Bio 12o Unit 3 Flashcards
Chapter 8, 9, and 10
2 Types of Energy Exist: Kinetic and Potential Energy
Kinetic: energy in motion
Potential: energy that is stored in position
1st Law of Thermodynamics
Energy can not be created or destroyed it can only be transfer or transformed
Potential Energy in Bonds= Chemical Energy
-Depends on positioned electrons
-Weaker bonds with equally shared electrons= high potential energy
-Stronger bones with unequally shared electrons= low potential energy
Reactants
-Weaker bonds with equally shared electrons
-HIGH potential energy
Products
-Stronger, shorter, more polar bonds
-LESS potential energy
What the engine needs»products of combustion
C8H18+12.508>8 CO2+9 H20
Isooctane+ oxygen> Carbone Dioxide+ Water
EntHalpy (H): total energy molecules
-Potential energy of the molecule effect of the molecule on the surrounding pressure and volume
-Net: total energy on bio systems
-Changes in enthalpy are primarily base on the difference in potential energy
-H< (neg.=products have lower pot. energy)
-H> (pos.= products have higher pot. energy)
Exothermic Reaction
-Release heat energy
-H<0
-Products have less pot. energy that reactant
- Ex. gas
Endothermic Reactions
-Heat energy is taken up
-H>0
-Products have higher pot. energy that reactant
-Ex. cooking and egg, melting ice
Entropy (S): amount of disorder
-Products of a chem reaction becomes less ordered than the reactant molecules
-Entropy increase
-S>0
2nd Law of Thermodynamic
-Entropy always increases
-Energy is transformed, there is always an increase of entropy
Entropy Order
Highly ordered» Increase entropy»disordered
Gibbs Free Energy(G): determines whether a reaction is spontaneous or requires add energy
Free energy change equation: G=H-TS
H= change in enthalpy
S change in entropy
T= temp. in degree Kelvin
Gibbs Free Energy (G)
G<0: Spontaneous reaction, reactions are exergonic
G>0: Nonspontaneous reactions that require energy, reactions are endergonic
G=0: reaction at equilibrium
Collision Theory
More collisions= Increase rate of reaction
Temp. & Concentration Affect Reaction Rates
-One or more chem. bonds have to break and others have to from
-Substances must collide in a specific orientation that brings the electrons involved near each other
-Higher concen. and higher temp. increase the number of collisions
-Higher concen. and higher temp. increase reaction rate
Energetic Coupling
-Between exergonic and endergonic reactions
-Allows chem. energy released from 1 reaction
-Drive another reaction
Ex. of Energetic Coupling: Redox RxNs
-Reduction, Oxidation reactions
-Redox reactions
-Chem. reactions have involve electron(e-) transfer= energy transfer
-Always occur together
-Represent energetic coupling of 2 half reactions
-During a redox reaction, e-: can be transferred or shifted
Redox RxNs Transfer Energy vis Electrons
Oxidation: loss of electrons, releases energy, exergonic
Reduction: gain of electrons, requires energy, endergonic
OIL RIG
-Oxidation Is Loss( of e-)
-Reduction Is Gain(of e-)
G=H-TS
Exergonic
G<0
Spontaneous
Reactants: Weaker bonds, higher potential energy»Products: stronger bonds, lower potential energy
Redox reactions are central in biology- they transfer energy in the form of electrons
The energy released from certain key redox reactions is used to drive the endergonic formation of ATP
ATP Transfers Energy via Phosphate Groups
Adenosine Triphosphate(ATP) is the energy currency for cells
-Provided the fuel for most cellular actives
ATP forms both between 3 neg. change phosphate groups.
-Neg. charges repel each other
-High-energy bonds store a large amount of potential energy
ATP Hydrolysis Releases Free Energy
Hydrolysis of the bond between the 2 outermost phosphate groups results.
Forms ADP and P(inorganic phosphate)
-Highly exergonic reactions+ 7.3 kilocalories of energy per mole of ATP
How does ATP Drive Endergonic Reactions
Energy release during ATP hydrolysis is transferred to a substrate by phosphorylation
-Phosphorylation is adding a phosphate group
-Usually causes a change in the proteins shape
Exergonic phosphorylation reactions are coupled to endergonic reactions
Hoe Enzymes Work
Most bio chem reactions occur fast enough only in the presence of an enzyme
-Enzymes are protein catalyst
-Bring reactants together in precise orientations
-Make reactions more likely
-Are specific for a single type of reactions
Enzymes Help Reactions Clear 2 Hurdles
Before a reaction can take place reactants must
1.Collide in a precise orientation
2.Have enough kinetic energy to overcome repulsion between electrons that come into contact as a bond forms
Collide in a precise orientation? Enzymes Bring Substates Together
Substrates bind to the enzymes active site
-Enzymes help them collide in a precise orientation
-Bonds break and form to generate products
Active site is very specific to the substrate
Many enzymes undergo a conformational change when the substrates are bound to the active site
-This change is celled in induced fit
Substrates bind via hydrogen bonding or other interactions with amino acid residues in the active site
-An unstable intermediate condition called Transition State is formed
-Activation energy(Ea) is required to strain substrates bonds so they can reach the transition state
Have enough kinetic energy… Enzymes Lower the Activation Energy
Interactions between the enzymes and the substate
-Stabilize the transition state
-Lower the activation energy required for the reaction to proceed
Enzymes are not consumed during the reaction
What limits the Rate of Catalytic Reactions(R)?
The speed of enzyme-catalyzed reaction
1. Increase linearly at a low substrate concentrations
2. Slows as substrate concertation increases
3. Reaches maximum speed at high substrate concentrations
Do Enzymes Work Alone?
Many enzymes are not regulated by molecules that are not part of the enzymes itself.
- Cofactors are inorganic ions, such as ZN2, Mg2 and Fe2 that are reversibly interact with enzymes
- Coenzymes are organic molecules such as NADH or FADH that interact with enzymes
- Prosthetic groups are non amino acid atoms or molecules that are permanently attached to proteins
An enzymes structure is critical to its function(dependent on folding)
Enzyme function is dependent on certain conditions
-Temp affects the folding and movement of the enzyme and its substrate
-pH affects the enzymes shape and reactivity
-Each enzymes has optimal temp and pH
Most Enzymes are Regulated: Non Covalent modifications
By regulatory molecules that are not part of the enzyme
-Can control when and where an enzyme functions by changing: Enzyme structure: Ability to bind its substrate
-Can activate or inactive the enzyme
-Does not permanently affect the enzyme structure: reversable
-Can be competitive inhibition or allosteric regulation
Competition inhibition
Occurs when a molecule competes with the substrate for the active site
Allosteric regulation(ACTIVATION)
Occurs when a molecule binds at a location other than the active site and cause a change in a enzyme shape…ACTIVATION
Allosteric Regulation(DEACTIVATION/INHIBITION)
Occurs when a molecule binds at a location other than the active side it causes a change in enzyme shape… DEACTIVATION/INHIBTION
Regulating Enzymes via Covalent Modification
Regulation may involve covalent modifications :
-Changes the enzymes primary structure
-Can be irreversible or reversible
Regulating Enzymes via Covalent Modification: Irreversible changes
Often result from cleaved of peptide bonds
Regulating Enzymes via Covalent Modification: Reversible changes of enzyme is the..
-Often through the addition of phosphate groups(phosphorylation)
-May activate or inactive the enzyme
Metabolic Pathways are Regulates by Feedback Inhibition
-When an enzyme in a pathway is inhibited
-By the final produce of that pathway
-Pathway can shut down when products are no longer needed by the cell
Metabolic Pathways: Anabolic & Catabolic
Anabolic: Small molecules are assembled into large molecules. Energy is required
Catabolic: Large molecules are broken into small ones. Energy is released
Overview of Cellular Respiration
-Life requires energy
-ATP fuels work in cells
-Metabolic pathways harvest energy from high energy molecules such as glucose
-The energy release is used to add a phosphate groups to ADP to make ATP
Overview of Cellular Respiration
Cells generally contain enough ATP to sustain from 30 sec to a few minute’s of activity
-ATP is unstable
-Most cells are making it all the time
Cells obtain glucose to make ATP
-Plants produce glucose during
photosynthesis
-Other organisms obtain glucose from food
Organisms store glucose as glycogen or starch
Oxidation of Glucose
As electrons are removed from glucose, it is oxidized to carbon dioxide by burning
-Some energy is release as heat/light
-Long series of carefully controlled redox reactions
-The released free energy is used to synthesize ATP
-These reactions comprise cellular respiration
Cellular Respiration is a set of 4 process
- Glycolysis: 6 carbon glucose is broken down into 2-3 carbon pyruvate
- Pyruvate processing: each pyruvate is oxidized to form a acetyl CoA
- Citric acid cycle: each acetyl CoA is oxidized to CO2
- Electron transport and Oxidative Phosphorylation: Electrons move through a transport chain and their energy is used to set up a proton gradient, which is used to make ATP
Cellular Reparation, is any set of reactions that use electrons from high energy molecules to make ATP
2 Fundamental requirements of cells:
1. Energy to generate ATP
2. A source of carbon to use as raw material for synthesizing macromolecules
Cellular Respiration Plays a Central Role in Metabolism
Catabolic Pathways: Breakdown molecules, harvest stored energy to produce ATP
Anabolic Pathways: Synthesis of larger molecules, often use energy in the form of ATP
Catabolic and Anabolic
Catabolic: For ATP Production
-Cells use carbs>then fats> and proteins
-Proteins, carbohydrate and fats can all furnish substrates for cellular respiration
Anabolic: Molecules found in carbohydrates metabolism are use to synthesize macromolecules
4 Steps of Cellular Respiration
- Glycolysis
2.Pyruvate Processing
3.Citric Acid Cycle
4.
Step 1. Glycolysis: is a sequences of 10 chemical reaction that occur in the cytosol
1.Starts by using ATP in the energy investment phase(1-5)
2. During the energy payoff phase(6-10) NADH is made and ATP is produced by substrate-level phosphorylation
3. The net yield is 2 NADH, 2 ATP and 2 Pyruvate
Glycolysis: 1-5
Energy Investment of ATP
Glycolysis: 6-10
Energy Payoff of 4 ATP
How is Glycolysis Regulated? Feedback Inhibition
High levels of ATP inhibit the 3rd enzyme: phosphofructokinase
Has 2 binding sites for ATP:
1. When ATP binds to the active site, the enzyme catalyzes the 3rd step in glycolysis
2. When ATP levels are high it binds to a regulatory site and inhibits the enzyme
Mitochondria have inner and outer membranes
Cristae: are extensions of the inner membrane, sac like
Mitochondria Matrix: inside the mitochondria
Intermembrane Space: between the inner and outer membrane
Step 2- Pyruvate produced during glycolysis is transported into mitochondria
Pyruvate process takes place inside an enormous enzyme called pyruvate dehydrogenase
-Located in the mitochondrial matrix in eukaryotes
-Located in the cytosol in prokaryotes
Step 2: Processing Pyruvate to Acetyl CoA
Pyruvate undergoes a series of reaction
-One of it’s carbons is oxidized to CO2
-NADH is produced
-Remaining 2 carbon unit is attached to coenzyme A, producing acetyl CoA
Pyruvate Processing :Regulated by Feedback Inhibition
When products of glycolysis and pyruvate processing are abundant Pyruvate dehydrogenase is phosphorylates changes shape and is inhabited
Step 3- Citric Acid Cycle: Oxidizing Acetyl CoA to CO2
-Each acetyl CoA from pyruvate processing is oxidized into 2 CO2
-Located in the mitochondrial matric in eukaryotes and cytosol in prokaryotes
-The reactions are organized in a cycle
The Citric Acid Cycle: Oxidizing Acetyl CoA to CO2
Some potential energy is used to
1. Reduce 3 NAD+ to NADH
2. Reduce 1 FAD to FADH
3. Phosphorylate 1 ADP(GDP) to from 1 ATP(GTP)
The cycle turns twice for each glucose molecule since 2 pyruvate are produced by glycolysis
TOTAL= 6 NADH, 2 FADH & 2 ATP
Series of Redox Reactions
Pyruvate is oxidized to CO2
NAD is reduced to NADH
FAD is reduced to FADH2
Aerobic versus Anaerobic Respiration: All Eukaryotes and many prokaryotes
-Use oxygen as the final electron acceptor for the ETC
-This is called aerobic respiration
Aerobic versus Anaerobic Respiration: Some Prokaryotes
-Especially those in oxygen poor environments
-Use other electron acceptors
-This is called anaerobic respiration
Aerobic versus Anaerobic Respiration: Oxygen is this most effective electron acceptor because…
- It it highly electronegative
- A large difference exist between the potential energy of electrons in NADH and O2
-It allows the generation of a large proton motive force
-Aerobic organisms grown and reproduce faster
Fermentation: What happens when there is no electron acceptor?
-The electrons have no place to go
-The ETC stops
Fermentation: NADH builds up and there is no NAD+ available to accept electrons
-Glycolysis, pyruvate processing and the critic acid cycle stop
-The situation is life threating
-NAD+ must be regenerated…through fermentation
Fermentation: is the pathway that regenerated NAD+ from NADH
-Electrons from NADH are transfer to pyruvate
-Serves as am emergency backup
-Glycolysis can continue to produce ATP by substrate level phosphorylation in the absence of oxygen
Different Fermentation Pathways Exist: Muscles
When our muscle cells cannot get enough oxygen they convert to lactic acid fermentation
-Pyruvate produced by glycolysis accepts electrons from NADH
-Lactate and NAD+ are produced
As muscle cells get more oxygen, lactate can be converted back to pyruvate
Different Fermentation Pathways Exist: Alcohol
Some yeast cells can perform alcohol fermentation
-Pryuvate is converted to acetaldehyde and CO2
-Acetaldehyde accepts electrons from NADH
-Ethanol and NAD+ are produced
Cells that preform other types of fermentation are used to make soy sauce, tofu, yogurt, cheese, etc
Prokaryotes that rely on fermentation are present in our intestines
Fermentation is an Alternative to Cellular Respiration
Fermentation is much less efficient then cellular respiration
-It produces 2 ATP per glucose, compared to about 38 ATP per glucose in cellular respiration
Some organisms can switch between fermentation and aerobic respiration= facultative anaerobes
They used fermentation only if an electron acceptor is not available
Overview of Photosynthesis
Photosynthesis s is the use of sunlight to manufacture carbohydrates
-Converts electromagnetic energy to chem. energy
-Organisms that use photosynthesis are AUTOTROPHS(self feeders)
-Non- photosynthetic organism are HETROTROPHS( different feeders)
Photosynthesis: 2 linked sets of reactions
1: Light Dependent reactions
-Produce O2 from H20
-Water is split to form O2(gas)
-Electrons are excited by lights energy
-High energy electrons are transferred to the electron carrier NADP+ forming NADPH
-ATP is also produced
2: Calvin Cycle reactions
-Produced sugar from CO2
-Electrons and ATP are used to reduce CO2
Photosynthesis occurs in the Chloroplast
-Green plants, algae, and other photosynthetic organisms
-Chloroplast are surrounded by 2 membranes
Interior is filled with thylakoids
-Flattened, vesicle like structures
-Form stacks call grana
-Space inside a thylakoid is lumen
-Space surrounding thylakoids is the stroma
Thylakoid membrane contain large quantities of PIGMENTS
Molecules that absorb only certain wavelengths of light and reflect or transmit others
-People see the reflected wavelength
Most common pigment in thylakoid= chlorophyll
-Reflects green light
-Responsible for green color of plants and algae
Different Pigments Absorb Different Wavelength of Light: 2 major classes of pigments in plants
1.The chlorophylls(A and B)
-Absorb red and blue light
-Reflect and transmit green
2. Carotenoid
-Absorb blue and green light
-Reflects and transmits yellow, orange and red light
3. Xanthophylls
-Absorb blue and green light
-Reflect and transmit yellow light
Carotenoid and xanthophylls are called accessory pigments
Light Reactions are a 2 Step Process
1: Photosystem II= ATP
2. Photosystem 1=NADH
What Happens during light reaction? Photosynthetic pigments absorb light
- When light(photons) is absorbed
- Excited electrons release energy, some of which is used to reduce molecules to manufacture sugar
What Happens during light reaction? Electrons are passed down an ETC
- In the thylakoid membrane
-Works like the ETC in mitochondria
-Produces a proton gradient
-Drive ATP production via ATP synthase
What Happens during light reaction? In the ETC Linear Pathway
-Electrons from photosystem II produce a proton-motive force that drives ATP synthesis
- Electrons from photosynthesis produce NADHP
Photosystem II: Electrons from light make ATP
- Transmits energy from excited e- to the reaction center in photosystem II
- The e- are passed then are reduced while chlorophyll pigment is oxidized
3.The e- are quickly shuttled away by the e0 acceptor - The e- is dropped and donates a H+ lowering the pH and creating an electrochemical gradient
- The gradient supplies the proton motive force for ATP synthases to phosphorylation ADP to ATP»> phosphorylation
Photosystem I: Electrons from water make NADHP
- Photosystem II re-aquires e- by oxidizing water
- The e- pass through to ferredoxin
- From ferredoxin they move to NADP+
- Reduces to NADPH
The Calvin Cycle: Reactions that produce sugar from CO2
-light Independent (aka dark Rxns/dark side)
_require that ATP and NADHP produced by the light dependent reactions
-Use carbon fixation to add CO2 to an organic compound.
Carbon Fixation
The process by which plants assimilate carbon from carbon dioxide in the atmosphere to form metabolically active compounds
The Calvin Cycle is a 3 step Process (in the stroma)
- Fixation
2.Reduction
3.Regeneration
1- Carbon Fixation
-CO2 reacts within a 5 carbon compound called ribulose bisphosphate(RuBP)
-This resulting 6 carbon molecule splits into 2, 3 carbon molecules of 3PGA
The Discovery of Rubisco
The CO2 fixing enzyme is rubisco
Rubisco is…
-found in all photosynthetic organisms that use Calvin cycle to fix carbon
- thought to be the most abundant enzyme on earth
- Rubisco is a very slow enzyme
Rubisco: Catalyzes the addtion of either CO2 or O2 to RuBP
-O2 and CO2 compete
- Slows the rate the CO2 reduction
-When O2 and RuBP react in rubisco’s active site one of the products undergoes a process called photorespiration
2- Reduction
-3 PGA are phosphorylated
by ATP and reduced by NADPH
-Producing glyceraldehyde 3 phosphate (G3P)
What happens to the sugar that is produced by photosynthesis?: G3P molecules produced by the Calvin Cycle
-Often used to make glucose and fructose by the process of gluconeogenesis
-Which can be combined to form sucrose
-When sucrose is abundant, glucose is polymerized to for, starch
-Starch is broken down into glucose at night
3- Regeneration
-Some G3P us used to make sugars or starches
-The remaining G3P us used in reactions that use ATP to regenerate RuBP
How is photosynthesis regulated?
-Light triggers production of photo. proteins and activates rubisco
-Hight sugar inhibits production of photo. proteins and stimulates production of proteins that process and store sugar
-Low CO2 inhibits rubisco: carbon fixation if favored over photorespiration when concentrations of CO2 are higher then O2
How is photosynthesis regulated? Plants have pores called stomata that allow gas exchange
-Oxygen and CO2 pass through stomata
-2 guard cells change shape to open or close the pore
Photorespiration “undoes” photosynthesis
- Consumes O2 and releases fixed CO2
-May have some benefit for the plant
-Some products involves in signaling
-May have a protective role
Oxygen photosynthesis and the evolution of earth
-The oxygen released from oxygenic photosynthesis was critical to the evolution of life as we know
-O2 was almost nonexistent on earth before enzymes evolved that could catalyze the oxidation of water
