BIOL Unit 1 - 3

Mad Cow Disease

  • Mad cow disease is an infectious disease caused by a misfolded protein known as a prion.

  • A single misfolded prion can lead to other prions misfolding, illustrating the disease's infectious nature.

  • This disease serves as an example of how misfolded proteins can fundamentally impact biological structure.

Protein Structure Levels

  • There are four levels of protein structure:

    • Primary (1°)

    • Secondary (2°)

    • Tertiary (3°)

    • Quaternary (4°)

Prions

  • Prions exhibit unusual resistance to proteinase K, an enzyme that cleaves proteins into their monomeric components.

  • Proteinase K breaks down proteins by cleaving specific types of bonds:

    • A. Hydrogen bonds

    • B. Hydrophobic interactions

    • C. Peptide bonds (correct answer)

    • D. Ionic bonds

Lecture Overview: Nucleic Acids

  • Chapter 4: Nucleic Acids and the RNA World

  • BioSkills 6: Separating and Visualizing Molecules

Key Learning Outcomes

  • Identification of monomers (building blocks) of nucleic acids, focusing on:

    • Name and chemical structure

    • Bonds linking them together

  • Functional groups in nucleotides and their role in nucleic acid synthesis.

  • Directionality of nucleic acid synthesis.

  • Analysis of DNA structure levels and relation to function.

  • Explanation of complementary base pairing.

  • Usage of base pairing rules to justify that in DNA,

    • %A = %T

    • %G = %C

  • Calculation of base composition in nucleic acid and prediction of complementary strand sequences.

  • Analysis of RNA structure levels and relation to function, discussing diversity between RNA, DNA, and protein structure and function.

Nucleic Acids Structure

  • Building blocks: Nucleotides

  • Main classes:

    • DNA (Deoxyribonucleic acid)

    • RNA (Ribonucleic acid)

Nitrogenous Bases

  • Comparison of nitrogenous bases in DNA and RNA:

    • DNA contains A, T, C, G

    • RNA contains A, U, C, G

  • Mnemonic: "CUT the Py" (Cytosine, Uracil, Thymine = Pyrimidines)

  • Pure silver metaphor indicating stability differences between the two structures.

Nucleotide Linkages

  • Nucleotides are bonded by Phosphodiester linkages.

  • Phosphate from one nucleotide links to the 3’ hydroxyl of another through a condensation reaction, forming the backbone of nucleic acids.

  • RNA has a unique 2’-hydroxyl group which distinguishes it from DNA.

Polymerization of Nucleic Acids

  • Activated nucleotides (triphosphates) serve as the building blocks for polymerization reactions.

  • The process of nucleic acid synthesis produces a directional sugar-phosphate backbone.

  • Directionality noted as 5’ to 3’ (denoted as 5’-UAGC-3’).

Levels of Nucleic Acid Structure

  • Similar to proteins, DNA and RNA exhibit primary (1°), secondary (2°), and tertiary (3°) structures.

  • Secondary Structure:

    • DNA’s secondary structure, as elucidated by Watson and Crick and supported by Rosalind Franklin, relies on:

    1. Complementary base pairs - hydrogen bonding.

    2. Base stacking interactions.

Stability and Function of DNA

  • DNA’s stable structure allows for the storage of genetic information and template formation for replication.

  • Key processes involved:

    • Strand separation

    • Complementary base pairing

    • Polymerization leading to semi-conservative replication.

RNA Structures

  • RNA can adopt complex structures, such as stem-and-loop configurations and pseudoknots, often distinct from DNA.

  • Major types of RNA discussed include:

    • Ribosomal RNA (rRNA)

    • Messenger RNA (mRNA)

    • Transfer RNA (tRNA)

    • Small nuclear RNA (snRNA)

    • Micro RNA (miRNA)

    • Catalytic RNA (Ribozymes)

Ribozymes and Their Functions

  • Ribosomes and ribosomal RNA catalyze peptide bond formation during translation.

  • Some ribozymes catalyze the cleavage of phosphodiester bonds during RNA processing events (splicing).

Learning Check: Nucleic Acids

  1. A nucleic acid sample has 35% Thymine. To determine the proportions of other bases:

    • Percentage of Adenine (A) = 35%

    • Percentage of Guanine (G) = 15%

    • Percentage of Cytosine (C) = 15%

    • Type of nucleic acid: DNA

  2. Predict the impact of monomer sequence changes on the structure of proteins, DNA, and RNA.

    • 1° Structure may change, impacting 2° and 3° Structures based on the nature of the change.

    • DNA and RNA may undergo similar changes in structure which could affect their overall function, but some structural aspects may remain intact.

Gel Electrophoresis Principles

  • Proteins and nucleic acids can be separated and visualized through gel electrophoresis.

  • Movement mechanics:

    • Nucleic acids and proteins move through the gel based on size and charge.

Comparative Analysis in Gel Electrophoresis

  • Compare aspects of samples in lanes of the gel, identifying specific characteristics such as size and structure.

  • Additional interpretation relating to molecular properties based on migration distances in gel electrophoresis setup.