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8,9 (enzyme (in enzymatic reactions, the substrate is held in the active…
8,9
enzyme
a catalytic protein that speeds up chemical reaction w/out being consumed by the reaction
chemical reaction between molecules involves both bond breaking and bond forming
changing one molecule into another generally involves contorting the starting molecule into a highly unstable state, until the reaction can proceed
to reach the contorted state where bonds can change reactant molecules must absorb energy from the surroundings
new bonds of the product molecules form energy Is released as heat and the molecules return to stable shapes
activation energy the energy required to contort the reactant molecules so the bonds break
enzyme catalyzes a reaction by lowering the activation energy so the reactants can absorb enough energy to reach the transition state
enzymes are specific for the reaction the catalyze, they determine which chemical processes will be going on in the cell at any given time.
the reactant an enzyme acts on is referred to as the enzymes substrate.
the enzyme binds to its substrate forming an enzyme substrate complex
while the enzyme and substrate are joined the catalytic action of the enzyme converts the substrate to the product
restricted region of the enzyme molecule actually binds to the substrate the region called the active site
the active site a pocket or groove on surface of the enzyme where catalysis occurs
the specificity of a enzyme is complementary fit between the shape of its active site and the shape of the substrate
induced fit, bring chemical groups of the active site into position that enhance their ability to catalyze the chemical reaction
in enzymatic reactions, the substrate is held in the active site by weak bonds, hydrogen and ionic bonds
metabolic reactions are reversible and an enzyme can catalyze either forward or the reverse reaction depending on direction has a negative delta g
in an enzymatic reaction the substrate binds to the active site of the enzyme
enzymes are fast acting and emerge from reactions in their original form
the active site can lower an Ea barrier by:
orienting substrates correctly
straining substrate bonds
providing a favorable microenvironment
more conducive to a type of reaction then the solution itself would be without the enzyme
covalently bonding to the substrate
enzyme activity
affected by environmental factors, temp and pH
enzymes work better under some conditions than others b/c these optimal conditions favor the most active shape for the enzyme
the rate of enzymatic reaction increases with increasing temp b/c substrates collide with active sites when molecules move rapidly
above temp range the enzyme speed declines sharply
thermal agitation of the enzyme molecule disrupts hydrogen, ionic and other weak bonds that stabilize the active shape for the enzyme and the protein denatures
enzyme has a pH were it is most active, range between the pH 6-8
enzymes require nonproteins helpers for catalytic activity they are called cofactors
cofactors mat be bound tightly to the enzyme as permanent residents or they are bound loosely and reversibly along the substrate
coenzyme, an organic cofactor that include vitamins
enzyme inhibitors
certain chemicals selectively inhibit the action of a specific enzyme
some inhibitors attach to the enzyme by covalent bonds making the inhibitor irreversible
other inhibitors bind to the enzyme by weak interactions making the inhibitor reversible
competitive inhibitors, reduce productivity of enzymes by blocking substrates from entering active sites
noncompetitive inhibitors, they impede enzymatic reactions by binding to another part of the enzyme
this interaction causes the enzyme molecule to change its shape in such a way the active site is less effective at catalyzing the conversion of substrate to product
allosteric regulation, either inhibit or stimulate the enzymatic activity
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feedback inhibition, metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway
catabolic pathways and production of ATP
one catabolic process fermentation degradation of sugars or other organic fuel that occurs without the use of oxygen
aerobic respiration, oxygen is consumed as a reactant along with organic fuel
anaerobic respiration, harvest chemical energy with out oxygen
cellular respiration includes both aerobic and anaerobic processes
catabolic pathways do not move flagella, pump solutes across membranes, polymerize monomers or perform cellular work
catabolism is linked to work by a chemical drive shaft ATP
catabolic pathways decompose and get energy, the transfer of electrons during the chemical reactions
in chemical reactions there is a transfer of one or more electrons from one reactant to another which are called oxidation reduction reactions or redox reactions
redox reaction the loss of electrons from one substance is called oxidation
the addition of electrons to another substrate is reduction
reducing agent is the electron donor
oxidizing agent is the electron acceptor
stages of cellular respiration
glycolysis occurs the cytoplasm breaks down glucose into two molecules of a compound called pyruvate breaks down glucose into two molecules of a compound called pyruvate
in eukaryotes, pyruvate enters the mitochondrion and is oxidized to s compound of acetyl CoA that enters the citric acid cycle. therefore the breakdown of glucose is completed
in prokaryotes these process take place in the cytosol
in some steps of glycolysis and citric acid cycle are redox reaction. which dehydrogenases transfer electrons from substrates to NAD+ forming NADH
the third stage of respiration the electron transport chain accepts electrons from the breakdown of products from the first two stages and passes electrons from one molecule to another
energy released at each step is stored in a form the mitochondrion can use to make ATP from ADP
this mode of ATP synthesis is called oxidative phosphorylation b/c it is powered by redox reaction of the electron transport chain
smaller amounts of ATP is formed directly in a few reactions of glycolysis and the citric acid cycle by substrate level phophorlaytion
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(9.2) glycolysis, "sugar splitting" glucose a six carbon sugar that splits into two three carbon sugars
there are oxidized and the remaining atoms rearranged to from two molecules of pyruvate
glycolysis is dived into two phases, the energy investment phase and the energy payoff phase
the energy investment phase, the cells spends ATP. this investment is paid with interest during energy payoff phase,...
when ATP is produced by substrate level phosphorylation and NAD+ is reduced to NADH by electron released from the oxidation of glucose
the net energy from glycolysis per glucose molecule is 2 ATP plus 2 NADH
glycolysis reactants, 1 glucose, 2NAD+ from ETS, 2ADP+2P, products, 2 ATP, 2 pyruvic acid, 2NADH got to ETS, 2H+
(oxidation of pyruvate to acetyl CoA)(9.3)upon entering the mitochondrion via active transport, pyruvate is converted to acetyl coenzyme A, or acetyl CoA
this step linking glycolysis and the citric acid cycle is carried out by a multienzyme complex that has three reaction.
1) pyruvates carboxyl group that is oxidized and has little chemical energy is removed and given off as a molecule of CO2, and is released during cellular respiration
2) the remaining two carbon fragment is oxidized forming acetate. extracted electrons are transferred to NAD+ storing energy in the form of NADH
3) coenzyme CoA, is attached via its sulfur atom to the acetate, forming the acetyl CoA.
the citric acid cycle (Krebs cycle), located in the mitochondrial matrix
functions as a metabolic furnace that oxidizes organic fuel derived from pyruvate
the cycle generates 1 ATP per turn by substrate level phosphorylation but most chemical energy is transferred to NAD+,...
and a related electron carrier the coenzyme FAD during the redox reactions
reduced coenzyme, NADH and FADH2 shuttle of high energy electrons into the electron transport chain
Krebs cycle reactants, 2 acetyl CoA, 6 NAD+ from ETS, 2 ADP + 2P, 2 FAD from ETS, products 4CO2, 6NADH go to ETS, 2 FADH2 go to ETS, 2 ATP
electron transport chain
embedded in the inner membrane of the mitochondrion in eukaryotic cells, & in prokaryotic reside on plasma membrane
the folding's of the inner membrane to form cristae which increases surface area, providing space for copies ETS in each mitochondrion
the infolded membrane structure is well suited for the series of sequential redox reactions that take place along the ETS
during electron transport along the chain, electron carriers alternate between reduced and oxidized states as they accept and donate electrons
electron transport chain in detail (figure 9.13)
electrons acquired from glucose by NAD+ during glycolysis and the critic acid cycle are transferred from NADH to the first molecule of the ETS
the next redox reaction, flavoprotein(FMN) returns to its oxidized form a it passes electrons to an iron sulfur protein
then the iron sulfur protein passes the electrons to a compound ubiquinone (Q), this electron carrier is small and hydrophobic and is not a protein
most of the remaining electron carriers between Q and oxygen are protein called cytochromes, their prosthetic group ( are nonproteins components essential for catalytic functions of certain enzymes)
their prosthetic group, a heme group has an iron atom that accepts and donates electrons
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FADH2 is another source of electrons for the ETS
the ETS makes no ATP directly, it breaks large free energy into a series of small steps that release in manageable amounts
ETS reactants, 10 NADH, 2 FADH2, O2, H+, ADP, P, and products H2O, 32 or 34 ATP, NAD+, FAD
transition reaction occurs between glycolysis and Krebs cycle.
reactants, 2 pyruvic acid, 2 NAD from ETS, 2 coenzyme A. the products, 2CO2, 2NADH go to ETS, 2 Acetyl CoA
metabolic pathways
begin with specific molecule, that is altered in steps resulting in certain products.
catabolic pathways
called breakdown pathways
breakdown of complex molecules to simpler ones
anabolic pathways
consume energy to build complicated molecules from simpler ones
ex: synthesis of an amino acid from simpler molecules
catabolic and anabolic are the uphill and downhill of metabolic pathways
energy released from downhill catabolic reaction can be stored and used to drive uphill reactions of anabolic pathways
bioenergetics, how energy flows through living organisms
ATP
three main kinds of work
chemical work, pushing endergonic reactions that do not occur spontaneously
transport work, pumping of substances across membrane against the direction of spontaneous movement
mechanical work, contraction of muscle cells , movement of chromosomes during cellular respiration
energy coupling, use of an exergonic process to drive an endergonic
if delta g of an endergonic reaction is less than the amount of energy released during ATP hydroloysis the two reactions...
..can be coupled so that the overall the coupled reaction are exergonic
this usually involves phosphorylation the transfer of a phosphate group from ATP to some other molecule such as a reactant.
the recipient molecule with the phosphate group covalently bonded to it is called a phosphorylated intermediate
the intermediate is key to the formation of exergonic and endergonic
transport and mechanical in the cell are usually powered by hydrolysis of ATP
ATP hydrolysis leads to the change in the proteins shape and its ability to bind to another molecule
the regeneration of ATP
ATP can be regenerated by the addition of phosphate to ADP, the free energy required to phosphorylate ADP comes from exergonic breakdown reactions in the cell
shuttling of inorganic phosphate and energy is called the ATP cycle, it couples the cells energy-yielding (exergonic) process to the energy consuming (endergonic) ones
the generation of ATP is endergonic
ATP formation from ADP and P is not spontaneous, free energy must be spent to make it occur
catabolic pathway, like cellular respiration provide energy for endergonic process of making ATP
glycolysis and the citric acid cycle connect to many other metabolic pathways
the digestive tract starch is hydrolyzed to glucose, then is broken down in the cells by glycolysis and the citric acid cycle
glycogen the polysaccharide humans and animals store in their liver an muscle cells can be hydrolyzed to glucose as fuel for respiration
catabolism can also harvest energy stored in fats obtained either from food or storage cells in the body
after fats are digested to glycerol and fatty acids the glycerol is converted to glyceraldehyde 3-phosphate an intermediate of glycolysis
metabolic sequence beta oxidation, breaks fatty acid down to two carbon fragments which enter the citric acid cycle as acetyl CoA
NADH and FADH2 are generated in beta oxidation they enter the ETS leading to more production of ATP
biosynthesis anabolic pathway
compounds formed as intermediates of glycolysis and the citric acid cycle can be diverted into anabolic pathways as precursors from which the cell can synthesize the molecules it requires
humans make about half of the 20 amino acid in proteins by modifying compounds siphoned away from the citric acid cycle the rest are essential amino acids
glucose can be made from pyruvate and fatty acid can be synthesized from acetyl CoA
however anabolic, biosynthetic pathways don not generate ATP, but consume it
regulation of cellular respiration via feedback mechanisms
if there is a glut for an amino acid the anabolic pathways that synthesize that amino acid from an intermediate of the citric acid cycle is switched off
common mechanism for control id feedback inhibition: the end product of anabolic pathway inhibits the enzyme that catalyze early step in the pathway
if the cell is working hard then its ATP concentration begins to drop, respiration speeds up
plenty of ATP meets demand then respiration slows down sparing valuable molecules for other functions
phosphofructokinase the enzyme that catalyzes step 3 of glycolysis
the first step that commits the substrate irreversibly to the glycolytic pathway, controlling the rate of this step the cell can speed up or slow down the entire catabolic process
phosphofructokinase is considered the pacemaker of respiration
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energy, capacity to cause change
ex: energy exists in various forms some can perform work,
forms of energy
kinetic energy
, relative motion of objects. moving objects can perform work by imparting motion to other matter
thermal energy
, is kinetic energy associated with random movement of atoms or molecules
thermal energy is transfer from one object to another is called heat
chemical energy
, refer to potential energy avaailable to release in a chemical reaction
complex molecules like glucose and are high in chemical energy
biochemical pathways carry out in context of cellular structures
enable the cell to release chemical energy from food molecules and use the energy to power life processes
potential energy
, when an object is not moving that may still posses energy
is it energy that matter posses b/c of its location and structure
the law of energy transformation
study of energy transformation that occur in a collection of matter is
thermodynamics
isolated system
, is unable to exchange energy or matter with its surroundings
open system
, energy and matter can transfer between the system and its surroundings.
first law of thermodynamics
energy of the universe is constant
energy can be transferred and transformed, but can neither be created or destroyed
second law of thermodynamics
every energy transfer or transformation increases entropy of the universe
entropy is a measure of disorder or randomness
spontaneous process (energetically favorable), an increase of entropy a process can proceed without requiring an input of energy
nonspontaneous process, decrease in entropy. will happen only if energy is supplied
NAD+ a coenzyme, and an electron carrier
carrier b/c it can cycle easily between oxidized and reduces states
as an electron acceptor NAD+ functions as an oxidizing agent during respiration
NAD+ is reduced to NADH, which shows that hydrogen is in the reaction
electron loose little potential energy when they are transferred from glucose to NAD+
each NADH molecule formed during cellular respiration represents stored energy
this energy can be tapped to make ATP when electron complete their fall in a series of steps down the energy gradient from NADH to oxygen
cellular respiration brings hydrogen and oxygen together to form water, but they are differences
first difference is in cellular respiration the hydrogen atom that reacts with oxygen is derived from organic molecules rather than H2
second, respiration uses electron transport chain to break the fall of electrons to oxygen into energy releasing steps
the electron transport chain mostly proteins built into the inner membrane of the mitochondria of eukaryotic cells, the plasma membrane in respiring prokaryotes
Free energy, energy that can do work when temp, and pressure are uniform as in a living cell
delta G= delta H -T delta S, free energy equation
delta H, the change in the systems enthalpy, delta S change in the systems entropy, and T absolute temp in Kelvin
delta G that is negative is always spontaneous
spontaneous process decreases the systems free energy and process that have a positive or zero delta G are nonspontaeous
delta g can only be negative when the process involves a loss of free energy during the change from initial to final state
chemical equilibrium, in which reactions are reversible and procced to the point of in which the forward and backward reaction occur at the same time
and there will be no net change in the concentrations of products and reactants
an
exergonic reaction
occurs with a net release of free energy b/c the chemical mixture loses free energy
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chemoiosmosis
populating the inner membrane of the mitochondrion or the plasma membrane(prokaryotes) are copies of protein complex called ATP synthase
ATP synthase is an enzyme that makes ATP from ADP and inorganic phosphate, ATP synthase works like an ion pump in reverse
ATP synthase uses the energy of the existing ion gradient to power ATP synthesis
the power source for ATP synthase is a difference in the concentration of H+ on opposite sides of the inner mitochondrial membrane
energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP called chemiosmosis
the H+ gradient that results is the proton motive force emphasizing the capacity of the gradient to perform work. the force drives H+ back across the membrane through the H+ channels provided by ATP synthase
in mitochondria energy for gradient formation comes from exergonic redox reactions and ATP synthase is the work performed
chloroplasts use chemiosmosis to generate ATP during photosynthesis in these organelles light drives both electron flow down an ETS and the H+ gradient formation
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certain cells can oxidize organic fuel and generate ATP w/out the use of oxygen: anaerobic respiration and fermentation
anaerobic respiration uses ETS, fermentation doesn't
fermentation is a way harvesting chemical energy w/out using oxygen or any ETS
glycolysis oxidizes glucose to two molecules of pyruvate, the oxidizing agent of glycolysis is NAD+ and neither oxygen or any ETS is present
glycolysis is exergonic and the energy available is used to produce 2 ATP by substrate level phosphorylation
if oxygen is present the ATP is made by oxidative phosphorylation when NADH passes electrons removed from glucose to the ETS
glycolysis generates 2 ATP whether oxygen is present or not depending on aerobic and anaerobic conditions
fermentation is an extension of glycolysis allowing continuous generation of ATP by the substrate level phosphorylation of glycolysis
for this occur there has to be a good supply of NAD+ to accept electrons during the oxidation step in glycolysis
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types of fermentation
alcohol fermentation, pyruvate is converted to ethanol.
step 1:releases carbon dioxide from the pyruvate which is converted to the two carbon compound acetaldehyde
step 2: acetaldehyde is reduced by NADH to ethanol, this regenerates the supply of NAD+ needed for the continuation of glycolysis
lactic acid fermentation
pyruvate is reduced by NADH to form lactate as an end product with no release of CO2
human muscle cells make ATP by lactic acid fermentation when oxygen is scarce