Enzymes

Enzyme Structure and Function

Structure Overview

• enzymes: biological catalysts; used to speed up biological processes

  • ribozymes: biological catalysts made of RNA

• active site: this part of an enzyme interacts with the substrate (reactant)

  • shape of the active site on an enzyme is specific to the enzyme and its function

    • substrate and active site shapes must match in order for enzyme to work

  • any charged r-groups on the amino acids within an active site of an enzyme must have compatible charges on the substrate

Environmental Factors that Affect Enzyme Functions

• enzymes catalyze at the most optimal temperature and pH levels

  • temp. is too low = less frequent collisions between enzyme and substrate; reaction slows down

  • temp. is too high = enzyme can denature; bonds between substrate and enzyme can be affected; enzyme shape can alter

  • pH levels are different = bonds in enzyme can be disrupted and tertiary structure of enzyme can change

• denaturation: changes to an enzyme’s structure; can limit an enzyme’s ability to catalyze chemical reactions

  • denaturation can sometimes be reversed if the reaction returns to optimal conditions

• competitive inhibitors: compete with substrates for the active site of the enzyme

  • competition lowers the rate of enzyme-substrate reactions occurring

  • effects of competitive inhibitors can be reduced by increasing the concentration of the substrate (reactant)

• non-competitive (allosteric) inhibitors: do not bind to active site and they bind to a different site on the enzyme; the binding changes the shape of the enzyme, which changes the shape of the active site and reduces the amount of enzyme-substrate bonding

  • higher concentration of substrate does not affect non-competitive inhibitors

  • non-competitive inhibitors function in feedback mechanisms by adjusting the rate of chemical reactions in the cell to suit changing environmental conditions

• cofactors: inorganic molecules and coenzymes (organic molecules): increase the efficiency of enzyme-catalyzed reactions

  • they usually increase efficiency by binding to the active site or the substrate to enhance the binding of the substrate to the active site

Activation Energy in Chemical Reactions

• all molecules have a given amount of free energy (G); chemical reactions in biological processes involve changes in molecules

• chemical reactions can be endergonic or exergonic

  • endergonic reaction: has products with higher free energy levels than its reactants; considered energetically unfavorable

  • exergonic reaction: has products with lower free energy levels than its reactants; considered energetically favorable

• all chemical reactions require an input of energy to reach a transition state/start the reaction

  • activation energy (Ea): the difference between the energy level of the reactants and the energy level of the transition state of the reaction

    • higher Ea: results in slower rate of chemical reactions

    • lower Ea: results in faster rate of chemical reactions

• enzymes can lower activation energy (Ea) in multiple ways:

  • bringing the substrates together in proper orientation for a reaction to occur

  • destabilizing chemical bonds in the substrate by bending the substrate

  • forming temporary ionic or covalent bonds with substrate

• enzymes can lower activation energy but they cannot change an endergonic reaction (energetically unfavorable) to an exergonic reaction (energetically favorable)

Energy and Metabolism/Coupled Reactions

• energy input into cell must be higher than energy requirements for cellular systems

• processes that release energy can be paired (coupled) with processes that require energy

  • coupled reactions: occur in multiple steps to allow for the controlled transfer of energy between molecules (leads to more efficiency)

• coupling exergonic reaction with endergonic reaction: allows the energy released by the exergonic reaction to “drive” the endergonic reaction

  • example:

    • exergonic step: breakdown of ATP into ADP and a phosphate group (Pi (inorganic)); releases approx. 30 kilojoules of energy per mole of ATP

    • endergonic reaction: the reaction that combines glucose with fructose to form sucrose requires approx. 27 kilojoules of ATP per mole of sucrose formed

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Photosynthesis

Overview

• heterotrophs: consume other organisms to obtain energy required for biological processes

• autotroph: produce their own organic molecules from inorganic molecules

  • photo-autotrophs: autotrophs that use light energy to power the process

• light-dependent reactions: use energy from sunlight to split water to produce oxygen gas, protons, and high-energy electrons

  • oxygen gas: released into atmosphere

  • protons and high-energy electrons: used to power the production of ATP and NADPH

    • ATP and NADPH are sent to the light independent reactions

• light-independent reactions: use ATP, NADPH, and carbon dioxide to produce sugars

  • ATP, Pi (inorganic phosphate group), and NADP+: sent back to light-dependent reactions

• plants: photosynthesis occurs in the chloroplasts

  • chloroplasts:

    • outer membrane: filled with liquid called stroma

    • stroma: has floating stacks of membranous sacs called grana; location of light-independent reactions

    • thylakoid: each individual membranous sac from the grana stack; location of light-dependent reactions

• prokaryotes: also perform photosynthesis (ex. cyanobacteria); do not contain chloroplasts

  • light-dependent reactions: occur on infoldings of plasma membrane

  • light-independent reactions: occur in the cytosol

Light-Dependent Reactions

• photophosphorylation: conversion of ADP to ATP using the energy of sunlight by activation of PSII

  • light energy excites the electrons in the chloroplasts to a higher energy level; energy is released as excited electrons move through chloroplasts

  • NADP+ accepts the electrons to form NADPH

    • NADPH: source of reducing power for light-independent reactions

• chlorophyll: light-absorbing pigment that captures the energy of photons from the sun; found in photosystems 1 and 2

  • photosystem: composed of proteins, chlorophyll, and accessory pigments; PSI and PSII contain different types of chlorophyll that absorb most light energy at slightly different wavelengths (PSI = 700 nm; PSII = 680 nm)

    • photosystems are located in the thylakoid membrane of the chloroplast; they are connected by an electron transport chain (ETC)

• accessory pigment: other light-absorbing pigments besides chlorophyll

The Process of Light-Dependent Reaction

• energy in p+ is used to boost e- in chlorophyll to higher energy level in PSII

• e-s from PSII are passed from one protein carrier to another in a series of redox reactions (like falling down a hill)

• the final e- donor in the ETC passes the e- to the PSI

• as the e-s pass through the ETC, energy is released and used to create a proton (H+) gradient

  • H+ ions are actively transported against concentration gradient across the thylakoid membrane

• electrons from PSII that fell down the ETC are now in PSI and need to be replaced in PSII

• photolysis: the splitting or decomposition of a chemical compound by means of light energy or photons

  • occurs when splitting of water molecules takes electrons from hydrogen atoms and produces H+ ions, electrons from PSII, and oxygen gas

• proton gradient generated by photolysis of water and the ETC powers the production of ATP by ATP synthase

  • chemiosmosis: process of using a proton gradient and ATP synthase to produce ATP; also used in mitochondria to generate ATP during cellular respiration

• the electron from the ETC that is now on PSI is boosted by a photon of light energy from the sun; the electron passes again through a series of carriers (much shorter than ETC) where it is finally transferred (along with a proton) to NADP+ by the enzyme NADP+ reductase

  • this produces a molecule of NADPH, which will provide the reducing power for the light-independent reactions

Light-Independent Reactions (Calvin Cycle)

• light-independent reactions occur in stroma of chloroplast

• the process can be broken down into 3 part:

  • fixation of carbon

  • reduction

  • regeneration of RuBP

Fixation of Carbon

• fixation: to turn a biologically unusable form to a usable form

• enzyme ribulose-biphosphate-carboxylase (rubisco) adds one molecule fo carbon dioxide to the 5-carbon molecule ribulose-biphosphate (RuBP)

  • this produces a 6-carbon intermediate that is unstable

• the unstable molecule is then broken down further into two 3-carbon molecules

Reduction

• the ATP and NADPH from the light-dependent reactions are used to reduce the 3-carbon molecules into glyceraldehyde-3-phosphate (G3P)

• G3P: can be used to make sugars; some of it is used during regeneration

Regeneration

• 5-carbon RuBP must be regenerated for the calvin cycle to continue

• for every 5 molecules of G3P, there are 15 carbon atoms present

• ATP from light-dependent reaction in used to rearrange the five G3P (3-carbon molecule) molecules to form 3 molecules of RuBP (5-carbon molecule)

  • this process requires energy that comes from the light-dependent reactions

Cellular Respiration

Overview

• cellular respiration includes the following processes:

  • glycolysis

  • oxidation of pyruvate

  • krebs cycle (citric acid cycle)

  • oxidative phosphorylation

• the presence of oxygen determines whether the process will be anaerobic or aerobic

  • anaerobic: without oxygen; anaerobic organisms (don’t have access to oxygen) can perform glycolysis and fermentation

  • aerobic: with oxygen; aerobic organisms (have access to oxygen) can perform all processes in the presence of oxygen and only glycolysis and fermentation in the absence of oxygen

    • can perform more processes than anaerobic, meaning they can extract more energy from organic compounds

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Glycolysis

• occurs in the cytosol of the cell (all organisms have cytosol, so all organisms can perform glycolysis)

• a 6-carbon molecule enters glycolysis alone with two molecules of NAD+ (electron carrier)

  • each NAD+ is reduced (loses hydrogen atom and electrons) to NADH

• two molecules of ATP are required for early steps of glycolysis

• four molecules of ATP are produced by glycolysis (net gain of ATP)

• at the end of glycolysis, the 6-carbon glucose molecule is split into two 3-carbon pyruvate molecules

  • 

Oxidation of Pyruvate

• occurs in the mitochondria

• the 3-carbon pyruvate molecule is oxidized (loses hydrogen atom and electron) and NAD+ is reduced (gains a hydrogen and its electrons) to become NADH

  • as this happens one of the carbons of the pyruvate molecule is reduced as CO2 (leaving behind a 2-carbon acetyl group)

• coenzyme A attaches to the 2-carbon acetyl group and delivers the acetyl group to the krebs cycle

• each molecule of glucose that enters glycolysis generates 2 pyruvate so oxidation of pyruvate occurs twice for each molecule of glucose

Krebs Cycle (Citric Acid Cycle)

• occurs in the matrix (liquid center) of the mitochondria

• coenzyme A brings the 2-carbon acetyl group to the cycle (initially attached as 4-carbon intermediate but forms 6-carbon molecule)

• the 6-carbon molecule goes through a series of enzyme-catalyzed reactions to regenerate the 4-carbon intermediate (and produces 2 molecules of CO2)

• at the end, all the carbon that was originally in the glucose molecule (at the start of glycolysis) has been released as CO2

• during the cycle:

  • one molecule of ATP is produced from substrate-level phosphorylation

    • phosphorylation: direct addition of a phosphate group to ADP without the use of an electron transport chain or chemiosmosis

  • three molecules of NAD+ are reduced to NADH

  • one molecule of FAD+ is reduced to FADH2

Total Products of Glycolysis, Oxidation of Pyruvate and Krebs Cycle for Each Molecule of Glucose

• all 6 carbons in glucose molecule have been released as CO2

• four molecules of ATP have been produced by substrate-level phosphorylation

• a total of 12 high-energy electron carriers (10 NADH and 2 FADH2) have been produced and will enter oxidative phosphorylation

Oxidative Phosphorylation

• involves the ETC and chemiosmosis (both of which occur in the membrane of the mitochondria)

• this process yields the most production of ATP in cellular respiration

• the electron carriers (NADH and FADH2) previously produced carry their electrons to the ETC

  • as they deliver their electrons they are oxidized to NAD+ and FAD+, which can be used earlier on in cellular respiration

  • as the electrons travel through the ETC their PE decreases and energy is released

• the released energy is used to pump H+ out of the matrix and int the intermembrane space of the mitochondria to create a proton gradient

• at the end of the ETC, molecular oxygen (O2) combines with four protons (H+) and four electrons (e-) to form 2 water molecules (2H2O)

  • this means oxygen is the final (terminal) acceptor of electrons in cellular respiration

• the proton gradient created by the ETC is used to produce ATP through chemiosmosis

  • protons flow from areas of higher concentration in intermembrane space to areas of lower concentration in the matrix through a channel in the ATP synthase enzyme

    • this flow of protons leads to a change in the shape of the enzyme; the new shape of the enzyme allows for ATP synthase to catalyze the production of ATP

• (ideally) 34 total ATP molecules can be produced:

  • 10 NADH x 3 ATP = 30 ATP

  • 2 FADH2 x 2 ATP = 4 ATP

  • FADH2 has a lower potential energy than NADH, so it produces less ATP

Fermentation

• when oxygen isn’t present, oxidative phosphorylation cannot occur (oxygen is the final electron acceptor)

• anaerobic conditions require the use of fermentation to regenerate NAD+ needed to keep the process of glycolysis going

• fermentation only occurs in the cytosol

• alcohol fermentation: pyruvate is reduced to an alcohol (usually ethanol) and CO2; NADH is oxidized to NAD+

  • example: yeast undergoing fermentation for bread to rise

• lactic acid fermentation: pyruvate is reduced to lactic acid (3-carbon molecule); NADH is oxidized to NAD+; no CO2 is produced

  • example: can occur in muscle cells if they do not have enough oxygen to carry out oxidative phosphorylation