PCB 3134 Matters Covered in Lectures Leading up to Exam 2

metabolism

all the chemical reactions in a cell (consists of many specific metabolic pathways)

two categories of metabolic pathways

anabolic pathways and catabolic pathways

anabolic pathways

synthesize cellular components, often polymers such as starch and glycogen

energy in anabolic pathways

• they usually involve an increase in order and a decrease in entropy

• they are endergonic (energy-requiring reactions)

catabolic pathways

involved in the breakdown of cellular constituents, such as the hydrolysis of glucose

energy in catabolic pathways

• these degredative pathways typically involve a decrease in order and increase in entropy

• they are exergonic (energy-releasing reactions)

ATP (adenosine triphosphate)

the molecule most commonly used as an energy intermediate (the primary energy currency of the biological world)

other high-energy molecules than ATP

• high-energy molecules, such as GTP and creatine phosphate, store chemical energy that can be converted to ATP

• chemical energy is also stored as reduced coenzymes such as NADH

other high-energy molecules represent

chemical potential energy - can be transferred to other molecules or used to power endergonic reactions

ATP structure

contains two energy-rich phosphoanhydride bonds

• contains the aromatic base adenine, the five-carbon sugar ribose, and a chain of three phosphate groups

• the phosphate groups are linked to each other by phosphoanhydride bonds and to ribose by a phosphoester bond

phosphoanhydride bonds

• referred to as energy-rich bonds

• free energy is released when the bond is hydrolyzed

• the energy is a characteristic of the reaction the molecule is involved in, and not of a particular bond in the molecule

factors that cause ATP hydrolysis to be highly exergonic

• charge repulsion between the adjacent negatively charged phosphate groups

• resonance stabilization of both products of hydrolysis

• increased entropy and solubility of the products of hydrolysis

ATP and ADP are higher-energy than…

AMP

ATP → ADP ΔG^o’ = -7.3

ADP → AMP ΔG^o’ = -7.3

AMP → adenosine ΔG^o’ = -3.6

ΔG^o’ is

the biological standard free energy change

why ΔG^o’ is an underestimate

• ΔG^o’ is based on equal concentrations of ADP and ATP (1 M each), meaning it’s an underestimate

• in most cells, ATP/ADP ratio is in the range of about 5:1

• ΔG^o’ is thus in the range of -10 to -14 kcal/mol

ATP is extremely important in

cellular energy metabolism

• ATP occupies an intermediate position among energy-rich phosphorylated compounds in the cell

• under standard conditions, a compound can phosphorylate a less energy-rich compound, but not a more energy-rich compound

ATP ΔG^o’ is

-7.3

ATP in glycolysis

• ATP can be formed from ADP by the transfer of a phosphate group from PEP but not from glucose-6-phosphate

• ATP can phosphorylate glucose but not pyruvate

ATP/ADP as intermediates in terms of bond energy

• the ATP/ADP pair represents a reversible means of conserving, transferring, and releasing energy within the cell

• as catabolic processes occur in the cell, the energy liberated is used to produce ATP from ADP

• then energy released from hydrolysis of ATP is used for essential processes of life that use energy

ATP → ADP is used for/releases

• synthetic work

• concentration work

• electrical work

• mechanical work

• bioluminescent work

• heat

ADP → ATP is used for/releases

oxidizable nutrients → products of catabolism

chemotrophic energy metabolism

describes the reactions and pathways by which cells catabolize nutrients and conserve the released energy in the form of ATP

involves energy-yielding oxidative reactions (oxidation)

oxidation in biological chemistry

• in biological systems, this involves the removal of hydrogen ions (protons) in addition to electrons

• this process is also a dehydrogenation

transfer of electrons

• because oxidation reactions involve the removal of 2 hydrogen atoms, many of the enzymes are called dehydrogenases

• the electrons must be transferred to another molecule, which is reduced

reduction

the addition of electrons; an endergonic process

reduction often involves…

hydrogenation

in reduction, the electrons that are transferred are frequently accompanied by protons, therefore, the overall reaction is a hydrogenation

coenzymes

• serve as electron acceptors in biological oxidations

• remove electrons and hydrogens during biological oxidation

• function along with enzymes, serving as carriers of electrons or small functional groups

• low in concentrations in the cell because they’re recycled

NAD⁺

• the most common coenzyme

• it serves as an electron acceptor, adding two electrons and a proton to its aromatic ring, generating NADH plus a proton

most chemotrophs meet their energy needs by…

oxidizing organic food molecules

• they depend on organic food molecules as oxidizable substrates

• oxidation of these organic compounds - carbohydrates, fats, and proteins - produces energy for the cell in the form of ATP and reduced coenzymes

• the six-carbon sugar glucose is the main energy source for most of the cells in the body

why the oxidation of glucose is highly exergonic

• glucose is a good source of energy because its oxidation is a highly exergonic process

• ΔG^o’ = 0686 kJ/mol for complete conversion of glucose to CO₂ and water, with oxygen as the final electron acceptor

glucose catabolism energy yield

• yields much more energy in the presence of oxygen than in its absence

• it’s not possible to obtain the full 686 kcal/mol for complete oxidation of glucose as energy conversion is not 100% efficient

• complete oxidation of glucose in the presence of oxygen is called aerobic respiration

anaerobic respiration

• even in the presence of oxygen, most organisms can extract limited energy from glucose

• done through glycolysis

glycolysis

• electrons removed during glucose oxidation are returned to an organic molecule later in the same pathway

• called fermentation

based on their need for oxygen, organisms are either…

aerobic, anaerobic, or facultative

obligate aerobes

have an absolute requirement for oxygen

obligate anaerobes

cannot use oxygen as an electron acceptor; oxygen is toxic to these organisms

facultative organisms

can function under aerobic or anaerobic conditions

glycolysis generates ATP by

catabolizing glucose to pyruvate

glycolysis phase 1 description

preparation and cleavage

• the 6-C glucose molecule is phosphorylated twice by ATP and split to form two molecules of glyceraldehyde-3-phosphate

• requires an input of 2 ATP per glucose

glycolysis phase 2 description

oxidation and ATP generation

• the 2 molecules of glyceraldehyde-3-phosphate are oxidized to 3-phosphoglycerate

• some of the energy from this oxidation is conserved as two ATP and two NADH molecules are produced

glycolysis phase 3 description

pyruvate formation and ATP generation

• the two 3-phosphoglycerate molecules are converted to pyruvate

• accompanying synthesis of two more ATP molecules

• results in a net gain of 2 ATP per glucose

enzymes that catalyze reactions in glycolysis

GLY-1: hexokinase

GLY-2: phosphoglucoisomerase

GLY-3: phosphofructokinase-1

GLY4: aldolase

GLY-5: triose phosphate isomerase

GLY-6: glyceraldehyde-3-phosphate dehydrogenase

GLY-7: phosphoglycerokinase

GLY-8: phosphoglyceromutase

GLY-9: enolase

GLY-10: pyruvate kinase

glycolysis phase 1: preparation and cleavage enzymes and reactions

Gly-1: phosphorylation - 1 ATP required

Gly-2: isomerization

Gly-3: phosphorylation - 1 ATP required

Gly-4: lysis - splitting 6-C glucose to two 3-C molecules

glycolysis phase 2: oxidation and ATP generation enzymes and reactions

Gly-5: isomerization

Gly-6: oxidation - NAD⁺ is reduced to NADH

Gly-7: dephosphorylation - generation of 1 ATP

Phase 3: pyruvate formation and ATP generation enzymes and reactions

Gly-8 isomerization

Gly-9: dehydration

Gly-10: dephosphorylation - generation of 1 ATP

important features of the glycolytic pathway

• the initial input of 2 ATP (gly-1 and gly-3)

• the sugar-splitting reaction, where glucose is split into two 3-C molecules (gly-4)

• the oxidative event that generates NADH (gly-6)

• the 2 steps at which the reaction sequence is coupled to ATP generation (gly-7 and gly-10)

summary of glycolysis

• the 2 molecules of ATP formed in the second phosphrylation event (gly-10) represent the net yield of ATP for the glycolytic pathway

• the pathway is highly exergonic in the direction of pyruvate formation; ΔG^o’ in a cell is about -20 kcal/mol

conservation of glycolysis

• the glycolytic pathway is one of the most common and highly conserved metabolic pathways known

• virtually all cells have the ability to convert glucose to pyruvate, extracting energy in the process

• the next steps depend on the availability of oxygen

Glycolysis splits 1 glucose molecule into 2 three-carbon ___ molecules, reduces 2 ____ to ___, and produces ___ (net) ATPs

pyruvate, NAD+, NADH, 2

important features of the glycolytic pathway

• the initial input of 2 ATP (Gly-1 and Gly-3)

• the sugar-splitting reaction, in which glucose is split into two three-carbon molecules (Gly-4)

• the oxidative event that generates NADH (Gly-6)

• the two steps at which the reaction sequence is coupled to ATP generation (Gly-7 and Gly-10)

summary of glycolysis

• the two molecules of ATP formed in the second phosphorylation event (Gly-10) represent the net yield of ATP for the glycolytic pathway

• the pathway is highly exergonic in the direction of pyruvate formation; ΔGʹ = -20 kcal/mol

formula summary of glycolysis

glucose + 2NAD⁺ + 2 ADP + 2 P_i —(reactions Gly-1 through Gly-10)→ 2 pyruvate + 2 NADH + 2 H⁺ + 2 ATP

in the absence of oxygen …

pyruvate undergoes fermentation to regenerate NAD+

regenerating NAD+ during fermentation

• fermentation must regenerate NAD+ from NADH so that glycolysis can continue

• cells monitor and stabilize the NAD+/NADH ratio, an indicator of the cell’s redox state (general level of oxidation of cellular components)

• electrons are transferred to pyruvate with two possible outcomes

anaerobic conditions

• when oxygen is absent, pyruvate is reduced so that NADH can be oxidized to NAD+

• required in reaction Gly-6 of glycolysis

common prodoucts of pyruvate reduction are

• lactate: in most animal cells and many bacteria

• ethanol and CO₂: in many plant cells and in yeasts and other microorganisms

enzymes that catalyze reactions under anaerobic conditions

PDH: pyruvate dehydrogenase

LDH: lactate dehydrogenase

PDC: pyruvate decarboxylase

ADH: alcohol dehydrogenase

the overall metabolism of glucose to lactate in the absence of oxygen can be summarized as

glucose + 2 ADP + 2 P_i → 2 lactate + 2 ATP

the overall metabolism of glucose to ethanol in the absence of oxygen can be summarized as

glucose + 2 ADP + 2 P_i + 2 H⁺ → 2 ethanol + 2 CO₂ + 2 ATP

propionate fermentation

bacteria reduce pyruvate to propionate

butylene glycol fermentation

bacteria that causes food spoilage

other fermentation pathways

yield acetone, isopropyl alcohol, or butyrate, all variations on the common theme of reoxidizing NADH by the transfer of electrons to an organic acceptor

fermentation taps only a fraction of the substrate’s free energy, but ___

conserves that energy efficiently as ATP

an essential feature of every fermentation process is

no external electron acceptor is involved, and no net oxidation occurs

fermentation and glucose

• fermentation gives a modest ATP yield of two ATP per glucose

• most of the free energy of the glucose molecule is still present in the lactate or ethanol

cancer cells ferment …

glucose to lactate even in the presence of oxygen

warburg effect

in the 1920s and 1930s, otto warburg showed that cancer cells consume glucose more rapidly than normal cells

many cancer cells get their energy…

mainly by fermenting glucose to lactate, even in the presence of oxygen

• called aerobic glycolysis

• despite its inefficiency, it allows cancer cells to outgrow normal cells

how do cancer cells outgrow cells that are carrying out aerobic respiration?

• dramatically increase amount of glucose consumed

• display increase in activity of nutrient transporters

• carry out aerobic glycolysis to produce carbon skeletons for biosynthesis of substances in high demand by proliferating cells

• don’t primarily use aerobic glycolysis for energy production

positron emission tomography

fluorodeoxyglucose, a radioactive glucose analogue, is given to patients and then imaged as it accumulates in cancer cells

the general principle that positron emission tomography highlights in biology and medicine

• the use of radiotracers can be used to follow the fate of individual types of molecules in the body

• radiotracers rely on the existence of naturally occurring isotopes of common elements

• isotopic labeling follows the fate of biochemical intermediates in metabolic studies

isotopic labeling

is used to follow the fate of biochemical intermediates in metabolic studies

alternative substrates for glycolysis

although glucose is a major substrate for both fermentation and respiration in a variety of organisms and some tissues, for some glucose isn’t significant at all; there are a variety of alternatives to glucose, which are often converted into an intermediate in the glucose catabolism pathway

alternates for the glycolytic pathway

• other sugars and glycerol are also catabolized by the glycolytic pathway

• many sugars are available to cells, either monosaccharides or disaccharides that can be readily hydrolyzed into monosaccharides

• the monosaccharides are then converted into a glycolytic intermediate

• glucose and fructose enter most directly after phosphorylation on carbon atom 6; mannose and galactose require more steps

cellular respiration

the flow of electrons through or within a membrane, from reduced coenzymes to an external electron acceptor usually accompanied by the generation of ATP

coenzymes involved in cellular respiration

FAD: flavin adenine dinucleotide

coenzyme Q: ubiquinone

the terminal electron acceptor

• in aerobic respiration, this is oxygen, and the reduced form is water

• others (sulfur, protons, and ferric ions) are used by other organisms, especially bacteria and archaea

• examples of anaerobic respiration

most aerobic ATP production in eukaryotic cells takes place in the ….

mitochondrion

mitochondria

• often present where the ATP needs are greatest

• found in virtually all aerobic cells of eukaryotes

• present in both chemotrophic and phototrophic cells

• frequently clustered in regions of cells with the greatest need for ATP, such as muscle cells

are mitochondria interconnected networks rather than discrete organelles?

• in electron micrographs, mitochondria usually appear as oval structures

• other work suggests that the oval profiles in electron micrographs of yeast cells reflect slices through a single large branched mitochondrion

intermembrane space

area between the outer and inner membranes

mitochondrial matrix

semifluid space inside the inner membrane`

cristae

folds of the inner membrane which generate much greater membrane surface area

mitochondrial functions

• specific functions and pathways have been localized within mitochondria by fractionation studies

• most enzymes involved in pyruvate oxidation, the citric acid cycle, and catabolism of fatty acids are found in the matrix

• most electron transport intermediates are integral inner membrane components

localization of metabolic functions within the mitochondria: inner membrane

• electron transport

• proton translocation for ATP synthesis

• oxidative phosphorylation

• pyruvate import

localization of metabolic functions within the mitochondrion: matrix

• pyruvate oxidation

• citric acid cycle

• ATP synthesis

completing the breakdown of pyruvate to CO₂

• in the presence of oxygen, pyruvate is oxidized fully to carbon dioxide with the released energy used to drive ATP synthesis

• pyruvate undergoes oxidative decarboxylation to produce an acetyl group which is attached to coenzyme A

• the two carbons of the acetyl group are fed into the citric acid cycle to complete the oxidation

pyruvate is converted to acetyl coenzyme A by …

oxidative decarboxylation

at the inner mitochondrial membrane, a specific symporter transports pyruvate into the matrix, along with a proton

the citric acid cycle begins with…

the entry of acetate as acetyl CoA

citric acid cycle

• with each round, two C atoms enter in organic form as acetate and leave in inorganic form as carbon dioxide

• in the first reaction CAC-1, the two-carbon acetate group is transferred from acetyl CoA to oxaloacetate (4C) to form citrate (6C)

• the remaining reactions strip two carbons off as CO₂ and recreate oxaloacetate

four of the eight steps of the citric acid cycle are oxidations

CAC-3

CAC-4

CAC-6

CAC-8

energy released in CAC-4 is used to

attach CoA to succinate

CAC-5 exergonically

removes CoA to phosphorylate GDP

oxaloacetate’s recreation in the citric acid cycle

it’s recreated in the final steps of the cycle and ready to receive two more carbons

redox of FAD and FADH₂

FAD is reduced to FADH₂: 2 H⁺ is added to the FAD

FADH₂ is oxidized to FAD: 2 H⁺ are removed from FADH₂ and released

summing up: the products of the citric acid cycle are…

CO₂, ATP, NADH, and FADH₂

the citric acid cycle accomplishes the following

1. two carons enter the cycle as acetyl CoA, which joins oxaloacetate to form the six-carbon citrate

2. decarboxylation occurs at two steps to balance the input of two carbons by releasing two CO₂

3. oxidation occurs at four steps, with NAD⁺ the electron acceptor in three steps and FAD in one

4. ATP is generated at one point, with GTP as an intermediate in the case of animal cells

5. one turn of the cycle is completed as oxaloacetate, the original 4C acceptor, is regenerated

chemical reactions of the CAC and glucose metabolism is summarized as

acetyl COA + 3 NAD⁺ + FAD + ADP + P_i → 2CO₂ + 3 NADH + FADH₂ + COA-SH + ATP

including glycolysis, pyruvate decarboxylation, and the citric acid cycle, the overall reaction is as follows

glucose + 10 NAD⁺ + 2 FAD + 4 ADP + 4 P_i → 6 CO₂ + 10 NADH + 2 FADH₂ + 4 ATP

glucose metabolism oversimplified

• glucose turns into 2 pyruvate through glycolysis

• glycolysis produces 2 NADH and 2 ATP in the process

• if no oxygen is present, the 2 pyruvate go through fermentation and 2 lactate or 2 ethanol + 2 CO₂ are produced

• if oxygen is present, the 2 pyruvate go through respiration where 2 NADH are released and 2 acetyl CoA + 2 CO₂ are produced

• the 2 acetyl CoA + 2 CO₂ then go through the citric acid cycle to be converted into 4 CO₂

• the citric acid cycle releases 6 NADH, 2 FADH₂, and 2 ATP as byproducts