Chemical Bonds, Water Properties, and Biological Macromolecules
Ionic Bonds
Mechanism
One atom loses electrons while another gains electrons, creating ions (positive cations and negative anions). Opposite charges attract, forming a bond. These are relatively weak in water because water is polar and surrounds the charged ions, causing dissociation.
Covalent Bonds
Mechanism
Atoms share electrons, typically between two non-metals. These are much stronger than ionic bonds.
Types of Covalent Bonds
- Nonpolar covalent: Equal sharing of electrons with no partial charge.
- Polar
Molecular Biology Methods for DNA and Protein Analysis
Enzyme-Linked Immunosorbent Assay (ELISA)
In an ELISA, an antigen is detected using a primary antibody and a secondary enzyme-linked antibody. The standard procedure involves:
- Antigen: Immobilization of the target.
- Wash: Removal of unbound substances.
- Primary Antibody: Binding to the specific antigen.
- Wash: Removal of unbound primary antibodies.
- Secondary Antibody: Binding to the primary antibody.
- Wash: Removal of unbound secondary antibodies.
- Substrate Addition: Adding HRP (Horseradish Peroxidase) to react
Origins and Biochemistry of Life: Key Concepts for Exams
Origins and Composition of Life (Ch. 1, L2)
Origins
- Earth formed: ~4.54 billion years ago (bya) (textbook consensus).
- Prebiotic world: before life emerged (~4.5–3.5 bya), the atmosphere contained H₂O, N₂, CO₂, CH₄, NH₃, SO₂, with energy from lightning and UV radiation.
- First evidence of life: ~3.5 billion years ago.
Composition of life
- ~70% water.
- Major dry weight: C, H, O, N (~87%), plus P, S, K, Ca, Mg.
Functional groups (must memorize)
- Amine (can be protonated at pH 7).
- Carboxyl (deprotonated
Molecular Cloning: Competent Cells, Ligation, and PCR
Preparation of Competent Cells
Aim: To prepare E. coli TOP10 cells capable of taking up foreign DNA (plasmid) using the calcium chloride method.
Core Principle
Calcium Chloride (CaCl₂) neutralizes the negative charges on the cell membrane (phospholipids) and the DNA backbone, reducing electrostatic repulsion. This, followed by a heat shock, creates transient pores for DNA entry.
Key Terms
- Competence: A cell’s ability to take up extracellular DNA.
- Transformation: The process of importing foreign DNA.
Aryl Diazonium Ion Formation and Stability
Diazonium Ion Synthesis and Stability Comparison
The synthesis of an aryl diazonium ion begins with an aniline ({{c1::Ar–NH₂}}), which may possess substituents such as a tert-butyl group. This transformation is achieved via N-nitrosylation/diazotization, typically employing NaNO₂, HCl, H₂O at approximately 0 °C.
Reaction Mechanism and Intermediate
This process first yields an N-nitrosamine intermediate, which subsequently decomposes to form the desired aryl diazonium ion ({{c1::Ar–N₂⁺}
Read MoreBiochemistry Essentials: Protein Folding, Hemoglobin, and Glycan Structure
Protein Structure and Function Fundamentals
Proteins are at the center of all biological processes. They catalyze reactions, regulate pathways, transport molecules, and form most of the structural framework of cells.
Core Principle: Structure → Function.
Historical Milestones in Protein Science
- Hsien Wu (1931): Showed that denaturation destroys non-covalent interactions, leading to unfolding and loss of function.
- Bernal & Hodgkin (1934): X-ray diffraction of pepsin revealed that proteins are ordered,