CHEM2770 Lecture #1 - Introduction to Biochemistry PDF

Lecture #1 An Introduction to Biochemistry  Chapter 1 The Cell The nature and structure of cells. Animal Cellprinciples Unifying vs Plant Cell of Biochemistry – for you to review. Animal Cell...

Lecture #1 An Introduction to Biochemistry  Chapter 1 The Cell The nature and structure of cells. Animal Cellprinciples Unifying vs Plant Cell of Biochemistry – for you to review. Animal Cell Plant Cell  What is Biochemistry? Bios means life in Greek Al kimya means the transmutation in Arabic – Chemistry explains ‘change’ using atoms All chemical change occurs as a consequence of electron rearrangement Biochemistry explains life in terms of the atomic structure of biological molecules The Periodic Table of the Elements Most Abundant Elements Essential Ions Common Trace Elements Less Common Trace Elements  Diversity of Life There are ~10 x 106 different species in the Biosphere Some are simple and unicellular while others are complex multicellular animals Biomolecule % in E. coli Protein 15 Nucleic Acid 7 Carbohydrate 3 Lipid 2 Water 70 Other 3  Diversity of Life All living cells use the same types of biomolecules and share common metabolic features – Suggests a common ancestor Evolution lends change over time – Change occurs as a result of chemical reactions  Metabolism Metabolism includes the sum of all catabolic and anabolic reactions occurring inside of the cell E. coli contains ~1000 metabolites that are interconverted by ~2000 enzymes http://www.manet.uiuc.edu/pathways.php  Metabolism Catabolism: reactions that degrade nutrient molecules – Release energy stored in chemical bonds Anabolism: reactions that assemble large molecules from smaller ones – Require energy supplied by catabolic reactions Five types of biochemical reactions occur by either forming or breaking chemical bonds: 1. Group Transfer 2. Internal Rearrangement 3. Cleavage 4. Condensation 5. Oxidation-Reduction  Chemical Bonds Electronegativity – Measures the ability of an atom to attract electrons to itself when involved in a chemical bond H 2.1 C 2.5 N 3.0 O 3.5 P 2.1 S 2.5 Saturated Hydrocarbons – Contain C-C and C-H covalent bonds – Referred to as aliphatic – Highly non-polar Characterized by covalent bonds with equal electron sharing  Functional Groups Molecule reactivity is determined by functional groups containing polar covalent bonds C=O carbonyl -O-C=O carboxyl H-O alcohol/hydroxyl H-N amino H-S thiol P-O phosphate  Functional Groups Biochemical Functional Groups Nucleophiles Nucleophiles:  Functional Groups Biochemical Functional Groups Electrophiles Electrophiles:  Functional Group Reactivity Nucleophile Reactivity Nucleophile reactivity Nucleophiles:  Functional Group Reactivity Electrophile Reactivity Electrophile reactivity Electrophiles:  Functional Group Reactivity Most biochemical reactions occur when nucleophiles and A lot of biochemistry electrophiles happens when nucleophiles meet make contact – electrophiles. Involves arrow pushing  Functional Group Reactivity Nucleophilic ThisAddition is a Group Transfer. Examples of group transfer – Nucleophilic addition reaction Nucleophilic Substitution – Nucleophilic substitution reaction This is a Group Transfer.  Functional Group Reactivity Condensation reactions Condensation  Thermodynamics Thermodynamics All living organisms require energy in order to sustain life activities All living organisms require a source of energy to live and The first law ofgrow. thermodynamics: – The total energy of the universe is constant 1st Law of Thermodynamics: The energy of the universe is – Energy is theconstant. capacity of a system to do work or release heat Measured in joules Energy is the capacity of a system to do work or release heat. The units for energy are Joules.  Thermodynamics Different energy forms include: – Kinetic Energy: energy an object has due to its motion – Potential Energy: energy an object has due to its position Ex) gravity – H: Enthalpy Heat energy of material at constant pressure – Heat Transfer of energy from a region of high temperature to a region of low temperature Associated with the motions of atoms or molecules  Thermodynamics Even though energy cannot be created or destroyed, durin physical or chemical change, energy may change its form Energy is able to change form during a physical or chemical In the picture below, the ball at rest has zero kinetic energ change lots of gravitational potential energy. The total energy in the whole system is unchanged – It is able to interconvert from one form to another – PE + KE= constant  Thermodynamics The second law of thermodynamics – The entropy of the universe increases – Entropy S A measure of the disorder of a system Tendency of energy to spread over time Measured in joules/Kelvin  Thermodynamics DH is not a good predictor of spontaneity H1 < H2 ice liq water Energy Level Diagram H2 H H1 Reaction H = H2 – H1 ~ +6 kJ / mole  Clearly, H is not a good predictor of spontaneity. Thermodynamics The following is aa spontaneous Consider change spontaneous change withHa=DH=0 in which 0. o o x o o o x x o x o x o o x x o x o x x o x x x o x x x o x o o x o o x x o o x o x x x o x o o x x x o o x x x o x o The gasesThe mix spontaneously gases andand mix spontaneously irreversibly irreversibly but there but there is no is no change in change in the energy of the atoms. the energy of the atoms The degree of disorder, entropy increases spontaneously. The entropy has spontaneously increased By combining the 1st and 2nd Laws we can predict spontaneous By combining the 1st and 2nd laws of thermodynamics we are able to change. predict spontaneous change  Thermodynamics Gibb’s Free Energy, G, is the energy available to do work at constant temperature and pressure H is the total energy of the system and TS is the wasted energy – DG is the useful energy – The greater the H, the more work can be done – The smaller the S, the greater the order, the more work can be done  Thermodynamics e.g. glucose Example: Glucoseà water and water + carbon carbon dioxide dioxide e.g. glucosewater and e.g. glucose water anddioxide carbon carbon dioxide G – G = H – H – T (S – S1) G2 – G21 = 1H2 – H21 – T1(S2 – S12) G2 – G1 = H2 – H1 – T (S2 – S1) G G= = H –HT – ST S In a chemical G change: = H –T S In aInchemical a chemical change: change: In a chemical change: H = HHC= +HHC D+–H(H DA– +(H HAB) + HB) H = HC + HD – (HA + HB) IfIf DH IfH isisH+, positive, isheat +, heat heat is absorbed: is absorbed is absorbed endothermic – Endothermic. – Endothermic. (ice melts) (ice melts) – Ice melting If H Ifis +, DH heat is is absorbed heat negative, – Endothermic. is released: (ice melts) exothermic If IfH isH–is, heat is evolved – , heat – Exothermic. is evolved – Exothermic.(glucose(glucose oxidation) oxidation) – Oxidation of glucose  Thermodynamics S = SC + SD – (SA + SB) S = SC + SD – (SA + SB) If S is +, disorder has increased. If DS is positive, disorder has increased If S is +, disorder has increased. If S is –, order has increased. If DS is negative, order has increased If G S=isG–, order + G has increased. – (G + G ) C D A B If DG is positive, free energy is absorbed: endergonic (non- IfG G= isG spontaneous + energy +,Cfree reaction)GD – is(G A + GBEndergonic. absorbed: ) G must have beenhave – G must added beentoadded the system. This will not occur spontaneously. to the system If G is +, free energy is absorbed: Endergonic. G must have If DG is Ifnegative, been addedfree G is –, free energy to energy the is released: is released: system. exergonic This Exergonic. will (spontaneous The not occur reaction is spontaneously. reaction) spontaneous. If G is –, free energy is released: Exergonic. The reaction is spontaneous.  Thermodynamics G = H – T S H S G – + – spont. + – + non-spont. + + ? ? – – ? ? The entropy The 2ndofLaw thestates universe that isSuniverse always >increasing 0 but living cells decrease entropyà How? But, as cells grow Scell < 0 Do living cells defy the laws of thermodynamics ?????  Thermodynamics No! Cells remove G from sunlight/nutrients in their surroundings Cells remove G from sunlight / nutrients in their surroundings, – Decreases the order in the surroundings decreasing the order in their surroundings, increasing the order – Increases the order within themselves within themselves. So all laws are obeyed. – All laws of thermodynamics are therefore obeyed Suniv = Scell + Ssurr > 0 But – Energy where within is theand glucose energy otherinnutrients glucose?is internal Kinetic energy from vibrations, rotations and translations Molecules Potential contain energy “internalinenergy”. of electrons chemicalThis bondsincludes kinetic energy of vibrations, rotations, and translations of the molecules and the potential energy of the electrons in chemical bonds.  Thermodynamics Consider the following reaction For the reaction inFor the reaction a closed system, the reaction will proceed until “equilibrium” is reached, after which, no change will occur. In a closed system, the reaction proceeds until equilibrium is reached – in a closed Once system, reached, changethe willreaction no longerwill proceed until “equilibrium” occur This is the Law of Mass Action. – isThe reached, afterAction Law of Mass which, no change will occur. Equilibrium can be described by the equilibrium constant. – Equilibrium is described by the equilibrium constant This is the Law of Mass Action. [C] [D] K eq [A] [B] Equilibrium can be described by the equilibrium constant. – Free energy changes drive reactants and products to equilibrium The reactants They fall and products are spontaneously [C] [D] driven down to equilibrium the free by free energy hill toward equilibrium which is there energylowest free energy changes. K They state spontaneously fall down the free energy eq is their lowest free energy state. hill toward equilibrium which [A] [B]  Thermodynamics The relationship The relationship between between freefree energy energy change change andequilibrium and equilibriumisisgiven by: given by: G R T * ln( K eq ) R = Gas Constant = 8.31 J / mol. K. T = Temp in K. If Keq = 19 at 25oC then, RT ln(K 'eq ) = – (8.315 J/mol K)(298 K)(ln19) = – 7,296 J/mol = – 7.3 kJ/mol