Biomolecules

Carbohydrates

• Overview: One of the main classes of biological molecules. Include monosaccharides, disaccharides, and polysaccharides.
• Subunits and examples:
  • Monosaccharides (basic subunit): simplest sugars (e.g., glucose, fructose, galactose).
  • Disaccharides: two monosaccharides linked together (e.g., sucrose, lactose, maltose).
  • Polysaccharides: long chains of monosaccharides (e.g., glycogen).
• Basic monosaccharides (from Page 3):
  • Glucose, Fructose, Galactose are isomers with the same molecular formula: $\mathrm{C<em>6H</em>{12}O_6}$.
  • Structural note: Monosaccharides display different arrangements but share the same formula; depicted with CH2OH groups in various orientations (illustrated on the slides).
• Monosaccharides details:
  • They can be isomers of each other, all with formula $\mathrm{C<em>6H</em>{12}O_6}$.
  • Glucose, Fructose, Galactose are common examples.
• Basic disaccharides (Page 4):
  • Sucrose = Glucose + Fructose.
  • Lactose = Galactose + Glucose.
  • Maltose = Glucose + Glucose.
  • Note: Each disaccharide is formed by a dehydration synthesis joining two monosaccharides.
• The polysaccharide glycogen (Page 5):
  • Structure: polymer of glucose units.
  • Glycogen is highly branched, enabling rapid release of glucose when needed.
• Where are the carbohydrates stored and found (Page 6):
  • Muscle glycogen: ~2000 kcal.
  • Muscle triglyceride (fat): ~4000 kcal. (Note: fats are a separate lipid store but listed here as a reference for energy storage comparison.)
  • Blood glucose: ~40 kcal.
  • Liver glycogen: ~300 kcal.
• Key concepts:
  • Carbohydrates serve as immediate energy sources (blood glucose), quick-access energy reserves (glycogen in liver and muscle), and stored energy in fats (triglycerides) elsewhere.
• Quick recap: Carbohydrates include monosaccharides, disaccharides, and polysaccharides such as glycogen; they differ in size and linkages but share common chemical fundamentals.

Lipids

• Overview: A diverse group including fatty acids, triglycerides, phospholipids, glycolipids, and steroids. Hydrophobic or amphipathic properties drive their functions.
• Fatty acids: saturated vs. unsaturated (Page 8).
  • Saturated fatty acids: no double bonds between carbon atoms (no kinks).
  • Unsaturated fatty acids: contain one or more double bonds; typically have cis configuration creating kinks that affect packing.
  • Diagrammatic note: double bonds introduce bends; saturated chains tend to be solid at room temperature, unsaturated often liquid.
• Triglycerides (Page 9):
  • Structure: glycerol backbone + three fatty acid chains.
  • Formation: Dehydration synthesis links three fatty acids to glycerol; yields triglyceride and 3 H2O.
  • Hydrolysis: Triglyceride + 3 H2O → Glycerol + 3 Fatty acids (release energy).
  • General equation (conceptual):
    $\text{Glycerol} + 3\ \text{Fatty acids} \xrightarrow{\text{dehydration synthesis}} \text{Triglyceride} + 3\,H<em>2O$$\text{Triglyceride} + 3\,H</em>2O \rightarrow \text{Glycerol} + 3\,\text{Fatty acids}$
• Phospholipids (Page 11):
  • Structure: glycerol backbone with two fatty acids and a phosphate group attached to a nonlipid molecule (often choline).
  • Polar head group vs. nonpolar tails: the phosphate-containing head is polar; the fatty acid tails are nonpolar.
  • Example: Lecithin (a common phospholipid used in membranes).
  • Diagrammatic components: choline (a common nonlipid head group), phosphate group, glycerol backbone, two fatty acid chains.
• Glycolipids: phospholipids with carbohydrate groups (as referenced in Fig. 2-18).
• Micelles and membrane context (Page 13):
  • In large numbers, phospholipids and glycolipids form micelles with hydrophilic heads facing water and hydrophobic tails inside.
  • This amphipathic behavior underlies the formation of cell membranes and lipid-based structures.
• Phospholipid bilayer (Page 14):
  • Basic membrane architecture: hydrophilic heads face aqueous environments on both sides; hydrophobic tails form the interior barrier.
  • This bilayer defines cell membranes and their barrier properties.
• Steroids (Page 15):
  • Four fused-ring structure.
  • Examples shown: Cholesterol, Estrogen, Testosterone.
  • Variations in ring substituents produce diverse biological roles (membrane fluidity, hormone signaling, etc.).
• Summary note: Lipids provide energy storage (triglycerides), form essential barriers and signaling molecules (phospholipids, glycolipids, steroids), and influence membrane structure and function.

Proteins

• Overview: Proteins are built from amino acids linked by peptide bonds; they perform virtually all cellular functions.
• Basic structure of an amino acid (Page 17):
  • Components: amino group (NH2), central carbon (Cα), carboxyl group (COOH), and an R group (side chain) that defines identity.
  • General formula: $\mathrm{NH_2-CH(R)-COOH}$
• Peptide bond formation (Page 18):
  • Condensation (dehydration synthesis) reaction linking the carboxyl group of one amino acid to the amino group of the next, releasing H2O.
  • Generic representation: $\text{Amino acid}<em>1 - \text{Amino acid}</em>2 \xrightarrow{\text{dehydration}} \text{Dipeptide} + H_2O$
  • Example shown: Glycine (Gly) to Alanine (Ala) illustrating peptide-bond formation.
• Amino acids and properties (Page 19):
  • Amino acids categorized by side-chain properties:
  • Nonpolar (hydrophobic): Gly (Gly, G); Ala (Ala, A); Val (Val, V); Leu (Leu, L); Ile (Ile, I); Pro (Pro, P); Met (Met, M); Trp (Trp, W); Phe (Phe, F); Cys (Cys, C) [note: Cys is often considered polarizable; included here as nonpolar in the slide].
  • Polar uncharged: Ser (Ser, S); Thr (Thr, T); Tyr (Tyr, Y); Asn (Asn, N); Gln (Gln, Q).
  • Polar charged (positive/basic): Lys (Lys, K); Arg (Arg, R); His (His, H).
  • Polar charged (negative/acidic): Asp (Asp, D); Glu (Glu, E).
  • This classification informs folding, interactions, and function.
• Primary structure (Page 20):
  • Definition: The linear sequence of amino acids in a polypeptide, e.g., A1, A2, A3, … along the chain.
  • Primary structure is the foundational sequence that determines higher-order structure.
• Secondary structure (Page 21):
  • Common motifs: alpha helix and beta pleated sheet (pleated sheet).
  • Primary determinant: hydrogen bonding along the polypeptide backbone.
  • Visual idea: alpha-helix = coiled arrangement; beta-pleated sheet = folded, sheet-like arrangement.
• Tertiary structure (Page 22):
  • Definition: The overall 3D folding of a single polypeptide chain.
  • Arises from interactions among R groups (side chains):
  • Hydrophobic interactions
  • Hydrogen bonds
  • Ionic bonds
  • Disulfide bridges (covalent S–S bonds between cysteine residues)
  • Mention of internal features such as heme units within some proteins (functional groups within tertiary structure).
• Quaternary structure (Page 23):
  • Definition: A protein composed of more than one polypeptide chain (subunits).
• Levels of protein organization (Page 23):
  • Primary: sequence of amino acids.
  • Secondary: local folding due to hydrogen bonds (alpha helix, beta-pleated sheet).
  • Tertiary: 3D folding due to interactions among R groups.
  • Quaternary: assembly of multiple polypeptide chains.
• Protein chemistry and biology (Page 24):
  • Ligand binding can change protein shape (conformational change).
  • Binding can alter affinity for other ligands.
  • Mechanistic basis for many physiological processes and functions:
  • Enzyme function
  • Muscle contraction
  • Action potentials
  • Hormone actions
  • Blood clotting
  • Immunity
• Notes on structure-function relationships:
  • The sequence (primary structure) directs higher-order structure and ultimately function.
  • Proper folding is essential for activity; misfolding can lead to dysfunction.

Nucleic Acids

• Overview: The genetic material of cells; include DNA and RNA.
• Subunits: Nucleotides.
• Components of a nucleotide (general knowledge):
  • Sugar (deoxyribose in DNA; ribose in RNA)
  • Phosphate group
  • Nitrogenous base (adenine, thymine or uracil, cytosine, guanine)
• Key note from transcript: Nucleic acids are composed of nucleotides, the basic building blocks for genetic information storage and transmission.

Connections, implications, and real-world relevance

• Energy and metabolism:
  • Carbohydrates provide immediate and stored energy; glycogen provides rapid glucose release; fats store large amounts of energy in triglycerides.
• Membrane biology and signaling:
  • Phospholipids form cell membranes (bilayers) and micelles; membrane composition influences permeability and signaling.
  • Steroids (cholesterol and steroid hormones) modulate membrane fluidity and regulate gene expression with hormones like estrogen and testosterone.
• Protein structure-function relationships:
  • Sequence dictates structure; structure determines function; ligand binding can regulate activity and signaling pathways.
  • Protein folding underpins enzyme catalysis, transport, immune defense, and many cellular processes.
• Genetic information:
  • Nucleic acids store and transmit genetic information through nucleotide sequences; DNA serves as the blueprint; RNA participates in decoding and expression.
• Practical implications:
  • Understanding biomolecule structure helps in drug design, nutrition, disease mechanisms, and biotechnology applications.