Download Black-Chapter 5 – Essential Concept of Metabolism

Essential Concept of Metabolism
METABOLISM: AN OVERVIEW
Metabolism is the sum of all chemical processes in a living organism. It consists of
anabolism, reactions that require energy to synthesize complex molecules from simpler
ones, and catabolism, reactions that release energy by breaking complex molecules into
simpler ones.
Autotroph, which use carbon dioxide to synthesize organic molecules, include
photoautotrophs (which carry on photosynthesis) and chemoautotrophs.
Heterotrophs, which use organic molecules made by other organisms, include
chemoheterotrophs, and photohetrotrophs (obtain chemical energy from light).
For growth, movement, and other activities, metabolic pathways use energy captured in
the catabolic pathways.
ENZYMES
Properties of Enzymes
Enzymes are proteins that catalyze chemical reactions in living organisms by lowering
the activation energy needed for a reaction to occur.
Enzymes have an active site, the binding site to which the substrate (the substance on
which the enzymes act) attaches to form an enzyme-substrate complex. Enzymes
typically exhibit a high degree of specificity in the reactions they catalyze.
Properties of Coenzyme and Cofactors
Some enzymes require coenzymes, nonprotein organic molecules that can combine with
the apoenzyme, the protein portion of the enzyme, to form holoenzyme. Some enzymes
also require inorganic ions as cofactors.
Enzyme Inhibition
Enzyme activity can be reduced by competitive inhibitors, molecules that compete with
the substance for the enzyme’s active site, or by noncompetitive inhibitors, molecules
that bind to an allosteric site, a site other than the active site.
Factors That Affect Enzyme Reaction
Factors that affect the rate of enzyme reactions include temperature, pH, and
concentrations of substrate, product, and enzyme.
Organic molecules have energy associated with the electrons that form bonds between
their atoms. When this energy is released, it is trapped into the bonds of ATP.
Biochemical Reactions
1. Metabolism
Chemical reactions that change or transform energy in cells.
a.Anabolic (synthesis) reactions
Chemical reactions that build large molecules from small ones.
require energy (endergonic) - products contain more energy than
reactants.
b.Catabolic (degredation) reactions
Chemical reactions that:
break down large molecules into small ones.
release energy (exergonic) - products contain less energy than reactants.
2. Oxidation - Reduction Reactions
Most energy transformations in organisms involve oxidation & reduction.
Oxidation - a molecule loses one or more electrons, lose a hhydrogen ion.
Reduction - a molecule gains one or more electrons, gain a hydrogen ion.
Oxidation and reduction reactions are always coupled; each time one substance is
oxidized, another is simultaneously reduced.
Cells take nutrients and degrade them from highly reduced compounds (with many
hydrogen atoms) to highly oxidized compounds.
Ex. electron transport chain
Electron transport chain
Fe3+ gains an electron - is reduced to Fe2+
Fe2+ loses an electron - is oxidized to Fe3+
Molecules Involved in Energy Transformations
1. ATP (adenosine triphosphate)
Energy currency of cells.
Generation of ATP
1). Substarte-level phosphorylation
ATP generated when a high energy phosphate is directly transferred from a
phosphorylated compound (a substrate) to ADP.
2). Oxidation phosphorylation
When electrons are transferred from organic compounds to electron carriers in an
electron transport chain – ATP generated from ADP through a process called
Chemiosmosis
Cells couple ATP formation & breakdown to other reactions.
2. Cofactors
Inorganic helpers (usually ions) needed by some enzymes to function.
Ex. Mg2+
3. Coenzymes
Organic cofactors (vitamin derived) needed by some enzymes to function, pick up
electrons when they are released.
Nicotinamide adenine dinucleotide (NAD+) - coenzyme that transfers
electrons; derived from niacin. Oxidized form is NAD+, reduced form is
NADH2.
Flavin adenine dinucleotide (FAD) - coenzyme that transfers electrons;
derived from riboflavin. Oxidized form is FAD, reduced form is FADH2.
4. Cytochromes
Iron containing molecules that transport electrons.
Ex. electron transport chains
5. Enzymes (biological catalysts)
Proteins that speed up chemical reactions without being altered in the process.
The generation of ATP
1. Energy released during certain metabolic reactions can be trapped to form ATP
from ADP and P.
2. Addition of a p to a molecule is called phosphorylation.
3. During substrate-level phosphorylation, a high-energy p from an intermediate in
catabolism is added to ADP.
4. During oxidative phosphorylation, energy is released as electrons are passed to a
series of electron acceptors (an electron transport chain) and finally to O2 or
another inorganic compound.
5. During photophosphorylation, energy from light is trapped by chlorophyll, and
electrons transfer release energy used for the synthesis of ATP.
Most cells break down glucose to make ATP by:
Cellular respiration (aerobic process) – converts the storage form to the direct
form of energy
Fermentation and anaerobic respiration – anaerobic process
CELLULAR RESPIRATION – AEROBIC AND ANAEROBIC METABOLISM:
AND FERMENTATION
Most of a cell’s energy is produced from the oxidation of carbohydrates.
Glucose is the most commonly used carbohydrates.
In aerobic,glucose is completely degrades through
a). glycolysis;
b). Kreb’s cycle (also known as tricarboxylic acid cycle
c). Electron transport chain.
Molecular oxygen is final acceptor for electrons and hydrogen:produces relatively
large amount of ATP; ex. many bacteria, fungi, protozoa and animals.
In anaeroboic , the metabolic reactions involve the same three steps as for aerobic
respiration, but does not use molecular oxygen as the final electron acceptor [rather
oxygen containing salts (nitrates, nitrite, carbonate, sulfate are final electron acceptors;
because only part of Kreb’s cycle operates under anaerobic conditions, ATP yield is
never as high as in aerobic respiration] ex. anaerobic microorganisms
Both processes start with Glycolysis
Glycolysis
Glycolysis is a metabolic pathway by which glucose is oxidized to pyruvic acid.
Under anaerobic conditions, glycolysis yields a net of two ATP’s per molecule of
glucose.
1. Glycolysis
Occurs in cells of most eukaryotes & some prokaryotes.
General equation for cellular respiration of glucose:
C6H12O6 + 6O2  6CO2 + 6H2O + 30 ATP
Cellular respiration occurs in 3 stages:
Eukaryotic cells
Cytoplasm - Glycolysis
Mitochondria - Krebs Cycle
inner membrane of Mitochondria - Electron Transport Chain
Glucose (6C) is split into two pyruvate (3C) molecules.
Glucose + NAD+ ADP + Pi  2 pyruvic acid (3Carbon) + 2 NADH + 2 ATP + 2 H+
does not require oxygen, in the cytosol.
energy harvested/glucose:
2 ATP (via substrate-level phosphorylation)
2 NADH (actively transported into mitochondria of eukaryotic cells)
First half of glycolysis activates glucose.
Second half of glycolysis extracts energy.
Total energy yield during the 2nd half of glycolysis is 4 ATPs and 2 NADHs.
Since 2 ATPs were used to activate glucose, there is a net gain of only 2 ATPs.
2 ATP are used to activate glucose to unstable fructose1,6-diphosphate then form
2 stable glyceraldehydes phosphate (P-GAL) - important intermediate compound.
Note: ATP is synthesized in glycolysis by substrate-level phosphorylation. This
means that an enzyme transfers a phosphate group from an organic molecule
(substrate) to ADP, forming ATP.
Pyruvic acid must be converted to Acetyl CoA before it can enter Krebs cycle.
Pyruvic acid breaks down to acetyl CoA produce 2 NADH
Pyruvic acid decarboxylation  add coenzyme A
CO2 releases
 Acetyl - CoA
Alternative to Glycolysis
1. Pentose-phosphate pathway is used to metabolize five-carbon sugars.
2. Entner-Doudoroff pathway yields one ATP and two NADH molecules.
Anaerobic respiration - Fermantation
Fermantation refers to the reactions of metabolic pathways by which NADH is oxidized
to NAD. An organic molecules is the final electron acceptor.
Six pathwayts of fermentation are summarized in figure 5.12.
Alcohol fermentation and Lactic acid fermentation (muscle cramp) most important
and commonly occurring fermentation pathways.
Oxygen is not required. Organic compounds are the final electron acceptors in
fermentation.
AEROBIC METABOLISM: RESPIRATION
Anaerobes do not use oxygen: aerobes use oxygen and obtain energy chiefly via
aerobic respiration.
The Krebs cycle
The Krebs cycle metabolizes two-carbon compounds to CO2 and H2O, produces one
ATP directly from each acetyl group, and transfers hydrogen atoms to the electron
transport chain.
In energy production the Krebs cycle processes acetyl-CoA, so that (in the electron
transport chain) hydrogen atoms can be oxidized for energy.
Fig. 7.7
Key to remember the Kreb cycle chemical compound:
CIA SS FMO, (CIA wants social security number for mails only)
Electron Transport and Oxidative Phosphorylation
Electron transport is the transfer of eklectrons to oxygen (the final electron acceptor).
Oxidative phosphorylation involves the electron transport chain for ATP synthesis
and is a membrane-regulated process not directly related to the metabolism of specific
substrates
Fate of electrons:
1. Electron transport chains splits the hydrogen atoms from NADH and
FADH2 into H+ and electrons.
2. the protons are forced into the space between inner and outer
mitochondrial membranes, where they accumulate high levels and
lower the pH.
3. The ETC transfer the electrons from one to another, until they are
finally accepted by the O2 molecules, which become reduced to Oions.
4. The protons are then allowed to diffuse through special openings in
the cristae membranes, this flow of protons is called chemiosmosis.
This flow of protons through ATP synthase to combine ADP + Pi
to form ATP – (Chemiosmotic phosphorylation).
Phosphorylation:adding a phosphate group to chemical
The theory of chemiosmosis explains how energy is used to synthesis ATP.
energy harvested/NADH: 3 ATPs (via chemiosmotic phosphorylation)
energy harvested/FADH2: 2 ATPs (via chemiosmotic phosphorylation)
2 NADH generated from glycolysis
2 NADH generated before entering Kreb’s cycle
6 NADH and 2 FADH produced from ETC
2 ATP was generated in glycolysis
2 ATP was generated in Kreb’s cycle
2 ATP was used in transporting NADH from glycolysis into
mitochondria
10 x 3 = 30, 2 x 2 = 4, 30 + 4 -2 = 32, 32 + 2 + 2 = 36 One glucose molecule
generates 36 ATP.
In eukaryotes, ETC are located in the inner mitochondrial membrane, in
prokaryotes, ETC are in the plasma membrane.
In prokaryotes , 38 ATP is produced, in Eukaryotes 36 ATP is produced.
The Significance of energy capture.
The prokaryotes, aerobic (oxidative) metabolism capture 19 times as much energy as
does anaerobic metabolisms.
THE METABOLISM OF FATS AND PROTEINS
Most organisms get energy mainly from glucose. But for almost any organic substance,
there is some microorganism that can metabolize it.
Fat metabolism
Fat metabolism involves hydrolysis and the enzymatic formation of glycerol and free
fatty acids. Fatty acids are in turn oxidized by beta oxidation to 2 carbon compound,
which results in the release of acetyl-CoA. Acetyl-CoA then enters the Krebs cycle.
Protein Metabolism
The metabolism of proteins involves the breakdown of proteins to amino acids, the
deamination of the amino acids, and their subsequent metabolism in glycolysis,
fermentation, or the Krebs cycle.
OTHER METABOLIC PROCESSES
Photoautotrophy
Photosynthesis is the use of light energy to synthesize carbohydrates:
(1) The light reactions can include cyclic photophsophorylation or photolysis
accompanied by noncyclic photoreduction of NADP;
(2) the dark reactions involve the reduction of CO2 to carbohydrate.
Photosynthesis in cyanobacteria and algae provides a means of making nutrients, as it
does in green plants; however, photosynthetic bacteria generally use some substances
besides water to reduce carbon dioxide.
Photoheterotrophy
Photoheterophy is the use of light as a source of energy. It requires organic compounds
as sources of carbon.
Chemoautotrophy
Chemoautotrophs, or chemolithotrophs, oxidize inorganic substances to obtain energy.
Chemolithotrophs require only carbon dioxide as carbon source.
THE USE OF ENERGY
Biosynthetic Activities
An amphibolic pathways is a metabolic pathway that can capture energy or synthesize
substances needed by the cell.
Figure 5.27 summarized the intermediate products of energy yielding metabolism and
some of the building blocks for synthetic reactions that can be made from them.
Bacteria synthesize a variety of cell wall polymers.
Membrane Transport and Movement
Membrane transport uses energy derived from the ATP-producing electron transport
system in the membrane to concentrate substances against a gradient. It occurs by active
transport and by the phosphotransferase system.
Movement in bacteria can be by flagella, by gliding or creeping, or by axial filaments.
Bioluminescence
The ability of an organism to emit light, may have evolved as a way to remove oxygen
from the surroundings of primitive anaerobic microbes early in the Earth’s history. Today
it often functions in symbiotic relationships with larger organisms.
Dr. Mohammad A.R. Ismaiel