Levels of Organization & Properties of Water

1. Atoms and Molecules

• Atoms are the smallest units of matter, and they consist of:

  • Protons: Positively charged, located in the nucleus.

  • Neutrons: Neutral charge, located in the nucleus.

  • Electrons: Negatively charged, orbiting the nucleus.

• Molecules are formed when two or more atoms join together through chemical bonds.

2. Types of Bonds

• Covalent Bonds: A pair of electrons are shared between two atoms.

  • Can be single (one pair of electrons shared) or double (two pairs shared).

  • Polar Covalent Bonds: Molecules that do not share electrons equally, creating partial charges (- or +).

  • Nonpolar Covalent Bonds: Molecules that share electrons equally

• Ionic Bonds: Electrons are transferred from one atom to another, creating full charges. (not partial charges like polar covalent bonds)

3. Isomers

• Isomers are molecules with the same chemical formula but different structures, leading to different properties.

• Example: Different arrangements of atoms or functional groups.

4. Organic vs. Inorganic Molecules

• Organic Molecules: Contain carbon and are the building blocks of life.

• Inorganic Molecules: Generally do not contain carbon.

Properties of Water

1. Basics of Water

• Water is a polar molecule, with partial negative charges near the oxygen atom and partial positive charges near the hydrogen atoms.

• This polarity gives water its unique properties.

2. Hydrogen Bonds

• Hydrogen Bonds: Weak bonds formed between the partial charges of water molecules.

3. Cohesion and Adhesion

• Cohesion: Water molecules sticking to each other due to hydrogen bonding.

• Adhesion: Water molecules sticking to other materials, helping plants in transpiration.

4. Moderation of Temperature

• High Specific Heat: Water absorbs and releases heat slowly, stabilizing temperatures in environments and organisms.

• Evaporative Cooling: When water evaporates, it cools the surface, stabilizing temperatures in bodies of water and in organisms (e.g., sweating in humans).

5. Expansion Upon Freezing

• Water expands when it freezes, forming a less dense solid (ice) that floats, insulating liquid water beneath and allowing life to survive under frozen surfaces.

6. Water as a Solvent

• Universal Solvent: Water can dissolve many substances due to its polarity, making it vital for life.

• Solution: A homogeneous mixture of two or more substances.

• pH Scale: Water is neutral with a pH of 7; acids have a pH below 7, and bases have a pH above 7.

Dehydration Synthesis and Hydrolysis

• Dehydration Synthesis: Water is removed to form a new compound, making a product plus a molecule of water.

• Hydrolysis: Water is added to break down a compound, meaning the water is a reactant and is added to the product.

Proteins

1. Protein Structure and Function

• Monomer/Subunit: Amino acids are the building blocks of proteins.

• General Structure of Amino Acids:

  • Consists of an amino group (-NH2), a carboxyl group (-COOH), and a variable R group that differentiates amino acids.

• Function:

  • Proteins play various roles in the body, such as making structures, working in the immune system, and supporting the cardiovascular system.

  • Important Note: Proteins do not provide energy.

2. Primary Structure

• Primary Structure: The sequence of amino acids in a protein, linked together by peptide bonds.

• Impact of Sequence: Changing the primary structure (amino acid sequence) alters the protein's function.

3. Protein Functions (with Examples)

• Enzymes: Speed up chemical reactions (e.g., lactase).

• Defense: Protects the body (e.g., antibodies).

• Storage: Stores nutrients (e.g., casein in milk).

• Transport: Carries molecules (e.g., hemoglobin for oxygen).

• Hormones: Regulate bodily functions (e.g., insulin).

• Receptors: Receive signals from the environment.

• Movement: Enable movement (e.g., motor proteins).

• Structure: Provide support (e.g., keratin).

4. Four Levels of Protein Structure

1. Primary Structure:

   • The specific sequence of amino acids in a polypeptide chain.

   • There are 20 different amino acids.

   • Peptide bonds link the amino acids.

2. Secondary Structure:

   • Formed by interactions between sections of the primary structure.

   • Alpha Helix: Helical shape.

   • Beta Sheet: Flat, sheet-like structure.

   • Proteins often contain a mix of both alpha helices and beta sheets.

3. Tertiary Structure:

   • The overall 3D shape formed by bonding between R groups of amino acids.

   • Bonds involved include hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions, and van der Waals interactions.

4. Quaternary Structure:

   • Formed when two or more polypeptides bond together to function as a single protein.

5. Protein Structure and Environmental Sensitivity

• Denaturation: Proteins can lose their shape (and function) if exposed to non-optimal pH or temperature.

• Importance of Structure: A change in protein structure leads to a change in its function.

• X-ray Crystallography: A technique used to determine the 3D structure of proteins.

Nucleic Acids

1. Function

• Store Hereditary Information: Nucleic acids store and transmit genetic information.

2. DNA vs. RNA

• DNA (Deoxyribonucleic Acid):

  • Structure: Double-stranded helix.

  • Nitrogen Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T).

  • Function: Stores hereditary information.

  • Size: Longer and larger than RNA.

  • Sugar: Deoxyribose.

• RNA (Ribonucleic Acid):

  • Structure: Single-stranded.

  • Nitrogen Bases: Adenine (A), Guanine (G), Cytosine (C), Uracil (U).

  • Function: Carries information from DNA to ribosomes.

  • Types: Includes mRNA, tRNA, rRNA, and RNAi.

  • Sugar: Ribose.

3. Nucleotides

• Monomer of DNA/RNA: Nucleotides.

• Structure of a Nucleotide: Each nucleotide consists of a sugar (either ribose or deoxyribose), a phosphate group, and a nitrogenous base.

Basics of Biochemistry

• Organic Chemistry: Focuses on carbon compounds.

• Organic Compounds: Contain Carbon and Hydrogen.

• Major Elements of Life: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur (CHNOPS).

• Carbon Properties:

  • Forms large, complex molecules.

  • Can form single, double, or triple covalent bonds.

  • Can be chains, ring-shaped, or branched.

  • Forms isomers (same molecular formula, different structures).

Common Functional Groups in Biomolecules

• Hydroxyl (-OH): Polar, found in carbohydrates, proteins, and nucleic acids.

• Carbonyl (-C=O): Polar, found in carbohydrates, and proteins.

• Carboxyl (-COOH): Polar, negatively charged, found in fatty acids, and amino acids.

• Phosphate (-OPO₃H₂): Polar, negatively charged, found in phospholipids, and nucleic acids.

• Amino (-NH₂): Polar, positively charged, found in amino acids, and proteins.

• Sulfhydryl (-SH): Polar, forms stable S-S bonds, found in proteins.

• Amide (-C(=O)NH): Polar, found in proteins.

• Methyl (-CH₃): Nonpolar, found in amino acids, proteins, and nucleic acids.

Carbohydrates

• Function: Serve as fuel and building material.

• Structure: Composed of simple sugars (monosaccharides) and polymers (polysaccharides).

  • Monosaccharides: Simple sugars (e.g., glucose, ribose).

  • Disaccharides: Formed from two monosaccharides.

  • Polysaccharides:

    • Storage: Starch (plants) and glycogen (animals).

    • Structure: Cellulose (plants) and chitin (arthropods).

• Glucose Forms:

  • Starch: α-glucose monomers (digestible by humans).

  • Cellulose: β-glucose monomers (indigestible by humans, structural component).

Lipids

• Types:

  • Fats (Triglycerides):

    • Composed of glycerol + 3 fatty acids.

    • Saturated Fats: No double bonds, solid at room temperature.

    • Unsaturated Fats: At least one double bond, liquid at room temperature.

  • Steroids: Cholesterol and hormones, help regulate cell membrane fluidity.

  • Phospholipids: Key component of cell membranes, form bilayers due to hydrophobic and hydrophilic interactions.

• Functions:

  • Energy Storage: Long-term energy, cushions organs.

  • Structural: Essential in the formation of cell membranes.