AP BIO UNIT 3 Flashcards
Metabolism
All of the chemical reactions in an organism
Metabolic Pathways
Series of chemical reactions that either build complex molecules or break down complex molecules
Catabolic Pathway
Pathways that release energy by breaking down complex molecules into simpler compounds
Anabolic Pathway
Pathways that consume energy to build complicated molecules from simpler compounds
Energy
The ability to do work
Organisms need energy to…
survive and function. A loss in energy flow results in death.
Kinetic Energy
Energy associated with motion.
Thermal Energy
Energy associated with the movement of atoms or molecules.
Potential Energy
Stored energy.
Chemical Energy
Potential energy available for release in a chemical reaction.
Thermodynamics
The study of energy transformations in matter. These laws apply to the universe as a whole.
1st Law of Thermodynamics
Energy cannot be created or destroyed. Energy CAN be transferred or transformed. (Example: the chemical energy (potential) stored in the nut will be transformed into kinetic energy for the squirrel to climb the tree.)
2nd Law of Thermodynamics
Energy transformation increases the entropy (disorder) of the universe. During energy transfers or transformations, some energy is unusable and often lost as heat. (Example: as the squirrel climbs the tree, some energy is released as heat)
∆G
Change in free energy
∆H
Change in total energy
T
Absolute temperature (K)
∆S
Change in entropy
Law of Thermodynamics Formula
∆G = ∆H - T∆S
Exergonic Reactions
Reactions that release energy (Example: cellular respiration)
Endergonic Reactions
Reactions that absorb energy (Example: photosynthesis)
Mechanical Work
Movement (Example: beating cilia, movement of chromosomes, contraction of muscle cells)
Transport Work
Pumping substances across membranes against spontaneous movement
Chemical Work
Synthesis of molecules (Example: building polymers from monomers)
ATP
(Adenosine Triphosphate) Molecules that organisms use as a source of energy to perform work
Organisms obtain energy…
By breaking the bond between the 2nd and 3rd phosphate in a hydrolysis reaction. (ATP –> ADP)
Phosphorylation
The released phosphate moves to another molecule to give energy
Regeneration of ATP
ADP can be regenerated to ATP via the ATP cycle. (ATP + H20 –> ADP + Pi)
Enzymes
Macromolecules that catalyze (speed up) reactions by lowering the activation energy. (Are not consumed by the reaction, type of protein, enzyme names end in “ase”)
Enzyme Structure
The enzyme acts on a reactant called a substrate
Active Site
Area for substrate to bind
Enzyme Function
Active site is open, substrates are held in active site by weak interactions, substrates are converted to products, products are released.
Induced Fit
Enzymes will change shape of their active site to allow the substrate to bind better.
Enzyme Catabolism
Enzyme helps break down complex molecules.
Enzyme Anabolism
Enzyme helps build complex molecules.
Effects on Enzymes
Enzymes are proteins, which means their 3D shape can be affected by different factors.
Factors that Affect the Efficiency of Enzymes
Temperature, pH, Chemicals
Optimal Conditions
The conditions (temperature & pH) that allow enzymes to function optimally.
Enzyme Activity (Temperature)
The rate of enzyme activity increases with temperature (due to collision) up to a certain point). After a certain point, the enzyme will denature.
Enzyme Activity (pH)
Enzymes function best at a specific pH. Being outside the normal pH range can cause hydrogen bonds to break changing the shape of the enzyme.
Enzyme Cofactors
Non-protein molecules that assist enzyme function. Inorganic cofactors consist of metals. Can be bound loosely or tightly.
Holoenzyme
An enzyme with the cofactor attached.
Coenzymes
Organic cofactors. (Example: vitamins)
Enzyme Inhibitors
Reduce the activity of specific enzymes.
Permanent Inhibition
Inhibitor binds with covalent bonds. (Example: toxins and poisons)
Reversible Inhibition
Inhibitor binds with weak interactions.
Competitive Inhibitors
Reduce enzyme activity by blocking substrates from binding to the active sites. Inhibition can be reverse with increased substrate concentrations.
Noncompetitive Inhibitors
Bind to the area other than the active site (allosteric site), which changes the shape of the active site preventing substrates from binding.
Regulation of Chemical Reactions
A cell must be able to regulate its metabolic pathways. Control where and when enzymes are active. Switch genes that code for enzymes on or off.
Allosteric Enzymes
Allosteric enzymes have two binding sites. 1 active site, 1 allosteric site (regulatory site, site other than the active site)
Allosteric Regulation
Molecules bind (noncovalent interactions) to an allosteric site which changes the shape & functions of the active site. May result in inhibition (by an inhibitor) or a stimulation (by an activator) of the enzymes activity.
Allosteric Activator
Substrate binds to allosteric site & stablilizes the shape of the enzyme that the active sites remain open.
Allosteric Inhibitor
Substrate binds to allosteric site and stabilizes the enzyme shape so that the active sites are closed (inactive form).
Cooperativity
Substrate binds to one active site (on an enzyme with more that one active site) which stabilizes the active form. Considered allosteric regulation since binding t one site changes the shape of other sites.
Feedback Inhibition
Sometimes, the end product of a metabolic pathway can act as an inhibitor to an early enzyme in the same pathway.
Photosynthesis
The conversion of light energy to chemical energy. (Plants are autotrophs (photoautotrophs))
Autotrophs
Organisms that produce their own food (organic molecules) from surrounding simple substances
Heterotrophs
Organisms unable to make their own food so they live off of other organisms
Evolution of Photosynthesis
Photosynthesis first evolved in prokaryotic organisms.
Cyanobacteria
Early prokaryotes capable of photosynthesis. Oxygenated the atmosphere of early Earth. Prokaryotic photosynthetic pathways were the foundation of eukaryotic photosynthesis.
Site of Photosynthesis
Leaves are the primary location of photosynthesis in most plants.
Chloroplast
Organelle or the location of photosynthesis. Found in the mesophyll, the cells that make up the interior tissue of the leaf
Stomata
Pores in leaves that allow CO2 in and O2 out
Chloroplasts are surrounded by a
double membrane
Stroma
Aqueous internal fluid
Thylakoids
Form stacks known as grana
Chlorophyll
Green pigment in the thylakoid membranes
Photosynthesis Formula
6 CO2 + 6 H2O + Light Energy –> C6H12O6 + 6 O2
Photosynthesis Reactants
6 CO2 + 12 H2O
Photosynthesis Products
C6H12O6 + 6 H2O + 6 O2
Redox Reactions
Reaction involving complete or partial transfer of one or more electrons from one reactant to another.
Redox Reactions in Photosynthesis
The electrons are transferred with H+ (from split H2O) to CO2 reducing it to sugar
Oxidation
Loss of e-
Reduction
Gain of e-
Two Stages of Photosynthesis
Light Reactions and the Calvin Cycle
Light
Electromagnetic energy. Made up of particles of energy called photons. Travel in ways.
Wavelength
The distance from the crest of one wave to the the crest of the next. The entire range is known as the electromagnetic spectrum. 380 nm to 750 nm is visible light.
Short Wavelengths
Higher energy
Long Wavelengths
Lower energy
When light interacts with matter it can be…
Reflected, transmitted, or absorbed. Pigments are able to absorb visible light. The color we see is the reflected wavelengths. Leaves are green because chlorophyll ABSORBS violet-blue and red light, and reflects green
Chlorophyll A
Primary pigment, involved in light reactions, blue/green pigment, absorb purple/blue/red, reflects blue/green.
Chlorophyll B
Accessory pigment, yellow/green pigment, absorbs blue
Carotenoids
Broaden the spectrum of colors that drive photosynthesis. Yellow/orange pigment.
Photoprotection
Carotenoids absorb and dissipate excessive light energy that could damage chlorophyll or interact with oxygen.
The Light Reactions Overview
Occur in the thylakoid membrane in the photosystems. Convert solar energy to chemical energy.
2 Forms of Chemical Energy
NADPH & ATP. The cell accomplishes this conversion by using light energy (photons) to excite electrons.
Light & Chlorophyll
Chlorophyll absorbs a photon of light. E- is boosted from a ground state to an excited state. E- is unstables. Falls back to ground state. Releases energy as heat. Emits photons as fluorescence.
Photosystems
Reaction center and light capturing complexes
Reaction Center
A complex of proteins associated with chlorophyll A and an electron acceptor.
Light Capturing Complexes
Pigments associated with proteins. THINK: antenna for the reaction centers.
Photosystem II
Reaction center P680. Absorbs light at 680 nm.
Photosystem I
Reaction center P700. Absorbs light at 700 nm.
Inside PS II
Light energy (photon) causes an e- to go from an excited state back to a ground state. This repeats until it reaches P680 pair of chlorophyll A molecules. The e- is transferred to a primary e- acceptor, forming P680+. H2O is split into 2e- reduced P680 +, 2H+ released into thylakoid space, 1 oxygen atom (which immediately bonds to another oxygen atom). Linear electron flow: each excited electron will pass from PSII to PSI via the electron transport chain.
Generation of ATP
The “fall” of electrons from PS II to PS I provides energy to form ATP. THe H+ gradient is a form of potential energy. ATP synthase couples the diffusion of H+ to the formation of ATP.
Inside PS I
LIght energy excites electrons i the P700 chlorophyll molecules. Become P700+. Electrons go down a second transport chain. NADP+ reductase catalyzes the transfer of e- from Fd to NADP+.
Light Reaction Inputs
H2O, ADP, NADP+
Light Reaction Outputs
O2, ATP, NADPH
Light Reactions Summary
Converts solar energy to chemical energy. Chemical energy is in 2 forms: NADPH and ATP. Water is split. Provides a source of electrons and protons (H+). Releases O2 as a by-product. Light absorbed by chlorophyll drives the transfer of electrons and hydrogen ions from H2O to an electron acceptor called NADP+. NADP+ is reduced to NADP. Generates ATP by phosphorylating ADP.
Calvin Cycle
The Calvin Cycle is cyclic electron flow. Uses ATP and NADH to reduce CO2 to sugar G3P. For net synthesis of 1 G3P molecule, the cycle must take place 3 times.
Three Phases of the Calvin Cycle
- Carbon Fixation
- Reduction
- Regeneration of RuBP
Carbon Fixation
CO2 is incorporated into the Calvin Cycle on at a time. Each CO2 attaches to a molecule of RuBP. Catalyzed by the enzyme rubisco. Form 3-phosphoglycerate.
Reduction
Each molecule of 3-phosphoglycerate is phosphorylated by ATP (uses 6 total). Becomes 1, 3-biphosphoglycerate. 6 NADPH molecules donate electrons to 1, 3-biphosphoglycerate. Reduces to G3P. 6 molecules of 63P are formed, but only one is counted as a net gain. The other 5 G3P molecules are used to regenerate RuBP.
Regeneration of RuBP
5 G3P molecules are used to regenerate 3 molecules of RuBP. Uses 3 ATP for regeneration. Cycle is now ready to take CO2 again.
Calvin Cycle Input
3 CO2, 9 ATP, 6 NADPH
Calvin Cycle Output
1G3P*, 9 ADP, 6 NADP+
Calvin Cycle Summary
Uses NADPH, ATP, and CO2. Produces a 3-C sugar G3P. Three Phases: Carbon Fixation, Reduction, Regeneration of RuBP.
Photorespiration
On very hot days plants close their stomata to stop water loss. Causes less CO2 to be present and more O2. Rubisco binds to O2 and uses ATP. The process produces CO2. No sugar is produced. BAD for the plant.
C4 Plant Adaptations
Spatial separation of steps, stomata partially closed to conserve water. Mesophyll cells fix CO2 into a 4-C molecule. Transferred to a bundle sheath cells. Releases CO2 to be used in the Calvin Cycle. (Examples: Maize, Grasses, Sugarcane)
CAM Plants
Open stomata at night and close during the day. CO2 is incorporated into organic acids and stored in vacuoles. During the day, light reactions occur and CO2 is released from the organic acids and incorporated into the Calvin Cycle. (Examples: Pineapples, Cacti, Succulents, Jade)
Cellular Respiration
Cells harvest chemical energy stored in organic molecules and use it to generate ATP. Organic molecules + oxygen (CO2 + H2O + energy). Starch is the major source of fuel for animals. Breaks down into glucose. The oxidation of glucose transfers e- to a lower energy state, releasing energy to be used in ATP synthesis.
Path of Electrons in Energy Harvest
glucose –> NADH –> ETC –> Oxygen
Energy Harvest
Glucose is broken down in steps to harvest energy. Electrons are taken from glucose at different steps. Each e- taken travels with a proton (H+). Dehydrogenase take 2e- & 2 protons from glucose. Oxidizing agent for glucose. Transfers 2e- & 1 proton to the coenzyme NAD+. Reduces to NADPH (stores energy). Other proton is released into surrounding solution as H+. NADH carries e- to the electron transport chain.
Electron Transport Chain (ETC) (Photosynthesis)
A sequence of membrane proteins that shuttle electrons down a series of redox reactions. Releases energy used to make ATP. ETC transfers e- to O2, the final e- acceptor, to make H2O. Releases energy.
Three Stages of Cellular Respirtion
- Glycolysis
- Pyruvate Oxidation
- Oxidative Phosphorylation (ETC & Chemiosmosis)
Glycolysis
Starting point of cellular respiration. Occurs in the cytosol. Splits glucose (6C) into 2 pyruvates (3C).
Energy Investment Stage (CR)
The cell uses ATP to phosphorylate compounds of glucose.
(2 ATP –> 2 ADP + P)
Energy Payoff Stage (CR)
Energy is produced by substrate level phosphorylation. Net energy yield per glucose: 2 ATP & NADH.
(4 ADP + P –> 4 ATP)
(2 NAD+ + 4e- + 4H+ –> 2 NADH + 2H+)
Net Glycolysis
2 Pyruvate + 2H2O
2 ATP
2 NADPH + 2H+
Pyruvate Oxidation and Citric Acid Cycle
If oxygen is present, the pyruvate enters the mitochondria (eukaryotic cells). Pyruvate is oxidized into Acetyl CoA. Acetyl CoA is used to make citrate in the citric acid cycle. 2 CO2 & 2 NADH are produced).
Pyruvate Oxidation
pyruvate –> acetyl CoA
Citric Acid Cycle
Also known as the Krebs Cycle. Occurs in the mitochondrial matrix. Turns acetyl CoA into citrate. Releases CO2. ATP is synthesized. Electrons transferred to NADH & FADH2).
Citric Acid Cycle Inputs
2 Acetyl CoA
Citric Acid Cycle Outputs
2 ATP, 6 NADH, 4 CO2, 2 FADH2
Oxidative Phosphorylation
Consists of ETC and Chemiosmosis
Electron Transport Chain (ETC) (Cellular Respiration)
The ETC is located in the inner membrane of the mitochondria. Collection of proteins, As the electrons “fall” proteins alternate between reduced (accepts e-) and oxidized (donates e- state). The cristae increase the surface area for the reactions to occur. Does not produce ATP directly. Helps manage the release of energy by creating several small steps for the “fall” of electrons. The final electron acceptor is oxygen. Each oxygen pairs with 2H+ and 2e- to form H2O. One major function of the ETC is to create a proton (H+) gradient across the membrane. As proteins shuttle electrons along the ETC, they also pump H+ into the intermembrane space. Use the exergonic flow of electrons from NADH and FADH2. This gradient will power chemiosmosis. Use hydrogen ions to power cellular work.
Chemiosmosis
ATP synthase: the enzyme that makes ATP from ADP + P. Uses energy from the H+ gradient across the membrane. H+ ions flow down their gradient through ATP synthase. ATP synthase acts like a rotor. When H+ binds, the rotor spins. Acivates catalytic sites to turn ADP + P into ATP. Produces about 26-28 ATP per glucose.
Cellular Respiration Summary
Glycolysis -
Input: 1 Glucose
Output: 2 Pyruvate, 2 ATP, 2 NADH
Pyruvate Oxidation -
Input: 2 Pyruvate
Output: 2 Acetyl CoA, 2 CO2, 2 NADH
Citric Acid Cycle -
Input: 2 Acetyl CoA
Output: 4 CO2, 2 FADH2, 2 ATP, 6 NADH
Oxidative Phosphorylation -
Input: 10 NADH, 2 FADH2
Output: 26-28 ATP
Total Output - 30 - 32 ATP
How do organisms produce ATP in the absence of oxygen?
Anaerobic Respiration
Fermentation
Anaerobic Respiration
Generates ATP using electron receptors in the absence of oxygen. Takes place n prokaryotic organisms that live in environments with no oxygen. The final electron acceptors are sulfates or nitrates.
Fermentation
Generates ATP without an ETC. Extension of glycolysis. Recycles NAD+, occurs in the cytosol, no oxygen. Two types: Alcoholic Fermentation and Lactic Acid Fermentation
Alcohol Fermentation
Pyruvate is converted into ethanol. (Example: bacteria, yeast)
Lactic Acid Fermentation
Pyruvate is reduced directly by NADH to form lactate. (Example: muscle cells. When muscle cells run out of oxygen, they can go through lactic acid fermentation to produce ATP. This causes the burning sensation you may feel when performing strenuous exercise).
Breakdown of Lactate
Muscles produce lactate, which goes into the blood, and is broken down back to glucose in the liver. When lactate is in the blood, it lower the pH. If lactate builds up and is unable to be broken down it can lead to lactic acidosis. Excessively low blood pH.
