Al N 14.01 29 44.96 39 14 4.003 8 7 28 Sc 55.85 13 26.98 26 21 C 12.01 10.81 Atomic mass number 1.008 6 74.92 Se 78.96 37 38 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe 85.47 87.62 88.91 91.22 92.91 95.94 98.00 101.1 102.9 106.4 107.9 112.4 114.8 118.7 121.8 127.6 126.9 131.3 55 56 57 72 73 74 75 76 77 78 79 80 81 82 83 84 Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po 132.9 137.3 138.9 178.5 180.9 183.8 186.2 190.2 192.2 195.1 197.0 200.6 204.4 207.2 209.0 209.0 210.0 222.0 87 88 89 104 105 106 107 108 109 110 111 112 112 114 115 116 117 118 Fr Ra Ac Rf Db Sg Bh Hs Mt Ds Rg Uub Uut 223.0 226.0 227.0 267.0 268.0 271.0 272.0 270.0 276.0 281.0 60 61 62 63 64 274 85 At 86 Rn Uuq Uup Uuh Uus Uuo 277 277 289.0 288.0 293.0 292.0 294.0 65 66 67 68 69 70 71 58 59 Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu 140.1 140.9 144.2 145.0 150.4 152.0 157.3 158.9 162.5 164.9 167.3 168.9 173.0 175.0 90 91 92 103 Th Pa 232.0 231.0 U 238.0 93 94 Np Pu 237.0 244.0 95 96 Am Cm 243.0 247.0 97 Bk 247.0 98 99 100 101 102 Cf Es Fm Md No 251.0 252.0 257.0 258.0 259.0 Lr 262.0 Increasing electronegaativity IA Figure 2.1b Copyright © The McGraw–Hill Companies, Inc. 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Most Common Elements of the Human Body Major elements (collectively compose more than 98% of body weight) Symbol (b) Lesser elements (collectively compose less than 1% of body weight) % Body weight Symbol % Body weight O Oxygen 65.0 S Sulfur 0.25 C Carbon 18.0 K Potassium 0.20 H Hydrogen 10.0 Na Sodium 0.15 N Nitrogen 3.0 Cl Chlorine 0.15 Ca Calcium 1.5 Mg Magnesium 0.05 P Phosphorus 1.0 Fe Iron 0.006 Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table The components of an atom • Atoms composed of three subatomic particles: – protons • mass of one atomic mass unit (amu) • positive charge of one (+1) – neutrons • mass of one amu • no charge – electrons • 1/1800th mass of a proton or neutron • negative charge of one (-1) • located at varying distance from the nucleus in regions called orbitals Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table The periodic table • Elements differ in number of subatomic particles • Periodic table displays: – chemical symbol • unique to each element • usually identified by first letter, or first letter plus an additional letter – C is carbon - atomic number number of protons in an atom of the element located above symbol name elements arranged by anatomic number within rows - average atomic mass mass of both protons and neutrons shown below the element’s symbol on the table Atoms, Ions, and Molecules: Matter, Atoms, Elements, and the Periodic Table Diagramming Atomic Structures • An atom has shells of electrons surrounding the nucleus – Each shell with a given energy level – Each shell holding a limited number of electrons – Innermost shell two electrons, second shell up to eight – Shells close to the nucleus: must be filled first Nucleus: Figure 2.2b Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Shell model Energy shell 8 protons 8 neutrons 8 electrons (b) Proton (+) Neutron (no charge) Electron shells: Electron (–) Atoms, Ions, and Molecules: Isotopes • Isotopes are different atoms of the same element – – – – Have same number of protons and electrons Have different numbers of neutrons Exhibit essentially identical chemical characteristics One usually predominant • Carbon exists in three isotopes: – carbon-12, with 6 neutrons • most prevalent type – carbon-13, with 7 neutrons – carbon-14 , with 8 neutrons Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Carbon–12 Carbon–13 Carbon–14 6 protons 6 neutrons 6 electrons 6 protons 7 neutrons 6 electrons 6 protons 8 neutrons 6 electrons Figure 2.3 Atoms, Ions, and Molecules: Isotopes Clinical View: Medical Imaging of the Thyroid Gland Using Iodine Radioisotopes – Radioisotopes- Are unstable because they contain excess neutrons – Lose nuclear components in the form of high energy radiation (alpha particles, beta particles, gamma rays) • introduced into the body during medical procedures – Used by cells in a similar manner to nonradioisotopes – Can trace products of metabolic reactions that use these elements – Thyroid gland darker in areas where less radioactive iodine taken up – Can help locate a nodule – Biological half-life, the time required for half of the radioactive material from a test to be eliminated from the body Atoms, Ions, and Molecules: Chemical Stability and the Octet Rule • Periodic table organized into columns based on number of electrons in outer shell (valence shell) – Column one, with hydrogen, lithium, sodium, potassium • all with one electron in their outer shell – Each consecutive column with one additional electron in outer shell – Elements in column VIIA with a full valence shell • results in chemical stability • helium, neon, etc., chemically inert (noble gases) Atoms, Ions, and Molecules: Chemical Stability and the Octet Rule • Elements tend to lose, gain, or share electrons to obtain complete outer shells with eight electrons – Known as the octet rule Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Number of valence electrons 1 IA Figure 2.4 2 IIA 3 IIIA 4 IVA 5 VA 6 VIA 7 VIIA 8 VIIIA He H Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Ions and Ionic Compounds • Chemical compounds – Stable associations between two or more elements combined in a fixed ratio – Classified as ionic or molecular • Ionic compounds are structures composed of ions held together in a lattice of ionic bonds • Ions – positive or a negative charge – Are produced from the loss or gain of an electron or electrons – Are used very commonly in the body with significant physiological functions • e.g., Na+ for electrical signals in neurons • e.g., Ca2+ for blood clotting and muscle contraction • e.g., Cl- in stomach acid, and many more Figure 2.5 Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Na 11p (a) Sodium atom (Na) + Cl 17p (b) Chlorine atom (Cl) = Na+ Cl– 11p 17p (c) Sodium ion (Na+) Chloride ion (Cl–) Cl– Na+ Cl– Na+ Cl– Na+ Cl– Na+ Cl– (d) Lattice salt crystal of NaCl Common Ions in the Human body and Their Physiological Significance (Table 2.1a) Common Ions in the Human body and Their Physiological Significance (Table 2.1b) Covalent Bonding, Molecules, and Molecular Compounds • Sharing of electrons between atoms results in a covalently bonded molecule • Most molecules are composed of two or more different elements – Termed molecular compounds • examples include carbon dioxide (CO2) but not molecular oxygen (O2) • Molecular formula – Shows the chemical constituents and their ratios in a molecule • Structural formula – Shows number and types of atoms – Also shows their arrangements within the molecule – Provides a mean for differentiating isomers • molecules with the same number and kind of elements arranged differently in space Covalent Bonding, Molecules, and Molecular Compounds: Molecular and Structural Formulas • Glucose versus galactose versus fructose – All with the same molecular formula, with 6 carbon, 12 hydrogen, and 6 carbon – Atoms arranged differently • Isomers may have different chemical properties Figure 2.6 Copyright © The McGraw–Hill Companies, Inc. 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Molecular formula Glucose Galactose Fructose (C6H12O6) (C6H12O6) (C6H12O6) 6 CH2OH 5C H 6 CH2OH O H HO H Structural formula 4C OH H H HO (a) 5C 5 O 4C C1 OH H H OH 3C C2 3C C2 H OH H OH (b) HOCH2 O OH H C1 4C C1 H OH H 3C OH (c) HO C2 H CH2OH Covalent Bonding, Molecules, and Molecular Compounds: Covalent Bonds • A covalent bond is formed when atoms share electrons – Occurs when both atoms require electrons – Occurs with atoms that have four to seven electrons in their outer shell • Four elements of the human body form covalent bonds most commonly: – – – – oxygen (O) carbon (C) hydrogen (H) nitrogen (N) Covalent Bonding, Molecules, and Molecular Compounds: Covalent Bonds The number of bonds an atom can form • Simplest covalent bond formation occurs between two hydrogen atoms – Each sharing its single electron • Oxygen needs two electrons to complete outer shell – Forms two covalent bonds • Nitrogen forms three bonds • Carbon forms four bonds Molecular Structure of Water and the Properties of Water: Molecular Structure • Water Figure 2.12 Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Water (H2O) + + – H H + + – – O + – + – – Hydrogen bonds form between water molecules. Water is a polar molecule due to unequal sharing of electrons. (a) Hydrogen bonds (b) – Composes two-thirds of the human body by weight – Polar molecule composed of one oxygen atom bonded to two hydrogen atoms – Oxygen atom with two partial negative charges – Hydrogen with a single positive charge – Can form four hydrogen bonds with adjacent molecules • central to water’s properties Phases of water • Water present in three phases, depending on temperature: – gas (water vapor) – liquid (water) • almost all water in the body in this phase – solid (ice) • Functions of liquid water: – transports • substances dissolved in water moved throughout the body – lubricates • decreases friction between body structures (e.g., serous fluid) – cushions • absorbs sudden force of body movements (e.g., cerebrospinal fluid) – excretes wastes • unwanted substances dissolved in water and eliminated Molecular Structure of Water and the Properties of Water: Properties Cohesion, surface tension, and adhesion • Cohesion – The attraction between water molecules due to hydrogen bonding • Surface tension – The inward pulling of cohesive forces at the surface of water – Causes moist sacs of air in the lungs to tend to collapse • surfactant (mixture of lipids and proteins) helps prevent this • Adhesion – The attraction between water molecules and a substance other than water Figure 2.4 6 Molecular Structure of Water and the Properties of Water: The Universal Solvent • Water is the solvent of the body • Substances that dissolve in water are called solutes • Water called the universal solvent because most substances dissolve in it – The chemical properties of a substance determine whether it will dissolve • Nonpolar molecules do not dissolve within water – Substances termed hydrophobic, “water-fearing” – Cohesive water molecule “force out” nonpolar molecules – Hydrophobic substances require carrier proteins to be transported within the blood • fats, cholesterol unable to dissolve within water Acidic and Basic Solutions, pH, and Buffers: pH, Neutralization, and the Action of Buffers • The pH is a measure of H+ – The relative amount of H+ in a solution – Expressed as a number between 0 and 14 • greater H+ = lower pH value • The pH of plain water is 7 Solutions with equal concentrations of H+ and OHAre neutral Have a pH of 7 Solutions with greater H+ than OHAre acidic Have a pH < 7 taste sour Solutions with greater OH- than H+ Are basic (alkaline) Have a pH >7 taste bitter Figure 2.15 Copyright © The McGraw–Hill Companies, Inc. 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H+ Concentration H+ H+ H+ 0 10–1 1 Hydrochloric acid (HCl): 1 10–2 2 Lemon juice, stomach acid: 2–3 [H+] 10–3 3 H+ H+ H+ Decreasing pH 10–4 H+ 4 10–5 5 H+ H+ H+ < OH– Decreasing [H+] Increasing pH H+ H+ H+ H+ > OH– Increasing H+ H+ H+ H+ H+ Examples 100 H+ H+ pH Value Wine: 2.4–3.5 Grapefruit juice: 3 Tomato juice: 4.7 Urine: 6 Milk, saliva: 6.3–6.6 Acidic 10–6 6 Neutral 10–7 7 Basic 10–8 8 10–9 9 10–10 10 Antacid: 10.5 10–11 11 Household ammonia: 10.5–11 10–12 12 Household bleach: 12 10–13 13 10–14 14 Pure water: 7 Human blood: 7.4 Seawater: 8 Sodium hydroxide (NaOH): 14 Acidic and Basic Solutions, pH, and Buffers: pH, Neutralization, and the Action of Buffers • Neutralization occurs when an acidic or basic solution is returned to neutral – Acids neutralized by adding base • e.g., medications to neutralize stomach acid containing base – Bases neutralized by adding acid • Buffers help prevent pH changes if excess acid or base is added – Act to accept H+ from excess acid or donate H+ to neutralize base • carbonic acid (weak acid) and bicarbonate (weak base) buffer blood pH • both help maintain pH in a critical range Biological Macromolecules: General Characteristics • Organic molecules, molecules that contain carbon – Most are a component of living organisms – Biological macromolecules (biomolecules) are a subset • Inorganic molecules, all other molecules • Four classes of biomolecules in living systems: – – – – lipids carbohydrates nucleic acids proteins Copyright © The McGraw–Hill Companies, Inc. 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Functional Group Structural Formula Properties Structural Diagram of Example Molecule Representative Molecules CH2OH Hydroxyl • Polar • Forms hydrogen bonds • Increases molecules’ solubility in water OH C • Carbohydrates • Proteins • Nucleic acids • Lipids O H C Figure 2.17 H H C OH H C C OH HO H OH Glucose • Polar • Forms hydrogen bonds • Increases molecules’ solubility in water O Carbonyl C • Carbohydrates • Nucleic acids H H O C C H H Acetaldehyde • Polar • Forms hydrogen bonds • Increases molecules’ solubility in water • Acts as an acid O Carboxyl (carboxylic acid) C OH • Polar • Forms hydrogen bonds • Increases molecules’ solubility i n water • Acts as a base H N Amine H H H H H H H H H H H H H H H H H H O • Proteins • Lipids C HO C 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 H H Fatty acid H • Proteins • Nucleic acids N H H O C C OH CH3 Alanine NH2 N C C N HC O Phosphate O O– P O– • Polar • Forms hydrogen bonds • Increases molecules’ solubility in water • Forms phosphodiester bonds • Acts as an acid (shown here with hydrogens released) N CH C N • Nucleic acids • Phospholipids • ATP O H2C O P O P O– O O O– P O– C C H O O C C OH OH H Adenosine triphosphate (ATP) NH2 Sulfhydryl S H • Forms disulfide bridge • Proteins H O C C CH2 S H Cysteine OH O– Biological Macromolecules: General Characteristics Polymers • Molecules made up for repeating subunits, termed monomers – Monomers identical or similar in chemical structure – Examples are carbohydrates, nucleic acids, proteins • carbohydrates with sugar monomers • nucleic acids with nucleotide monomers • proteins with amino acid monomers Biological Macromolecules: General Characteristics Copyright © The McGraw–Hill Companies, Inc. 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Dehydration • Dehydration synthesis (condensation) Anabolic reaction – – – – Occurs during the synthesis of biomolecules One subunit looses an –H Other subunit loses an –OH New covalent bond formed and water produced H2O Synthesis (a) • Hydrolysis reaction Catabolic reaction Hydrolysis H2O – Occurs during the breakdown of biomolecules – An –H added to one subunit – An –OH added to another subunit Digestion (b) Biological Macromolecules: Lipids • Lipids – made from fatty acids – Functions: energy storage, insulation, and cushioning – Are in cell membranes and hormones – Occur in four primary classes: • Triglycerides- energy storage – – – – Most common form of lipid in living things Used for long-term energy storage in adipose tissue Also used for structural support, cushioning, and insulation Formed from a glycerol molecule and three fatty acids • Phospholipids- cell membranes • Steroids – Composed of hydrocarbons arranged in a multiringed structure – Include cholesterol, steroid hormones (e.g., testosterone), and bile salts • Eicosanoids – Have functions in the inflammatory response, in the nervous system, and all body systems ex. prostaglandins Biological Macromolecules: Lipids • Fatty acids – vary in length – Are varied in the number of double bonds • saturated if they lack double bonds • unsaturated if they have one double bond • polyunsaturated if they have two or more double bonds • Adipose tissue – Forms triglycerides when energy is excess • termed lipogenesis – Breaks down triglycerides when needed • termed lipolysis Other lipids Glycolipids lipid molecules with carbohydrate attached associated with the plasma membrane involved in cellular binding Fat soluble vitamins vitamins A, E, and K Figure 2.25a Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. (a) Lipids Nonpolar and amphipathic molecules with four major subclasses Triglycerides (storage form) H H C OH H C OH H C OH Fatty acid (saturated or unsaturated) H Triglycerides are the most Adipose connective tissue common form of lipid in living cells with fat droplets things. They are used for long-term energy storage, structural support, cushioning, and insulation of the body. Glycerol Fatty acid Blood Eicosanoids (local acting molecules) Phospholipids Steroids Component of plasma membrane Cholesterol Precursor for steroid hormones and bile salts Plasma membrane Chemical barrier of cells Polar head Nonpolar tails Prostaglandins Prostacyclins Thromboxanes Leukotrienes Major Classes of Lipids (Table 2.3) Biological Macromolecules: Lipids Clinical View—Fatty Acids: Saturated, Unsaturated, and Trans Fats • Most animal fats are saturated – Most solid at room temp • Most vegetable fats are unsaturated – Most liquid at room temp – Generally healthier – Can be converted to saturated fats through hydrogenation • Partial hydrogenation can lead to trans fats – Increase the risk of heart attack and stroke Biological Macromolecules: Carbohydrates • Carbohydrates – An –H and an –OH usually attached to every carbon – Chemical formula is (CH2O)n • n the number of carbon atoms – Monosaccharides • simple monomers(sugars) • Formula: • Examples: – Disaccharides • formed from two monosaccharides • Formula: • Examples: – Polysaccharides • formed from many monosaccharides • Examples: Biological Macromolecules: Carbohydrates Glucose and Glycogen • Glucose – – – – – Six-carbon carbohydrate Most common monosaccharide Primary nutrient supplying energy to cells Concentration carefully maintained Bound into the polysaccharide glycogen during glycogenesis • Liver and skeletal muscle store excess glucose following a meal – Broken down from glycogen during glycogenolysis • Liver breaks down glucose from glycogen as needed Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Figure 2.20 Glycogenesis CH2OH C O H C H OH H H C OH HO C C H OH (a) Glucose Glycogenolysis (b) Glycogen Figure 2.21 Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Monosaccharides 6–carbon sugars (hexose) CH2OH CH2OH O HO H OH H OH H OHCH2 O H H H 5–carbon sugars (pentose) HO CH2OH OH Galactose O H HO OH OHCH2 H H H O OH H OH H H OH OH Ribose Fructose H H H OH H Deoxyribose (a) Disaccharides CH2OH CH2OH O H H OH H HO O H O H H OH OH HO Sucrose H O H H OH CH2OH H (b) CH2OH H H OH OH H H CH2OH H O H HO H H OH O CH2OH Lactose O H H OH OH H HO H CH2OH H O H O H OH Maltose H H H OH OH OH Biological Macromolecules: Proteins • Proteins serve a vast array of functions – – – – – – – Serve as catalysts (enzymes) in metabolic reactions Act in defense Aid in transport Contribute to structural support Cause movement Perform regulation Provide storage Protein Functions (Table 2.5) Biological Macromolecules: Proteins General protein structure • Proteins composed of one or more strands of monomers • Monomers are amino acids – 20 total in living organisms – Have an amine and a carboxylic acid functional group • both covalently linked to same carbon atom – Carbon also covalently bonded to a hydrogen and different side chain structures • referred to as the R group • distinguish different amino acids from one another – Amino acids covalently linked by peptide bonds Figure 2.24 Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Amino acid Carboxylic acid Amine H Peptide bond Peptide bond H H O N C C R R group (1 of 20 different structures) OH H H H O N C C OH R (a) H H H O N C C OH R H2O (b) Polymer protein Carboxylic acid Amine H H H O H H O H H O H H O H H O H H O H H O H H O H H O N C C N C C N C C N C C N C C N C C N C C N C C N C C N–terminal (c) R R R R R R R R R OH C–terminal Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Glycine (Gly) Nonpolar H O C C OH NH2 Isoleucine (Ile) H O C C OH H O NH2 C C H C CH3 CH H CH3 CH3 Alanine (Ala) NH2 H O C C Leucine (Leu) OH NH2 Phenylalanine (Phe) H O C C OH NH2 CH2 CH2 CH2 CH3 CH3 CH3 H O C C OH Tryptophan (Trp) H O NH2 C C CH2 OH CH2 C HN OH CH3 Polar Serine (Ser) NH2 H O C C Threonine (Thr) H OH Asparagine (Asn) O NH2 C C OH C CH3 CH2 NH2 OH CH3 OH H O C C OH Glutamine (Gln) NH2 H O C C CH2 CH2 C CH2 NH2 O Tyrosine (Tyr) OH NH2 Charged NH2 H O C C NH2 CH2 CH2 O H O C C Histidine (His) NH2 OH H O C C CH2 CH2 C C O C C C O– HC O– OH Lysine (Lys) OH NH2 H O C C Arginine (Arg) OH CH2 H N N H+ CH NH2 H O C C CH2 CH2 CH2 CH2 CH2 NH3+ NH NH2 Cysteine (Cys) NH2+ CH2 CH O C O– CH2 CH2 NH2 H O C C Methionine (Met) OH NH2 H O C C CH2 CH2 S CH2 H S OH CH3 Allows bends in protein chain Forms disulfide bond Always the first amino acid in a protein sequence (may be removed following synthesis of protein) OH CH2 CH2 Proline (Pro) OH (+) Charge Aspartic acid (Asp) OH O C (–) Charge Glutamic acid (Glu) H CH2 NH2 O Special functions Figure 2.26 NH2 Valine (Val) NH2+ Protein Structure: Amino Acid Sequence and Protein Conformation • Primary structure, linear sequence of amino acids Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Primary structure Linear sequence of amino acids joined by peptide bonds Figure 2.27a Peptide bond Amino acid H H N O R C C C N R H (a) C H O Biological Macromolecules: Nucleic Acids – Macromolecules that store and transfer genetic information in cells – Two classes deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. Nitrogenous base The nucleotide monomer – Three components: sugar, phosphate group, and a nitrogenous base • sugar a five-carbon pentose • phosphate group attached at carbon five • nitrogenous base attached to same sugar at carbon one • nitrogenous base with single-ring or double-ring structure NH2 P N Phosphate group O –O P N O N CH2 O– O Sugar OH in RNA OH H in DNA (a) Nucleotide monomer Figure 2.22a Deoxyribonucleic acid (DNA) Double-stranded nucleic acid Found in chromosomes in the nucleus and in mitochondria Has deoxyribose sugar, phosphate, and one of four nitrogenous bases: adenine, guanine, cystosine, or thymine does not contain uracil Double-strands held together by hydrogen bonds thymine paired with adenine; guanine paired with cytosine – Responsible for directing the synthesis of proteins • essential for multiple body functions • over 10,000 different proteins in the human body •Ribonucleic acid (RNA) –Single-stranded nucleic acid –Found in the nucleus and within cytoplasm of the cell –Has ribose sugar, phosphate, and one of four nitrogenous bases: •adenine, guanine, cystosine, or uracil •does not contain thymine Figure 2.22b Pyrimidines Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. NH2 O C C HC N HC C CH3 C Cytosine (C) (both DNA and RNA) Purines O C N C C NH C C HC HC N H CH C N Adenine (A) (both DNA and RNA) (b) Nitrogenous bases N H N NH HC C O Uracil (U) (RNA only) O N HC N H Thymine (T) (DNA only) NH2 C C N H N H N C NH HC O O NH2 Guanine (G) (both DNA and RNA) Figure 2.22c-d Copyright © The McGraw–Hill Companies, Inc. Permission required for reproduction or display. U Unique to RNA P O 5′ Phosphate group Nitrogenous base G P Sugar–phosphate “backbone” Nitrogenous base Nucleotide Deoxyribose sugar O Ribose sugar Nucleotide Phosphate group P A A P P O T G P Phosphodiester bonds C P T P Unique to DNA C P A O P Hydrogen bonds between nitrogenous bases OH 3′ (c) RNA (single–stranded) 3′ (d) DNA (double–stranded) 5′ Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Chromosome Figure 4.31b T A Hydrogen bonds C G Complementary base-pairing A T C Sugarphosphate backbone C Coiled chromatin A T DNA Histones C G G Nucleosome (b) Levels of organization Nitrogenous bases A Function of the Nucleus and Ribosomes— Transcription: Synthesizing RNA Process of Transcription • Three types of RNA produced during transcription: – messenger RNA (mRNA) – transfer RNA (tRNA) – ribosomal (rRNA) • Three events of transcription: – Initiation DNA unwound by specific enzymes – Bonds broken between DNA DNA strand copied by mRNA, termed template strand – Other strand, coding strand, not copied – Termination Rewinding of DNA into double helix Function of the Nucleus and Ribosomes— Translation: Synthesizing Protein • Translation – – – – – – Synthesis of a new protein mRNA threaded through ribosome Code in nucleotide sequence of mRNA translated Converted into amino acids to produce protein Takes place at ribosomes within the cytoplasm mRNA transcribed from genes • linear sequence of nucleotides • carries “instructions” for synthesizing proteins • read three bases at a time, in codons – Types of codons: • start codon, AUG, signal to begin protein synthesis • consecutive codons, code for amino acids • stop codon, where mRNA reading ends Function of the Nucleus and Ribosomes— Translation: Synthesizing Protein Required Structures – Transfer RNA (tRNA) • brings specific amino acids to a specific mRNA codon • “cloverleaf” shape • has region termed anticodon – base pairs with complementary codon in mRNA • has amino acid acceptor region – where specific amino acid attaches to tRNA – based on tRNA’s anticodon sequence – Amino acids • building blocks for protein synthesis • 20 found in proteins of living things Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Figure 4.35 Summary of transcription and translation Transcription of DNA in the nucleus forms RNA molecule mRNA is processed prior to exiting nucleus Translation of mRNA into protein occurs at a ribosome in the cytoplasm 1 Transcription. Occurs within the nucleus. Pre-mRNA is transcribed from DNA and processed to form mature mRNA prior to leaving the nucleus. Events in nucleus mRNA Template strand Nucleus mRNA processing Mature mRNA exits the nucleus Protein 2 Translation. Follows transcription; mRNA is read to direct tRNAs in adding amino acids; protein molecule is formed. Events in cytoplasm tRNA mRNA Ribosome Transcription – mRNA carries the code DNA C–G T–A G–C A–T C–G G–C mRNA tRNA amino acid C G U A aspartic acid G C A U C G cysteine G C (transcription) (translation) (codons) anticodons Translation – tRNA translates the code Protein synthesis – rRNA makes the protein rRNA assemble amino acids make the protein Biological Macromolecules: Nucleic Acids Other important nucleotides • Adenosine triphosphate (ATP) – Nucleotide composed of nitrogenous bases adenine, ribose sugar, and three phosphate groups – Covalent bonds between last two phosphate groups • release energy when broken – Central molecule in chemical energy transfer within cells • Nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD) – Nucleotides participating in the formation of ATP Energy, Chemical Reactions, and Cellular Respiration • All living organisms require energy • We need energy to: – – – – – – power muscle pump blood absorb nutrients exchange respiratory gases synthesize new molecules establish cellular ion concentrations • Glucose broken down through metabolic pathways – Forms ATP, the “energy currency” of cells Energy: Forms of Energy Chemical Energy (A Form of Potential Energy) energy stored in a molecule’s chemical bonds Molecules function in chemical energy storage – Triglycerides • long-term energy storage in adipose tissue – Glucose • glycogen stores in liver and muscle – ATP • stored in all cells • produced continuously and used immediately – Protein • can be used as a fuel molecule but has more important functions Figure 3.3a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (a) Potential and Kinetic Energy Potential Energy: The energy of position Na+ Na+ ions have potential energy due to concentration gradient difference between the outside and inside of the cell. Na+ The Two States of Energy Kinetic Energy: The energy of motion Na+ Na+ Na+ Na+ ions exhibit kinetic energy as they move down the concentration gradient. Na+ Na+ Na+ Na+ Na+ Chemical Reactions: Chemical Equations • Metabolism – Collective term for all chemical reactions in the body • Chemical reactions – Occur when chemical bonds in existing molecular structures are broken – New bonds formed – Summary of changes written as a chemical equation Chemical Reactions: Classification of Chemical Reactions • Classified based on three criteria: – changes in chemical structure, changes in chemical energy, and whether the reaction is irreversible or reversible Classification Based on Changes in Chemical Structure • Catabolism – Collective term for all decomposition reactions • Anabolism – Collective term for all synthesis reactions • Metabolism – Collective term for all chemical reactions in the body Chemical Reactions: Classification of Chemical Reactions • Decomposition reaction – Initial large molecule broken down into smaller structures • e.g., the hydrolysis reaction of sucrose into glucose and fructose Figure 3.4a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Decomposition reaction: A large molecule is broken down into smaller chemical structures; AB CH2OH CH2OH H O H OH H HO H O H O H CH2OH CH2OH H OH CH2OH OH OH Sucrose (a) H H H2O A+B O H OH + H HO OH H OH Glucose O H H H OH HO CH2OH OH H Fructose Chemical Reactions: Classification of Chemical Reactions Classification Based on Changes in Chemical Structure Synthesis reaction – Two or more structures combined to form a larger structure • e.g., the dehydration synthesis reaction forming a dipeptide Figure 3.4b Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Synthesis reaction: Two or more atoms, ions, or molecules are combined to form a larger chemical structure; A + B H2O Amino acids (b) Dipeptide AB Chemical Reactions: Classification of Chemical Reactions Classification Based on Changes in Chemical Energy • Exergonic reactions – Reactants with more energy within their chemical bonds than products – Energy released with net decrease in potential energy – E.g., decomposition reactions • Endergonic reactions – Reactants with less energy within their chemical bonds than products – Energy supplied with a net increase in potential energy – E.g., synthesis reactions Chemical Reactions: Classification of Chemical Reactions • ATP cycling – The continuous formation and breakdown of ATP – ATP formed from energy released in exergonic reactions • fuel molecules from food oxidized • energy in their bonds transferred to ADP and free phosphate to form ATP – ATP oxidized • released energy used for energy-requiring processes – Only a few second worth of ATP present at a time • formation of ATP occurs continuously to provide energy Figure 3.7 Copyright © The McGraw-Hill Companies, Inc. 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ATP (a) ATP formation (Endergonic reaction) Triphosphate group P Energy supplied P Adenine (b) Splitting ATP (Exergonic reaction) P High-energy bond Ribose Energy released ADP P Phosphate (Pi) Adenine Diphosphate group P P Ribose P Cellular Respiration • Exergonic multistep metabolic pathway • Organic molecules oxidized and disassembled by a series of enzymes • Potential energy in chemical bonds released • Energy used to make ATP (endergonic process) • Oxygen required Cellular Respiration: Overview of Glucose Oxidation • Enzymes for glucose oxidation are found in both: – The cytosol, semifluid cell contents – The mitochondria, small organelles within the cell • Stages of glucose oxidation: – Glycolysis (anaerobic cellular respiration) • occurs in cytosol • can occur without oxygen – citric acid cycle – electron transport system • other three collectively referred to as aerobic cellular respiration • require oxygen • occur in mitochondria The role of mitochondria in the production of the high-energy compound ATP Although most ATP production occurs inside mitochodria, the first steps take place in the cytosol. In this reaction sequence, called glycolysis (glycos, sugar + -lysis, a loosening), each glucose molecule is broken down into two molecules of pyruvate. The pyruvate molecules are then absorbed by mitochondria. Glucose CYTOPLASM The energy released during a series of steps performs the enzymatic conversion of ADP to ATP, which leaves the mitochondrion. 2 Pyruvate MITOCHONDRION Citric acid cycle Enzymes and ADP + phosphate coenzymes of cristae MATRIX In the mitochondrial matrix, a CO2 molecule is removed from each absorbed pyruvate molecule; the remainder enters the citric acid cycle, of TCA (tricarboxylic acid) cycle, an enzymatic pathway that systematically breaks down the absorbed pyruvate remnant into carbon dioxide and hydrogen atoms. The hydrogen atoms are delivered to enzymes and coenzymes of the cristae which catalyze the synthesis of ATP from ADP and phosphate. At the end of this process, oxygen combines with the hydrogen atoms to form water molecules. Figure 3.6 2 Figure 3.15 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cytosol Mitochondrion Cellular Respiration Anaerobic cellular respiration (glycolysis occurs in cytosol) Glycolysis Intermediate stage Citric acid cycle Electron transport system Aerobic cellular respiration (intermediate stage, citric acid cycle, and electron transport system occur in mitochondria) Cellular Respiration—Glycolysis: Anaerobic Cellular Respiration • Glycolysis – Anaerobic process in the cytosol – Glucose broken down into two pyruvate molecules • pyruvate’s fate dependent on oxygen availability – Net production of 2 ATP and 2 NADH molecules – Pathway contains ten enzymes Summary of Glycolysis • Glucose initial substrate • Pyruvate final product • Net 2 ATP formed (2 invested, 4 formed) • Two NADH formed Cellular Respiration—Glycolysis: Anaerobic Cellular Respiration The Fate of Pyruvate • Chemical changes made to pyruvate depend upon oxygen availability – If sufficient O2 available, pyruvate enters mitochondria – If insufficient O2 available, pyruvate converted to lactate Cellular Respiration—Aerobic Cellular Respiration: Citric Acid Cycle “KREB’S” Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Cyclic metabolic pathway – ATP, 3 NADH, and 1 FADH2 formed during one cycle – Occurs in mitochondria – Requires oxygen – Acetyl CoA initial substrate – Two CO2 and one CoA produced – 1 ATP, 3 NADH, 1 FADH2 formed per cycle – Oxaloacetic acid involved in first step and regenerated in last step – Two “turns” for one glucose molecule • 2 ATP, 6 NADH, 2 FADH2 Pyruvate Acetyl CoA CoA OAA regenerated CO2 NADH NAD+ Citric acid cycle FADH2 NAD+ NADH CO2 FAD NAD+ ATP ADP NADH (a) Net chemical reaction of citric acid cycle Cellular Respiration—Aerobic Cellular Respiration: The Electron Transport System Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • The electron transport system Cristae Matrix – Involves the transfer of electrons from NADH and FADH2 • energy released used to make ATP – Involves structures located in the inner membrane of mitochondria ATP synthetase Electron carriers Outer compartment Q H+ H+ H+ H+ Outer membrane • electron carriers, H+ pumps, ATP (a) Structures of the electron transport system synthetase enzymes (Figure 3.20) H+ C H + pumps Figure 3.20c Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Glycolysis NADH NADH Intermediate stage Matrix NADH e- FADH2 Citric acid cycle e- ATP 1 O 2 2 e- ADP + Pi H+ ATP synthetase H2O H+ H+ H+ H+ H+ H+ H+ H+ Electron carriers H+ pumps 1 Electrons are transferred from NADH and FADH2 through a series of electron carriers within the cristae. O2 is the final electron acceptor. (c) Details of the electron transport system 2 Energy of electrons “falling” is used to move H+ up its concentration gradient from the matrix to the outer compartment. 3 ATP synthetase harnesses the kinetic energy of the H+ “falling” down its concentration gradient to bond ADP and Pi to form ATP. Cellular Respiration: ATP Production • ATP in glucose breakdown Stage/Total Glycolysis Intermediate Stage Citric Acid Cycle Substrate level phosphorylation 2 ATP –– 2 ATP Total 4 ATP Oxidative phosphorylation 2 NADH to 6 ATP 2 NADH to 6 ATP 6 NADH to 18 ATP 2 FADH2 to 4 ATP 34 ATP – Transport of NADH during glycolysis takes 1 ATP per NADH – Total = 4 ATP + 34 ATP – 2 ATP = 36 ATP for one molecule glucose Enzymes: Function of Enzymes • Enzymes – – – – Are catalysts that accelerate normal chemical activities Decrease the activation energy of cellular reactions Only facilitate reactions that would already occur Increase the rate of product formation • Chemical reactions – Are termed uncatalyzed reactions if no enzyme present – Are termed catalyzed reactions if enzyme present Enzymes: Structure and Location Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Active site Active site’s specificity of shape: Substrate – permits only a single substrate to bind – helps catalyze only one specific reaction Enzyme (Figure 3.9) Enzyme-substrate complex Enzymes: Structure and Location • Enzyme produced from normal protein synthesis within cells – Some remain within cells • e.g., DNA polymerase which helps form DNA – Some become embedded in plasma membrane • e.g., lactase in walls of small intestine cells • helps digest lactose – Some are secreted from the cell • e.g., pancreatic amylase • released from pancreas to participate in starch digestion Cofactors – Molecules or ions required for normal enzyme function – Associate with particular enzyme – Nonprotein organic or inorganic structure • organic cofactors called coenzymes – e.g., vitamins or modified nucleotides serving as coenzymes Figure 3.10a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Decomposition reaction: Lactose digested to glucose and galactose Lactose 1 The substrate binds Glucose Enzyme-substrate complex (a) 3 The bond is broken between glucose and galactose. 4 Products: Glucose Substrate: Lactose Enzyme: Lactase shape, resulting in an induced fit between substrate and enzyme. O Galactose 2 The enzyme changes to the enzyme, forming an enzyme-substrate complex. and galactose are released, and the enzyme is free to bind other substrates. Enzymes: Classification and Naming of Enzymes • Enzyme names – Generally based on: • the name of substrate or product • sometimes subclass • suffix –ase – E.g., pyruvate dehydrogenase transferring hydrogen from pyruvate – E.g., DNA polymerase helping form DNA – E.g., lactase digesting lactose Enzymes: Enzymes and Reaction Rates Effect of Temperature • Three-dimensional shape of enzymes dependent on temperature – Human enzymes function best at optimal temperature • normal to slightly elevated body temperature (95-104° F) – Moderate fever • results in more efficient enzyme activity – Severe increases in temperature • cause protein denaturation with loss of function Enzymes: Enzymes and Reaction Rates Effect of pH • Enzymes function best at optimal pH – – – – Between pH of 6 and 8 for most enzymes Changes in H+ disrupting electrostatic interactions Enzyme loss of shape, denaturation Optimal pH may differ • e.g., enzymes working in the lower pH of the stomach Cellular Respiration: Other Fuel Molecules That Are Oxidized in Cellular Respiration • Other fuel molecules can be oxidized to generate ATP – Increases during conditions of starvation – Fatty acids • preferred molecule for muscle tissue at rest • provide long-term energy reserves • enzymatically changed two carbons at a time to form acetyl CoA (beta-oxidation) • acetyl CoA enters pathway at citric acid cycle • can only be used aerobically – Proteins • different amino acids enter pathway at different points • amine group removed and waste converted to urea and excreted 88 Membrane Transport— Passive Processes: Diffusion • Diffusion – Describes net movement of a substance – Moves from area of greater concentration to area of lesser concentration – Molecules and ions in constant motion due to kinetic energy – If unopposed, continues until substance reaches equilibrium • molecules evenly distributed throughout a given area – “Steepness” of concentration gradient • difference in concentration between two areas • steeper gradient with a faster rate of diffusion – Temperature • higher movement with higher temperature • results in faster rate of diffusion Figure 4.7 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Membrane Transport— Passive Processes: Diffusion Cellular Diffusion • Simple diffusion – – – – Molecules passing between phospholipid molecules Include respiratory gases (O2 and CO2), some fatty acids, ethanol, urea Movement dependent on concentration gradient alone Continue to move as long as gradient exists • Facilitated diffusion – Require assistance from plasma membrane proteins – Maximum rate of transport determined by number of channels and carriers • higher rate with greater number of transport proteins Figure 4.8 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Small nonpolar solutes move down their concentration gradients. Interstitial fluid Oxygen Cytosol Carbon dioxide Figure 4.9a Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Ions move down their concentration gradient through water-filled channels. Na+ Interstitial fluid Cytosol (a) Channel-mediated diffusion Na+ leak channel K+ leak channel K+ Figure 4.9b Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Carrier proteins change shape to transport molecules across the plasmamembrane. Carrier-mediated diffusion Interstitial fluid Glucose Cytosol Glucose carrier protein (b) Carrier-mediated diffusion Small, polar molecules assisted across membrane by carrier protein Transport substances such as glucose Binding of substance causing change in carrier protein shape Move substances down their gradient Membrane Transport— Passive Processes: Osmosis • Osmosis – Passive movement of water through selectively permeable membrane • membrane allowing passage of water • membrane preventing passage of most solutes – Occurs in response to differences in water concentration • different concentrations on either side of a membrane Semipermeable membrane allowing for passage of water only Side A with more solutes initially Water moving from side B to side A by osmosis Continues until fluids equal in concentration Figure 4.11 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Side A Side B Side A Side B Non-permeable solutes (glucose, Na+, protein) Water molecules Higher solute Semipermeable concentration, membrane lower water concentration Lower solute concentration, higher water concentration Initial setup: Side A contains proportionately more solute and less water. Semipermeable membrane Final setup: Water moved by osmosis from side B down the water gradient to side A until the concentrations of side A and side B are equal. Osmosis Osmosis Isotonic solution – Both cytosol and solution with same relative concentration of solutes – saline with a concentration of 0.9% NaCl Isotonic to erythrocytes – No net movement of water • Hypotonic solution – – – – Solution with a lower concentration of solutes than cytosol E.g., erythrocytes in pure water Water moving down concentration gradient May cause cell lysis (rupture) • hemolysis, term for ruptured red blood cells • Hypertonic solution – – – – Solution with a higher concentration of solutes than cytosol E.g., erythrocytes in 3% NaCl pure water Water moves down concentration gradient May cause cell to shrink • termed crenation Figure 4.12 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Isotonic solution Hypotonic solution Interstitial fluid is less concentrated than cytosol. Interstitial fluid is the same concentration as cytosol. Erythrocyte Water leaves cell. Erythrocyte Erythrocyte SEM 11,550x SEM 9030x SEM 6900x Interstitial fluid is more concentrated than cytosol. Water enters cell. No net movement of water. Normal erythrocytes (a) Hypertonic solution Erythrocytes nearing hemolysis (b) Erythrocytes undergoing crenation (c) a: © Dennis Kunkel Microscopy, Inc./Phototake; b: © Dennis Kunkel Microscopy, Inc./Phototake; c: © Dennis Kunkel Microscopy, Inc./Phototake Membrane Transport: Active Processes Active Transport – – – – Opposes the movement of solutes by diffusion Solutes moved against a concentration gradient Maintains gradient between cell and interstitial fluid Uses energy directly from breakdown of ATP Membrane Transport: Active Processes Figure 4.13 • Ion pumps – Active transport proteins that move ions across membrane – Help cell maintain internal concentration of ions – E.g., Ca2+ pumps in plasma membrane of erythrocytes • prevent cell rigidity from accumulated calcium Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Erythrocyte ADP +Pi ATP Ca2+ pump Ca2+ Cytosol Interstitial fluid Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cytosol Interstitial fluid Secretory vesicle Plasma membrane Figure 4.16 Vesicle membrane 1 Vesicle nears plasma membrane Vesicular Transport Requires vesicles Membrane proteins membrane-bounded sac filled with materials Requires energy to transport vesicles – Exocytosis • vesicle fuses with membrane • releases substances outside the cell • E.g., release of neurotransmitters from nerve cells – Endocytosis 2 Fusion of vesicle membrane with plasma membrane Plasma membrane opens 3 Plasma membrane opens to outside of cell 4 Release of vesicle components into the interstitial fluid and integration of vesicle membrane components into the plasma membrane • vesicle encloses material outside cell • fuses with membrane to release inside cell • phagocytosis, pinocytosis Membrane Transport: Active Processes • Phagocytosis – – – – Occurs when cell engulfs large particle external to cell Forms large extensions termed pseudopodia Surround particle, enclosing it in membrane sac Fuses with lysosome • contents digested here – Only in a few cell types • E.g., white blood cells engulfing microbes • Pinocytosis – – – – – Internalization of droplets of interstitial fluid Multiple, small vesicles formed All dissolved solutes taken into cell Performed by most cells E.g., cells of capillary wall