AP Biology - Unit 3

determination of if rxn occurs

environmental factors

catalysts definition

substances that accelerate chemical rxns w/out being changed

Enzymes are…

proteins and follow rules of protein construction (primary, secondary, tertiary structure)

enzyme conformed =

physical location for reactant molecules to attach to (substrates)

interaction b/w enzyme & substrate

shape dependent; substrate properties and shape must be compatible w/active site

substrate relation

closely related based on highly similar structure and properties

enzymes w/decomposition rxns

interact with 1 substrate & produce lots of products

enzymes catalysing synthesis rxn

accepts many substrates & product one product

substrate bonding to active site triggers…

shape change

shape change results in…

stress on bonds w/in substrate = bonds weakened and less potential energy required for rxn

enzyme not changed by rxn

concentration of substrate/enzyme changes as time passes

as rxn progress =

substrate molecules are less available and slows rxn down

every enzyme has set environment conditions where it functions most effectively

temperature; pH; concentration of enzyme &/or substrate; concentration of other solutes; presence of cofactors and coenzymes

cofactor

substance other than substrate whose presence is required for enzyme function

coenzyme

organic non-protein based compound that binds to enzymes reversible assisting in function

denatured

enzyme lost its function conformation bc of change in environmental conditions

change in enzyme shape =

down or loss of enzymatic activity

weaker interactions/loss of shape

more likely to be interfered/prevents enzyme function

allosteric site (in some enzymes)

regulatory molecules binds and locks enzyme into confirmation → regulating an enzyme

enzyme action halted by…

blocking active site

competitive inhibition

involves molecule (non-substrate) binding to active site (no chem-rxn and blocks substrate)

non-competitive inhibition

form of allosteric regulation → occurs when molecules binds to enzyme somewhere other than active site = conformational change to enzyme

biochemical pathways

involve series of enzymes functioning like relay-race

feedback inhibition

end product reversibly binds to allosteric site of 1st enzyme in pathway → changes first conformation = prevents initial rxn occuring

metabolic pathways

pathways used to convert substrates into products

drivers of pathways

enzymes → proteins that work to assist chemical rxns by building or breaking down molecules

rate of reaction

can speed, slow, or stop based on cell needs

allosteric site role

prevents cells from wasting resources/energy to maintain homeostasis

Greater concentration of substrate than competition inhibitor

rxn occurs

competition inhibitor has higher concentration

rxn halted

stages of photosynthesis

light-dependent rxns & calvin cycle

consumers

consuming/ingesting organic molecules for energy

producer

taking energy and forming into more energy

energy

can’t be created or destroyed; only transferred & transforms as moves from one organism to another

energy forms

light; gravitational; kinetic (motion); nuclear

chemical energy

a form of potential energy; result of molecular structure

law of thermodynamics

study of energy transformations

first law of thermodynamics

energy cannot be created or destroyed

second law of thermodynamics

less energy is available after each transformation (release of heat); transformations favor a disorderly state

entropy

measures the disorder of a system (relative); use as little energy as possible; related to building and breaking molecules

catabolic reaction

large molecules broken into small products

anabolic reaction

smaller reactants made into larger products

free energy

energy available for a system to do work

catabolic rxn ex.

glucose → O & H molecules

anabolic rxn. ex.

O & H molecules → glucose

chemical rxns and free energy

chemical rxns change amount of free energy in a system

-ΔG

spontaneous rxn & release of energy

+ΔG

non-spontaneous rxn & requires energy

when is equilibrium achieved

when rates of forward & reverse rxns are identical

why is equilibrium never achieved in living system

constant supply of matter/energy input

metabolic pathway

pathways linked together by using products from one rxn as reactants of another

words associated with breaking down molecules

catabolic; +ΔS (increasing entropy); exergnoic (releasing energy); -ΔG (decreasing free energy); spontaneous

words associated with building up molecules

anabolic; -ΔS (decreasing entropy); endergonic (storing energy); +ΔG (increasing free energy); non-spontaneous

chemical rxns involve…

all chemical rxns involve breaking/building chemical bonds by transferring of electrons

reduced atoms

atoms receiving electrons

oxidized atoms

atoms giving electrons r

redox…

can’t occur independently of each other

whether rxn occurs =

release or storage of energy depends on bond energies of reactant and product

ATP hydrolyzed

free phosphate ion bonds to reactant molecules (phosphorylation)

ADP → ATP

addition of phosphorus ion

Phosphorylation

addition of phosphoryl group to a molecule

photosynthesis captures energy from ….. and produces….

sun; sugars

what did photosynthesis first evolve from

prokaryotes; evolved in organisms like cyanobacteria

evolution of photosynthesis contributed to…

oxidation of atmosphere

visible light is produced by sun and used as energy

1% of sunlight is used for photosynthesis

pigments

molecules that absorb some wavelengths of light and reflect others to appear as a color

chlorophyll molecule has a

high concentration in plant = green color

chlorophyll A

primary pigment responsible for initiating rxns of photosynthesis → absorbs blue and red wavelengths

light energy from sun drives…

anabolic endergonic rxns

where is chloroplast density hightest?

on the top surface of the leaf in mesophyll cells to be efficient w/using light energy

stomata

pores on bottom of the leaf that open and close to regulate exchange of gases (CO2 in and O2 out)

chloroplast

stroma; thylakoids; photosystems; thylakoid space; granum

stroma

large internal space where Calvin Cycle occurs

thylakoid

membrane bound structure stacked on each other and have photosystems & electron transport chains; location of dependent rxns

photosystems

clusters of photosynthetic pigments embedded in membrane

thylakoid space

internal space of thylakoids and interconnected w/other thylakoids; provides a concentration gradient of H+ (protons) to be est.

granum

stack of thylakoids

light dependent rxns

light energy to chemical energy

Photosystem 2

1. lgiht strikes photosynthetic pigments embedded in thylakoid membrane and light is transferred

2. E- removed from cholorphyll A and boosted to highter energy level → replaced with E- from H2o

   1. oxygen gas is produced as waste

Electron transport chain

links photosystem 1 & 2 by series of proteins embedded in TK membrane

ETC processes

1. E- travel from protein to protein in TK in ETC (pumps H+ to in stroma)

2. ATP is generated as E- are transferred

2. ETC processes

proteins of ETC use energy from E- transfer to actively transport protons from stroma into TK space; concentration gradient of protons = facilitated diffusion of protons back into stroma thru ATP synthase

photosystem 1

1. E- from ETC deposited @ chlorophyll A

2. E- boosted to higher energy level by light

3. 2 E- & proton transferred to E- carrier (NADP+ → NAPDH)

reactants and products of dependent rxns

water and o2 gas; ATP and NADPH are NOT net products

atp and nadph from dependent =

provides energy to power calvin cycle

napdh deliver electrons from

h2o to form new covalent bonds to build organic molecules

3 stages of calvin cycle

carbon fixation; reduction; regeneration

carbon fixation

1. co2 from atmosphere enters stomata

2. Rubisco joins co2 to acceptor → RuBP

3. RuBP added to crbon = 6C 2 phosphate molecule that is unstable = 6 molecules each with 3C and 1 phosphate

RuBP

five carbon molecules with two phosphates

Reduction

1. ATP broken down; gives 2nd phosphate to 3c molecules

2. NAPDH delivers E- to 3c molecules → rearranged and lose phosphate = 6 glyceraldehyde 3 phosphate molecules

   1. 1 G3P molecule exits calvin cycle and remaining 5 complete it

after reduction NADP+ and ADP and free phosphates

returns to dependent rxns for reconstruction to be sent back and used again

Regeneration of CO2 acceptor (RuBP)

rearranges 5 G3P molecules into 3 molecules of RuBP to continue calvin cycle

1 full completion of photosynthesis =

1 G3P molecule

G3P can be used as reactant to form…

biochem pathways for mono/polysaccgarudes; mentose sugars; fatty acids; glycerol; amino acids

photorespiration

CO2 levels fall, O2 levels rise = rubisco fixes oxygen to RuBP

Stomata is important for…

exchange of gases bus especially H2O evaporate from plants

why do plants regulate stomata

to slow/speed evaporation process (ex. hot dry days, plants close stomata to avoid water loss)

why is photorespiration unstainable over long periods?

because it won’t make enough G3P to survive

alternatives to C3 photosynthesis

C4 plants - spatial separation; CAM plants - Temporal seperation

Spatial Separation - C4 Plants

1. fixes co2 to organic acid

2. shipped off to another cell for rest of calvin cycle

   1. *bc carbonfixation and calvin cycle occur in two different locations (cells)