Chapter 5 THE FLOW OF ENERGY WITHIN ORGANISMS

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Chapter 5 THE FLOW OF ENERGY WITHIN ORGANISMS

• Starting chemical reactions
• Energy flow and change in living systems
• The structure of ATP
• How ATP stores, transfers, and releases energy
• Enzymes lower activation energy
• Enzymes bind substrates at active sites
• Factors that affect enzyme activity
• Cofactors and coenzymes

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Starting Chemical Reactions

• Chemical Reactions one substance is changed into
  another
• Reactants molecules entering into the chemical
  reaction
• Products changed molecules at the end of the
  reaction
• Energy is needed to initiate the reaction between
  molecules (also called Free Energy of Activation)
• There are two types of chemical reactions, termed
  exergonic (energy out) reaction and endergonic
  (energy in) reaction.

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Exergonic Reaction
Endergonic reaction

• Energy added to products during the reaction
  called endergonic reactions.
• Endergonic reactions DO NOT occur spontaneously.
• Anabolic reactions are endergonic reactions that
  use energy to build complex molecules form
  simpler molecules.

• Energy released from the reactants during the
  reaction called exergonic reaction.
• Energy released due to reactions breaking down
  complex molecules into simpler molecules called
  catabolic reactions.

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Energy Management in Organisms

• In living organisms, the exergonic and endergonic
  reactions are coupled together to form coupled
  reactions.
• Thus, energy released from exergonic reactions is
  used to power endergonic reactions
• Energy Flow and Change in Living Systems
• Life can be viewed as a constant flow of energy
  that is channeled by the organisms to do the work
  of living.
• Forms of Energy
• mechanical, heat, sound, electricity, light,
  radioactivity, and magnetism

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The structure of ATP

• Each ATP molecule has three subunits
• -Ribose sugar
• -Adenine
• -Triphosphate group formed by the linkage of
  three phosphate groups (PO4).

How ATP stores, transfers, and releases energy

• ATP stores energy released from other exergonic
  reactions in the covalent bonds that link the
  phosphate groups in ATP, called phosphoanhydride
  bonds.
• The phosphoanhydride bonds are fairly unstable
  and require only small amount of free energy to
  break it, a process called hydrolysis.
• The hydrolysis of terminal phosphoanhydride bond
  releases stored energy.

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ATP is the Energy Currency of Cells

• ATP couples energy-releasing (exergonic) and
  energy-storing (endergonic) enzymatic reactions
  in cells.
• ATP, ADP, and phosphate are continually being
  recycled within living cells as cells use group
  transfer to capture, carry, and release energy.

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Group Transfer by Phosphorylation

• The stored energy in ATP is easily transferred,
  along with the PO4 group, to another molecules in
  a process called phosphorylation.
• ATP has high group transfer potential.

ATP loses stored energy due to hydrolysis to
produce ADP and phosphate group. Compound A gains
more energy due to phosphorylation.
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States of Energy

• Energy exists in two states
• Kinetic energy energy of motion ability to do
  work
• Potential energy stored energy

Laws of Thermodynamics

• Laws of thermodynamics
• First law energy is constant cannot be created
  or destroyed, just changed from one form to
  another
• Second law entropy (chaos, disorder) continually
  increases in the universe

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Living Things obey Laws of Thermodynamic

• Organisms transform energy from one form or state
  to another, termed energy flow.
• Living organisms transform potential energy
  stored in food into kinetic energy to do cellular
  works.
• How do the laws of thermodynamics apply to cells?
• As organisms use energy to perform cellular
  works, some potential energy may lose as heat,
  which induce a disorder in the system (entropy
  increase).
• The lost heat energy is also necessary for many
  living things to keep them warm.
• All things in the universe tend toward disorder.
• Thus, cells need a continual, external source of
  useful energy to do work, overcome entropy,
  remain organized, stay alive!

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Energy from the Sun

• Earth continuously receives new energy from the
  sun.
• Some of this energy is captured by green plants
  (producers) and transformed into usable energy
  forms.
• Chemical reactions transform the energy of
  sunlight or fuel into usable energy called
  photosynthesis.
• Cells can use this energy to do their work
• synthesis, movement, organization, reproduction,
  communication, etc.

Metabolic pathways

• The flow of energy in an organism consists of a
  complicate network of coupled reactions, that
  transfer energy released from exergonic reactions
  to either power endergonic reactions or to
  transform into different energy storage forms.
• The chains of all chemical reactions in an
  organism that moves, stores, and releases energy
  is called metabolic pathways.

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Enzymes Act as Catalysts

• Activation energy is needed to control the start
  of chemical reactions.
• Increase temperature helps to induce the chemical
  reactions.
• Catalysts increase the rate of reaction by
  lowering activation energy.
• Enzymes endow cells with the remarkable capacity
  to exert kinetic control over thermodynamic
  potentiality
• Enzymes are the agents of metabolic function

Enzymes can accelerate reactions as much as 1016
over uncatalyzed rates! Ex. Urease Catalyzed
rate 3x104/sec Uncatalyzed rate 3x10-10/sec
Ratio is 1x1014 !
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Enzymes Act as Catalysts
Enzymes act as catalysts in the living systems
that induce the chemical reactions under the
moderate temperature condition.
Ribozymes - segments of RNA that display enzyme
activity in the absence of protein Ex. RNase P
and peptidyl transferase Abzymes - antibodies
raised to bind the transition state of a reaction
of interest
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Life is Regulated by Enzymes

• Enzymes are proteins that act as biological
  catalysts to reduce the amount of free energy of
  activation needed for chemical reactions to take
  place.
• All the metabolic reactions in cells are
  controlled by enzymes. Life is therefore a
  process regulated by enzymes.
• Specificity
• Enzymes selectively recognize proper substrates
  over other molecules
• Enzymes produce products in very high yields -
  often much greater than 95
• Specificity is controlled by structure - the
  unique fit of substrate with enzyme controls the
  selectivity for substrate and the product yield

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Enzyme/Substrate Interactionsare Specific

• Enzymes typically catalyze only one or a few
  chemical reactions.
• Each cell in your body contains from 1000 to 4000
  different types of enzymes.

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Enzymes contain Active Site

• Active site is the groove or cleft on enzyme
  formed by tertiary structure of protein.
• Active site is the location in enzyme that binds,
  orients, and strains substrate in both endergonic
  and exergonic reactions.
• The active site of each enzyme has a specific
  shape complementary to the shape of the
  substrates (substances on which enzyme act).

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Induced-Fit Model of Enzyme Activity

• To allow chemical reaction to occur, substrate(s)
  must fit into the active site of an enzyme.
• The binding of substrates may induce the
  adjustment of the shape of active sit allowing a
  better fit, called an induced fit.

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Enzymes Catalyze Reactions between Two Substrates

• The chemical reaction is less likely to occur by
  the random collision between two reactants.
• Enzyme acts like a marriage broker to get two
  reactants together.

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Factors that Affect Enzyme Activity

• Enzymes activity is sensitive to the change in
  their 3-dimensional shape.
• Temperature and pH are two factors that may make
  enzyme to lose its shape or denature.

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Inhibitors and Activators

• The 3-D shape of an enzyme can also be affected
  by the binding of specific chemicals called
  activators (facilitate chemical reactions) and
  inhibitors (turn-off chemical reactions).
• Enzyme activity within an organism is often
  regulated by inhibitors under the process called
  negative feedback.
• End-product inhibition

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Cofactors and Coenzymes

• Special non-protein molecules called cofactors
  and coenzymes help enzymes to catalyze chemical
  reactions
• Cofactors, generally metal ions, assist enzymes
  in catalyzing chemical reactions.
• Coenzymes are small organic molecules (e.g.,
  vitamins).
• Vitamins Many vitamins are "coenzymes" -
  molecules that bring unusual chemistry to the
  enzyme active site
• Vitamins and coenzymes are classified as
  "water-soluble" and "fat-soluble"
• The water-soluble coenzymes exhibit the most
  interesting chemistry

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Cofactors and Coenzymes
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Vitamin B1 Thiamine pyrophosphate (TPP) ???

• Thiamine - a thiazole ring joined to a
  substituted pyrimidine by a methylene bridge
• Thiamine-PP is the active form
• TPP is involved in carbohydrate metabolism
• It catalyzes decarboxylations of a-keto acids and
  the formation and cleavage of a-hydroxyketones

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Nicotinamide, Riboflavin and the
Flavins ????,???,??

• These coenzymes are electron carriers, involved
  in redox reactions
• They transfer hydride anion (H-) to and from
  substrates
• Riboflavin (???), first isolated in 1879, is also
  called vitamin B2

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Coenzyme A

• Pantothenic acid (vitamin B3) is a component of
  Coenzyme A
• Functions
• Activation of acyl groups for transfer by
  nucleophilic attack
• activation of the a-hydrogen of the acyl group
  for abstraction as a proton
• Both these functions are mediated by the reactive
  -SH group on CoA, which forms thioesters

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Vitamin B6

• Pyridoxine and pyridoxal phosphate
• Catalyzes reactions involving amino acids,
  including transaminations, decarboxylations,
  eliminations, racemizations and aldol reactions

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Vitamin B12 Cyanocobalamin

• B12 can prevent pernicious anemia
• Not synthesized by animals or by plants
• B12 is converted into two coenzymes in the body
• 5'-deoxyadenosylcobalamin
• methylcobalamin
• B12 catalyzes 3 kinds of reactions
• Intramolecular rearrangements
• Reductions of ribonucleotides to
  deoxyribonucleotides
• Methyl group transfers

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Vitamin C

• Ascorbic acid
• Most plants and animals make ascorbic acid - for
  them it is not a vitamin
• Only a few vertebrates - man, primates, guinea
  pigs, fruit-eating bats and some fish (rainbow
  trout, carp and Coho salmon) cannot make it!
• Vitamin C is a reasonably strong reducing agent
• It functions as an electron carrier
• Many functions in the body
• Hydroxylations of proline and lysine (essential
  for collagen) are Vitamin C-dependent, treatment
  or prevention of scurvy
• Metabolism of Tyr in brain depends on C
• Fe mobilization from spleen depends on C
• C may prevent the toxic effects of some metals
• C ameliorates allergic responses
• C can stimulate the immune system

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Biotin Vitamin H

• Biotin, also vitamin H (from German haut,
  meaning skin)
• Functions curing or preventing dermatitis???,
  loss of hair, and paralysis in rats
• Biotin functions as a mobile carboxyl group
  carrier, so, whenever you see a carboxylation
  that requires ATP and CO2 or HCO3-, think biotin!
  
• Bound covalently to a lysine, the biotin ring
  system is tethered to the protein by a long,
  flexible chain
• The "tether" allows the carboxyl group to be
  shuttled from the carboxylase subunit to the
  transcarboxylase subunit of ACC-carboxylase

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Folic Acid Coenzyme One Carbon Donor

• Folic acid participates in the generation and
  utilization of 1 C functional groups, methyl,
  methylene, and formyl
• Discovered in 1930s, found to cure megaloblast
  anemia (????????) (reduced level of erythrocytes)
  with yeast or liver extract
• Megaloblast anemia caused reduced level of
  erythrocytes, cells are large and immature,
  suggesting a role of vitamin in cell
  proliferation and/or maturation
• Abundant in leafy green vegetables such as
  spinach, named folic acid
• Three distinct moieties
• (1) a bicyclic heterocyclic pteridine ring,
  6-methylpterin
• (2) p-aminobenzoic acid (PABA), required for
  many bacterial growth
• (3) glutamic acid

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Vitamin A and Rod Cell

• Vitamin A - also called all-trans-retinol, is an
  isoprenoid alcohol that plays a key role in
  vision and a role in controlling animal growth.
• Vitamin A must either be present in the diet, or
  derived from b-carotene, an isoprenoid compound
  prominent in carrots.
• Dehydrogenation of retinol yields the aldehyde,
  retinal, which has a role in vision.
• Retinoids (derivatives of retinol) act like
  steroid hormones and interact with specific
  receptor proteins in the cell nucleus.

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Vitamin A

• Retinol, retinyl esters and retinal are forms of
  Vitamin A
• Retinol-binding proteins (RBPs) help to mobilize
  and transport vitamin A and its derivatives
• Retinol is converted to retinal in the retina of
  the eye and is linked to opsin (???) to form
  rhodopsin (?????), a light-sensitive pigment
  protein in the rods and cones
• Vitamin A, obtained from animal diet or plant
  b-carotene, affects growth and differentiation,
  prevent night blindness

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Vitamin D

• Ergocalciferol and cholecalciferol
• Cholecalciferol is made in the skin by the action
  of UV light on 7-dehydrocholesterol
• Major circulating form is 25-hydroxyvitamin D,
  1,25-dihydroxyvitamin D3) is the most active form
  
• Functions regulate calcium (bone formation,
  ricket, muscle contraction, nerve impulse
  transmission, blood clotting, membrane structure)
  and phosphate (DNA, RNA, lipid, protein
  phosphorylation) homeostasis

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Vitamins E and K

• Less understood vitamins
• Vitamin E (?-tocopherol) is a potent antioxidant
• Molecular details are almost entirely unknown
• Vitamin E may prevent oxidation of unsaturated
  fatty acid in membrane
• Vitamin K is essential for blood clotting
• Carboxylation of 10 glutamyl residues on
  prothrombin (to form ?-carboxy-Glu residues) is
  catalyzed by a vitamin K-dependent enzyme, liver
  microsomal glutamyl carboxylase