Module 3 Euk Exam 1

bioenergetics

the study of various types of energy transformations that occur in living organisms

energy

the capacity to do work

two different types of energy in a force field

• potential energy

  • PE=mgh

  • determined by an object’s position in the force field

• kinetic energy

  • KE=1/2(mv²)

  • object is moving

first law of thermodynamics

• conservation of energy: closed system energy is conserved

• energy can be converted into various types, never lost or created

closed system

• no communication between the system and its surroundings

  • no energy exchange

• it is difficult to find a closed system in the real world

systems vs surroundings

• system: a certain space or certain amount of matter under study

• surroundings: the remainder of the universe outside of the system

internal energy

• the energy inside the system

• ΔE=Q-W

  • Q is heat energy

  • W is work

  • ΔE represents change in internal energy

• exothermic: reactions that lose heat (negative value)

• endothermic: reactions that gain heat (positive value)

• ΔE cannot predict the direction of the reaction

  • energy can increase if it enters the system, and vise versa

second law of thermodynamics

• events in the universe tend to proceed “downhill” from a state of higher energy to a state of lower energy, which is a spontaneous event

• entropy increases naturally, so energy spreads out and loses its ability to do work (low energy)

• this law determines the direction of a reaction

• energy input is required to go from a low energy to high energy state, which is a non-spontaneous event

entropy

• spontaneous events lead to increase in randomness or disorder

  • going from highly organized to disorder

• measure of randomness or disorder in the universe, a system, or its surroundings

• energy of the system changes with an increase in entropy: ΔE=TΔS

enthalpy

the total energy content of a system

free energy

• the thermodynamic laws indicate that the energy of the universe is constant, but the entropy continues to increase toward a maximum

• part of the energy that can be used to do work

• -ΔG means spontaneous reaction

• free energy determines direction of the reaction

free energy equation

• ΔH= ΔG + TΔS or ΔG= ΔH - TΔS

• ΔH is the change in enthalpy or total energy of the system

• ΔG is the change in free energy (change in useful energy)

• T is temp

• ΔS is change in entropy of the system (change in energy that is unavailable to do work)

• when ΔG is negative, the reaction is exergonic/favorable

  • system used some of its free energy

• when ΔG is positive, the reaction is endergonic/unfavorable

  • system gained free energy

  • energy had to be added to increase free energy of the system

free-energy changes in chemical reactions

• K is a rate constant for each direction a reaction can proceed

• view a reaction as a system

• at equilibrium, the rate constants are equal to each other

equilibrium

• no net change in the reaction, but the reaction does not stop

• concentrations of products and reactants are equal

• equilibrium constant is Keq

• Keq= [product]/[reactant]

standard conditions

• 25 degrees celsius (room temp), 298 K

• pressure is 1 atm

• concentrations are all 1 mol/L, except water which is present at 55.6 mol/L

• pH=7

• under these conditions, we can calculate the free energy of a reaction: ΔG^o= RTlnKeq = -2.303 RTlogKeq (equation is not tested though)

  • just understand R is the gas constant (1.987 cal/mol K) and T is absolute temperature

ΔG and equilibrium

• If ΔG^o is negative, the reaction will go to the left

• If ΔG^o is positive, the reaction will go to the right

• ΔG^o is the driving parameter on which way the reaction goes

• when ΔΔG^o is negative, Keq is large, meaning a large concentration of products

• when ΔG^o is positive, Keq is small, meaning a large concentration of reactants

ΔG^o vs ΔG

• ΔG is used when the concentrations are different

• ΔG= ΔG^o + 2.303 RT log Keq

• changing concentrations of the products or reactants changes ΔG

roles of ATP hydrolysis

• promote reactions and activities inside the cell because ATP hydrolysis releases energy

• separate charges across the membrane

  • pump ions into and out of the cell to create an electrical difference between the inside and outside of a cell

• concentrate solute in the cell

  • move solutes against a concentration gradient (i think)

• drive unfavorable reactions

• slide filaments across one another

• phosphorylation of proteins

  • kinases use ATP

2 ways cells achieve a negative ΔG

• change the product and reactant ratio to change ΔG

  • reduce product concentration or remove product once its formed so the reaction drives forward

• couple endergonic and exergonic reactions

steps of glycolysis and its free energy profile

• glucose is the substrate

• glucose oxidized in the cytosol and becomes pyruvate

• 10 steps, but 3 steps have a big energy release

  • the first step

  • the third step

  • the last step

• these 3 steps drive the pathway forward

• these 3 steps release so much energy, they are irreversible

• the other steps have a small free energy change, so it can be reversed by changing product and reactant concentrations.

  • both ways are catalyzed by the same enzyme

equilibrium vs steady-state metabolism

• as reactions reach eqilibrium, the free enegy available decreases toward a minimum, while entropy increases toward a maximum.

• if ΔG=0, the reaction is at equilibrium

• steady-state: can be or can not be at equilibrium. A condition where the concentration of substances remains constant because they are produced and consumed at equal rates, while the system continues to operate.

• equilibrium: Forward reaction rate = reverse reaction rate → no net reaction. (balanced reactions)

• Steady state: Rate of production = rate of consumption → constant concentration, but material is continuously flowing through the system. (balanced inputs and outputs)

open system

• takes energy and releases waste

• maintain ratio of ATP and ADP because food is available to make ATP

• ATP / ADP is a steady state

enzyme

• biological catalysts- speed up a reaction

• proteins

  • many are conjugated proteins with nonprotein components (cofactors)

• cofactors may be inorganic (metals) and organic (coenzymes)

enzyme properties

• Are required only in small amounts

• Are not altered irreversibly during course of reaction

• Have no effect on reaction thermodynamics (does not determine reaction direction)

• Are highly specific for their Substrates

• Produce only appropriate metabolic products

• Can be regulated to meet the needs of a cell

enzymes vs inorganic catalysts

• enzymes are more effective

• inorganic catalysts catalyze a reaction under extreme conditions, while enzymes catalyze under mild cnditions

• enzymes are highly specific and will only catalyze one reaction, while inorganic catalysts can catalyze different kinds of reactions

• enzymes are “metabolic traffic directors” which means one pathway in metabolism can branch into two pathways, and that pathway is determined by the enzyme

  • whichever enzyme is more active will determine what pathway it will channel the substrate into

• enzyme activity can be regulated to meet particular cellular needs at particular time

activation energy

• enzymes lower this energy to help the reaction proceed

  • more substrates will reach the threshold to convert to products

• the energy required for a reaction to occur (to overcome the transititon state)

transition state

• covalent bonds become weak and easily can be broken so the reaction can occur

• once bonds are broken, new bonds will form

• activation energy needs to be reached to exit transition state and make products

mechanisms used by enzymes and heat to increase rate of reaction

• increasing temperature increases rate of reaction because energy of the substates increases

  • shifts energy diagram to the right (more enzymes in the threshold of high energy to overcome Ea)

  • this method leaves Ea unchanged

  • if enzymes are added while using this method, high temp might denature them

• decreasing activation energy (adding enzyme)

enzyme-substrate complex

• enzyme has an active site where it has a complementary shape with the substrate

• substrate binds to active site

• after bound, enzyme can catalyze the reaction and the product will be released. another subsrate can come in after product is released

active site

• typically buried in a cleft or crevice that leads from the aqueous surroundings into the depth of the protein to create a hydrophobic environment within the protein

  • allows the substrate to interact with the enzyme instead of water molecules

• where substrate binds to enzyme

noncovalent interaction between enzyme and its substrate

• the enzyme’s active site and the substrate are complementary, which allows binding at a high degree of precision

• this precise binding is performed by noncovalent bonds

• a transient covalent bond between enzyme and substrate could also be formed

mechanisms of enzyme catalysis

• substrate orientation

  • the enzyme positions the substrate(s) in the correct orientation so the reacting groups are close together and properly aligned, making the reaction easier and faster.

• changing substrate reactivity

  • enzyme can help change the charge inside the substrate, allowing covalent bonds to be broken

  • enzyme changes the distribution of electrons at a specific position or specific bond so the enzyme can break the bonds within the substrate

• inducing strain in a substrate

  • once the substrate is bound, it causes a conformational change of the enzyme, so it causes a strain inside the substrate, which can break covalent bonds

enzyme kinetics

• Vmax: the initial velocity when the enzyme approaches a state of saturation

• Km (Michaelis constant): the substrate concentration when reaction velocity is one-half of Vmax. (substrate’s affiinity for the enzyme)

  • independent of substrate and enzyme concentration

  • for most enzymes, ranges between 10^-1 M and 10^-7 M, with a typical value around 10^-4 M

• when [S] is set at Km, V=Vmax/2

  • Km=[S] when V=Vmax/2

effects of pH and temperature on enzyme-catalyzed reactions

• enzymes only work in their specific pH level

• enzymes only work in their specific temperature range

  • changing temperature will decrease activity

lineweaver burk plot

• x-intercept: -1/Km

• y-intercept: 1/Vmax

• slope: Km/Vmax

• useful because it makes it easier to determine enzyme kinetics parameters and the type of inhibition.

• by comparing how the lines change with/without inhibitor can help us determine inhibitor type

enzyme inhibitors

• molecules that are able to bind to an enzyme and decrease its activity

• cells use inhibitors to regulate the activity of many enzymes.

• researchers use inhibitors to study the properties of enzymes.

• enzyme inhibitors can be used as drugs, antibiotics, or pesticides.

• ireversible inhibitors: bind very tightly to an enzyme, often by

  forming a covalent bond to one of its amino acid residues.

  • kills and removes enzymes from the system

  • antibiotics and pesticides are usually irreversible inhibitors

• reversible inhibitors: bind only loosely to an enzyme, and thus are

  readily displaced.

  • competitive inhibitors: compete with a substrate for access to

    the active site of an enzyme.

• noncompetitive inhibitors: act at a site other than the enzyme’s

  active site.

  • changes conformation of active site/enzyme so substrate will not fit. enzyme reverts back to original conformation once noncompetitive inhibitor leaves

effects of inhibitors on enzyme kinetics

• competitive inhibition:

  • increase substrate concentration; Vmax can still be reached, so it does not change

  • Km will increase because substrate concentration increases

• noncompetitive inhibitor:

  • enzyme activity is reduced, so Vmax will decrease

  • Km is unchanged because same amount of substrate can be used to reach half of max speed

metabolism

• collection of biochemical reactions occuring in a cell

• all reactions are diverse, and they are different types of reactions

• reactions function together to form a pathway

• multiple enzymes catalyze these reactions so they can occur in one compartment

• reactions occur in different locations, so they do not have to occur at the same time

• enzymes can form a complex to increase efficiency of metabolic pathways

  • substrate enters complex and finishes pathway within it

metabolic intermediates/metabolite

• molecules that are produced, consumed, or transformed during metabolic reactions; intermediates are the molecules between steps of a pathway.

• no specific function

energy metabolism

• catabolic pathway: the complex molecules are broken down into simpler products

  • provide raw materials for synthesis

  • provide energy for cell activities in the forms of high-energy phosphates (ATP) and high-energy electrons (NADPH)

• anabolic pathways: synthesis of more complex compounds from simpler starting materials

3 stages of energy metabolism

1. big macromolecules are broken down into building blocks

2. building blocks are further degraded to common metabolites

3. small metabolites are completely oxidized or degraded to yield ATP

oxidation and reduction

• “oxidized” means to lose electrons

  • the “reducing agent” is oxidized since it reduces the other molecule

• “reduced” means to gain electrons

  • the “oxidizing agent” is reduced since it oxidizes the other molecule

• in the organic world, electrons are not completely transferred, oxidation and reduction is based on the polarization of shared electrons

• organic molecules have covalent bonds, so electrons cannot be transferred; the electrons polarize the bond instead (unequal sharing)

  • the more the electron is pulled away from the atom we are looking at, the more the molecule has been oxidized

• the more hydrogen, the more reduced

• the more nitrogen or oxygen, the more oxidized

oxidation of glucose

• in glycolysis and TCA cycle, glucose is completely oxidized

• energy is released

• produces 36 molecules of ATP

• step one and step three require ATP input

• after glycolysis, there is a net of 2 ATP and 2 NADH

• ΔG⁰ is different for each step

NADH/NAD+

• coenzymes (organic compounds)

• NAD+ can take two electrons and one proton to form NADH

• NADH is a reduced form, NAD+ is an oxidized form

oxidative vs substrate level phosphorylation

• two ways to make ATP

• oxidative phosphorylation: energy released during electron transport is utilized to form ATP

• substrate-level phosphorylation: a direct formation of ATP by a transfer of a phosphate group from substrates to ADP

  • high-energy phosphate group from a phosphorylated substrate to ADP.

  • cannot transfer a low-energy phosphate

anaerobic vs aerobic respiration

• both oxidize glucose to pyruvate

• aerobic respiration produces 36 ATP

• anaerobic respiration produces 2 ATP

fermentation

• oxygen is not present but we need ATP

• yeast cells under anaerobic conditions

• skeletal mucle cells undergoing strenuous contraction

• goal of fermentation is to generate NAD+

  • produces ethanol (yeast)

• NADH produces lactate to make NAD+, which makes our muscles burn

metabolic regulation

• regulated by regulating enzymes

• covalent modification

  • regulation of a protein or enzyme by adding or removing a chemical group through a covalent bond, which changes its activity.

  • ex: adding or removing a phosphate group

• allosteric modification (site other than the active site)

  • allosteric inhibition

  • allosteric activation

  • an example is feedback inhibition, which helps save resources by turning off when product is not needed and turning on when product is needed

  • as product is produced, it binds to the allosteric site and changes the enzyme conformation, so substrate can no longer bind. substrate can bind once product unbinds and is used in the next pathway

quaternary structure and allosteric activation

one subunit binds to oxygen, causing a conformation change. other subunits will also have a conformationc change of their active site. the change in conformation increases the affinity for oxygen in all subunits.

regulation of catabolic and anabolic pathways

• in opposite pathways (like glycolysis and gluconeogenesis), reversible steps use the same enzyme in each pathway

• the irreversible steps must use a different enzyme

• regulation of enzymes (especially in the irreversible steps) drives the reactions downward or upward (glycolysis or gluconeogenesis)