BIOL 111 Chapter 8

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Metabolism

How do the following items relate to each other?

Energy	Matter (elements, atoms)
Enzymes	Electron movements
Chemical reactions	Concentration gradients

BIG Picture

Energy flow in natural systems:

Chloroplasts in autotrophs ^{[vocab 1]} (photosynthesis)
Organic molecules + O₂
Mitochondria in heterotrophs ^{[vocab 2]} (cellular respiration) → ATP
CO₂ + H₂O
(repeat)

Energy

$E=mc^{2}\,\!$

Even the smallest amount of matter has the potential for enormous amounts of energy

Types:

kinetic ^{[vocab 3]} – energy due to motion (light, heat, sound)
- More free energy (higher $\Delta G$ )
- Less stable
- Greater work capacity
potential ^{[vocab 4]} – energy stored due to position or structure (chemical, atomic)
- Less free energy (lower $\Delta G$ )
- More stable
- Less work capacity

Energy is measured in calories ^{[vocab 5]}. $1000{\text{cal}}=1{\text{kcal}}=1{\text{ Calorie (in food)}}$

Thermodynamics ^{[vocab 6]}

2 laws:

Energy and matter can be transferred but cannot be created or destroyed.
In every energy transfer, some energy becomes unusable (heat), which increases entropy ^{[vocab 7]} or disorder of the universe.

Spontaneous Reactions

No input energy required
Increases entropy ^{[vocab 7]}

Gibbs Free Energy

In order to measure the entropy of a closed system, we use Gibbs Free Energy equation:

$\Delta G=\Delta H-T\Delta S\,\!$

$\Delta G$ : Change in free energy (E available for work)
$\Delta H$ : Change in enthalpy (potential energy)
$T$ : Temperature in Kelvin
$\Delta S$ : Change in entropy

It measures the energy in a "system" like a living cell. The value of $\Delta G$ predicts spontaneity of a reaction:

Negative result = spontaneous and exergonic ^{[vocab 8]}
- Products are normally more stable but have less free energy
Positive result = NOT spontaneous; endergonic ^{[vocab 9]}
- Products are less stable but have more free energy

Cellular Respiration

CO₂ + H₂O → C₆H₁₂O₆ + O₂: NOT endergonic; $+\Delta G$

C₆H₁₂O₆ + O₂ → CO₂ + H₂O: spontaneous; endergonic $-\Delta G$; ΔG_glucose = –686kcal/mol

Protein Enzyme Catalyst ^{[vocab 10]} required to speed up the natural combustion reaction for cellular use.

How is this related to Biology?

Organisms use energy in different ways depending on whether they are autotrophs ^{[vocab 1]} or heterotrophs ^{[vocab 2]}

Metabolism

2 types:

Anabolic ^{[vocab 11]} – requires energy
Catabolic ^{[vocab 12]} – produces energy

^[1]

Metabolic Disequilibrium

If you put reactions in a test tube, the reaction will run until the chemicals reach equilibrium ( $\Delta G=0$ )

In cell system, material is constantly entering and leaving, so equilibrium never obtained. The products of one or more reactions are often used as the reactants of another reaction.

Thursday, September 30, 2010

Enzymes

Lowers activation energy ^{[vocab 13]}:

Active site of enzyme bonds to substrate; the enzyme changes shape to form induced fit ^{[vocab 14]}, which applies forces to break bonds and form new ones

Measuring activity

Lab used a spectrophotometer:

Measures amount of light transmitted or absorbed by a sample. Certain chemicals absorb certain wavelengths of light. Enzymes alter the chemicals and therefore the light-absorbing properties.

Reaction Rate Factors

Enzyme Concentration
Substrate Concentration
Temperature
pH
organic and inorganic cofactors ^{[vocab 15]} like coenzymes from vitamins & minerals (organic) and metal ions (inorganic)
inhibitors ^{[vocab 16]}
- competitive: able to bind to active site and takes it out of commission.
- noncompetitive: binds to another point on the enzyme and alters the active site.

Adenosine Triphosphate (ATP)

ATP structure

Adenine Ribose bonded with three phosphate molecules.

Phosphates are negatively charged, so the want to get away from each other. The hydrolysis of phosphate molecules releases a burst of energy

Coke machine analogy

Glucose has a lot of free energy: $\Delta G=-686{\text{kcal/mol}}$ ($20 bill)

ATP has a smaller unit of free energy: ΔG_ATP = –7.3 kcal/mol ($2 bill)

Theoretically, 1mol of glucose can provide 93.9mol of ATP:

{\frac {-686}{-7.3}}\approx 93.9

How ATP Works

The energy released by donating a phosphate to the reactant (phosphorylation ^{[vocab 17]}), thereby making it more reactive for a moment. Phosphate is then released into cytoplasm.

Consider the following reaction:

Glu + NH₃ → Glutamine ( $\Delta G=+3.4{\text{kcal/mol}}$ )

Glu+ATP → Glu–P + ADP ( $\Delta G=-7.3$ ) Glu–P + NH₃ → Glutamine + P_i

The ATP lowered the net $\Delta G$ input required to -3.9kcal/mol

Redox Reactions

reduction ^{[vocab 18]} + oxidation ^{[vocab 19]}

Redox reactions happen due to electronegativity ^{[vocab 20]}

Xe^– + Y → X + Ye^– : X becomes oxidized, Y becomes reduced

OIL RIG: Oxidation Is Loss, Reduction Is Gain (of e^– electron, that is)

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + Energy

carbon in glucose becomes oxidized: (follow the carbons in order to match up the reactants with their products)
oxygen becomes reduced into water: it goes from an equal sharing in O₂ to accepting electrons from H

Vocabulary

↑ ^1.0 ^1.1 autotrophic organisms make their own food
↑ ^2.0 ^2.1 heterotrophic organisms get their energy from outside sources
↑ kinetic energy is energy due to active motion
↑ potential energy is energy due to a current position or structure
↑ a calorie (little c) is the amount of heat required to raise 1g of water by 1°C
↑ Thermodynamics is the study of the energy flow in natural systems.
↑ ^7.0 ^7.1 entropy is the disorder of the universe. On a smaller scale, more kinetic energy usually means more entropy
↑ exergonic reactions have a net release of energy
↑ endergonic reactions absorb/store free energy
↑ catalysts lower the activation energy for a reaction and therefore speed the reaction up
↑ anabolic metabolism builds molecules, requires energy
↑ catabolic metabolism breaks down molecules, produces energy. Cats can really break things down and tear them apart :)
↑ activation energy is the amount of input energy required to start a reaction
↑ reduced fit describes the shape of the enzyme after the substrate has bonded with it
↑ cofactors are nonprotein molecules that aid enzyme catalysis
↑ inhibitors are the reverse of cofactors: they stop enzyme activity. Inhibitors are mostly found in toxins and poisons.
↑ when ATP phosphorylates other molecules, it adds a phosphate group to the reactant, making it more reactive
↑ reduction is the addition of electrons (reduces overall charge)
↑ oxidation is the systematic removal of electrons or loss of electrons
↑ electronegativity is the attraction of an atom for the electrons of a covalent bond. elements on the right side of the periodic table are generally more electronegative

References & Footnotes

↑ Sigma Aldrich. Metabolic Pathways of a Cell. http://www.sigmaaldrich.com/img/assets/4202/MetabolicPathways_6_17_04_.pdf

[autotroph-1] 1.0 ^1.1 autotrophic organisms make their own food

[heterotroph-2] 2.0 ^2.1 heterotrophic organisms get their energy from outside sources

[3] kinetic energy is energy due to active motion

[4] potential energy is energy due to a current position or structure

[5] calorie (little c) is the amount of heat required to raise 1g of water by 1°C

[6] Thermodynamics is the study of the energy flow in natural systems.

[entropy-7] 7.0 ^7.1 entropy is the disorder of the universe. On a smaller scale, more kinetic energy usually means more entropy

[8] exergonic reactions have a net release of energy

[9] endergonic reactions absorb/store free energy

[10] catalysts lower the activation energy for a reaction and therefore speed the reaction up

[11] anabolic metabolism builds molecules, requires energy

[12] catabolic metabolism breaks down molecules, produces energy. Cats can really break things down and tear them apart :)

[14] activation energy is the amount of input energy required to start a reaction

[15] reduced fit describes the shape of the enzyme after the substrate has bonded with it

[16] cofactors are nonprotein molecules that aid enzyme catalysis

[17] inhibitors are the reverse of cofactors: they stop enzyme activity. Inhibitors are mostly found in toxins and poisons.

[18] when ATP phosphorylates other molecules, it adds a phosphate group to the reactant, making it more reactive

[19] reduction is the addition of electrons (reduces overall charge)

[20] oxidation is the systematic removal of electrons or loss of electrons

[21] electronegativity is the attraction of an atom for the electrons of a covalent bond. elements on the right side of the periodic table are generally more electronegative

[13] Sigma Aldrich. Metabolic Pathways of a Cell. http://www.sigmaaldrich.com/img/assets/4202/MetabolicPathways_6_17_04_.pdf

[vocab 1]

[vocab 2]

[vocab 3]

[vocab 4]

[vocab 5]

[vocab 6]

[vocab 7]

[vocab 8]

[vocab 9]

[vocab 10]

[vocab 11]

[vocab 12]

[1]

[vocab 13]

[vocab 14]

[vocab 15]

[vocab 16]

[vocab 17]

[vocab 18]

[vocab 19]

[vocab 20]

BIOL 111 Chapter 8

Contents

Metabolism

BIG Picture

Energy

Thermodynamics ^{[vocab 6]}