Biochemistry : Chemistry in biological systems
Biochemistry is the study of the chemical processes and transformations in living organisms Key metabolic processes are common to many organisms. Most of biochemical reactions are done by enzymes, the catalysts of biological systems
Biochemistry Berg Tymoczko Stryer Part 1. The molecular design of life Part 2. Transducing and sorting energy : degradation of molecules (CH, FA, Pr) Part 3. Synthesizing the molecules of life : AA, NT (DNA, RNA), Lipids, Pr
Part 1. The molecular design of life Chapter 1. Prelude: Biochemistry and the genomic revolution Chapter 2. Biochemical evolution Chapter 3. Protein structure and function Chapter 4. Exploring proteins Chapter 5. The flow of genetic information Chapter 6. Exploring genes Chapter 7. Exploring genes Chapter 8. Enzymes: Basic concepts and kinetics
Chapter 1: Prelude: Biochemistry
Geological and biochemical findings support a time line for the evolutionary path
Cystic fibrosis DNA: The storage of genetic information
The tree of life. A possible evolutionary path from a common ancestor cell to the diverse species present in the modern world can be deduced from DNA sequence analysis.
Base: A, C, G, T DNA is constructed from four building blocks
Covalent structure of DNA
Two single strands of DNA combine to form a double helix
Double Helix: Watson AND Click propsosed in 1953
Watson-Crick base pairs: A-T & G-C
DNA structure explains heredity and storage of information 1.The structure is compatible with any sequence of bases. 2. Because of base pairing, the sequence of base along one strand completely determines the sequence along the other strand.
* RNA is an intermediate in the flow of genetic information Ribose instead of Deoxyribose Uracil instead of Thymine * Proteins, encoded by nucleic acids, perform most of functions
Concept from Chemistry 1.Types of chemical bonds 2.Thermodynamics 3.The principle of Acid-base chemistry
Covalent Bonds
Resonance Structures A molecule that can be written as several resonance structures has greater stability than does a molecules without multiple resonance structures.
Non-covalent Bonds 1.Electrostatic interactions: E=kq 1 q 2 /Dr 2 2.Hydrogen bonds 3.van der Waals interactions r q1q1 q2q2
Properties of water 1.Water is a polar molecule 2.Water is highly cohesive
Structure of water molecule Distribution of charge is asymetric
Structure of ice Highly ordered and open structure
at pH 7 Polar and non polar biomolecules
Hydrogen bonds are highly directional and capable of holding two hydrogen bonded molecules or groups in a specific geometric arrangement.
The strength of hydrophobic interactions results from the system’s achieving greatest thermodynamic stability by minimizing the number of ordered water molecules required to surround hydrophobic portions of the solute molecules. The hydrophobic Effect
DNA double helix: Expression of the rules of chemistry
1.Types of chemical bonds 2.Thermodynamics 3.The principle of Acid-base chemistry
Heat is released in the formation of the double helix
Energy coupling links reaction in Biology
1.Types of chemical bonds 2.Thermodynamics 3.The principle of Acid-base chemistry
The movement of hydrinium and hydroxide ions in the electric field is anomalously fast
Neutral pH The ionization of water (K w ) is expressed by an equilibrium constant
Acid-Base reactions can disrupt the double helix The pK a for the proton on N-1 of guanine is 9.7 ; When pH equals the pKa, the concentration of the deprotonated form is equal to the concentration of the protonated form.
Henderson-Hasselbalch equation The tendency of any acid (HA) to lose a proton and form its conjugated base (A-).
pKa Buffer action Biological systems need a solution system to resist a signficant change in pH
At pH 9, the ratio of acetate ion and acetic acid is very high (18000). At pH 3, the ratio is about pKa = 4.75 Conclusion: Buffers function best close to the pKa values of their acid component.