Undergraduate
  1. General chemistry  1.1. Introduction to Chemistry  1.2. Atomic Structure  1.2.1. Subatomic particles  1.2.2. Atomic Model  1.2.3. Quantum numbers  1.2.4. Electron Configuration  1.2.5. Periodic trends  1.2.6. Isotopes and their applications  1.3. Chemical bond  1.3.1. Ionic bond  1.3.2. Covalent bonds  1.3.3. Metal Bond  1.3.4. Hybridization  1.3.5. Molecular geometry and VSEPR theory  1.3.6. Bond polarity and dipole moment  1.4. Stoichiometry  1.4.1. Mole concept  1.4.2. Empirical and molecular formula  1.4.3. Limiting reactant and excess reactant  1.4.4. Percent Yield and Purity  1.4.5. Dilution calculation  1.5. States of matter  1.5.1. Gas Laws  1.5.2. Matter and Intermolecular Forces  1.5.3. Solid and Crystal Structures  1.5.4. Phase diagram  1.5.5. Plasma and supercritical fluid  1.6. Chemical reactions  1.6.1. Types of Chemical Reactions  1.6.2. Balancing Chemical Equations  1.6.3. Thermochemical reactions  1.6.4. Reaction energy profiles  1.7. Solutions and Mixtures  1.7.1. Concentration units  1.7.2. Syndrome properties  1.7.3. Solubility and Solubility Rules  1.7.4. Henry's Law and Raoult's Law  1.7.5. Partition coefficient  1.8. Chemical equilibrium  1.8.1. Law of mass action  1.8.2. Le Chatelier's principle  1.8.3. Reaction quotient  1.8.4. To use this online calculator for Equilibrium Constant, enter Equilibrium Constant (Eq.) and hit the calculate button. Here is how the Equilibrium Constant calculation can be explained with given input values -> 0.05 = 0.05/0.  1.8.5. Acid-base balance  1.9. Acids and bases  1.9.1. Arrhenius, Brønsted–Lowry, and Lewis definitions  1.9.2. pH and pOH  1.9.3. Acid-base titration  1.9.4. Buffer Solution  1.9.5. Acid-base indicator  1.9.6. Polyprotic Acids and Bases  1.10. Electrochemistry  1.10.1. redox reactions  1.10.2. Galvanic and Electrolytic Cells  1.10.3. Nernst equation  1.10.4. Electrolysis  1.10.5. Faraday's laws of electrolysis  1.11. Thermodynamics  1.11.1. Laws of Thermodynamics  1.11.2. Enthalpy, entropy and Gibbs free energy  1.11.3. Spontaneity of reactions  1.11.4. Thermodynamic cycles (Hess's law, Carnot cycle)  1.12. Kinetics  1.12.1. Rate law and reaction order  1.12.2. Activation Energy and Catalyst  1.12.3. Collision theory  1.12.4. Reaction mechanism  1.12.5. Transition state theory
  2. Organic chemistry  2.1. Structure and relationships  2.1.1. Hybridisation in Carbon Compounds  2.1.2. Resonance and aromatization  2.1.3. Molecular orbitals  2.1.4. Inductive and mesomeric effects  2.2. Hydrocarbons  2.2.1. Hydrocarbons  2.2.2. Alkene  2.2.3. Alkynes  2.2.4. Aromatic compounds  2.2.5. Cycloalkanes and Conformation  2.3. Functional Group  2.3.1. Alcohols and phenols  2.3.2. Ethers and epoxides  2.3.3. Aldehyde and ketone  2.3.4. Carboxylic acids and derivatives  2.3.5. Amin  2.3.6. Esters and amides  2.3.7. Thiols and sulfides  2.4. Stereoscopic  2.4.1. Isomerism in Stereochemistry  2.4.2. Chirality and optical activity  2.4.3. Structural analysis  2.4.4. Diastereomers and Enantiomers  2.5.1. Substitution reactions  2.5.2. Elimination reactions  2.5.3. Addition reactions  2.5.4. Radical reactions  2.5.5. Rearrangement reactions  2.5.6. Pericyclic Reactions  2.6. Spectroscopy and structural analysis  2.6.1. Infrared Spectroscopy  2.6.2. Nuclear magnetic resonance spectroscopy  2.6.3. Mass Spectrometry  2.6.4. UV-visible spectroscopy  2.6.5. X-ray crystallography  2.7. Polymer chemistry  2.7.1. Addition and Condensation Polymers  2.7.2. Polymerization mechanism  2.7.3. Biodegradable Polymer  2.7.4. Conducting and smart polymers
  3. Inorganic chemistry  3.1. Coordination chemistry  3.1.1. Ligands and coordination compounds  3.1.2. Crystal field theory  3.1.3. Molecular Orbital Theory in Coordination Compounds  3.1.4. Jahn–Taylor distortion  3.2. Main Group Chemistry  3.2.1. Alkali and alkaline earth metals  3.2.2. Halogens and Noble Gases  3.2.3. Transition metals and their complexes  3.2.4. Lanthanides and Actinides  3.3. Solid state chemistry  3.3.1. Crystal lattices and unit cells  3.3.2. Defects in solids  3.3.3. Electrical and magnetic properties  3.3.4. Superconductivity  3.4. Bio-inorganic chemistry  3.4.1. Metal ions in biology  3.4.2. Enzymatic reactions with metals  3.4.3. Metal poisoning and detoxification  3.4.4. Metalloproteins and Metalloenzymes
  4. Physical chemistry  4.1. Quantum Chemistry  4.1.1. Wave–particle duality  4.1.2. Schrödinger Equation  4.1.3. Quantum Numbers and Orbitals  4.1.4. Atomic and molecular spectroscopy  4.2. Statistical mechanics  4.2.1. Maxwell–Boltzmann distribution  4.2.2. Partitioning functions  4.2.3. Bose–Einstein and Fermi–Dirac statistics  4.3. Chemical thermodynamics  4.3.1. Gibbs Free Energy  4.3.2. Phase transition  4.3.3. Thermodynamic efficiency  4.4. Surface chemistry  4.4.1. Absorption and Catalysis  4.4.2. Colloids and Emulsions
  5. Analytical Chemistry  5.1. Classical methods  5.1.1. Gravimetric Analysis  5.1.2. titrimeter  5.2. Instrumental methods  5.2.1. Chromatography  5.2.2. Spectroscopy  5.2.3. Electroanalytical methods  5.2.4. X-ray diffraction
  6. Industrial Chemistry  6.1. Petrochemistry  6.2. Chemical engineering principles  6.3. Green Chemistry  6.4. Pharmaceuticals and Drug Synthesis
  7. Biochemistry  7.1. Carbohydrates  7.2. Proteins and enzymes  7.3. Lipids and membranes  7.4. Nucleic acids  7.5. Metabolism and Bioenergetics  7.6. Enzyme kinetics and mechanism

Undergraduate → Biochemistry ↓


Proteins and enzymes


Proteins and enzymes play important roles in the life processes of all organisms. While proteins are the fundamental building blocks of living tissues, enzymes are specific types of proteins that catalyze biochemical reactions. Understanding these biomolecules is essential in biochemistry, especially in undergraduate chemistry.

Understanding proteins

Proteins are large, complex molecules that are important for many functions within organisms. They are polymers of amino acids, which are organic compounds composed primarily of carbon, hydrogen, nitrogen, oxygen, and sometimes sulfur. Proteins serve a variety of functions in the body, including structural, regulatory, and catalytic roles.

General formula of an amino acid: H2N-CHR-COOH

1. Structure of proteins

Proteins have unique structures that enable them to perform specific functions. They are organized into several layers of structure, which are mainly classified into primary, secondary, tertiary and quaternary structures:

  • Primary structure: The sequence of amino acids linked by peptide bonds, which forms a polypeptide chain.
  • Secondary structure: Local folding of the polypeptide chain into structures such as alpha-helix and beta-pleated sheet, which are stabilized by hydrogen bonding.
  • Tertiary structure: The three-dimensional structure of a polypeptide, determined by interactions such as hydrogen bonds, ionic bonds, van der Waals interactions, and disulfide bridges.
  • Quaternary structure: An arrangement of multiple polypeptide subunits in a protein, each of which has its own tertiary structure.

2. Functions of proteins

Proteins play both structural and functional roles, such as:

  • Structural support: Proteins such as collagen and elastin provide support and structure to tissues and organs.
  • Enzymatic activity: Enzymes are proteins that speed up biochemical reactions.
  • Transport and storage: Hemoglobin transports oxygen in the blood, while ferritin stores iron.
  • Signal transduction: Hormones like insulin are proteins that help in cell signaling.
  • Immune response: Antibodies are proteins that identify and neutralize pathogens such as bacteria and viruses.

Visual example of protein structure

Protein Structure Primary Structure: AABCD Secondary Structure: Helix and Sheet Tertiary structure: 3D folding Quaternary structure: multiple chains

Understanding enzymes

Enzymes are proteins that act as biological catalysts, speeding up the rate of chemical reactions in cells without being consumed in the process. Nearly all metabolic processes in the body require enzyme catalysis to occur at a rate fast enough to sustain life.

1. Structure of enzymes

Enzymes, like all proteins, are made up of long chains of amino acids. Their specific folding and resulting 3D structure allows them to bind to specific substrate molecules. The active site of an enzyme is the region where the substrate molecules bind and undergo a chemical reaction.

2. Enzyme functionality

Enzymes act by lowering the activation energy of reactions, thereby increasing the reaction rate. They do this by binding to the substrate and stabilizing the transition state. There are several key points about enzyme action:

  • Specificity: Each enzyme is specific for a particular reaction or type of reaction.
  • Induced fit: Upon binding, enzymes slightly change their shape to fit more closely onto the substrate.
  • Reusability: Enzymes are not spent in the reaction and can be reused many times.
  • Regulation: Enzyme activity can be regulated by factors such as temperature, pH, and the presence of inhibitors or activators.

Visual example of enzyme activity

I S Enzymes Substrate Binding

Enzyme kinetics

Enzyme kinetics is the study of the rates of enzyme-catalyzed reactions. Understanding enzyme kinetics is essential for determining enzyme activity, understanding metabolic pathways, and developing drugs.

1. Michaelis-Menten kinetics

This is a common model used to describe enzyme kinetics. It is based on the formation of the enzyme-substrate complex:

E + S ⇌ ES → E + P

In this model:

  • E is an enzyme.
  • S is the substrate.
  • ES is an enzyme-substrate complex.
  • P is the product.

The rate of the reaction is given by the Michaelis-Menten equation:

v = (Vmax [S]) / (Km + [S])

where v is the reaction rate, [S] is the substrate concentration, Vmax is the maximum rate, and Km is the Michaelis constant.

Importance of proteins and enzymes in living organisms

Proteins and enzymes are essential for life. They are necessary for cell structure, function, and the regulation of the body's tissues and organs. Without proteins and enzymes, vital processes such as metabolism, DNA replication, and cell signaling would not be able to occur.

1. Role in metabolism

Enzymes are vital to metabolic pathways, which are sequences of chemical reactions in the cell. Each step is catalyzed by a specific enzyme. This allows for regulation, efficiency, and speed of metabolic processes.

2. Role in disease and medicine

Many diseases can be caused by malfunctioning enzymes or proteins. Understanding these biomolecules extends to medical applications such as drug design, where inhibitors or activators can be used to correct improper enzyme function.

Conclusion

Understanding proteins and enzymes is important in biochemistry. Their diverse structures and functions make them key components of life. By studying proteins and enzymes, scientists can develop new techniques and treatments to improve health and understanding of biological processes.


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Proteins and enzymes

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