L2 Nature of DNA and protein binding

P1.7. Describe the structure of DNA, its nature, and its discovery. Include nucleosides, nucleotides, and Watson and Crick.

• DNA Structure:

  • Composed of a sugar-phosphate backbone with nitrogenous bases (Adenine, Thymine, Cytosine, Guanine).

  • DNA strands are anti-parallel and held together by hydrogen bonds between complementary base pairs.

  • Watson and Crick (1953) elucidated the double-helical structure of DNA, using Rosalind Franklin's X-ray diffraction data.

• Nucleosides and Nucleotides:

  • Nucleosides: Composed of a nitrogenous base and a sugar (deoxyribose in DNA).

  • Nucleotides: Nucleosides with one or more phosphate groups attached.

Complementary:

• A pairs with T (2 hydrogen bonds), and G pairs with C (3 hydrogen bonds).

• This complementarity is essential for accurate DNA replication and transcription.

Central Dogma:

• Describes the flow of genetic information: DNA → RNA → Protein.

• Transcription occurs in the nucleus, while translation occurs in the cytoplasm.

Different RNAs:

• mRNA: Carries the genetic message from DNA to ribosomes.

• tRNA: Transfers specific amino acids during protein synthesis.

• rRNA: Structural and catalytic component of ribosomes.

Overview of Transcription, Translation, and Genetic Code:

• Transcription: DNA is used as a template to synthesize mRNA.

• Translation: mRNA is decoded by ribosomes to synthesize proteins.

• Genetic Code: Triplet codons on mRNA correspond to specific amino acids.

Importance of a Point Mutation:

A single nucleotide change can significantly alter protein structure and function.

Sickle Cell Anemia:

Caused by a point mutation (Glu → Val) in the β-globin gene, leading to hemoglobin aggregation and deformation of red blood cells.

P2.1. Understand the building blocks of proteins and how they are made up.

• Proteins are composed of amino acids linked by peptide bonds.

• Each amino acid has a central carbon (Cα), a hydrogen atom, a carboxyl group, an amino group, and a variable R group (side chain).

• The sequence and properties of R groups determine protein structure and function.

P2.2. Describe the nature of RNA and DNA and understand the fundamental differences between the two.

• DNA: Double-stranded, contains deoxyribose, and uses Thymine (T).

• RNA: Single-stranded, contains ribose, and uses Uracil (U) instead of Thymine.

P2.3. Explain how proteins fold and why this is important with respect to binding DNA and RNA.

• Protein folding is driven by interactions like hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.

• Proper folding creates specific 3D shapes, allowing proteins to bind DNA/RNA with high specificity (e.g., transcription factors binding promoter regions).

misfolded proteins are associated with diseases like Alzheimer's and Parkinson's.

Specific Shape for Binding: fits like key

DNA Replication and Repair:allow them to bind to damaged DNA

Recognition of Sequences:creates pockets or grooves

RNA Binding for Translation:bind to mRNA to either stabilize it or help the ribosome read the message and build the corresponding protein.

P2.4. Describe the following bonding forces and understand the bonding strength of each:

• Van der Waals Forces: Weak, nonspecific interactions between close molecules.

• Hydrogen Bonds: Attraction between a hydrogen atom and an electronegative atom like oxygen or nitrogen.

• Ionic Bonds: Electrostatic attraction between oppositely charged ions.

• Hydrophobic Bonds: Interactions between nonpolar molecules in an aqueous environment.

P2.5. Understand why these bonds are important in molecular biology.

These bonds facilitate the specific interactions necessary for molecular recognition, enzymatic activity, and the stability of macromolecular structures like DNA, RNA, and proteins.

P2.6. Explain what a polar molecule is.

• A polar molecule has an uneven distribution of electron density, leading to partial positive and negative charges (e.g., water, H₂O).

P2.7. Define the constitution of an amino acid and explain how amino acids are joined into protein chains.

• Constitution of Amino Acids: Central carbon, hydrogen, carboxyl group, amino group, and R group.

• Amino acids are joined by peptide bonds, formed through a condensation reaction between the carboxyl group of one amino acid and the amino group of another.

P2.8. Explain which amino acids are hydrophobic, hydrophilic, nonpolar, polar uncharged, polar negatively charged, polar positively charged, and nonpolar aromatic.

• How to Figure It Out:

  1. Look at the Side Chain (R Group):

     • Nonpolar (hydrophobic) amino acids typically have side chains made of hydrocarbons (carbon and hydrogen) or aromatic rings.

     • Polar (hydrophilic) amino acids usually have hydroxyl groups (OH), amine groups (NH₂), or carboxyl groups (COOH), making them able to interact with water.

     • Charged amino acids (either positive or negative) have side chains that either have a positive charge (basic) or negative charge (acidic) at physiological pH.

  2. Remember Key Terms:

     • Hydrophobic = Avoids water = Often nonpolar.

     • Hydrophilic = Loves water = Often polar or charged.

P2.9. Understand how to separate proteins based on the following terms:

• Ion Exchange: Separates proteins based on charge differences.

• Gel Exclusion (Size Exclusion): Separates based on molecular size.

• Affinity Resin: Exploits specific binding properties between proteins and ligands.

• Gel Electrophoresis: Separates based on size and charge, typically using SDS-PAGE.