2_Basic_Chemistry

Chapter 2: Basic Biochemistry

Matter

• Biochemistry is the study of the chemical processes within living organisms.

• Matter is anything that has mass and takes up space, and it includes energy.

• Energy is the capacity to perform work, measured by its effects on matter. It exists in kinetic form (motion) and potential form (stored energy, e.g., ATP).

Functional Characteristics

• Organization: Living beings maintain distinct internal and external environments.

• Acquisition & Metabolism: Encompasses movement, uptake of materials and energy, and waste excretion.

• Response & Regulation: Ability to respond to environmental changes.

• Reproduction & Growth: Organisms reproduce and develop.

• Adaptation: Ability to adjust to environmental changes.

Basic Chemistry: Matter

• Matter consists of elements and compounds.

• Elements: Substances that cannot be separated into simpler substances, consisting of only one type of atom.

• Known Elements: Over 100 elements exist, with 92 occurring naturally.

Elements

• Atoms: The smallest unit of an element that retains its properties.

• Atoms consist of protons (positively charged), neutrons (neutral), and electrons (negatively charged).

• Carbon (C): Example of an atom with 6 protons and 6 neutrons, defining its characteristics.

Isotopes

• Isotopes: Variants of elements differing in the number of neutrons.

• Radioisotopes: Unstable isotopes that emit particles and energy, causing radioactive decay.

The Periodic Table

• Discusses the arrangement of elements based on atomic number, properties, and periodicity.

• Elements are grouped into categories such as alkali metals, alkaline earth metals, and transition metals.

Biologically Important Elements (CHNOPS)

• CHNOPS: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur are essential for life.

• Bulk Elements: Make up most of the body mass (C, H, O, N).

• Trace Elements: Required in small amounts (e.g., Iron, Iodine).

Electron Distribution and Chemical Properties

• The behavior of an atom is influenced by its electron arrangement in shells. Electrons in the outermost shell (valence electrons) are pivotal in bonding and reactivity.

• Periodic table rows represent energy levels, while columns correlate with valence electrons.

Molecular Structure and Chemical Bonds

• Orbitals: Regions of space where electrons are likely to be found; can accommodate only two electrons.

• Covalent Bonds: Forms when atoms share electrons, contributing to molecular stability.

• Ionic Bonds: Occur when electrons are transferred between atoms, creating cations and anions, which are charged particles.

• Hydrogen Bonds: Weaker interactions that occur between polar molecules, significant in biological structures and processes.

Functional Groups and Molecular Shape

• Functional groups influence a molecule's reactivity and solubility.

• The 3D shape of molecules is critical for their biological function, exemplified by how enzymes interact with substrates.

Energy and Biochemical Reactions

• Metabolism: The total of chemical reactions that occur in an organism, partitioned into anabolic (building up) and catabolic (breaking down) processes.

• Energy transformation follows the Laws of Thermodynamics, emphasizing energy conservation and loss in conversions.

Chemical Reactions: Metabolism

• Reactions involve changes in chemical bonds, with defined reactants and products that maintain mass conservation.

• Equilibrium occurs when the rate of forward and reverse reactions are equal, resulting in stable concentrations of reactants/products.

Synthesis and Decomposition Reactions

• Dehydration Synthesis: Forms larger molecules by removing water.

• Hydrolysis: Breaks down larger molecules by adding water.

Free Radicals and Antioxidants

• Free radicals are unstable molecules that can cause cellular damage, linked to various diseases; antioxidants can neutralize these radicals.

Bonds Between Elements

• The three primary types of bonds are covalent, ionic, and hydrogen, which create molecular structure and determine biochemical interactions.

• Understanding these bonds is vital to comprehending enzyme reactions and metabolic pathways.

Enzymes and Metabolic Pathways

• Enzymes, biological catalysts, lower activation energy to facilitate chemical reactions in cells.

• They form complexes with substrates, and their activity can be influenced by factors such as temperature, pH, and concentrations of substrates/products.

Regulation of Metabolic Processes

• Enzyme activity is regulated through competitive inhibition, noncompetitive inhibition, and allosteric modulation, allowing fine-tuned metabolic control.

Conclusion

• Biochemistry encompasses the principles of chemistry as they apply to biological systems, essential for understanding life processes.

1. Definitions:

   • Polar molecule: A molecule with a net dipole moment due to the presence of polar bonds, resulting in partially positive and negative charges.

   • Nonpolar molecule: A molecule that does not have a net dipole moment; has an even distribution of electrical charge.

   • Hydrophilic: Substances that are attracted to water (water-loving).

   • Hydrophobic: Substances that repel water (water-fearing).

   • Amphipathic: Molecules that have both hydrophilic and hydrophobic regions.

   • ECF (extracellular fluid): The fluid outside of cells; ISF (interstitial fluid): The fluid in the spaces between cells.

   • ICF (intracellular fluid): The fluid within cells.

   • Solute: A substance that is dissolved in a solution.

   • Solvent: A substance in which a solute is dissolved.

   • Solution: A homogeneous mixture of solute and solvent.

   • Osmolarity: The measure of solute concentration, defined as the number of osmoles of solute per liter of solution.

   • Osmolality: The measure of solute concentration, defined as the number of osmoles of solute per kilogram of solvent.

   • pH: A measure of the acidity or basicity of a solution, calculated as the negative logarithm of the hydrogen ion concentration.

   • Buffer: A solution that resists changes in pH when acids or bases are added.

   • Kinetic energy: Energy of motion.

   • Potential energy: Stored energy, often due to position or structure.

   • Chemical energy: Energy stored in the bonds of chemical compounds.

   • Electrical energy: Energy caused by the movement of electrons.

   • Reactant: A substance consumed in a chemical reaction.

   • Product: A substance produced in a chemical reaction.

   • Equilibrium: The state in a reaction where the rate of forward and reverse reactions are equal.

   • Oxidation: The loss of electrons or an increase in oxidation state by a molecule.

   • Reduction: The gain of electrons or a decrease in oxidation state by a molecule.

   • Anabolism: The metabolic process that builds larger molecules from smaller ones.

   • Catabolism: The metabolic process that breaks down larger molecules into smaller ones.

   • Exergonic: A reaction that releases energy.

   • Endergonic: A reaction that absorbs energy.

   • Catalyst: A substance that increases the rate of reaction by lowering activation energy without being consumed.

   • Agonist: A substance that activates a receptor to produce a biological response.

   • Antagonist: A substance that inhibits or blocks a receptor's biological response.

   • Saturation: The point at which all active sites of an enzyme are occupied by substrates.

   • Glycolysis: The metabolic pathway that converts glucose into pyruvate, producing ATP.

   • Transition reaction: Converts pyruvate into acetyl-CoA before entering the Krebs cycle.

   • Electron transport system (ETS): A series of protein complexes that transfer electrons to generate ATP.

   • Chemiosmosis: The movement of ions across a selectively permeable membrane, generating ATP.

   • Aerobic respiration: A process that requires oxygen to produce ATP.

   • Anaerobic respiration: A process that occurs without oxygen to produce ATP.

   • Fermentation: A metabolic process that converts sugar to acids, gases, or alcohol without the use of oxygen.

2. Laws of Thermodynamics:

   • First Law: Energy cannot be created or destroyed; it can only change forms. In the body, this means energy transformations during metabolic reactions.

   • Second Law: The entropy of the universe increases over time; in body reactions, some energy is lost as heat.

3. Energy: The capacity to perform work, stored in the body primarily as chemical energy (in ATP), and can be converted from one form to another (e.g., from food).

4. An element: A pure substance consisting of one type of atom; A molecule: Two or more atoms bonded together; An ion: An atom or molecule that has gained or lost one or more electrons, resulting in a charge; An isotope: Variants of a particular chemical element that have the same number of protons but different numbers of neutrons.

5. Periodic Table: Columns (groups) indicate elements with similar properties; rows (periods) correspond to the number of electron shells. Valence electrons determine bonding behavior.

6. Orbitals matter as they dictate the arrangement of electrons, influencing the molecular structure and therefore biological functions (structure and reactivity).

7. Free radicals: Unstable molecules that can damage cells; controlling them is important to prevent cellular damage and diseases like cancer.

8. Biologically important elements: Mainly CHNOPS - Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur.

9. Three types of bonding: Covalent (sharing electrons), Ionic (transfer of electrons), and Hydrogen (weak bonds between polar molecules).

10. Polar covalent bonds are important because they result in partial charges within molecules, creating dipoles that influence interactions. A dipole is a molecule with two poles, one positive and one negative.

11. Hydrogen bonding is critical for the structure of proteins and nucleic acids; it stabilizes their structures and influences their interactions.

12. A cation is a positively charged ion, an anion is a negatively charged ion, and a salt is a compound formed from the ionic bond between cations and anions.

13. Water is the most important inorganic molecule in the human body; its chemical properties include being a solvent, regulating temperature, and participating in biochemical reactions.

14. Amphipathic molecules have both hydrophilic and hydrophobic parts, crucial for plasma membrane structure, allowing for selective permeability. Phospholipids form bilayers in membranes due to their amphipathic nature.

15. Molarity (moles of solute per liter of solution) vs. Molality (moles of solute per kilogram of solvent); osmolality is more relevant in physiological contexts due to its relation to the number of particles in a solution.

16. Salts are termed electrolytes because they dissociate into ions in solution, conducting electrical current.

17. pH: A measurement of hydrogen ion concentration; acids increase [H+], while bases decrease it.

18. Buffers: Solutions that stabilize pH changes; the carbonic acid/bicarbonate buffering system helps maintain blood pH around 7.35-7.45.

19. Organic molecules contain carbon and common elements include C, H, O, N; their functional groups dictate their biochemical activities.

20. Four types of organic molecules: Carbohydrates (energy), Lipids (membranes), Proteins (structure and function), Nucleic Acids (genetic information).

21. Functions of proteins include catalysis (enzymes), signaling (hormones), and structural roles; formed through specific amino acid sequences (primary structure).

22. ATP is crucial for energy transfer within cells and a primary energy source for cellular processes.

23. Components of chemical reactions include reactants, products, energy changes, and catalysts.

24. Dehydration synthesis: Combining molecules with the removal of water; Hydrolysis: Breaking down molecules with the addition of water; both often occur during metabolism.

25. Oxidation: Loss of electrons; Reduction: Gain of electrons; Redox: Coupled reactions of oxidation and reduction.

26. Anabolism (building) and Catabolism (breaking down) are coupled processes; together, they manage energy and matter in metabolism.

27. Exergonic reactions release energy, while endergonic reactions require energy input; coupled reactions enable balance in metabolic pathways.

28. Activation energy is the energy needed to start a reaction; enzymes lower this barrier, facilitating reactions at physiological conditions.

29. Net free energy influences reaction direction; if negative, reactions proceed spontaneously, influencing metabolic pathways.

30. Enzymes are biological catalysts; substrates are the reactants; ligands bind to enzymes; the ES complex is the enzyme-substrate complex; specificity and affinity are critical for enzyme function.

31. Factors affecting protein binding include concentration, temperature, and pH.

32. Active site: Region on the enzyme where substrates bind; Induced fit model: Enzyme changes shape upon substrate binding; Catalytic cycle: Sequence of events in enzyme action.

33. Law of Mass Action states that a change in concentration of reactants/products will shift equilibrium; equilibrium means no net change in concentrations of reactants and products.

34. Enzyme regulation occurs through inhibitions (competitive/non-competitive), allosteric modulation, and cooperativity, allowing dynamic metabolic control.

35. Factors affecting enzymatic function include temperature, pH, and substrate concentrations.

36. Saturation means all active sites on an enzyme are filled; ligand and enzyme concentrations affect how quickly saturation is reached.

37. Enzymatic reactions are classified by their specific functions (e.g., kinases transfer phosphate groups).

38. Metabolic pathways follow specific control points where enzymes can be regulated to manage flow and speed of biochemical reactions.

39. Steps of glucose metabolism: Glycolysis -> Krebs cycle -> Electron transport chain; ATP is produced primarily during the Krebs cycle and ETS.

40. Glycolysis occurs in the cytoplasm, producing 2 ATP; it is anaerobic as it does not require oxygen.

41. The aerobic pathway depends on oxygen for complete glucose metabolism, while the anaerobic pathway leads to lactate or ethanol formation.

42. Transition Reaction: Converts pyruvate to acetyl-CoA, occurring in mitochondria.

43. ETS generates ATP and creates a proton gradient, which affects body pH by absorbing H+ during ATP production.

44. Oxygen is critical for aerobic metabolism; insufficient oxygen leads to reliance on anaerobic pathways, causing accumulation of lactic acid during intense exercise.