Unit 3 - Enzymes and Metabolism

Focusing on enzymes and metabolism, explores how biological catalysts speed up chemical reactions and how cells harness energy

Metabolism

All of the chemical reactions in an organism.

Metabolic Pathways

Series of chemical reactions that either build complex molecules or break down complex molecules.

Catabolic Pathways

Pathways that release energy by breaking down complex molecules into simpler compounds.

Anabolic Pathways

Pathways that consume energy to build complicated molecules from simpler compounds.

Kinetic Energy

Energy associated with motion.

Potential Energy

Stored energy that can be converted into kinetic energy.

First Law of Thermodynamics

Energy cannot be created or destroyed; it can only be transferred or transformed.

Second Law of Thermodynamics

Energy transformation increases the entropy or disorder of the universe.

Free Energy

Energy that determines the likelihood of reactions occurring; ΔG = ΔH - TΔS.

Exergonic Reactions

Reactions that release energy and occur spontaneously.

Endergonic Reactions

Reactions that absorb energy and do not occur spontaneously.

Adenosine Triphosphate (ATP)

Molecule that organisms use as a source of energy to perform work.

Enzymes

Macromolecules that catalyze reactions by lowering the activation energy.

Active Site

Area of an enzyme where substrates bind.

Induced Fit

Change in the shape of an enzyme’s active site to better fit the substrate.

Cofactors

Non-protein molecules that assist enzyme function.

Competitive Inhibitors

Substances that reduce enzyme activity by blocking substrates from binding to the active site.

Noncompetitive Inhibitors

Substances that bind to an allosteric site, changing the shape of the enzyme and preventing substrate binding.

Allosteric Regulation

Regulation of enzyme activity by binding molecules to sites other than the active site.

Feedback Inhibition

Process where the end product of a metabolic pathway inhibits an early enzyme in the pathway.

Cooperativity

When substrate binding to one active site stabilizes the active form of the enzyme at other active sites.

Photosynthesis

The conversion of light energy to chemical energy

Autotroph

Organisms that produce their own food (organic molecules) from simple substances in their surroundings

Heterotroph

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

Cyanobacteria

Early prokaryotes capable of photosynthesis that played a crucial role in Earth's oxygenation.

Chloroplast

organelle for the location of photosynthesis found in the mesophyll, the cells that make up the interior tissue of the leaf where chlorophyll captures light energy.

Stomata

pores in leaves that allow CO2 in and O2 out

Stroma

aqueous internal fluid of chloroplasts where the Calvin cycle occurs.

Thylakoids

form stacks known as grana

Chlorophyll

green pigment in thylakoid membranes

Redox Reaction

reaction involving complete or partial transfer of one or more electrons from one reactant to another

In photosynthesis: the electrons are transferred with H+ (from split H2O) to CO2 reducing it to sugar

Light

electromagnetic energy; made up of particles of energy called photons; travel in waves

Wavelength

the distance from the crest of one wave to the crest of the next; the entire range is known as the electromagnetic spectrum; 380 nm to 750 nm is visible light

Chlorophyll a

Primary pigment; Involved in the light reactions; Blue/green pigment

Chlorophyll b

Accessory pigment; Yellow/green pigment

Carotenoids

Broaden the spectrum of colors that drive photosynthesis; Yellow/orange pigment

Photoprotection

carotenoids absorb and dissipate excessive light energy that could damage chlorophyll or interact with oxygen

Light Reactions

Occur in the thylakoid membrane in the photosystems; Converts solar energy to chemical energy; Chemical energy is in two forms: NADPH and ATP; The cell accomplishes this conversion by using light energy (photons) to excite electrons

Photosystems

reaction center and light capturing complexes

Reaction center

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

Light capturing complexes

pigments associated with proteins

Photosystem 2

reaction center P680; Absorbs light at 680 nm

Photosystem 1

reaction center P700; absorbs light at 700 nm

Photosystem II

Light energy (photon) causes an e- to go from an excited state back to a ground state. This repeats until it reaches the P680 pair of chlorophyll a molecules; The e- is transferred to a primary e- acceptor, forming P680+; H2O is split into: 2 e-, 2 H+, and 1 oxygen atom (which immediately bonds to another oxygen atom)

Linear electron flow

each excited electron will pass from PS II to PS I via the electron transport chain

Photosystem I

Light energy excites electrons in the P700 chlorophyll molecules to become P700+; Electrons go down a second transport chain; NADP⁺ reductase catalyzes the transfer of e^- from Fd to NADP⁺

Calvin Cycle

cyclic electron flow; Uses ATP and NADH to reduce CO2 to sugar (G3P); For net synthesis of 1 G3P molecule, the cycle must take place 3 times

Carbon fixation

CO2 is incorporated into the calvin cycle one at a time; Each CO2 attaches to a molecule of RuBP; Catalyzed by the enzyme rubisco; Forms 3-phosphoglycerate

Reduction

Each molecule of 3-phosphoglycerate is phosphorylated by ATP (uses 6 total); Becomes 1,3-bisphosphoglycerate; 6 NADPH molecules donate electrons to 1,3-bisphosphoglycerate; Reduces to G3P; 6 molecules of G3P are formed, but only one is counted as a net gain; The other 5 G3P molecules are used to regenerate RuBP

Regeneration of RuBP

5 G3P molecules are used to regenerate 3 molecules of RuBP'; Uses 3 ATP for regeneration; Cycle is now ready to take in CO2 again

Photorespiration

On very hot days plants close their stomata to stop water loss; Causes less CO2 to be present, and more O2; Rubisco binds to O2 and uses ATP; The process produces CO2; NO sugar is produced; BAD for the plant

C4 Plants

Spatial separation of steps; Stomata partially close to conserve water; Mesophyll cells fix CO2 into a 4-C molecule; Transferred to bundle sheath cells; Releases CO2 to be used in the Calvin cycle

Examples: maize (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 reactions occur and CO2 is released from the organic acids and incorporated into the Calvin cycle

Examples: pineapples, cacti, succulents, jade

Cellular Respiration

Cells harvest chemical energy stored in organic molecules and use it to generate ATP; Starch is the major source of fuel for animals

Electron transport chain (ETC)

a sequence of membrane proteins that shuttle electrons down a series of redox reactions; Releases energy used to make ATP; ETC transfers e- to O2 (the final e- acceptor) to make H2O; Releases energy

Glycolysis

Starting point of cellular respiration; Occurs in the cytosol; Splits glucose (6C) into 2 pyruvates (3C)

Energy investment stage

the cell uses ATP to phosphorylate compounds of glucose

Energy payoff stage

energy is produced by substrate level phosphorylation

Pyruvate Oxidation

If oxygen is present, the pyruvate enters the mitochondria (eukaryotic cells); Pyruvate is oxidized into acetyl coA; Acetyl coA is used to make citrate in the citric acid cycle; 2 CO2 and 2 NADH are produced

Citric Acid Cycle

Also known as the Krebs cycle; Occurs in the mitochondrial matrix'; Turns acetyl CoA into citrate; Releases CO2; ATP synthesized; Electrons transferred to NADH and FADH2

Oxidative Phosphorylation

consists of: Electron transport chain and Chemiosmosis

Chemiosmosis

H+ ions flow down their gradient through ATP synthase; ATP synthase acts like a rotor; When H+ binds the rotor spins; Activates catalytic sites to turn ADP + P into ATP; Produces about 26-28 ATP per glucose

ATP synthase

the enzyme that makes ATP from ADP + P; Uses energy from the H+ gradient across the membrane

Anaerobic Respiration

generates ATP using an ETC in the absence of oxygen; takes place in prokaryotic organisms that live in environments with no oxygen; the final electron acceptors: sulfates or nitrates

Fermentation

generates ATP without an ETC; Extension of glycolysis; Recycles NAD+; Occurs in the cytosol; NO oxygen

Alcohol fermentation

pyruvate is converted into ethanol

Examples: bacteria, yeast

Lactic acid fermentation

pyruvate is reduced directly by NADH to form lactate

Example: Muscle Cells