unit 3 biology

12th grade ap biology

metabolism

metabolism

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

metabolic pathways

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

catabolic pathways

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

anabolic pathways

consume energy to build complicated molecules from simpler compounds

energy

- 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
- the laws apply to the universe as a whole

1st law of thermodynamics

energy cannot be created or destroyed, only transferred or transformed

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

free energy

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

exergonic reactions

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

endergonic reactions

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

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

mechanical work

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

transport work

pumping substances across membranes against spontaneous movement

chemical work

- synthesis of molecules
- ex: building polymers from monomers

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)

phosphorylation

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

enzymes

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

enzyme structure

acts on a reactant called a substrate

enzyme function

active site (area for substrate to bind)

induced fit

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

enzyme catabolism

helps break down complex molecules

enzyme anabolism

helps build complex molecules

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

enzyme cofactor

- nonprotein 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
- ex: vitamins

enzyme inhibitors

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

permanent inhibition

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

reversible inhibition

inhibitor binds with weak interactions

competitive inhibitors

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

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

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

allosteric enzymes

two binding sites (1 active and 1 allosteric)

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

allosteric activator

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

allosteric inhibitor

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

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)

feedback inhibition

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

photosynthesis

conversion of light energy to chemical energy

autotrophs

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

heterotrophs

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

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

site of photosynthesis

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

mesophyll

cells that make up the interior tissue of the leaf

stomata

pores in leaves that allow CO2 in and O2 out

chloroplast structure

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

photosynthesis reaction

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

photosynthesis stages

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

pigment

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

chlorophyll a

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

chlorophyll b

- accessory pigment
- yellow/green pigment

carotenoids

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

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

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

photosystems

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

reaction center

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

light capturing complexes

pigments associated with proteins

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

linear electron flow

each excited electron will pass from PS2 to PS1 via ETC

ETC (photosynthesis)

in light reaction on thylakoid membrane

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

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

light reaction inputs and outputs

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

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

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

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

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)

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

calvin cycle inputs and outputs

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

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

C4 plants

- stomata partially close to conserve water
- ex: corn, 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 reaction occur and CO2 is released from the organic acids and incorporated into the calvin cycle
- ex: cactus, succulents, jade, pineapples

cellular respiration

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

cellular respiration reaction

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

starch

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

path of electrons in energy harvest

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

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

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

oxygen

final electron acceptor to make water

stages of cellular respiration

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

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

energy investment stage

the cell uses ATP to phosphorylate compounds of glucose

energy payoff stage

energy is produced by substrate level phosphorylation

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

oxidative phosphorylation

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

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

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

respiration without oxygen

organisms will produce ATP through anaerobic respiration or fermentation

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

fermentation

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

alcohol fermentation

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

lactic acid fermentation

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

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)