The Working Cell - KOCWcontents.kocw.net/KOCW/document/2014/hanyang/bertbinas/... · 2016-09-09 ·...

CHAPTER 5

The Working Cell

The working cell • Energy in biology

• The nature of energy • The molecule ATP and cellular work

• Enzymes – biological catalysis • The nature of catalysis • How enzymes work • The regulation of enzymes

• Functions of biomembranes • Passive transport • Osmosis and water balance • Active transport • Exocytosis and endocytosis

“…there is a certain quantity, which we call energy, that does not change in manifold changes which nature undergoes. … It is not a description of a mechanism, or anything concrete; it is just a strange fact that we can calculate some number, and when we finish watching nature go through her tricks and calculate the number again, it is the same.” Richard Feynman (Physicist, Nobel laureate)

• What is energy?

Some Basic Energy Concepts

•Energy is a capacity of a system to perform work.

•Work is movement of an object against an opposing force (a non-random movement).

•In principle, any change of a system can perform work

Any “hidden energy” or “internal energy” that can be released may be called “potential

energy”

•Mechanical potential

•Energy of chemical bonds

•Energy of bonds between elementary particles in the nucleus

Heat •Is a type of kinetic energy contained in the random motion of atoms and molecules. •Is a product of all energy conversions. •Randomized energy, the energy of aimless molecular movement •It is impossible to convert heat completely into work

•Entropy is the quantitative measure of disorder (= randomness) •Entropy can only increase in an isolated system

Potential energy can never be completely converted into

useful (working) energy = “free energy” of the system, because any change of an isolated system is accompanied by an increase of randomness of the universe (nature’s “heat tax”).

• Robert Mayer formulated the law of energy conservation and he and others calculated the mechanical equivalent of heat.

• He also was the first to describe oxidation as the primary source of energy for life.

• This is one of the rare cases when a major discovery was made by an amateur scientist (a medical doctor)

• Because he was an amateur, Mayer had to fight hard for recognition. He became mentally ill and tried to commit suicide

• The first exact measurement of the mechanical equivalent of heat was made by Prescott Joule ( Joule as modern unit of energy), and Mayer was largely forgotten Robert Julius Mayer, 1814-1878

Conservation of Energy

Copyright © 2007 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Chemical Energy

• How can food molecules provide energy for our cells? • Chemical energy

– Is a form of potential energy. – Arises from the arrangement of atoms – Is found in food, gasoline, and other fuels.

•Respiration is the major form energy “production” in the cell –The combustion of fuel in cells –Is the energy-releasing chemical breakdown of fuel molecules. –Provides energy for the cell to do work. Body heat: keep the body at a constant temperature

• There is no principal difference in the way cars and cells use chemical energy

Efficiency ~ 40%

Efficiency ~ 25%

The car example shows: There is no special form of energy that can be called “biological energy”

•Rather, the energy of a living creature is stored and released simply in the form of chemical energy


Food Calories = kilocalories •1calorie = the amount of energy that raises the temperature of 1g of water by 1 oC. •1 calorie = 4.184 Joule (J) •1,000 calories = 1 kilocalorie (kcal) = 1 “food calorie” (Cal)

•… and burned off by many activities. •Chemical energy is taken with food

Nature uses a universal molecule that transports and delivers energy

•There is a large variety of energy-yielding molecules (“food molecules”) especially sugars, lipids, proteins

•Every type of food molecule is broken down with specialized mechanisms

•There is also a variety of energy-requiring processes (mechanical work, transport work, chemical work)

•The energy-yielding processes need to be coupled to the energy-requiring processes

A

Y

X

Z

W

E D C B

A

Y

X

Z

W

E D C B ATP

5 x 4 = 20 Number of coupling mechanisms between energy-yielding processes A, B, C, D, E and energy-consuming processes W, X, Y, Z

5 + 4 = 9 Number of coupling mechanisms between energy-yielding processes A, B, C, D, E and energy-consuming processes W, X, Y, Z

• The energy coupler ATP reduces the number of coupling mechanisms and is freely diffusible a simple, universal way of energy transport from the site of energy production to the site of energy consumption

• Situation without a universal energy transporter

ATP and Cellular Work •The chemical energy of organic molecules is captured by fermentation and respiration in the form of chemical bonds within ATP

Adenosine triphosphate (ATP)


•ATP (adenosine triphosphate) is a “spring” loaded against electrical charges

• In cells, [ATP] = 1-10 mM, which is ~ 1000x higher than [ADP]

- - - - - -

Adenosine P ∼ P

Adenosine P ∼ P ∼ P Adenosine P ∼ P P +

Adenosine P P +

Adenosine P Adenosine P +

Adenosine P ∼ P ∼ P Adenosine P P P +

7.3 kcal/mol

3.0 kcal/mol

7.3 kcal/mol

14.6 kcal/mol

pyrophosphate

Inorganic phosphate

•High-energy phosphate bonds


Phosphate Transfer •ATP can energize other molecules by transferring phosphate groups. –This energy can be used to drive cellular work.

•Mechanical work

•Transport work

•Chemical work


•The chemical energy is now stored in an intermediate activated form

•Mechanical work: A conformational change in the muscle protein

•Transport work: A conformational change in the membrane protein

•Chemical work: An energy-rich intermediate molecule forms


• ATP is spent on cellular work and regenerated from ADP and Pi through fermentation and respiration

• Energy coupling: The transfer of energy from processes that yield energy to processes that consume energy

• A working muscle cell recycles all of its ATP once each minute (10 million ATP molecules spent and regenerated per second per cell)

The ATP Cycle: Energy Coupling

• ATP is an energy molecule • ATP is a precursor for nucleic acid synthesis

• ATP is a ribonucleotide (oxygen in 2’ position), can together with GTP, CTP, UTP be used for RNA synthesis

• ATP is also precursor of dATP (= desoxyATP) for DNA synthesis

The double life of ATP

Karl Lohmann (1929) No Nobel prize

Discoverer of ATP

Summary – Energy in biology

•Energy is a capacity of a system to perform work. •There are various forms of energy, such as mechanical, chemical, electrical, … •The energy used to sustain life is largely the energy of chemical bonds. •There is no form of energy that would be specific for life: there is no “biological energy”.

•Cells use ATP (adenosine triphosphate) as a universal molecule to transport/deliver energy: •ATP (a “spring-loaded” molecule because of its 3 negative phosphates) has two energy-rich bonds. •Energy-yielding breakdown reactions of ATP are ATP ADP + P or ATP AMP + PP or PP P + P (here, P stands for inorganic phosphate, not for phosphor).

•The phosphate is not simply released (this would only create heat). Rather, the energy-rich phosphate bond is transferred (“phosphate transfer reactions”) to proteins, amino acids, or other molecules.

•Splitting of energy-rich phosphate bonds in proteins causes conformational changes driving muscle contraction (mechanical work) or pumping molecules (transport work); energy-rich phosphate bonds in small molecules are used to synthesize more complex molecules (biosynthetic work).

•ATP is ideal for energy transport and delivery since it is small and water soluble, so it can diffuse well. Using only one type of molecule (ATP) for coupling the various energy-yielding with the various energy-consuming processes also reduces complexity.

•ATP is constantly re-synthesized from ADP (or AMP) and P; the synthesis will be discussed in other lectures.

•The double life of ATP •ATP is a nucleotide, more precisely a ribonucleotide (has oxygen in 2’ position). •As such, there is nothing special in ATP as compared to other nucleotides (GTP, CTP, UTP). •Therefore ATP can also be used for RNA synthesis or (after removal of the 2’ O) for DNA synthesis. •The preferred use of ATP (rather than the other nucleotides) as energy transporter/deliverer probably reflects divisions of labor optimized during evolution.

요약- 생물학에서 에너지

• 에너지는 계 (system)가 일을 할 수 있게 하는 능력이다.

• 기계적, 화학적, 전기적 에너지와 같은 다양한 형태의 에너지가 존재한다. • 생명을 유지하기 위해 사용되는 에너지는 대부분 화학결합 에너지이다. • 생명을 위한 특이적 에너지의 형태는 존재하지 않는다: “생물학적 에너지”는 없다.

• 세포들은 ATP(아데노신 3 인산)를 에너지를 전달/수송하기 위한 보편적인 분자로 사용한다.

• ATP (PO₃³- 때문에 “스프링이 장착된” 분자로 표현된다)는 두 개의 고(高)에너지 결합을 가지고 있다. • ATP의 에너지를 생산하기 위한 분해반응은 ATP → ADP + P 또는 ATP → AMP + PP 또는 PP → P + P (여기에서, P는 인이 아닌, 무기물의 인산염을 의미). • 인산염은 단순히 방출되지 않는다 (오직 열만 생산). 그것보다는, 고 에너지 인산결합은 단백질, 아미노산, 또는 다른 분자로 전달된다 (“인산염 전달 반응”). • 단백질에서 고 에너지 인산결합의 분해는 근육수축을 진행하는 (기계적 일) 형태학적 변화나, 분자 펌핑(pumpinh, 수송의 일)을 유발한다; 작은 분자에서 고 에너지 인산염 결합은 더 복잡한 분자를 합성하기 위해 사용되기도 한다 (생합성적 일). • ATP는 작고 물에 잘 녹기 때문에 에너지 수송과 전달에 이상적이며, 그래서 이것은 잘 확산될 수 있다. 다양한 에너지 소비과정을 다양한 에너지 생산과 연결하기 위해, 오직 한 종류의 분자 (ATP)를 사용하는 것은 또한 복잡성을 줄일 수 있다. • ATP는 ADP (또는 AMP) 와 P로부터 지속적으로 재합성될 수 있다; 합성은 다른 강의에서 다시 논의될 것이다.

• ATP의 또 다른 역할.

• ATP는 뉴클레오타이드, 더 정확하게는 리보뉴클레오타이드 (2‘ 위치에 산소를 가진다)이다. • 다른 뉴클레오타이드 (GTP, CTP, UTP)와 비교하였을 때, ATP는 특별한 분자가 아니다. • 결과적으로 ATP는 또한 RNA 합성 또는 DNA 합성 (2' 위치에 산소 제거 후)에 사용될 수 있다. • 에너지의 수송자/전달자로서 ATP의(다른 뉴클레오타이드보다) 호의적 사용은 아마도 진화하는 동안 최적화된 일의 분배를 반영한 것일 것이다.

• Energy in biology • The nature of energy • The molecule ATP and cellular work

• Enzymes – biological catalysis • The nature of catalysis • How enzymes work • The regulation of enzymes

• Functions of biomembranes • Passive transport • Osmosis and water balance • Active transport • Exocytosis and endocytosis


Enzymes

• Metabolism is the sum of all chemical reactions in an organism.

• Most metabolic reactions are facilitated by catalysts

• Catalysts are substances that facilitate chemical reactions without being consumed

• Enzymes are biomolecules with catalytic ability

• Biocatalysis was first shown by E. Buchner ~1900: yeast extracts can ferment glucose

• By 1930, it was shown that enzymes are proteins

• In the 1980s, it was discovered that RNA molecules can also be enzymes (“ribozymes”)

Eduard Buchner, Nobel Prize 1907

The nature of enzyme catalysis

• Every chemical reaction has an energy barrier that requires an activation energy to overcome

• Catalysts, including enzymes, lower this barrier

How does an enzyme lower the activation energy?

•Every chemical reaction goes through a transition state •The catalyst (enzyme) stabilizes this transition state

What is so special about enzymes compared to simple catalysts?

Enzymes are extremely specific

• The region in the enzyme that creates the stabilizing environment is called the active site.

• Enzymes are extremely specific because they recognize the shape of the reactant molecules (= enzyme substrate)

• The ability of the enzyme to recognize and bind to its specific substrate depends on the enzyme’s shape.

• Proximity Effect. The active site brings the reactants together for collision. The effective concentration of the reactants is increased; this also favors transition state formation.

• Orientation Effect. Substrate collisions in solution are random and are less likely to be the specific orientation that promotes the approach to the transition state. The amino acids that form the active site orient the substrate.

• Promotion of Acid-Base Reactions. For many enzymes, the amino acids that form the active site have functional side chains that donate or accept hydrogen ions from the substrate.

• Exclusion of Water. Most active sites are somewhat hydrophobic to exclude water. This nonpolar environment can lower the activation energy for certain reactions. In addition, substrate binding to the enzyme is mediated by many weak non-covalent interactions. The presence of water with the substrate can often disrupt these interactions.

How does the active site work?

http://en.wikipedia.org/wiki/Enzyme

Induced fit

•When a substrate molecule slips into the active site, the active site changes shape slightly.

•This interaction is called “induced fit”.

Enzyme Regulators

I. Competitive inhibitors (Substrate imposters) = usually artificial compounds or natural poisons

Inhibitor: Viagra Normal enzyme substrate: cGMP (cyclic Guanosine monophosphate)

Example of competitive enzyme inhibitor

Enzyme: cGMP specific phosphodiesterase type 5

Note that the two molecules are structurally similar but not identical

II. Allosteric regulators (inhibitors and activators) bind at a remote site (allo = different steric = spatial location)

Allosteric regulators are the most important regulators of enzyme activity in the living cell

A frequent and important case of allosteric inhibition: Negative feedback by final product of a metabolic pathway

Example of an allosteric inhibitor

Enzyme 3 Enzymes at the crossroads of biochemical pathways integrate information of multiple allosteric signals Glucose Glycogen

CO2 + H2O

Nucleotides

Enzyme 1

Enzy

me

2

Allosteric enzymes act like analog computers

http://flipper.diff.org/app/items/info/5362

Multienzyme complexes efficiently couple consecutive reaction steps

• Reduces diffusion paths and increases local concentrations

• Requires mutual recognition of enzymes

Why are biological catalysts (enzymes) large compared to simple catalysts? • Cell compartments perform multiple chemical reactions in a highly complex

mix of small organic molecules Need for selective and specific binding of substrate ability of enzymes to form very specific, complex shapes

• Cell milieu not optimal for the given reaction Need for a optimized local milieu ability of form “nanomilieu” in “cavities”

• Changing needs for products Need for integrating regulatory inputs by many different compounds allostery

• Coupling of consecutive chemical reactions Formation of multienzyme complexes Need for specific interaction with other proteins

Summary: Why are enzymes large?

Summary – Enzymes

•Catalysts = Substances that facilitate chemical reactions without being consumed. •Enzymes = Biomacromolecules (proteins or RNA) with catalytic ability.

•For many years, it was thought that all enzymes are proteins, now it’s known that RNA can also be.

•Nature of catalysis: Lower the activation energy of a reaction. •Mechanism: Increase the probability of formation of transition state / stabilize the transition state. This is achieved by proximity effect, orientation effect, promotion of acid-base reactions, or exclusion of water.

•Catalysis does not require an input of energy.

•What is special about enzymes compared to simple catalysts? •Presence of multiple metabolites in a mix need for more selective substrate binding substrate binding sites have complex shapes. Shapes of active sites change slightly upon binding (induced fit).

•Co-occurrence of multiple chemical reactions in the cell creation of an optimized nanomilieu for each given reaction by formation of “cavity” (active site).

•Changing physiological conditions need for enzyme regulation (usually the rate-limiting enzymes of a pathway) need to integrate multiple inputs need for allosteric binding sites with complex shapes, and need for ability to switch between different conformations.

•Optimization of pathways: Coupling of consecutive chemical reactions in multienzyme complexes need for specific binding sites for other enzymes.

All these functions require the enzyme to be a very large, flexible molecule.

•Regulatory properties make many enzymes “nanocomputers”. •Allosteric regulation is the natural form of regulation. Typical case is negative feedback of first enzyme of a pathway by end product. Inputs by alternative pathways are also common. •Competitive inhibitors, which clog the catalytic site, play a major role as medical drugs.

요약- 효소 • 촉매 = 기질을 소비 없이 화학반응 시키는 것.

• 효소 = 촉매능력이 있는 생체고분자 (단백질 또는 RNA).

• 오랜 시간 동안, 모든 효소는 단백질이라 생각되어왔으나, 현재는 RNA 또한 가능하다고 밝혀졌다.

• 촉매의 특징: 반응의 활성화 에너지를 낮춤.

• 기작: 전이상태의 형성 가능성을 증가시키거나 안정화시킴. 거리상의 가까움에 의한 효과, 방향에 의한 효과, 산-염기 반응의 촉진 또는 탈수반응에 의한 효과에 의해 이루어진다.

• 촉매는 에너지의 투입이 필요하지 않다.

• 단순한 촉매제와 비교하였을 때 효소는 무엇이 특별한가? • 혼합물 내 다중 대사 산물이 존재 → 더 선택적인 기질 결합이 필요 → 기질 결합 부위는 복잡한 형태를 가짐. 활성화 부위의 형태는 결합할 때 약간 변한다 (유도적합).

• 세포 내 다중 화학반응이 동시발생 → “공동 (空洞,cavity)”의 형성 (활성화 부위)에 의해 각 주어진 반응에 대한 최적화된 미세환경을 형성함.

• 생리학적 조건의 변화 → 효소조절이 필요 (일반적으로 반응속도를 결정하는 효소, rate-limiting enzyme) → 다중 투입물의 통합이 필요 → 복잡한 형태를 가진 입체구조적 결합부위와 다른 형태 사이의 전환능력이 필요.

• 대사경로의 최적화: 다중 효소 복합체에서 연속적인 화학반응의 결합. → 다른 효소들에 대한 특이적 결합 부위가 필요. → 이들 모든 기능은 효소가 매우 크고 유연한 분자가 되어야 가능하다.

• 조절 특징들은 많은 효소들을 “초미세 컴퓨터” 로 만든다.

• 입체구조적 조절은 조절의 자연적인 형태이다. 일반적인 형태는 최종산물이 첫 번째 효소의 대사를 방해하는 네거티브 피드백 (negative feedback)이 있다. 대체경로에 의한 투입물 역시 일반적이다.

• 촉매 부위를 막는 경쟁적 저해제는 약품으로서 주요한 역할을 한다.

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