Lecture 12: Introduction to Metabolism Flashcards Preview

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Flashcards in Lecture 12: Introduction to Metabolism Deck (46):
1

First Law of thermodynamics

- for any physical or chemical change, the total amount of energy (in the universe) remains constant

--> when energy is converted from one form to another, the total energy before and after the conversion is the same

--> energy is neither created or destroyed

2

Second law of thermodynamics

 

- when energy is converted from one form to another, some of that energy becomes unavailable to do work, resulting in increased entropy (in the universe)

3

Entropy

 

- measure of the disorder in as system and is based on the fact that energy transformation processes are never 100% efficient

--> it takes energy to impose order on a system

--> unless energy is applied to a system, it will be randomly arranged or disordered

4

Enthalpy

- total energy = the usable energy (free energy G) plus the unusable energy (entropy)

H = G + TS

T = temperative in kelvin

5

Change in energy

 

 delta G = delta H -  T (delta S)

 

positive = energy consumed

negative  = energy released and reaction can occur spontaneously

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Exergonic

 

release free energy (delta G negative) and are spontaneous

--> catabolism

7

Endergonic

 

- consume free energy

- delta G is positive and are nonspontaneous

--> anabolism

8

Free energy for reaction in a biological system

 

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Values for k Eq in biological reactions

 

K eq > 1 : - delta G, proceeds forward

K = 1 : delta G = 0, is at equilibrium

K < 1 : + delta G, proceeds in reverse

10

Types of metabolic pathways

metabolism: sum of chemical reactions in an organism

catabolism: sum of energy releasing (exergonic) processes. the degenerative phase of metabolism

anabolism: sum of energy using (endergonic) processes. biosynthetic phase of metabolism

 

* catabolism provides the building blocks and energy for anabolism

 

overall sequence = metabolic pathways

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anabolism: precursor and cell macromolecules

 

precursors: amino acids, sugars, fatty acids, nitrogenous bases

 

macromolecules: proteins, polysaccharides, lipids, nucleic acids

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catabolism: energy containing nutrients and energy depleted end products

 

nutrients: carbohydrates, fats, proteins

 

energy depleted end products: C02, H20, NH3

13

Five priniciple characteristics of metabolic pathways

 

* stem from their function of generating products for cellular

1. metabolic pathways are IRREVERSIBLE due to at least one highly exergonic reaction conferring directionality

2. they have INDEPENDENT CATABOLIC and ANAMOLIC interconversion routes for intermediates

3. they each have a FIRST COMMITTED STEP

4. they are REGULATED, most often on the level of enzymes catalyzing specific metabolic steps

5. they occur in SPECIFIC CELLULAR LOCATIONS

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Irreversibility of metabolic pathways

- at least one highly exergonic reaction conferring directionality

15

metabolic pathways: catabolic and anabolic interconversion routes

independent routes for the two processes

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Metabolic pathways: first step

 

committed

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metabolic pathways: regulation

most often on the level of enzymes catalyzing specific metabolic steps

 

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metabolic pathways: locations

- specific cellular locations

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Metabolic pathways: connection and arrangement

 

highly interconnected and nonlinearly arranged

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Types of metabolic reactions:

 

1. reactions that make and break bonds of carbons with other carbons

2. internal rearrangements, isomerizations, eliminations

3. free radical reactions

4. group trasnfer reactions

5. oxidation-reduction reactions

 

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reactions that make and break bonds of carbons with other carbons

 

- aldol condensation

- claisen ester condensation

- decarboxylation of a b-keto acid

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internal rearrangements, isomerizations, eliminations

 

glucose 6 phosphate --> fructose 6 phosphate

other?

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free radical reactions

 

coproporphyrinogen III

coproporphyrinogenyl III radical

protoporophyrinogen IX

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group trasnfer reactions

 

glucose --> glucose 6 phosphate

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oxidation reduction reactions

 

lactate --> puryvate

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transfer potentials

 

- protons, electrons or functional groups can be transferred during biochemical reactions

--> tendency of such reactions to occur can be quantified

27

Cellular work

- types

- process

- chemical

- transport

- mechanical

 

- to do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an andergonic one

--> most energy coupling in cells is mediated by ATP

28

phosphorylated adenosine derivatives

 

1 = AMP

2=ADP

3 = ATP

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29

ATP hydrolysis and Mg 2+

 

- formation of Mg2+ complexes partially shields the negative charges and influences the conformation of phosphate groups in necleotides such as ATP and ADP

 

- between 2 end ones for ATP: MgATP2-

- between only 2 for ADP: MgADP-

30

Daily human requirement for ATP

 

- the average adult human consumes approximately 11,700 Kj of food energy per day

- assuming thermodynamic efficiency of 50%, about 5860 KJ of this energy ends up in form of ATP

- Assuming 50Kj of energy required to synthesize one mole of ATP, the body must cycle through 5860/50 or 117 moles of ATP per day (=65kg of ATP per day)

- the typical adult human body contains 50 g ATP/ADP

- each ATP must be recycled nearly 1300 times per day

31

How many times is each ATP molecule recycled per day

 

1300

32

How many grams does the typical adult human body contain

 

50 g ATP/ADP

33

ATP-ADP cycle

- revolving door through which energy passes during its transfer from catabolic to anabolic pathways

- using energy from catabolic reactions in the cell, ATP is regenerated by the addition of a phosphate group to ADP in three diff ways

1. substrate level phosphorylation

2. oxidative phosphorylation

3. photophosphorylation

34

ATP-ADP cycle summary

 

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Substrate level phosphorylation

 

- transfer of a high-energy PO4- from a phosphorylated compounds to ADP

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Oxidative phosphorylation

 

- energy released by transferring clectrons from one compound  (oxidation) to another (reduction) along an electron trasnport chain to a final acceptor (such as oxygen) is used to create a proton gradient and hence to synthesize ATP

37

photophosphorylation

 

- light causes chlorophyll to release excited electrons and the energy from this electron trasnfer of chlorphyll through a system of carrier molecules is used to reate a proton gradient and hence to synthesize ATP (as well as other energy sources)

38

Redox reactions

 

chemical reactions that transfer electrons between reactants (donor and acceptor) are called oxidation-reduction reactions

Fe3+ + Cu+ --> Fe2+ + Cu2+

 

can be divided in two 2 half reactions:

Fe3+ + e- --> Fe2+

Cu+ --> Cu2+ + e-

39

Other ways for electron transfer to occur in redox reactions:

 

- hydrogen atoms

AH2 --> A + 2e- + 2H+

AH2 + B --> A + BH2

- hydride ion (H-) has 2 electrons

- direct combination with oxygen: which acts as an electron acceptor that is covelantly incorporated into the product (oxidation of a hydrocarbon to an alcohol)

 

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Dehydrogenations in biological systems

 

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NAD/NADP-dependent reactions

 

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NAD(P) binding in dehydrogenases

where does binding occur?

 

- Rossman fold

43

FAD/FMN-dependent reactions

 

44

Redox potential

 

- when two redox pairs are together in solution, electron trasnfer from the electron donor of one pair to the electron acceptor of the other may proceed spontaneously

- the tendency for such a reaction depends on the relative affinity of the acceptor of each redox pair for electrons

- the redox potential (or electromotive force, emf) Enot, a measure (in volts) of this affinity, can be determined experimentally using the:

H+ + e- --> 1/2 H+

as a reference  (arbitrarily assigned as Enot = 0.00V)

45

Using electrochemical cell

Half-cell that takes electrons from the standard hydrogen cell is assigned a positive E not ( a negative E not when it donates electrons)

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Quantification of REdox potential

- redox potential depends not only on the chemical species present, but also on their activities, approximated by their concnetrations

- the standard redox potential Enot related to the actual redox otential E at any concentration of oxidized and reduced species in a living cell nu the Nernst equation

 

 

E0 at pH 7 and 250c

 

ΔG = -nF ΔE