Biochemistry: Anatomy & Physiology I

Overview of Biochemistry

• Topic: BI 150: Anatomy & Physiology I
• Institution: SUNY ERIE (State University of New York)

Elements in Biochemistry

1. Definition of Elements

• Matter that contains only ONE TYPE of atom.
• Cannot be decomposed into simpler substances by ordinary CHEMICAL means.
• Examples: Carbon (C), Hydrogen (H), Oxygen (O).

1. Molecule

   • Definition: Two or more atoms joined together by chemical bonds (specifically covalent bonds).
   • Examples:
     • H₂O (water)
     • O₂ (molecule of Oxygen)

2. Compound

   • Definition: Two or more atoms bonded together, can be decomposed into different substances through ordinary chemical means (covalent or ionic bonds).
   • Examples:
     • H₂O (water)
     • CO₂ (carbon dioxide)
     • NaCl (sodium chloride)
     • HCl (hydrochloric acid)

Atoms

1. Definition

   • Smallest unit of an element retaining its chemical properties.

2. Principal Parts of an Atom:

   • Nucleus: Contains the main mass of an atom.
   • Electron Orbits (Shells): Regions where electrons spin around the nucleus.

3. Atomic Structure:

   • Electron orbits depicted as 2D circles or clouds.

4. Atomic Particles

   • Proton: Mass = 1 amu, Charge = +1, Location = nucleus.
   • Neutron: Mass = 1 amu, Charge = 0, Location = nucleus.
   • Electron: Mass ≈ 0 amu, Charge = -1, Location = orbit (shell).

5. Energy Levels

   • Different electron orbits that electrons can occupy.
   • Specific numbers of electrons fill each energy level:
     • 1st orbit: Max. of 2 Electrons
     • 2nd orbit: Max. of 8 Electrons
     • 3rd orbit: Max. of 8 Electrons (for atomic numbers ≤ 20).

6. Inert vs. Active Atoms

   • Inert: Atoms that do not bond with others, having full electron shells.
   • Active: Atoms that do bond with others due to incomplete shells.

Energy

1. Definition

   • Energy: Capacity to do work or move matter.

2. Types of Energy

   • Potential Energy: Stored energy.
   • Kinetic Energy: Energy of motion, transferrable between atoms or molecules.
   • Chemical Energy: A form of potential energy stored within chemical bonds.

3. Conversion

   • Potential energy can be converted to kinetic energy and vice versa.
   • Note: Heat is released during energy conversion.

Ions and Atoms

1. Definition of an Atom

   • An atom has equal numbers of electrons and protons, resulting in an overall charge of 0.

2. Definition of an Ion

   • An ion is an atom with unequal numbers of electrons and protons, resulting in an overall charge (positive or negative).
   • Gaining or losing electrons causes an atom to become an ion.

Types of Bonds

1. Ionic Bonds

   • Formed by transferring of electrons.
   • One atom takes one or more electrons from another atom, resulting in both atoms achieving full outer electron shells.

2. Covalent Bonds

   • Formed by the sharing of electrons.
   • Atoms share electron pairs, ensuring each has a filled outermost electron shell.
   • Examples:
     • Hydrogen Molecule (H₂): Formed by a single covalent bond (1 shared pair of electrons).
     • Oxygen Molecule (O₂): Formed by a double covalent bond (2 shared pairs of electrons).
     • Carbon Dioxide (CO₂): Formed by two double covalent bonds (O=C=O).

Atomic Properties

1. Atomic Number

   • The number of protons in the nucleus, identifying the atom in the Periodic Table.

2. Atomic Mass

   • Total number of protons and neutrons in an atom.

3. Isotopes

   • Atoms sharing the same identity (same proton number) but differing in atomic mass (different neutron number).
   • Example: Hydrogen isotopes (Hydrogen-1, Hydrogen-2 (deuterium), Hydrogen-3 (tritium)).

Chemical Reactions

1. Metabolism

   • All chemical reactions occurring in the cells and tissues at a given moment.

2. Reactions

   • Hydrolysis: Breaking down via addition of water (e.g. A-B + H₂O → A-H + HO-B).
   • Dehydration Synthesis: Combining to form new bonds with water as a product (e.g. A + B → AB, where A-H + HO-B → A-B + H₂O).

3. Adenosine Triphosphate (ATP)

   • Definition: Energy carrier of the cell.
   • Structure: Adenine-containing ribose nucleotide with two additional phosphate groups.
   • ATP is vital for cellular work, like muscle contractions, transport work, and key chemical reactions.
   • Comparison: ATP functions like gasoline for cars, supplying energy for cellular activities.

Cellular Respiration

1. What is Cellular Respiration?

   • The process by which ATP is produced from glucose.
   • Aerobic Respiration (with Oxygen) equation:
     C₆H₁₂O₆ + O₂ → CO₂ + H₂O + ATP.

2. Site of Cellular Respiration

   • Mitochondria: Where aerobic respiration occurs.

3. Anaerobic Respiration

   • Occurs when there is insufficient oxygen, producing lesser amounts of ATP.

4. Consequences of ATP Depletion

   • Failure in cellular functions, including synthesis and transport activities, leading to cell and tissue death.

Organic Substances

1. Definition

   • Organic substances contain carbon attached to at least one hydrogen.

2. Four Subtypes:

   • Carbohydrates: Sugars, starches, and cellulose.
   • Lipids: Fats.
   • Proteins: Major structural component of cells and tissues.
   • Nucleic Acids: RNA, DNA, and ATP.

Carbohydrates

1. Identify a Carbohydrate:

   • Contains only Carbon, Hydrogen, and Oxygen in a ratio of 2:1 for hydrogen to oxygen.
   • Structural forms: Hexagon or Pentagon shapes for different sugars (Hexoses and Pentoses).

2. Functions of Carbohydrates:

   • Short-term energy storage (4 calories per gram).

3. Types:

   • Monosaccharides: Simple sugars (e.g. glucose, fructose, galactose).
   • Disaccharides: Formed by two monosaccharides (e.g. sucrose, lactose, maltose) through dehydration synthesis (A-H + HO-B → A-B + H₂O).
   • Polysaccharides: Complex carbohydrates (e.g. glycogen in animals, starch & cellulose in plants).

4. Important Properties:

   • Glycogen: Energy reserve stored in liver and muscle cells.
   • Cellulose: Indigestible for humans, contributing to dietary fiber; benefitting digestion and cholesterol management.

Lipids

1. Types of Lipids:

   • Neutral Fats (Glycerides): Formed by dehydration synthesis of glycerol & fatty acids.
   • Phospholipids: Similar to glycerides but contain a phosphorus group.
   • Steroids: Derived from cholesterol.

2. Functions of Fats:

   • Long-term energy source (9 calories per gram).
   • Essential for making steroid hormones.
   • Component in cell membranes, insulation for organs.

3. Formation & Breakdown:

   • Formed through dehydration synthesis and broken down via hydrolysis, yielding glycerol and fatty acids.

4. Saturated vs Unsaturated Fats:

   • Saturated: Single covalent bonds in fatty acids, solid at room temperature.
   • Unsaturated: One or more double bonds, liquid at room temperature.

Proteins

1. Composition

   • Contains carbon, hydrogen, oxygen, and nitrogen.
   • Proteins are not stored due to toxic nitrogenous wastes (e.g. urea).

2. Building Blocks:

   • Made of amino acids (20 total, 9 of which are essential).

3. Functions of Proteins:

   • Emergency energy source (4 calories per gram).
   • Structural components (keratin, collagen, elastin).
   • Regulatory molecules (insulin, growth hormones).
   • Contractile proteins (actin, myosin).
   • Immune response (antibodies).
   • Catalytic functions (enzymes like cellulase, lactase, sucrase).

4. Peptide Bonds:

   • Chemical bonds linking amino acids; when formed, they create peptides.

5. Levels of Protein Structure:

   • Primary: Sequence of amino acids.
   • Secondary: Folding & twisting (alpha-helix & beta-pleated sheets).
   • Tertiary: Overall 3D shape.
   • Quaternary: Multiple polypeptide chains.

6. Denaturation:

   • Structural alteration due to pH changes or temperature increases, leading to loss of function.

Nucleic Acids

1. Definition

   • Chains of nucleotides made up of a phosphate group, sugar, and nitrogenous base.
   • Types: Deoxyribonucleic Acid (DNA), Ribonucleic Acid (RNA).

2. Functions:

   • DNA: Permanent storage of genetic information; self-replicating.
   • RNA: Temporary storage and transfer of genetic information; involved in protein synthesis (messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA)).

3. Importance of Denaturation:

   • Affects function; can lead to conditions like diabetes (lack of insulin) or anemia (lack of hemoglobin).

Inorganic Compounds

1. Water:

   • Makes up 60-80% of body mass; vital for temperature control, solvent function, and participation in chemical reactions.

2. Acids, Bases & Salts

   • Definitions:
     • Acid: Substance yielding H⁺ when added to water.
     • Base: Yields OH⁻ when added to water.
     • Salt: Yields neither H⁺ nor OH⁻ when added to water.
   • Electrolytes: Ions conducting electric charge (e.g. Na⁺, K⁺, Ca²⁺).

3. pH:

   • Measurement of H⁺ concentration; sensitive to changes, with extreme values causing denaturation.

4. Buffers:

   • Composed of weak acids and bases; help maintain stable pH levels in the body.

Conclusion

• Fundamental understanding of biochemistry is critical for anatomy and physiology.
• Involves the study of elements, compounds, organic substances, and various types of biological reactions and processes.