• Two factors determine fate of chemical reaction: Direction and Rate

6.1 Energy comes in different forms

• Kinetic Energy: energy associated with movement

• Potential Energy: energy that a substance/object possess due to its structure and location

Types of energy used in bio

• Light: Form of electromagnetic radiation visible to the eye, composed of photons

• Heat: transfer of kinetic energy from one object to another

• Mechanical: energy from an object due to its motion

• Chemical Potential: potential energy stored between chemical bonds

• Electron/Ion Gradient: the movement of charges creates energy and electrochemical gradient

Thermodynamics

• First law: Energy cannot be created or destroyed, only transferred or transformed

• Second law: Energy transfers/transformation increases disorder the the system, called entropy

Change in free energy determines direction of chemical reaction

• Enthalpy (H) = total energy

• Free Energy (G) = Useable energy

• System’s Entropy (S) = unusable energy

• T = temperature in Kelvin

Scientists use the change in free energy (delta G) to determine the direction of the reaction

formula: delta G = delta H - (T)delta S

• If delta G < 0, reaction is exergonic, so energy is released

  • this is spontaneous

• If delta G > 0, reaction is endergonic, so energy is used to start reaction

  • this favors formation of reactants

6.2 Enzymes

• Enzymes catalyzed reactions occur at higher & faster rates

• Activation energy: initial input of energy needed for rearrangement of bonds

• Transition state: when original bonds stretch to create new products

• Activation energy is a barrier to the formation of new products

  • Enzymes can lower the activation energy needed

• Enzymes do this via 2 methods

  • Straining reactants: large enzyme proteins bind to smaller reactants, which strains the bonds of reactants, making it easier for them to reach transition state

  • Positioning reactants close together: Involves 2 or more reactants, enzymes can provide sites (active site) where reactants are close together

    

Enzymes recognize their substrate

• Active site: where the chemical reaction takes place on an enzyme

• Substrate: the reactant molecules that bind to active site

  • process is called enzyme-substrate complex

    

Additional factors influence enzyme function

• enzymes sometimes require help to perform functions

  • Prosthetic Groups: small molecules that are permanently bonded to the surface of the enzyme, aids in enzyme function

  • Cofactors: usually inorganic ions that temporarily bond to surface of an enzyme, promotes chemical reactions

  • Coenzymes: organic molecules that temporarily bond to an enzyme

• Ability of enzymes are affected by temp, pH, and ionic conditions

6.3 Metabolic Pathways

• Series of steps if chemical reactions

  • each step is catalyzed by different enzymes

• Catabolic Enzymes: The breakdown of larger molecules to smaller ones

• Anabolic reactions: Smaller molecules are synthesized into larger ones

Catalytic reactions recycle organic building blocks

• Breaking down larger molecules lets the body recycle the building blocks for other molecules

  • This can also release energy as the bonds of certain molecules contain a lot of chemical potential energy

    • ATP → ADP + Phosphate

Redox reactions transfer electrons

• Oxidation: the removal of electrons during the breakdown of small molecules

  • oxygen is often involved in this process

• Reduction: the addition of one or more electrons to an atom or molecules

Metabolic pathways are regulated in 3 general ways

• Gene Regulation: enzymes are proteins coded by genes

  • These genes can be turned off/on

• Cell-Signaling Pathways: cells react to signals from their environment and adjust their metabolic pathways to adapt

• Biochemical Regulation: noncovalent bonding of a molecule to an enzyme

  • called Feedback Inhibition

6.4 Overview of Cellular Respiration

• The process of metabolic reactions that a cell uses to get energy from organic molecules and release waste products

Occurs in Four stages

• Glycolysis

  • Glucose is broken down into 2 Pyruvate

  • occurs in cytosol

  • Creates 2 NADH and 4 ATP

    • Net total is 2 ATP

• Breakdown of Pyruvate

  • 2 Pyruvate is broken into 2 acetyl groups, which then bind to Coenzyme A (CoA)

  • Occurs in Mitochondrial Matrix

  • Creates one CO2 molecule

• Citric Acid Cycle

  • 2 acetyl groups are incorporated into organic molecule

  • Creates 4 CO2, 2 ATP, 6 NADH, and 2 FADH2

• Oxidative Phosphorylation

  • NADH & FADH contain high energy electrons that are transferred in a redox reaction to other molecules

    • when removed, creates H+ electrochemical gradient

  • Mainly the process of electron transport and ATP synthesis

  • This occurs in the Cristae of the mitochondria

    

6.5 Glycolysis

• Occurs in 3 main phases

  • Energy Investment Phase: 2 ATP is hydrolyzed into ADP and 2 phosphate groups

    • these phosphate groups are then attached to glucose

    • This helps make later reactions exergonic

  • Cleavage

    • Glucose is broken down into 2 pyruvate

  • Energy liberation

    • produces 4 ATP, 2 NADH, and 2 Pyruvate

      

6.6 Breakdown of Pyruvate

• Pyruvate is oxidized by enzyme pyruvate hydrogenase

  • CO2 is removed and remaining acetyl groups are bonded to CoA

  • The removed electrons are transferred to NAD+, creating 2 NADH

6.7 Citric Acid Cycle

• Cyclical metabolic cycle

• Acetyl CoA is converted into 4 CO2, 6 NADH, 2 ATP, and 2 FADH2

• Regulated by the availability of substrates

  

6.8 Oxidative Phosphorylation

Electron Transport Chain creates electrochemical gradient

• consists of protein complexes inside mitochondrial membrane

• As ETC moves through complexes, pumps H+ across membrane, creating an electrochemical gradient

ATP synthase makes ATP

• ATP is synthesized by ATP Synthase

• H+ electrochemical gradient is passive energy, aiding in the synthesis of ATP

  • H+ passes through ATP synthase, causing the top to spin, which creates ATP

• Around 30 - 34 molecules of ATP are produced per cycle

  

6.9 Not really important

• Proteins and fats can enter glycolysis and citric acid cycle at different times

6.10 Anaerobic respiration and fermentation

• anaerobic: without oxygen

• In an environment with little oxygen, cells use 2 ways to remedy it

Anaerobic Respiration

• Some species evolved enzymes that trigger oxidative phosphorylation without oxygen

Fermentation

• Molecules can make ATP through glycolysis in anaerobic environments

  • in anaerobic environments, citric acid cycle or ETC isn’t needed to make ATP

• Glycolysis requires NAD+ to create NADH

  • in anaerobic environments, NADH increases, while NAD+ decreases

    • this causes NADH to haphazardly give away volatile electrons, damaging DNA and proteins

    • A decrease in NAD+ doesn’t maintain glycolysis

  • In muscle cells, lactate is secreted from pyruvate, which can maintain glycolysis until O2 is found