unit 3 biology

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12th grade ap biology

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98 Terms

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metabolism

- all chemical reactions in an organism
- substrate -> intermediate -> intermediate -> product

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metabolic pathways

- series of chemical reactions that either build complex molecules or break down complex molecules
- two types: catabolic, anabolic

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catabolic pathways

release energy by breaking down complex molecules into simpler compounds (ex: hydrolysis)

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anabolic pathways

consume energy to build complicated molecules from simpler compounds

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energy

- ability to do work
- organisms need energy to survive and function
- a loss in energy flow results in death

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kinetic energy

energy associated with motion

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thermal energy

energy associated with the movement of atoms or molecules

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potential energy

stored energy

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chemical energy

potential energy available for release in a chemical reaction

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thermodynamics

- the study of energy transformations in matter
- the laws apply to the universe as a whole

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1st law of thermodynamics

energy cannot be created or destroyed, only transferred or transformed

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2nd law of thermodynamics

- energy transformation increases the entropy (disorder) of the universe
- during energy transfers, some energy is unusable and often lost as heat

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free energy

determines whether or not the reaction occurs spontaneously/ are energetically favorable

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exergonic reactions

- release energy
- reaction is spontaneous
- ex: cellular respiration

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endergonic reactions

- absorb energy
- reaction is not spontaneous
- ex: photosynthesis

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cells and energy

- living cells have a constant flow of materials in and out of the membrane
- cells are not at equilibrium
- cells perform three kinds of work: mechanical, transport, chemical

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mechanical work

- movement
- ex: beating cilia, chromosome movement, muscle cells contraction

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transport work

pumping substances across membranes against spontaneous movement

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chemical work

- synthesis of molecules
- ex: building polymers from monomers

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ATP

- molecule that organisms use as a source of energy to perform work
- most potential energy
- couples exergonic to endergonic reactions to power cellular work
- organisms obtain energy by breaking the bond between the 2nd and 3rd phosphate in hydrolysis (ATP -> ADP)

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phosphorylation

the released phosphate moves to another molecule to give energy (donating a phosphate)

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enzymes

- macromolecules that catalyze (speed up) reactions by lowering the activation energy
- not consumed by the reaction
- type of protein
- names end in -ase

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enzyme structure

acts on a reactant called a substrate

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enzyme function

active site (area for substrate to bind)

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induced fit

enzymes will change the shape of their active site to allow the substrate to bind better

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enzyme catabolism

helps break down complex molecules

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enzyme anabolism

helps build complex molecules

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effects on enzymes

- affected by temperature, pH, and chemicals
- change in shape = change in function
- optimal conditions: enzyme will denature outside of its optimal range of temp or pH

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enzyme cofactor

- nonprotein molecules that assist enzyme function
- inorganic cofactors consist of metals
- can be bound loosely or tightly

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holoenzyme

an enzyme with the cofactor attached

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coenzymes

- organic cofactors
- ex: vitamins

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enzyme inhibitors

- reduce the activity of specific enzymes
- can be permanent or reversible

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permanent inhibition

- inhibitor binds with covalent bonds
- ex: toxins, poisons

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reversible inhibition

inhibitor binds with weak interactions

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competitive inhibitors

- reduce enzyme activity by blocking substrates from binding to the active site
- can be reversed with increased substrate concentrations

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noncompetitive inhibitors

- bind to an area other than the active site (allosteric site), which changes the shape of the active site preventing substrates from binding
- type of allosteric inhibition

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regulation of chemical reactions

a cell must be able to regulate its metabolic pathways by controlling where and when enzymes are active and switching genes that code for enzymes on or off

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allosteric enzymes

two binding sites (1 active and 1 allosteric)

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allosteric regulation

- molecules bind (noncovalent interactions) to an allosteric site which changes the shape and function of the active site
- may result in inhibition or stimulation of the enzymes activity

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allosteric activator

substrate binds to allosteric site and stabilizes the shape of the enzyme so that the active sites remain open

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allosteric inhibitor

substrate binds to allosteric site and stabilizes the enzyme shape so that the active site are closed (inactive form)

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cooperativity

substate binds to one active site (on an enzyme with more than one active site) which stabilizes the active form (considered allosteric regulation since binding at one site changes the shape of other sites)

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feedback inhibition

sometimes the end product of a metabolic pathway can act as an inhibitor to an early enzyme in the same pathway

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photosynthesis

conversion of light energy to chemical energy

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autotrophs

- organisms that produce their own food (organic molecules) from simple substances in their surroundings
- ex: plants (specifically photoautotrophs)

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heterotrophs

organisms unable to make their own food so they live off of other organisms

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photosynthesis evolution

- first evolved in prokaryotic organisms
- cyanobacteria: early prokaryotes capable of photosynthesis and oxygenated the atmosphere of early earth
- prokaryotic photosynthetic pathways were the foundation of eukaryotic photosynthesis

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site of photosynthesis

- leaves: primary location in most plants
- chloroplast: organelle location, found in mesophyll

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mesophyll

cells that make up the interior tissue of the leaf

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stomata

pores in leaves that allow CO2 in and O2 out

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chloroplast structure

- surrounded by a double membrane
- stroma: aqueous internal fluid
- thylakoids form stacks called grana
- chlorophyll: green pigment in thylakoid membranes

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photosynthesis reaction

6CO2 + 6H2O + light energy -> C6H12O6 + 6O2

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photosynthesis stages

- light reactions (light dependent)
- calvin cycle (light independent/dark reaction)

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pigment

- absorb visible light
- the color we see is the reflected wavelengths

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chlorophyll a

- primary pigment
- involved in light reactions
- blue/green pigment

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chlorophyll b

- accessory pigment
- yellow/green pigment

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carotenoids

- photoprotection: absorb and dissipate excessive light energy that could damage chlorophyll or interact with oxygen
- yellow/orange pigment

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light reaction

- occur in thylakoid membrane in the photosystems
- concert solar energy to chemical energy (NADPH and ATP)
- happens bc light energy (photons) is used to excite electrons

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chlorophyll and light

1. chlorophyll absorbs a photon of light
2. electron is boosted from a ground state to an excited state
3. electron is unstable and falls back to ground state
4. releases energy as heat and emits photons as fluorescence

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photosystems

- reaction center and light capturing complexes
- in the thylakoid membrane, there are two: PS2 and PS1

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reaction center

a complex of proteins associated with chlorophyll a and an electron acceptor

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light capturing complexes

pigments associated with proteins

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photosystem 2

1. light energy (photon) causes an electron to go from an excited state back to a ground state. repeats until it reaches the P680 pair of chlorophyll a molecules
2. electron is transferred to a primary electron acceptor, forming P680+
3. H2O splits into 2e-, 2H+, and O2

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linear electron flow

each excited electron will pass from PS2 to PS1 via ETC

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ETC (photosynthesis)

in light reaction on thylakoid membrane

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photosystem 1

1. light energy excites electrons in P700 chlorophyll molecules, becoming P700+
2. electrons go down a second transport chain
3. NADP+ reductase catalyzes the transfer of electrons from Fd to NADP+
4. results in NADPH

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generation of ATP

- "fall" of electrons from PS2 to PS1 provides energy to form ATP
- proton gradient is a form of potential energy
- ATP synthase couples the diffusion of H+ to the formation of ATP

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light reaction inputs and outputs

- inputs: H2O, ADP, NADP+
- outputs: O2, ATP, NADPH

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light reaction summary

- water is split providing a source of electrons and protons and releasing oxygen
- light absorbed by chlorophyll drives the transfer of electron and hydrogen ions from H2O to an electron acceptor, NADP+
- NADP+ is reduced to NADPH
- generates ATP by phosphorylating ADP

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calvin cycle

- cyclic electron flow
- uses ATP and NADPH to reduce CO2 to sugar (G3P)
- for net synthesis of 1 G3P molecule, the cycle must take place 3 times (GP -> G2P -> G3P)
- three phases: carbon fixation, reduction, regeneration of RuBP

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carbon fixation

1. CO2 is incorporated into calvin cycle one at a time (3 times to produce 1 net G3P)
2. each CO2 attaches to a molecule of RuBP and catalyzed by enzyme rubisco
3. forms 3-phosphoglycerate

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reduction

1. 3-phosphoglycerate is phosphorylated by ATP and becomes 1,3-biphosphoglycerate
2. NADPH donate electron to 1,3-biphosphoglycerate
3. reduces to G3P: 6 molecules of G3P are formed (1 is a net gain and the other 5 are used to regenerate RuBP)

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regeneration of RuBP

1. 5 molecules of G3P are used to regenerate 3 RuBP
2. cycle is now ready to take in CO2 again
- 3 ATP are used

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calvin cycle inputs and outputs

- inputs: CO2, ATP, NADPH
- outputs: G3P, ADP, NADP+

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C3 plants problem

- photorespiration: on hot days plants close their stomata to stop water loss
- causes less CO2 to be present and more O2
- wastes energy and no sugar is produced

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C4 plants

- stomata partially close to conserve water
- ex: corn, grasses, sugarcane

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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 reaction occur and CO2 is released from the organic acids and incorporated into the calvin cycle
- ex: cactus, succulents, jade, pineapples

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cellular respiration

cells harvest chemical energy stored in organic molecules and use it to generate ATP

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cellular respiration reaction

C6H12O6 + 6O2 -> 6CO2 + 6H2O + energy (ATP and heat)

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starch

- major source of fuel for animals
- breaks down into glucose

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path of electrons in energy harvest

- during cellular respiration, most electrons will follow this "downhill" exergonic path
- glucose -> NADH (e- carrier) -> ETC -> oxygen

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energy harvest

- glucose is broken down in steps to harvest energy
- electrons are taken from glucose at different steps
1. each electron taken travels with a proton
2. transfers 2 electrons and 1 proton to the coenzyme NAD+ and reduces to NADH (stores the energy)
3. NADH carries electron to the ETC

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electron transport chain

- a sequence of membrane proteins that shuttle electrons down a series of redox reactions
- releases energy used to make ATP
- transfers electrons to oxygen

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oxygen

final electron acceptor to make water

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stages of cellular respiration

1. glycolysis
2. pyruvate oxidation and the citric acid cycle
3. oxidative phosphorylation

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glycolysis

- occurs in cytosol
- splits glucose into 2 pyruvates
- two stages: energy investment, energy payoff
- input: 1 glucose
- output: 2 pyruvate, 2 ATP, 2 NADH

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energy investment stage

the cell uses ATP to phosphorylate compounds of glucose

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energy payoff stage

energy is produced by substrate level phosphorylation

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pyruvate oxidation and the citric acid cycle

- if oxygen is present, the pyruvate enters the mitochondria (eukaryotic cells)
- occurs in mitochondrial matrix
- pyruvate oxidation: pyruvate is oxidized into acetyl CoA
- citric acid: acetyl CoA turns into citrate, electrons transferred to NADH and FADH2
- input (pyruvate oxidation): 2 pyruvate
- output (pyruvate oxidation): 2 acetyl CoA, 2 CO2, 2NADH
- input (citric acid): 2 acetyl CoA
- output (citric acid): 4 CO2, 2 ATP, 6 NADH, 2 FADH2

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oxidative phosphorylation

- occurs in inner membrane of mitochondria
- ETC and chemiosmosis
- input: 10 NADH, 2 FADH2
- output: 26-28 ATP

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oxidative phosphorylation (ETC)

- do not produce ATP directly
- creates a proton gradient across the membrane that will power chemiosomosis by using hydrogen ions to power cellular work

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oxidative phosphorylation (chemiosmosis)

- ATP synthase: the enzyme that makes ATP from ADP + P
- uses energy from the proton gradient across the membrane
- H+ ions flow down their gradient through ATP synthase
- produces about 26-28 ATP per glucose

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respiration without oxygen

organisms will produce ATP through anaerobic respiration or fermentation

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anaerobic respiration

- generates ATP using an ETC in the absence of oxygen
- takes place in prokaryote organisms that live in environments with no oxygen
- final electron acceptors: sulfates, nitrates

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fermentation

- generates ATP without an ETC
- extension of glycolysis (recycles NAD+, occurs in cytosol, no oxygen)
- two types: alcohol, lactic acid

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alcohol fermentation

- pyruvate is converted in ethanol
- ex: yeast, bacteria

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lactic acid fermentation

- pyruvate is reduced directly by NADH to form lactate
- ex: muscle cells

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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 lowers the pH
- if lactate builds up and is unable to be broken down, it can lead to lactic acidosis (excessively low blood pH)