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• Principles that govern energy resources

Metabolism/Energy Transformations

p g gyin chemistry, physics and engineering also apply to biology

• Metabolism – all of an organism’s chemical reactions – an emergent property

• Bioenergetics – the study of how organisms manage their energy resources

• Metabolic pathway – alteration of molecules in steps

• Catabolic pathways – breakdown of complex molecules

Chemical reactions in cells are organized into Metabolic Pathways

complex molecules– release energy

• Anabolic pathways – build complex molecules– consume energy– Energy released by catabolic pathways

drives anabolic pathways

Figure 8.2 Transformations between potential and kinetic energy

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Energy transformations of life are subject to two laws of thermodynamics

• Thermodynamics:study of energy transformations

• First law: energy can

Fig. 8.3a

• First law: energy can be transferred or transformed, but cannot be created or destroyed

Chemical energy (e.g., food) is a form of potential energyin molecules because of the arrangement of atoms

Energy transformations of life are subject to two laws of thermodynamics

Second law: every energy transfer or transformation increases the disorder (entropy) of the universe– Entropy: a measure of disorder, or randomness

• The more random a collection of matter, the greater its entropy– Much of the increased entropy of the universe takes the

form of increasing heat• Heat (random molecular motion) is energy in its most random state

Fig. 8.3b

Order as a characteristic of life

• Do living organisms violate the second law of thermodynamics?– NO! Order can increase locally (e.g., a cell), but net effect is

randomization of the universe• Living organisms take in organized forms of matter and

energy, and replace them with less ordered forms

Fig. 8.4

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The relationship of free energy to stability, work capacity, and spontaneous changein systems with higher energy initial states and more stable final states

Initial state – higher energy

.

Free energy change ('G) – portion of a system’s energy that is able to perform work

Fig. 8.5 Final state – more stable

Free energy changes ('G) in exergonic (left) and endergonic (right) reactions

Free energy change ('G) – portion of a system’s energy that is able to perform work (constant T)

'G = 'H – T'S'H = ' total energy (biology); T = temperature (o Kelvin); 'S = ' entropy

At equilibrium, 'G = 0 (cell is dead…)([HUJRQLF�UHDFWLRQ

&DQ SURFHHG VSRQWDQHRXVO\(QGHUJRQLF�UHDFWLRQ

&DQQRW SURFHHG VSRQWDQHRXVO\&DQ�SURFHHG�VSRQWDQHRXVO\ &DQQRW�SURFHHG�VSRQWDQHRXVO\

Fig. 8.6

Equilibrium and work in an isolated (closed) hydroelectric system

Reactions in a system isolated from its surroundings reach equilibrium ('G = 0) and can then do no work

Fig. 8.7

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An open hydroelectric system

Open systems can exchange energy (and often matter) with their surroundings – system does not reach equilibrium

Living organisms are open systemsFig. 8.8a

Figure 8.7c Equilibrium and work in isolated (closed) and open systems

A cell breaking down glucose occurs in a series of reactions that power the work of the cell

Fig. 8.8b

Structure of adenosine triphosphate (ATP)

Fig. 8.9a (also review Chap 4)

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ATP hydrolysis to ADP and Pi

In the cell:'G ~ -13 kcal/mol

Fig. 8.9b (also review Chap 4)

The ATP cycle

In the cell:'G ~ -13 kcal/mol

Fig. 8.12

ATP hydrolysis drives cellular work

TransportExample: ion pumping across membranes (Na+, K+, Ca2+)

Example: pyruvate transport across inner mitochondrial membrane

Mechanical workExamples: cilia beating, muscle contraction, chromosome movement

ChemicalExample: polypeptide synthesis Fig. 8.11

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Energy coupling using ATP hydrolysis

Endergonic ('G > 0)

Coupled reactions:net reaction is exergonic ('G < 0)

Fig. 8.10

'G = -7 kcal/mol

Hydrolysis of sucrose

Fig. 8.13 –Energy profile of an

EXERGONIC reactionDoes this reaction occur spontaneously?Yes…But…VERY slowlyHigh activation energy (EA)EA - extra energy required to start a reaction

EXERGONIC reaction

�(1=<0(6�DUH�ELRORJLFDO�FDWDO\VWV� • Catalyst – changes

reaction rate without being consumed (changed)– Enzyme – a

catalytic protein

• Enzymes speed reactions by lowering EA– Enables transition state to be reached at cell temperature

• Enzymes do not change 'G• Enzymes only affect the reaction rate

Fig. 8.14

– Ribozyme – a catalytic RNA (lectures on: polypeptides; translation)

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• Substrate – reactant that binds to an enzyme• Substrate binds to active site of enzyme

– Structure of active site ĺ specific for substrate binding/catalysis

• Substrate converted to products (may be reversible)

Enzymes are substrate specific

(enzyme that hydrolyzes sucrose)

Enzyme +Substrate

Enzyme-substratecomplex

Enzyme +Products

Induced fit between an enzyme and its substrate:glucose binding to active site of hexokinase

Fig. 8.15

Active site and catalytic cycle of an enzyme

A + B ļ C + D

Fig. 8.16

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• Substrates are typically held in the active site by weak interactions– e.g., H-bonds; ionic bonds

• Catalysis– Thousands of reactions per second– Involves -R groups of a few amino acids at active site

ff d b h i bl ( l !)

Active site is an enzyme’s catalytic center

– Enzymes unaffected by the reaction: reusable (catalyst!)• Most metabolic enzymes catalyze reactions in both

forward and reverse directions– Reversible reactions– Direction (net reaction over many reaction cycles) at any time

depends on the relative concentrations of products and reactants• Concentrations affect 'G

– Enzymes catalyze reactions in the direction of equilibrium

Reaction rate depends on substrate concentration…Michaelis-Menton kinetics…

n

substrate concentration

rate

of r

eact

io

…and enzyme concentration.

n 2 [ ]

substrate concentration

rate

of r

eact

io

1x [enzyme]

2x [enzyme]

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Environmental factors affect enzyme activity

temperature

Fig. 8.17

pH

Inhibition of enzyme activity (some pharmaceuticals, poisons, etc.): COMPETITIVE INHIBITION

Fig. 8.18a,b

Inhibition of enzyme activity (some pharmaceuticals, poisons, etc.):NONCOMPETITIVE INHIBITION

Fig. 8.17a,c

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Allosteric regulation of a multi-subunit enzyme

Most allosterically regulated enzymes contain multiple subunits(multiple polypeptides; quaternary structure)

- each subunit has it’s own active site

Fig. 8.19a

The Evolution of Enzymes

� Enzymes are proteins encoded by genes

� Changes (mutations) in genes lead to changesin amino acid composition of an enzyme

� Altered amino acids in enzymes may result in

© 2014 Pearson Education, Inc.© 2014 Pearson Education, Inc.

y ynovel enzyme activity or altered substrate specificity

� Under new environmental conditions a novelform of an enzyme might be favored

� For example, six amino acid changes improved substrate binding and breakdown in E. coli

Figure 8.19

Active siteTwo changed amino acids werefound near the active site.

© 2014 Pearson Education, Inc.

Two changed amino acidswere found on the surface.

Two changed amino acidswere found in the active site.

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Concept 8.5: Regulation of enzyme activity helps control metabolism� Chemical chaos would result if a cell’s metabolic

pathways were not tightly regulated

� A cell does this by switching on or off the genes that encode specific enzymes or by regulatingthe activity of enzymes

© 2014 Pearson Education, Inc.© 2014 Pearson Education, Inc.

the activity of enzymes

Feedback inhibition in a metabolic pathway for synthesis of isoleucine (an amino acid)

METABOLICMETABOLICPATHWAY

Isoleucine is a non-competitive inhibitor of the

initial step in the pathway

Fig. 8.21

Allosteric Regulation of Enzymes

� Allosteric regulation may either inhibit or stimulate an enzyme’s activity

� Allosteric regulation occurs when a regulatory molecule binds to a protein at one site andaffects the protein’s function at another site

© 2014 Pearson Education, Inc.© 2014 Pearson Education, Inc.

affects the protein’s function at another site

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Figure 8.20a

Regulatorysite (oneof four)

Allosteric enzymewith four subunits Active site

(one of four)

Active formActivator

Stabilizedactive form

(a) Allosteric activators and inhibitors

© 2014 Pearson Education, Inc.

OscillationNon-functionalactive site

InhibitorInactive form Stabilized

inactive form

Cooperativity in an enzyme with multiple subunits

Fig. 8.20b

BSC 2010 Chase

Energy and the Laws of Thermodynamics Motivation: Synthesis of biological macromolecules and the organization (structure) associated with life require continuous input and use of energy (according to the laws of thermodynamics). In the next two lectures, we’ll see how living organisms use specific proteins (enzymes) to transform energy in a highly organized way. Objectives: ¾ Explain the role of catabolic and anabolic pathways in cellular metabolism. ¾ Distinguish between kinetic and potential energy. ¾ Explain why an organism is considered an open system. ¾ Explain the first and second laws of thermodynamics. ¾ Explain why highly ordered living organisms do not violate the second law of

thermodynamics. ¾ Write and define each component of the equation for free energy change ('G). ¾ Distinguish between exergonic and endergonic reactions in terms of free energy change

('G). ¾ Describe the relationship between free energy and equilibrium. ¾ Describe the three main kinds of cellular work. ¾ Describe the structure of ATP and explain in general terms how ATP performs cellular

work. Metabolism Bioenergetics Metabolic pathways

Catabolic pathways Anabolic pathways Energy Chemical energy Thermodynamics First law of thermodynamics Second law of thermodynamics Entropy

BSC 2010 Chase

Free energy

Free energy change ('G) Exergonic reaction Endergonic reaction Adenosine triphosphate (ATP) Energy coupling Phosphorylated intermediate

BSC 2010 Chase

Enzymes and catalysis (Motivation continues from last lecture) Objectives: ¾ Describe the function of enzymes in biological systems. ¾ Explain why an investment of activation energy (EA) is necessary to initiate a

spontaneous reaction. ¾ Explain how enzyme structure determines enzyme specificity. ¾ Describe several mechanisms by which enzymes lower activation energy. ¾ Explain how substrate concentration affects the rate of an enzyme-catalyzed reaction. ¾ Explain how temperature, pH, cofactors, and enzyme inhibitors can affect enzyme

activity. ¾ Explain how metabolic pathways are regulated. ¾ Explain how the location of enzymes in a cell influences metabolism.

Catalyst Activation energy

Enzyme Substrate Product Active site Conformational change Evolution

Activity

Environmental factors Cofactors Inhibitors Activators Allosteric regulation

BSC 2010 Chase

Feedback inhibition Negative feedback Positive feedback Cooperativity