Bioenergetics Unit Vocab

Chlorophyll

Green Pigment

Main photosynthetic pigmnet

Absorbs primarily violet-blue and red wavelengths

Metabolism

the totality of an organisms chemical reactions that result from interactions between molecules within the cell

Cellular Respiration

The process by which cells produce energy (ATP)

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

(oxidative process)

Thylakoids

dense interconnected membranous sacs where the light reactions occur

metabolic pathway

a sequence of chemical reactions undergone by a compound in a living organism, start with substrate end with product

ATP

Consists of adenosine plus 3 phosphates; source of immediate energy

(know this structure)

Grana

stacks of thylakoid

catabolic

breaking a complex molecule down into its simpler parts, releasing energy. ie. cellular respiration

Glycolysis

Anaerobic phase of cellular respiration that breaks down glucose into 2 molecules of pyruvate

- Occurs in cytoplasm

- Makes 2 Net ATP molecules and 2 molecules of NADH

Fermentation

A process that produces a small amount of energy in the absence of oxygen

- Begins with glycolysis and produces 2 molecules of pyruvate and then alcohol or lactic acid

- Converts NADH to NAD+ by transferring electrons to pyruvate

anabolic

using energy to build complex molecules from simpler molecules. ie. protein synthesis

Granum

singular of grana

Chloroplast

sites of photosynthesis

Bioenergetics

the study of how organisms manage their energy resources

Aerobic Respiration

Consists of Krebs cycle and electron transport chain (ETC) and oxidative phosphorylation

- Requires oxygen

- Occurs after the anaerobic respiration

- Produces 34 ATP

- Occurs in the mitochondria

Photosynthesis

conversion of light energy into chemical energy stored in sugar and other organic molecules

energy

capacity to cause change, do work

Citric Acid Cycle

Synonym for Krebs Cycle

Photosynthesis Equation

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

heat(thermal energy)

kinetic energy associated with random movement of molecules

Anaerobic Respiration

respiration without oxygen present, common synonym for fermentation

Aerobic

With oxygen

chemical energy

potential energy available for release in a chemical reaction, energy within bonds

Carbon Dioxide

source of inorganic carbon used in photosynthesis

Anaerobic

Without oxygen

Electromagnetic Spectrum

Electromagnetic energy which travels in waves

exergonic reaction

a reaction with a net release of free energy, negative free energy, spontaneous

endergonic reaction

a reaction that absorbs free energy from its surroundings, non-spontaneous, positive free energy

Krebs cycle

Uses 2 acetyl co-A to produces 6 NADH, 2 FADH2, and 2 ATP and CO2 as waste

- Occurs in the mitochondrial inner matrix

- Part of aerobic respiration

- Turns twice for each molecule of glucose

(also known as Citric Acid Cycle)

Colors

Light we see is reflected off objects and light we don't see is absorbed by objects

White

All colors reflected

catalyst

a chemical agent that speeds up chemical reactions without being consumed by the reaction

Acetyl co-A

coenzyme combined with pyruvate created in middle step; raw material of Krebs cycle

ATP synthase

An enzyme that produces ATP as protons (H+) flow down a gradient through chemiosmosis or oxidative phosphorylation

enzymes

a catalytic protein, speeds up metabolic reactions by lowering activation energy, very specific, reusable, unchanged by reaction

Black

All colors absorbed

activation energy

initial energy needed to start a chemical reaction, free energy for activating reaction, given off by heat

Electron Transport Chain

Energy-coupling reaction that creates H+ gradient in the membrane necessary for the production of ATP through chemiosmosis or oxidative phosphorylation

- Energy released from the exergonic flow of electrons is used to pump protons across the membrane to create a proton gradient

- Electrons flow down the chain from one carrier molecule to the next in a series of redox reactions

- The final hydrogen (H+) acceptor in the chain is oxygen (H2+1/2O2 --> H2O) / Water is the waste product and is exhaled

Pigment

a molecule that absorbs wavelengths in the visible light spectrum

induced fit

brings the chemical groups of the active site into positions that enhance their ability to catalyze the reaction, makes the enzyme more effective

Oxygen

Final electron acceptor in the ETC

Carotenoid

Group of pigments that absorb blue and blue-green wavelengths, appear orange, yellow, and red

Water

Waste product created by at the end of the ETC

Chemiosmosis

A process by which ATP is formed as protons flow down a proton gradient through the ATP synthase complex

Light Reactions

Occur in thylakoid membrane and are also called light dependent reactions

Substrate

the REACTANT that an enzyme acts on

Substrate-Level Phosphorylation

Process that produces a small amount of ATP during glycolysis and the Krebs cycle

During this process, the enzyme kinase transfers a phosphate from a susbtrate directly to ADP, forming ATP

Photosystem

Consists of a reaction-center complex surrounded by light-harvesting complexes which split water to create electrons that get transferred to NADP+ to create NADPH and H+ which are used to create ATP

Enzyme-Substrate Complex

The enzyme and substrate bound together

Active Site

region on the enzyme where substrate binds

Oxidative Phosphorylation

The production of ATP using energy from the electron transport chain. Ends with the production of water.

Light-Harvesting Complex

Contains chlorophyll a, chlorophyll b, and carotenoids (within the photosystem) that will trap light energy for use in the light reactions

Photosystem 1

Has P700 chlorophyll a in reaction-center complex, thought to have evolved first because it can work alone to create primary acceptors, 2nd of the photosystems

Hydrogen and Ionic Bonds

substrate held in active site by WEAK interactions

NADH

Primary electron transporter to the ETC from glycolysis and Krebs cycle

FADH2

Secondary electron transporter to the ETC from Krebs cycle, entering at lower energy levels than NADH

Lock and Key

active site on enzyme fits substrate exactly

Photosystem 2

Has P680 chlorophyll a in reaction-center complex, first of the photosystems. splits water into electrons, oxygen, and hydrogen ions

Ways enzymes lower activation energy

can do this by having a favorable environment, straining substrate molecules, orienting substrates correctly

NAD+

Oxidized form of NADH

Cytochrome

Protein in the electron transport chain of the photosystems that transfers the electrons to create NADPH

Calvin Cycle

Light-Independent reactions

Occurs in stoma, does not use light directly. Uses the enzyme Rubisco to create 2 molecules of G3P which is then either used to create glucose or recycled back into RuBP to restart the cycle

hydrolysis

The addition of water to a polymer to split it into monomers.

FAD

Oxidized form of FADH2

Rubisco

The most abundant protein on Earth

Carbon Fixation is catalyzed by Rubisco

cofactors

non-protein enzyme helpers ex. zinc, iron, copper

Redox Reactions

Reduction and oxidation

Reduction

gain of electrons; gain of hydrogen -> for storing energy

coenzymes

organic enzyme helpers

Denature

A change in the shape of a protein (such as an enzyme) that can be caused by changes in temperature or pH (among other things).

Oxidation

loss of electrons; loss of hydrogen -> for releasing energy

1 Cycle of Calvin Cycle

1 CO2 is fixed

3 ATP are used

2 NADPH are used

1 RuBP is regenerated

6 cycles needed to make 1 glucose molecule

C4 Photosynthesis

A method that bypasses photorespiration

Happens in corn, sugarcane, and other plants in hot, dry environments

Converts carbon dioxide to a 4-carbon intermediary which is then stored in bundle-sheath cells

Renature

removing reagent that denatures protein brings to this state

Cytochromes

Proteins that help make up the ETC; transport electrons

C3 Plant

Plants that use the Calvin Cycle without creating carbon intermediaries, take in carbon dioxide through stomata. An enzyme called RuBisCO helps the carbon dioxide combine to make sugar.

Feedback inhibition

A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.

Inner-membrane space

Mitochondrial part where the ETC pumps protons

Matrix

Site of Krebs cycle in mitochondria

Allosteric Regulation

can accelerate or inhibit production and enzyme activity by attaching to another part of the protein. this changes the shape of the active site which inhibits substrates from bonding and producing more products

CAM Plants

Plants that only open stomata at night. They convert carbon dioxide to malic acid which is then converted back into carbon dioxide during the day for the Calvin cycle

Activator

one of the allosteric regulators, stabilizes and keeps active site open for production, wedges open

Inner mitochondrial membrane

site of oxidative phosphorylation and the electron transport chain

Inhibitor

a substance that interferes with the action of a catalyst

Competitive Inhibitor

inhibitor that mimics original substrate by blocking the original substrate

noncompetitive inhibitor

bind to another part of enzyme to change shape and block substrate from producing

Conditions that affect enzymes

environment, pH, temp, salinity, chemicals that infuse enzyme, increase activity by increasing substrate concentration

reducing agent

The electron donor in a redox reaction. The reducing agent gets oxidized.

oxidizing agent

Accepts electrons and becomes reduced.

pyruvate oxidation

Conversion of pyruvate to acetyl CoA and CO2 that occurs in the mitochondrial matrix in the presence of O2.

Link reaction

Stage of aerobic respiration that links glycolysis with the Krebs cycle. In eukaryote cells it occurs in the mitochondrial matrix. (sometimes called the prep reaction or the oxidation of pyruvate)

prep reaction (link reaction)

Reaction that oxidizes pyruvate with the release of carbon dioxide; results in acetyl CoA and connects glycolysis to the citric acid cycle. (sometimes called the oxidation of pyruvate)

cyclic electron flow

A route of electron flow during the light reactions of photosynthesis that involves only photosystem I and that produces ATP but not NADPH or oxygen.

linear electron flow

the primary pathway, involves both photosystems and produces ATP and NADPH using light energy (non-cyclic electron flow)

glucose

C6H12O6

A simple sugar that is an important source of energy.

Contains potential energy in the form of chemical bonds

Engelmann's experiment

He took a plant and put it under different colored lights to see how that affected rates of photosynthesis (like a boss)