Midterm 1 Notes Biochemistry PDF

Biochemistry aims to explain biological form and function in chemical/molecular terms. - Living organisms share remarkable similarity in their chemical makeup, distinct from non-living matter. - Fewer than 30 naturally occurring chemical elements are essential to organisms. - Hydrogen, Ox...

Biochemistry aims to explain biological form and function in chemical/molecular terms. - Living organisms share remarkable similarity in their chemical makeup, distinct from non-living matter. - Fewer than 30 naturally occurring chemical elements are essential to organisms. - Hydrogen, Oxygen, Nitrogen, and Carbon make up 99% of living matter. Lightest elements capable of forming 1, 2, 3, 4 bonds. - The lightest elements form the strongest bonds. - Trace elements are important for enzymes (later this quarter) and other specific functions of proteins. For instance hemoglobin requires iron in order to transport oxygen in your blood. Red- structural components of cells, required to eat grams/day. Yellow – trace elements required for specific pathways, requires only a few mg/day  Biomolecules are compounds of Carbon with a variety of functional groups - Versatility of carbon bonding likely a major factor in the selection of carbon compounds for molecular machinery during evolution - No other element can form molecules of such widely different sizes, shapes, composition  Freedom of rotation differs for C-C single and double bonds - Free rotation around each single bond (unless very large or charged groups are attached) - Length of a single bond ~ 0.154 nm - Double bonds are shorter and do not allow free rotation. Note the carbons and bonded atoms lie in the same plane. - Later in quarter: Implications in protein folding (what shape gets created) - Major theme: connection between form and function Common Functional groups of macromolecules you should know (carboxyl)  Functional groups in a biomolecule - Many biomolecules are polyfunctional, i.e. they contain multiple functional groups - Chemical “personality” of a molecule is determined by the chemistry of its functional groups and their orientation in 3D space.  Macromolecules - Dissolved inside of the aqueous phase (cytoplasm) of all cells. dissolved inzo - Most are Polymers with molecular weights above ~5,000 D.a. (daltons) - Assembled from relatively simple monomers. The synthesis of macromolecules is a major energy-consuming activity for cells. La Cocina in Dixon!  Macromolecules - Examples? - Monomers are usually smaller molecules, MW - Cytoplasm Water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes > - assume always there unless stated otherwise  - How does water generally compare to other common solvents ? Water has relatively higher melting and boiling points. Requires more energy for a phase change. What might explain these observations of water’s properties ? These properties are a consequence of attractions between adjacent water molecules – hydrogen bonding. "Stickyners"  Structure of a Water Molecule Attractions between adjacent water molecules results in great internal Partial is cohesion of water charges what allows for hydrogen bonding - At RT, thermal energy is of same order of magnitude required to break H-bonds. What does this mean for water? Form break rapidly ; unstable ~20 kJ/mol - What do you notice about these bond two types of bonds? - H-bonds are longer and weaker than covalent bonds. H-bonds are ~ 10% covalent, 90% ~470 kJ/mol electrostatic. - shorter bond; stronger hold - requires more energy to break  The Electron Structure of Water - Oxygen nucleus attracts electrons more strongly than hydrogen. Oxygen is more electronegative. - Shared electrons are on average more often near oxygen, resulting in two dipoles - Therefore each hydrogen has partial positive charge and oxygen has partial negative charge - As a result of these partial charges, there is an electrostatic attraction between the hydrogen of one water molecule and the oxygen of another. I bonding * partial charges are critical for how proteins are able to function in their biochemical role z Electronegativity in a polypeptide lone - pair e-  The Electron Structure of Water: - Oxygen nucleus attracts electrons more strongly than hydrogen. Oxygen is more electronegative - Shared electrons are on average more often near oxygen, resulting in two dipoles - Therefore each hydrogen has partial positive charge and oxygen has partial negative charge - As a result of these partial charges, there is an electrostatic attraction between the hydrogen of one water molecule and the oxygen of another. - What would happen if water were a linear molecule? Cancels out dipoles ; will lose properties (H-bonding) multiple of same motec will influence shape of other same moler. In Jame volution.  Draw a single water molecule hydrogen bonding with its neighboring water molecules How many other water molecules can it H-bond with? ↑! * Don't forget %0 lone pair Regular crystal lattice of water molecules in ice One water molecule interacts with: 3.4 on average in water molecular dynamics (water molecules are disorganized and in constant motion) 4 in ice (each water molecule is fixed in space) -- this crystal lattice structure is why ice is less dense than liquid water and why ice can float on water  Hydrogen bonding in water At any given time, most of the molecules in liquid water are hydrogen bonded … but the lifetime of each H bond is how long??? 1-20 picoseconds! “flickering clusters” : short- lived groups of water molecules interlinked by H- bonds in water Water. Theme in Biochem: The molecular world is highly dynamic!  Molecular Modeling of H-Bonding in Liquid Water H-bonding is more like a network - always moving Similar to Spider web - short lived interactions H-bonds are short lived due to weak bond strength https://www.youtube.com/watch?v=Zl74NCVbA5A  Hydrogen Bonds: Examples A Must bond to electrone atom - - - Hydrogen bonds are not unique to water - H-bonds form between electronegative atoms (acceptors) and hydrogens covalently bounded to another electronegative atom (donors) - Is water a hydrogen bond donor or acceptor? BOTH Biological Relevance of Hydrogen Bonds Hydrogen Bonds can Impart Directionality on Interacting Molecules is stronger straight because It can be equally shared when they are aligned vertically - H-bonds are strongest when the bonded molecules are oriented to maximize electrostatic interaction - This occurs when the H atom and the two atoms that share it are in a straight line. Puts the positive charge of H directly between two partially negative charges. - Thus H-bonds are capable of holding two molecules or functional groups in a particular 3D arrangement.  H-bonds are weak. Having hundreds makes the bonds , stronger. (Net overall) Are all of these scenarios possible? Why or why not? NO · can't have NO. carbon 2 I bonded Yes. electro-positive together , both It bonded to 2 are partial positiv electro neg.. atoms Property of water: Water as a solvent Water is a polar solvent – Compounds that dissolve easily: hydrophilic proteins (most) , nucleic acid) carbohydrates Examples? , – Non-polar molecules don’t dissolve easily: hydrophobic lipids Examples? – Water dissolves polar molecules by replacing solute-solute H-bonds with solute-water H-bonds. Ho replaces H-bonds between 2 molecules, with new H-bonds from the water.  NO His mean no electroneg makes partial. for strong covalent bonds 3 partial charges - makes them charges , very Polar. no electro negativity will be hydrophobic polar = loves H20 - Amphipathic: compounds that have both polar and nonpolar groups so they have both characteristics eX. amino acids  Every day compound: NaCl To vaporize table salt/ separate Na and Cl in air, you would need to raise the temp to ? ~800 oC! Nat Care strongly bonded , so high s is required To break those bonds Salt dissolves in water at ? Room temp ~24oC breaks bonds H2 easily What is going on? Natsclare able to find complimentary charges  Water as a solvent Water interacts Water shields the ion’s charges so they electrostatically with can separate "Aydration shells" charged solutes  Water as a Solvent - Proteins and other macromolecules with polar groups are surrounded by a dynamic water “shell” Not static shell - , H20 constantly moving - This hydration shell plays a part in molecular interactions. In order for these molecules to touch each other , they must displace Ho overcome the "shell" which is HIGHLY energetically costly· positive value; thus DG is negative. solution. What about dissolving Nonpolar Gases Are Poorly Soluble in Water gasses Nonpolar Compounds in Unfavorab Force Energetically The molecules of the biologically important gases CO2, Changes in the Structure of Water water? O2, and N2 are nonpolar. In O2 and N2, electrons are shared equally by both atoms. In CO2, each CPO bond is polar, but the two dipoles are oppositely directed and When water is mixed with benzene or hexane, t phases form; neither liquid is soluble in the other. N cancel each other (Table 2–3). The movement of mole- polar compounds such as benzene and hexane Are biologically important gases like carbon cules from the disordered gas phase into aqueous solu- tion constrains their motion and the motion of water hydrophobic—they are unable to undergo energetica favorable interactions with water molecules, and th molecules and therefore represents a decrease in entropy. interfere with the hydrogen bonding among wa dioxide and oxygen are highly soluble in The nonpolar nature of these gases and the decrease in molecules. All molecules or ions in aqueous solut entropy when they enterNO solution combine andto makeare interfere with thesohydrogen bonding of some wa water? CO2 O2 interact with Hy not. they would. not polar , TABLE 2–3 Solubilities of Some Gases in Water Solubility Gas Structure* Polarity in water (g/L)† Nitrogen NqN Nonpolar 0.018 (40 8C) Oxygen OPO Nonpolar 0.035 (50 8C) Carbon dioxide !" !" Nonpolar 0.97 (45 8C) OPCP O Ammonia H H Polar 900 (10 8C) A H G D N !" Hydrogen sulfide H H Polar 1,860 (40 8C) G D S !" *The arrows Must bethere ispolar represent electric dipoles; to(d2)interact a partial negative charge with at the head of the arrow, a partial H2O positive charge (d1 ; not  Some solutions to this problem that have evolved water soluble carrier proteins (ex. Hemoglobin) change into a form that is water soluble (ex. Carbon dioxide forms carbonic acid H2CO3 in water and travels as the very soluble bicarbonate ion HCO3 -) 202 + H20 > HzCoz # Coz is sombre  Weak interactions 1. Hydrogen bonding weak compared to covalent 2. Electrostatic interactions/ Ionic interactions 3. Hydrophobic interactions 4. Van der Waals interactions All of the above are NONCOVALENT Noncovalent bonds are crucial to biological processes These interactions are affected by water in importantly different ways If covalent bonds had to be broken for every biological · process , It would be energetically costly  Molecular Interactions vs. Bonds - Molecular interactions are attractive or repulsive forces between molecules and between non-bonded atoms. Are non-covalent. Intra 3 Inter forces. can occur at R. - Bonds hold atoms together within molecules. Are covalent. - Bonds break and form during chemical reactions. Fire: chemical reaction where bonds within cellulose break, while bonds of carbon dioxide and water form. Bond energies typically 400 KJ/mol, much greater than RT, so bonds do not break at RT. - T/F: Covalent Bonds remain intact when - 1) ice melts True OnlyI bonds break.. - 2) DNA strands separate True OnlyIt bonds. break - 3) When salt dissolves in water False Ions.. find Complimentary charged ions to form new molecules.  Hydrogen Bonds Remember, not unique to water. Hydrogen atom is partially shared by two electronegative atoms such as N or O. H-bond donor is the group that includes the H and electronegative atom. c02Water.indd Page 50 27/08/12 1:48 PM user-F408 8 H-bond acceptor is a separate2.electronegative atom with an unshared Hydrogen Bonds. These interactions are largely ionic inte CHAPTERelectron pair. 1 Biochemistry: partial charges on nearby atoms attracting one another. Hydro An Evolving Science Strongest H-bonds tend to beresponsible for specific base-pair straight, important formation in orienting in the DNA dou interacting molecules. 50hydrogen atom in a hydrogen bond is partially shared by tw Water tive atoms such as nitrogen or oxygen. The hydrogen-bond don Hydrogen- Hydrogen- that includes both the atom to which the hydrogen atom is bond donor bond acceptor linked and R the hydrogen atom itself, whereas the hydrogen-bo N H N the atomAless tightly linked to the hydrogen R atom (Figure 1.9) !− !+ !− A O negative Aatom to which the hydrogen N H O O atom is covalently bond tron density away from the hydrogen H Strong A atom, which thus dev O H N H Weaker positive charge (d!).bond hydrogen Thus, the hydrogen O atom with hydrogen bond a partial p O Ginteract K G K O H O canO P with an atom havingOP a partial negative charge (d D ionic D interaction. FIGURE 1.9 Hydrogen bonds. Hydrogen Hydrogen bonds are much weaker than FIGURE 2–5 Directionality of the hydrogen bond. covalent bonds. Th The attraction between bonds are depicted by dashed green lines. 1 The positions of the partial charges (d! gies ranging from 4 to 20 kJ mol (from 1 to 5 kcal mol" " the partial electric charges (see Fig. 2–1) is greatest when the three atoms and d") are shown. bonds are also somewhat longer than covalent bonds; their involved in the bond (in this case O, H, and O) lie in a straight line. When (measured from the hydrogen atom) range from 1.5 Å to 2. the hydrogen-bonded moieties are structurally constrained (when they distance ranging from 2.4 Å to 3.5 Å separates the two nonhy  G noted Ionic Interactions (or repulsions) Between peptide bonds O G D D CP O H N nonco enzym neuro Ionic interactions O result B Attraction O!NH3 "O O CO the la subst Repulsion O!NH3 H3N! O provid molec ing bi - Also called “salt bridges” in proteins (later in course) intera Water - Charged groups on one molecule attract the oppositely Hydrophobic group CH3 CH3 charged group on the same or another interactions G D molecule. W CH (Fig. - Strength depends on the ions andAdistance between Box 4 CH2 them A so tig CH2 - Can have attraction and repulsion of charges A the sa van der Waals Any two atoms in These interactions close proximity be de reson  Hydrophobic Interactions - Are the result of an intrinsic attraction of hydrophobic molecules for one another True or False hydrophobic molecules do not have Intrinsic attraction - Results from the system achieving the greatest to each other thermodynamic stability by minimizing the number of ordered water molecules required to surround the hydrophobic portion of the solute molecules hydrophobic interactions - 2nd Law of Thermodynamics: tendency of nature towards arise from : disorder. Total entropy of the universe is always increasing Total entropy of universe is always increasing What happens when a hydrophobic molecule enters water? - Water molecules become more ordered around the hydrophobic molecule. - Is this thermodynamically favorable? NO. goes against 2nd law. - This reduces Ho interactions < thus reducing entropy  Second Law of Thermodynamics the tendency in nature is toward ever greater disorder in the universe (2nd law) the total entropy of the universe is continually increasing can not tumble around freely More movement more interaction Which is more = ordered? "diffusional " capabilities are more limited · #20around hydrophobic molecules - Entropy of the OR system is REDUCED when a hydrophobic molecule is added to water Minimizing order by clustering the hydrophobic bits Entropy is reduced when a hydrophobic molecule is present Non polar regions cluster together to present the smallest area to the aqueous environment clusters mean lessordered around to molecules than Results in the least amount of Individual ordered water, thus the hydrophobic molecures greatest thermodynamic stability  Minimizing order by clustering “Flickering clusters” of H2O molecules in bulk phase the hydrophobic bits Highly ordered H2O molecules form “cages” around the hydrophobic alkyl chains (a) Cl Amphipathic compounds such as many m FIGURE 2–7 Amphipathic lipids, form micelles compoundswhere all the in aqueous solution. (a) Long- On hydrophobic parts of the molecule are chain fatty acids have very hydrophobic alkyl chains, each of which is at surrounded by a layer of highly ordered water molecules. (b) By cluster- shielded from water, while the ing together in micelles, the fatty acid molecules expose the smallest th or hydrophilic parts are exposed to water. possible hydrophobic surface area to the water, and fewer water mole- Fe cules are required in the shell of ordered water. The energy gained by ar en The forces that hold the the non-polar freeing immobilized water molecules stabilizes the micelle. regions together are hydrophobic interactions. molecules in theirIt’s strengthvicinity, immediate results but frompolar or Entropy the system charged solutesachieving it’s greatest (such as NaCl) compensate for lost increased thermodynamic water-water hydrogenstability. bonds by forming new solute- water interactions. The net change in enthalpy (DH) M for dissolving these solutes is generally small. Hydro- Al Theresolutes, phobic is no however, attraction between offer no such the compensation, gr hydrophobic and their additionparts of the to water maymolecules. Thein a therefore result se wa association small is driven gain of enthalpy; by thermodynamics the breaking of hydrogen bonds sh to minimize between organization water molecules takesofupwater energy from the m molecules. system, Sometimes requiring the input of called energythefrom the sur- m en hydrophobic roundings. effect. In addition to requiring this input of energy, inc dissolving hydrophobic compounds in water produces a measurable decrease in entropy. Water molecules in the immediate vicinity of a nonpolar solute are con- (b) strained in their possible orientations as they form a Micelle Formation Hydrophobic Effect  tron d Van der Waals interactions O H N positiv O H O can int ionic i FIGURE 1.9 Hydrogen bonds. Hydrogen Hy bonds are depicted by dashed green lines. The positions of the partial charges (d! gies ra At any instant, distribution of electronic charge and d") are shown. bonds around an atom is fluctuating and not perfectly (measu distan symmetrical in a hy Hydrogen- Hydrogen-bond bond donor acceptor Th Happens when two uncharged atoms are very 0.9 Å 2.0 Å straigh N H O hydrog close – surrounding electron clouds influence each earity other 180° one an the pr describ Random variations in where the electrons are 3. van around one nucleus can create a transient dipole , that th Repulsion which induces a transient opposite diploe in a van der Waals time. A nearby atom, causing attraction. contact distance This t throug Energy Distance 0 electro As nuclei get closer, they begin to get repelled by neighb Attraction overlapping electron clouds come contac Waals Energy associated with VdW forces is small (less becaus FIGURE 1.10 Energy of a van der Waals than H-bond), but can add together for large interaction as two atoms approach each En amounts of atoms in close contact (like in folded other. The energy is most favorable at the van der Waals contact distance. Owing to typica proteins) electron–electron repulsion, the energy mol"1 H-bonding is 2 separate partial charged atoms rises rapidly as the distance between the. togeth atoms becomes shorter than the contact and th Vander waals is 1 atomIts electrons. distance. We  attraction between nonpolar moieties. Rather, it results known as London forces). As the two nuclei draw closer from the system’s achieving the greatest thermody- together, their electron clouds begin to repel each other. namic stability by minimizing the number of ordered At the point where the net attraction is maximal, the Van der Waals interactions water molecules required to surround hydrophobic por- tions of the solute molecules. Many biomolecules are amphipathic; proteins, pig- ments, certain vitamins, and the sterols and phospholipids nuclei are said to be in van der Waals contact. Each atom has a characteristic van der Waals radius, a measure of how close that atom will allow another to approach (Table 2–4). In the “space-filling” molecular models of membranes all have both polar and nonpolar surface shown throughout this book, the atoms are depicted in regions. Structures composed of these molecules are sta- Nonpolar sizes proportional molecules to their or nonpolar van der Waals radii. parts bilized by hydrophobic interactions among the nonpolar to aggregate in water owing to a phenom regions. Hydrophobic interactions among lipids, and between lipids and proteins, are the most important hydrophobic effect. Because water molecu determinants δof" structure in biological membranes. TABLE hydrogen 2–4 vanbonds der Waals withRadii nonpolar and Covalent substanc δ! δ! δ" Hydrophobic interactions between nonpolar amino acids form “cages” (Single-Bond) of relatively Radii of Some rigidElements hydrogen-b also stabilize the three-dimensional structures of proteins. van der Waals nonpolar Covalentmolecules radius for ( Hydrogen bonding between water and polar solutes and hexagons around Element radius (nm) single bond (nm) also causes an ordering of water molecules, but the This state is energetically unfavorable bec H energetic effect is less significant than with nonpolar the entropy, or0.11 randomness, of 0.030 the populat solutes. Disruption of ordered water molecules is part of O 0.15 0.066 the driving force for binding of a polar substrate (reac- ecules. (The role of entropy in chemical sys N 0.15 0.070 Covalent van derpolar tant) to the complementary Waalssurface of an enzyme: in Section 2.4.) If nonpolar molecules in a radius C 0.17 0.077 entropy increases radius as the enzyme displaces ordered ronment aggregate with their hydrophobi (0.062 nm) the substrate, water from (0.14 nm) and as the substrate displaces S 0.18 0.104 ordered water from the enzyme surface (Fig. 2–8). each P other, the 0.19 net hydrophobic 0.110 surface FIGURE 210 Two oxygen molecules in van der Waals contact. water is reduced I 0.21(Figure 2-11, right). 0.133 As a In this model, red indicates negative van der Waals charge and Interactions blue indicates positive Are Weak water is needed to form the cages surroun charge. Transient dipoles in theAttractions electron clouds of all atoms give rise to Sources: For van der Waals radii, Chauvin, R. (1992) Explicit periodic trend of van der Waals Interatomic radii.lar molecules, Chem. 96, 9194–9197.entropy increases relative to weak attractive forces, Whencalled two van der Waals uncharged interactions. atoms are broughtEach type very of close J. Phys. each Chemical element Bond, 3rd edn, Cornell For covalent radii, Pauling, L. (1960) Nature University Press, Ithaca, NY. state, and an energetically more favorable has of the Note: van der Waals radii describe the space-filling dimensions of atoms. When two atoms atom has a characteristic vantheir together, der Waals radiuselectron surrounding at whichclouds van der Waals influence are lessdistance Waals radii, because the joined atomsoptimal it's are In acovalently, joined sense, own then, the atomic radii atwater squeezes the point of bonding thanthe the vannonpol der interactions with other eachatoms are optimal. other. Random Because variations in the atoms repel positions of theone elec- are pulled together by the shared electron pair. The trons around one nucleus may create a transient electric aggregates. distance between nuclei in a vanRather than der Waals interaction constituting or a covalent bond is about equal to an another if they are close enough together for their outer electrons to dipole, which induces a transient, opposite electric dipole due asof ain length to hydrogen carbon–carbon it's the sum of the van der Waals or covalent single bond bonds, structure radii, respectively, is about 0.077 nmthe1 0.077 hydrophobic. for the two atoms. Thus the nm 5 0.154 nm. ef overlap without being shared in a covalent bond, the van der Waals ra- dius is a measure of the size of the electron cloud surrounding an atom. an avoidance of an unstable state—that is The covalent radius indicated here is for the double bond of O=O; the cages around individual nonpolar molecule single-bond covalent radius of oxygen is slightly longer. Nonpolar molecules can also associat through van der Waals interactions. The hydrophobic effect and van der Waals inte  Geko’s and Van der Waals trillions of H-bonds sums to very 1 strong interaction (force  Weak interactions are crucial for life Why wouldn’t we want all bonds to be covalent? To costly to break = rearrange covalent bonds. What examples of weak interactions are there in biology? DNA double helix , proteins? Water (hydration Shell) , carboxyl group 3 amino group in amino acids  Weak interactions are crucial for life Allow for dynamic interactions (lots of energy required to break covalent bonds) The cumulative effects of many weak interactions can be very significant protein folding, enzyme-substrate binding, DNA and RNA structure, hormone binding to its receptor, etc. within the same molecule inter : between 2 molecules Intra : amino acids, lipids cannot readily dissolve in the blood, the OH O C OH O C aqueous circulatory system that transports molecules and cells throughout the body. Instead, lipids such as cholesterol Ionic bond must be packaged into special hydrophilic carriers, called lipoproteins, that can themselves dissolve in the blood and C O HN Hydrogen bond C O HN be transported throughout the body. There can be hundreds CH3 H3C Hydrophobic to thousands of lipid molecules packed into the center, or and van der CH3 H3C core, of each lipoprotein. The hydrophobic core is sur- Waals rounded by amphipathic molecules that have hydrophilic CH3 H3C interactions parts that interact with water and hydrophobic parts that interact with one another and the core. The packaging of lipids into lipoproteins (discussed in Chapter 14) permits C O HO C O H3C their efficient transport in blood and is reminiscent of the containerization of cargo for efficient long-distance trans- Protein A Protein B Protein A Protein C Stable complex Less stable complex port via cargo ships, trains, and trucks. High-density lipoprotein (HDL) and low-density lipo- FIGURE 212 Molecular complementarity permits tight protein  Intro to Thermodynamics of Life The chemical composition of living organisms differs from their surroundings, even in face of constantly changing environments eX· Temperature Change doesn't change the fundamental chemistry in our body Though the overall chemical composition of organisms changes little through time, population of molecules within organisms is not static! Body is constantly making new molecules; same exact mol. Small molecules and macromolecules are constantly being synthesized and broken down in chemical reactions – constant flux of mass and energy through the system. Hemoglobin molecules in you right now were synthesized within last month and next month, all new molecules will be present. Rate of synthesis approximately equals rate of breakdown – dynamic steady state. Dynamic steady state is FAR from equilibrium and requires constant input of energy to maintain. What is another word for ‘equilibrium’ in this context? Death, no longer imputting energy no flux of mass  Living Systems Transform Energy and Matter from Their Surroundings Organisms are open systems – they exchange matter and energy with their surroundings. They obtain energy in two ways: 1. consumption of chemical fuels (glucose), and 2. absorb energy from sunlight. (plants) all energy on earth comes from the Sun. 1st Law of Thermodynamics is total amount of energy in universe remains constant. Therefore organisms use energy but do not destroy it. They convert it from one form to another. Example: Convert potential energy in chemical bonds (ATP) to kinetic energy of movement (muscle movement).  ng water can this process roundings. FIGURE 1–25 Some energy transformations in living organisms. As met- theThe surroundings end products ofundergo this oxidative anmetabo- increa the Randomization of Heat lism, CO2 and H2O, are Entropy abolic energy is spent to do cellular work, the randomness of the system (a) returned to (S) the surroundings. In f erated the burner Nutrients in environment entropy, whereas plus surroundings (expressed quantitatively as entropy) increases as the (complex molecules such from boiling sugars, fats)water can as the organism itself remains in a s this process the surroundings undergo an increase in potential energy of complex nutrient molecules decreases. (a) Living Potential energy organisms extract energy from their surroundings; (b) convert some of it C (the pose we turn “sys- off the burner state and undergoes entropy, into useful forms of energy to produce work; (c) return some energy to Sunlight whereas the the surroundings as heat; and (d) release end-product molecules that are noorganism change itselfin its internal remains in a steady o ”)water andat(b)allow100 8C (the “sys- Although - 2some state and of nd Law entropy undergoes arises no Thermodynamics change from is that inthe the itstotal dissipati internal entropyorder. of less well organized than the starting fuel, increasing the entropy of the universe. One effect of all these transformations is (e) increased order e “surroundings”) and allow Although some the Universe (decreased randomness) in the system in the form of complex macromol- Energy Chemical transformations entropy is always arises from increasing the dissipation and systems tend toward of is done, but heat, entropy also ecules. We return to a quantitative treatment of entropy in Chapter 13. transductions t cools, within cells accomplishno work is done, but ever entropy heat, arises greater randomness from another (entropy) also arises from kind another kind of disorder,of diso urroundings, work akettle to the Cellularsurroundings, work: chemical synthesis illustrated by the illustrated Increasing by# equation the equationfor molecules = the for the oxidation oxidation increasing of gluc of glucose: entropy of the surroundings (the (randomness) ndings (the mechanical work C6H12O6 1 6O2 88n 6CO2 1 6H2O mally small amount osmotic and electrical gradients until com- C 6 12O6 1 6O2 88n 6CO2 1 6H2O H nt until ned. At this com- light point production all parts genetic information transferof We can represent this schematically as ntitchen all parts are at of (c) precisely We the can represent this schematically as free energy Heatthat was once 7 molecules 12 molecules precisely the ettle of hot water at 100 8C, at oingwas work,once has Increased disappeared. randomness O2 7 molecules 12 moleculesCO2 (a gas) er nergy at is100 still 8C, present in the (entropy) in the surroundings (a gas) H2O CO (d) e., the “universe”) Metabolism produces but has disappeared. ndomized throughout. compounds simpler than initial fuel molecules: COThis the , 2 Glucose O2 (a solid) (a g (a liquid) esent in the 2! NH , H O, HPO 3 2 4 (a gas) e”) but has Decreased randomness Glucose - End products are returned to organism’s surroundings, H ides ghout. Energy for(entropy) (e) This Organisms (a solid) ing these two largewhile groups theof organisms itselfinterdependent (a li in the system increasing entropy, organism has remained Simple compounds polymerize Virtually at steady all energy transductions in cells can be traced state. derive theirtomacromolecules: energy, directly form information-rich DNA, RNA, to this flow of electrons from one molecule to another, in ant energy of sunlight. In the proteins a “downhill” flow from higher to lower electrochemica of asallyhuman callednature, increasing. “negative it is To bring about thevery entropy.” synthesis In tures, fact, of macro- immensely thefree-energy branch change, of rich DG, in in is determined itmolecules hasmathematics called entropy-poor. “negative entropy.” In fact, the branch of Gibbs and Free Energy from their monomeric units, free energy must change, DH, reflecting the kinds and num m- called information be supplied to the system (in this case, the cell). theory, entropy-poor. which is bonds and noncovalent interactions brok escom-basic to mathematics the programming called logicinformation of computers, and the entropy theory, which ischange, DS, describingisth he KEY CONVENTION: closelyTherelated randomness to or thermodynamic disorder of the com- theory. choes basicsystem ponents of a chemical -toGibbs isthe programming developed expressed as entropy, logicLiving system’s the theory of energy of computers, randomness: changes during is e- organisms are highly 1–3).ordered, nonrandom struc- ¢G 5 ¢H 2 T ¢S d ry the closely S (Box related chemical Anytochange reactions. thermodynamic in theory. Living tures, immensely randomness richof the in system information is and thus ics, of hake- the ten- thermodynamics, organisms entropy, the expressed ten- are as S; highly entropy entropy-poor. - Showed the free-energy content, and change, the entropy, ordered, absolute where, S; nonrandom G, of any releases heat, temperature, by definition, and the closed DH is negative for absolute and DS is positivestruc- tem for order s veryin thetures, ever-greater disorder Thewhich by in immensely DS, system definition the can convention rich be quantitatively a positive value when random- of has The infree definition energy information defined increasesin terms of is free of three the system’s G and energy 5 randomness. H thus 2 i parameters: is the of continu- universe isnesschemical entropy-poor. continu- increases. J. Willard - 1. Enthalpy reaction (heatchemical Gibbs, content), occurs A reaction process H, reflecting attendsconstant numberoccurs attem to occur spontaneo co who developed the theory of is negative (if free energy is released i bout is of the n- macro- synthesis entropy, S; and of themacro- free-energy energy and kinds absolute changes of bonds free-energy change, temperature, during chemi- (chemical, DG, weak (in T cell Yet change, is determined interactions). Kelvin). function largelyis depends DG, on deby mo he meric The definition units, free energy freeJ/mol calof reactions, energy must showed is Gchange, 5.H 2 that TS. and proteins DH, When reflectinga acids,the nucleic kinds for which the energy u- must chemical reaction change, - 2. Entropy, the free-energy DH, occurs atcontent, reflecting S. J/mol constant the kinds and numbe K formation is positive: the molecules are G, temperature, the no- this ell). case, the cell).bonds of any- closed 3. system canbonds and Temperature, noncovalent T (in be Kelvin)and more noncovalent interactions highly interact broken ordered than a mixture of t he ten- entropy, free-energy change, definedS;inand terms the DG, is absolute determined of three quan- bytemperature, the components.enthalpy To carry (inthese T out Kelvin ther st change, - and DH, reflecting the theof entropy kinds and andenergy the change, benumbers entropy ofGchemical DS, change, describing DS, des the in ness the or J. Willard The disorder Gibbs, definition tities: of Free the enthalpy, energy com- H,free can reflecting then defined is unfavorable, as: 5 H 2 TS. energy-requiring When (endergo of the 1839–1903 com- bonds the number and and noncovalent interactions system’s kinds of bonds; broken randomness: cellsand couple them to other reactions th formed, ntinu- m is expressedand thechemical as- system’s entropy Whenreaction entropy, change, a chemical randomness: occurs rxn occursat DS, describing at aconstant the constant in change temperature, T, the the free th as entropy,free-energy macro- m- energy change, change is defined DG,as:is determined by ¢G the5enthalp ¢H 2 (Box y, change in 1–3). system’s Any change randomness: in ¢G 5 ¢H 2 T ¢S y must ndomness ofchange, the DH, system ¢G reflecting is¢H T the ¢S kinds and numbers of chemic in epressed system isbonds 5 Kelvin does not change and noncovalent 2 where, much interactions by definition, broken and is neg DH forme is as entropy where, where, change, * Note by definition, DH is by definition, isnegative negative releases for rxn forthat DH heat, releases a reaction isheat negative and thatand DS isisfor posi a opy e, , whichchange, by releases and theand convention heat, entropy releases positiveDSforhas change, isrxn heat, that increases positive DS, and for describing system’s a DS reaction is randomness the change positive that for inath e com- increases the system’s random  Inorganic phosphate (Pi) G 5 H 2 TS. spontaneous When ¢G 5 !a = more forward without ¢H 2 T ¢S the imput of energy nstant temperature, ere, OH by definition, ermined by the O ! the enthalpy Free Energy DH is negative for a reaction that O P O P OH " P Adenosine (Adenosine monophosphate, AMP) eases heat, and and numbers DS is positive for a reaction that of chemical reases Gibbs the free O energy system’s O (G) expresses randomness. the amount of energy capable of doing ons broken and formed, work during Inorganic a reaction (at pyrophosphate (PPconstant ) temp. and pressure) amount of energy cribing the change in the i available to react A process tendstends A process to occur to occurspontaneously spontaneouslyonly only ifif DG is negative (free negative energy (if free is released). energy isAlso called exergonic released rxn. AG in the process). = - free energy released Tcell Yetenergy ¢S function (exergonic celldepends function largely relies onreactions), on rxns that requireso molecules, such that energy the(building asinput overallDNA ing ab teins andprocess nucleic isacids, exergonic: the sum for which the freeof the free-energy energy of changes simple ative forfrom nucleotides) a reaction that because final products are more highly ordered than ispositive: negative. mation isconstituents. the molecules are less stable and An ob ive for a reaction that re highly ordered Cells than usuala energy mixture of their monomeric ess. How? The couple sourcerequiring of freerxns energy in coupled (endergonic) to otherbio- rxns that amoun mponents. To carry logical liberate free out (exergonic) reactions energy these thermodynamically is the energy so thatreleased the overall byprocess breakage of is exergonic. tends avorable,i.e. pontaneously energy-requiring theonly sum if phosphoanhydride (endergonic) of DG is negative. bonds such as reactions, those in adenosine of posi s couple leased in them to the process). triphosphate Common other source reactions (ATP; Fig.rxn of exergonic that is toliberate 1–26) free and phosphoanhydride break guanosine triphos- bonds: priate y on molecules, ATP, phate such as GTP(GTP). Here, each P represents a phosphoryl group: to ano which the free energy of ules are Amino n protein acids and less stable DG1 is positive (endergonic) ture of their n AMP 1 P — P ATPmonomeric DG2 is negative (exergonic) [or ATP n ADP 1 P ] ese thermodynamically (a) endergonic) reactions, When these reactions are coupled, the sum of DG1 and ctions that liberate free  A Coupled Reaction positive (endergonic) negative (exergonic) (a) Mechanical example Spontaneous AG , = - he sum of DG1 and !G > 0 !G < 0 s is exergonic. By does not require Imput to synthesize and of energy Work Loss of ers essential to life. done potential raising energy of object position Biology he study of energy is the means by or light capture is reactions. In think- Endergonic Exergonic (b) Chemical example nd chemical processes. Reaction 2: es potential energy that ATP → ADP " Pi Reaction 3: made available by spon- Glucose " ATP →