Notes on Lipids and Proteins (Part 3-4)

Part 3: Lipids

  • Context

    • Lipids are an exception among macromolecules: they are not polymers, though they can form larger structures (e.g., triglycerides).
    • They can be studied via diagrams showing glycerol, fatty acids, and triglycerides (fat molecules) and the ester linkages that connect fatty acids to glycerol.
    • Example fatty acid shown: Palmitic acid.

  • Structure involved in triglyceride formation

    • Glycerol has three hydroxyl (–OH) groups that react with fatty acids (carboxyl –COOH groups) via dehydration synthesis to form ester linkages.
    • General ester linkage formation (simplified):
    • extR−COOH+extHO−R′→R-CO-O-R’+H2Oext{R-COOH} + ext{HO-R'} \rightarrow \text{R-CO-O-R'} + \mathrm{H_2O}
    • Overall biosynthesis of a triglyceride from glycerol and three fatty acids releases three water molecules (one per ester bond formed):
    • extGlycerol+3 Fatty Acids→extTriglyceride+3 H2Oext{Glycerol} + 3\ \text{Fatty Acids} \rightarrow ext{Triglyceride} + 3\ \mathrm{H_2O}

  • Answers to the questions in the diagram

    • a) How many water molecules are formed in the biosynthesis of a triglyceride?
    • 33
    • b) What 2 atoms are in high abundance in fat? What kind of covalent bond forms between these 2 atoms?
    • The atoms: Carbon (C) and Hydrogen (H).
    • Bond type between C and H: nonpolar covalent bond (C–H).
    • c) Why does the presence of so many C–H bonds explain why lipids have a low affinity for water?
    • C–H bonds are nonpolar, making hydrocarbon tails hydrophobic.
    • Lipids lack polar groups that can form hydrogen bonds with water; the hydrophobic (nonpolar) character of the hydrocarbon chains repels water, leading to low water solubility and low affinity for water.

  • Key concepts and terms

    • Dehydration synthesis (condensation) in lipid assembly: removes water to form bonds.
    • Ester linkage: the covalent bond formed between glycerol’s hydroxyl group and a fatty acid’s carboxyl group, producing triglycerides.
    • Triglyceride composition: glycerol backbone + three fatty acids.
    • Palmitic acid: a common saturated fatty acid example (illustrated in the diagram).
    • Hydrophobicity of long hydrocarbon chains as a driver of lipid behavior in aqueous environments.

  • Quick connections

    • Relation to fatty acid saturation: saturated vs. unsaturated fatty acids affect packing and melting temperature, but both contribute to the lipid’s hydrophobic character.
    • Role in cells: triglycerides store energy in adipose tissue; lipids also form membranes as phospholipids, though that’s beyond the triglyceride focus here.

Part 4: Proteins

  • Generic amino acid structure (13)

    • A typical amino acid can be represented as:
    • H2N−CH(R)−COOH\mathrm{H_2N-CH(R)-COOH}
    • Elements attached to the central (alpha) carbon ((\alpha) carbon):
    • Amino group:
      • −NH2\mathrm{-NH_2} (contains nitrogen and hydrogen)
    • Carboxyl group:
      • −COOH\mathrm{-COOH} (contains a carbon, two oxygens, and one hydrogen)
    • Hydrogen atom: represented as (\text{H}) on the (\alpha) carbon
    • Side chain (R group): variable group that determines the amino acid’s identity and properties
    • The diagram prompt (13) asks to fill the empty box with the missing atoms to make a generic monomer an amino acid, identify the functional groups where the H and OH are located.
    • Answer (conceptual): Add the amino group ((-\mathrm{NH_2})) and the carboxyl group ((-\mathrm{COOH})) to the central (\alpha) carbon, while including the hydrogen and the variable side chain R.
    • Functional groups where H and OH are located:
    • Hydrogen (H) is bonded to the amino group on the amino end ((\mathrm{NH_2})) from which the hydrogen atoms can participate in bonding.
    • Hydroxyl (OH) is part of the carboxyl group ((-\mathrm{COOH})); the OH is the acidic hydrogen donor that participates in forming the peptide bond in condensation reactions.
    • Core representation of an amino acid:
    • Amino acid=H2N−CH(R)−COOH\text{Amino acid} = \mathrm{H_2N-CH(R)-COOH}

  • The analogy to letters of the alphabet (14)

    • The analogy in the diagram compares amino acids to letters that form words (or sentences).
    • Completed analogy (Biology side):
    • The 20 amino acids used in making a protein are like the letters of the alphabet.
    • Arranging these amino acids into a specific order (not yet a protein) creates a polypeptide chain (a peptide, a sequence of amino acids).
    • If the order of amino acids is changed, it creates a different protein with a different function.

  • Filled version of the table (conceptual)

    • Analogy: The 26 letters in the English alphabet are used to create sentences.
    • Biology: The 20 amino acids used in making a protein.
    • Arranging these amino acids into a specific order (not a protein yet) creates a polypeptide (peptide chain).
    • If the order of amino acids is changed, it creates a different protein with a different function.

  • Key concepts and terms

    • Amino acid components: amino group ((-\mathrm{NH_2})), carboxyl group ((-\mathrm{COOH})), hydrogen, and variable side chain (R).
    • Primary structure of proteins is the sequence of amino acids in a polypeptide chain.
    • The order of amino acids determines the protein’s chemical properties and function after folding.

  • Connections and implications

    • Relationship to metabolism: peptide bonds form via dehydration synthesis, releasing a molecule of water per bond formed.
    • The side chain (R group) diversity leads to the vast array of protein structures and functions (enzymes, structural proteins, signaling molecules, etc.).
    • Ethical/practical relevance: understanding amino acid sequences underpins fields like biotechnology, medicine, and synthetic biology (e.g., designing proteins with specific functions).