AP Bio: Cell Energetics (unit 3)

ENZYMES

ENZYME PROPERTIES

• proteins; biological catalysts; reusable

• essential (without them, biological reactions would progress too slowly to sustain life)

  • enzymes help overcome low concentration of substrates by holding onto them and giving them more time to react (more of a chance than spontaneous collisions)

  • lower activation energy of reactions

• highly specific (each one acts on a specific narrow range of chemical reactions)

  • induced fit hypothesis:

    • explains how enzymes catalyze similar chemical reactions. the active site changes shape to conform to each substrate, forming an enzyme-substrate complex.

    • is like a handshake

    • disproves the previous “lock and key” hypothesis that enzymes and substrates are in a 1-1 specific relationshi

• appearance:

  • 3º or 4º structures

  • active site

    • substrate binds here

  • cofactor “site”

    • cofactors: molecules that enhance enzyme activity; like vitamins

  • allosteric sites

    • binding sites for regulatory molecules; switches enzymes on/off to regulate its activity

• “ase”

  • kinases → enzymes that phosphorylate substrates (and more)

factors affecting enzyme activity:

• general protein-related factors:

  • pH

  • temperature

    • freezing: enzyme activity slows down a lot, but low temp. does not denature the protein. enzyme activity resumes when temperatures heat up again

    • heat: excessive heat denatures the enzyme, as the bonds break and the amino acids unravel, changing the active site

  • salinity

    • the presence of extra ions change the attraction of ionic bonds holding tertiary structures together

• inhibitors

  • competitive

    • compete with the substrate for the active site

    • block the substrate from accessing the active site

    • reaction rate slows

      • reduces maximum reaction rate

  • non-competitive

    • binds to an allosteric site away from the active site

    • causes the active site to change shape, so that the substrate no longer fits and can’t react

    • permanent/temporary binding

    • shuts off the enzyme

      • maximum reaction rate can be reduced to zero

• concentration of enzyme/substrate

  • ^ enzyme: faster reactions (more processors/locations that substrates can react)

  • ^ substrate: longer overall reaction → more things that are needed to be processes

enzyme kinetics:

rate = substrate consumed/time OR products/time

an enzyme has a maximum rate and it can’t go any faster than that

ENZYME REGULATION

feedback inhibition

• the end product plays a role in regulating the first enzyme

  • in some pathways, the end product may turn off the first enzyme by acting as a competitive inhibitor

  • ATP → ADP + P_i → AMP + P_i

  • ATP is an inhibitor

    • too much ATP? don’t make more! ATP bind to the enzyme and blocks the process

  • AMP is an activator

    • AMP rises after ATP is burned—it activates enzymes to make more ATP after the ATP is used up

allosteric regulation

• inhibit and activate enzyme activity

• occurs in enzymes with 4º structures in the metabolic pathway

• enables finer control of the on/off mechanism

  • milliseconds!! of on/off to conserve energy

cooperativity

• makes it easier for a substrate to bind to an active site

• once the first substrate binds, the following substrates have an easier time binding to their active sites

  • spontaneous binding to the active site

  • only some enzymes do this

  • most common in 4º structures with more than 1 active site

    • but…can happen in tertiary structures (but it must have more than one active site)

  • EX: hemoglobin

    • 4 subunits (2 alpha chains and 2 ß chains)

    • binding of one O₂ happens spontaneously, which causes favorable changes in the other subunits

    • now, the other O₂ molecules have an easier time binding to their active sites

INTRO TO METABOLISM

metabolism: a metabolic pathway involving enzyme-catalyzed steps

catabolism: breaking down substances

anabolism: synthesizing substances

OIL RIG: oxidation is loss, reduction is gain

redox reactions:

reduction-oxidation reactions transfer energy by adding/removing electrons.

• C₆H₁₂O₆ + O₂ → CO₂ + H₂O

  • glucose: oxidation (glucose loses electrons and H)

  • O2: reduction (CO2 gains electrons and H)

• biological redox reactions: electrons “fall” from molecules containing lots of hydrogen

• oxygen is reduced—gain e^- and H+—becoming H2O

• glucose carbons are oxidized—they lose H and e^-

cellular respiration

• a process that generates ATP by metabolizing food using O₂

• turns one glucose molecule → ~36 ATP

• equation: C₆H₁₂O₆ + 6O₂ + 6H₂O → 6CO₂ + 12H₂O + energy (ATP)

• glucose vs ATP: ATP is important because glucose releases too much energy per molecule. Too much energy all at once causes cellular overheating and results in the loss of excess heat and energy

  • C-H bonds in glucose hold most of the chemical energy

  • cellular respiration: glucose oxidizes into CO2

  • H+ and electrons are carried away by NAD+ and FAD

  • energy is transferred and held onto by ATP

ATP (adenosine triphosphate)

• transfers energy released from exergonic reactions to endergonic reactions

• holds onto potential energy

• renewable and recyclable

• hydrolysis of ATP produces energy

  • 7.3 kcal per mole of ATP

NAD+/NADH

• metabolic energy carrier

• accepts one H+ and 2e^- from C-H bond → transfer that energy during ETC

  • then transfers it to ADP, then ATP

• common oxidizing agent; oxidizing agents get reduced

• NAD+ is an “electron bus”

• NAD⁺ + 2e^- + H⁺ → NADH

FAD/FADH₂

• metabolic energy carrier

• accepts 2H+ and 2e^- from C-H bond → transfer that energy during ETC

  • then transfers it to ADP, then ATP

• common oxidizing agent; oxidizing agents get reduced

• FAD + 2e^- + 2H⁺ → FADH₂

GLYCOLYSIS

glucose → 2 pyruvic acid

• in: 6-carbon glucose, 2 ADP+2P, 2NAD+

• out: 2 3-carbon pyruvic acids, 2ATP, 2NADH & 2H+

• location: cytoplasm

  • no organelles are needed

math:

• “energy investment”: 2 ATPs used in 1st steps

• “energy payout”: 2 ATPs generated in last steps

• net production of 2 ATP

  • ADPs get re-phosphorylated

• glucose → 2 pyruvate + 2 ATP + 2 NADH

history:

• no O2 for billions of years…so glycolysis evolved

• inputs (glucose/simple sugars) matched to early earth’s conditions

• most widespread metabolic pathway today (almost everything undergoes this)

FERMENTATION

the step that follows glycolysis—used to clear up NADH that builds up from glycolysis

• cells need a way to regenerate NAD+ (after it’s used up by glycolysis)

  • otherwise, glycolysis cannot continue and no more ATP can be made

• fermentation: a way to regenerate NAD+ from NADH; it strips the electrons from NADH

  • DOES NOT PRODUCED ATP

alcohol (ethanol) fermentation:

• common in fungi, yeast, and some bacteria

  • used to make bread, wine, beer, hard cider, old soft drinks

equation:

• 2 pyruvate (3C) → 2 acetaldehyde (2C) + 2 CO₂ (1C)

• 2 acetaldehyde (2C) + 2 NADH → 2 ethanol (2C) + 2 NAD+

  • input: 2 pyruvate

  • output: 2 CO₂, 2 ethanol, 2 NAD+

    • NAD+ is the end product goal; the thing that we mainly want from this reaction

diagram:

lactic acid fermentation:

• common in bacteria, animals

  • used to make cheese, vinegar, sauerkraut, kimchi, pickles, sour cream, yogurt, etc.

    • acidity curdles milk and crates a sour taste. the high acid content limits enzymes in the pathway.

• strenuous exercise → anaerobic muscle cell response

  • lactic acid builds up in muscle cells, causing fatigue (and then pain)

  • lactic acid is eventually moved from muscle cells → bloodstream → liver

    • liver cells connect lactic acid back to pyruvate, and then breaks it down aerobically

equation:

• 2 pyruvate (3C) + 2 NADH → 2 lactate (3C) + 2 NAD+

  • no intermediate reaction; pyruvate accepts electrons from NADH

KREBS TRANSITION AND KREBS CYCLE

krebs transition:

• moves 2 pyruvate made from glycolysis in the cytoplasm into the matrix

• enters 2 acetyl-coA into the Krebs cycle

• equation: 2 pyruvate → 2 Acetyl-coA + 2CO₂ + 2NADH

krebs cycle:

• extracts energy from Acetyl-coA

  • carbons are given off as CO₂

  • makes ATP

  • energy stored in NAD+ and FA

• it takes 2 krebs cycles to metabolize one glucose molecule (2 pyruvate)

• yield per cycle: 3 NADH, 1 FADH, 1 ATP

  • total yield: 6 NADH, 2 FADH, 2 ATP

steps:

• acetyl-coA binds to oxaloacetate → citrate

• 7 more steps to remove 2 carbons from acetyl-coA and generate oxaloacetate

• byproducts: 6NADH, 2FADH_2, 4CO₂, 2ATP

diagram:

ELECTRON TRANSPORT CHAIN (ETC)

electron transport chain: a series of protein complexes and other molecules that transfer electrons and create an electrochemical gradient

after krebs cycle:

• __NADH (2e, one H+ each) and __FADH₂ (2e, 2H+ each) carry over their cargo to the ETC

• this remaining energy in NADH and FADH₂ is used to convert ADP → ATP

• yield: 3 ATP per NADH, and 2 ATP per FADH₂

  • FADH yields less because it is more electronegative and holds onto its electrons longer during the ETC

process:

• ETC uses proteins in the inner mitochondrial membrane

• NADH and FADH are oxidized (lose electrons) and give electrons to these proteins

• passing electrons down the ETC pumps H+ ions into intermembrane space

• the proton gradient provides the energy to convert ADP → ATP (chemiosmosis)

• final electron acceptor: oxygen

  • this is the main reason for why we breathe!!

  • oxygen accepts the electrons from the integral proteins, freeing them up to keep cycling more electrons through

    • oxygen accepts the electrons and protons and use them to form water

  • without oxygen, the ETC can’t continue because their hands are full with electrons that they can’t let go of

• H+ ions in intermembrane space flow back into the matrix through ATP synthase, which has a rotor mechanism that connects ADP back to P, creating ATP

• ATP Synthase:

  • a channel protein for H+ ions to pass through.

  • the movement of H+ through the protein makes the rotor spin and phosphorylate ADP (creating ATP)

  • this is an ancient molecule that’s also used in photosynthesis

• chemiosmosis: movement of H+ ions through ATP synthase

  • H+ gradient is established by the ETC

  • H+ easily flows back into the matrix through ATP Synthase (facilitated diffusion)

yield:

input:

• 10 NADH (2 from glycolysis, 2 from 2 krebs transitions, 6 from 2 krebs cycles)

• 2 FADH₂ (2 from 2 krebs cycles)

output:

• max 38 ATP

  • 3 × (10 NADH)

    • yield 3 ATP per NADH

  • 2 × (2 FADH₂)

    • yield 2 ATP per FADH₂

  • 2 ATP from glycolysis

  • 2 ATP from krebs cycle