In-depth Notes on Carbon and Organic Molecules

Why Carbon?
- Carbon can form 4 covalent bonds due to its 4 electrons in the valence shell.
- It can link up to 4 other atoms, making it highly versatile for building large, stable molecules (macromolecules).
- Capable of forming single, double, or triple bonds which allows for diverse structural shapes.

Types of Organic Molecules:
- Proteins
- Carbohydrates
- Lipids
- Nucleic Acids
These molecules are polymers, consisting of repeating structural units known as monomers.
They can be very large, with molecular weights (MW) over 1000 g/mol, hence the term macromolecules.

Functional groups are small groups of atoms in organic molecules that affect their chemical properties:
- Determine polarity and charge of molecules.
- Influence interactions with other molecules and with water.

The function of macromolecules often reflects their structure.
Similar molecules across different species suggest common ancestry, enabling organisms to utilize raw materials via consumption.

Condensation Reactions:
- Link monomers by forming covalent bonds.
- Release a water molecule and require energy.
Hydrolysis Reactions:
- Break bonds between monomers by adding a water molecule.
- Release energy and are essential for digesting polymers.

Examples of Proteins:
- Hormones, antibodies, receptor proteins, transport proteins, structural proteins, enzymes.
Amino Acids:
- Building blocks of proteins, consisting of 20 different amino acids.
- Proteins form through chains of amino acids linked by peptide bonds through condensation reactions.
Polypeptide chains fold into 3D shapes, determined by the sequence of amino acids.

Primary Structure:
- Linear sequence of amino acids.
Secondary Structure:
- Folding due to hydrogen bonds between backbone amino acids, forming either alpha-helices or beta-pleated sheets.
Tertiary Structure:
- 3D shape formed by interactions among R-groups (ionic bonds, hydrogen bonds, hydrophobic interactions, and disulfide bridges).
Quaternary Structure:
- Arrangement of multiple polypeptide chains into a final functional protein structure.

The protein's function is closely tied to its shape; R-groups interact with other molecules through ionic, hydrophobic, and hydrogen bonding.

Temperature: Increased temperature disrupts H-bonds and hydrophobic interactions.
pH changes: Can alter ionic interactions.
Solvent polarity: Affects H-bonding and hydrophobic interactions.
Loss of 3D structure leads to denaturation.

Chaperone Proteins: Assist in the proper folding of newly synthesized or denatured proteins to ensure correct structure.

Abnormal protein folding can lead to diseases caused by prions (e.g., BSE, Kreutzfeld-Jakob disease).
Misfolded proteins can induce normal proteins to misfold, causing degenerative effects on neural tissues causing cell death.

General Structure: Formulas generally: $C<em>mH</em>{2n}O_n$ .
Serve primarily as energy sources but also as building blocks for other molecules.

Monosaccharides: Simple sugars like glucose ( $C<em>6H</em>{12}O_6$ ).
Disaccharides: Formed by linking two monosaccharides through a condensation reaction (e.g., sucrose = glucose + fructose).

Long chains of monosaccharides that may serve as energy storage (e.g., starch, glycogen) or structural materials (e.g., cellulose).
Polysaccharides can be branched or linear.

Starch: Energy storage in plants, comprised of glucose, moderately branched.
Cellulose: Main component of plant cell walls, unbranched, chemically stable.
Glycogen: Short-term energy storage in animals, highly branched for rapid access.

Glucosamine: Modified glucose important for joint fluid.
Chitin: Derived from glucosamine, forms the exoskeleton of arthropods and fungal cell walls.

Lipids are nonpolar hydrocarbons, not water-soluble, aggregate in water.
Types include triglycerides, phospholipids, steroids, and waxes.

Triglycerides: Composed of glycerol and three fatty acids for energy storage.
- Saturated fatty acids: No double bonds, straight chains (solids at room temp).
- Unsaturated fatty acids: Contain double bonds, causing kinks (liquids at room temp).
Phospholipids: Tails (fatty acids) are nonpolar, while the head is polar, forming cell membranes through bilayer structure.

Steroids: Consist of multiple carbon rings; cholesterol serves as a cell membrane component and precursor for hormones.
Waxes: Hydrophobic and pliable, used for waterproofing and coating surfaces in animals and plants.

Polymers for storing and transmitting genetic information; include DNA and RNA.
Nucleotides are the building blocks, linked by phosphodiester bonds, consisting of sugar, phosphate, and nitrogenous base.

DNA strands are anti-parallel; base pairs formed by hydrogen bonding are complementary: A-T and C-G.

Replication: DNA makes exact copies before cell division.
Transcription: RNA is synthesized based on DNA sequence for protein synthesis.