Metabolis lism is the totality of an organism s chemical reactions - - PDF document

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Chapter 8 Metabo bolis lism

Chemical Reactions of Life

Metabolis lism is the totality of an organism’s chemical reactions Metabolic lic Pathway: linked reactions where end product of

• ne reaction becomes reactant of next reaction until final

end product is created

• chem rxns divided into many small steps

Types of Metabolic Pathways

Catabolic lic pathways:

• Breaking bonds to release energy (complex molecules  simpler molecules)
• Hydrolysis reactions
• Exergonic

ex: digestive enzymes break down food  release energy

Anabolic lic pathways

• Forming bonds by consuming energy (simple  complex molecules)
• Dehycration synthesis/ condensation reactions
• Endergonic
• Ex: formation of proteins from amino acids

Forms of Energy

Energy: capacity to do work Kine netic energy (KE): energy associated with motion Thermal energy (heat): KE associated with random movement of atoms or molecules Potent ntial energy (PE): stored energy as a result of its position or structure

• Chemical energy is PE available for release in a chemical reaction

ex: glucose has PE in its bonds Energy can be converted from one form to another ex:. chemical  mechanical  electrical

Conversion of Energy Forms Laws of Energy Transformation

Thermodynamic amics: study of energy transformations that

• ccur in nature
• System: matter under study
• Surroundin

ing: everything else in the universe

• Open system: energy and matter can be transferred between

the system and its surroundings

• Closed system: unable to exchange energy or matter with its

surroundings (like liquid in a thermos) Orga ganis isms are open systems

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First Law of Thermodynamics

The energy of the universe is constant Energy can be transferred and transformed but energy cannot be created or destroyed ** also known as the law of Conservatio ion of Energy gy**

chemical reactions in brown bear will convert chemical (PE) in fish into KE of running

Second Law of Thermodynamics

Every energy transfer or transformation increases the entropy (disorder/randomness) of the universe.

• Energy is unusable or lost (converted to heat) during the transfers or

transformations

• Heat can be put to work if there if heat flows from warm  cooler

areas

• If temp is stable it can only be use warm body
• f matter (true of cells)

As bear runs entropy is increased by release of heat and CO2 Spont ntane neous us Process: process that occurs without any input

• f energy “energetically favorable”
• Increases entropy of the universe (fast or slow process)

ex: explosions rusting of a car

• Living systems increase entropy of their surroundings

ex: catabolic pathways break down food molecules animal release CO2 and H2O (depletion of chemical energy) result: heat generated during metabolism **If entropy of a system is decreased, the entropy

• f the surroundings must increase

Free Energy

Free energy: part of a system’s energy available to perform work (Gibbs free energy) when pressure and temperature are uniform throughout a system G = change in free energy = ability to do work G = H H - TS H = total energy in system T = absolute temperature in Kelvin (K = *C = 273) S = change In system’s entropy Used to predict whether process will be spont ntane neous (not require energy) Allows scient ntists to determine ne which reactions supply cellula ular energy for work

Free Energy

G G represents the difference between the free energy of the final stage and the free energy of the initial al stage

• Measure of a system’s instability- its tendency to change to a more stable state

(equilibrium) G = G final stage - G initial al stage

Stability

G is only negative when process loses free energy from initial to final stage Higher energy  lower energy Final state of system has less free energy gy and is Less likely to change so therefore considered more stable

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Equilibrium

State of maxim imum stabilit lity

• no further net change in concentration of reactants & products
• G is at lowest possible value in the system
• System cannot do any work at equilibrium
• Process is spontaneous and can perform work only when it is

moving ng toward equilibrium Metabolism is never at equilibrium um becaus use living ng cells are not in equilibrium um (cons nstant nt flow of material in and out of cells)

Free Energy and Metabolism

Exergo gonic ic reactio ion “energy outward” Energy is released Spontaneous reaction Decreases system’s free energy G < 0 (negative) ex: ice to water Endergo gonic ic react ctio ion “energy inward” Energy is required Absorbs free energy G > 0 ex: steam to water

• G

The greater the decrease in free energy, the greater the amount of work that can be done

+ G

Equilibrium and Work

Cellular respiration is similar to this system: Glucose is broken down in a series of exergonic reactions that power the work of the cell. Product of each reaction becomes reactant for the next so no reaction reaches equilibrium.

Energy Coupling in ATP

Orga ganis isms need energy gy to live. A cell l does three main kinds of work:

• 1. mechanical (cilia beating, muscle contraction)

2 transport (pumping substances against gradient)

• 3. chemical (pushing of endergonic reactions)

Cells do work by energy gy couplin pling exergo gonic ic react ctio ions (release energy) to drive endergo gonic ic react ctio ions (needing energy)

Structure and Hydrolysis of ATP

ATP (adenosin ine tripho phospha phate) is the cell’s main energy source in energy coupling ATP = adenine + ribose + 3 phosphates When the bonds between the phosphate groups are broken by hydrolysis  energy gy is rele leased This release of energy comes from the chemical change to a state

• f lower free energy, not in the phosphate bonds themselves

When a terminal phosphate bond is broken a molecule of inorganic phosphate (HOPO3) Pi leaves the ATP and becomes ADP ATP + H2O  ADP + Pi G = 7.3 kcal/mol

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Energy released during ATP hydrolysis performs the three types

• f cellular work.
• Phosphate group from ATP is transferred to another molecule

Phospho phoryla lated intermedia iate:

• molecule that accepts phosphate
• more reactive/less stable than unphosphorylated

molecule

Regeneration of ATP

ATP Cycle le: shuttling of inorganic phosphate and energy

• Coupled exergonic/ endergonic reactions
• Very quick process: muscle regenerates ATP in < 10 min.
• Endergonic process: reversible process
• Uses free energy

Energy and Chemical Reactions

Oxid idatio ion/ Reduct ctio ion Reactio ions (Redox): reactions in which electrons are transferred between atoms * reactions always come in pairs

• Oxid

idatio ion: reactant loses one or more electrons becomes positively charged

• Reductio

ion: reactant gains

• ne or more electrons

becomes negatively charged

Energy and Chemical Reactions

Activ ivatio ion energy gy: (Ea): initial investment of energy to start a reaction (usually heat) Cataly lyst: substance that can change the rate of a reaction without being altered in the process (lowers Ea needed to start rxn.) Enzyme: biological catalyst

Enzymes

Biological catalysts (end in “ase”)

• Globular proteins
• Required for most biological reactions
• Increase rate of reaction without being consumed
• Reduce activation energy
• Don’t change free energy (G) released or required
• Needed to maintain homeostasis
• Mode of action: enzyme substrate comple

plex

• Highly specifiic- thousands of different enzymes in cells

ex: protease- proteins lactase- lactose

Substrate Specificity

Substrate: reactant that binds to enzyme Product ct: end result of reaction Enzyme- substrate comple plex: temporary association

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Induced Fit Model

• “Chemical handshake”
• 1. 3-D sturcture of enzyme fits substrate
• 2. Substrate binds
• 3. Enzyme changes shape leading to a tighter fit
• Conformational change
• Brings chemical groups in position to catalyze

reaction

• Can catalyze 1000’s of substrate/second

“

Factors that Affect Enzyme Activity

Temperat ature

• Optim

imal l tempe perature - humans (35- 40 C)

• greatest number of molecular collisions
• Decr

crease tempe perature = decreased rate

• molecules move slower
• decreased collisions
• slows reaction rate
• Incr

crease above optimum tempe perature

• Denatures enzyme = rate slows or stops

Factors that Affect Enzyme Activity

pH pH

• Optimal pH for most organisms(6-8)
• pH too high or low (add or remove H+)
• disrupts bonds, 3D shape (conformation)
• Denatures enzyme

Effect of Temperature and pH Other Factors Affecting Activity

Enzyme me concentrat ation

• increase enzyme = higher rate until substrate used up

Substrat ate concentrat ation

• Increase substrate = higher rate until enzymes saturated

Salinity (salt concentration)

• High- disrupts bonds and 3D shape (Dead Sea)
• Denatures enzyme

Other Factors Affecting Activity Activat vator

• rs:: compounds that help enzymes

Cofacto ctors

• Non-protein inorganic compounds and ions (Mg, K, Ca, Zn, Fe)
• Found in enzyme molecule

Coenzy zyme mes

• No-protein organic molecules
• Bind near enzyme active site

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Other Factors Affecting Activity

Inhibitors: causes decreased enzyme action

• Can be beneficial or destructive to organism
• 1. Compe

petit itiv ive Inhibit itio ion

• inhibitor (very similar shape to substrate) binds to enzyme
• inhibitor competes with substrate
• prevents substrate from binding

ex: aspirin anti-cancer drugs blood pressure drugs AIDS drugs

• overcome by

increasing substrate

.

2. 2. Non-co competit itiv ive inhib ibit itio ion

• inhibitor binds to another site on enzyme
• changes shape of enzyme
• prevents binding of intended substrate
• often permanent change

ex: insecticides lead poisoning nerve gas 3. 3. Feedback ck Inhibit itio ion (nega gativ ive feedback ck)

• normal process in cells: regulates chemical reactions
• end product of a pathway accumulates as metabolic

demand for it declines

• end product binds to

regulatory enzyme at start of pathway Prevents wasting chemical resources Increases efficiency of cell ex: synthesis of isoleucine from threonine

Regulation of Enzyme Activity

To regula late metabolic lic pathways, the cell l switche ches on/off the genes that encode specif ific ic enzymes. Allosteric ic regu gula latio ion: protein’s function at one site is affected by binding of a regu gula latory molecu cule le to a separate site (allosteric ic site)

• Most enzymes allosterically regulated have 2+ subunits

(polypeptide chain with its own active site)

• Complex oscillates between two shapes
• Cataly

lytica ically lly active or inactiv ive

Types of Allosteric Regulation

• 1. Activator: keeps

enzyme in active form

• 2. Inhibitor: keeps

enzyme in inactive form 3.

• 3. Cooperat

ativity:

• Substrate acts as an activator
• Causes conformational change in enzyme
• Induced fit
• Favors binding of substrate at second site
• Makes enzyme more active and effective

ex: hemoglobin