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Protein Structure and Nucleic Acids - Vocabulary Flashcards

Primary structure of proteins

  • The necklace with colored beads represents amino acids; each color stands for a different amino acid type. The sequence shown (purple, pink, purple, green, green, purple, pink, green, yellow, yellow, pink, orange, purple, pink, yellow, orange, pink) is the primary structure of a protein.
  • Primary structure is the order of amino acids in a polypeptide chain; this order largely determines the protein’s final shape and function.
  • An ordinal/degreeted notation is used for positions in the sequence (the degree symbol denotes an ordinal). For example, primate, secondate, tertiary, etc., are used to label structural levels and positions conceptually, with the sequence dictating where hydrogen bonds will form downstream.
  • The sequence dictates where hydrogen bonds will form between backbone groups (the amine and carboxyl ends) and not between the side chains (R groups). These backbone hydrogen bonds drive formation of secondary structures.

Secondary structure

  • Secondary structures arise from hydrogen bonds between the backbone amide H and carbonyl O atoms, not the side chains.
  • Common motifs:
    • Alpha helix: a right-handed coil stabilized by intramolecular hydrogen bonds along the backbone.
    • Beta-pleated sheet: the chain runs in a pleated fashion, with hydrogen bonds forming between strands that run in parallel or antiparallel directions.
  • The dotted lines in typical diagrams represent these backbone hydrogen bonds between adjacent residues in the chain, stabilizing the secondary structure.
  • Some stretches of the protein may be straight or unoriented; not every region must form a helix or sheet.

Tertiary structure

  • Tertiary structure is the three-dimensional folding of a single polypeptide chain into its functional form.
  • Contributions to folding:
    • Interactions between side chains (R groups):
    • Ionic bonds between acidic and basic residues can bridge distant parts of the chain.
    • Covalent disulfide bonds (–S–S–) between cysteine residues can form a very strong constraint to stabilize the fold.
    • Hydrophobic side chains tend to cluster away from water, driving core formation.
    • Hydrophilic side chains tend to be exposed on the exterior surface interacting with the aqueous environment.
  • The overall 3D shape (tertiary structure) is critical for protein function.

Quaternary structure

  • Some proteins are functional only when multiple polypeptide chains come together.
  • Quaternary structure refers to the arrangement of multiple polypeptide subunits.
  • Example: Hemoglobin consists of two alpha chains and two beta chains (two slightly different chains). Each subunit has its own tertiary and secondary structures, but the functional protein is the assembled quaternary complex.
  • The presence of more than one polypeptide is what defines quaternary structure; each chain contributes to the overall function.

Denaturation and protein function

  • Denaturation is the process of altering a protein’s shape, typically by heat, pH changes, or chemical denaturants, which disrupt hydrogen bonds and other interactions.
  • Example: Cooking an egg denatures egg proteins. Heat unfolds globular proteins, allowing random hydrogen bonds and ionic interactions to form a solid protein matrix; upon cooling, the structure may stay solid and not revert to the original liquid state.
  • Denatured proteins often lose their function because the active site or structural arrangement is disrupted.
  • Reversible denaturation is possible in some cases (renaturation), but many denatured proteins do not fully regain original function.
  • Perming hair is a chemical denaturation process: chemicals denature keratin proteins to change shape, then the hair is reshaped and rehydrated to renature in the new configuration.

Nucleic acids: DNA and RNA basics

  • Monomer: nucleotide.
  • Each nucleotide consists of a sugar, a phosphate, and a nitrogenous base; the bases are polar and can form hydrogen bonds.
  • DNA vs RNA sugars:
    • DNA uses deoxyribose (deoxyribonucleic acid,
      ext{DNA} = ext{deoxyribo} ext{nucleic acid}) with a missing 2′-OH group on the sugar.
    • RNA uses ribose (ribonucleic acid,
      ext{RNA} = ext{ribo} ext{nucleic acid}) with a 2′-OH group.
  • Bases:
    • DNA: adenine (A), cytosine (C), guanine (G), thymine (T).
    • RNA: adenine (A), cytosine (C), guanine (G), uracil (U) replaces thymine.
  • DNA structure:
    • Double helix held together by hydrogen bonds between bases on opposite strands.
    • Base pairing rules in DNA: A ext{ pairs with } T ext{ (two hydrogen bonds)}, G ext{ pairs with } C ext{ (three hydrogen bonds)}.
  • RNA structure:
    • Mostly single-stranded; can fold into various shapes.
    • mRNA is a copy of a DNA gene, carrying the instructions to build a protein.
    • In RNA base pairing, A ext{ pairs with } U (not with T).
  • General: hydrogen bonds between bases hold the DNA double helix together; the sequence encodes information for protein synthesis.
  • Cellular context:
    • DNA is found primarily in the nucleus in eukaryotes; RNA is synthesized in the nucleus and then moves to the cytoplasm.
    • Helicase unwinds DNA; polymerase synthesizes new strands; ligase joins fragments.

Nucleotides, base pairing, and information flow

  • The sequence information in DNA specifies the order of amino acids (via transcription and translation).
  • RNA processing and translation follow later lectures; here the basics include:
    • DNA bases: A, C, G, T; RNA bases: A, C, G, U.
    • Base pairing rules as noted above; the hydrogen bonds are relatively weak but numerous, providing stability to the helix.

Adenosine triphosphate (ATP) and cellular energy

  • ATP is the most common universal, single-use, energy-carrying molecule in cells.
  • Structure: adenosine plus three phosphate groups (triphosphate).
  • High-energy phosphate bonds are indicated by the red bonds in diagrams; these energy-rich bonds can be hydrolyzed to perform work.
  • ATP hydrolysis:
    • Reaction (simplified):
      ext{ATP} + ext{H}2 ext{O} ightarrow ext{ADP} + ext{P}i +
      abla G
  • Uses of ATP energy:
    • Muscle contraction: myosin binding to actin powered by ATP hydrolysis.
    • Active transport: Na^+/K^+ pump and other transporters use ATP-driven conformational changes.
  • Regeneration: ADP and inorganic phosphate (
    ext{ADP} + ext{P}_i
    ightarrow ext{ATP} ) are formed when energy is available from nutrients; the cell regenerates ATP using energy from food (carbohydrates, proteins, fats).
  • Energy sources to reform ATP include breakdown products from sugars, amino acids, and lipids.
  • Electrolytes and ATP production:
    • Electrolytes (e.g., Mg^{2+}, K^+, Ca^{2+}) play roles in ATP production and enzyme function but cannot generate ATP by themselves simply by ingestion.
    • Drinking water and electrolytes supports homeostasis but does not by itself create ATP; fat and carbohydrate oxidation provides energy to reform ATP.
  • Cholesterol discussion:
    • Cholesterol cannot be burned directly to make ATP; its synthesis and breakdown are not a reversible source for ATP in the sense used here.
  • Quick note on terminology:
    • Hydrolysis is the chemical process used to break bonds with water; the transcript mentions "hydromysis" which is a common misnomer—correct term is hydrolysis.

Quick recap: connections and implications

  • Structure-function relationship:
    • Primary sequence determines secondary structures (alpha helices, beta sheets) via backbone hydrogen bonding.
    • Secondary structures fold into tertiary structure, driven by side-chain interactions (ionic bonds, disulfide bonds, hydrophobic/hydrophilic patterns).
    • Multiple polypeptides form quaternary structures, expanding functional capabilities (e.g., hemoglobin).
  • Denaturation and function:
    • Denaturation disrupts 3D structure and often inactivates function, though some denatured proteins can renature under suitable conditions.
  • Information flow:
    • DNA stores genetic information; RNA serves as an intermediary; protein synthesis translates this information into functional polypeptides.
  • Energy and metabolism:
    • ATP, generated via catabolic processes, powers cellular work; its regeneration is tied to nutrient availability and overall metabolic state.

Practice prompts (concept checks)

  • If a protein’s primary sequence changes, how might that affect secondary, tertiary, and quaternary structures? Explain the cascade.
  • Why are hydrogen bonds crucial for secondary structures but weaker than covalent bonds? How does this relate to protein folding and stability?
  • Distinguish between alpha helices and beta sheets in terms of backbone hydrogen bonding and geometry.
  • Explain how disulfide bonds stabilize a protein and under what conditions they are most likely to form.
  • Describe the base pairing rules for DNA and RNA and explain why RNA is typically single-stranded while DNA is double-stranded.
  • Write the ATP hydrolysis reaction and explain the energetic role of this process in muscle contraction and active transport.
  • Why can’t you simply “eat” a protein and expect it to become part of your own tissues? Explain protein digestion and reassembly briefly.

Lab and classroom notes (context from transcript)

  • Week one lab focuses on microscopy and drawing observations: students should print or prepare drawing circles and bring pencils to sketch what they observe under the microscope; digital drawing with a mouse/ stylus is not acceptable for the lab task.
  • Instructor encourages questions and emphasizes revisiting fundamentals from inorganic, organic biochemistry to support understanding of biological macromolecules.
  • If unsure about a concept, students are advised to email questions or bring them to class for discussion.