AP bio unit 3

catalysis

something that speeds up a reaction (without being a reactant) by reducing the activation energy

enzymes

catalysts in biological systems

catalyst

factor that’s added to lower the activation energy

substrates

molecules that bind to the proteins of an enzyme

active site

area where 2 substrates bind

activation energy

the amount of energy that must be put in for the reaction to begin

transition state

the unstable state a molecule takes to be able to allow bonds to break

exergonic reaction

a reaction that goes from reactant to product

endergonic

a reaction that goes from products to reactants

temperature

an affecting factor of enzymes/active sites; higher temp = higher reaction rates

pH

affecting factor of enzymes/active sites; changes in pH change residues within active site amino acids, making it harder for substrates to bind

acidic pH

below 7 on the pH scale

basic pH

above 7 on the pH scale

enzyme concentration

affecting factor on enzymes/active sites; increasing concentration = faster reaction

substrate concentration

affecting factor of enzymes/active sites; can increase reaction rate

induced fit

an enzyme changes shape slightly when it binds to its substrate

competitive inhibition

a competitor reaches an active site first, preventing the substrate from binding to it

allosteric competitive inhibition

a competitor binds to an allosteric (different) site on the enzyme but has the same effect of preventing the substrate from binding to its active site

noncompetitive inhibition

a substrate & an inhibitor can bind to their sites, but the reaction will no longer proceed, which forces them to unbind

regulatory molecules

activator/inhibitor molecules that bind specifically to an enzyme; can turn enzyme activity up or down

cofactors

nonprotein helper molecules; can be attached to enzyme permanently by covalent bonds or temporarily by hydrogen/ionic bonds

compartmentalization

storing enzymes in specific compartments can keep them from doing damage or provide the right conditions for activity

feedback inhibition

end product of a metabolic pathway acts on the key enzyme regulating entry to that pathway, which keeps more of the end product from being produced

activators

molecules that increase the activity of an enzyme

inhibitors

molecules that decrease the activity of an enzyme

allosteric enzymes

enzymes that are allosterically regulated have a unique set of properties that set them apart. typically have multiple active sites located on different protein subunits

cooperativity

a substrate can act as an allosteric activator, causing the activity of another site to go up

coenzymes

subset of cofactors that are organic molecules

thermodynamics

the study of energy transfers in molecules or groups of them

system

the item of collection of items that is the focus

surroundings

everything that is not in the system

open system

exchanges energy & matter with its surroundings

closed system

can only exchange energy with its surroundings, not matter

first law of thermodynamics

energy can’t be created or destroyed; can only change form or be transferred from one object to another

heat

thermal energy moving from one object to another; can be released as unusable energy that is a byproduct of a reaction

entropy

the degree of randomness or disorder in a system

second law of thermodynamics

every energy transfer that takes place will increase the entropy of the universe & reduce the amount of usable energy to do work

photosynthesis

the process in which plants turn co2, h2o, & sunlight into carbohydrates & oxygen; converts light energy to chemical energy in form of sugars

photoautotrophs

organisms that produce their own food using light energy

heterotroph

organisms that can’t convert co2 to organic compounds

light reactions

stage of photosynthesis that is light dependant. require photons & water and results in ATP, NADPH, and molecules oxygen. take place in the thylakoid membrane

OIL

Oxidation Is Losing an electron

RIG

Reduction Is Gaining an electron

dark reactions (Calvin cycle)

stage of photosynthesis that is light independant. requires co2, ATP, & NADPH to produce pgal/g3p (molecules used to produce glucose). takes place in the stroma

mesophyll

cells in the middle layer of leaf tissue that are the primary site of photosynthesis

stomata

small pores found on the surface of leaves that let co2 diffuse into the mesophyll layer & oxygen diffuse out

chloroplasts

organelles in each mesophyll cell that are specialized to carry out the reactions of photosynthesis

thylakoids

disc-like structures in chloroplasts

grana

thylakoids arranged in piles

chlorophylls

green colored pigments found in thylakoid that absorb light

stroma

space around grana that is filled with fluid

thylakoid space

space inside the thylakoid discs

photosystems

large complexes of proteins and pigments that are optimized to harvest light

p700

special pair of chlorophyll molecules found at the core of photosystem I

p680

special pair of chlorophyll molecules found at the core of photosystem II

non-cyclic photophosphorylation

electrons are removed from water and passed through photosystem 2 and 1 before ending up in nadph

resonance energy transfer

a pigment is excited by light and transfers energy to a neighboring pigment through direct electromagnetic interactions

A0

a chlorophyll that is the primary electron acceptor in p.s. 1

pheophytin

primary elections acceptor in p.s. 2 that is an organic molecules resembling chlorophyll

ATP synthase

enzyme that harnesses the flow of protons to make ATP from ADP and phosphate

chemiosmosis

the process of making ATP using energy stored in a chemical gradient

linear phosphorylation

electrons travel from water to nadph through photosystem 2 and 1

cyclic photophosphorylatoin

electrons break this pattern and loop back to the first part of the electron transport chain, repeatedly cycling through p.s. 1 instead of ending up at nadph

carbon fixation

first step in calvin cycle. co2 molecule combines with a 5-carbon acceptor molecule RuBP, making a 6-carbon compound that splits into 2 molecules of a 3-carbon compound (3-pga)

rubisco

enzyme that catalyzes carbon fixation

reduction

second step in Calvin cycle. ATP and NADH are used to convert the 3-pga molecules into molecules of a 3-carbon sugar, g3p

regeneration

third step in Calvin cycle. some g3p molecules go to make glucose and other are recycled to regenerate the RuBP acceptor

cellular respiration

process in which we derive energy from fuel and glucose; energy produced in CR is used to produce ATP

glycolysis

first step of cr. requires 2 ATP and produces 2 additional ATP; nad+ is converted into nadh. 2 pyruvate are produced. only step in CR that is anaerobic.

pyruvate oxidation

second step of cr. pyruvates from glycolysis enter the mitochondrial matrix are converted into a 2-carbon molecule bound to acetyl coA. co2 is released and NADH is generated

krebs cycle (citric acid cycle)

third step of cr. acetyl coA from pyruvate oxidation step combines with a 4-carbon molecule and goes through a cycle of reactions, which ends up regenerating the 4-carbon start molecule. ATP, NADH & fadh2 are produced and co2 is released

oxidative phosphorylation

last step of cr. nadh and fadh2 from previous steps deposit their electrons in the ETC and return to their original form.

electron transport chain

included in oxidative phosphorylation; energy is released and used to pump protons out of the matrix as electrons move down the chain, forming a gradient.

atp synthase

enzyme in which protons flow through; makes atp

chemiosmosis

the process in which energy from a proton gradient is used to make ATP

catabolic reactions

reactions that extract energy from molecules like glucose

substrate-level phosphorylation

within the steps of a glucose molecule being broken down and releasing energy (that’s eventually captured as atp), a phosphate group is transferred from a pathway intermediate straight to ADP.

oxidative phosphorylation

an electron is passed through the electron transport chain & the energy it releases is used to pump protons out of the matrix of the mitochondrion (forming an electrochemical gradient). H+ protons flow back down their gradient & through an enzyme known as atp synthase, which drives the synthesis of atp.

electron carriers/shuttles

small organic molecules that pick up electrons from one molecule and drop them off to another. 2 important ones are nad+ and fad

redox reactions (oxidation-reduction reactions)

reactions involving electron transfers; one molecule loses electrons and is oxidized & the other molecule gains electrons and is reduced