Biomolecules - EN-DIOL ARRANGEMENT

• The en-diol arrangement is a structural feature commonly found in many biomolecules.

• It involves the formation of a double bond between two adjacent carbon atoms, which are also bonded to hydroxyl groups.

• This arrangement is important for the stability and reactivity of biomolecules.

• Examples of biomolecules with en-diol arrangement:

  • Glucose:

    • Glucose is a monosaccharide that contains an en-diol arrangement.
    • The hydroxyl groups on the C2 and C3 carbon atoms can form a double bond, resulting in the en-diol structure.

  • Ribose:

    • Ribose, a sugar molecule found in RNA, also exhibits the en-diol arrangement.
    • The C2 and C3 carbon atoms can form a double bond, creating the en-diol structure.

• Importance of the en-diol arrangement:

  • The en-diol structure provides stability to biomolecules.
  • It can participate in various reactions, such as oxidation and reduction.
  • The presence of an en-diol structure can contribute to the reactivity and functionality of biomolecules.

• Equilibrium between en-form and diol-form:

  • The enol form (double bond) and the keto form (diol) can exist in dynamic equilibrium.
  • The enol form is generally less stable than the keto form due to the strain created by the double bond.
  • The equilibrium between these forms can be influenced by factors like temperature, pH, and solvent.

Slide 2: Carbohydrates

• Carbohydrates are essential biomolecules composed of carbon, hydrogen, and oxygen atoms.

• They are classified into three main groups: monosaccharides, disaccharides, and polysaccharides.

• Monosaccharides:

  • Monosaccharides are the simplest form of carbohydrates.
  • They cannot be further hydrolyzed into smaller units.
  • Examples include glucose, fructose, and galactose.

• Disaccharides:

  • Disaccharides are formed by the condensation reaction between two monosaccharide units.
  • Glycosidic bonds connect the monosaccharide units.
  • Examples include lactose, sucrose, and maltose.

• Polysaccharides:

  • Polysaccharides are composed of long chains of monosaccharide units.
  • They serve as storage molecules (e.g., starch and glycogen) or structural components (e.g., cellulose and chitin).
  • Polysaccharides are often used by living organisms for energy storage and structural support.

Slide 3: Lipids

• Lipids are a group of biomolecules that are largely insoluble in water but soluble in organic solvents.

• They are composed of carbon, hydrogen, and oxygen atoms.

• Lipids are diverse and serve various functions in living organisms.

• Types of lipids:

  • Triglycerides:

    • Triglycerides are the most common type of lipids.
    • They consist of glycerol and three fatty acid molecules.
    • Triglycerides function as energy storage molecules.

  • Phospholipids:

    • Phospholipids are major components of cell membranes.
    • They consist of a hydrophilic head (phosphate group) and two hydrophobic tails (fatty acid chains).

  • Steroids:

    • Steroids, such as cholesterol, are crucial for maintaining cellular structure and functions.
    • They also serve as hormones and precursors for the synthesis of other important molecules.

• Functions of lipids:

  • Energy storage: Lipids act as an efficient energy storage molecule due to their high energy content.
  • Insulation: Lipids help in maintaining body temperature by acting as insulators.
  • Protection: Lipids provide cushioning and protection to vital organs.
  • Cell membrane structure: Phospholipids form the basic structure of cell membranes.

Slide 4: Proteins

• Proteins are essential biomolecules composed of amino acids.

• They perform various critical functions in the body, such as providing structural support, catalyzing reactions, and transporting molecules.

• Structure of proteins:

  • Proteins have a complex hierarchical structure.
  • Primary structure: The sequence of amino acids in a protein chain determines its primary structure.
  • Secondary structure: Proteins can form alpha-helix or beta-sheet structures.
  • Tertiary structure: The three-dimensional folding of proteins.
  • Quaternary structure: Some proteins consist of multiple polypeptide chains.

• Functions of proteins:

  • Enzymes: Proteins act as biological catalysts, speeding up chemical reactions in the body.
  • Structural support: Proteins like collagen provide structural integrity to connective tissues.
  • Transport: Proteins like hemoglobin transport oxygen in the bloodstream.
  • Immunity: Antibodies are proteins that defend against foreign substances.
  • Hormones: Some proteins, like insulin, act as chemical messengers.

Slide 5: Enzymes

• Enzymes are specialized proteins that catalyze biochemical reactions in living organisms.

• They are involved in numerous physiological processes, such as digestion, metabolism, and DNA replication.

• Characteristics of enzymes:

  • Highly specific: Enzymes are specific to particular substrates due to the shape of their active sites.
  • Efficient catalysts: Enzymes increase the rate of reactions without being consumed in the process.
  • Sensitive to environmental factors: The activity of enzymes is influenced by factors like temperature and pH.

• Enzyme-substrate interaction:

  • Enzymes bind to their specific substrates through the lock-and-key or induced fit model.
  • The active site of an enzyme undergoes conformational changes to accommodate the substrate.
  • This interaction facilitates the formation of an enzyme-substrate complex.

• Enzyme regulation:

  • Enzymes can be regulated to control biochemical reactions.
  • Regulation can occur through various mechanisms, such as allosteric regulation or competitive inhibition.
  • The regulation of enzymes ensures that reactions occur when needed and are inhibited when not required.

Slide 6: Nucleic Acids

• Nucleic acids are biomolecules involved in the storage, transmission, and expression of genetic information.

• They are composed of nucleotides, which consist of a sugar molecule, a phosphate group, and a nitrogenous base.

• Types of nucleic acids:

  • Deoxyribonucleic acid (DNA):

    • DNA carries genetic information in all living organisms.
    • It consists of two polynucleotide strands that form a double helix.
    • DNA dictates the synthesis of proteins through the process of transcription and translation.

  • Ribonucleic acid (RNA):

    • RNA plays a role in protein synthesis.
    • It is single-stranded and can adopt various secondary structures.
    • RNA can also function as an enzyme (ribozyme) and as a regulator of gene expression.

• DNA replication:

  • DNA replication is the process by which a DNA molecule is copied to produce two identical DNA molecules.
  • It occurs during cell division and is crucial for the transmission of genetic information to subsequent generations.
  • Enzymes called DNA polymerases catalyze the synthesis of new DNA strands.

Slide 7: Acid-Base Reactions

• Acid-base reactions are fundamental chemical reactions that involve the transfer of protons.

• Acids donate protons (H+ ions), while bases accept protons.

• Bronsted-Lowry acid-base theory:

  • According to the Bronsted-Lowry theory, an acid is a substance that donates a proton, and a base is a substance that accepts a proton.
  • The acid-base reaction results in the formation of a conjugate acid and a conjugate base.

• Examples:

  • Acid: Hydrochloric acid (HCl)

    • HCl donates a proton, forming the chloride ion (Cl-) as the conjugate base.

  • Base: Ammonia (NH3)

    • NH3 accepts a proton, forming the ammonium ion (NH4+) as the conjugate acid.

• pH scale:

  • The pH scale is used to measure the acidity or basicity of a solution.
  • On the pH scale, values below 7 are acidic, 7 is neutral, and values above 7 are basic.
  • The scale is logarithmic, with each unit representing a tenfold change in acidity or basicity.

Slide 8: Redox Reactions

• Redox reactions, or oxidation-reduction reactions, involve the transfer of electrons between species.

• Oxidation is the loss of electrons, while reduction is the gain of electrons.

• Redox reaction components:

  • Reducing agent: The species that undergoes oxidation and donates electrons.
  • Oxidizing agent: The species that undergoes reduction and accepts electrons.
  • Electron transfer occurs between the reducing agent and the oxidizing agent.

• Examples of redox reactions:

  • Combustion reactions: Organic compounds reacting with oxygen to produce carbon dioxide and water.
  • Oxidation of metals: The reaction between a metal and an oxidizing agent, resulting in the conversion of the metal to its oxide form.

• Redox indicators:

  • Redox reactions can be detected using indicators.
  • Common indicators for redox reactions include potassium permanganate, which changes color from purple to colorless upon reduction.

Slide 9: Equilibrium and Le Chatelier’s Principle

• Chemical equilibrium occurs when the rate of the forward reaction is equal to the rate of the reverse reaction.

• Le Chatelier’s principle states that if a system at equilibrium is subjected to a stress, it will respond by shifting in a direction that minimizes the stress.

• Factors that affect equilibrium:

  • Concentration: Changes in the concentration of reactants or products can shift the equilibrium position.
  • Temperature: Increasing temperature favors an endothermic reaction, while decreasing temperature favors an exothermic reaction.
  • Pressure: Changes in pressure mostly affect reactions involving gases.
  • Catalysts: Catalysts do not affect the position of equilibrium but can increase the rate at which equilibrium is achieved.

• Equilibrium constant (K):

  • The equilibrium constant, expressed as K, is a mathematical representation of the ratio of product concentrations to reactant concentrations at equilibrium.
  • K is specific to each reaction and is constant at a given temperature.

Slide 10: Chemical Kinetics

• Chemical kinetics is the study of the rates of chemical reactions and the factors that affect them.

• It provides insights into reaction mechanisms and helps predict reaction rates under different conditions.

• Factors influencing reaction rates:

  • Concentration: Increasing the concentration of reactants generally increases the reaction rate.
  • Temperature: Higher temperatures enhance the movement of particles, resulting in increased reaction rates.
  • Catalysts: Catalysts increase reaction rates by providing an alternative reaction pathway with lower activation energy.

• Rate law:

  • The rate law expresses the relationship between the concentrations of reactants and the rate of a reaction.
  • It is experimentally determined and can be used to determine the order of reaction with respect to each reactant.
  • The overall order of reaction is the sum of the orders with respect to each reactant.

• Activation energy:

  • Activation energy is the minimum energy required for a reaction to occur.
  • Higher activation energies result in slower reactions.
  • Catalysts lower the activation energy, making it easier for the reactants to reach the transition state and form products. Slide 11: Chemical Bonding

• Chemical bonding is the process by which atoms combine to form molecules or compounds.

• The type of chemical bond formed depends on the electronegativity difference between atoms.

• Types of chemical bonds:

  • Ionic bonds: Formed between a metal and a non-metal through the transfer of electrons.

    • Example: NaCl (Sodium chloride) - Sodium donates an electron to chlorine to form an ionic bond.

  • Covalent bonds: Formed between non-metals through the sharing of electrons.

    • Example: H2 (Hydrogen gas) - Two hydrogen atoms share electrons to form a covalent bond.

  • Metallic bonds: Formed between metal atoms due to the delocalization of electrons.

    • Example: Copper (Cu) - Metal atoms share a sea of electrons, forming metallic bonds.

• Lewis dot structures:

  • Lewis dot structures are a way to represent the valence electrons in an atom or molecule.
  • Valence electrons are represented as dots around the atomic symbol in a Lewis dot structure.

Slide 12: Periodic Trends

• Periodic trends are patterns observed in the periodic table that help predict the properties of elements.

• Atomic radius:

  • Atomic radius refers to the size of an atom, measured as the distance from the nucleus to the outermost electron shell.
  • Atomic radius generally increases down a group and decreases across a period.
    • Example: Atomic radius increases from top to bottom in Group 1 (alkali metals).

• Ionization energy:

  • Ionization energy is the energy required to remove an electron from an atom or ion.
  • Ionization energy generally decreases down a group and increases across a period.
    • Example: Ionization energy increases from left to right in Period 2.

• Electronegativity:

  • Electronegativity is the ability of an atom to attract electrons in a chemical bond.
  • Electronegativity generally increases across a period and decreases down a group.
    • Example: Fluorine (F) has the highest electronegativity among the elements.

• Metallic character:

  • Metallic character refers to the tendency of an atom to lose electrons and form cations.
  • Metallic character generally increases down a group and decreases across a period.
    • Example: Group 1 elements (alkali metals) have high metallic character.

Slide 13: Organic Chemistry Basics

• Organic chemistry is the study of carbon-based compounds and their reactions.

• Organic compounds have a wide range of applications, including medicine, fuels, and polymers.

• Carbon bonding in organic compounds:

  • Carbon can form covalent bonds with other carbon atoms and with other elements such as hydrogen, oxygen, nitrogen, and halogens.
  • Carbon often forms single, double, or triple bonds with other atoms.

• Functional groups:

  • Functional groups are specific arrangements of atoms in organic molecules that contribute to their chemical properties.
  • Examples include hydroxyl group (-OH), carbonyl group (>C=O), and amino group (-NH2).

• Isomerism:

  • Isomerism refers to the existence of multiple compounds with the same molecular formula but different structural arrangements.
  • Isomers can have different physical and chemical properties.
  • Examples include structural isomers, geometric isomers, and optical isomers.

• Hydrocarbons:

  • Hydrocarbons are organic compounds composed of only carbon and hydrogen atoms.
  • They can be classified into alkanes, alkenes, and alkynes based on the type of carbon-carbon bonds present.

Slide 14: Organic Reactions

• Organic reactions involve the breaking and formation of chemical bonds in organic compounds.

• These reactions are commonly categorized into addition, elimination, substitution, and rearrangement reactions.

• Addition reactions:

  • Addition reactions involve the addition of atoms or groups to carbon-carbon multiple bonds.
  • Example: Addition of hydrogen to an alkene to form an alkane.

• Elimination reactions:

  • Elimination reactions involve the removal of atoms or groups from a molecule, usually resulting in the formation of a double bond.
  • Example: Dehydration of an alcohol to form an alkene.

• Substitution reactions:

  • Substitution reactions involve the replacement of an atom or group in a molecule by another atom or group.
  • Example: Halogenation of an alkane, where a hydrogen atom is replaced by a halogen atom.

• Rearrangement reactions:

  • Rearrangement reactions involve the redistribution of atoms within a molecule to form an isomer.
  • Example: Rearrangement of a carbocation to form a more stable carbocation.

Slide 15: Thermodynamics

• Thermodynamics is the study of energy and its transformations in chemical reactions.

• It helps understand the direction and extent of reactions.

• First law of thermodynamics:

  • The first law states that energy is conserved in a chemical reaction.
  • It is also known as the law of conservation of energy.

• Enthalpy (H):

  • Enthalpy is a measurement of the total heat content of a system.
  • It accounts for the internal energy (U) of a system and the work done (PΔV).
  • ΔH represents the change in enthalpy during a reaction.

• Entropy (S):

  • Entropy is a measure of the disorder or randomness in a system.
  • ΔS represents the change in entropy during a reaction.

• Gibbs free energy (G):

  • Gibbs free energy relates enthalpy, entropy, and temperature (T) of a reaction.
  • ΔG represents the change in Gibbs free energy during a reaction.
  • ΔG = ΔH - TΔS.

Slide 16: Kinetics of Chemical Reactions

• Kinetics is the study of the rates of chemical reactions and the factors that influence them.

• It provides insights into the reaction mechanism and helps predict reaction rates.

• Rate of a chemical reaction:

  • The rate of a reaction is the change in concentration of a reactant or product over time.
  • It is determined by the rate law, which relates the rate of the reaction to the concentrations of reactants and other factors.

• Activation energy:

  • Activation energy (Ea) is the minimum energy required for a reaction to occur.
  • It represents the energy barrier that must be overcome for the reaction to proceed.
  • Catalysts can lower the activation energy, increasing the rate of the reaction.

• Factors affecting reaction rates:

  • Concentration: Increasing the concentration of reactants generally increases the reaction rate.
  • Temperature: Higher temperatures increase the kinetic energy of particles, resulting in more frequent and energetic collisions.
  • Catalysts: Catalysts provide an alternate reaction pathway with a lower activation energy, increasing the reaction rate.

Slide 17: Equilibrium Constants

• Equilibrium constants (K) are mathematical expressions that relate the concentrations of reactants and products at equilibrium.

• They provide information about the extent of a reaction at a given condition.

• Equilibrium constant expression:

  • The equilibrium constant expression is written using the concentrations of products divided by the concentrations of reactants, each raised to the power of their stoichiometric coefficient.
  • Example: For the reaction A + B ⇌ C + D, the equilibrium constant expression is K = [C][D]