AP Biology, Chapter 6
An Introduction to Metabolism

Summary
Introduction

METABOLISM, ENERGY, AND LIFE
	Intro
	The chemistry of life is organized into metabolic pathways
	1. Contrast catabolic and anabolic pathways and describe their energetic relationship. 
			a. Catabolism breaks down molecules, anabolism builds them up
			b. Catabolism harnesses energy as ATP, anabolism uses that energy
	Organisms transform energy
		2. Define potential energy, kinetic energy, open system, closed system.
			a. Potential energy = energy stored by position or structure
			b. Kinetic energy = energy of motion
			c. Open system = matter and energy can enter or leave
			d. Closed system = matter and energy cannot enter or leave
	The energy transformations of life are subject to two laws of thermodynamics
		3. Explain the first and second laws of thermodynamics.
			a. 1st law
				i. Energy can be transformed but neither created nor destroyed
				ii. Except in radioactive decay, nuclear fusion, quantum fluctuations, 
				photon-photon interactions, etc.
			b. 2nd law
				i. In every process, system entropy increases
				ii. Matter scatters and/or energy dissipates
		4. Explain why highly ordered living systems do not violate the second law of 
		thermodynamics.
			a. Living systems are open systems
			b. As they order matter into proteins, new cells, etc. the degrade energy
	Organisms live at the expense of free energy
		5. What types of systems tend to change spontaneously?
			a. ΔG < 0
			b. Examples
				i. A lot of heat is given off like burning, respiration, explosion
				ii. Molecules breakdown into many smaller molecules like digestion
		6. Write and define each component of the equation for free-energy change.
			a. ΔG = ΔH - TΔS
				i. ΔG is the free energy of the system
				ii. ΔH is the heat content or enthalpy of the system
				iii. TΔS is the entropy which increases with temperature
			b. Two types of reactions
				i. Exergonic, ΔG < 0, releases free energy
				ii. Endergonic, ΔG > 0, absorbs free energy
		7. Explain how changes in temperature influence the maximum amount of usable energy 
		that can be harvested from a reaction.
			a. Amount of entropy (disorder) is subtracted from the usable energy
			b. The greater the temperature, the larger the entropy term becomes
		8. Describe the relationship between free energy and equilibrium.
			a. In general, reactions are reversible
			b. Energy is present in the form of photons and the motions of the molecules
			c. A large negative ΔG will drive the reaction one direction
			d. The opposite, endergonic, reaction will occasionally occur
			e. Equilibrium = when the rates are the same, cancel each other out, and ΔG=0
		9. Explain why metabolic disequilibrium is one of the defining features of life.
			a. Organisms are constantly degrading energy and scattering matter
			b. Organisms require matter and high-quality energy from our environment
			c. ΔG < 0
	ATP powers cellular work by coupling exergonic reactions to endergonic reactions
		10. Describe three main types of cellular work.
			a. Mechanical: organisms, cells and parts of cells move
			b. Transport: actively, across membranes against diffusion
			c. Chemical: coupling endergonic reactions with exergonic reactions
		11. Describe the function of ATP in a cell.
			a. Temporarily stores small amounts of chemical energy
		12. List the three components of ATP and identify the major class of macromolecules to 
		which ATP belongs.
			a. ATP = adenine + ribose + 3phosphate
			b. Required for nucleic acid synthesis
		13. Explain how ATP performs cellular work.
			a. Adds energy by phosphorylation = transferring high-energy phosphate
			b. Example
				i. Glutamic acid + ammonia  glutamine; ΔG = +3.4 kcal/mole; non-
				spontaneous
				ii. ATP  ADP + Pi; ΔG = -7.3 kcal/mole; spontaneous
				iii. Coupled (added) together; ΔG = -3.9 kcal/mole; spontaneous
				iv. Starts with ATP + glutamine  glutamine-P + ADP

ENZYMES
	Intro
	Enzymes speed up metabolic reactions by lowering energy barriers
		14. Describe the function of enzymes in biological systems.
			a. Change the rate of chemical reactions but aren't consumed
			b. Lowers the amount of activation energy required to reach transition state
			c. Does not change ΔG
	Enzymes are substrate-specific
		15. Explain the relationship between enzyme structure and enzyme specificity.
			a. Active site shape matches substrate shape
			b. Most enzymes are very specific for substrates of a certain shape
		16. Explain the induced-fit model of enzyme function and describe the catalytic cycle of 
		an enzyme.
			a. Induced fit 
				i. Substrate enters the active site
				ii. Weak bonds form to hold it there
				iii. Enzyme pulls on substrate, substrate pulls on and flexes the enzyme
			b. Catalytic cycle
				i. Enzyme and substrate are available
				ii. Substrate binds to enzyme (= enzyme-substrate complex)
				iii. Substrate is converted to product(s)
				iv. Product(s) released
	The active site is an enzyme’s catalytic center
		17. Describe several mechanisms by which enzymes lower activation energy.
			a. Hold reactants in the proper orientation
			b. Bend and stretch the bond that needs to break
			c. Active site may have acidic side chains for low pH reactions
			d. Active site may directly, covalently, participate
		18. Explain how substrate concentration affects the rate of an enzyme-controlled 
		reaction.
			a. Initially, the more substrate, the faster the reaction
			b. When active site is always occupied, further increases have no effect
	A cell’s physical and chemical environment affects enzyme activity
		19. Explain how enzyme activity can be regulated or controlled by environmental factors, 
		co-factors, and enzyme inhibitors.
			a. Increased temperature
				i. Faster motion, faster reaction
				ii. Above optimum active site becomes unstable
			b. pH
				i. Acid may be required for the reaction
				ii. Outside an acceptable range the active site changes shape
			c. Cofactors
				i. Metals, vitamins required besides the amino acid chain
				ii. May store energy or bind reactants
			d. Enzyme inhibitors
				i. Competitive have shape similar to substrate, block active site
				ii. Non-competitive bind elsewhere, change the shape of active site	

THE CONTROL OF METABOLISM
	Metabolic control often depends on allosteric regulation
		20. Explain how metabolic pathways are regulated.
			a. Allosteric regulation
				i. Allosteric activators and inhibitors bind where subunits join
				ii. Activators stabilize the subunits in active shape
				iii. Inhibitors stabilize the subunits in nonfunctional shape
			b. Feedback inhibition
				i. Synthetic pathways are assembly lines of enzymes
				ii. Once enough end-product of a pathway is made it inhibits the first 
				enzyme in the pathway
			c. Cooperativity: binding of substrate in one active site stabilizes the others
	The localization of enzymes within a cell helps order metabolism
		21. Explain how the location of enzymes in a cell influences metabolism.
			a. Multienzyme complexes help organize pathways
			b. Synthetic pathways may require delivery of enzymes into an organelle in a 
			specific order
			
	The theme of emergent properties is manifest in the chemistry of life:  a review