bsc 2010 - exam i lectures and text pages

BSC 2010 - Exam I Lectures and Text Pages• I. Intro to Biology (2-29)

• II. Chemistry of Life– Chemistry review (30-46)

– Water (47-57)

– Carbon (58-67)

– Macromolecules (68-91)

• III. Cells and Membranes– Cell structure (92-123)

– Membranes (124-140)

• IV. Introductory Biochemistry– Energy and Metabolism (141-159)

– Cellular Respiration (160-180)

– Photosynthesis (181-200)

Energy & Metabolism

• Metabolism, Energy and Life– Metabolism = all of an organism’s chemical

rxns and energy conversions

– Metabolism transforms the energy and material resources of a cell

– Cells use energy to perform various types of work

– Metabolic reactions occur in specific pathways, catalyzed by specific enzymes (proteins)

The Energy of Life• The living cell

– Is a miniature factory where thousands of reactions occur

– Converts energy in many ways and uses energy to perform work, such as active transport.

• Some organisms convert energy to light, as in bioluminescence

Figure 8.1

Organization of the Chemistry of Life into Metabolic Pathways

• A metabolic pathway has many steps

– That begin with a specific molecule and end with a product

– That are each catalyzed by a specific enzyme

Enzyme 1 Enzyme 2 Enzyme 3A B C D

Reaction 1 Reaction 2 Reaction 3Starting

moleculeProduct

Catabolic Pathways

– Break down larger molecules into smaller ones

– Release energy that can be captured in the bonds of ATP

– Example: Cellular Respiration (glucose CO2 + H2O + ATP)

Anabolic Pathways

– Synthesize complicated molecules from simpler ones

– Consume energy (use ATP or another E source)

– are biosynthetic pathways (use energy)

– Example: Photosynthesis (CO2 + H2O + sunlight energy O2 + glucose)

Energy Coupling

• Anabolism is fueled by the energy released from catabolism

– Anabolic pathways use the energy produced by catabolic pathways. The transfer of energy is accomplished by ATP.

Forms of Energy

• Energy

– Is the capacity to cause change, to do work, to move or rearrange matter

– Exists in various forms, of which some can perform work

Kinetic Energy

– Is the energy associated with motion/work

– Ex = leg muscles turning a bike wheel

– Heat = thermal energy = kinetic energy assoc. w/ random movement of molecules

– Moving matter does work by transferring its motion to other matter.

Potential Energy

– Is energy stored in the location or structure of matter

– Includes chemical energy – potential energy available from a reaction that is stored in the arrangement of atoms in molecules

Energy Can Be Converted– From one form to

another

– Plants convert light energy (kinetic) into chemical energy (potential) in sugars.

On the platform, a diverhas more potential energy.

Diving converts potentialenergy to kinetic energy.

Climbing up converts kineticenergy of muscle movement to potential energy.

In the water, a diver has less potential energy.

Figure 8.2

Metabolism is Subject to the Laws of Thermodynamics

• An organism’s metabolism transforms matter and energy into various forms, but always subject to the laws of thermodynamics

The Laws of Energy Transformation

• Thermodynamics

– Is the study of energy transformations

• A System = matter under study

– a. Closed system is isolated from surroundings

– b. Open system = energy can be transferred between the system & surroundings

• Ex = organisms

The First Law of Thermodynamics

• According to the first law of thermodynamics energy cannot be created or destroyed

• The energy of the universe is constant. This is the principle of the conservation of energy

• So energy can be transferred & transformed but NOT created or destroyed

Figure 8.3 

First law of thermodynamics: Energy can be transferred or transformed but Neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b).

(a)

Chemicalenergy

The Second Law of Thermodynamics• According to the second law of thermodynamics,

spontaneous changes that do not require outside energy increase the entropy, or disorder, of the universe

Figure 8.3 

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.

(b)

Heat co2

H2O+

The Second Law of Thermodynamics• Every energy transformation/transfer increases the

entropy (disorder) of the universe.

– No energy transfer is 100% efficient, some is always converted to heat.

– Heat (kinetic energy) has a high entropy value. It is the least ordered form of energy.

• Order can increase locally (energy input), but is constantly decreasing globally

– Organisms are low-entropy islands in an increasingly random universe. They live at the expense of free energy. Organisms are open systems and can become more ordered, but only with the input of energy, and that is at the expense of the surroundings. Organisms take in food (a highly ordered form of energy) and put out heat, water, and carbon dioxide.

Biological Order and Disorder

• Living systems

– Increase the entropy of the universe

– Use energy to maintain order50µm

Figure 8.4Buttercup root cross-section

Organisms Live at the Expense of FREE ENERGYThe reactions in our bodies use up energy. Reactions will

only run without the input of additional outside energy IF they are spontaneous reactions. Non-spontaneous reactions require the input of outside energy.

• a. Reactions that happen on their own (w/out energy input) are spontaneous. Spontaneous processes always increase entropy.

• b. “How do we know if a rxn is spontaneous?” It occurs without the input of external energy and it will only do so if it decreases the free energy of the system.

Organisms Live at the Expense of FREE ENERGYGibbs free energy (G) is the portion of a system’s energy

that is available to do work when temperature and pressure are held constant.

• Reactions with a -∆G are spontaneous. Those reactions decrease the total free energy and/or increase the disorder (entropy [S]) and thereby increase the stability of the system.

Change in Free Energy

• The change in free energy, ∆G during a biological process

– Is related directly to the enthalpy change (∆H) and the change in entropy

∆G = ∆H – T∆S

H = enthalpy (total energy in biological systems)S = entropy (disorder, energy not available for work)T = temperature (K = C + 273)

An unstable system is rich in free energy and has a tendency to change to a more stable state and potentially perform work in the process.

Free Energy and Equilibrium or “Why Care About Spontaneity”?

In terms of rxn equilibriums (see Ch 2):

• a. ∆G = Gfinal - Ginitial (smaller value is more stable)

• b. Equilibrium = state of maximum stability

• c. When equilibrium reached G is lowest in that system

• d. In chemical reactions, equilibrium is when the forward and backward reactions proceed at the same rate and ∆G = 0, so no net free energy change.

• e. A cell that has reached equilibrium is DEAD (∆G is lowest & no work can be done)

– Lack of equilibrium (life) maintained by making products of one rxn the reactants of another (with a steady supply of glucose + O2)

– Organisms are open systems. Life is constantly supplied with free E from the sun. That energy must be added to the system to move it away from equilibrium (death).

Free Energy, Stability, and Equilibrium

• Organisms live at the expense of free energy

• During a spontaneous change

– Free energy decreases and the stability of a system increases

At Maximum Stability– The system is at equilibrium

Chemical reaction. In a cell, a sugar molecule is broken down into simpler molecules.

.

Diffusion. Molecules in a drop of dye diffuse until they are randomly dispersed.

Gravitational motion. Objectsmove spontaneously from ahigher altitude to a lower one.

• More free energy (higher G)• Less stable• Greater work capacity

• Less free energy (lower G)• More stable• Less work capacity

In a spontaneously change • The free energy of the system decreases (∆G<0) • The system becomes more stable• The released free energy can be harnessed to do work

(a) (b) (c)

Figure 8.5 

Free Energy and MetabolismFree E and living systems (metabolism):

a. Exergonic rxn (fig 8.6a) = E releasing (negative ∆G) spontaneousThe greater the decrease in ∆G greater amt of work can be doneEx: Respiration∆G for C6H12O6 + O2 6CO2 + 6H2O = -686 kcal/mol

b. Endergonic rxn (fig 8.6b) = E absorbing (positive ∆G) NOT spontaneousSunlight (E) drives photosynthesis (reverse of respiration)∆G for 6CO2 + 6H2O C6H12O6 + O2 = +686 kcal/mol

c. The energy released by an exergonic reaction (-∆G) is equal to the energy required by the reverse endergonic reaction (+∆G)

d. Metabolic disequilibrium is essential to life. Respiration and other cell reactions are reversible and could reach equilibrium if the cell did not maintain a supply of reactants and use up or dispose of products.

e. The cell must couple the energy of exergonic processes to power endergonic processes.

Exergonic and Endergonic Reactions in Metabolism

• An exergonic reaction

– Proceeds with a net release of free energy and is spontaneous

Figure 8.6

Reactants

ProductsEnergy

Progress of the reaction

Amount ofenergyreleased (∆G <0)

Free

ene

rgy

(a) Exergonic reaction: energy released

Exergonic and Endergonic Reactions in Metabolism• An endergonic reaction

– Is one that absorbs free energy from its surroundings and is nonspontaneous

Figure 8.6

Energy

Products

Amount ofenergyrequired (∆G>0)

Reactants

Progress of the reaction

Free

ene

rgy

(b) Endergonic reaction: energy required

Equilibrium and Metabolism

• Reactions in a closed system

– Eventually reach equilibrium

Figure 8.7 A

(a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium.

∆G < 0 ∆G = 0

Maintaining Disequilibrium in Living Systems

• Cells in our body

– Experience a constant flow of materials in and out, preventing metabolic pathways from reaching equilibrium

Figure 8.7

(b) An open hydroelectric system. Flowing water keeps driving the generator because intake and outflow of water keep the system from reaching equlibrium.

∆G < 0

An analogy for cellular respiration

Figure 8.7 (c) A multistep open hydroelectric system. Cellular respiration is analogous to this system: Glucoce is broken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction reaches equilibrium.

∆G < 0∆G < 0

∆G < 0

ATP – Energy Currency of the Cell

ATP powers cellular work by coupling exergonic reactions to endergonic reactions

• Energy coupling

– Is a key feature in the way cells manage their energy resources to do work

• A cell does three main kinds of work

– Mechanical

– Transport

– Chemical

The Structure and Hydrolysis of ATP

• ATP (adenosine triphosphate)

– Is the cell’s energy shuttle

Figure 8.8

O O O O CH2

H

OH OH

H

N

H H

ON C

HC

N CC

N

NH2Adenine

RibosePhosphate groups

O

O O

O

O

O

-- - -

CH

Energy is released from ATP– When the terminal phosphate bond is broken

Figure 8.9

P

Adenosine triphosphate (ATP)

H2O

+ Energy

Inorganic phosphate Adenosine diphosphate (ADP)

PP

P PP i

ATP hydrolysis (and the energy released)– Can be coupled to other reactions

Endergonic reaction: ∆G is positive, reaction is not spontaneous

∆G = +3.4 kcal/molGlu Glu

∆G = - 7.3 kcal/molATP H2O+

+ NH3

ADP +

NH2

Glutamicacid

Ammonia Glutamine

Exergonic reaction: ∆ G is negative, reaction is spontaneous

P

Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous ∆G = –3.9 kcal/molFigure 8.10

How ATP Performs Work

• ATP drives endergonic reactions

– By phosphorylation, ATP transfers a high-energy phosphate to other molecules

– Energy to perform work becomes available when the phosphate is released from its substrate.

The three types of cellular work

• Are powered by the hydrolysis of ATP

(c) Chemical work: ATP phosphorylates key reactants

P

Membraneprotein

Motor protein

P i

Protein moved(a) Mechanical work: ATP phosphorylates motor proteins

ATP

(b) Transport work: ATP phosphorylates transport proteinsSolute

P P i

transportedSolute

GluGlu

NH3

NH2P i

P i

+ +

Reactants: Glutamic acid and ammonia

Product (glutamine)made

ADP+

P

Figure 8.11

The Regeneration of ATP

• Catabolic pathways provide energy to

– Drive the regeneration of ATP from ADP and phosphate

ATP synthesis from ADP + P i requires energy

ATP

ADP + P i

Energy for cellular work(endergonic, energy-consuming processes)

Energy from catabolism(exergonic, energy yieldingprocesses)

ATP hydrolysis to ADP + P i yields energy

Figure 8.12