Green- touched on in class

Bioenergetics is the study of what?

Yellow- key concepts  

Bio 126 Notes Week 5

TEXTBOOK CHAPTER 8

An Introduction to Metabolism  

An organism’s metabolism transforms matter and energy, subject to  the laws of thermodynamics (8.1)  

∙ Metabolism: the totality of an organism’s chemical reactions  o Occurs in a metabolic pathway that begins with a specific  molecule  

o Manages material and energy resources of the cell

o Catabolic pathways release energy by breaking down complex  molecules into simpler compounds -> cellular respiration  o Anabolic pathways consume energy to build complex  molecules (biosynthetic)  

Catabolic pathways refer to what?

 EX: synthesis of amino acids  

o Bioenergetics: study how energy flows through a living  organism  

∙ Energy is the capacity to change

o Kinetic energy is the relative motion of objects

o Thermal: kinetic energy associated with random movement of  atoms and molecules, in transfer it is called heat

o Potential energy: the object is not presently moving but  energy the matter possesses is due to its location or structure  o Chemical energy is potential energy that is available in a  reaction Don't forget about the age old question of What is the difference between carbon-12 and its isotope carbon-14?

∙ Thermodynamics: the study of energy transfer in atoms that occur in matter (an isolated system, one that can’t exchange energy or matter  with surroundings, vs an open system)  

Anabolic pathways refer to what?

o 1st Law of thermodynamics: the energy in universe is  constant, it cannot be created or destroyed; the conservation of  energy  

o 2nd law of thermodynamics: every energy transfer or  transformation increases the entropy of the universe  

 entropy: a measure of disorder/randomness, helps  

describe why some processes are energetically favorable  and occur on their own (in a spontaneous process, the  

process leads to increased entropy, can proceed without  

requiring energy input, vs unspontaneous process), in  

the universe, a closed system, it is continuously increasing

 organisms cannot create energy they must capture energy from their surroundings  

o energy flows into most ecosystems as light energy and exits as  heat We also discuss several other topics like What is the equipartition theorem?

The free-energy change of a reaction tells us whether of not the  reaction occurs spontaneously (8.2)  

∙ the universe is equivalent to “the system” plus “the surroundings”  ∙ free energy: the portion of a systems energy that can perform work  when the temperature and the pressure are uniform throughout the  system (represented by ΔG)  

o chemical reaction ΔG = ΔH - TΔS

o Δ H = change in enthalpy (total energy)

o Δ S = change in systems entropy

o T = absolute temperature in Kelvin  

o Tells us if a process is spontaneous (Δ G (-) then the reaction is  spontaneous), allows us to predict which change can happen  without the input of energy  

o Δ G = G final state – G initial state, Δ G can be (-) only when  process involves less free energy  

o free energy is the measurement of a systems instability (the  higher the free energy the more unstable)  

o equilibrium describes stability  

∙ Chemical reactions can be:  Don't forget about the age old question of What are the four types of regime change?

o Exergonic reaction: process with net release of free energy.  Because a chemical mixture loses free energy (G decreases), Δ G is (-), meaning it occurs spontaneously. The magnitude of Δ G  represents the maximum amount of work the reaction can  perform, catabolic  We also discuss several other topics like Which hormone is produced by the hypothalamus and stored in the posterior pituitary?

o Endergonic reaction: one that absorbs free energy from its  surroundings, essentially stores free energy in molecules so the  Δ G is (+), meaning it is unspontaneous. The magnitude of Δ G is the quantity of energy to drive a reaction, anabolic 

∙ Metabolism as a whole is never at equilibrium  

ATP powers cellular work by coupling exergonic reactions to  endergonic reactions (8.3)  

∙ A cell does three main kinds of work:

o Chemical: pushing of endergonic reactions that would not  occur spontaneously (the synthesis of polymers from monomers) o Transport: pumping of substances across membranes against  direction of spontaneous movement

o Mechanical: beating of cilia, contraction of muscle cells  ∙ Energy coupling: use of an exergonic process to drive and  endergonic one; ATP does this mostly, ATP links endergonic and  exergonic reactions If you want to learn more check out Discuss each of the four economic resources.

∙ ATP: immediate energy for cell; sugar ribose, nitrogenous base  adenine, and a change of 3 phosphate groups that can be broke down  by hydrolysis  

o When thermal phosphate (third phosphate group, high energy  phosphate)is broken, ADP is produced

o ATP + H2O -> ADP + Pi  

o Δ G = -7.3 kcal/mol  

∙ cell proteins harness energy released during ATP hydrolysis in several ways to performs 3 types of cellular work  

∙ if Δ G of endergonic reaction is less that the amount of energy  released by ATP, then 2 reactions are coupled so it becomes exergonic o usually involves phosphorylation (the transfer of phosphorus  group from ATP to another molecule)  

o The recipient molecule bonded with the phosphate group  covalently in a process is called the phosphorylates  

intermediate

∙ Transport/mechanical functions are nearly always powered by he  hydrolysis of ATD  

o Leads to change in proteins shape and often its ability to bind to another molecule  Don't forget about the age old question of How do rocks melt?

∙ ATP cycle is endergonic: ADP + Pi -> ATP + H2O  

Enzymes speed up metabolic reactions by lowering energy barriers  (8.4)  

∙ Recall: an enzyme is a macromolecule that acts as a catalyst, it speeds up reactions without being consumed by it  

∙ Initial investment of energy for starting reaction is called the  activation energy (EA), oftentimes it is heat

∙ An enzyme lowers the activation energy required for a reaction ∙ The transition state occurs when the energy equivalent has been  absorbed  

∙ The laws of thermodynamics favor the breakdown of proteins, DNA,  and other cell molecules (has the potential to decompose  spontaneously)  

∙ Instead of heat (which kills cells at certain temps and speeds up all  reactions not just the ones needed) cells use catalysts (enzymes)  o Lowers the EA barrier  

∙ Substrate: reactant enzyme acts on, binds forming enzyme  substrate complex

o Enzyme + substrate = enzyme substrate complex – enzyme +  product(s)

∙ The area the enzyme binds to the substrate is called the active site o It is induced to fit between the substrate and enzyme, helps  break and form bonds 

∙ In most enzymatic reactions, the enzyme and the substrate are held  together by hydrogen and ionic bongs  

∙ Most metabolic reactions are reversible, it depends mainly on the  relative concentration of reactants and products. Reactions ALWAYS go towards equilibrium  

∙ Enzymes operate under optimal conditions  

o Up to a point, increased temperature speeds up reactions- past  that point it drops. (most human optimal temperature is 34-40o C/ pH 6-8)

∙ Cofactors: nonprotein helpers for enzymatic reactions, can be  bound/permanent residents (most are inorganic, of organic it is called  a coenzyme)  

∙ Inhibitors are:

o competitive: they reduce productivity by blocking substrates o noncompetitive: do not directly compete but decreases  production, binds at a different site and alters the shape of the  enzyme

 both are reversible 

o An inhibitor is irreversible if it is bound and stops the enzyme  completely 

∙ EVOLUTION -> enzymes were created by a mutation that occurred  and it was favored over time  

Regulation of enzyme activity helps control metabolism (8.5)  

∙ Regulatory molecules change enzymes shape and the functioning of the active site by binding to the enzyme at another site  

∙ Allosteric regulation proteins function at one site affected by  binding of regulatory molecule to separate site -> inhibition and  stimulation

∙ ADP and Pi play a role in balancing the flow between  

anabolic/catabolic pathways

∙ Cooperactivity: substrate binds to 1 active site in a multisubunit  enzyme, it triggers shape change in all the subunits

∙ Feedback inhibition: metabolic pathway is halted by inhibitory  binding of the product to enzyme that cats early in the pathway, the  end product inhibits the earlier reaction- enzymes keep doing what  theyre doing until they are broken down or shut off  

∙ Closed system

o no energy exchange with surroundings

∙ open system  

o organisms  

o exchange energy with surroundings  

∙ KEY  

o Energy can’t be created or destroyed 

o Organisms are open systems, they Use energy from surrounding to do work  

o Processes involved with evolution are consistent with the laws  of thermodynamics  

∙ Catabolism  

o degregation of large complex molecules into simpler smaller  ones

o exergonic  

∙ anabolism 

o synthesis of complex molecules from smaller ones

o endergonic  

∙ photoautotrophs 

o use light energy as source of energy  

o incorporate atmospheric carbon dioxide into organic molecules ∙ chemoheterotrophs  

o obtain energy by oxidizing chemicals

o obtain carbon from other organisms

o thought to be the first organisms on earth  

∙ photosynthesis 

o light energy is converted to chemical energy (carbohydrates)  o hydrogens from water reduce carbon dioxide  

o oxygen from water is oxidized

Green- touched on in class

Yellow- key concepts  

Bio 126 Notes Week 5

TEXTBOOK CHAPTER 8

An Introduction to Metabolism  

An organism’s metabolism transforms matter and energy, subject to  the laws of thermodynamics (8.1)  

∙ Metabolism: the totality of an organism’s chemical reactions  o Occurs in a metabolic pathway that begins with a specific  molecule  

o Manages material and energy resources of the cell

o Catabolic pathways release energy by breaking down complex  molecules into simpler compounds -> cellular respiration  o Anabolic pathways consume energy to build complex  molecules (biosynthetic)  

 EX: synthesis of amino acids  

o Bioenergetics: study how energy flows through a living  organism  

∙ Energy is the capacity to change

o Kinetic energy is the relative motion of objects

o Thermal: kinetic energy associated with random movement of  atoms and molecules, in transfer it is called heat

o Potential energy: the object is not presently moving but  energy the matter possesses is due to its location or structure  o Chemical energy is potential energy that is available in a  reaction

∙ Thermodynamics: the study of energy transfer in atoms that occur in matter (an isolated system, one that can’t exchange energy or matter  with surroundings, vs an open system)  

o 1st Law of thermodynamics: the energy in universe is  constant, it cannot be created or destroyed; the conservation of  energy  

o 2nd law of thermodynamics: every energy transfer or  transformation increases the entropy of the universe  

 entropy: a measure of disorder/randomness, helps  

describe why some processes are energetically favorable  and occur on their own (in a spontaneous process, the  

process leads to increased entropy, can proceed without  

requiring energy input, vs unspontaneous process), in  

the universe, a closed system, it is continuously increasing

 organisms cannot create energy they must capture energy from their surroundings  

o energy flows into most ecosystems as light energy and exits as  heat 

The free-energy change of a reaction tells us whether of not the  reaction occurs spontaneously (8.2)  

∙ the universe is equivalent to “the system” plus “the surroundings”  ∙ free energy: the portion of a systems energy that can perform work  when the temperature and the pressure are uniform throughout the  system (represented by ΔG)  

o chemical reaction ΔG = ΔH - TΔS

o Δ H = change in enthalpy (total energy)

o Δ S = change in systems entropy

o T = absolute temperature in Kelvin  

o Tells us if a process is spontaneous (Δ G (-) then the reaction is  spontaneous), allows us to predict which change can happen  without the input of energy  

o Δ G = G final state – G initial state, Δ G can be (-) only when  process involves less free energy  

o free energy is the measurement of a systems instability (the  higher the free energy the more unstable)  

o equilibrium describes stability  

∙ Chemical reactions can be:  

o Exergonic reaction: process with net release of free energy.  Because a chemical mixture loses free energy (G decreases), Δ G is (-), meaning it occurs spontaneously. The magnitude of Δ G  represents the maximum amount of work the reaction can  perform, catabolic  

o Endergonic reaction: one that absorbs free energy from its  surroundings, essentially stores free energy in molecules so the  Δ G is (+), meaning it is unspontaneous. The magnitude of Δ G is the quantity of energy to drive a reaction, anabolic 

∙ Metabolism as a whole is never at equilibrium  

ATP powers cellular work by coupling exergonic reactions to  endergonic reactions (8.3)  

∙ A cell does three main kinds of work:

o Chemical: pushing of endergonic reactions that would not  occur spontaneously (the synthesis of polymers from monomers) o Transport: pumping of substances across membranes against  direction of spontaneous movement

o Mechanical: beating of cilia, contraction of muscle cells  ∙ Energy coupling: use of an exergonic process to drive and  endergonic one; ATP does this mostly, ATP links endergonic and  exergonic reactions 

∙ ATP: immediate energy for cell; sugar ribose, nitrogenous base  adenine, and a change of 3 phosphate groups that can be broke down  by hydrolysis  

o When thermal phosphate (third phosphate group, high energy  phosphate)is broken, ADP is produced

o ATP + H2O -> ADP + Pi  

o Δ G = -7.3 kcal/mol  

∙ cell proteins harness energy released during ATP hydrolysis in several ways to performs 3 types of cellular work  

∙ if Δ G of endergonic reaction is less that the amount of energy  released by ATP, then 2 reactions are coupled so it becomes exergonic o usually involves phosphorylation (the transfer of phosphorus  group from ATP to another molecule)  

o The recipient molecule bonded with the phosphate group  covalently in a process is called the phosphorylates  

intermediate

∙ Transport/mechanical functions are nearly always powered by he  hydrolysis of ATD  

o Leads to change in proteins shape and often its ability to bind to another molecule  

∙ ATP cycle is endergonic: ADP + Pi -> ATP + H2O  

Enzymes speed up metabolic reactions by lowering energy barriers  (8.4)  

∙ Recall: an enzyme is a macromolecule that acts as a catalyst, it speeds up reactions without being consumed by it  

∙ Initial investment of energy for starting reaction is called the  activation energy (EA), oftentimes it is heat

∙ An enzyme lowers the activation energy required for a reaction ∙ The transition state occurs when the energy equivalent has been  absorbed  

∙ The laws of thermodynamics favor the breakdown of proteins, DNA,  and other cell molecules (has the potential to decompose  spontaneously)  

∙ Instead of heat (which kills cells at certain temps and speeds up all  reactions not just the ones needed) cells use catalysts (enzymes)  o Lowers the EA barrier  

∙ Substrate: reactant enzyme acts on, binds forming enzyme  substrate complex

o Enzyme + substrate = enzyme substrate complex – enzyme +  product(s)

∙ The area the enzyme binds to the substrate is called the active site o It is induced to fit between the substrate and enzyme, helps  break and form bonds 

∙ In most enzymatic reactions, the enzyme and the substrate are held  together by hydrogen and ionic bongs  

∙ Most metabolic reactions are reversible, it depends mainly on the  relative concentration of reactants and products. Reactions ALWAYS go towards equilibrium  

∙ Enzymes operate under optimal conditions  

o Up to a point, increased temperature speeds up reactions- past  that point it drops. (most human optimal temperature is 34-40o C/ pH 6-8)

∙ Cofactors: nonprotein helpers for enzymatic reactions, can be  bound/permanent residents (most are inorganic, of organic it is called  a coenzyme)  

∙ Inhibitors are:

o competitive: they reduce productivity by blocking substrates o noncompetitive: do not directly compete but decreases  production, binds at a different site and alters the shape of the  enzyme

 both are reversible 

o An inhibitor is irreversible if it is bound and stops the enzyme  completely 

∙ EVOLUTION -> enzymes were created by a mutation that occurred  and it was favored over time  

Regulation of enzyme activity helps control metabolism (8.5)  

∙ Regulatory molecules change enzymes shape and the functioning of the active site by binding to the enzyme at another site  

∙ Allosteric regulation proteins function at one site affected by  binding of regulatory molecule to separate site -> inhibition and  stimulation

∙ ADP and Pi play a role in balancing the flow between  

anabolic/catabolic pathways

∙ Cooperactivity: substrate binds to 1 active site in a multisubunit  enzyme, it triggers shape change in all the subunits

∙ Feedback inhibition: metabolic pathway is halted by inhibitory  binding of the product to enzyme that cats early in the pathway, the  end product inhibits the earlier reaction- enzymes keep doing what  theyre doing until they are broken down or shut off  

∙ Closed system

o no energy exchange with surroundings

∙ open system  

o organisms  

o exchange energy with surroundings  

∙ KEY  

o Energy can’t be created or destroyed 

o Organisms are open systems, they Use energy from surrounding to do work  

o Processes involved with evolution are consistent with the laws  of thermodynamics  

∙ Catabolism  

o degregation of large complex molecules into simpler smaller  ones

o exergonic  

∙ anabolism 

o synthesis of complex molecules from smaller ones

o endergonic  

∙ photoautotrophs 

o use light energy as source of energy  

o incorporate atmospheric carbon dioxide into organic molecules ∙ chemoheterotrophs  

o obtain energy by oxidizing chemicals

o obtain carbon from other organisms

o thought to be the first organisms on earth  

∙ photosynthesis 

o light energy is converted to chemical energy (carbohydrates)  o hydrogens from water reduce carbon dioxide  

o oxygen from water is oxidized