Macromolecules

General Principles: Building and Breaking Macromolecules
- Monomer: A single, basic molecular subunit that can bond to other identical or similar molecules (e.g., monosaccharides, amino acids, nucleotides).
- Polymer: A large molecule (macromolecule) built from repeating chains of bonded monomers.
- Dehydration Synthesis (Condensation Reaction):
- Process: Bonds two monomers together by removing a molecule of water ( $H_2O$ ).
- Mechanism: One monomer loses a hydrogen atom ( $-H$ ) and the other loses a hydroxyl group ( $-OH$ ). A new covalent bond forms between the monomers, releasing free water ( $H_2O$ ).
- Requires: Energy input and specific enzymes.
- Diagram:text [ Monomer 1 ]-OH + H-[ Monomer 2 ] \ / \ / ---> Dehydration Synthesis (removes H2O) v v [ Monomer 1 ]-[ Monomer 2 ] + H2O

Hydrolysis:
- Process: Breaks polymers down into individual monomers by adding a molecule of water ( $H_2O$ ).
- Mechanism: Water splits into $-H$ and $-OH$ . The covalent bond between monomers breaks; $-H$ attaches to one monomer and $-OH$ attaches to the other.
- Releases: Energy (used in cellular digestion).
- Diagram:text [ Monomer 1 ]-[ Monomer 2 ] + H2O / \ / \ ---> Hydrolysis (adds H2O to split) v v [ Monomer 1 ]-OH + H-[ Monomer 2 ]       
- Memory Hook:
- Dehydrate = lose water (synthesizes/builds a bond).
- Hydro-lysis = water-splitting (breaks a bond).

Carbohydrates
- Empirical Formula:
- Monosaccharides follow the stoichiometric ratio: $C_n H_{2n} O_n$ (ratio of $1\text{C} : 2\text{H} : 1\text{O}$ , e.g., hexose is $C_6 H_{12} O_6$ ).
- Main Functions:
- Immediate and short-term energy supply (via cellular respiration).
- Energy storage (glycogen in animals, starch in plants).
- Structural materials (cellulose in plant cell walls, chitin in fungal walls and arthropod exoskeletons).
- Cellular markers and recognition (glycoproteins on cell membranes).
- Classification of Carbohydrates:
- Monosaccharides (Simple Sugars): Single ring units.
  - Glucose ( $C_6 H_{12} O_6$ ): Primary blood sugar and instant cellular fuel. A 6-membered ring (hexose).
  - Ribose ( $C_5 H_{10} O_5$ ): 5-carbon sugar (pentose) found in RNA and ATP.
- Disaccharides: Double sugars formed by linking two monosaccharides via a glycosidic bond (formed by dehydration synthesis).
  - Maltose ( $\text{Glucose} + \text{Glucose}$ ): Malt sugar.
  - Sucrose ( $\text{Glucose} + \text{Fructose}$ ): Table sugar.
  - Lactose ( $\text{Glucose} + \text{Galactose}$ ): Milk sugar.
- Polysaccharides: Long polymer chains made of many linked glucose units.
- Structural Recognition Diagrams (Sugars):
- Glucose (Hexose Ring):text CH2OH | C------O / \ H-C C-H / \ / \ OH C------C OH | | H OH

Ribose (Pentose Ring):text HOCH2 O \ / \ C C-OH / \ / \ H C---C H | | OH OH       
Disaccharide Formation (Glycosidic Linkage):text [ Sugar Ring 1 ]-OH + HO-[ Sugar Ring 2 ] | v (Dehydration: -H2O) [ Sugar Ring 1 ]--- O ---[ Sugar Ring 2 ] (Glycosidic Bond)       
Comparison of Key Polysaccharides:
- Starch:
- Function: Energy storage in plant cells.
- Type of Bonding: Alpha-glycosidic bonds (spiral/helical structure; easily broken down by human amylase enzymes).
- Branching: Moderately branched (amylopectin) or unbranched spirals (amylose).
- Glycogen:
- Function: Energy storage in animals (stored primarily in liver and skeletal muscles).
- Type of Bonding: Alpha-glycosidic bonds.
- Branching: Highly branched (frequent branching allows multiple enzymes to cleave glucose simultaneously for rapid energy release during fight-or-flight).
- Cellulose:
- Function: Rigid structural support in plant cell walls.
- Type of Bonding: Beta-glycosidic bonds (alternating upside-down glucose units; creates straight, rigid chains stabilized by hydrogen bonds; indigestible to humans, serves as dietary fiber/roughage).
- Branching: Completely unbranched; runs in tight parallel bundles (microfibrils).
- Visual Comparison of Polysaccharide Architectures: ```text Starch: O-O-O-O-O-O-O-O (Coiled helix, slight branching)
```
                O-O-O
```
  Glycogen: O-O-O-O-O-O-O-O (Extensively branched) \ \ O-O O-O-O \ \ O-O O-O
  Cellulose: O-O-O-O-O-O-O-O-O (Straight, parallel, unbranched chains ::::::::::::::::: held tightly by hydrogen bonds) O-O-O-O-O-O-O-O-O ```

Lipids
- General Characteristics:
- Hydrophobic and nonpolar (insoluble in water; dissolve only in nonpolar organic solvents).
- Composed predominantly of carbon and hydrogen atoms, with very few oxygen atoms (high ratio of $C-H$ bonds gives twice the energy per gram compared to carbohydrates).
- Saturated vs. Unsaturated Fatty Acids:
- Saturated Fatty Acid:
  - Structure: No carbon-carbon double bonds; carbons are fully saturated with hydrogen atoms.
  - Shape: Perfectly straight hydrocarbon tail.
  - State at Room Temperature: Solid (chains pack tightly together, e.g., butter, animal lard). text H H H H H H O | | | | | | // H - C - C - C - C - C - C ... C - OH | | | | | | H H H H H H [ Straight chain: all C-C single bonds ]

Unsaturated Fatty Acid:
- Structure: Contains one or more double bonds ( $C=C$ ).
- Shape: A prominent kink or bend at each double bond.
- State at Room Temperature: Liquid (kinks prevent tight molecular packing, e.g., vegetable oils, olive oil). text H H H H H O | | | | | // H - C - C - C = C - C - C ... C - OH | | | | | H H H H H ^ Double bond creates a bend/kink!       
Neutral Fats (Triglycerides):
- Structure: 1 molecule of glycerol bonded to 3 fatty acid tails via ester linkages (formed by 3 dehydration reactions).
- Location: Stored inside adipocytes (fat cells) in adipose tissue beneath the skin (subcutaneous) and cushioning visceral organs.
- Function: Long-term energy storage, thermal insulation (prevents heat loss), and physical shock absorption/cushioning.
- Diagram of Glycerol and Triglyceride: text Glycerol: Triglyceride ("E" Shape): H H | | H - C - OH H - C - O - C(=O) - [ Fatty Acid Tail 1 ] | | H - C - OH ---> H - C - O - C(=O) - [ Fatty Acid Tail 2 ] | | H - C - OH H - C - O - C(=O) - [ Fatty Acid Tail 3 ] | | H H       
Phospholipids:
- Structure: 1 glycerol molecule bonded to 2 fatty acid tails (hydrophobic/nonpolar) and 1 negatively charged phosphate group bonded to a choline or other polar group (hydrophilic/polar head). This dual nature is termed amphipathic.
- Location: The principal component of all biological membranes (plasma membrane and organelle membranes).
- Function: Spontaneously forms the semi-permeable phospholipid bilayer that creates a protective boundary around cells.
- Diagram of a Phospholipid: text [ Polar, Hydrophilic Head ] <--- Phosphate group + Glycerol / \ / \ [ Saturated Tail ] [ Unsaturated Tail (bent) ] (Hydrophobic) (Hydrophobic)       
Steroids:
- Structure: A characteristic carbon skeleton composed of 4 fused carbon rings (three 6-carbon rings labeled A, B, C fused to one 5-carbon ring labeled D) with functional groups attached.
- Location: Intercalated inside animal cell membranes (cholesterol) and circulating in the bloodstream/endocrine system.
- Function:
- Cholesterol: Regulates membrane fluidity and stability over varying temperatures; acts as the precursor molecule for all other steroid hormones.
- Steroid Hormones: Chemical messengers (e.g., testosterone, estrogen, progesterone, cortisol, aldosterone).
- Diagram of Steroid Skeleton: text / \ / \ | B | | C | / \ / \ / \ / \ | D | | A | | | \ / \ / \ / [ 4 Fused Rings: 6-6-6-5 structure ]

Proteins
- Major Functions:
- Enzymatic Catalysis: Accelerate chemical reactions (e.g., amylase, pepsin, DNA polymerase).
- Structural Support: Provide architectural integrity (e.g., keratin in hair/nails, collagen in skin/bones).
- Transport: Carry substances across membranes or throughout the body (e.g., hemoglobin transports oxygen; sodium-potassium pumps).
- Immune Defense: Target and neutralize foreign antigens (e.g., antibodies/immunoglobulins).
- Movement/Contractile: Facilitate muscle contraction and intracellular motion (e.g., actin and myosin).
- Signaling: Peptide hormones regulate homeostasis (e.g., insulin).
- Amino Acid Structure:
- All 20 amino acids share an identical central backbone and vary solely by their unique $R\text{-group}$ (side chain).
- Components:
  - Central alpha carbon ( $C_\alpha$ )
  - Amine group ( $-NH_2$ )
  - Carboxyl group / carboxylic acid ( $-COOH$ )
  - Lone hydrogen atom ( $-H$ )
  - Variable side chain ( $R\text{-group}$ , gives individual chemical properties: polar, nonpolar, acidic, or basic)
- Generalized Diagram:text H O | // H - N - C - C | | | \ H H R OH | | | | [Amine] [Alpha-C] [Carboxyl] | [R-Group]

Peptide Bond Formation (Dipeptides & Polypeptides):
- Peptide Bond: A covalent bond linking the carboxyl carbon of one amino acid to the amine nitrogen of the next via dehydration synthesis.
- Dipeptide: 2 amino acids joined by 1 peptide bond.
- Polypeptide: A continuous chain of many amino acids linked by multiple peptide bonds.
- Diagram of Peptide Bond in a Dipeptide:text H H O H H O | | || | | || H - N - C - C - OH + N - C - C - OH | | | R1 H R2 | v (Dehydration: -H2O) H H O H H O | | || | | || H - N - C - C --- N - C - C - OH | | | R1 H R2 ^ [ Peptide Bond ]       
Four Levels of Protein Structure:
- Primary Structure ( $1^\circ$ ):
- Description: The unique, linear sequence of amino acids in a polypeptide chain dictated by genetic code.
- Bonding: Strong covalent peptide bonds only.
- Significance: Even a single amino acid substitution can disrupt total protein function (e.g., sickle cell anemia).
- Secondary Structure ( $2^\circ$ ):
- Description: Localized folding or coiling of the polypeptide backbone into regular recurring shapes.
  - Alpha-helix ( $\alpha\text{-helix}$ ): A delicate right-handed spiral coil.
  - Beta-pleated sheet ( $\beta\text{-sheet}$ ): Parallel or anti-parallel strands folded like an accordion accordion pleat.
- Bonding: Hydrogen bonds between the backbone carbonyl oxygen ( $C=O$ ) and amide hydrogen ( $N-H$ ). $R\text{-groups}$ are not directly involved in these bonds.
- Tertiary Structure ( $3^\circ$ ):
- Description: The overall three-dimensional globular conformation of a single polypeptide chain.
- Bonding: Interactions strictly between the variable $R\text{-groups}$ :
  - Hydrophobic interactions: Nonpolar side chains cluster in the protein interior away from water.
  - Hydrogen bonds: Between polar uncharged side chains.
  - Ionic bonds: Between positively and negatively charged side chains.
  - Disulfide bridges: Strong covalent bonds between two cysteine sulfhydryl groups ( $-S-S-$ ).
- Quaternary Structure ( $4^\circ$ ):
- Description: The biological assembly formed when two or more distinct polypeptide subunits come together to form one multi-subunit functional protein complex.
- Examples: Hemoglobin (composed of 4 interacting subunits: 2 alpha and 2 beta globins) and collagen (triple-helical fiber).
- Bonding: The same non-covalent interactions and disulfide bridges seen in tertiary structure, occurring across separate polypeptide chains.
- Visual Summary of Structural Levels: ```text Primary (1°): (Met)-(Gly)-(Ala)-(Leu)-(Val) [Peptide bonds]
  Secondary (2°): Alpha-Helix Beta-Sheet [Backbone H-bonds] @@@@@ /\/\/\/\ @@@@@ \/\/\/\/
  Tertiary (3°): [ Single complex 3D globular ball ] (Held by R-group bonds: S-S, ionic, hydrophobic)
  Quaternary (4°): [ Subunit A ] === [ Subunit B ] [ Subunit C ] === [ Subunit D ] (Multi-subunit protein complex, e.g., Hemoglobin) ```