Cell Chemistry and Bioenergetics

• Until the 19th century, people knew “Vital Force” to be responsible for all the distinctive properties.

• Organic Chemistry: It is the study of hydrocarbons and their derivatives.

Why chemistry of life is indeed special?

• Firstly, it is based on carbon compounds.

• Secondly, cells are 70% water, and life depends largely on chemical reactions.

• Thirdly, cell chemistry is enormously complex.

Chemical components of cell:

• It is made up of mainly four elements including carbon(C), hydrogen(H), nitrogen(N), and oxygen(O).

• A cell is formed from carbon compounds.

  • Carbon has a property of catenation which helps in the self-linking of atoms of an element to form chains and rings.

  • Carbon has a covalency of four.

  • It confers stability to form large molecules.

• A cell also contains small organic molecules:

  • Sugars

  • Fatty Acids

  • Nucleotides

  • Amino Acids

• Types of bonds:

  • Covalent Bond: A chemical bond that involves the sharing of electrons to form electron pairs between atoms.

  • Non-Covalent Bond: The bond in which no sharing of electron pairs takes place is called a non-covalent bond.

  • Hydrogen Bond: A hydrogen bond is the interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen, or fluorine from another molecule.

• Non-Covalent attractions:

  • Electrostatic attractions (ionic bonds)

  • Hydrogen Bonds

  • Vander Waal attractions

  • Hydrophobic force

• Acids: Substances that release protons when they dissolve in water thus forming H3O+ are termed acids.

  • Strong Acids: Those who lose their protons quickly. Eg: Hydrochloric acid (HCL).

  • Weak Acids: Those who hold on to their proton more tightly when dissolved in water. Eg: Acetic Acid (C2H5COOH)

• Bases: The opposite of acid is a base. Substances that accept a proton from a water molecule are called bases.

  • Strong Base: Those who readily dissociate in water to form respective ions. Eg: Sodium Hydroxide (NaOH)

  • Weak Base: Those who have a weak tendency to reversibly accept a proton from water. Eg: Ammonia (NH3)

• pH Scale: The concentration of H3O+ is expressed using a logarithmic scale called as pH scale.

  • Pure water has a pH of 7.0.

  • An acidic solution has a pH of <7.

  • The basic solution has a pH of >7.

• Buffers: It is a solution that can resist pH change upon the addition of an acidic or basic component.

• Types of molecules:

  • Macromolecule: It is composed of a much larger number of atoms than ordinary molecules.

  • Micromolecule: It is a small molecule that often joins together to form a larger type of molecule. It is often referred to as monomers.

Cell Metabolism

• It is the set of chemical reactions that occur to maintain life.

• Metabolism = Catabolism + Anabolism

• Catabolic Reactions: These reactions break down molecules into smaller units.

• Anabolic Reactions: These reactions use the small molecules and the energy harnessed by catabolism to drive the synthesis of molecules.

• Thermodynamics: (branch of science which deals with the energy changes taking place in all physical and chemical processes)

  • Thermo (heat) + Dynamics (flow/motion)

Key terms:

• Work: The product of force and displacement is called work

  • w = (- P ΔV )

    • w= work done; P= pressure; ΔV = change in volume

• System: It is any region of space that is under thermodynamic investigation.

  • Open system: This type of system can exchange energy as well as matter with the surrounding.

  • Closed system: This type of system can exchange energy, but not matter with the surroundings.

• Surrounding: It comprises the rest of the universe apart from the system.

• Universe: It comprises the system and its surroundings together.

• Boundary: A wall or layer separating the surrounding.

  • A boundary can be rigid or non-rigid.

  • A boundary can be conducting or non-conducting.

  • A boundary can be real or imaginary.

• Internal Energy (E): It is defined as the sum of different energies associated with its atoms and molecules.

Laws of thermodynamics:

• The first law of thermodynamics:

  • This law is based on the law of conservation of energy.

  • Energy can neither be created nor be destroyed but can be transformed from one form to another.

  • The total energy of the universe is always constant.

  • ΔE= q + w (a mathematical form of 1st law of thermodynamics)

    • q: energy given to the system; w: work done on the system; ΔE: change in internal energy.

• Enthalpy (H): Heat contained in the system measured at constant pressure. {H = E + PV}

• The second law of thermodynamics: States that in the universe or any isolated system the degree of disorder always increases.

• Spontaneity: It defines whether a chemical reaction will occur or not.

  • Causes of spontaneity:

    • Decrease in potential energy (stored energy at rest).

    • Increase in randomness or disorder.

• Reactions proceeds in that direction where randomness increase.

• Reactions are of two types:

  • Spontaneous Reaction: Reaction which can occur by itself without any external force.

  • Non-Spontaneous Reaction: Reaction which cannot occur by itself.

• Entropy: It is a measure of randomness or disorder in a system. The greater the disorder, the greater the entropy.

• Gibb’s Energy (G): It is the part of the total energy of the system which can be converted to useful work. (∆G = ∆H -- T∆S)

  • ∆G: change in Gibbs energy; ∆H: change in enthalpy; ∆S: change in entropy.

  • For a reaction Y → X at 37°C, ∆G° is related to ∆G as follows:

    ∆G = ∆G° + RT ln [X] /[Y]

• Relationship between standard Gibb’s energy change (∆G°) and Equilibrium Constant (Keq):

  ∆G° = - RT ln Keq

Key terms for different energy reactions:

• Oxidation: It is the loss of electrons or an increase in the oxidation state of a chemical or atoms within it.

• Reduction: It is the gain of electrons or a decrease in the oxidation state of a chemical or atoms within it.

• Hydrogenation: It is a chemical reaction between molecular hydrogen (H2) and another compound or element, usually in the presence of a catalyst.

• Dehydrogenation: It is the process by which hydrogen is removed from an organic compound to form a new compound.

• Activation Energy: It is the minimum amount of energy that must be provided for compounds to result in a chemical reaction.

• Enzymes: A substance produced by a living organism that acts as a catalyst to bring about a specific biochemical reaction.

• Coenzymes: Coenzymes are small molecules. They cannot by themselves catalyze a reaction but they can help enzymes to do so.

• Substrates: Each enzyme binds tightly to one or more molecules called substrates.

• Catalysts: A substance that can lower/increase the activation energy of a reaction.

Important Abbreviations to understand the different processes:

• ATP: Adenosine Tri Phosphate

• ADP: Adenosine Di Phosphate

• NADH: Nicotinamide Adenine Dinucleotide

• NADPH: Nicotinamide Adenine Dinucleotide Phosphate

• FADH2: Flavin Adenine Dinucleotide

• AMP: Adenosine Mono Phosphate

• PPi: Pyrophosphate

How do cells obtain energy from food?

• Glycolysis: The major process of oxidizing sugars is the sequence of reactions known as glycolysis.

  • It is common in both aerobic (in presence of oxygen) and anaerobic (without the presence of oxygen) reactions.

  • It takes place in the cytoplasm of the cell.

  • It starts with 6-carbon glucose to finally result in two molecules of 3-C pyruvate. In plants, this glucose is derived from sucrose.

  • Total ATP produced: 8ATP

• Fermentation:

  • Alcoholic Fermentation:

    • It occurs in yeast.

    • The process is hazardous either acid or alcohol is produced. Yeats poison themselves to death when the concentration reaches about 13%.

    • It yields ethyl alcohol as the final product.

    • Total ATP produced: 2ATP

• Lactic Acid Fermentation:

  • It occurs in the muscles of humans during an intense workout.

  • it yields lactic acid as the final product.

  • Total ATP produced: 2ATP

• Oxidative Phosphorylation:

  The process that connects glycolysis and Krebs’s Cycle.

• Krebs’s Cycle:

  It occurs in the mitochondria matrix of the eukaryotic cell but in prokaryotes, it occurs in the cytoplasm.

Stored food in organisms:

• Fungi: Oil and glycogen

• Humans: Glycogen

• Plants: Starch