Biology Chapter 6
Terms in this set (128)
The ability to promote change or do work
Energy associated with movement, such as movement of a baseball bat from one location to another
Energy that is a substance or object possesses due to its structure or location, such as the location of an arrow when it is drawn back
Energy contained within covalent bonds in molecules is a type of potential energy
Study of energy transfers and transformations
First Law of Thermodynamics
"Law of conservation of energy"
Energy cannot be created or destroyed. However, energy can be transferred from one place to another
Cells couple heat-generating reactions to processes that maintain order
Second Law of Thermodynamics
Any energy transfer or transformation from one form to another increases entropy (the degree of disorder of a system)
Highly ordered to more disordered
Energy can be lost as heat!
___ is a from of electromagnetic radiation that is visible to the eye. The energy of ____ is packaged in photons. Used during photosynthesis. Energy is used to reduce carbon, thus producing organic molecules
___ is the transfer of kinetic energy from one object to another or from an energy source to an object. In biology, ___ is often viewed as kinetic energy that can be transferred due to a difference in temperature between two objects locations. Many organisms, including humans, maintain their bodies at a constant temperature. This is achieved, in part, by chemical reactions that generate ____.
___ energy is the energy possessed by an object due to its motion or its position relative to other objects. In animals, ___ energy is associated with movements due to muscle contraction such as walking
____ energy is potential energy stored in the ____ bonds of molecules. When the bonds are broken and rearranged, large amounts of energy may be released. The covalent bonds in organic molecule, such as glucose and ATP, store large amounts of energy. When bonds are broken in larger molecules to form smaller molecules, the ____ energy that is released can be used to drive cellular processes.
Electrical/ Ion gradient
The movement of charge or the separation of charge can provide energy. Also a difference in __ concentration across a membrane constitutes an electrochemical gradient, which is a source of potential energy. During a stage of cellular respiration called oxidative phosphorylation an H+ gradient provides the energy to drive ATP synthesis.
A measure of the randomness of molecules in a system. When a physical system becomes more disordered, the __ increases. As the energy becomes more evenly distributed, that energy is less able to promote change or do work.
Free Energy (G)
The amount of available energy that can be used to promote change or do work
A chemical reaction that has a NEGATIVE free-energy change. The products have less free energy than the reactants, and therefore, free energy is RELEASED during product formation. Spontaneous!
- ΔG<0 (negative free energy change)
If a reaction has a POSITIVE free-energy change, requiring the ADDITION of free energy from the environment. Not a spontaneous reaction.
- ΔG>0 (positive free energy change)
- Requires addition of energy to drive reactions
A molecule commonly used to drive cellular processes.
The rate of formation of products equals the rate of formation of reactants.
In the coupled reaction, a phosphate is directly transferred from ATP to glucose.
An agent that speeds up the rate of chemical reaction without being permanently changed or consumed by it.
Enzyme increases the rate of chemical reactions
Decreases the activation energy needed to facilitate a chemical reaction
This greatly increases the rate of the reaction
Most common catalysts in cells, proteins
Proteins that help molecules clear the activation barrier
They bind substrates and hold them in such a way that reduces the activation energy
Not actually used up in the reaction
Increase the rates of chemical reactions
Used to overcome repulsion, as an initial input of energy. This allows the molecules to get close enough to cause a rearrangement of bonds.
Energy barrier which needs to be overcome by the molecules to have the reaction occur
Allows molecules to get close enough to cause bond rearrangement
With the input of activation energy, glucose and ATP can achieve ____ in which the original bonds have stretched to their limit. Once the reactants have reached the ____ the chemical reaction can readily proceed to the formation of products.
Stretched out and held in a certain way to make the reaction work better
How Enzymes Lower Activation Energy
Straining bonds in reactants to make it easier to achieve transition state
Positioning reactants close together to facilitate bonding
Changing local environment of reactants- Direct participation through very temporary bonding between the enzyme and the reactants.
Location in Enzyme where reaction takes place
Enzymes are generally large proteins that bind relatively small reactants. When bound to an enzyme, the bonds in the reactants can be strained, thereby making it easier for them to achieve the transition state.
Positioning Reactants Close Together
When a chemical reaction involves two or more reactants, the enzyme provides sites in which the reactants are positioned very close to each other in an orientation that facilitates the formation of new covalent bonds
Changing the Local Environment Of The Reactants
Amino Acids in an enzyme may have properties, such as a negative or positive charges, that affect the chemistry of the reactants
Reactants that bind to active site
For an enzyme are the reactant molecules that bind to an enzyme at the active site and participate in the chemical reaction.
Enzyme- Substrates Complex
Binding between an enzyme and substrate
Enzymes have a high specificity for their substrate
Lock and key metaphor for substrate and enzyme binding- only the right key (substrate) will fit in the lock (enzyme)
Induced fit phenomenon- Interaction also involves conformational changes.
The attraction of an enzyme for a substrate
Can be strong- enzyme binds even when substrate is at low concentration
Weak- enzyme only binds at high substrate concentration
Reaction velocity increases until it reaches __ - a plateau where nearly all active sites are occupied by substrate
Vmax= velocity of reaction near maximal rate
Michaelis Constant, (KM)
Substrate concentration where velocity is half maximal value
Higher __ enzyme needs higher substrate concentration
Measure of substrate concentration required for chemical reaction to occur
Inversely related to affinity between enzyme and substrate
Molecules which bind non covalently to the active site. Inhibit the ability for the substrate to bind.
Molecule binds to the active site
Inhibits ability of substrate to bind
Apparent KM increases- more substrate needed
Lowers Vmax without affecting Km
Inhibition binds to allosteric site, not active
Site which causes change to occur in the enzyme, on and off switch essentially
Bind covalently to an enzyme to inhibit function
May covalently bind to amino acid in active site, blocking it permanently
IE: Nerve Gas, Binds covalently to acetylocholinerstase. Neurons and muscles can't communicate
Cells normally use reversible inhibitors instead
Usually inorganic ion that temporarily binds to enzyme
Organic molecule that participates in reaction but is left unchanged afterward
These conformational changes cause the substrates to bind more tightly to the enzyme
Break down food molecules into useful material for the cell
Break down cellular components
Synthesize Cellular molecules.
Putting together molecules, need an input of energy.
Endergonic (coupled reactions needed)
Catabolic and Anabolic pathways
Cells Obtain Energy
Energy of sunlight
Manufacturing them though photosynthesis (plants)
Cellular respiration- Eating Food(animals)
usable energy+ unusable energy
Amount of energy available to do work
Energy that can be extracted from a system to do work
Free Energy Change
G of products- G of reactants
Measures amount of disorder created
Energetically favorable to have a negative ΔG to happen spontaneously other wise it needs to be coupled with another reaction
Standard Free Energy
ΔG of a reaction depends on two main things
Energy stored in bonds of the molecules
The concentration of reactants
ΔG° standard free energy. Defined concentration, temperature, pressure
H= G+ TS
H= Enthalpy or total energy
G= Free Energy
S= Entropy or unusable energy
T= Absolute temperature in Kelvin (k)
Not necessarily fast, can be slow. Breakdown of sucrose to CO2 and H2O is spontaneous, but will take a long time for sugar in a sugar bowl to break down
Still needs an initial input of energy
Features of Enzymes
Highly selective- speed up only one particular chemical reaction
Have unique shape containing an active site- where substrate bind
Remain unchanged after the reaction
Molecules need to clear an energy barrier before they can undergo a reaction that moves it to a lower energy state.
Hydrolysis of ATP
ΔG =-7.3 kcal/mole
Reaction favors formation of products
The energy liberated is used to drive a variety of cellular processes
An endergonic reaction can be ___ to an exergonic reaction
Net Free Energy Change
The reactions will be spontaneous if the _____ for both processes is negative
Add together the ΔG, if they are negative than they can be coupled
Are molecules that bind noncovalently to the active site of an enzyme and inhibit the ability of the substrate to bind.
This binds to the enzyme away from the active site, altering the shape of the enzyme so that even if the substrate can bind, the active site functions less effectively. Usually reversible.
Place where non competitive inhibitor binds
Small molecules that are permanently attached to the surface of an enzyme and aid in the enzyme
Usually inorganic ions, such as Iron and Zinc that temporarily bind to the surface of an enzyme and promote a chemical reaction
Enzymes are affected by envioronment
Most enzymes function maximally in a narrow range of a temperature and pH
Organic molecules that participate in reaction but is left unchanged
Some of these ___ are synthesized by cells, but many of them are taken in as dietary vitamins by animal cells
Chemical reactions are coordinated with each other and occur in sequences called _____. Each step of which is catalyzed by a different enzyme.
2. Breakdown of Pyruvate
3. Citric Acid Cycle
4. Oxidative Phosphorylation
Results in the breakdown of of larger molecules into smaller ones. Exergonic
Breakdown of reactants, used for recycling building blocks
Used for energy to drive endergonic reactions -energy stored in intermediate such as ATP, NADH
Synthesis of larger molecules from smaller precursor molecules. Endergonic, but must be coupled with an exergonic reaction
Make large macromolecules or smaller molecules not available from food
Requires energy inputs from intermediates (NADH or ATP) to drive reactions
When a cell breaks covalent bonds in organic molecules they do not directly use the energy released in this process. The released energy is stored in ____, molecules such as ATP which are directly used to drive endergonic reactions in cells.
Oxygen is frequently involved in chemical reactions that remove electrons from other molecules
The addition of electrons to an atom or molecule. The addition of a negatively charged electron reduces the net charge of a molecule
Generally means the addition of a hydrogen atom
A molecule is reduced if the number of C-H bonds increase
Short for reduction-oxidation reaction. A substance that has been oxidized has less energy, a substance which has been reduced has more energy
During the oxidation of organic molecules such as glucose the electrons are used to reduce energy intermediates such as NADH. Organic molecules has been reduced to NADH.
Turn genes on or off
Enzymes in every metabolic pathway are encoded by genes , cells control this by ___.
Regulation vis Cell-Signaling Pathways
Often activate protein kinases.
Metabolic reactions are also coordinated at the cellular level. Cells integrate signals from their environment and adjust their chemical reactions to adapt to those signals.
Flight or Fight
Product of pathway inhibits early steps to prevent over accumulation of product
Noncompetitive inhibition is a type of regulation called ___, where the product of a metabolic pathway inhibits an enzyme that acts early in the pathway, thus preventing the over accumulation of the product.
Rate Limiting Step
The slowest step in a pathway. If this is inhibited or enhanced the changes will have the greatest influence on the formation of the product of the metabolic pathway.
Process by which living cells obtain energy from organic molecules and release waste products. Primary reason is to make ATP and NADH
Produces CO2 and water which are oxidized products of organic molecules
Aerobic respiration uses oxygen
Primarily use glucose but other organic molecules also used
Stage 1 of Catabolism
Breakdown of large macromolecules to simple subunits
Polysaccharides- Simple Sugars
Fats-Fatty Acids and Glycerol
Digestion and it occurs outside cells, in our intestines, or inside the cell with lysosomes
Break larger macromolecules into their monomeric subunits
These small organic molecules are then transported into the cytosol
Stage 2 of Catabolism
Breakdown of simple subunits to acetyl CoA; Accompanied by production of limited amounts of ATP and NADH
A chain of reactions called glycolysis takes place in the cytosol
Metabolic pathway converts 1 glucose molecule into 2 pyruvate molecules
Pyruvate is transported into the mitochondrial matrix where it is converted to acetyl CoA
Other sugars and fats can be broken down to acetyl CoA as well
Stage 3 of Catabolism
Complete oxidation of acetyl CoA to water and Co2. Large amounts of ATP produced in mitochondrion
Acetyl CoA is completely broken down in the citric acid cycle
Takes place entirely in the mitochondria
Large amounts of NADH are generated
Electron-Transport chain is used to produce large amounts of ATP
Oxygen is used and Carbon Dioxide is released via the oxidation of organic molecules. IE breathing
Greek: "sweet", "splitting"
Stage 1 of cellular respiration
Can occur with our without oxygen
Ten steps in three phases
Probably evolved very early in evolution
1. Energy investment
3. Energy Liberation
Glucose is broken down to two pyruvate molecules, producing a net energy yield of two ATP molecules and two NADH molecules.
In Eukaryotes this occurs in the cytosol
Produces a small amount of ATP without using any oxygen
A phosphate is transferred directly from a substrate to ADP
2 ATP hydrolyzed to create fructose-1,6 bisphosphate
6 carbon molecules broken into two 3 carbon molecules of glyceraldehyde-3-phosphate
Two Glyceraldehyde-3-phosphate molecules broken down into two pyruvate molecules - produces 2 NADH and 4 ATP
Adding a phosphate group to a molecule
Catalyzes the rearrangement of bonds within
Catalyzes the oxidation of a molecule by removing a hydrogen atom plus an electron
Catalyzes the shifting of a chemical group from one position to another within a molecule
Substrate Level Phosphorylation
Two ATP's made during glycolysis are synthesized which occurs when an enzyme is directly transfers a phosphate from an organic molecule to ADP
Breakdown of Pyruvate to an Acetyl Group
Two Pyruvate molecules enter the mitochondrial matrix, where each one is broken down to an acetyl group (with two carbons each) and one Carbon Dioxide molecule. For each pyruvate broken down via oxidation, one NADH molecule is bade by the reduction of NAD+
Citric Acid Cycle
Stage 3 of cellular respiration
Some molecules enter while others leave
Series of organic molecules regenerated in each cycle
Acetyl is removed from Acetyl CoA and attached to oxaloacetate to form citrate (citric acid)
Oxaloacetate is regenerated to start the cycle again
Each acetyl group is incorporated into an organic molecule, which is later oxidized to liberate two CO2 molecules. One ATP, three NADH and one FADH2 are made in this process.
There are two acetyl groups, the total yield is four carbon dioxides, two ATP via substrate-level phosphorylation, six NADH and two FADH. This process occurs in the mitochondrial matrix.
The NADH and FADH2 made in the three previous stages contain high-energy electrons that can be readily transferred in a redox reaction to other molecules.
Energy stored in the H+ electrochemical gradient is used to synthesize ATP from ADP and P. The overall process of electron transport and ATP synthesis is called oxidative phosphorylation because NADH or FADH2 have been oxidized and ADP has become phosphorylated to make ATP.
In eukaryotes, oxidation phosphorylation occurs along the __ which are invaginations of the inner mitochondrial membrane.
Electron removed from one molecule is added to another
Oxidation of Sugar
A. Direct Burning of Sugar in nonliving system
B. Stepwise oxidation of sugar in cells
Electrons removed by oxidation of organic molecules are used to create energy intermediates like ___
1. Releases a lot of energy when oxidized that can be used to make ATP
2. Can donate electrons during synthesis reactions to energize them
Step Wise Fashion
Stepwise oxidation of sugar in cells
Some free energy stored in activated carrier molecules
Activated Energy Carriers
NADH and NADPH
Major role in oxidation-reduction
When Hydrogen is added it will be reduced and more negative
KNOW OXIDIZED OR REDUCED FORM!
Adding an oxygen or taking hydrogen away is oxidized
Feedback inhibition prevents the formation of too much product of a metabolic pathway
Living Organisms Use Energy
Molecules such as glucose store a large amount of energy
The breakdown of glucose is used to make energy intermediates, such as ATP molecules which drive many types of cellular processes
Many disease associated with alterations in carbohydrate metabolism
Used to diagnose cancer in PET scans
Glycolytic enzymes over expressed in 80% of all types of cancers
May be due to low oxygen levels inside tumors, with over expression of glycolysis genes in response
Cancer cells preferentially use glycolysis while decreasing oxidative phosphorylation
If oxygen is present
In aerobic cells will convert __ to acetyl-CoA
Then this enters the citric acid cycle in the mitochondria
Generates a lot of ATP through oxidative phosphorylation
No oxygen presents
in anaerobic cells pyruvate undergoes fermentation
Without oxygen, only 5% of the energy available in glucose is captured in the 2 ATP molecules
Breakdown of Pyruvate
Stage 2 of cellular respiration
In Eukaryotes, pyruvate is transported into the mitochondrial matrix
broken down by pyruvate dehydrogenase
Molecule of CO2 removed from each pyruvate
Remaining acetyl group attached to CoA to make acetyl CoA
Yield= 1 NADH for each pryuvate
Pyruvate Dehydrogenase Complex
This giant complex of three enzymes converts pyruvate to acetyl-CoA
Are present in all eukaryotic cells
Generate chemical energy for the cell
consume oxygen and release CO2- cellular respiration
Membrane- Based ATP production
High energy electrons are transferred along a series of poteins in the memebrane
The energy released is used to pump protons across the memebrane
Creates an ion gradient across the memebrane
Membrane- Based ATP production
Protons flow down their electrochemical gradient through a complex called ATP synthase
The flow allows the enzyme to catalyze ATP synthesis form ADP and inorganic phosphate
Chemiosmotic coupling- Linking electron transport, proton pumping and ATP synthesis
NADH dehydrogenase complex
Catalyzes the removal of the hydride ion from NADH
Small, hydrophobic molecule
carries the electrons to cytochrome b-c1 complex
Series of proteins embedded in the inner mitochondrial membrane
As the electrons pass through the chain, protons are pumped across the membrane
The electrons are passed to oxygen to form water
Consists of 3 respiratory enzyme complexes- transfer electrons and pump protons
There are 2 mobile carriers that shuttle electrons between the complexes
Stage 1 of Chemiosmotic Coupling
As the electrons pass through the chain, protons are pumped across the membrane
The electrons are passed to oxygen to form water
Cyanide and Azide
Bind tightly to cytochrome oxidase and half electron transport
Electron Transport--> proton pumping
Hydrogen atoms are by far the most abundant type of atom
Water serves as a reservoir for donating and accepting protons during reduction and oxidation reactions
So whenever a molecule acquires an electron, its rapidly neutralized by a H+
2nd respiratory enzyme complex
Carrie the electrons to cytochrome oxidase complex
cytochrome oxidase complex
combines the electrons with O2 to form H2O
This is an oxygen requiring step of cellular respiration
Cytochrome oxidase complex
holds on to 4 electrons
transferes them to oxygen
this prevents formation of the superoxide radical oxygen
Electron transport and proton pumping
The transfer of high energy electrons can drive proton pumping
Electrons carries are arranged so that they:
- pick up a proton on one side of the membrane when they accept the electron
-release the proton on the other side of the membrane when the electron is passed
Most carriers use metal containing groups to transfer electrons
Redox potential and electron flow
Indicates the affinity for electrons - The larger the number, the higher the affinity
Electrons are passed to carriers with a progressively higher redox potential
The energy released during each step is used to pump protons
Capture free energy as H+ ions flow through
The enzyme converts energy from the proton motive force of the H+ gradient to the chemical bond energy in ATP
__ is a rotary machine that makes ATP as it spins
H+ carrier F0
Forms the channel for the protons
As protons move through, it causes the stalk to spin rapidly
Inside the matrix
Rotation causes the altering of protein conformation in stationary head
Mechanical deformation is converted into chemical bond energy of ATP
Catalyzes formation of ATP from ADP + Pi
100 ATP / second
This mechanism of ATP synthesis
Involves the consumption of oxygen and the addition of a
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