hChapter 8 Study Guide 8.

1 Metabolism/ Thermodynamics
Metabolism: totality of an organisms chemical reactions Metabolism is emergent life property, cell interactions with environment

Metabolic Pathways
Metabolic pathway: begins with a specific molecule, which is altered through a series of defines steps resulting in a certain product, each step catalyzed by an enzyme Catabolic pathways: release energy by breaking down complex molecules to simpler, degradative process (cellular respiration) Pathways can have more than one starting molecule Anabolic pathways: consume energy to build complicated molecules from simpler ones, aka biosynthetic pathways (protein from amino acids) Energy released from the downhill reaction of catabolism can be stored and used to drive the uphill reaction of the anabolic pathways Bioenergetics: the study of how organisms manage their energy resources

Forms of Energy
Energy is the capacity to cause change. (Ability to rearrange collection of matter) Kinetic energy: relative motion of objects Heat, thermal energy: kinetic energy associated with random movement of atoms or molecules Potential energy: energy no kinetic, energy that a matter possesses because of location and structure Chemical energy: potential energy available for release in a chemical reaction Diver climbs up releasing food chemical energy, muscle movement causes kinetic energy transformed into potential (increase in height)

Laws of Energy Transformation

Thermodynamics: study of energy transformations that occur in a collection of matter Closed system is isolated from surroundings, open system is when energy can be transferred between the system and surroundings First law of thermodynamics: the energy of the universe is constant. Energy can be transferred and transformed, but not created or destroyed. This is known as the principle of conservation of energy Second law of thermodynamics: every energy transfer or transformation increases the entropy of the universe Entropy: measure of disorder or randomness

During every energy transformation some energy becomes unusable (not able to do work) Heat dissipates into surroundings, heat is associated with random motion of atoms or molecules Increasing entropy in decay of an unmaintained building, or cheetah producing heat Spontaneous: a process that can occur without an input of energy A spontaneous process increases entropy Nonspontaneous: a process that cannot occur on its own, will happen only if energy is added to the system For a process to occur spontaneously, it must increase the entropy of the universe

Biological order and disorder

Organisms can also take organized forms of matter and replace with less ordered Animals take in starch and proteins and release carbon dioxide and water, small molecules store less chemical energy, accounted fro the heat generated The entropy of a particular system may actually decrease, so long as the total entropy of the universe increases

8.2 Free Energy Change

Free energy G
In 1878 J Gibbs defined the Gibbs free energy of a system (without considering surroundings)= G Free energy: measures the portion of a systems energy that can perform work when temperature and pressure are uniform throughout the system Change in free energy: G = H TS G=change in free energy H=change in a systems enthalpy (total energy) S=change in a systems entropy T = absolute temperature in Kelvin Processes with a negative G are spontaneous Spontaneous reactions either give up enthalpy (H decreases) or give up order (TS increase) or both Every spontaneous process decreases the systems free energy positive or zero G are never spontaneous

Stability and equilibrium

G is the difference between the free energy or the final state and the initial state G = G(final) G(initial) G can only be negative when the amount of free energy decreases There is less free energy in its final state, so less likely to change, so more stable Higher G=less stable and lower G=more stable

Equilibrium: state of maximum stability Systems never spontaneously move away from equilibrium Systems at equilibrium can not spontaneously change so they can do no work

Metabolism
Exergonic reaction proceeds with a net release of free energy, G decreases and G is negative (spontaneous) The magnitude of G for exergonic reactions represent the amount of work the reaction can perform Greater the decrease in free energymore amount of work Endergonic reaction absorbs free energy from its surroundings Stores free energy so G increases and G is positive (Nonspontaneous) Cells dies at equilibrium because no reactions G=0 Metabolism as a whole is never at equilibrium Constant flow of materials in and out keeps metabolic pathways from reaching equilibrium, and the cell continues to do work Product of one reaction is a reactant of the next step

8.3 ATP with exergonic and endergonic reactions

A cell does three main kinds of work: 1. Mechanical: beating of cilia, contracting of muscles, movement of chromosomes during cellular reproduction 2. Transport: pumping of substances across membranes against the direction of spontaneous movement 3. Chemical: pushing of endergonic reactions, which would not occur spontaneously such as the synthesis of polymers from monomers Energy coupling: the use of an exergonic process to drive and endergonic one

Structure and hydrolysis of ATP

ATP (adenosine triphosphate) phosphate group is functional, sugar ribose, nitrogenous base adenine, and chain of 3 phosphate groups bonded Bonds between the phosphate group of ATPs tail can be broken by hydrolysis When terminal bond is broken a molecule of inorganic phosphate leaves and it becomes adenosine diphosphate ATP + H20 ADP + P If the change in free energy (G) of an endergonic reaction is less that the amount of energy released by ATP hydrolysis then they can be couples and are exergonic All three phosphates are negatively charged, repulsion contributes to instability

How ATP performs work

Cell couples the energy from ATP hydrolysis to endergonic processes Transfer the P from ATP to another molecule like a reactant

The recipient of the phosphate group is the phosphorylated and undergoes a change that performs work Mechanical, transport, and chemical works are almost always powered by hydrolysis of ATP In the synthesis of amino acid glutamine, glutamic acid and ammonia are usedATP phosphorylates glutamic acid making it less stableammonia displaces the phosphate group forming glutamine

Regeneration of ATP
ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP ATP cycle it couples with exergonic processes to the endergonic ones If ATP could not be regenerated by phosphorylation of ADP then humans would use their body weight in ATP each day Regeneration is endergonic, not spontaneous, free energy must be spent Plants use light energy to produce ATP, cellular respiration also has catabolic processes Chemical potential energy is stored in the ATP

8.4 Enzymes lower energy barrier

Catalyst: a chemical agent that speeds up reactions without being consumes by the reaction Enzyme: catalytic protein Changing one molecule requires contorting the starting molecule into a highly unstable state before the reaction can proceed To reach this state, reactant molecule must absorb energy from surroundingnew bonds are formed and energy is released as heat, stable again Free energy of activation or activation energy: EA initial investment of energy for starting reactions Activation energy is amount of energy needed to push reactants over energy barrier Energizing or activation is uphill free energy increasing, down hill is loss of energy Activation energy often supplied in form of heat, colliding more likely for bonds to break Enzymes lower EA barrier enabling reactant molecules to absorb enough energy to reach transition state even at moderate temperatures

Substrate Specificity
Substrate: the reactant an enzyme acts on Enzyme-substrate complex: enzymes bind to its substrates Active site: restricted region of the enzyme that binds to the substrate Induced fit: interactions between the chemical groups on the substrate and enzyme cause it to change shape slightly so it fits more snug

Catalysis in Active Site Substrate held by weak hydrogen and ionic bonds R groups of amino acids on the enzyme catalyze reaction, and product departs Enzymes normally can do both forward and reverse reactions, direction of equilibrium 1. Substrate enters active site, induced fit 2. Held by weak hydrogen or ionic bonds 3. Active site the r groups of amino acids lower EA barrier and speed rate Provides a template for orientation Stressing the substrates and stabilizing the transition state Favorable microenvironment Participating directly in catalytic reaction (may need covalent bond) 4. Substrates are converted into products 5. Products are released 6. Active site is available When enzyme population is saturated, the only way to increase rate is to add more enzymes

Local Conditions on Enzyme Activity

Above a certain temperature, thermal agitation on enzyme molecules disrupts bonds that stabilize active site formationdenatures Has optimal temperature where greatest rate without denaturing. Human are from 35-40C bacteria in hot springs are &0C Optimal pH is 6-8, pepsin in stomach 2, tripsin in intestine is 8

Cofactors
Cofactors: non protein helpers fro catalytic activities, can be tightly bound permanent, or bind loosely Coenzyme: when a cofactor is organic molecule

Enzyme Inhibitors
If attaches by covalent bonds it is normally irreversible Bind by weak bonds normally Competitive inhibitors: resemble the normal substrate and compete for admission, they reduce productivity of enzymes by blocking active sites Can be overcome by increasing concentration of the substrate Noncompetitive inhibitors: do not directly compete, impede enzymatic reactions by binding to another part Enzyme will change its shape and the active site will be less effective Toxins and poisons are irreversible Antibiotics are inhibitors of bacterial enzymes

8.5 Regulation of Enzyme Activity

Allosteric regulation: proteins function at one site is affected by the binding of a regulatory molecule to a separate site Enzymes have either active or inactive form Regulatory sites are where subunits join Activator: binds to regulatory site that stabilizes the active form and has functional active sites Inhibitor: stabilizes the inactive form of an enzyme ATP can bind to catabolic enzymes lowering affinity for substrate and inhibiting activity ADP functions as an activator of the same enzyme Another type of allosteric activity is when a substrate binds to the active site of one subunit it stimulates catalytic powers of the others Cooperativity: amplifies the response of enzymes to substrates, substrate binds to one subunit and causes induced fit for the rest Feedback inhibitory: a metabolic pathway is switched off by the inhibitory binding of its end product to and enzyme that acts early in the pathway Prevent cells from wasting resources on synthesizing more than necessary