Metabolism

FADH2

Gibbs Free Energy

Laws of Thermodynamics

ATP

Enzymes

Important Terms

Energy

Metabolism

Thermodynamics

free energy

change in free energy can be calculated by ΔG =ΔH - TΔS

Greek word metabol, meaning change

Metabolism is the totality of an organisms chemical reactions

Metabolic Pathways

Catabolic Pathways

Anabolic Pathways

a specific molecule which is then altered in a series of defined steps, resulting in a certain product

release energy by breaking down complex molecules into simpler compounds. (ex. cellular respiration)

consume energy to build complicated molecules from simpler ones.

known as the capacity to cause change

also called biosynthetic pathways

ex. the synthesis of amino acids from simpler molecules

Types of Energy:

Kinetic

Thermal

Potential

Chemical

energy that is not kinetic, or an object that is not presently moving

energy associated with the relative movement of objects(ex. rollercoaster)

kinetic energy associated with the random movement of atoms or molecules

potential energy available for release a chemical reaction

heat

thermal energy transferred from one object to another

study of energy transformations that occur in a collection of matter

First Law

the energy of the universe is constant

Second Law

every energy transfer or transformation increase the entropy of the universe

energy can be transferred and transformed but it cannot be created or destroyed

entropy

a measure of molecular disorder, randomness

spontaneous process

"energetically favorable"

systems

surroundings

isolated systems

open systems

everything outside of the system

unable to to exchange either energy or matter with its surroundings

energy an matter can be transferred between the system and its surroundings(ex. organisms)

Biological Order/Disorder

Order

Disorder

portion of a systems energy that can perform work when temperature and pressure are uniform throughout the system.

ΔG is only negative when the process involves a loss of free energy during the change from initial state to final state.

ΔH symbolizes the change in the systems enthalpy

ΔS is the change in the systems entropy

T is the absolute temperature in Kelvin(K)

used to measure for any reaction

values will depend on conditions(pH, temperature, and concentrations)

developed by J. Willard Gibbs in 1878

measure of a systems instability, or its tendency to change to a more stable state.

equilibrium is a state of maximum stability

am process is spontaneous and can perform work only when it is moving toward equilibrium

Endergonic

energy inward

Exergonic

energy outward

absorbs free energy from its surroundings

proceeds with a net release of of free energy, when a chemical mixture loses free energy, ΔG is a negative.

stores free energy in molecules, G increases therefore ΔG is positive.

Metabolism is never at equilibrium

cellular respiration reaction: C6H12O6 --> 6 CO2 + 6 H2O

adenosine triphosphate

ATP contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups

used to make RNA

powers cellular work

chemical work

transport work

mechanical work

push of endergonic reactions that would not occur spontaneously (ex. synthesis of polymers and monomers)

pumping substances across membranes against the direction of spontaneous movement

contraction of muscle cells and the movement of chromosomes during cellular reproduction.

energy coupling

how cells manage their energy resources. the use of an exergonic process to drive an endogenic one.

during shivering the body uses ATP hydrolysis during muscle contractions to warm the body.

phosphorylated intermediate

the recipient molecule with the phosphate group covalently bonded to

a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction

activation energy

initial investment of energy, used to start a reaction

transition state

when molecules have absorbed enough energy to for the bonds to break the reactants are in an unstable state

catalysis

process by which a catalyst selectively speeds up a reaction without without itself being consumed

an enzyme cannot change the ΔG for a reaction; it cannot make an endergonic reaction exergonic.

substrate

the reactant an enzyme acts on

enzyme-substrate complex

the enzyme binds to its substrate

active site

pocket or groove on the surface of the enzyme where catalysis occurs

induced fit

tightening the binding after initial contact

saturated

cofactors

non-protein helpers for catalytic activity

coenzyme

an organic cofactor

enzyme inhibitors

competitive

non-competitive

do not directly compete with the substrate to bind to the enzyme at the active site.

reduce productivity of enzymes by blocking substrates from entering active sites.

allosteric regulation

any case in which a proteins function at one site is affected by the binding of a regulatory molecule to a separate site.

cooperativity

amplifies the response of enzymes to substrates

feedback inhibition

a decrease in entropy is said to be non spontaneous--will happen only if energy is supplied

meaning organized

doesn't violate the second law of thermodynamics

un organized

the formation of this is key to coupling exergonic and endergonic reactions

more reactive-less stable, more free energy than the original unphosphorlyated molecule

changes the proteins shape and its ability to bind to other molecules

proteins move along the cytoskeletal track

Regeneration of ATP

ATP is regenerated by the addition of a phosphate to ADP

ATP cycle

muscle cells recycle its entire pool of ATP in under a minute.

free energy must be spent to cause ATP formation

Active Sites:

with two or more reactants the active site will provide a template on which substrate can come together in which order for a proper reaction

enzymes may stretch the substrate molecules toward their transition state from, stressing and bending chemical bonds to be broken during a reaction

active site may provide a microenvironment that is more conductive to a particular type of reaction

amino acids of the enzyme and substrate will covalently bond and restore side chains to their original state so the active site is the same after the reaction as it was prior to

high concentration of substrates means the enzyme is saturated

rate of reaction after this can only be increases by adding more enzymes

more than 4,000 discovered in various species

mutation

permanent change in a gene.

metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway

Cellular Respiration

Photosynthesis

Events in Cellular Respiration

Equation for Cellular Respiration:

Relevant Terms

Events in Photosynthesis

Equation for Photosynthesis:

Relevant Terms

C6 H12 O6 + O6 ----> 6CO2 + 6H2O + ATP

Goal of Cellular Respiration

to generate the energy molecules that serve as the "currency" of energy exchange in the cell called ATP

Important Proteins and Chemicals

How does this relate to Gibbs Free Energy?

6 CO2 + 6 H2O +O2 -- (light)--> C6 H12 O6

Goal of Photosynthesis

converting light into food or sugar molecules.

Important Proteins and Chemicals

How does this relate to Gibbs free energy?

ATP Synthase

1. Glycolysis occurs in the cytoplasm

1. Light Reactions occurs in the thylakoids

2. Pyruvate Oxidation(Intermediate Step)( occurs in the mitochondria)

3. Citric Acid Cycle/Krebs Cycle **(occurs in the matrix of the mitochondria)**

4. Oxidative Phosphorlyation. (occurs in the inner membrane of the mitochondrion)

photo system 2

2. Dark Reactions/Calvin Cycle occurs in the stroma

GLU is taken in by the cells-6 carbon molecules. GLU is then broken into two pyruvates (containing 3 carbons each) (catabolic reaction) (exergonic reaction)

2 pyruvates are transported to the mitochondrion

Acetyl-CoA binds to a 4 carbon molecule called oxaloacetic acid

Start with a net gain of 4 ATP, 10 NADH, and 2 FADH2

Activation energy for this is released in the form of 4 ATPs & 2 NADH coenzymes. (catabolic)(exergonic)

Only 2 of the ATPs are used--there is a net gain of 2 ATPs

if O is not available, NADH will recycle its H ions back onto the pyruvate creating lactic acid

this is called fermentation

in this case only 2 ATP are produced.

one of the 3 carbons are released and bind to oxygen-creating CO2

this CO2 is released as waste by the organism as it respires (exergonic reaction)(catabolic reaction)

the remaining 2 carbons are oxidized = 1 NADH

these 2 carbon molecules are called acetyl-CoA

this forms a 6 carbon molecule called citric acid

this is then broken down. 2 carbons are removed and excreted as waste in the form of CO2 (catabolic reaction) (exergonic reaction)

the remaining 4 carbons bind to another incoming acetyl-CoA

the cycle then repeats, each time producing 1 ATP, 3 NADH, and 1 FADH2

one GLU molecule will generate two turns of the citric acid cycle since it makes two pyruvates

the coenzymes NADH & FADH2 provide electrons to the electron transport chain, embedded in the cristae

electrons are passed from one enzyme to another. enzymes "pump" hydrogen to the inter-membrane(in between the inner and outer) of the mitochondria

this creates a high concentration if hydrogen ions in the INTER membrane space

at the end of the chain the electrons bind to hydrogen ions and oxygen atoms to form a water molecule--the other waste product of cellular respiration

special enzyme called ATP synthase is able to turn low-energy ADP, into high energy molecule. (anabolic reaction)(endergonic reaction)

lactic acid

facilitated diffusion provides the energy for the movement of hydrogen ions from the inter membrane back into the mitochondrial matrix

1 NADH can provide the needed energy via the electron transport chain in order to phosphorylate 3 ADP and turn them into ATP

ATP

1 FADH2 can produce enough energy to phosphorylate 2 ADPs

therefore 1 GLU can produce 10 NADH and 2 FADH2

these molecules enter the electron transport chain to generate up to 34 additional ATPs (exergonic)(catabolic)

electron transport chain

fermentation

cristae

facilitated diffusion

phosphoylate

pyruvate

NADH

respires

FADH2

ADP

Acetyl-oA

cellular respiration is a measure in the change of entropy, or a change in disorder.

when something gains entropy or gains disorder, it loses energy. Which is the process of cellular respiration.

photosynthesis is a measure in the change of enthalpy, or the change in order in a system.

when enthalpy increases there is more order in a system

aerobic respiration

cell wall

cytoplasm

chloroplast

stroma

grana

thylakoids

cytochrome complex

photosystem 1

NADP+ reductionase

ATP synthase

water & light enters through the cell wall and into the membrane of the chloroplast (anabolic)(endergonic)

starts with the ATP produced earlier in the light reactions that was left in the stroma of the thylakoid

this produces oxygen, NADPH, and ATP

sequence of electron carrier molecules that shuttle electrons down a series of redox actions that release energy used to make ATP.

catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces ethyl alcohol or lactic acid

infolding of the inner membrane of the mitochondrion. inner membrane houses electron transport chains and molecules of the enzyme catalyzing the synthesis of ATP

passage of molecules down their concentration gradient; requires no energy

addition of a phosphate to an organic compound

to exhale; breath

catabolic pathway for organic molecules using oxygen as the final electron acceptor in a electron transport chain; ultimately produces ATP

the enzyme responsible for making ATP from ADP and inorganic phosphate

ATP is produced by lactic acid when oxygen is scarce in the body

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1 glucose molecule forms 2 pyruvates

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pyruvate is converted into this, it is fully oxidized giving off CO2

temporarily stores electrons during cellular respiration

1 of 2 light-capturing units in a chloroplast's thylakoid membrane

iron containing protein that is a component of electron transport chains in the mitochondria and chloroplasts

a light capturing unit in the chloroplast's thylakoid membrane

the oxidized form of nicotinamide adenine dinucleotide phosphate; an electron carrier that can accept electrons becoming NADPH- this temporarily stores energized electrons

complex of several membrane proteins that use energy of a hydrogen ion concentration gradient to make ATP

structure of the plant cell (boarder)

the contents of the cell bound by the plasma membrane

organelle in the plant cell responsible for

a microscopic pore surrounded by guard cells in the epidermis of leaves and other stems that allows gas exchange between the environment and the interior of the plant

stacks of thylakoids embedded in the stroma of a chloroplast

structure of the chloroplast organelle responsible for

(the energy produced goes into the Calvin cycle later on) where CO2 goes in and glucoses goes out

light and water enter the first membrane protein called photo system 2

light powers the movement of an electron through an electron transport chain--this electron is changed into NADPH

a water molecule is then split, leaving a oxygen molecule that will leave the cell as a waste product(catabolic) (exergonic)

protons are entered into the inside of the thylakoid

protons exit though ATP Synthase to produce more ATP(catabolic) (exergonic)

1 carbon + 5 carbon(RuBisCo), forming a 6 molecule carbon

this then breaks into a 3 carbon molecule (catabolic) (exergonic)

the molecule then gains energy from ATP + NADPH (anabolic) (endergonic)

the molecule is then transformed into G3P

G3P is then turned into a glucose molecule(something useful to the cell)

G3P is either released or recycled to make RUBP (catabolic) (exergonic)

the cycle then repeats.