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Bioenergetics and Biochemical Reaction types

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1 Bioenergetics and Biochemical Reaction types
Chapter 13

2 Chemical energy, photosynthetic energy
A property of the living organism: (1) alive, (2) grow, (3) reproduce Ability to harness energy Ability to channel it into biological work A fundamental properties of all living organism Simple precursor Synthesis of complex and highly ordered marcromolecules Chemical energy, photosynthetic energy Movement of heart: chemical energy  concentration gradient and electrical gradient Fireflies and deep-sea fish: chemical energy  light Biological energy transductions obey the same chemical and physical laws that govern all other natural processes  to understand these laws and how they apply to the flow of energy in the biosphere Bioenergetics and thermodynamics Bioenergetics: quantitative study of energy transductions (changes of one form of energy into another) 1. Biological energy transductions obey the law of thermodynamics Two fundamental laws of thermodynamics For any physical or chemical change, the total amount of energy in the universe remains constant; energy may change form or it may be transported form one region to another, but it cannot be created or destroyed In all natural processes, the entropy of the universe increase; the universe always tends toward increasing disorder

3 Some definition (again)
Gibbs free energy (G): the amount of energy capable of doing work during a reaction at constant temperature and pressure  ΔG (free energy change); joules/mole Enthalpy (H): the heat content of the reacting system; reflects the number and kinds of chemical bonds in the reactants and products  the heat content of the products is less than that of the reactants (ΔH is a negative); joules/mole Entropy (S): a quantitative expression for the randomness or disorder in a system The units of ΔG, ΔH = joule/mole =calories/mole (1 cal =4.194 J) The units of entropy (S) = joules/mole·Kelvin (J/mol·K) ΔG = ΔH - T Δ S Changes of free energy, enthalpy and entropy are related to each other quantitatively Energy transform into another Randomness or disorder increase Form products

4 2. Cells requires sources of free energy
Cells are isothermal systems (constant temperature system)  heat flow is not a source of energy The energy that cell can and must use is free energy from chemical reaction Heterotrophic cells: acquire free energy from nutrient molecules Photosynthetic cells: acquire free energy from absorbed solar radiation Transform to ATP 3. Standard free-energy change is directly related to the equilibrium constant Keq: equilibrium constant aA + bB cC+ dD [C]c [D]d when equilibrium status: no driving force, no net charge change when not equilibrium status: move toward equilibrium, net charge change; free energy change for the reaction Keq = [A]a [B]b Standard condition: (1) 1 M concentration or kilopascals (kPa) (2) temperature (298 K = 25 oC) the force deriving the system toward equilibrium  standard free-energy change, ΔGo [H+] = 1 M, pH = 0 In biological condition = well buffered condition at pH = 7.0; [H+] = 10-7 M, [H2O] = 55.5 M, [Mg2+] = 1 mM Physical constants: standard transformed constants = standard free-energy changes In physical condition ΔG’ o = –RT lnK’eq

5

6 4. Actual free-energy changes depend on reactant and product concentration
Keq: equilibrium constant [C]c [D]d Mass-action ratio (Q) aA + bB cC+ dD Keq = [A]a [B]b [C]c [D]d Actual free-energy change, ΔG = ΔG’ o + RT InK’eq = ΔG’ o + RT In = ΔG’ o + RT In Q [A]a [B]b Initially reaction proceeding toward to equilibrium: ΔG = negative Negative of ΔG becomes less and more less, eventually zero when equilibrium is reached. [C]eq [D]eq 0= ΔG = ΔG’ o + RT In Q = ΔG’ o + RT In = ΔG’ o + RT InK’eq [A]eq [B]eq ΔG’ o = - RT InK’eq 5. Standard free-energy changes are additive ΔG1’o ΔG2’o ∴ A C, ΔG’ o = ΔG1’o + ΔG2’o A B C Glucose + Pi Glucose-6-phosphate + H2O: ΔG’ o = 13.8 kJ/mol ATP + H2O ADP + Pi: ΔG’ o = kJ/mol ATP + Glucose ADP + Glucose-6-phosphate: ΔG’ o = kJ/mol

7 ΔG’ o is a way of expressing the equilibrium constant for a reaction
[glucose-6-phosphate] K’eq1 = = 3.9 X 10-3 M-1 [glucose] [Pi] H2O is not include this reaction because its concentration (55.5 M) is assumed to remain uncharged by the reaction [ADP] [Pi] K’eq2 = = 2.0 X 105 M [ATP] The equilibrium constant for the two coupled reaction [glucose-6-phosphate][ADP][Pi] Keq1 = = (K’eq1)(K’eq2) = (3.9 X 10-3 M-1) (2.0 X 105 M) = 7.8 X 102 [glucose] [Pi] [ATP]

8 13. 2. Chemical logic and common biochemical reactions
Most of the reactions in living cells fall into one of five general categories Reactions that make or break carbon-carbon bonds Internal rearrangements, isomerizations, and eliminations Free-radical reactions Group transfer Oxidation-reduction Two basic chemical principles A covalent bond consists of a shared pair of electrons, and the bond can be broken in two general ways Homolytic cleavage: each atom leaves the bond as a radical, carrying one unpaired electron Heterolytic cleavage (more common): one atom retains both bonding electrons (2) many biochemical reactions involve interactions between nucleophiles and electrophiles nucleophiles: functional groups rich in and capable of donating electrons) Electrophiles: electron-deficient functional groups that seek electrons)

9 1) Reactions that make or break carbon-carbon bonds
Heterolytic cleavage of a C-C bond yields a carbanion and a carbocation Carbanions and carbocations are generally so unstable, thus reaction intermediates can be energentically inaccessible even with enzyme catalysts Nucleophile carbonion electrophile carbonion Carbonyl groups are particularly important in the chemical transformations of metabolic pathways The carbon of a carbonyl group has a partial positive charge due to the electron-withdrawing property of the carbonyl oxygen electrophilic carbon Carbonyl group facilitate the formation of a carbanion’s on an adjoining carbon by delocalizing the carbanion’s negative charge A imine group can serve a similar function The capacity of carbonyl and imine groups to delocalize electrons can be further enhanced by a general acid catalyst or by a metal ion such as Mg2+

10 Three major class of reaction in which C-C bonds are formed or broken
Aldol condensation: a common route to the formation of a C-C bond Claisen condensation: the carbonion is stabilized by the carbonyl of an adjacent thioester Decarboxylation: involves the formation of a carbanion stabilized by a carbonyl group neucleophiles electrophiles Example for carbocations in carbon-carbon bond formation by prenyltransferase reaction in the pathway of cholesterol biosynthesis

11 2) Internal rearrangements, isomerizations, and eliminations
Intramolecular rearrangement: redistribution of electrons results in alterations of many different types without a change in the overall oxidation state of the molecule (1) different group in the molecule may undergo oxidation-reduction, with no net change in oxidation state of the molecule (2) groups at a double bond may undergo a cis-trans rearrangement (3) the positions of double bonds may be transposed rearrangement Conversion of Glucose-6-phosphoate to fructose-6- phosphate Isomerization Nucleophilic groups Nucleophiles Ionizable groups in the enzyme (c) elimination Loss of water from an alcohol  introduction of a C=C bond

12 3) Free-radical reactions
Homolytic cleavage of covalent bond  produce free radical Isomerizations that make use of adenosylcobalamin (vitamin B12) or S-adenosylmethionine Certain radical-initiated decarboxylation reaction Oxygen-independent coproporphysinogen III oxidase catalyzes decarboxylation 3) Some reduction reaction, such as that catalyzed by ribonucleotide reductase 4) Some rearrangement reactions, such as that catalyzed by DNA photolyase

13 4) Group transfer reactions
The trasnfer of acyl, glycosyl, and phosphoryl groups from one nucleophile to another is common in living cells 1) Acyl transfer: acyl group transfer generally involves the addition of a nucleophile to the carbonyl carbon of an acryl group to form a tetrahedral intermediate Fig. 6-21 2) Glycosyl group transfers involves nucleophilic substitution at C-1 of a sugar ring Fig. 6-25

14 3) phosphoryl group is the attachment of a good leaving group to a metabolic intermediate to “activate” the intermediate for subsequent reaction - inorganic orthophosphate (Pi): the ionized form of H3PO4 at neutral pH, a mixture of H2PO4- and HPO42- - inorganic pyrophosphate (PPi): P2O74- Nucleophilic substitution: attachment of a phosphoryl group to an poor leaving group (-OH): occur in hundreds of metabolic reactions Phosphorous can form five covalent bonds All four phosphorous-oxygen bonds with some double bond character. Because oxygen is more electronegative than phosphorus, the sharing of electrons is unequal: the central phosphorus bears a partial positive charge and can therefore act as an electrophile A phosphoryl group (-PO32-) can be transferred to an alcohol ( forming a phosphate ester), or to a carboxylic acid (mixed anhydride) When nucleophile attacks the electrophilic phosphorus atom in ATP, a relatively stable pentacovalent structure forms as a reaction intermediate. Kinases: enzymes that catalyze phosphoryl group transfer

15 5) Oxidation-reduction reactions
Thioalcohols (thiols): the oxygen atom of an alcohol is replaced with a sulfur atom 5) Oxidation-reduction reactions Carbone atoms can exist in five oxidation status, depending on the elements with which they share electrons The transition of these status are of crucial importance in metabolism Biological reaction (commonly), a compound loses two electrons and two hydrogen ions: dehydrogenations (catalyzed by dehydrogenases) In some biological oxidation (but not all), a carbon atom becomes covalently bonded to an oxygen atom (a enzyme catalyze these reaction calls oxidases) Oxygenases: if oxygen is derived directly from molecular oxygen (O2). Oxidation reaction generally coupled with reduction Oxidation reaction generally releases energy Most of living cells obtain the energy needed for cellular work by oxidizing metabolic fuels such as carbohydrates or fats Many of reactions are facilitated by cofactors: coenzymes and metals

16 1. Biochemical and chemical equations are not identical
Phosphorylated compounds: can exist in several ionization status and the different species can bind Mg2+. Ex, at pH7 and 2 mM Mg2+, ATP exists in forms ATP4-, HATP3-, H2TAP2-, MgHATP-, Mg2ATP Biochemical equation: ATP + H2O ADP + Pi Because H+ and Mg2+ is constant Chemical equation at a pH above 8.5 in the absence of Mg2+ ATP4- + H2O ADP3- + HPO42- + H+ ΔG’o and K’eq in this book: determined at pH7 and 1 mM Mg2+

17 13. 3. Phosphoryl group transfers and ATP
Heterotrophic cells: obtain free energy in a chemical form by the catabolism of nutrient molecules In this chapter, we will study here the chemical basis for the large free-energy changes 1. The free-energy change for ATP hydrolysis is large and negative Ionized immediately because the concentration of the direct products of ATP hydrolysis are far below the concentrations at equilibrium Standard condition However, actual free energy of hydrolysis (ΔG) of ATP in living cells is very different because ----

18 However, actual free energy of hydrolysis (ΔG) of ATP in living cells is very different because
the cellular concentration of ATP, ADP, and Pi are not identical ATP, ADP, and Pi concentration are much lower than the 1.0 of standard condition Mg2+ in the cytosol binds to ATP and ADP ΔGp= ΔG’o + RT ln = -52 kJ/mol (Work example: 13-2) [ADP][Pi] [ATP] 2. Other phosphorylated compounds and thioesters also have large free energies of hydrolysis Immediate reaction less stable more stable

19 The several resonance forms available to Pi stabilize this product relative to the reactant, contributing to an already negative free-energy change

20 Thioesters: a sulfur atom replaces the usual oxygen in the ester bond
Free energy hydrolysis for thioester and oxygen ester Becauae of orbital overlap in O and C atoms For hydrolysis reactions with large, negative, standard free-energy changes, the products are more stable than the reactants for one or more of the following reasons The bonds strain in reactants due to electrostatic repulsion is relieved by charge separation, as for ATP The products are stabilized by ionization, as for ATP, acyl phosphates, and thioesters The products are stabilized by isomerization (tautomerization), as for PEP The products are stabilized by resonance, as for creatine released from phosphocreatine, carboxylate ion released from acyl phosphates and thioesters and phosphate (Pi) released from anhydride or ester linkages

21 3. ATP provides energy by group transfers, not by simple hydrolysis
General ATP hydrolysis Some process do involve direct hydrolysis of ATP (or GTP) Muscle contraction (5-31) The movement of enzymes along the DNA (25-35) The movement of ribosomes along the RNA (27-30) The phosphate compounds found in living organisms can be divided two groups High-energy compounds: ΔG’o : < -25 kJ/mol Low energy compounds: ΔG’o : > -25 kJ/mol Pi, PPi, AMP are can be transferred ATP: although thermodynamically unstable, it is kinetically stable (200 to 400 kJ/mol)  ATP does not spontaneously donate phosphoryl group to water Phosphoryl group donate when specific enzymes are presented  can regulate the disposition of the energy carried by ATP

22 4. ATP donates phosphoryl, pyrophosphoryl, and adenylyl groups
Electrophilic targets Nucleophilic attack: an alcohol (ROH), a carboxyl group (RCOO-) or a phosphoanhydride (a nucleoside mono- or diphosphate : adenylylation 5-phosphoribosyl-1-pyrophosphate: a key intermediate in nucleotide synthesis Transfer of phosphoryl group to glutamate or glucose Hydrolysis of a-b phosphoanhydride bond: ~46 kJ/mol Hydrolysis of b-g phosphoanhydride bond: ~31 kJ/mol Adenylation: produce PPi Pi: 19 kJ/mol  further energy “push” for the adenylylation reaction: thermodynamically favorable reaction (ex, activation of fatty acids) Inorganic pyrophosphatase

23 5. Assembly of informational macromolecules requires energy
Activation of fatty acid AMP transfer from ATP to carboxyl group of FA  Form fatty acyl adenylate and liberating PPi: exergonic: ΔG’o = -45 kJ/mol Displaces the adenylyl group to thiol group of CoA  form thioester with fatty acid: endergonic: ΔG’o = 31.4 kJ/mol PPi  2 Pi: kJ/mol: total = kJ/mol Favorable reaction 5. Assembly of informational macromolecules requires energy Assembly of ordered sequences (DNA, RNA, Protein) from the monomers energy obtains from the cleavage of a-b phosphoanhydride linkage (AMP, GMP, CMP and UMP transferred as a transferring moieties

24 6. ATP energizes active transport and muscle contraction
Transport processes are major consumers of energy Phosphoryl group donor: ATP Phosphoryl group transfer: to enzyme, not to substrate Phosphorylation: induces conformational change of enzyme Muscle contraction ATP bind with head of myosin (not covalent)  dissociate from actin  ATP hydrolysis induces conformational change (still ADP and Pi bound tightly)  Pi release  conformational change of the head of myosin  actin move

25 7. Transphosphorylations between nucleotides occur in all cell types
ATP: (1) cell’s energy currency and donor of phosphoryl groups (2) primary high-energy phosphate compound produced by catabolism, in process of glycolysis, oxidative phosphorylation, photophosphorylation (in photosynthetic cell) What about others such as GTP, UTP, CTP, dATP, dGTP, dTTP and dCTP  energetically equivalent with ATP (free energy changes associated with hydrolysis of their phosphoanhydride linkage) However, phosphoryl group from ATP can be transferred to other nucleotides Mg2+ ATP + NDP (or dNDP) ADP + NTP (or dNTP) Nucleoside diphosphate kinase Ping-pong mechanism of nucleoside diphosphate kinase Phosphoryl group transfer from ATP  increase ADP  muscle contraction Intense ATP demand  cells lowers the ADP concentration  replenish ATP by the action of adenylate kinase Mg2+ 2ADP ATP + AMP ΔG’o ≒ 0 Adenylate kinase

26 8. Inorganic polyphosphate is a potential phosphoryl group donor
Phosphocreatine (PCr = creatine phosphate): serves as a ready source (reservoir) of phosphoryl groups for the quick synthesis of ATP from ADP Phosphagens: PCr-like molecules in the lower phyla organism Mg2+ ADP + PCr ATP + Cr ΔG’o = kJ/mol Adenylate kinase 8. Inorganic polyphosphate is a potential phosphoryl group donor Inorganic polyphosphate ((polyP)n): linear polymer of Pi (p511) Present in all organism In yeast, polyP accumulated in vacuoles (= 200 mM) Serve as a phosphagen (Reservoir of phosphoryl group) The shortest polyP is PPi (n=2): can serve as the energy source for active transport of H+ in plant cells (across vacuolar membrane) Phosphoryl group donor of phosphofructokinase in plants Mg2+ ATP + polyPn ADP + polyPn ΔG’o = -20 kJ/mol Polyphosphate kinase-1 (PPK-1) Polyphosphate synthesis Present in pathogenic bacteria Mg2+ GDP + polyPn GTP + polyPn Polyphosphate kinase-2 (PPK-2) GTP, ATP synthesis

27 13. 4. Biological oxidation-reduction reactions
Central feature of metabolism 1) Phosphoryl group transfer 2) Electron transfer in oxidation-reduction Loss of electron (oxidation), gain of electron (reduction) In nonphotosynthetic organism, source of electron: food In photosythetic oranism, source of electron: chemical compound excited by the absorption of light Electrons move from various metabolic intermediates to specialized electron carriers in enzyme-catalyzed reaction  energy release 1. The flow of electrons can do biological work Electromotive force (emf): In battery, because the two chemical species differ in their affinity for electrons, electrons flow spontaneously through the circuit, driven by a force proportional to the difference in electron affinity Living cells have an analogous biological “circuit”, with relatively reduced compound such as glucose (the source of electron donor) Glucose  enzymatically oxidized  release electron  spontaneously flow through electron-carrier intermediates to another chemical species, such as O2: exergonic reaction because O2 has a higher affinity for electrons than do electron-carrier intermediates In the mitochondrion, membrane-bound enzymes couple electron flow  a production of transmembrane pH difference and a transmembrane electrical potential  accomplish osmotic and electrical work Thus, the proton potential has potential energy: electron-motive force ATP synthetase: use electron-motive force to produce ATP from ADP + Pi - Bacterial flagellar motion: use proton-motive force

28 2. Oxidation-reductions can be described as half-reactions
Fe2+ + Cu Fe3+ + Cu+ (1) Fe Fe3+ + e- Two half-reaction (2) Cu2+ + e Cu+ Electron donor: reducing agent Conjugate redox pair Electron acceptor: oxidizing agent The oxidation of reducing sugar by cupric acid (Fig. 7-10) R-COH + 4OH- + 2Cu R-COOH + Cu2O + 2H2O (1) R-COH + 2OH R-COOH + 2e- + H2O (1) 2Cu2+ + 2e- + 2OH Cu2O + H2O Doubled cupric to cuprous take balance the overall equation

29 3. Biological oxidations often involve dehydrogenation
“Owns”: more electronegative atom O is more electronegative. Thus O is the “owns”. This means that C loss electron  undergone oxidation The carbon in living cells exists in a range of oxidation status Electronegativity: H<C<S<N<O oxidation Alkane: -CH2-CH Alkene: -CH=CH- Oxiation = dehydrogenation Enzymes that catalyze oxidation call dehydrogenase reduction 6H+ + 6e- + N NH3

30 **Electrons are transferred from one molecule to another in one of four ways
1) Directly as electrons: Fe2+/Fe2+ redox pair can transfer an electron to the Cu/Cu2+ redox pair Fe2+ + Cu Fe3+ + Cu+ 2) As hydrogen atoms: hydrogen atom consists of a proton (H+) and a single electron (e-) AH A + 2 e- + 2H- Hydrogen/electron donor AH2/A: conjugate redox pair  can reduce another compound B AH2 + B A+ + BH2 3) As a hydride ion (:H-) Has two electrons This reaction occurs in NAD-linked dehydrogenase 4) Through direct combination with oxygen R-CH3 + 1/2O R-CH2-OH Oxygen covalently incorporated into product: Electron donor Electron acceptor

31 4. Reduction potentials measure affinity for electrons
When two conjugate redox pairs are together in solution, electron transfer may proceed spontaneously depended on the relative affinity of the electron acceptor of each redox pair for electrons  measure of this affinity (volts): Standard reduction potential (Eo) Standard half reference of the half reaction: H+ + e /2H2 5. Standard reduction potentials can be used to calculate free-energy change Electrons tend to flow to the half-cell with the more positive E  the strength ΔE (difference in reduction potential)  free energy change ΔG = ΔE ΔG = -n ΔE or ΔG ’o = -n ΔE ’o When acetaldehyde is reduced by the biological electron carrier NADH, ΔG = kJ/mol

32 6. Cellular oxidation of glucose to carbon dioxide requires specialized electron carriers
The principles of oxidation-reduction energetics  can apply to the many metabolic reactions that involve electron transfers Glucose oxidation: C6H12O6 + 6O CO2 + 6H2O, ΔG ’o = -2,840 kJ/mol > ATP synthesis in cells: kJ/mol need Cells does not convert to CO2 in a single, high energy releasing reaction but rather in a series of controlled reactions, some of which are oxidation for the ATP synthesis from ADP through NAD+ and FAD coenzyme 7. A few of coenzymes and proteins serve as universal electron carriers NAD, NADP, FMN and FAD: water-soluble coenzymes and undergo reversible oxidation and reduction in many of the electron-transfer reactions of metabolism NAD and NADP: move rapidly from one enzyme to another Flavin nucleotides (FMN, FAD): usually very tightly bound to the enzymes (=flavoproteins)  serve as prosthetic group Lipid-soluble quinones (ubiquinones and plastoquinone): act as a electron carriers and proton donors in the nonaqueous evironment of membranes Iron sulfur protein and cytochromes: serve as electron-carriers in many oxidation-reduction reactions

33 8. NADH and NADPH act with dehydrogenase as soluble electron carriers
NAD: nicotinamide adenine dinucleotide  NAD+: oxidized form NADP: nicotinamide dinucleotide phosphate (close analog of NAD) Oxidized form has positive charge in nitrogen atom Reduction produces a new, broad absorbance with a maximum at 340 nm Total concentration of NAD+ + NADH in most tissues: 10-5 M - Concentration ration: NAD+ > NADH  favoring hydride transfer from a substrate to NAD+ to form NADH  function in oxidation  occur in mitochondrial matrix Total concentration of NADP+ + NADPH in most tissues: 10-6 M - Concentration ration: NADP+ < NADPH  favoring hydride transfer from NADPH to a substrate  function in reduction  occur in cytosol

34 More than 200 enzymes are known to catalyze reactions in which NAD+ (or NADP+) accepts a hydride ion from a reduced substrate or NADPH (or NADH) donates a hydride ion to an oxidized substrate Oxidized substrate General reaction AH2 + NAD A + NADH + H+ oxidoreductase reduced substrate A + NADPH + H AH2 + NADP+ CH3CH2OH + NAD CH3CHO + NADH + H+ ethanol acetaldehyde When reduction NAD+ or NADP+  NADH or NADPH Hydride ion is transferred to A or B side Front side Have specificity, not both Back side - ex, yeast alcohol dehydrogenase: A side transfer - B side transfer

35 Most dehydrogenases: Contain a conserved domain called the Rossmann fold Rossmann fold: consists with a six-stranded parallel b sheet and four associated a helics Rosssmann fold serves as binding with a cofactor The association between dehydrogenases and cofactor is loose  the coenzyme readily diffuse from one enzyme to another  act as a water-soluble carrier of electron form one metabolite to another (1) Glyceraldehyde 3-phosphate + NAD phosphoglycerate + NADH + H+ (2) Acetaldehyde + NADH + H ethanol + NAD+ Glyceraldehyde 3-phosphate + Acetaldehyde phosphoglycerate + ethanol In overall reaction, there is not net production or consumption of NAD+ or NADH  no concentration change of NAD+ or NADH and recycle repeatedly NAD+ or NADH.

36 9. Dietary deficiency of Niacin, the vitamin form of NAD and NADP, causes pellegra
Most coenzyme: derived from vitamins NAD and NADP: derived from vitamin niacin (=nicotinic acid) Human cannot synthesize sufficient quantities of niacin Maize: content low tryptophan Niacin deficiency: affects all the NAD(P)-dependent dehydrogenase  causes the serious human disease pellagra (=rough skin): characterized by the Three Ds (dermatitis, diarrhea and dementia)  death Too much alcohol drink  reduce niacin absorption from the intestine

37 10. Flavin nucleotides are tightly bound in flavoproteins
Fully reduced: 360 nm Partially reduced: 450 nm Fully oxidized: 370 and 440 nm Flavoproteins  derived from the vitamin riboflavin The fused ring structure of the flavin nucleotide (isoalloxazine ring): Cryptochromes (light receptor): a flavoprotein act as a (1) mediate the effects of blue light on plant development and (2) the effects of light on mammalian circadian rhythms


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