B.sc. biochemistry sem 1 introduction to biochemistry unit 1 foundation of biochemistry
B.sc. biochemistry sem 1 introduction to biochemistry unit 4 metabolism and bioenergetics
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Transcript of B.sc. biochemistry sem 1 introduction to biochemistry unit 4 metabolism and bioenergetics
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Course: B.Sc. Biochemistry
Sub: introduction to biochemistry
Unit -4
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Metabolic Concepts Metabolism, the sum of all the chemical transformations
taking place in a cell or organism, occurs through a series of enzyme-catalyzed reactions that constitute metabolic pathways.
Each of the consecutive steps in a metabolic pathway brings about a specific, small chemical change, usually the removal, transfer, or addition of a particular atom or functional group.
The precursor is converted into a product through a series of metabolic intermediates called metabolites.
The term intermediary metabolism is often applied to the combined activities of all the metabolic pathways that interconvert precursors, metabolites, and products of low molecular weight (generally, Mr 1,000).
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Catabolism is the degradative phase of metabolism in which organic nutrient molecules (carbohydrates, fats, and proteins) are converted into smaller, simpler end products (such as lactic acid, CO2, NH3).
Catabolic pathways release energy, some of which is conserved in the formation of ATP and reduced electron carriers (NADH, NADPH, and FADH2); the rest is lost as heat.
In anabolism, also called biosynthesis, small, simple precursors are built up into larger and more complex
molecules, including lipids, polysaccharides, proteins,
and nucleic acids.
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Anabolic reactions require an input of energy, generally in the form of the phosphoryl group transfer potential of ATP and the reducing power of
NADH, NADPH, and FADH2 (Fig. 3).
Some metabolic pathways are linear, and some are branched, yielding multiple useful end products from a single precursor or converting several starting materials into a single product. In general, catabolic pathways are convergent and anabolic pathways divergent .
Some pathways are cyclic: one starting component of the pathway is regenerated in a series of reactions that converts another starting component into a product.
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Three types of nonlinear metabolic pathways. (a) Converging, catabolic; (b) diverging, anabolic; and (c) cyclic, in which one of the starting materials (oxaloacetate in this case) is regenerated and reenters the pathway. Acetate, a key metabolic intermediate, is the breakdown product of a variety of fuels (a), serves as the precursor for an array of products (b), and is consumed in the catabolic pathway known as the citric acid cycle (c).
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Bioenergetics Life is an energy intensive
process.
It takes energy to operate muscles, extract wastes, make new cells, heal wounds, even to think.
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BioenergeticsA discipline within
biochemistry dedicated to the study of energy flow within living systems
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Why Study Bioenergetics?
The understanding of metabolism provides the directions to better understand how skeletal muscles generate energy, and how and why the body responds to exercise the way it does.
The study of metabolism is aided by studying Bioenergetics.
The Laws of Bioenergetics provide the rules upon which metabolism functions.
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Thermodynamics The study of energy transformations that occur in a
collection of matter.
Two Laws:
1. First Law of Thermodynamics
2. Second Law of Thermodynamics
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First Law of Thermodynamics
Energy cannot be created or destroyed, but only converted to other forms.
This means that the amount of energyin the universe is constant.
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The First Law is not much help...What prevents a melting ice cube from
spontaneously refreezing?
Why doesn’t water flow uphill?
Will L-alanine convert into D-alanine?
The energy of the system and its surrounds won’t
change.
If it does not occur, what is driving force?
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What can we learn from the 1st law of bioenergetics
1. The main forms of energy within the body are;
• heat light mechanical
• chemical
• “free energy”
• entropy
2. Entropy is a form of energy that cannot be re-used in chemicalreactions, and is defined synonomously with increasedrandomness or disorder.
3. “Free energy” is referred to as Gibb’s free energy, and isabbreviated “G”. Typically, during energy transfers there is achange in energy forms, which is indicated by the “∆“ symbol.Thus, a change in Gibb’s free energy is expressed as a “∆G”.
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The Second Law helps resolve problem
Only those events that result in a net increase in disorder will occur
spontaneously
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Second Law of Thermodynamics
All energy transformations are inefficient because every reaction results in an increase in entropy and the loss of usable energy as heat.
Entropy: the amount of disorder in a system.
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Second law: The second law of thermodynamics, which can be
stated in several forms, says that the universe always tends toward increasing disorder: in all natural processes, the entropy of the universe increases.
Living organisms consist of collections of molecules much more highly organized than the surrounding materials from which they are constructed, and organisms maintain and produce order, seemingly oblivious to the second law of thermodynamics. But living organisms do not violate the second law; they operate strictly within it.
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Lessons learnt from the 2nd law of bioenergetics
1. All reactions proceed in the direction of:
a) ↑ entropy
b) a release of free energy (-∆G,(Kcal/Mol))
2. The more negative the ∆G, the greater the release of freeenergy during a chemical reaction.
3. Chemical reactions that have a -∆G are termed exergonicreactions.
4. By convention, reactions that require free energy input toproceed are termed endergonic reactions, but there are nosuch reactions in the human body!
5. The free energy not used to do work is expressed as heat.
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6. Reactions that have no net change in substrate or product are termed equilibrium reactions, and have no change in free energy (∆G=0).
7. All reactions are potentially reversible.
8. The directionality and amount of free energy release of a chemical reaction can be modified by altering substrate and product concentrations.
- ↑’ing products may reverse the direction of the reaction
- ↑’ing substrates can make the ∆G more negative
Of course, if the reaction is reversed, what were the
products are now the substrates, and vice-versa
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The second Law; The entropy (disorder) of the universe is increasing
3
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Mitochondria:
1
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STATE STANDARD:
“Students know that in both plants and animals,
mitochondria make stored chemical bond
energy available to cells by completing the
breakdown of glucose to carbon dioxide!”
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Mitochondria:
1
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• have complex folded inner membranes (cristae), increasing their surface area
Mitochondria:
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• have complex folded inner membranes (cristae), increasing their surface area
• have a fluid-filled interior (the matrix)
Mitochondria:
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• have complex folded inner membranes (cristae), increasing their surface area
• have a fluid-filled interior (the matrix)
• act like combustion chambers in an engine,a ‘safe’ place to ‘burn’ fuel with oxygen
Mitochondria:
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A Combustion Chamber?
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A Combustion Chamber?LET’S COMPARE!
A gasoline engine . . . . and a mitochondria,in cross-section.
2
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Before combustion canoccur, however, we have to
get some “fuel” !
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For that, we will need to break down glucose(or other sugars) OUTSIDE
the mitochondria, in a process called . . . .
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is the breakdown of glucose (orother sugars)
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is the breakdown of glucose (orother sugars)
requires an activation energy
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is the breakdown of glucose (orother sugars)
requires an activation energy
occurs in the cytoplasm
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Polymers of glucose, like starch, are first broken into individual sugars through
hydrolysis
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The single sugars produced containstored energy in their chemical bonds,
but they are still too big to pass through the mitochondrial membrane.
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ATP provides the initial activation energy. The 6-carbon sugar willbe broken down in a series of steps
that do not involve oxygen.
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There will be a net gain of 2 ATP. The final products of glycolysis are two 3-carbon molecules of pyruvate (pyruvic
acid)
C3H3O3
3
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Pyruvate is small enough tobe easily transported through the mitochondrial
membrane, where a new series of chemical reactionstake place. . .
C3H3O3
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TheKrebsCycle
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The Krebs Cycle:
• takes place in the matrix
4
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The Krebs Cycle:
• takes place in the matrix
• begins by converting each of the 3-carbonpyruvates into a special complex calledacetyl CoA
C3H3O3 “acetyl CoA”
. . Co-enzyme A is added
Pyruvate entersthe matrix. . . . . .a waste product ,
CO2 , is released . . .
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The Krebs Cycle:Acetyl CoA
begins the cycleAcetyl CoA
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The Krebs Cycle:Acetyl CoA
begins the cycle
As the cycle proceeds, CO2
are removed
CO2
CO2
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The Krebs Cycle:There is a netgain in ATP,
and . . .
. . .an electron transport chain
is charged!
ATP
CO2
CO2e-
e-
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Electron Transport:
• takes place in the cristae
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Electron Transport:
• takes place in the cristae
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Electron Transport:
• takes place in the cristae
• will draw in H+, creating a highconcentration which can be used to
drive a proton pump
Electron Transport:
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Proton Pumping:
• powers the enzyme, ATP synthase
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Proton Pumping:
• powers the enzyme, ATP synthase
…which is then used to make ATP
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DOING THE MATH:
Glycolysis, in cytoplasm, no O2 4 ATP
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DOING THE MATH:
Glycolysis, in cytoplasm, no O2 4 ATP
Krebs Cycle, in matrix, no O2 2 ATP
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DOING THE MATH:
Glycolysis, in cytoplasm, no O2 4 ATP
Krebs Cycle, in matrix, no O2 2 ATP
Electron transport chains, with O2 32 ATP
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DOING THE MATH:
Glycolysis, in cytoplasm, no O2 4 ATP
Krebs Cycle, in matrix, no O2 2 ATP
Electron transport chains, with O2 32 ATP
TOTAL: 38 ATP
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DOING THE MATH:
Glycolysis, in cytoplasm, no O2 4 ATP*
Krebs Cycle, in matrix, no O2 2 ATP
Electron transport chains, with O2 32 ATP
TOTAL: 38 ATP(-2 ATP)*---------------
(*minus 2 ATP used for activation energy in glycolysis)
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DOING THE MATH:
Glycolysis, in cytoplasm, no O2 4 ATP*
Krebs Cycle, in matrix, no O2 2 ATP
Electron transport chains, with O2 32 ATP
TOTAL: 38 ATP(-2 ATP)*---------------
NET YIELD, 1 glucose: 36 net ATP
(*minus 2 ATP used for activation energy in glycolysis)
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MINERALS A mineral is a naturally occurring substance that is
solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and has an ordered atomic structure. It is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regard to it having an ordered atomic structure. The study of minerals is called mineralogy.
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Functions of Minerals Some participate with enzymes in metabolic
processes (cofactors, e.g. Mg, Mn, Cu, Zn, K)
Some have structural functions (Ca, P in bone; S in keratin)
Acid-base and water balance (Na, K, Cl)
Nerve & muscle function (Ca, Na, K)
Unique functions: hemoglobin (Fe), Vitamin B12
(Co), thyroxine (I).
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Classification
Macro or Major minerals
Sodium (Na), potassium (K), magnesium (Mg), calcium (Ca), phosphorus (P), sulfur (S), chloride (Cl)
Present in body tissues at concentrations >50 mg/kg
requirement of these is >100 mg/d
Micro or Trace minerals(body needs relatively less) Manganese(Mg), iron(Fe),
cobalt(Co), chromium(Cr),molybdenum(Mo), copper(Cu), zinc(Zn), fluoride(F), iodine(I), selenium(Se)
Present in body tissues at concentrations <50 mg/kg
requirement of these is ﹤100 mg/d
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Nutritionally Important Minerals
Macro Trace
Element g/kg Element mg/kg
Ca
P
K
Na
Cl
S
Mg
15
10
2
1.6
1.1
1.5
0.4
Fe
Zn
Cu
Mo
Se
I
Mn
Co
20-50
10-50
1-5
1-4
1-2
0.3-0.6
0.2-0.5
0.02-0.1
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Minerals in Foods Found in all food groups.
More reliably found in animal products.
Often other substances in foods decrease absorption(bioavailability) of minerals Oxalate, found in spinach, prevents
absorption of most calcium in spinach.
Phytate, form of phosphorous in most plants makes it poorly available
Oxalate
Phytate
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Factors Affecting Requirements
Physiological state/level of production
Interactions with other minerals
4
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Deficiencies and Excesses Most minerals have an optimal range
Below leads to deficiency symptoms
Above leads to toxicity symptoms
Mineral content of soils dictates mineral status of
plants (i.e., feeds)
May take many months to develop
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Requirements and Toxicities
Element Species Requirement, mg/kg
Toxic level, mg/kg
Cu Cattle
Swine
5-8
6
115
250
Co Cattle 0.06 60
I Livestock 0.1 ?
Se Cattle
Horses
0.1
0.1
3-4
5-40
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Calcium (Ca)
Most abundant mineral in animal tissues 99% Ca in skeleton 1% Present in:
Blood & other tissues
Lots of functions Bone structure Nerve function Blood clotting Muscle contraction Cellular metabolism
5
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Dietary requirements
Dietary requirements:
Adult : 800 mg/day;
Women during pregnancy, lactation and post-
menopause: 1.5 g/day;
Children (1-18 yrs): 0.8-1.2 g/ day;
Infants: (< 1 year): 300-500 mg /day
Food Sources:
Best sources: milk and milk product;
Good sources: beans, leafy vegetables, fish, cabbage, egg
yolk.
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Major minerals
Sodium-sources- table salt, processed foods-metabolism- water balance
-acid base balance (excretion ofhydrogen ions in exchange for sodium ions in kidney)
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Major minerals
Chloride-sources- table salt, processed foods-metabolism- water balance
-hydrochloric acid
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Major minerals
Potassium--sources-all whole foods, meats, milk,
fruits, grains
-metabolism- water balance-supports cell integrity-promotes steady heartbeat
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Major minerals
Calcium
-sources-milk and milk products, small fish with bones, tofu, broccoli, chard
-metabolism- bone and teeth formation
-cell signalling
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Major minerals
Phosphorous-sources-all animal tissues
-metabolism- buffers-part of DNA/RNA-phosphorylation of many
enzymes and B vitamins to make them biochemically active
-ATP-phospholipids-cell signalling
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Major minerals
Magnesium
-sources-nuts, legumes, whole grains, dark green vegetables,
seafood, chocolate
-metabolism- enzyme co-factor (glucose use in body plus
synthesis of protein, lipids and nucleic acids)
-part of enzyme that transforms ADP to ATP
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Major minerals
Sulphur-sources-all protein containing foods
-metabolism- protein structure-part of thiamine and
biotin
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Minor minerals
Definition of minor minerals
-present in body in amounts less than 5 grams
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Minor minerals
Inorganic elements
•Iron
•Zinc
•Iodine
•Selenium
•Copper
•Manganese
•Fluoride
•Chromium
• Molybdenum
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Minor minerals
Body's handling of minerals
-iron uses carriers for absorption, transport and proteins for storage-no free iron- oxidation issue-example of minor mineral requiring no carriers or storage proteins iodine
Variable Bioavailability-phytates reduce iron absorption
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Minor minerals
Nutrient Interactions-slight manganese overload may exacerbate iron deficiency
-combined iodine and selenium deficiency reduces thyroid hormone function more than just iodine deficiency alone
Varied roles-iron-oxygen carrying-zinc- part of enzymes
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Minor minerals
Iron-sources-red meats, fish, poultry,
shellfish, eggs, legumes, dried fruits
-metabolism- oxygen carrier-part of electron carriers
in electron transport chain
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Minor mineralsZinc
-sources-protein containing foods:meats fish, poultry, whole grains, vegetables
-metabolism- part of many enzymes-synthesis of DNA/RNA-heme synthesis-fatty acid metabolism-release hepatic stores of
vitamin A-carbohydrate metabolism-synthesis of proteins-dispose of damaging free radicals
-oxygen carrying
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Minor minerals
Iodine-sources-iodised salt, seafood, bread,
dairy products, plants grown on iodine rich soil and animals that eat such plants
-metabolism- thyroid hormones-metabolic rate(rate of oxygen use),body temperature
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Minor minerals
Selenium-sources-seafood, meat, whole grains, and
depending on soil selenium content- vegetables
-metabolism- anti-oxidation (via enzyme)- regulates thyroid hormone
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Minor mineralsCopper
-sources-seafood, nuts, whole grains, seeds, legumes
-metabolism- part of many enzymes all of which have common feature of
consuming oxygen or oxygen radicals-eg -hemoglobisynthesis
-collagen synthesis-free radical control-electron transport
chain
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Minor minerals
Manganese-sources-nuts, whole grains, leafy
vegetables
-metabolism- essential for iron absorption and use in formation of hemoglobin -part of several enzymes
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Minor minerals
Fluoride
-sources-fluoridated drinking water, tea, seafood
-metabolism- formation of bones and teeth, resistance to tooth decay
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Minor minerals
Chromium-sources-meat, unrefined foods, fats,
vegetable oils
-metabolism- enhancing insulin activity
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Minor minerals
Molybdenum-sources-legumes, cereals, organ meats
-metabolism- co-factor for several enzymes
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References/Sources All images are from Lehninger Principles of biochemistry by Nelson and Cox except1.https://lh4.ggpht.com/0HlIrSFqDcCtidmS1T6x70CquY2CThQM6i_eY3ZuxEt4lC0_yLvjFTwsBiuS6isLH
Azb=s1232.https://lh4.ggpht.com/J4qU9fcv42V2pQj7Wt99lTqMZQZedjEaafMd4CahkTo9euleEuWRbjwSTcnDK1
VIzPbTLg=s933. https://lh5.ggpht.com/CYhZcxlIn01H7O77jW4gz-
6MPxYJ59IzvMJbV6utSh2FX0505P7Ab1fLHQcFE2Zxbv-JBVk=s854.https://lh3.ggpht.com/cc8HBCMzPlDFxXgQKwjk9ZYkOJLotGmbUa4ZzwusqvslbQY7W2UVhXUgVd_
Oj8YGtK6wWw=s1395.
https://lh3.ggpht.com/cHAfbDE2a1aKZfi_VuC9uzkrvK2YjakVMmONrNPcchJcwcsOaYYgOk4wXL_YzeX0E15iEw=s97
6.https://lh3.ggpht.com/eWm_hMna_I6Wapkaq33984aHnCZk8cjgh354pbqKU1BNtZ9kAcNNnaEwGVUZT5FtwR27eow=s85
Books/ Web resources Lehninger Principles of biochemistry by Nelson and Cox www.nlm.nih.gov/medlineplus/minerals.html https://chemistry.osu.edu/~woodward/ch121/ch5_law.htm biochem.co/2010/02/glycolysis www.elmhurst.edu/~chm/onlcourse/CHM103/Rx24citricacidcycle