1
Q
catabolism vs anabolism
A
- Catabolic pathways release energy by breaking down complex molecules into simpler compounds.
Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism. - Anabolic pathways consume energy to build complex molecules from simpler ones. (ex glucose anabolism)
The synthesis of protein from amino acids is an example of anabolism.
2
Q
potential energy
A
Potential energy is energy that matter possesses because of its location or structure.
Being on top of the platform, the energy within the bonds of glucose.
3
Q
kinetic energy
A
Kinetic energy is energy associated with motion.
Climbing up the ladder, a beating flagellum.
4
Q
heat energy
A
Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules.
5
Q
open system
A
In an open system, energy and matter can be transferred between the system and its surroundings.
Organisms are open systems.
6
Q
The First Law of Thermodynamics
A
According to the first law of thermodynamics, the energy of the universe is constant.
Energy can be transferred and transformed,but it cannot be created or destroyed.
The first law is also called the principle of conservation of energy.
7
Q
The Second Law of Thermodynamics
A
During every energy transfer or transformation, some energy is unusable, and is often lost as heat.
According to the second law of thermodynamics
Every energy transfer or transformation increases the entropy (disorder) of the universe.
- ex: the conversion of chemical energy in food to kinetic energy is inefficient, resulting in the generation of heat and the waste products CO2 and H2O
8
Q
entropy
A
A measure of the disorder or randomness of a system.
The more randomly arranged a collection of matter is, the more entropy it has.
- a block of salt has less entropy (has a more organized structure) than a pile of salt (more dispersed).
- a protein molecule has less entropy than the individual amino acids that make it up.
To lower the entropy of a system (make it more organized) requires an input of energy.
9
Q
entropy of biological systems
A
- Biological systems usually have great order (low randomness), and therefore exist in a state of low entropy.
- To maintain this state of low entropy requires a constant expenditure of energy: a biological organism is an island of low entropy in a universe of increasing entropy.
- An organism can only be maintained by constantly using energy to reduce its entropy (maintain its order).
10
Q
free energy
A
Free energy (G). The amount of energy in a system that is available to do work. G = Gibbs Free Energy
A ordered system (i.e. has a low degree of entropy) has a greater amount of free energy.
deltaG = Gproducts - Greactants
11
Q
exergonic vs endergonic rxn
A
exer:
- energy released
- spontaneous
- deltaG < 0
- reactants have higher free energy than prodcuts
ender:
- energy required
- nonspontaneous
- deltaG > 0
- reactants have lower free energy than products
12
Q
in a spontaneous change,
A
- higher to lower free energy
- less to more stable
- more to less work capacity
- the released free energy can be harnessed to do work
- ex: gravitational motion, diffusion
13
Q
The Structure and Hydrolysis of ATP
A
- ATP is composed of ribose (a sugar), adenine(a nitrogenous base), and three phosphate groups.
- The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis (HD,DP hydrolysis depolymerization).
- Energy is released from ATP when the terminal phosphate bond is broken (the reaction is exergonic).
14
Q
The Regeneration of ATP
A
- ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP).
- The energy to phosphorylate ADP comes from the catabolism (breakdown) of energy-containing bonds of macromolecules (e.g. glucose).
- Hydrolysis of ATP provides energy to perform cellular work (for endergonic processes)
15
Q
ATP powers cellular work by
A
- coupling exergonic reactions to endergonic reactions.
- ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant.
The recipient molecule is now called a phosphorylated intermediate.
16
Q
A cell does three main kinds of work
A
(all endergonic)
Chemical
Transport
Mechanical
17
Q
transport work
A
ATP hydrolysis leads to a change in transport protein shape and binding ability.
18
Q
mechanical work
A
ATP hydrolysis leads to a change in motor protein shape and binding ability.
- ATP binds noncovalently to motor
proteins and then is hydrolyzed. (This moves a vesicle, attached to a motor protein, along a cytoskeletal track.)
19
Q
enzymes
A
- Enzymes speed up metabolic reactions by lowering energy barriers (lowering EA).
- A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction. They do not cause reactions that could not ordinarily occur.
- An enzyme is a catalytic protein.
- Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction.
20
Q
activation energy
A
- Every chemical reaction between molecules involves bond breaking and bond making.
- The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA).
- Even exergonic reactions need to get over the activation energy “hump”.
- The energy for this is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings.
- EA is the difference in free energy btwn reactants in the transition state (highest) and reactants at the beginning (lower)
21
Q
How Enzymes Speed Up Reactions
A
- Enzymes catalyze reactions by lowering the EA barrier.
- Enzymes do not affect the change in free energy (∆G); instead, they hasten reactions that would occur eventually.
- EA w/ enzyme is LOWER
- Course of rxn w/o enzyme has higher “hump” than w/ enzyme
22
Q
substrates
A
- Enzymes bind specific reactant molecules called substrates.
- Substrates bind to a specific site on the enzyme surface called the active site, where catalysis takes place.
- Some enzymes are very specific. They bind specific substrates and catalyze particular reactions under particular conditions
23
Q
hexokinase
A
adds a phosphate group to glucose
24
Q
The catalytic cycle of an enzyme (steps)
A
- substrates enter active site; enzyme changes shape such that its active site enfolds the substrates (induced fit)
- in this enzyme-substrate complex, substrates are held in active site by weak interactions, such as H bonds and ionic bonds
- active site can lower EA and speed up a rxn
- still in the active site, substrates are converted to products
- products released
- active site available for new substrate molecules
25
How do enzymes alter the activation state of a reaction?
At the active sites enzymes and substrates interact by breaking old bonds and forming new ones. Enzymes catalyze reactions using one or more of the following mechanisms:
1) Enzymes can orient substrates.
2) Enzymes can add charges to substrates.
3) Enzymes can alter the shape of the substrates.
26
1. Enzymes can orient substrates.
- While free in solution, substrates move randomly. So the probability for an interaction at the angle necessary to change chemical interactions is low.
- When bound to enzymes, two substrates can be oriented in such a way that a reaction becomes more likely.
27
2) Enzymes can add charges to substrates.
- The R groups (side chains) of an enzyme’s amino acids may directly participate in making substrates more chemically reactive.
- Some enzymes work by acid-base catalysis: acidic or basic side chains of amino acids form the active site and transfer H+ to or from the substrate, destabilizing a covalent bond in a substrate.
28
3) Enzymes can alter the shape of the substrates.
The stretching of the bonds decreases their stability, making them more reactive.
29
Competitive inhibitors
bind to the active site of an enzyme, competing with the substrate.
30
Noncompetitive inhibitors
bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective.
31
Allosteric regulation of enzyme activity
- Allosteric regulation occurs when a regulatory molecule binds to a enzyme at one site and affects the enzyme's function at another site.
- Allosteric refers to an action at a site “other” than the active site.
- Enzymes that are allosterically regulated usually consist of multiple subunits each with its own active site
32
cooperativity
- Cooperativity is a form of allosteric regulation that can amplify enzyme activity.
- One substrate molecule primes an enzyme to act on additional substrate molecules more readily.
- Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site.
33
Metabolism is organized into
- Metabolism is organized into sequences of enzyme-catalyzed chemical reactions called pathways.
- Each step A to B to C to D occurs appropriately because of enzymes. For example, one enzyme converts A to B; a second enzyme converts B to C
34
feedback inhibition
In feedback inhibition, the end product of a metabolic pathway shuts down the pathway.
Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.
35
feedback inhibition example
- threonine (the initial substrate) binds to active site on enzyme, threonine deaminase.
- this sets of a string of reactions involving many different phosphorylated intermediates. the end product of these reactions is isoleucine
- isoleucine binds to allosteric site. this is the feedback inhibition -- this makes the active site unavailable, halting the pathway
- after isoleucine is used up by the cell, the active site is available once more
36
covalent bonds and energy
The relocation of electrons in covalent bonds releases energy.
Electrons in covalent bonds between atoms of equal electronegativity have a greater potential energy than those between atoms with unequal electronegativity.
Covalent C — H bonds have greater potential energy than O — H or C — O bonds because the electrons are more equally shared by C and H.
37
Glucose Anabolism
photosynthesis; positive deltaG
38
Glucose Catabolism
cell resp; negative deltaG
- Glucose is transformed from a
less stable and more complex state (low entropy) to a
more stable and less complex state (higher entropy)
39
3 stages of cell resp
1) glycolysis
2) citric acid (or Krebs) cycle
3) electron transport chain & oxidative phosphorylation
40
oxidizing and reducing agent
An oxidizing agent (an agent that oxidizes another agent) accepts an electron.
A reducing agent (an agent that reduces another agent) donates an electron.
41
redox in glucose catabolism
- During the catabolism of glucose, glucose is the reducing agent (and is oxidized), while oxygen is the oxidizing agent (and itself is reduced).
- electrons are transferred along a series of electron donors and acceptors (electron carriers) in a way that produces energy in small packets.
42
e- carriers
The coenzyme nicotinamide adenine dinucleotide (NAD) is a key electron carrier in redox reactions.
Another electron carrier is flavin adenine dinucleotide (FAD).
43
NAD oxidized/reduce
NAD exists in an oxidized form, NAD+, and a reduced form, NADH + H+.
The reduction reaction is: NAD+ + 2 H --> NADH + H+ and requires an input of energy.
44
oxygen and NADH
NADH + H+ + 1/2O2 --> NAD+ + H2O
The deltaG of this oxidation reaction is -52.4 kcal/mol.
(For comparison, the deltaGG of the ATP to ADP reaction is -12 kcal/mol.)
Think of NAD as a packaging agent for free energy.
45
Potential energy in glucose
contained in the reduced hydrocarbon bonds.
| To use this energy, glucose must be oxidized to CO2 and water.
46
6 maj steps of releasing energy from glucose
- The transport of glucose into the cell using glucose transporters.
- Splitting glucose into two pyruvate molecules in glycolysis.
- Oxidation of pyruvate to produce acetyl CoA, which is then metabolized further in:
- The citric acid (or Krebs) cycle where Acetyl CoA is oxidized to produce ATP.
- The electron transport chain uses NADH/ FADH2 from the citric acid cycle and glycolysis to establish a proton gradient across the inner mitochondrial membrane.
- This gradient drives an enzyme, ATP synthase, to produce ATP.
47
cell resp compartmentalization
- The compartmentalization of these
processes within the cell is critical for the
efficient release of energy from glucose.
- They occur in different cell compartments. The movement of molecules between compartments is an important aspect of metabolism.
48
compartmentalization: gluose transport
The transport of glucose between the extracellular and intracellular compartments requires transport proteins.
49
compartmentalization: glycolysis
Glycolysis requires soluble cytosolic enzymes.
50
compartmentalization: pyruvate and citric acid cycle
Pyruvate moves from the cytosol to the mitochondrial matrix, where enzymes required for the citric acid cycle are located.
51
glycolysis
a metabolic pathway made up of a series of cytosolic enzymes that metabolize glucose - a 6 carbon compound - into two 3 carbon compounds (pyruvate).
- energy investment and payoff phases
52
glycolysis energy investment
kinases use ATP to phosphorylate glucose and some of the molecules that are produced as glucose begins to be broken down.
53
glycolysis energy payoff
the energy from the some of the first C-H bonds of glucose that are broken is shunted to ATP and NADH2.
54
glycolysis products
production of ATP and NADH2 and two molecules of pyruvate.
55
how can Substrates other than glucose can also be used as sources of energy?
1. large macromolecules broken down into simple subunits
2. breakdown of simple subunits into acetyl CoA accompanied by production of limited amounts of ATP and NADH
3. complete oxidation of acetyl CoA to H2O and C2O accmopanied by production of large amounts of NADH and ATP in mitochondrion
56
mitochondria vs chloroplast energy conversion
- Mitochondria convert energy from food (e.g. fats and carbohydrates) and consume oxygen to produce water and carbon dioxide.
- Chloroplasts convert energy from sunlight and consume water and carbon dioxide to produce oxygen and carbohydrates. In both systems a proton gradient is established.
57
The pH gradients
across the membranes
of mitochondria and chloroplasts.
M:
- matrix: 7.5
- intermembrane space: 7
C:
- stroma: 7.5
- intermembrane space: 7
- thylakoid: 5
58
C3 leaves
Most plants have C3 leaves (generate G3P, a 3 carbon sugar). Mesophyll cells carry out photosynthesis (have chloroplasts).
59
photorespiration
On hot, dry days, plants close stomata, which conserves H2O but also limits photosynthesis because closing of stomata reduces access to CO2 and causes O2 to build up.
These conditions favor a wasteful process called photorespiration. Plant use oxygen and release CO2 without producing ATP or sugar (instead of the other way around).
60
calvin cycle uses ___ to ___
The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar.
61
Tracking atoms through photosynthesis
(O2 is derived from H2O not CO2)
62
Photosynthesis vs. Aerobic Respiration
Photosynthesis is also a redox process, but here the electron flow is in the opposite direction.
H2O is split, and the electrons from the more polar H - O bonds are transferred along with the protons to CO2 reducing it to a sugar and generating less polar C - H bonds.
The energy required for this process is derived from sunlight.
It is stored as potential energy in the C - H bonds of the sugar.
63
chlroplasts
Chloroplasts are found mainly in cells of the mesophyll, the interior tissue of the leaf.
64
stomata
CO2 enters and O2 exits the leaf through pores called stomata.
65
electromagnetic spectrum
The electromagnetic spectrum is the entire range of electromagnetic energy, or radiation.
Visible light consists of wavelengths (including those that drive photosynthesis) that produce colors we can see.
66
Determining an absorption spectrum
1. White light is split into component colors with a prism.
2. Filter passes green light only.
3. Light is passed through chlorophyll solution.
4. Transmitted light is detected with photoelectric sensor. Galvanometer indicates low absorption.
- When experiment is
repeated with blue
light, little light get
past solution of
chlorophyll.
- The absorption spectrum of chlorophyll suggests that non-green light is used for photosynthesis.
67
Which wavelengths of light are most effective in driving photosynthesis?
- Exposed different segments of a filamentous alga to different wavelengths of light.
- Areas receiving wavelengths favorable to photosynthesis produced excess O2.
- Aerobic bacteria clustered along the alga as a function of O2 production.
68
two types of chlorophyll:
Plants contain two types of chlorophyll:
Chlorophyll a
Chlorophyll b
They differ slightly in structure.
- CHO in b, CH3 in a
69
chlorophyll molecule structure
- head: porphyrin ring; absorbs light
| - tail: hydrocarbon tail; interacts with hydrophobic regions of proteins inside thylakoid membranes of chloroplasts.
70
carotenoids
Plants also contain carotenoids that can absorb excessive light that would damage chlorophyll.
71
photosystems
- In chloroplasts, chlorophyll molecules are organized with proteins to form photosystems that are located in the thylakoid membrane.
- The light-harvesting complexes (pigment molecules bound to proteins) transfer the energy of photons to the reaction center (like a funnel).
- A primary electron acceptor in the reaction center accepts excited electrons from a special pair of chlorophyll molecules.
72
Linear electron flow
- the primary electron flow pathway, involves both photosystems and produces ATP and NADPH using light energy.
1. A photon hits a pigment in the light harvesting (antenna) complex and its energy is passed among pigment molecules until it excites P680 (the special pair inside the reaction center).
2. An excited electron from P680 is transferred to the primary electron acceptor (pheophytin). P680 is now called P680+ (think of it as having a “hole” since it lost its electron).
3. H2O is split by enzymes, and the electrons are transferred from the hydrogen atoms to P680+, thus reducing it back to P680 (its hole is “filled”). O2 is released as a by-product of this reaction.
4. Each electron “falls” down an electron transport chain from the primary electron acceptor of PS II.
5. Energy released by the fall drives the creation of a proton gradient across the thylakoid membrane. Diffusion of H+ (protons) across the membrane drives ATP synthesis.
6. In PS I (like PS II), transferred light energy captured by pigments in the light harvesting (antenna) complex excites P700, which loses an electron to an different primary electron acceptor. P700+ (P700 that is missing an electron) accepts an electron passed down from PS II via the electron transport chain to fill its “hole” (recall that PS II got its electron from water).
7. Each electron “falls” down an electron transport chain from the primary electron acceptor of PS I to the protein ferredoxin (Fd).
8. The electrons are then transferred to NADP+ and reduce it to NADPH
The electrons of NADPH are available for the reactions of the Calvin cycle.
73
calvin cycle uses more __ than __
The Calvin cycle uses more ATP than NADPH.
| Cyclic electron transfer provides the required extra ATP.
74
linear vs cyclic e- transfer
Linear electron transfer can generate ATP and NADPH.
Cyclic electron transfer generates ATP, but not NADPH.
Why does the cyclic pathway exist?
- At least in some cases, chloroplasts seem to switch from linear to cyclic electron flow when the ratio of NADPH to NADP+ is too high (when too little NADP+ is available to accept electrons).
- In addition, cyclic electron flow may be common in photosynthetic cell types with especially high ATP needs (such as the sugar-synthesizing bundle-sheath cells of plants that carry out C4 photosynthesis).
75
cyclic e- flow
In cyclic electron flow, electrons cycle back from Fd to the PS I reaction center.
Cyclic electron flow uses only photosystem I and produces ATP, but not NADPH (since electrons are routed away from NADP+ reductase)
No oxygen is released.
76
In summary, light reactions
generate ATP and increase the potential energy of electrons by moving them from H2O to NADPH.
77
redox potentials
- Larger redox potentials are associated with increased electron affinity (the more positive the potential, the greater the species' affinity for electrons and tendency to be reduced).
- Light lowers the redox potential of chlorophyll enabling electrons to be transferred to other molecules that would otherwise have lower redox potentials.
- Example: plastoquinone has redox potential of about -150 mV. PSII has redox potential of 1.1 V. Light absorption decreases redox potential of PSII to about -500 mV so transfer of electron to plastoquinone can occur.
- Another Example: PS I redox potential is 500 mV. In order for electron to be transferred to NADP+ (redox potential of -200 mV), PS I’s redox potential is reduced to -1200 mV by light energy so electron can be transferred via ferredoxin.
78
ATP synthase direction
ATP synthase catalytic site (knob) faces stroma in chloroplast and matrix in mitochondrion.
79
How chloroplast acquired three membranes and how ATP synthase is oriented.
1. Prehistoric photosynthetic bacterium has ATP synthase on its (only) membrane. Catalytic knob is facing inside.
2. Bacterium invaginates its membrane (akin to the ER formation in eukarytoic cells).
3. Membrane pinches off inside forming an intracellular organelle with knob facing cytosol.
4. Bacterium is subsequently phagocytosed
by (less) prehistoric soon-to-be plant cell.
5. ATPase of present day plant cell
faces stroma.
80
control of metabolism
The amount and balance of products a cell has is regulated tightly.
This balance is achieved via allosteric regulation of enzyme activities. Control points use both positive and negative feedback mechanisms.
The main control point in glycolysis is the enzyme phosphofructokinase.
This enzyme is inhibited by ATP and citrate and activated by ADP and AMP.
When ATP is low, phosphofructokinase is active; when ATP is high, it is inactive.
81
phosphofructokinase activator/inhibitor
a: ADP, AMP
i: ATP, citrate
82
ATP synthase: synthesis vs hydrolysis
s: H+ intro matrix
h: H+ out of matrix
ATP synthase can hydrolyze ATP (and pump protons) if proton-motive force is reversed.
83
Other functions of the proton-motive force.
- voltage gradietn drives ADP-ATP exchange
- pH gradient drives pyruvate import
- " " " phosphate import
84
How protons can get pumped across a membrane.
A has high energy electron and donates it freely to B.
To maintain neutrality, B also accepts a proton from water.
When B donates the electron to C (because C has a higher affinity for electrons than B) the proton is released to water (which can be on the other side of the membrane).
85
baccteria and ATP synthase
Bacteria use ATP synthase in reverse to consume ATP and maintain proton gradient to drive cotransport of metabolites and extrusion of Na+.
86
When there is an insufficient oxygen
a cell cannot re-oxidize cytochrome c and ubiquinone-H2 (can’t “pull” the chain along.)
- Therefore, NAD+ and FAD are not regenerated from their reduced form.
- This back-up continues until pyruvate oxidation stops because of a lack of NAD+. Then reactions in the citric acid cycle stop.
- If the cell has no other way to obtain energy, it dies.
87
anaerobic conditions
Without oxygen (anaerobic conditions) some cells can continue glycolysis to produce a limited amount of ATP by fermentation. (pyruvate products do not necessarily have to enter the Krebs cycle—they can be metabolized anaerobically if insufficient oxygen is present)
Two types are involved:
Ethanol fermentation
Lactic acid fermentation
88
lactic acid fermentation
glucose undergoes glycolysis; get 2 pyruvate, which are converted into 2 lactate
- accompanying this conversion is
2NADH + 2H+ --> 2NAD+
89
alcohol fermentation
glucose undergoes glycolysis; get 2 pyruvate, which are converted into 2 acetylaldehyde, which are converted into 2 ethanol
- accompanying this last conversion (to ethanol) is
2NADH + 2H+ --> 2NAD+
