Topic 9

spontaneous reactions

• depend on the change in energy and entropy of a system

• reactants have less potential energy than products

metabolism

the sum of all chemical reactions that take place in an organism

negative delta G

exergonic reaction

positive delta G

endergonic reaction

hydrolysis reaction

• breakdown of ATP in an aqueous environment

• releases free energy, resulting in the formation of adenosine diphosphate and orthophosphate

Activation energy

molecules that gain energy to make bonds unstable and ready to be broken

mechanisms of enzyme action

• bringing reacting molecules closer together

• exposing the reactant molecule to altered charge environments that promote catalysis

• changing the shape of a substance molecule

the enzyme cycle

A series of steps that describes how enzymes interact with substrates, including binding, catalysis, and product release, followed by enzyme recovery for reuse.

factors that affect enzyme activity

• enzyme and substrate conditions

• enzyme inhibitors

  • temperature and pH

presence of excess substrate

can increase the rate of reaction until the enzyme is saturated. Once saturated, rate of reaction levels off

low substrate concentrations

reaction rate slows, enzymes and substrates collide infrequently

enzyme inhibitors

non-substrate molecules that can bind to an enzyme and decrease its activity

Competitive inhibition

inhibitor competes with normal substrate for active site

non-competitive inhibition

inhibitor does not compete with normal substrate for active site but combine withs sites elsewhere on enzyme

penicillin

a competitive inhibitor that acts by inhibiting the synthesis of peptidoglycan, a key component of the bacterial cell wall

aerobe

an organism that requires oxygen to survive and grow.

anaerobe

an organism that does not require oxygen for survival and may even be harmed by it.

facultative anaerobe

an organism that can survive with or without oxygen, adapting its metabolism accordingly.

aerobic respiration

• the process by which organisms convert glucose and oxygen into energy, carbon dioxide, and water.

• the acceptor molcule is oxygen

anaerobic respiration

the process by which organisms convert glucose into energy without using oxygen, producing byproducts like lactic acid or alcohol.

• inorganic molecules

fermentation

a metabolic process that converts sugar to acids, gases, or alcohol in the absence of oxygen.

• organic molecules

reduction

• partial or full gain of electrons

  • the substance that gains the electrons becomes reduced

oxidation

• partial or full loss of electrons

  • the substance from which electrons are lost (the electron donor) is oxidized

glycolysis

6 carbon glucose is broken down to 3 carbon pyruvate (oxidation)

energy investment phase

• the initial stages of glycolysis where ATP is used to phosphorylate glucose.

• endergonic that requires 2 ATP investment

cleavage phase

the stage in glycolysis where 6-carbon molecules are split into 3-carbon molecules called glyceraldehyde 3-phosphate.

pyruvate grooming

• conversion of pyruvate to acetyl-CoA

mitochondiral matrix

where pyruvate grooming and the krebs cycle occurs

pyruvate dehydrogenase

An enzyme that catalyzes the conversion of pyruvate into acetyl-CoA, producing NADH and carbon dioxide in the process.

cytosol

where glycolysis occurs and where pyruvate is formed

citric acid cycle

• fueled by acetyl-coA

• chemical reactions complete the metabolic breakdown of glucose molecules to CO2

glycolysis reactanta

• 6-C glucose

• 2 ATP

• 4 ADP

• 2 NAD+

glycolysis products

• 2× 3-C pyruvate

• 4 ATP

• 2 NADH

citric acid cycle

Oxidizes acetyl-CoA to CO₂ while producing NADH, FADH₂, and GTP/ATP for oxidative phosphorylation.

step 1 of the citric acid cycle

acetyl-CoA enters the cycle and combines with oxaloacetate to form citrate (4 carbons to 6 carbons)

step 2 of citric acid cycle

Citrate is converted into isocitrate through an intermediate called cis-aconitate.

step 3 and 4 of citric acid cycle

NAD+ is reduced to NADH, releases CO2, citrate loses a carbon molecule at each step

step 5 of citric acid cycle

energy from release of CoA generates GTP to ATP

step 6 of citric acid cycle

FAD is reduced to FADH2

step 7 of citric acid cycle

hydration of fumarate to malate

step 8 of citric acid cycle

NAD is reduced to NADH

the products of the citric acid cycle (per glucose)

6 NADH, 2 FADH2, 2 ATP

molecules that carry the most energy to the electron transport chain

NADH and FADH2

electron transport chain

a sequence of electron-carrier molecules that shuttle electrons during redox reactions, with the release of energy

inner mitochondrial membrane

where electron transport chain occurs

chemiosmosis

production of ATP using a proton gradient across membranes to phosphorylate ADP

proton gradient

a difference in proton concentration across a membrane that drives ATP synthesis

• is a form of potential energy

ATP synthase

an enzyme that uses the proton gradient to convert ADP and inorganic phosphate into ATP during chemiosmosis.

• is an exergonic process that drives endergonic reactions

fermentation

• a metabolic process that converts sugar to acids, gases, or alcohol in the absence of oxygen

• NADH molecules transfer their hyrdogen atoms to organic molecules, thus regeneration of the NAH+ enables cells to keep glycolysis going

alcoholic fermentation

yeasts and bacteria convert pyruvate produced by glycolysis to CO2 and ethanol

lactic acid fermentation

NADH is oxidized from glycolysis, producing lactic acid

autotrophs/primary producer

able to carry out carbon fixation using CO2 as a carbon source

heterotrophs

unable to synthesize its own carbon-based compounds from inorganic sources, feed on organic matter

phototrophs

photosynthetic organisms, use light as an energy source

chemotrophs

obtain energy by the oxidation of reduced compounds (electron donors) in their environment

chlorophyll a

• absorbs red and blue pigments, reflecting green

• initiates light-dependent reaction, primary electron donor in electron transport chain

chlorophyll b

extends absorption spectrum and acts as an accessory pigment that also participates in light absorption

caratenoids

• pigments that absorb light in the blue and green wavelengths, reflecting yellow, orange, and red

photosystem

a light-harvesting unit of a chloroplast thylakoid membrane, containing a reaction center and antenna (light harvesting) complexes

reaction center

• the core of a photosystem where energy is converted into chemical energy through electron transfer.

• primary electron acceptor

antenna (light harvesting) complexes

• structures within a photosystem that capture and funnel light energy to the reaction center, maximizing light absorption.

step 1 of electron transport chain (photosynthesis)

• light excited electrons (P680) are passed to a primary acceptor

• P680 returns to reduced state by donation of electrons from water, producing O2

step 2 of electron transport chain (photosynthesis)

• electrons are passed by mobile carrier PQ to cytochrome complex, then to plastocyanin and PSI

• some energy used to pump H+ to lumen, creating a H+ gradient across the thylakoid membrane

step 3 of electron transport chain (photosynthesis)

• electrons re-energized by light, P700 reduced, electrons passed on to Ferredoxin (used to reduce NADP+ to NADPH)

step 4 of electron transport chain (photosynthesis)

• energy produced by protons move through ATP synthase used to generate ATP

NADPH

NADPH is released into the __________ and will be used for carbon fixation

the final products of electron transport chain

ATP and NADPH

photophosphorylation

is the process of generating ATP from ADP and inorganic phosphate, driven by light energy during photosynthesis.

cyclic electron flow

is a process in photosynthesis that generates ATP without producing NADPH or oxygen. It involves the cycling of electrons through photosystem I.

RUBISCO

• produces 2x 3 carbon compound molecule in the first step of the calvin cycle. Catalyzes the fixation of CO2

• most abundant protein on earth

step 1 of the calvin cycle

involves the fixation of carbon dioxide by RUBISCO to form 3-phosphoglycerate.

step 2 of the calvin cycle

involves the reduction of 3-phosphoglycerate to glyceraldehyde-3-phosphate (G3P), utilizing ATP and NADPH.

step 3 of the calvin cycle

involves the regeneration of ribulose bisphosphate (RuBP) from G3P, enabling the cycle to continue.

G3P

can be converted to glucose or fructose in an exergonic reaction

the calvin cycle

• occurs in the stroma

• uses carbon (CO2), ATP and NADHP to convert carbon dioxide into organic compounds, primarily through steps of fixation, reduction, and regeneration.