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,
The Core Biomolecules: Carbohydrates, Proteins, and More
Carbohydrates
Definition
Optically active polyhydroxy aldehydes or ketones, or compounds that yield these upon hydrolysis.
General Formula and Name Origin
General Formula: Cₓ(H₂O)ᵧ
Name Origin: The name comes from “carbo” (meaning carbon) and “hydrate” (meaning water).
Classification of Carbohydrates
| Type | Definition | Examples |
|---|---|---|
| Monosaccharides | Cannot be hydrolyzed further into simpler units. | Glucose, Fructose, Ribose |
| Oligosaccharides | Yield 2–10 monosaccharide units upon hydrolysis. | Disaccharides: Sucrose, |
Cellular Metabolism: Energy, Lipid Synthesis, and Gene Regulation
Fatty Acid Oxidation
Fatty acids carry more energy per carbon because they are more reduced. They also carry less water along because they are nonpolar. In contrast, glucose and glycogen are for short-term energy needs and quick delivery, with fat stored in adipose tissue.
Lipids are transported in the blood as chylomicrons. Unsaturated fatty acids have a bent structure.
Glycerol Activation
- Glycerol kinase activates glycerol at the expense of ATP.
- Subsequent reactions recover more than enough ATP to