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: C<em>6H</em>12O6\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 C<em>6H</em>12O6\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):
      Glycerol+3 Fatty acids→dehydration synthesisTriglyceride+3 H<em>2O\text{Glycerol} + 3\ \text{Fatty acids} \xrightarrow{\text{dehydration synthesis}} \text{Triglyceride} + 3\,H<em>2OTriglyceride+3 H</em>2O→Glycerol+3 Fatty acids\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: NH2−CH(R)−COOH\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: Amino acid<em>1−Amino acid</em>2→dehydrationDipeptide+H2O\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.