Exam II Flashcards
- There are five general principles governing metabolic pathways:
o A complex chemical transformation occurs in a series of separate, intermediate reactions that form a metabolic pathway
o Each reaction is catalyzed by a specific enzyme
o Most metabolic pathways are similar in all organisms, from bacteria to plants to humans
o In eukaryotes, many metabolic pathways are compartmentalized, with certain reactions occurring inside specific organelles
o Each metabolic pathway is controlled by key enzymes that can be inhibited or activated, thereby determining how fast the reactions will goo
- Free energy
– chemical energy available to do work
- Law of thermodynamics
A biochemical reaction may change the form of energy but not the net amount
- A biochemical reaction is a type of energy
– exergonic if it releases energy from the reactants or endergonic if energy must be added to the reactants
ATP Cycle
Cells use adenosine triphosphate as an energy currency. Some of the energy that is released in exergonic reactions is captured in chemical bonds when ATP is formed from adenosine diphosphate and inorganic phosphate (hydrogen phosphate; commonly abbreviated to Pi). The ATP can be hydrolyzed at other sites in the cell, releasing free energy to drive endergonic reactions.
- An ATP molecule - consists of the
of the nitrogenous base adenine bonded to ribose (a sugar), which is attached to a sequence of three phosphate groups. The Hydrolysis of a molecule of ATP yields free energy, ADP, and the inorganic phosphate ion
o ATP + H20 -> ADP + Pi+ Free Energy
- The change in free energy from the hydrolysis is
about -7.3 kcal/mol (-30 kJ/mol). Recall that a negative change in free energy means that the product molecules have less energy than the reactant, so the change is negative
- A molecule of ATP can also be hydrolyzed to – adenosine monophosphate and a pyrophosphate ion (P2O7^4-; commonly abbreviated as PPi).
- Two characteristics of ATP account for the free energy released by the loss of one or two of its phosphate groups:
o The free energy of the P-O bond between phosphate groups (called a phosphoanhydride bond and often denoted by wavy lines in chemical structures) is much higher than the energy of the O-H bond that forms after hydrolysis. So some usable energy is released by the following hydrolysis
o Because phosphate groups are negatively charged and so repel each other, it takes energy to get phosphate near enough to each other to make the covalent bond that links them together in the ATP molecule.
- In some reaction, ATP is formed by substrate level phosphorylation
because it involves the transfer of phosphate to ADP. This is the case for some reactions of glycolysis. But most of the ATP in living cells is formed by oxidative phosphorylation.
- Redox reactions
a reaction in which one substance transfers one or more electrons to another substance.
o Reduction – is the gain of one or more electrons by an atom, ion, or molecule
o Oxidation – the loss of one or more electrons
- Oxidation and reduction ALWAYS
occur together: as one chemical is oxidized, the electrons it loses are transferred to another chemical, reducing it. Thus some molecules are called oxidizing agents and others are reducing agents
- When a Molecule loses a hydrogen atom, it becomes oxidized
- The more reduced a molecule is, the more energy is stored in its covalent bonds.
- In a redox reaction,
some energy is transferred from the reducing agent to the reduced product. Some energy remains in the reducing agent (now oxidized), and some is lost to entropy
- Cells use the coenzyme
coenzyme nicotinamide adenine dinucleotide as an electron carrier in redox reactions This coenzyme exists in two chemically distinct forms, one oxidized (NAD+) and the other reduced (NADH). The reduction reaction:
o NAD+ + H^+ +2e^- ->NADH
o Involves the transfer of a proton and two electrons, which are released by the accompanying oxidization reaction. This reaction is highly endergonic, with a positive G about four times greater than the positive G for ATP formation.
- Within the cell, the electrons do not remain with NADH.
Oxygen is highly electronegative and readily accepts electrons from the reduced NADH molecule. The oxidation of NADH by O2 (which occurs in several steps:
o NADH + H^+ + 1/2O^2 -> NAD^+ + H2O
o Is highly exergonic, releasing energy with a lambda G of -52.4 kcal/mol (-219 kj/mol). Note that the oxidizing agent appears here a s1/2 O2 instead of O. This notation emphasizes that it is molecular oxygen, O2, that acts as the oxidizing agent
- Because the oxidation of NADH released more energy than the hydrolysis of ATP,
NADH can be thought of as a larger package of free energy than ATP.
- NAD+ is a common electron carrier in cells, but not the only one.
Others include FAD, which also transfers electrons during glucose metabolism, and NADP+ which is used in photosynthesis.
- We can summarize the two energy coupling coenzymes as follows
o ADP traps chemical energy to make ATP
o NAD+ traps the energy released in redox reactions to make NDH.
- Most chemical energy in cells is stored in the
C-H bonds of carbs and lipids. The release and reuse of this energy can be summarized as follows:
o Energy is released in catabolism by oxidation; this energy can be trapped by the reduction f coenzymes such as NADH
Energy for many anabolic and other energy requiring processes is supplied
by ATP. For example, active transport requires ATP
o Most of the energy releasing reactions in the cell produces
NADH, but most of the energy consuming reactions require ATP.
o Cells need a way to connect the two coenzymes;
; that is, to transfer energy from NADH to the phosphoanhydride bond of ATP. This transfer is accomplished in a process called oxidative phosphorylation-
the coupling of the oxidation of NADH
• NADH -> NAD+ + N+ + 2e- + energy
To the production of ATP
• Energy + ADP + Pi -> ATP
o This coupling is achieved via a mechanism called chemiosmosis- the diffusion of protons across a membrane, driving the synthesis of ATP.
o Chemiosmosis relies on
If the concentration of a substance is greater on one side of a membrane than the other, the substance will tend to diffuse across the membrane to its region of lower concentration
If a membrane blocks this diffusion, the substance at the higher c0oncentration has potential energy, which can be converted to other forms of energy
o Because the interior of a membrane is nonpolar, protons cannot readily diffuse across the membrane.
proton motive force
o Chemiosmosis convers the potential energy of a energy gradient across a membrane into the chemical energy in ATP.
o In prokaryotes, the gradient
is set up across the plasma membrane
o In eukaryotes, chemiosmosis occurs in the mitochondria and chloroplasts.
In the mitochondria, the H+ gradient is set up across the inner membrane, using energy released by the oxidation of NADH.
In chloroplasts, the H+ gradient is set up across the thylakoid membrane using energy from light.
o A membrane protein called ATP synthase uses
the potential energy of the H+ gradient to drive ATP synthesis.
o ATP synthase is a molecular motor composed of two parts
: the F0 unit, which is a trans membrane domain that functions as the H+ channel; and the F1 unit, which contains the active sites fir ATO synthesis.
o The f1 unit consists of six subunits (three each of two polypeptide chains), arranged like the segments of an orange around a central polypeptide. The potential energy set up by the proton gradient drives the passage of protons through the ring of polypeptides that make up the F- component. This ring rotates as the proton pass through the membrane, causing the F1 unit to rotate as well. ADP and Pi bind to active sites that become exposed on the F1 unit as it rotates, and ATP is made. The structure and function of ATP synthase are shared by living organisms as diverse as bacteria and humans. The molecular motors make ATP at rates of up to 100 molecules per second
- An oxidation reaction is always coupled with a reduction. When NADH is oxidized to
NAD+ in the mitochondria, the corresponding reduction reaction is the formation of water
o H+ + 1/2O2 -> H2O
- So the key role of O2 cells-
the reason we breath and have a blood system to deliver O2 to tissues- is to act as an electron acceptor and become reduced. In chloroplasts, the molecule ultimately reduce is NADP+, a relative of NAD+
- Chemiosmosis can be demonstrated experimentally.
- What happens if the H+ gradient is destroyed by the presence of a membrane channel that is always open to protons?
Obviously, ATP cannot be made, but the oxidation of NADH still occurs and O2 is reduced, releasing considerable energy. The released energy forms heat instead of being used to make ATP.
- Cellular respiration is
the catabolism of organic molecules within cells, and it is one of the key ways in which cells obtain energy.
- The chemical energy released from complete oxidation of glucose to CO2 is considerable, and the cell traps the energy by forming ATP:
o Glucose + 6O2 -> 6CO2 + 6H2O + Energy
o This energy is lost as heat 686 kcal/mol.
o In the cell, much of the released energy is trapped as ATP 234 kcal.
- In the catabolism of glucose under aerobic conditions (in the presence of O2), the small steps can be grouped into three linked biochemical pathways
o In glycolysis, the six carbon monosaccharide glucose is converted into two three carbon molecules of pyruvate
o In pyruvate oxidation, two three carbon molecules of pyruvate are oxidized to two two carbon molecules of acetyl CoA and two molecules of CO2
o In the citric acid cycle, two two carbon molecules of acetyl CoA are oxidized to four molecules of CO2
- Glycolysis
- Glycolysis takes place in the cytosol and involved ten enzyme catalyzed reactions. During glycolysis, some of the covalent bonds between carbon and hydrogen atoms in glucose molecule are oxidized, releasing some of the stored energy. The final products are two molecules of ATP, two molecules of ATP, and two molecules of NADH.
Glycolysis can be divided into two stages
the initial energy-investing reactions that consume chemical energy stored in ATP, and the energy-harvesting reactions that produce ATP and NADH.
- These are examples of two types of reactions that occur repeatedly in glycolysis and in many other metabolic pathways
o Oxidation-reduction – In this exergonic reaction, more than 50 kcal/mol of energy are released in the oxidation of glyceraldehyde 3 phosphate. The energy is trapped via the reduction of NAD+ to NADH
o Substrate level phosphorylation – The second reaction in this series is also exergonic, but in this case less energy is released. It is enough to transfer a phosphate from substrate to ADP, forming ATP.
o The end product of glycolysis, pyruvate, is somewhat more oxidized than glucose. In the presence of 02, further oxidation can occur. In prokaryotes these subsequent reactions take place in the cytosol, but in eukaryotes they take place in the mitochondrial matrix
- The next step in the aerobic catabolism of glucose
involves the oxidation of pyruvate to a two carbon acetate molecule and CO2.
- The formation of acetyl CoA
is a multistep reaction catalyzed by the pyruvate dehydrogenase complex, containing 60 individual proteins and 5 different coenzymes. The overall reaction is exergonic, and one molecule of NAD+ is reduced. The main role of acetyl CoA is to donate its acetyl group to the four carbon compound oxaloacetate, forming the six carbon molecule citrate.
- Acetyl CoA is the starting point for the citric acid cycle
This pathway if eight reactions completely oxidizes the two carbon acetyl group to two molecules of C02.
- The free energy released from these reactions is captured by ADP and the electron carriers NAD+ and FAD.
- This oxidation reaction is exergonic and the released energy is trapped by NAD+, forming NADH. With four such reactions (FADH2 is reduced coenzyme similar to NADH), the citric acid cycle harvests a great deal of chemical energy from the oxidation of acetyl CoA
- As previously mentioned, NADH is reoxidized to NAD+.
In the process, O2 is reduced to H2O:
o NAD + H+ + 1/2O2 -> NAD+ H2O
- This doesn’t happen in a single step but rather in a series of redox carrier proteins called the respiratory chain embedded in the inner membrane of the mitochondrion.
- The electrons from the oxidation of NADH and FADH2 pass from one carrier to the next chain, in the process called electron transport. The oxidation reactions are exergonic and they release energy that is used to actively transport H+ ions out of the mitochondrial matrix. Thus, a proton gradient is set up across the inner membrane. In addition to the electron transport carriers, the inner membrane contains an ATP synthase that uses the H+ gradient to synthesize ATP by chemiosmosis.
- The inner membrane provides compartments needed for separation of H+ and formation the H+ gradient.
- Oxidative phosphorylation yields a lot of ATP. For each NADH that begins the chain, two or three ATP molecules are formed under the conditions in the cell. Taking an average of 2.5, the 4 molecules of reduced coenzyme produced by each turn of the citric acid yield 100 molecules of ATP. Two molecules of acetyl OA are produced from each glucose, so the total is about 20 ATPs per molecule of glucose. Add to this the NADH produced by glycolysis and pyruvate oxidation, and the ATP formed by substrate level phosphorylation during glycolysis and the citric acid cycle, and the total is about 32 molecules of ATP produced per fully oxidized glucose.
- Under anaerobic conditions the respiratory chain cannot operate.
Without an alternative, the NADH produced by glycolysis would not be reoxidized and glycolysis would stop, because there would be no NAD+ for step of glycolysis.
- To solve this, organisms use fermentation to reoxidized the NADH, thus allowing glycolysis.
- Like glycolysis, fermentation pathways occur in the cytoplasm
- The overall yield of ATP from fermentation is
reduced to only the ATP made in glycolysis (two per glucose)
- Two fermentation pathways are usually found:
o Lactic acid fermentation (lactate)
o Alcoholic fermentation (ethanol)
- In lactic fermentation,
, pyruvate serves as the electron acceptor and lactate is the product.
- Alcoholic fermentation
takes place in certain yeasts and some plant cells under anaerobic conditions. Pyruvate is converted to ethanol.
- Carbon skeletons (molecules with covalently linked carbon atoms) can
enter catabolic pathways and be oxidized to release their energy, or they can enter anabolic pathways to be used in the formation of the macromolecules that are the major constituents of the cells
- Catabolic interconversions
polysacs, lipids, and proteins can all be broken down to provide energy
- Polysac are hydrolyzed to
to glucose. Glucose then passes through glycolysis, pyruvate oxidation, and then respiratory chain, where its energy is captured in ATP
- Lipids are broken down into
their constituents-glycerol and fatty acids. Glycerol is converted into dihydroxyacetone phosphate, an intermediate in glycolysis. Fatty acids are highly reduced molecules that are converted to acetyl CoA in the process called beta oxidation. This is carried out by a series of oxidation enzymes inside the mitochondrion. The beta oxidation of C16 fatty acid occurs in several steps
o C16 fatty acid + CoA -> C16 fatty acyl CoA
o C16 fatty acid CoA + CoA -> C16 fatty acyl CoA + acetyl CoA
o Repeat 6 times -> 8 acetyl CoA
- Proteins are hydrolyzed to
their amino acid building blocks. The 20 amino acids feed into glycolysis or the citric acid cycle at different points
- Anabolic interconversions
many catabolic pathways can operate essentially in reverse. Glycolytic and citric acid cycle intermediates, instead of being oxidized to form C02, can be reduced and used to form glucose in a process called gluconeogenesis. Likewise, acetyl CoA can be used to form fatty acids. The most common fatty acids have even numbers of carbon: 14, 16, 18. These are formed by the addition of two carbon acetyl CoA “units” one at a time until the appropriate chain length is reached
- Photosynthesis is
an anabolic process by which the energy of sunlight is captured and used to convert CO2 and H20 into carbohydrates and oxygen gas
o 6CO2 + 6H20 -> C6H12O6 + 6O2
o This is a highly endergonic reaction equation.
- Photosynthesis involves two pathways
o Light reaction converts light energy into chemical energy in the form of ATP and the reduced electron carrier NADPH. This molecule is similar to NADH but with an additional phosphate group
o Carbon fixation reactions do not use light directly, but instead use the ATP and NADPH made by the light reactions, along with C02, to produce carbs
- Both the light reactions and the carbon fixation reactions stop
in the dark because ATP synthesis and NADP+ reduction require light.
- In photosynthetic prokaryotes
the light reactions take place on internal membranes and the carbon fixation reactions occur in the cytosol.
- Light
traveling in waves, light also behaves as particles, called photons, which have no mass. Receptive molecules absorb photons in order to harvest their energy for biological processes. These receptive molecules absorb only specific wavelengths of light-photons with specific amounts of energy
- When a photon meets a molecule, one of three an happen
o The photon may bound off the molecule – it may be scattered or reflected
o The photon may pass through the molecule-it may be transmitted
o The photon may be absorbed by the molecule, adding energy to the molecule
o Neither of the first to causes any change. However, in absorption, the photon disappears and its energy is absorbed by the molecule.
o The photon’s energy cannot disappear, because according to the first law of thermodynamics, energy is neither created nor destroyed.
- The increase in energy boosts on of the electrons within the molecule into a shell farther from its nucleus;
pigments
- Molecules that absorb wavelengths in the visible spectrum
- When a beam of white light falls on a pigment
certain wavelengths are absorbed. The remaining wavelengths are scattered or transmitted and make the pigment appear to us as colored.
Absorption spectrum
plot light absorbed by a purified pigment against wavelength
- Action spectrum
a plot of the biological activity of an organism against the wavelengths of light
- In plants, two chlorophylls absorb light energy to drive the light reactions
: chlorophyll a and chlorophyll b. These two molecules differ only slightly in their molecular structures. Both have a complex ring structure, similar to that of the heme group of the hemoglobin, with a magnesium ion at the center. A long hydrocarbon tail anchors the chlorophyll molecule to integral proteins in the thylakoid membrane of the chloroplast.
- Chlorophyll absorb blue and red light.
In addition, plants possess accessory pigments that absorb photons intermediate energy between the red and blue wavelengths, and then transfer a portion of that energy to the chlorophylls. Among these accessory pigments are carotenoids such as beta carotene, which absorb photons in the blue and blue green wavelengths and appear deep yellow.
- The phycobilins are found in red algae and in cyanobacteria
, absorb various yellow green, yellow, and orange wavelengths
For most chlorophyll molecules embedded in the thylakoid membrane, the released energy
is
- A ground state chlorophyll molecule at the reaction center (Chl) absorbs the energy from the
adjacent chlorophylls and becomes excited (Chl*), but when this chlorophyll returns to the ground state, something very different occurs. The reaction center converts the absorbed light energy into chemical energy. The chlorophyll molecule in the reaction absorbs sufficient energy that it actually gives up its excited electron to a chemical acceptor
o Chl* + acceptor -> Chl+ + acceptor-
o This is the first consequence of light absorption by chlorophyll: the reaction center chlorophyll loses its excited electron in a redox reaction and becomes Chl+. As a result of this transfer of an electron, the chlorophyll gets oxidized, while the acceptor molecule is reduced.
T
- he final electron acceptor is NADP+, which gets reduced:
o NADP+ + H+ 2e- -> NADPH
o Photosystem I
absorbs energy at 7000 nm and passes an excited electron to NADP+, reducing it to NADPH
Photosystem II
absorbs light energy at 680 nm and produces ATP and oxidizes water molecules
- After an excited chlorophyll gives up its energetic electron to reduce a chemical acceptor molecule,
the chlorophyll lacks an electron and is very unstable. It has a strong tendency to grab an electron from another molecule to replace the one it lost- in chemical terms, it is a strong oxidizing agent. The replenishing electrons come from water
o H20 -> 1/2O2 + 2H+ + 2E-
o 2E- + 2CHL+ -> CHL
o Overall: 2CHL* + H2O -> 2CHL + 2H+ + 1/2O2
- Back to the electron acceptor in the electron transport system: the energetic electrons are passed through a series of membrane bound carriers to a final acceptor at a lower energy level.
As in the mitochondrion, a proton gradient is generated and is used by ATP synthase to store energy in the bounds of ATP
- In photosystem I, an excited electron from the Chl* at the reaction center reduces an acceptor.
The oxidized chlorophyll now grabs an electron, but in this case the electron comes from the last carrier in the electron transport system of photosystem II. This links the two photosystems chemically. They are also linked spatially, with the two photosystems adjacent to one another in the thylakoid membrane. The energetic electrons from photosystem I pass through several molecules and end up reducing NADP+ to NADPH
