Biology Notes CHAPTER 3: Lipids, Phospholipids, Proteins, Enzymes, and Collagen

Lipids: Triacylglycerols, Diacylglycerols, Cholesterol, and Phospholipids

• Triacylglycerols and diacylglycerols are discussed; steroids (cholesterol) are another lipid type.
• Cholesterol
  • An extremely important component of cell membranes; helps maintain membrane movement and prevents it from becoming too static or too rigid.
  • Serves as a precursor for steroid hormones, including estrogen and testosterone.
  • It will be revisited in the context of cell membranes next week when more detail is covered.
• Phospholipids
  • Primary component of cell membranes.
  • Amphipathic: molecules have both hydrophobic and hydrophilic regions.
  • In membranes, typically have two fatty acid tails: one saturated and one unsaturated, contributing to membrane fluidity.
  • The tails/heads arrange themselves to form the bilayer with hydrophobic tails inward and hydrophilic heads outward, enabling a selective barrier.
  • Memorization cue for structure is not required for this course, but understanding amphipathicity and bilayer formation is essential.

Proteins: Overview and Structure

• Proteins are composed of amino acids linked together; there are 20 standard amino acids.

• Amino acids share a common backbone: a central (alpha) carbon with:

  • an amino group (-NH₂),
  • a carboxyl group (-COOH),
  • a hydrogen atom, and
  • a side chain R group that distinguishes each amino acid.

• The R group determines the amino acid’s chemical properties (hydrophobic/hydrophilic, polar/nonpolar, acidic/basic).

• The order of amino acids in a protein determines its final shape and function; structure dictates function.

• Amino acids are linked by peptide bonds to form polypeptides; the peptide bond is formed via a dehydration synthesis (condensation) reaction, where a molecule of water is removed.

• Dehydration synthesis (condensation) example:
  ext{AA}1- ext{COOH} + ext{AA}2- ext{NH}2 ightarrow ext{AA}1- ext{CO-NH}- ext{AA}2 + ext{H}2 ext{O}

• Primary structure

  • The linear sequence of amino acids in a protein.
  • Often described with the analogy: beads on a string (Mardi Gras beads represent amino acids; the string between beads is the peptide bond).
  • No actual folding has occurred in the primary structure yet.

• Secondary structure

  • Arises from hydrogen bonds forming between the backbone of amino acids.
  • Common motifs include:
  • Alpha helices
  • Beta pleated sheets (beta sheets)
    • Can be parallel or antiparallel.
    • Parallel beta sheets run in the same direction and tend to be more compact; antiparallel sheets run in opposite directions and create a larger distance between paired strands.
  • The concept of hydrophobic exclusion: hydrophobic (water-fearing) side chains tend to face inward, away from water, influencing folding into a stable structure.

• Tertiary structure

  • The overall three-dimensional shape of a single polypeptide.
  • Stabilized by multiple interactions:
  • Hydrogen bonds
  • Ionic bonds
  • Covalent bonds (e.g., disulfide bridges)
  • Van der Waals interactions
  • Disulfide bridges
  • Formed between cysteine residues via sulfhydryl (-SH) groups.
  • A cysteine pair can form a disulfide bond (R-S-S-R), which is a strong covalent link that stabilizes the protein's tertiary structure.
  • These bridges can occur within a single protein or between two different proteins.
  • Subunits and naming (alpha and beta)
  • Some proteins have subunits named alpha and beta (e.g., in hemoglobin).
  • The reason for different names is that the alpha and beta subunits have different primary structures (amino acid sequences) and can perform different roles.
  • Comparison: histone proteins illustrate how small sequence differences can have large functional consequences (e.g., two amino acid changes out of ~
    \ extapprox 100 total in histone cores found in cows vs. peas) can alter function.

• Quaternary structure

  • Not detailed in the transcript, but generally refers to the assembly of multiple polypeptide subunits into a functional protein complex.

• Protein folding and function

  • Proper folding is essential for function; misfolding disrupts activity.
  • If a protein folds incorrectly, it usually cannot function properly in most cases.
  • The environment surrounding a protein can affect folding and function (e.g., denaturation).
  • Denaturation is the unfolding of a protein due to environmental factors; often irreversible, making refolding unlikely.

• Denaturation and stability

  • Environmental changes (pH, temperature, solvents) can cause denaturation.
  • In some cases, cells can synthesize a new protein instead of refolding an unfolded one.

• Proteins and enzymes

  • Enzymes are proteins that act as biological catalysts to accelerate chemical reactions.
  • An enzyme’s active site is the region where the substrate binds and the reaction occurs.
  • Substituting amino acids within the active site can disrupt function (e.g., replacing a hydrophobic residue with a hydrophilic one may prevent proper active-site catalysis).
  • Enzymes will be discussed in more depth later in the course; this section introduces the concept and relevance.

• Collagen and connective tissue

  • Collagen is a major protein in skin and connective tissue.
  • There is growing interest in collagen supplementation for skin health and connective tissue maintenance; it appears in some drinks and supplements.

Connections and Real-World Relevance

• Structure-function relationship in biology: the three levels of protein structure (primary, secondary, tertiary, and quaternary) determine function. Changes at the sequence level can ripple through folding to alter function.
• Membrane composition and fluidity influence cell physiology, signaling, and transport.
• Post-translational features (e.g., disulfide bridges) contribute to protein stability in variable environments.
• Enzymes provide speed and specificity for metabolic pathways; active-site integrity is essential for catalytic activity.
• Collagen’s role in skin and connective tissue underlies cosmetic and medical interest in collagen supplementation.

Transcription and Translation Context (Course Schedule)

• The transcript notes that transcription and translation are covered over multiple days and revisited toward the end of the semester for enzymes and regulation; these processes are foundational for how proteins are produced and regulated in cells.

Quick Reference: Key Terms and Concepts

• Amphipathic: a molecule with both hydrophobic and hydrophilic regions.
• Hydrophobic exclusion: hydrophobic residues tend to cluster away from water inside a folded protein.
• Peptide bond: bond between amino acids linking carboxyl and amino groups; formed via dehydration synthesis.
• Dehydration synthesis / Condensation reaction: removal of water to form a bond between monomers.
• Primary structure: amino acid sequence.
• Secondary structure: alpha helices and beta pleated sheets stabilized by hydrogen bonds.
• Tertiary structure: three-dimensional folding driven by multiple types of interactions (hydrogen bonds, ionic bonds, disulfide bridges, Van der Waals).
• Disulfide bridge: strong covalent bond between cysteine residues (-S-S-).
• Quaternary structure: assembly of multiple polypeptide subunits (not elaborated in this transcript).
• Denaturation: unfolding of protein due to environmental factors; often irreversible.
• Enzyme: protein that speeds up chemical reactions; active site is where catalysis occurs.

Notes on Memorization for This Course

• Do not memorize all amino acid R-group structures for this class.
• Focus on understanding how amino acid properties influence folding and function, and how environment can alter structure and activity.