Biochemistry: Fundamentals and Biomolecules

Fundamentals of Biochemistry

• This is an introductory presentation on the fundamentals of biochemistry, by D. en C. Octavio Barragán Mares.
• Biochemistry is defined as the branch of science studying chemical and molecular processes in living beings.

Assessment and Course Content

• Classwork and assignments are 30% of the final grade.
• Lab practice work is 15% of the final grade.
• Quizzes are 5% of the final grade.
• The midterm exam counts for 40% of the final grade.
• Vocational practices contribute 10% of the final grade.
• The thematic content includes the importance of water as a biomolecule, structure, classification, and function of nucleotides, amino acids, carbohydrates, and lipids from a metabolic perspective.
• Focus is placed on the physicochemical properties, structure, metabolism, and functions of water and nucleotides to understand biochemistry as a science that studies life.
• Analysis includes the concept of metabolism which encompasses anabolism and catabolism, and its relationship to the ATP cycle and bioenergetics.
• Discussion focuses on basic structure, nomenclature, biological function, and metabolic processes of carbohydrates and lipids.
• The importance of lipids and carbs in metabolic processes, and moderating intake for health, are valued.

Impact of Biochemistry

• Biochemistry helps understanding how molecules like water interact and function in organisms.
• Biochemical understanding is key to creating drugs and therapies for treating diseases, by targeting biochemical processes involved in diseases to restore health.
• Biochemistry advances biotechnology, allowing manipulation of organisms to produce useful substances like therapeutic proteins, vaccines, and bioenergy.
• Biochemical principles are applied in bioengineering for the creation of biocompatible materials and medical devices.
• Biochemistry contributes to improved crops, livestock, and their nutritional value.
• Biochemistry plays a crucial role in food processing and human nutrition research.

Basic Concepts in Chemistry and Biology

• Chemical bonds
• Intermolecular forces
• Elemental composition of the human body.

Ionic Bonds

• Ionic bonds involve the transfer of electrons to form ions.
• Typically form between a metal and a nonmetal.
• Electronegativity difference is greater than 1.7.
• Conduct electricity in solution.

Covalent Bonds

• Covalent bonds involve shared electrons.
• Covalent bonds occur between two nonmetals.
• Do not conduct electricity.
• Nonpolar covalent bonds form between atoms with an electronegativity difference less than 0.4.
• Polar covalent bonds form when the electronegativity difference is between 0.4 and 1.7.

Coordinate Bonds

• Coordinate bonds, also known as dative bonds, are a type of covalent bond.
• Coordinate bonds happen when one atom provides both electrons that are shared in the bond.
• Commonly found in metallic complexes and other structures.
• An atom or ion donates a lone pair of electrons to another atom or ion with an empty orbital.

Intermolecular forces

• Hydrogen bonds occur in molecules containing hydrogen bonded to a highly electronegative element (O, N, F) with a small atomic radius.
• Dipole-dipole forces maintain the molecule in a polar substance.
• London dispersion forces are weak but can bond molecules that are nonpolar.

Elemental Composition of the Human Body

• Main elements:
  • Oxygen: 65%
  • Carbon: 18.5%
  • Hydrogen: 10%
  • Nitrogen: 3%
  • Calcium: 1.5%
  • Phosphorus: 1%
• Secondary elements:
  • Potassium: 0.30%
  • Sulfur: 0.25%
  • Sodium: 0.20%
  • Chlorine: 0.15%
  • Magnesium: 0.05%
  • Iron: 0.005%
• Trace elements consist of very small percentages.
  • Fluorine: 0.001%.
  • Copper: 0.0002%.
  • Iodine: 0.00004%.
  • Manganese: 0.00003%.
  • Zinc, Cobalt, and Molybdenum are present in trace amounts.

Biomolecules

• Biomolecules are molecules present in living organisms and are essential for biological processes.
• These biomolecules include:
  • Water
  • Mineral salts
  • Carbohydrates
  • Lipids
  • Nitrogen compounds
  • Amino acids
  • Proteins
  • Enzymes and hormones
  • DNA and RNA

Physical Properties of Water

• Boiling and Freezing Points: Water boils at 100°C and freezes at 0°C under standard conditions.
  • Changes in the state of water can cause damage to the structure of cells.
  • The study of these property is crucial with cell preservation.
• Water is most dense at 4°C with a density of 1 g/cm³.
  • Water density affects buoyancy and the distribution of molecules.
• Surface Tension: Water has high surface tension due to strong cohesive forces between its molecules.
• The importance in Biochemistry: Surface tension is essential for the formation and stability of cell membranes.
• Specific Heat Capacity: It has a high specific heat capacity (4.18 J/g°C) and can absorb or release heat.
  • This helps stabilize internal temperature and allows reactions within organisms.

Chemical Properties of Water

• Polarity: Water is a polar molecule with an uneven charge distribution.
  • Polarity allows formation of hydrogen bonds.
  • Polarity supports the construction of macromolecules.
• Reactivity: It can react with a wide range of substances, acting as both an acid and a base.
  • The ability to act as an acid and a base is essential for metabolic reactions.
• Electrical Conductivity: Pure water has low electrical conductivity, but conductivity increases with dissolved ions.
  • The conductivity affects membrane potentials and signals in the nervous system.
• Autoionization: Water can ionize to form hydronium (H3O+) and hydroxide (OH-) ions.
  • Autoionization is crucial for control of pH levels.

Electrolytes and Metallic Ions

• Metallic ions play a crucial role in biological functions.
• Metallic ions act as cofactors in enzymatic reactions.
• Metallic ions help in the delivery of nerve signals.
• Important for maintaining the liquid pH balance.
• The concentration of ions must be cautiously regulated.
• Imbalances cause health concerns.
• Some ions function as electrolytes and conduct electricity.

Calcium (Ca2+)

• Function: Essential for the formation of bones and teeth, blood coagulation, muscle contraction, and nerve transmission, and it works as an electrolyte.
  • Deficiency: Causes osteoporosis, rickets
  • Excess: Causes hypercalcemia.

Potassium (K+)

• Function: Potassium regulates fluid balance, muscle contraction, and nerve function, acting as an electrolyte.
  • Deficiency: Hypokalemia causes muscle weakness, cramps, and cardiac arrhythmias.
  • Excess: Hyperkalemia can cause severe cardiac arrhythmias.

Sodium (Na+)

• Function: Sodium maintains fluid balance, nerve function, and muscle contraction, and is an electrolyte.
  • Deficiency: Hyponatremia can cause nausea, vomiting, confusion, and seizures.
  • Excess: Hypernatremia can lead to hypertension and dehydration.
• Bartter syndrome is a renal tubular disease characterized by impaired sodium reabsorption.

Magnisium (Mg2+)

• Magnesium has electrolyte behavior.
• Magnesium is essential for synthesizing proteins, as well as muscular, and neural functions.
• A magnesium deficit in the body can cause muscle cramps, cardiac arrhythmia or convulsions.
• High levels of magnesium in the body can cause hypotension, nausea and muscle weakness.

Zinc (Zn2+)

• Important in the synthesis of DNA as well as immune system functions.
• Critical for tissue and wound healing
  • Deficiency: can cause stunted growth, appetite deficiencies or immune dysfunction.
  • Excess: Can cause gastrointestinal issues and nervous system complications.

Iron (Fe2+/Fe3+)

• Essential for the formation of hemoglobin and oxygen transport.
  • Deficiency: Iron deficiency causes anemia, which leads to tiredness and pallor.
  • Excess: Hemochromatosis causes organ damage

Copper (Cu2+)

• Copper is needed to support red blood cell formation and a healthy nervous system.
  • Deficiency: Anemia and Neutropenia.
  • Excess: Wilson’s disease and Hemolytic.

Body Water Content

• Relative distribution of body water
  • In men: 60% water - 45% intracellular fluid, 15% extracellular, 10% interstitial fluid, and 5% plasma.
  • In women: 55% water - 40% intracellular fluid, 15% extracellular, 10% interstitial fluid, and 5% plasma.
  • In infants: 77% water - 48% intracellular fluid, 29% extracellular, 24% interstitial fluid, and 5% plasma.
• Values are expressed as percentages.
  • LIC stands for intracellular fluid.
  • LEC stands for extracellular fluid.
  • LIT is used to define interstitial fluid.

Water Balance

• Daily water balance:
  • Water Input (ml):
    • Fluids: 1400
    • Food: 800
    • Metabolic water: 300
    • = 2500 mL
  • Water Output (ml):
    • Urine: 1500
    • Perspiration: 850
    • Feces: 150

Ionograms

• Plasmatic ionograms analyze principal components of blood plasma.
• The components are:
  • Sodium (Na)
  • Potassium (K)
  • Chlorine (Cl)
  • Bicarbonate (CO2H-)
• Urinary ionograms are useful to complement plasmatic ionograms.
• They're both useful to observe hydrolitic unbalance and control in organs.

Osmosis

• Osmosis is water travelling from high concentration to low concentration. Tonicity reflects solute concentration and solution behavior.
  • Hypertonic solutions: cells shrink.
  • Isotonic solutions: no change.
  • Hypotonic solutions: cells swell.
• Acid solutions contain (H+).
• Basic solutions contain (OH-).
• Neutral substances contain an even amount of chemicals.

PH Calculations

• Acids have a pH value of 0-6.
• Neutrals have a pH value of 7.
• Bases have a pH value of 8-14.
• Strong acids has a pH value from 0-3.
• A weak acid has a pH value of 4-6.
• Weak bases has a pH value of 8-10.
• A strong bases has a pH value 11-14.