Unit 4 Metabolism & Matabolic Disorder
Unit 4 Metabolism & Matabolic Disorder
Unit 4 Metabolism & Matabolic Disorder
Unit 4
Cellular Metabolism and Metabolic Disorders
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4. Cellular Metabolism and Metabolic Disorders
4.1 Cellular metabolism
Living cells are in a constant activity.
Macromolecules are assembled & broken down,
substances are transported across cell membranes, &
genetic instructions are transmitted.
All of these cellular activities require energy.
Living organisms are unique in that they can extract energy to
carry out activities such as
– movement,
– growth and development,
– reproduction.
How living organisms or, their cells extract energy?
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Metabolism is thus the sum of all chemical reactions that takes
place within each cell of a living organism.
– provides energy & synthesizing of new organic materials.
• Broadly, these reactions can be divided into
– catabolic reactions that convert nutrients to energy &
– anabolic reactions that lead to the synthesis of larger
biomolecules.
Metabolic pathway:
Catabolic pathways release energy by breaking down larger
molecules into smaller molecules.
Anabolic pathways use the energy released to build larger
molecules from smaller molecules
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The reactants & products of these chemical reactions are
metabolites.
include proteins, carbohydrates, nucleotides, lipids,
coenzymes, & cofactors.
these metabolites involved in cellular respiration (e.g.,
glycolysis, Kreb‘s cycle, other pathways) &
in the production of building blocks for synthesis of large
biopolymers DNA, RNA, proteins, & oligosaccharides.
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4.1.1. Enzymes and their role in metabolism
most chemical reactions require biological catalyst called
enzymes.
are protein catalysts
speed up chemical reactions;
make a chemical reaction millions times faster than without it.
almost all metabolic processes in cell need enzyme catalysis
Enzymes bind with particular reactants until the chemical reaction
occurs, then free themselves.
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How do enzymes speed up chemical reactions?
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4.1.2 Chemical nature and classification of enzymes
All known enzymes are proteins except recently discovered
RNA enzymes.
Some enzymes contain additional non-protein group.
Enzymes are high molecular weight cpds made up of chains of
aa linked together by peptide bonds.
Many enzymes require other compounds (cofactors) before their
catalytic activity can be exerted.
This entire active complex is referred to as the holoenzyme;
i.e., apoenzyme (protein portion) + cofactor (coenzyme,
prosthetic group or metal-ion-activator).
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Thus, based on chemical nature, enzymes may be described as
follows:
Simple enzymes: are made up of only protein (polypeptide).
– contain no chemical groups.
– e.g: digestive enzymes (pepsin & trypsin).
Conjugate enzymes: is formed of two parts;
– a protein part called apoenzyme (e.g., flavoprotein) & a
non-protein part cofactor.
• apoenzyme + cofactor holoenzyme
• only enzymatic activity present when both components
(apoenzyme & cofactor) are present together.
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• The cofactor is sometimes a
– simple divalent metallic ion (e.g. Ca, Mg, Zn, Co, etc), &
– sometimes a nonprotein organic compound.
• If the cofactor is firmly bound to the apoenzyme, it is called
prosthetic group.
– e.g. cytochromes are the enzymes that possess porphyrins as
their prosthetic groups.
• If, instead of being more or less permanently bound to the
apoenzyme,
– the cofactor attaches itself to the apoenzyme only at the time
of reaction, it is called a coenzyme.
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Metallo-enzymes:
• metal cofactors involved in enzymic reactions are
– monovalent (K+) & divalent cations (Mg++, Mn++ & Cu++).
• These may be loosely held by the enzyme, or as in some cases,
go into the composition of the molecule itself.
• If the metal forms part of the molecule, as iron of haemoglobin or
cytochrome is, the enzymes are called metallo-enzymes.
Isoenzymes (Isozymes):
• are enzymes that differ in amino acid sequence but catalyze the
same chemical reaction.
e.g. lactate dehydrogenase
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Classes of enzymes based on the substrate they act up on
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4.1.3 Mechanisms of enzyme action
Mechanisms of enzyme catalysis vary, but are all similar in
principle to other types of chemical catalysis
The reduction of activation energy increases the fraction of
reactant molecules that can overcome this barrier & form the P.
An E attracts S to its active site, catalyzes the chemical reaction
by which P are formed, & then allows the P to separate.
The combination formed by an E & its S is called the E-S
complex.
The S are attracted to the active site by electrostatic &
hydrophobic forces, which are called noncovalent bonds
– because they are physical attractions & not chemical bonds.
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4.1.4 Factors affecting enzymatic activities
The activity of an enzyme is affected by its environmental
conditions such as T & pH.
Temperature (T):
Increasing T increases the kinetic energy of molecules.
Since E catalyse reactions by randomly colliding with S, increasing
T increases the rate of reaction, forming more P.
2.0
Enzym atic activity
1.5
1.0
0.5
10 20 30 40 50 60 Temp. (C)
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However, increasing T also increases the vibrational energy that
E have, which damage the bonds that hold them together.
As T increases, weaker hydrogen & ionic bonds, will break
Breaking bonds within the E will cause the active site to change
shape.
change in shape of active site, is less complementary to the shape
of the S, so that it is less likely to catalyse the reaction.
Higher T will denature the E & will no longer function.
Optimal temperature (To) is the T at which an E has the
maximal catalytic power.
This is different for different E.
Reaction rates increase by 2 folds for every 10C rise.
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pH - Acidity and Basicity:
Lower pH values mean higher [H+] & lower [OH-].
H+ & OH- ions are charged & so, interfere with H & ionic bonds
that hold together an E, since they will be attracted or repelled by
the charges created by the bonds.
This interference causes a change in shape of E & its active site.
Different E have different optimum pH values.
At the optimum pH, the rate of reaction is at an optimum.
Any change in pH above or below the optimum will quickly cause a
decrease in the rate of reaction.
Small changes in pH above or below the optimum do not cause a
permanent change to the enzyme.
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However, extreme changes in pH can cause enzymes to denature &
permanently lose their function.
E in different locations of our body have different optimum pH
values since their environmental conditions may be different.
For example, the enzyme pepsin functions best at around pH-2 & is
found in the stomach, which contains HCl.
most living systems are highly buffered; i.e., they have mechanisms
that enable them to maintain a constant acidity.
trypsin
pH 7.0 is suitable for most 1.0
enzymes.
pH (pepsin) = 1.8 0.5
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Enzyme concentration
Increasing [E] will increase the rate of reaction, as more E
will be colliding with S molecules.
However, this too will only have an effect up to a certain
concentration, where the [E] is no longer the limiting factor.
Velocity, or how fast the
reaction is going
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Concentration of enzyme18
4.1.5 Enzyme inhibitors
E activity can be inhibited in various ways.
Inhibition could be reversible or irreversible.
Reversible inhibition
Competitive inhibition:
• occurs when molecules very similar to the S molecules bind to the
active site & prevent binding of the actual S.
• Penicillin, is a competitive inhibitor that blocks the active site of
an E that many bacteria use to construct their cell walls.
E + ES E +
Inhibitors can be normal S P
+
body metabolites & I
foreign substances
(drugs and toxins). EI
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Noncompetitive inhibition:
• occurs when an inhibitor binds to the E at a location other than
the active site.
• In some cases, the inhibitor is thought to bind to the E in such a
way as to physically block the normal active site.
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Frequently, an end-product of a metabolic pathway serves as an
allosteric inhibitor on an earlier enzyme of the pathway.
This inhibition of an enzyme by a product of its pathway is a form
of negative feedback.
Activators: allosteric control can involve stimulation of E action
as well as inhibition.
An activator molecule can be bound to an allosteric site and
induce a reaction at the active site by changing its shape to fit a S.
Common activators include hormones & the products of earlier
enzymatic reactions.
Allosteric stimulation & inhibition allow production of energy &
materials by the cell when they are needed & inhibit production
when the supply is adequate.
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Irreversible inhibition
covalently modify an E, & inhibition can not be reversed.
often contain reactive functional groups.
Is different from reversible E inactivation.
are generally specific for one class of E &
do not inactivate all proteins;
they do not function by destroying protein structure but by
specifically altering the active site of their target
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4.2 Bioenergetics and biosynthesis
4.2.1 Cellular respiration
Most living organisms obtain energy by breaking down organic
molecules during cellular respiration.
cellular respiration is to harvest electrons from C cpds (glucose)
use that energy to make ATP.
ATP is used to provide immediate energy for cells to do work.
This catabolic process can be divided into 3 phases.
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Phase I - breakdown polysaccharides, proteins & lipids into their
- respective building blocks (hydrolysis).
-this stage do not release much energy. Glycolysis
Phase II - these building blocks are oxidized to acetyl-CoA.
Also, pyruvate or other TCA intermediates may be formed
Phase III - consists of TCA followed by ETC & oxidative
phosphorylation.
Energy released by ETC to O2 is coupled to ATP synthesis.
TCA cycle & ETC release much energy.
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Cellular respiration occurs in two main parts:
– glycolysis and
– aerobic respiration.
glycolysis is an anaerobic process.
• do not require O2.
Aerobic respiration are Krebs cycle & ETC.
• processes require O2.
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Glycolysis: anaerobic respiration
Glucose is a key metabolite in metabolism.
Various pathways that are concerned with the utilization, storage,
& regeneration of glucose exist.
Glycogen is a polymeric storage form of glucose in human & in
the liver & in striated muscle, some is found in other tissues.
• Glycogen is synthesized when glucose supply is high, &
– its degradation helps to maintain the blood glucose level
when we are fasting.
• When glycogen is depleted, more glucose is synthesized from
scratch in gluconeogenesis.
• Gluconeogenesis occurs in the liver & in the kidneys.
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The first step in the degradation of glucose is glycolysis.
breaks down glucose to pyruvate.
glycolysis generate ATP.
A modest amount of ATP is produced in glycolysis directly.
much more ATP is formed downstream of glycolysis through
complete oxidation of pyruvate.
Glycolysis is found in animals, plants & microorganism.
This pathway is used by anaerobic as well as aerobic organisms.
The process takes place in the cytoplasm of prokaryotes &
eukaryotes & does not require O2.
Under aerobic conditions, pyruvate undergoes complete oxidative
to CO2 & H2O.
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• Pyruvate intended for complete degradation is transported to the
mitochondria,
– where it is decarboxylated to acetyl-CoA by pyruvate
dehydrogenase.
• Acetyl-CoA is completely degraded in the TCA cycle.
• The H2 that is produced here is not gaseous but bound to co-
substrates as,
– NADH & FADH2, which is subsequently oxidized in the
respiratory chain.
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Glycolysis involves ten enzymatic reactions;
The first five are preparatory phases or investment phase.
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6. GADP glyceraldehyde-3-phosphate dehydrogenase 1,3-PG
7. 1,3-PG + ADP phosphoglycerate kinase ATP + 3-PG
8. 3-PG phosphoglycerate mutase 2-PG
9. 2PG enolase phosphoenolpyruvate (PEP).
10. PEP + ADP pyruvate kinase Pyruvate + ATP
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11/30/2024 Fig: 4.1a. Glycolysis steps 31
Fig: 4.1b. Glycolysis steps
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TCA cycle and ETC: Aerobic respiration
One fate of pyruvate is, it enters to TCA for complete oxidation.
But there are intermediate processes that convert pyruvate to a
acetyl-CoA.
The enzyme complex converts pyruvate into Acetyl-CoA by the
following chemical changes:
Decarboxylation of pyruvate (loss of CO2)
Formation of acetyl group
Linkage of acetyl group to coenzyme A forming acetyl-CoA.
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The Tricarboxylic Acid (TCA) Cycle (Phase III)
The TCA cycle is considered as central pathway of aerobic
metabolism, as it serves two purposes-
– bioenergetics & biosynthesis:
Bioenergetic - the cycle carries out complex degradation of
acetyl group in acetyl-CoA to CO2,
– resulting in release of energy (ATP or GTP) & reducing
power (NADH & FADH2).
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Steps of the Krebs cycle
Prior to the Krebs cycle, pyruvate first reacts with coenzyme A
(CoA) to form acetyl-CoA.
At the same time, CO2 is released & NAD is converted to NADH.
Then acetyl-CoA moves to the mitochondrial matrix resulting
2CO2 & 2NADH.
The Krebs cycle begins with acetyl-CoA combining with a 4-C
compound to form a 6-C compound known as citric acid.
Citric acid is then broken down in the next series of steps, releasing
2CO2 &1GTP, 3NADH, & 1FADH2.
FAD is another electron carrier similar to NADH and NADPH.
Finally, acetyl-CoA & citric acid are generated & the cycle
continues.
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Fig: 4.2a. The TCA cycle
Fig: 4.2b. The TCA cycle
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Recall that two pyruvate molecules are formed during glycolysis,
resulting in two turns of the Krebs cycle for each glucose
molecule.
The net yield from the Krebs cycle is
6CO2 molecules,
2GTP (ATP),
8NADH, &
2FADH2.
NADH & FADH2 move on to play a significant role in the next
stage of aerobic respiration.
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Electron Transport Chain
In aerobic respiration, electron transport is the final step in the
break-down of glucose.
It is the point at which most of the ATP is produced.
High-energy electrons & H+ from NADH & FADH2 produced in
the TCA are used to convert ADP to ATP.
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• The prerequisite elements for biosynthesis include:
– precursor compounds,
– chemical energy (e.g. ATP), &
– catalytic enzymes which require coenzymes (e.g.NADH,
NADPH).
• These elements create monomers, the building blocks for
macromolecules.
• Some important biological macromolecules include:
– Proteins composed of aa monomers &
– DNA composed of nucleotides joined via phosphodiester
bonds.
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Photosynthesis
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Photosynthesis is essential to all life on earth.
It is the only biological process that captures energy from sunlight
converts it into chemical energy in the form of G3P
which in turn made into sugars, proteins, lipids, & nucleic acids.
Plants use these compounds in all of their metabolic processes;
plants do not need to consume other organisms for food
Unlike plants, animals need to consume other organisms
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The process of photosynthesis
• During photosynthesis,
– molecules in leaves capture sunlight & energize electrons,
– then stored in the covalent bonds of carbohydrate molecules.
– those covalent bonds are broken to release energy by cell respiration.
• Photoautotrophs (self-feeders using light).
– Plants, algae, & cyanobacteria
• Heterotrophs (other feeders): animals, fungi, & most bacteria,
– rely on photosynthetic organisms for their energy needs.
• Chemoautotrophs:
– synthesize sugars by extracting energy from inorganic chemical,
– Do not using sunlight’s energy. e,g, other bacteria
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• Those carbohydrates are the energy source that heterotrophs use to
power the synthesis of ATP via respiration.
• Therefore, photosynthesis powers 99% of Earth’s ecosystems.
• Energy path: sun light vegetation to deer finally to wolf.
E.g,
Wolf
Dear
Vegetation
Sunlight
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Other variant of photosynthesis
Oxygenic photosynthesis.
Anoxygenic photosynthesis.
Oxygenic photosynthesis,
Commonly seen in plants, algae & cyanobacteria.
light energy transfers e- from H2O to CO2, to produce
carbohydrates.
the CO2 is "reduced," or receives electrons, and
the water becomes "oxidized," or loses electrons.
Ultimately, oxygen is produced along with carbohydrates.
Reaction:
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Anoxygenic photosynthesis,
– uses electron donors other than water.
– occurs in purple bacteria & green sulfur bacteria
– does not produce oxygen.
– What is produced depends on the electron donor.
e.g, many bacteria use H2S, producing solid S as a byproduct.
Reaction is written as follows:
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The photosynthetic apparatus
Plastids
Photosynthetic eukaryotic contain organelles called plastids in their
cytoplasm.
Plastids contain pigments or can store nutrients.
The undifferentiated protoplastids in plants can differentiate into
several types, each with a distinct function
Chloroplasts contains chlorophyll for photosynthesis
Chromoplasts for pigment storage (contain carotenoids)
Proteinoplasts for protein storage
Leucoplasts for storage of fats & starch; colorless & nonpigmented
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The grana is the innermost portion; a collection of disc-shaped
membranes, stacked into columns like plates.
The individual discs are called thylakoids.
It is here that the transfer of electrons takes place.
The empty spaces b/n columns of grana constitute the stroma.
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Fig: 4.4. Structure of chloroplast 50
Pigments
are molecules that bestow color on plants, algae & bacteria,
responsible for effectively trapping sunlight.
Pigments of d/t colors absorb d/t wavelengths of light.
The three main groups pigments are:
1. Chlorophylls:
are green-colored pigments
are capable of trapping blue & red light.
have 3 subtypes, chlorophyll a, b & c.
also a bacterial variant named bacteriochlorophyll,
– which absorbs infrared light.
– mainly seen in purple & green bacteria, which perform anoxygenic
photosynthesis.
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2. Carotenoids:
these red, orange or yellow-colored.
absorb bluish-green light.
e.g, xanthophyll (yellow) & carotene (orange) from which
carrots get their color.
Carotenoids cannot transfer sunlight energy directly to the
photosynthetic pathway,
– For this reason, they are called accessory pigments. e,g fucoxanthin
3. Phycobilins:
these red or blue pigments
absorb wavelengths of light that are not well absorbed by
chlorophylls & carotenoids.
They are seen in cyanobacteria & red algae.
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Antennae
A large collection of 100-5,000 pigment molecules constitutes antennae.
capture light energy from the sun, in the form of photons.
Ultimately, light energy transferred to a pigment-protein complex that
can convert it to chemical energy, in the form of electrons.
In plants, light energy is transferred to chlorophyll pigments.
The conversion to chemical energy is accomplished when a chlorophyll
pigment expels an electron, which can then move on to an appropriate
recipient.
The pigments & proteins, which convert light energy to chemical
energy & begin the process of electron transfer, are known as reaction
centers.
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The photosynthetic process
• Plant photosynthesis are divided those that require sunlight & those
that do not.
• Both types of reactions take place in chloroplasts:
– light-dependent reactions in the thylakoid &
– light-independent reactions in the stroma.
Light-dependent reactions:
Called light reaction.
A photon of light hits the reaction center, a pigment chlorophyll
releases an electron.
The released e- escape through ETC, to generate ATP & NADPH.
The "electron hole" in the original chlorophyll pigment is filled by
taking an electron from water.
As a result, oxygen is released into the atmosphere.
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Light-independent reactions:
• called dark reactions & known as the Calvin cycle.
• Light reactions produce ATP & NADPH, which are the rich energy
sources that drive dark reactions.
• NADPH & ATP provide cells with large amounts of energy
– But these molecules are not stable enough to store chemical
energy for long periods of time.
Thus, there is a second phase of photosynthesis called the Calvin
cycle in which energy is stored in organic molecules such as
glucose.
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• Three chemical reaction steps make up the Calvin cycle:
carbon fixation,
reduction &
regeneration.
• These reactions use water & catalysts.
• The carbon atoms from CO2 are ''fixed,'' when they are built into
organic molecules that ultimately form 3C sugars.
• These sugars are then used to make glucose or are recycled to
initiate the Calvin cycle again.
• RuBisCo is biological enzymes converts inorganic CO2 into organic
molecules that can be used by the cell.
• Calvin Cycle is known as the C3 pathway because the first stable
organic molecule formed is a 3C sugar!
e.g, C3 plants are: grass, oak trees, maple trees, rose bushes, etc.
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Alternative Pathways
The environment in which an organism lives can impact the
organism’s ability to carry out photosynthesis.
Environments in which the amount of water or CO2 is
insufficient can decrease the ability of a photosynthetic organism
to convert light energy into chemical energy.
e.g, plants in hot, dry environments are subject to excessive
water loss that can lead to decreased photosynthesis.
Many plants in extreme climates have altered native
photosynthesis pathways to maximize energy conversion.
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C4 plants adaptive pathway that helps to maintain photosynthesis
by minimizing water loss is called C4 pathway.
e.g; sugar cane & corn.
Are called C4 plants because they fix CO2 into 4C cpds instead of
3C during the Calvin cycle.
C4 plants have significant structural modifications in the
arrangement of cells in the leaves.
C4 plants keep their stomata (pores) closed during hot days, while
the 4C cpds are transferred to special cells where CO2 enters the
Calvin cycle.
This allows for sufficient CO2 uptake, while simultaneously
minimizing water loss.
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CAM plants another adaptive pathway used by some plants to
maximize photosynthetic activity is called crassulacean acid
metabolism (CAM photosynthesis).
The CAM pathway occurs in water conserving plants that live in
deserts, salt marshes, & other where access to water is limited.
CAM plants, such as cacti, orchids, & pineapple allow CO2 to
enter the leaves only at night, when the atmosphere is cooler and
more humid.
At night, these plants fix CO2 into organic compounds.
During the day, CO2 is released from these compounds & enters
the Calvin cycle.
This pathway also allows for sufficient CO2 uptake, while
minimizing water loss.
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4.3 Metabolic disorders, diagnosis and treatments
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Inherited causes of metabolic disorders include:
Carbohydrate disorders; examples include
Diabetes insipidus, (large amount of dilute urine)
hereditary fructose intolerance, (unable to break fructose)
Galactosemia, (accumulation galactose)
pyruvate metabolism disorders, (build up of lactic acid)
von Gierke’s disease, (glycogen)
McArdle disease, (deficiency of muscle phosphorylase)
Pompe’s disease, and
Forbes’ disease
Fatty acid oxidation defects; examples include
– Gaucher’s disease,
– Niemann-Pick disease,
– Fabry’s disease, and
– medium-chain acyl-coenzyme A dehydrogenase (MCAD) deficiency
Amino acid disorders; examples include
– Tay-Sachs disease,
– phenylketonuria,
– tyrosinemia,
– maple syrup urine disease, and
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Some of the disorders associated with metabolism.
Acid-base imbalance
Disorders of calcium metabolism
DNA repair-deficiency disorders
Iron metabolism disorders
Mitochondrial diseases
Phosphorus metabolism disorders
Malabsorption syndromes
Water-electrolyte imbalance
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Other causes of metabolic disorders
• Metabolic disorders can be due to other factors, such as a
combination of inherited and environmental factors.
• Some of the conditions that can cause metabolic disorders include:
– Alcohol abuse, Diabetes (chronic, affects body’s ability to use sugar)
– Diuretic abuse, Gout (type of arthritis caused by a buildup of uric
acid in the joints)
– Ingestion of poison or toxins, including excessive aspirin,
bicarbonate, alkali, ethylene glycol, or methanol
– Kidney failure, Pneumonia, respiratory failure, or collapsed lung
– Sepsis (life-threatening bacterial blood infection)
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4.3.1. Risk factors of metabolic disorders
• A number of factors increase the risk of developing metabolic disorders.
• Not all people with risk factors will get metabolic disorders.
• Risk factors for metabolic disorders include:
– chronic medical conditions, such as lung or kidney disease and
Diabetes
– Family history of genetic metabolic disorder.
– Race and ethnicity: blacks people are at higher risk than whites for
type 2 diabetes.
– HIV/AIDS and other diseases;
– Age- the risk of metabolic syndrome increases with age.
– Obesity and lack of exercise:
– Hormone imbalance:
– Insulin resistance: a body cannot use insulin properly.
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4.3.2 Diagnosis of metabolic disorders
Metabolic syndrome is more effectively diagnosed by testing
different;
– blood markers (specific markers of insulin resistance),
– obesity (especially abdominal obesity),
– high blood pressure, and
– lipid abnormalities.
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Specifically, metabolic syndrome is diagnosed if any three of the
following five markers are present:
– Elevated waist circumference: 40 inches or more for men; 35 inches
or more for women
– Elevated triglycerides: 150 mg/dL or higher
– Reduced high-density lipoprotein (HDL) levels (AKA ''good''
cholesterol): less than 40 mg/dL in men; less than 50 mg/dL in
women
– Elevated blood pressure: 130/85 mm Hg or higher or are already
taking blood pressure medications
– Elevated fasting glucose: 100 mg/dL or higher or are already taking
glucose-lowering medications
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4.3.3 Treatments of metabolic disorders
• Treatment approach depends on the specific metabolic disorder.
• Multiple treatment options are available for inborn (inherited) errors
of metabolism and examples include:
– bone marrow transplantation,
– enzyme replacement therapy in selected patients,
– gene therapy in selected patients,
– medications to reduce symptoms, such as pain or low blood sugar,
– mineral supplementation,
– periodic assessment,
– physical therapy
– nutritional counseling & support,
– surgery to relieve pain or symptoms,
– vitamin supplementation and etc.
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• Acquired metabolic disorder treatment will include
– normalizing the metabolic balance by both reversing the cause
and administering medications.
Potential complications of metabolic disorders include;
– organ failure/dysfunction,
– seizures and tremors, and
– unconsciousness and coma.
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