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Chapter 6

Lecture Outline

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Chapter 6

An Introduction to Energy, Enzymes, and Metabolism

Key Concepts:

• Energy and Chemical Reactions

• Enzymes and Ribozymes

• Overview of Metabolism

• Recycling of Organic Molecules

Energy and Chemical Reactions

• Energy = ability to promote change or do work

• Two forms

Kinetic Energy – associated with movement

Potential Energy – due to structure or location

• Chemical energy, the energy in molecular bonds, is a form of potential energy

Figure 6.1

a) Kinetic energy b) Potential energy

a: ©moodboard/Corbis; b: ©amanaimages/Corbis

Table 6.1

Table 6.1 Types of Energy That Are Important in Biology

Energy type Description Biological example

Light Light is a form of electromagnetic radiation that is visible to the eye. The energy of light is packaged in photons.

During photosynthesis, light energy is captured by pigments in chloroplasts (described in Chapter 8). Ultimately, this energy is used to produce organic molecules.

Heat Heat is the transfer of kinetic energy from one object to another or from an energy source to an object. In biology, heat is often viewed as kinetic energy that can be transferred due to a difference in temperature between two objects or locations.

Many organisms, including humans, maintain their bodies at a constant temperature. This is achieved, in part, by chemical reactions that generate heat.

Mechanical Mechanical energy is the energy possessed by an object due to its motion or its position relative to other objects.

In animals, mechanical energy is associated with movement due to muscle contraction, such as walking.

Chemical potential Chemical potential energy is potential energy stored in the electrons of molecules. When bonds are broken and rearranged, energy may be released.

The covalent bonds in organic molecules, such as glucose and ATP, store large amounts of energy. When bonds are broken in larger molecules to form smaller molecules, the energy that is released can be used to drive cellular processes.

Electrical/ion gradient The movement of charge or the separation of charges can provide energy. Also, a difference in ion concentration across a membrane constitutes an electrochemical gradient, which is a source of potential energy.

During a stage of cellular respiration called oxidative phosphorylation (described in Chapter 7), an

H  gradient

provides the energy to drive ATP synthesis.

Laws of Thermodynamics

First Law of Thermodynamics

“Law of conservation of energy” Energy cannot be created or destroyed, but can be transformed from one type to another

Second Law of Thermodynamics

Transfer of energy from one form to another increases the entropy (degree of disorder) of a system As entropy increases, less energy is available for organisms to use to promote change

Figure 6.2 1

Figure 6.2 2

Change in free energy determines direction of chemical reactions 1

• Total energy = Usable energy + Unusable energy

• Energy transformations involve an increase in entropy (disorder that cannot be harnessed to do work)

• Free energy (G) = amount of energy available to do work

Also called Gibbs free energy

Change in free energy determines direction of chemical reactions 2

H = enthalpy or total energy

G = free energy or amount of energy for work

S = entropy or unusable energy

T = absolute temperature in Kelvin (K)

Spontaneous reactions 1

• Occur without input of additional energy

• Not necessarily fast, can be slow Breakdown of sucrose to CO2 and H2O is spontaneous, but will take a long time for sugar in a sugar bowl to break down

• Key factor is the free energy change – if ΔG is negative, then process is exergonic and spontaneous

Spontaneous reactions 2

• Exergonic = spontaneous

ΔG < 0 (negative free energy change)

Energy is released by reaction

• Endergonic = not spontaneous

ΔG > 0 (positive free energy change)

Requires addition of energy to drive reaction

Hydrolysis of ATP

ΔG= −7.3kcal/mole

Reaction favors formation of products

The energy liberated is used to drive a variety of cellular processes

Cells use ATP hydrolysis to drive reactions

• An endergonic reaction can be coupled to an exergonic reaction

• The reactions will be spontaneous if the net free energy change for both processes is negative

ATP drives endergonic reactions

2 2

2 Glucose Phosphate Glucose 6 phosphate H O

    ‐ ‐

ΔG=+3.3Kcal/mole(endergonic)

4 2 2

2 i ATP ADP P

       

ΔG=−7.3Kcal/mole(exergonic)

Coupled reaction:

4 2 2 Glucose ATP Glucose 6 phosphate ADP

     ‐ ‐

ΔG=−4.0Kcal/mole(exergonic) = spontaneous

Figure 6.4

Table 6.2

Table 6.2 Examples of Proteins That Use ATP for Energy

Type Description

Metabolic enzymes

Many enzymes use ATP to catalyze endergonic reactions. For example, hexokinase uses ATP to attach phosphate to glucose, producing glucose- 6-phosphate.

Transporters Ion pumps, such as Na K ATPase  – , use ATP to pump ions against a gradient (see Chapter 5).

Motor proteins Motor proteins, such as myosin, use ATP to facilitate cellular movement, as in muscle contraction (see Chapter 45).

Chaperones Chaperones are proteins that use ATP to aid in the folding and unfolding of cellular proteins (see Chapter 4).

DNA-modifying enzymes

Many proteins, such as helicases and topoisomerases, use ATP to modify the conformation of DNA (see Chapter 11).

Aminoacyl-tRNA synthetases

These synthetases are enzymes that use ATP to attach amino acids to tRNAs (transfer RNAs; see Chapter 12).

Protein kinases Protein kinases are regulatory proteins that use ATP to attach a phosphate to a protein, thereby phosphorylating the protein and affecting its function (see Chapter 9).

Many Proteins Bind ATP and Use That ATP as a Source of Energy

• Each ATP undergoes 10,000 cycles of hydrolysis and resynthesis every day

• Particular amino acid sequences in proteins function as ATP- binding sites

• We can predict whether a newly discovered protein uses ATP or not

• On average, 20% of all proteins bind ATP

• Likely an underestimate because there may be other types of ATP-binding sites

• This illustrates the enormous importance of ATP as an energy source

Enzymes and Ribozymes

• A spontaneous reaction is not necessarily a fast reaction

• Catalyst – an agent that speeds up the rate of a chemical reaction without being consumed during the reaction

• Enzymes – protein catalysts in living cells

• Ribozymes – RNA molecules with catalytic properties

Activation energy

• Initial input of energy to start reaction

• Allows molecules to get close enough to cause bond rearrangement

• Can now achieve transition state where bonds are stretched

• Common ways to overcome activation energy Large amounts of heat

Using enzymes to lower activation energy

Figure 6.5

An enzyme strains chemical bonds in the reactant molecules and/or brings them close together.

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How enzymes lower activation energy

• Straining bonds in reactants to make it easier to achieve transition state

• Positioning reactants together to facilitate bonding

• Changing local environment Direct participation through very temporary bonding

Other enzyme terminology

• Active site – location where reaction takes place

• Substrates – reactants that bind to active site

• Enzyme-substrate complex – formed when enzyme and substrate bind

Figure 6.6

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Substrate binding

• Enzymes have a high specificity for their substrate

• Lock and key metaphor for substrate and enzyme binding – only the right key (substrate) will fit in the lock (enzyme)

• Induced fit phenomenon – interaction also involves conformational changes

Enzyme reactions

• Saturation Plateau where nearly all active sites are occupied by substrate

velocity of reaction near maximal rate max

• Michaelis constant, M

Substrate concentration where velocity is half maximal value

High M

K enzyme needs higher substrate concentration

Inversely related to affinity between enzyme and substrate

Figure 6.7a

a) Reaction velocity in the absence of inhibitors

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Inhibition

• Competitive inhibition

Molecule binds to active site

Inhibits ability of substrate to bind

Apparent M

K increases – more substrate needed

• Noncompetitive inhibition

Lowers maxV without affecting mK

Inhibitor binds to allosteric site, not active site

Figure 6.7b and c

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Other requirements for enzymes

• Prosthetic groups – small molecules permanently attached to the enzyme

• Cofactor – usually inorganic ion that temporarily binds to enzyme

• Coenzyme – organic molecule that participates in reaction but is left unchanged afterward

Enzymes are affected by environment

• Most enzymes function maximally in a narrow range of temperature and pH

Discovery of Ribozymes

Until 1980s, scientists thought all biological catalysts (enzymes) were proteins

Ribonuclease P (RNase P) is found in all living organisms, and involved in cleaving tRNA molecules

RNase P is a Ribonucleoprotein, with an RNA subunit and a protein subunit – which part is the catalyst?

Experiments found the RNA subunit alone is able to cleave substrate

The RNA is a true catalyst

• it accelerates rate without being altered itself

Figure 6.10 Steps 1 and 2

HYPOTHESIS The catalytic function of RNase P is carried out by its RNA subunit or by its protein subunit.

KEY MATERIALS Purified precursor tRNA (ptRNA) and purified RNA and protein subunits of RNase P from E. coli.

1. Into each of five tubes, add ptRNA.

2. In tubes 1 to 3, add a low concentration of MgCI2; in tubes 4 and 5, add a high MgCI2 concentration.

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Figure 6.10 Steps 3 through 7

HYPOTHESIS The catalytic function of RNase P is carried out by its RNA subunit or by its protein subunit.

KEY MATERIALS Purified precursor tRNA (ptRNA) and purified RNA and protein subunits of RNase P from E. coli.

3. Into tubes 2 and 5, add the RNA subunit of RNase P alone; into tube 3, add both the RNA subunit and the protein subunit of RNase P. Incubate to allow digestion to occur. Note: Tubes 1 and 4 are controls that have no added subunits of RNase P.

4. Carry out gel electrophoresis on each sample. In this technique, samples are loaded into a well on a gel. They move toward the bottom of the gel and are separated according to their masses: Molecules with higher masses are closer to the top of the gel. The gel is exposed to ethidium bromide, which stains RNA.

5. THE DATA 6. CONCLUSION The RNA subunit alone catalyzes the breakage of a covalent bond in ptRNA at high MgCI2 concentrations. It is a ribozyme.

7. SOURCE Altman, S. 1990. Enzymatic cleavage of RNA by RNA. Bioscience Reports 10:317 to 337.

(4 to 5): Altman. S 1990. Enzymatic Cleavage of RNA by RNA. Bioscience Reports. 10:317 to 337, Figure 7. ©The Nobel Foundation

Overview of Metabolism

• Chemical reactions occur in metabolic pathways

• Each step is coordinated by a specific enzyme

• Catabolic pathways Breakdown cellular components Exergonic

• Anabolic pathways Synthesis cellular components Endergonic Must be coupled to exergonic reaction

Figure 6.11

Catabolic reactions

• Breakdown of reactants

• Used for recycling building blocks

• Used for energy to drive endergonic reactions

Energy stored in intermediates such as ATP, NADH

Two ways to make ATP

• Substrate-level phosphorylation

Enzyme directly transfers phosphate from one molecule to another molecule

• Chemiosmosis

Energy stored in an electrochemical gradient is used to make ATP from ADP and

i P

Redox reaction

Electron removed from one molecule is added to another

• Oxidation – removal of electrons

• Reduction – addition of electrons

A is oxidized, B is reduced

NADH

• Electrons removed by oxidation of organic molecules are used to create energy intermediates like NADH

• NAD  Nicotinamide adenine dinucleotide

• NADH useful in two ways: Releases a lot of energy when oxidized that can be used to make ATP Can donate electrons during synthesis reactions to energize them

Figure 6.12

The 2 electrons and H can be added to this ring, which now has 2 double bonds instead of 3.

Two electrons are released during the oxidation of the nicotinamide ring.

Anabolic reactions

• Biosynthetic reactions

• Make large macromolecules or smaller molecules not available from food

• Require energy inputs from intermediates (NADH or ATP) to drive reactions

Regulation of metabolic pathways

Gene regulation Turn genes on or off

Cellular regulation Cell-signaling pathways like hormones

Biochemical regulation Feedback inhibition – product of pathway inhibits early steps to prevent over accumulation of product

Feedback inhibition

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Recycling of organic molecules 1

• Most large molecules exist for a relatively short period of time

• Half-life – time it takes for 50% of the molecules to be broken down and recycled

• All living organisms must efficiently use and recycle organic molecules

Recycling of organic molecules 2

• Expression of genome allows cells to respond to changes in their environment

RNA and proteins made when needed

Broken down when they are not

• mRNA degradation important

Conserve energy by degrading mRNAs for proteins no longer required

Remove faulty copies of mRNA

Proteasome

• A large complex that breaks down proteins using protease enzymes

• Proteases cleave bonds between amino acids

• Ubiquitin tags target proteins to the proteasome to be broken down and recycled

• Ubiquitin tagging allows the cell to: Degrade improperly folded proteins Rapidly degrade proteins to respond to changing cell conditions

Figure 6.14a

a) Structure of the eukaryotic proteasome

Figure 6.14b

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Lysosomes

• Lysosomes contain hydrolases to break down proteins, carbohydrates, nucleic acids, and lipids

• Digest substances taken up by endocytosis

• Autophagy – recycling worn out organelles using an autophagosome

Figure 6.15

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