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Chemistry and Physics of Life Animal diversity is shaped (and limited) by constraints imposed by a the rules of physics and chemistry • Orderliness increases as an organism develops from a fertilized egg into an adult • The increase in orderliness requires a constant input of energy • When energy intake stops, metabolism stops, and the order is lost. Energy Categories Figure 2.2 • Animals rely on five forms of energy, which are interconvertible Radiant & Thermal energy • Radiant energy travels by waves or particles • Chemical reactions in organisms produced heat that must “radiate” out from animals and plants • Thermal regulation is a big “issue” in physiology Radiant energy from a cat Thermal Energy • An increase in thermal energy results in movement of molecules, and greatly affecting the rate of chemical reactions. • In physiology, rate of chemical reactions is often synonymous with metabolic rate • Most chemical reactions involve changes in thermal energy • Exothermic reactions – release heat • Endothermic reactions – absorb heat Food Webs & energy conversion 1. Radiant energy – 2. Mechanical energy 3. Electrical energy 4. Thermal energy – 5. Chemical energy – Figure 2.3 Electrical energy: Electrochemical Gradients Potential and Kinetic energy that results from the movement of charged particles 1. Organisms invest energy to delay diffusion 2. The unequal distribution of charged particles is a form of energy storage 3. Gradients can be chemical, electrical or both depending on the nature of the molecule 4. Gradients across a cell membrane (Membrane potential) are extremely important Electromotive force: emf • The electrochemical gradient is maintained by active transport across cell membranes • The energy of diffusion is a major source of potential physiological energy & one that is often overlooked Temperature Influences Chemical Reactions • Increasing temperature more molecules reach activation energy • Increases the likelihood of endothermic reactions Figure 2.5 Chemical Reaction Vocabulary • Enthalpy – average thermal energy of a collection of molecules • Activation energy – energy required for a molecule to reach a transition state • Transition state – intermediate structure between a substrate and a product • Change in enthalpy (DH) = Hproducts – Hsubstrates • Exothermic: DH is negative • Endothermic: DH is positive Things to keep in mind • Chemical reactions proceed according to the rules of thermodynamics • In physiology, as (as in every science, The law of conservation of energy holds firm. • Entropy – the universe is becoming more chaotic DG = DH - TDS 1. If DG is (-); the reaction is exergonic, and the process is spontaneous 2. If DG is (+), the reaction is Endergonic, and the reaction must be driven by external energy Reduction of Free energy drives chemical and biochemical processes Free energy is a measure of the ratio between heat energy, and the change in entropy DG = DH - TDS Consider the breakdown of glucose: – The large molecule is broken down to carbon dioxide and water (entropy increases) – Heat is released to the environment DH is negative – enthalpy decreases – Change in free energy will be negative Exergonic and Enderngonic pairs Catabolism-degradative, oxidative, energy yielding Anabolism-synthetic, reductive, energy consuming What is taking place in terms on enthalpy, entropy and free energy? DG =? DG =? Chemical energy is all about bonds • Ionic bonds • Covalent bonds • Intermolecular bonds Covalent Bonds • Atoms with unpaired electrons can form covalent bonds with other atoms with unpaired electrons, i.e., share electrons • Atoms with more than one unpaired electron can form multiple covalent bonds • Geometry of the resultant molecule is influenced by the bond angle Figure 2.6 van der Waals Interaction • Each electron within an atom is constantly moving • The nucleus is more negative when the electron is closer; positive when further away • Transient dipole – polarity created by asymmetry in electron distribution • van der Waals interaction – atom with transient dipole affects the distribution of electrons in a second atom • Effective only over a narrow range of distances Bond Energy Chemical bond energy is the principle currency used by organisms to maintain homeostasis, to grow, and to engage in life activities Table 2.1 Water • Most cells are primarily composed of water • Aquatic organisms live in water • Cells of terrestrial animals are bathed in water • Many physiological processes arose to meet challenges of the physical and chemical properties of water Hydrogen Bonds • Asymmetric sharing of electrons between two atoms • e.g., Organization of water molecules • Hydrogen (+) of one water molecule is attracted to oxygen (-) of another Figure 2.9 Water: The Unique Solvent • The hydrogen bonds that form between water molecules account for some of the essential — and unique — properties of water. Non-covalent Bonds (Weak Bonds) • Control macromolecule structure • Arise between atoms with asymmetrical distributions of electrons • Types of intermolecular bonding – van der Waals forces – Hydrogen bonds – Hydrophobic bonds Figure 2.8 Functional Groups: order among chaos • Combinations of atoms and bonds that recur in biological molecules Figure 2.7 Binding of ions to Marcromolecules • A site with a partial negative charge attracts cations •A site with a partial positive charge attracts cations Cation binding sites on organic molecules are generally oxygen atioms in silicates, carbonyls, carboxylates, and esthers The oxygen atom is electron-hungry and draws electrons from the surrounding atoms Hydrophobic Bonds • Due to mutual aversion to water • No significant dipoles (polarity) • Cannot interact with polar molecules like water • e.g., oil congealing into droplets – not attracted to each other, but repelled by water Weak Bonds & Temperature • Weak bonds are sensitive to temperature because of lower bond energies • Affects three-dimensional macromolecule structures • Denature – macromolecules unfold due to rising temperature • e.g., protein, membranes, DNA Amphipathic compound contain a polar and nonpolar group. The hydrophobic, nonpolar “tails” will “huddle in the center The polar heads isll face outward – and interact with the water The formation of a micelle crucial to the formation of biological membranes in living cells Solvents and Solutes • Solvent – most abundant molecule in a liquid • Solute – the other molecules in a liquid • Solution – solvents and solutes • In biological systems the solvent is usually water Concentration, of solutions, and colligative properties Molarity Moles of solute 1000g solution Molality Moles of solute 1000g solvent 1. The amount of solute to solvent is the most important measure physiologically – so molality “should be used” 2. Molality is generally inconvenient – most physiologists use molarity 3. Colligative properties depend on the concentration of solute particles in a solution. Water is Affected by Temperature • Temperature changes the organization of water molecules • High temperature: molecules posses enough thermal energy to escape the force of surface tension, i.e., boil • Low temperature: stabilize molecules as a result of additional hydrogen bonds, i.e., it solidifies or freezes Figure 2.11 Density of Water • Temperature influences the density of water • Ice is less dense than liquid water – Ice has more hydrogen bonds, but molecules are held further apart • Water is most dense at 4°C – Most deep waters are 4°C – Surface waters can be colder or warmer Water is a Very Stable Liquid • High melting point • High boiling point • High heat of vaporization – amount of energy to cause liquid water to boil Table 2.2 Solutes can Dissolve in Water • Solutes form hydrogen bonds with water molecules • Hydration shell – solute surrounded by water molecules Figure 2.12 Water dissolves polar molecules What's in your water? • A compound added to gasoline to help it burn more cleanly • Methyl Tertiary Butyl Ether (MTBE). Solutes Affect Properties of Water • Colligative properties • Decrease freezing point • Increase – Boiling point – Vapor pressure – Osmotic pressure • Depend on the number of solutes, not their size or charge Solutes Impose Osmotic Pressure • Semipermeable membrane – allow some molecules to cross while restricting others • Osmotic pressure – force associated with the movement of water • Osmolarity – ability of solution to induce water to cross a membrane Figure 2.13 Relative Osmolarity and Tonicity Figure 2.14 pH and the Ionization of Water • Dissociation of a water molecule into ions – H:O:H H:O:- + H+ • pH = -log10 [H+] – Brackets denote concentration • Pure water is pH 7 (-log 10-7) Figure 2.5 Neutrality • Neutrality - [H+] = [OH-] or pH = pOH • Affected by temperature – pH at neutrality (pN) varies inversely with temperature • 5°C: pN = 7.28 • 25°C: pN = 7.00 • 45°C: pN = 6.72 Acids and Bases Alter the pH of Water • Acids – release protons pH – HA H+ + A- • Bases – accept protons pH • Mass action ratio = ([H+] X [A-]) / [HA] • Equilibrium constant (Keq) - [HA] reaches a minimum and [H+] and [A-] reach a maximum – pK = -log10 Keq – pK = pH –log [A-] / [HA] • pK reflects the strength of acids or bases Strength of Acids and Bases Table 2.3 pH Affects Ionization State Figure 2.16 Temperature Affects Ionization State • pK increases as temperature decreases • Each ionizable groups has a characteristic sensitivity to temperature DpK/°C Buffers Limit Changes in pH • Buffer – chemical found in solution that dampens the effect of added acid or base • Mixture of protonated and deprotonated molecules • Most buffers rely on weak acids • Buffers work only over a particular range of pH values Figure 2.17 Biomolecules • • • • • Four main types Carbohydrates Lipids Proteins Nucleic acids • Metabolism – Sum of metabolic pathways for the interconversion of these macromolecules and their breakdown for energy Carbohydrates • Lots of hydroxyl (-OH) groups • No other general structural features • Glucose is the most common carbohydrate in animal diets • Energy metabolism • Biosynthesis: precursor to most other carbohydrates Monosaccharides • Used for energy and biosynthesis • Small carbohydrates with three to seven carbons – six is most common Figure 2.18 Disaccharides • Two monosaccharides connected by a covalent bond • Broken down when used Figure 2.19 Carbohydrates + other Macromolecules • Glycosylation – addition of carbohydrates to other macromolecules • Alters molecular profile of the macromolecule • e.g., glycolipids, glycoproteins – Both are typically found in plasma membranes and the extracellular fluid Complex Carbohydrates • • • • Polysaccharides Long chain of monosaccharides Energy storage or structural molecules e.g., glycogen, starch, cellulose Complex Carbohydrates , Cont. Figure 2.20 Complex Carbohydrates, Cont. • Structural carbohydrates – Chitin – exoskeleton of arthropods – Hyaluronate – gel-like spacer between cells in vertebrates Figure 2.21 Lipids • All are hydrophobic • Composed of a carbon backbone – Linear – aliphatic – Ring – aromatic • e.g., fatty acids, triglycerides, phospholipids, steroids Fatty Acids • Long chains of carbon ending with a carboxyl group • Saturated – no double bonds • Unsaturated – one or more double bonds Figure 2.22 Triglycerides • Fatty acids are stored as triglycerides • Fatty acids are esterified to a glycerol backbone – e.g., Mono-,di-, tri-acylglycerol • High concentration in lipids Figure 2.23 Phospholipids • Dominate biological membranes • Constructed from diacylglycerol • Two classes – Phosphoglycerides – Sphingolipids Phospholipids, Cont. Figure 2.24a Phospholipids, Cont. Figure 2.24b Steroids • Four hydrocarbon rings • Synthesis involves many intermediates Figure 2.25 Proteins • Make up almost half of cell volume (excluding water) • Mediate all cellular processes • Contribute to cell structure • Have complex structure Amino Acids • Proteins are polymers of amino acids • Amino acids: amino group (-NH2) and a carboxylic acid group (-COOH) • Termed a-amino acids because -NH2 and -COOH are located on the 1st carbon • Distinguished by side groups (R) • Can be nonpolar (hydrophobic), polaruncharged (hydrophilic) and polarcharged (hydrophilic) Amino Acids, Cont. Figure 2.26 (1 of 2) Amino Acids, Cont. Figure 2.26 (2 of 2) Protein Structure Figure 2.28 Primary Structure Figure 2.27 • Linear sequence of amino acids joined by covalent peptide bonds between the carboxyl and amino group Secondary Structure: a-helix & b-sheet Results from hydrogen bonding between the carboxyl oxygen and the hydrogen of the amine group. It is the most stable configuration hair, fingernails, claws, horns Tertiary Structure • Covalent bonds (disulfide bonds) and weak bonds (van der Waals forces, ionic bonds, and hydrogen bonds) Figure 2.30 Quaternary Structure • Multiple polypeptide chains • Dimer – 2 subunits – Homodimer – identical proteins – Heterodimer – different proteins • Trimer – 3 subunits • Tetramer – 4 subunits Molecular chaperones and Stress proteins • A family of proteins that helps the formation of the folded structure, and for the preservation of the complex structure • Commonly called heat-shock proteins Nucleic Acids • Two types • DNA – deoxyribonucleic acid – Genetic blueprint • RNA – ribonucleic acid – Read and interpret DNA to make protein – Three main forms • Transfer RNA (tRNA) • Ribosomal RNA (rRNA) • Messenger RNA (mRNA) Nucleic Acids, Cont. • Polymers of nucleotides linked by phosphodiester bonds • Nitrogenous base (4 types) attached to sugar linked to a phosphate – Cytosine – Adenine – Guanine – Thymine (DNA only) – Uracil (RNA only) Nucleic Acids, Cont. Figure 2.32 (1 of 2) Nucleic Acids, Cont. Figure 2.32 (2 of 2) DNA • Nucleotides can form bonds with only one other nucleotide – A + T: two hydrogen bonds – G + C: three hydrogen bonds 1. Doublestranded a-helix 2. Two strands are linked by hydrogen bonds DNA Structure Figure 2.33 Histones • Strand of mammalian DNA is several meters long • DNA is compressed by DNA-binding proteins (histones) • Advantages of compression by histones – Large amounts of DNA fit into small volumes – Reduces damage caused by radiation and chemicals • Must be uncompressed for DNA and RNA synthesis Figure 2.34 DNA Organization • Genome - entire collection of DNA within a cell • Chromosome – separate segments of DNA • Genes – DNA sequence within a chromosome • Exons – genes that encode RNA • Introns – interspersed DNA sections Figure 2.35 Genome Size • Highly variable • Little relationship between genome size and animal complexity Figure 2.36 Enzymes • • Catalysts that accelerate chemical reactions Enzymes have three properties 1. Active at low concentrations 2. Increase the rate of reactions but are not altered 3. Do not change the products • • Most are made of proteins Some are made of RNA (ribozymes) Cofactors • Nonprotein components of enzymes • Many are loosely associated with enzymes • Prosthetic group – cofactor covalently bonded into the enzyme • Coenzymes – organic cofactors usually derived from vitamins • Inorganic ion cofactors – copper, iron, magnesium, zinc Reaction Acceleration • Enzymes accelerate reactions by reducing reaction activation energy (EA) • Uses the same substrate and yields the same product • Reaction follows a different path with a different intermediate at the transition state • S + E ES ES* EP* EP E + P • Active site – location in enzyme where substrate binds Reaction Acceleration, Cont. Figure 2.37 Enzyme Kinetics • Conditions that influence the rate of enzymatic reactions • Not the fastest rate, but the appropriate rate • Changing the concentration of substrate and product will affect reaction rates Figure 2.38 Michaelis-Menton Rectangular Hyperbola • • • • V = Vmax X [S] / ([S] + Km) V = initial velocity Vmax = maximum velocity Km = indicator of affinity of enzyme for the substrate Figure 2.39 Sigmoidal Relationships • Homotropic enzymes – show a sigmoidal relationship between V and [S] • Cooperativity – enzymes show increased affinity for S with increasing [S] • Hill coefficient – degree of cooperativity (slope at inflection) Figure 2.41 Environmental Effects • Enzyme activity is affected by temperature, pH, salinity, and hydrostatic pressure Figure 2.42 Environmental Effects, Cont. • Enzymes are affected in different ways • Changes in weak bonds alter three-dimensional structure • Changes in ionization state of amino acids within the active site • Changes in the ability of the enzyme to undergo structural changes necessary for catalysis Non-catalytic Molecules • Do not participate directly in catalysis, but can alter enzyme kinetics Figure 2.44a, b Non-catalytic Molecules, Cont. Figure 2.44c Energy Storage &Reducing Energy • Two main forms of storage: – Reducing energy – High energy bonds • The Reducing equivalents are a vitamin + nucleotide – e.g., NAD, NADP, FAD, FMN • Oxidoreductases are enzymes that store energy in reducing equivalents by converting them from an oxidized (energy-poor) form to a reduced (energy-rich) form – e.g., NAD+ NADH • Redux status – reducing energy within a cell = reduced form/oxidized form – e.g., [NADH/NAD+]