Title: Cell Chemistry 1
Cells are Made of Molecules
A molecule consists of one or more atoms bonded together.
Atom: Comprised of an equal number of protons and neutrons in the nucleus.
Electrons:
Negatively charged (-) and orbit the nucleus.
Same number of electrons and protons: neutral.
More electrons than protons: anion (-).
Fewer electrons than protons: cation (+).
Hydrogen (H): Unique as it has no neutrons.
Electron Shells
Electrons occupy discrete areas around the nucleus known as shells.
Each shell has a maximum capacity for electrons.
The closest shells to the nucleus must be filled first.
Unfilled Electron Shells
Atoms with partially filled outer shells are less stable than those with filled outer shells.
Stability and Interaction
Atoms attempt to fill their outer shells for increased stability.
Methods to achieve this:
Covalent Bonds: Share electrons.
Ionic Bonds: Transfer electrons.
Covalent Bonds
Atoms with nearly filled outer shells share electrons to form a covalent bond, resulting in a molecule.
Covalent bonds are relatively strong and stable.
Types of Covalent Bonds
Single Bonds: Flexible and allow rotation.
Double Bonds: Shorter, stronger, less flexible.
Triple Bonds: Less common (e.g., nitrogen gas N2, acetylene C2H2).
Strength of Covalent Bonds
Bond strength is the energy difference between free atoms and the molecule formed.
Stronger bonds (e.g., CO2, H2O) are more stable with less energy.
Weaker covalent bonds can store energy (e.g., CH2O).
Electron Sharing
Electronegativity: Different atoms attract electrons to varying degrees.
Atoms with different electronegativities can create polar molecules.
Polar molecules are crucial in biology.
Polar Covalent Bonds
Small differences in polarity can lead to attractions between polar molecules.
Hydrogen Bond: A vital electrostatic attraction between hydrogen and electronegative atoms.
Although individually weak, many hydrogen bonds can collectively form strong interactions.
Acids and Bases
When polar differences are large, molecules act as acids or bases.
Acids can donate protons (H+) in polar bonds, often interacting with water, forming hydronium ions (H3O+).
Water as an Acid
Water can act as an acid, donating H+ to bases, maintaining a dynamic equilibrium of H+ in cells, essential for cellular chemistry.
Electron Transfer to Fill Outer Shells
Atoms can transfer electrons to fill outer shells, resulting in cations (+) and anions (-).
Ionic Bonds
Ionic compounds, or salts, are formed from the electrostatic attraction between oppositely charged ions.
Nature of Ionic Bonds
Ionic bonds exhibit strong electrostatic attraction, similar to hydrogen bonds but much stronger due to full charges.
Dissolution of Ionic Bonds
Ionic bonds are strong but can dissolve in polar solvents like water.
Approximately 70% of a cell is water, keeping most salts in ionic form.
Other Interactions
Hydrophobic Interactions: Nonpolar molecules tend to associate and avoid water.
Van der Waals Attractions: Weak attractions between the fluctuating electron clouds of polar molecules.
Van der Waals Radii: Defines the minimum distance between two atoms based on electron cloud dimensions.
Summary of Interactions
Interactions defined:
Covalent Bonds: Strong and stable.
Ionic Bonds: Strong in nonpolar environments.
Hydrogen Bonds: Common interaction in polar molecules.
Van der Waals Attractions: Weak but significant in number.
Hydrophobic Interactions: Weak interactions.
Complementary Molecules
Characteristics:
High degree of fit between three-dimensional shapes.
Multiple weak non-covalent interactions allow alignment and stability.
Biological Molecules
The Most Important Biological Molecule
Water: Essential for life; makes up approximately 70% of cell weight.
Biological Molecules
Biological molecules possess special properties; main atoms involved include:
Hydrogen (H), Carbon (C), Nitrogen (N), Oxygen (O).
Less common but essential: Sodium (Na), Magnesium (Mg), Phosphorus (P), Sulfur (S), Chlorine (Cl), Potassium (K), Calcium (Ca).
Carbon is notably important despite not being the most abundant.
Cells are Made From Carbon
All non-water molecules in cells contain carbon.
Carbon can form covalent bonds with 2, 3, or 4 other atoms due to having 4 missing electrons.
Carbon molecules can be small or form large polymers (organic molecules).
Cells as Chemical Factories
Reactions within cells predominantly involve four types of organic molecules:
Amino acids, Sugars, Nucleotides, Lipids.
Primary Reactions in Cells
Catabolic Reactions: Breakdown of large organic molecules, releasing energy and producing smaller molecules.
Details on Catabolic Reactions
Significant energy release during the breakdown of high-energy organic molecules.
Anabolic Reactions
Anabolic Reactions: The small molecules produced during catabolism are built into larger molecules, utilizing some released energy.
Metabolism: The sum of catabolic and anabolic reactions occurs at millions per second.
Biochemical Reactions
Basic principles, yielding products from reactants:
Energetically Favorable: Products have less energy than reactants (exothermic).
Energetically Unfavorable: Products have higher energy than reactants (endothermic).
Energy Dynamics in Reactions
Energy difference signifies the stability of electrons and molecules.
Ionic bonds and other weaker interactions do not store energy.
Energetically Stable States
In the presence of O2, carbon's stable state is CO2, and the stable state of hydrogen is water (H2O).
Organisms utilize energy to break down CO2 and H2O into free, unstable atoms, later stabilizing them at CH2O.
Photosynthesis Overview
Reaction process involves sunlight energy, CO2, and H2O conversion into CH2O and O2 while releasing heat energy.
CH2O holds chemical energy between its states.
Importance of CH2O
Key points:
Carries chemical energy.
Provides usable carbon source for processes.
Gibbs Free Energy
ΔG: Represents the change in free energy between reactants and products.
Negative ΔG: Favorable, energy lost in reactions (catabolism).
Positive ΔG
Positive ΔG: Unfavorable, requires energy input (anabolism).
Reduction and Oxidation
Energy transfer correlated with electron gain/loss:
Reduction: Gain of electrons, more negative charge.
Oxidation: Loss of electrons, more positive charge.
Occurs in complementary redox reactions.
Understanding Electrons
Electrons are units of energy and charge; not all have the same energy, influencing processes accordingly.
Second Law of Thermodynamics
States that disorder in an isolated system is always increasing.
Entropy: Measure of disorder, with elements striving for high entropy (low energy state).
Reaction Rates
Favorable reactions result in products with lower energy states, increasing disorder and releasing heat.
Assessment of Reaction Dynamics
Rate of reactions can be favorable or unfavorable, independent of product energy assessment.
Reaction Speed example
Example of wood decay: a favorable reaction taking time due to necessary molecular contact for bond breaking.
Activation Energy
Energy needed to produce sufficient thermal motion for reactions to occur and pass through unstable intermediates.
Influencing Reaction Rate
The rate of reactions can be increased (e.g., through heat) while maintaining thermodynamic properties.
Control through Cells
Oxidation in cells occurs gradually to allow energy harvesting efficiently through enzymes.
Enzyme Function
Enzymes lower activation energy by stabilizing reactants and intermediates, conducting reactions on demand.
Energy Recovery through Enzymes
Reaction energy is captured for future use while maintaining ΔG and Δentropy consistency.
Unfavorable Reactions
Reactions with positive ΔG require energy input and yield higher energy products that are more organized.
Enzyme Role in Coupling Reactions
Enzymes couple unfavorable reactions with favorable ones to drive processes efficiently.
Metabolism Flow
Encompasses both catabolism and anabolism, indicating energy transition within biological systems.
Activated Carriers
Molecules like ATP serve as activated carriers for energy and biosynthetic pathways, crucial for metabolic processes.
Integrated Control of Biosynthesis
Both anabolism and catabolism are coordinated and managed by proteins, ensuring efficiency and stability in cellular chemistry.