Ground Rules of Metabolism
Chapter 6
Hsueh-Fen Juan
Oct. 2, 2012
Impacts, Issues:A Toast to Alcohol Dehydrogenase
In the liver, alcohol dehydrogenase helps break down toxic alcohols, but at the expense of liver function and energy metabolism
Video: Alcohol, enzymes, and your liver
6.1 Energy and the World of Life
Assembly of the molecules of life starts with energy input into living cells
Energy Disperses
First law of thermodynamics• Energy is neither created nor destroyed, but can
be transferred from one form to another
Second law of thermodynamics• Entropy (a measure of dispersal of energy in a
system) increases spontaneously• The entropy of two atoms decreases when a
bond forms between them (endergonic reaction)• 熵要仔細看課本
Motion: A Form Of Energy
Entropy
One Way Flow of Energy
The total amount of energy available in the universe to do work, called free energy, is always decreasing• Each time energy is transferred, some energy
escapes as heat (not useful for doing work)• Free energy 和總能量以熵及相關
On Earth, energy flows from the sun, through producers, then consumers• Living things need a constant input of energy
Energy Conversion
Only about 10% of the energy in food goes toward building body mass, most is lost in energy conversions
Fig. 6-5, p. 95
energy input, mainly from sunlight
ENERGY IN
Sunlight energy reaches environments on Earth. Producers of nearly all ecosystems secure some and convert it to stored forms of energy. They and all other organisms convert stored energy to forms that can drive cellular work.
PRODUCERS plants and other self-
feeding organisms
nutrient cycling
ENERGY OUTCONSUMERS
animals, most fungi, many protists, bacteria
With each conversion, there is a one-way flow of a bit of energy back to the environment. Nutrients cycle between producers and consumers.
energy output, mainly heat
Energy Flow
6.2 Energy in the Molecules of Life
All cells store and retrieve energy in chemical bonds of the molecules of life
Free energy• The amount of energy in a molecule that is
available to do work
Energy In, Energy Out
Reaction• A chemical change that occurs when atoms, ions,
or molecules interact
Reactant• Atoms, ions, or molecules that enter a reaction
Product• Atoms, ions, or molecules remaining at the end of
a reaction
Chemical Reactions
Reactions Require or Release Energy
We can predict whether a reaction requires or releases energy by comparing the bond energies of reactants with those of products
Endergonic (“energy in”)• Reactions that require a net input of energy
Exergonic (“energy out”)• Reactions that end with a net release of energy
Endergonic and Exergonic Reactions
Why the World Doesn’t Go Up in Flames
Activation energy• The minimum amount of energy needed to get a
reaction started• Some reactions require a lot of activation energy,
others do not
Activation Energy
ATP – The Cell’s Energy Currency
ATP (adenosine triphosphate)• A nucleotide with three phosphate groups • Transfers a phosphate group and energy to other
molecules
Phosphorylation• A phosphate-group transfer• ADP binds phosphate in an endergonic reaction
to replenish ATP (ATP/ADP cycle)
Fig. 6-9a, p. 97
Fig. 6-9b, p. 97
Fig. 6-9c, p. 97
Animation: Mitochondrial chemiosmosis
6.1-6.2 Key Concepts:Energy Flow in the World of Life
Energy tends to disperse spontaneously; each time energy is transferred, some of it disperses
Organisms maintain their organization only by continuously harvesting energy
ATP couples reactions that release usable energy with reactions that require energy
6.3 How Enzymes Make Substances React
Enzyme• A catalyst that makes a specific reaction occur
much faster than it would on its own• Enzymes are not consumed or changed by
participating in a reaction• Most are proteins, some are RNA
Substrate• The specific reactant acted upon by an enzyme
How Enzymes Work
Enzymes lower the activation energy required to bring on the transition state, when substrate bonds break and reactions run spontaneously
Active sites• Locations on the enzyme molecule where
substrates bind and reactions proceed• Complementary in shape, size, polarity and
charge to the substrate
Active Site of an Enzyme
Fig. 6-10b, p. 98
Fig. 6-10c, p. 98
Activation Energy
Animation: Activation energy
Animation: Enzymes and activation energy
Mechanisms of Enzyme-Mediated Reactions
Binding at enzyme active sites may bring on the transition state by four mechanisms1. Helping substrates get together (拉近距離 )
2. Orienting substrates in positions that favor reaction (有效碰撞 )
3. Inducing a fit between enzyme and substrate (induced-fit model)
4. Shutting out water molecules (隔絕水分子 )
Effects of Temperature, pH, and Salinity
Raising the temperature boosts reaction rates by increasing a substrate’s energy• But very high temperatures denature enzymes
Each enzyme has an optimum pH range• In humans, most enzymes work at ph 6 to 8
Salt levels affect the hydrogen bonds that hold enzymes in their three-dimensional shape
Enzymes and Temperature
Enzymes and pH
Help from Cofactors
Cofactors• Atoms or molecules (other than proteins) that
are necessary for enzyme function• Example: Iron atoms in catalase• 常固定在酶的內部 (或為結構中心 )、反應後不變
Coenzymes• Organic cofactors such as vitamins• May become modified during a reaction• 細胞質內自由飄移,反應後結構常被改變
Catalase and Cofactors
Catalase is an antioxidant that neutralizes free radicals (atoms or molecules with unpaired electrons that attack biological molecules)
自由基很不好,因為容易搶別人電子讓人氧化,隨著年紀增加,體內自由基含量也會增加。抗氧化劑(通常是酶 )藉由中心金屬吸引自由基的未成對電子以「解毒」 (注意!僅吸引,未進行氧化還原 )
Catalase works by holding a substrate molecule close to one of its iron atoms (cofactors)• Iron pulls on the substrate’s electrons, bringing on
the transition state
6.3 Key Concepts:How Enzymes Work
On their own, reactions proceed too slowly to sustain life
Enzymes tremendously increase the rate of metabolic reactions
Environmental factors such as temperature, salt, and pH influence enzyme function
6.4 Metabolism – Organized, Enzyme-Mediated Reactions
ATP, enzymes, and other molecules interact in organized pathways of metabolism (activities by which cells acquire and use energy)
Types of Metabolic Pathways
A metabolic pathway is any series of enzyme-mediated reactions by which a cell builds, rearranges, or breaks down an organic substance• Anabolic pathways build molecules• Catabolic pathways break apart molecules• Cyclic pathways regenerate a molecule from the
first step (例子:光合作用暗反應的卡爾文循環 )
Controls Over Metabolism
Concentrations of reactants or products can make reactions proceed forward or backward
Feedback mechanisms can adjust enzyme production, or activate or inhibit enzymes
Regulatory molecules can bind to an allosteric site to activate or inhibit enzymes (結構變異區 )• Feedback inhibition
Allosteric Control
Animation: Allosteric activation
Animation: Allosteric inhibition
Feedback Inhibition
Animation: Feedback inhibition
Redox Reactions
Oxidation-reduction reactions (paired reactions)• A molecule that gives up electrons is oxidized• A molecule that accepts electrons is reduced• Coenzymes can accept molecules in redox
reactions (also called electron transfers) (電子轉移者、電子攜帶者… etc.) (NADH, FADH2之類 )
ATP Synthesis
細胞不能承受一次放能太多,要讓放能過程拆解成一個個小步驟,而這些小步驟幾乎都是氧化還原反應
Coenzymes deliver electrons to electron transfer chains for ATP synthesis
Electron transfer chain• A series of redox reactions in membrane-
bound enzymes or molecules (特別注意強調固定在膜上的 ) that release energy in small, controlled steps
Uncontrolled and Controlled Reactions
Overview: Energy Pathways
6.4 Key Concepts:The Nature of Metabolism
Metabolic pathways are energy-driven sequences of enzyme-mediated reactions
They concentrate, convert, or dispose of materials in cells
Controls over enzymes that govern key steps in metabolic pathways can shift cell activities fast
6.5 Night Lights
Bioluminescence is visible evidence of metabolism
Bioluminescence• Light emitted from metabolic reactions in living
organisms
Enzymes of Bioluminescence
Bioluminescent organisms emit light when enzymes (luciferases) convert chemical bond energy in luciferins to light energy
luciferin + ATP → luciferin-ADP + Pi
luciferin-ADP + O2 → oxyluciferin + AMP + CO2 + light
Bioluminescence: Fireflies
A Research Connection
Researchers can transfer genes for bioluminescence from one species to another• Example: bacteria with jellyfish genes
6.5 Key Concepts:Metabolism Everywhere
Knowledge about metabolism, including how enzymes work, can help you interpret some natural phenomena
Key Players in Metabolic Reactions
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