Biochemistry

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=kq1q2/Dr2

2. Hydrogen bonds

3. van der Waals interactions

rq1 q2

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 iceHighly 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 (Kw) is expressed by an equilibrium constant

Acid-Base reactions can disrupt the double helix

The pKa 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 0.03.

pKa = 4.75

Conclusion:Conclusion:Buffers function best close Buffers function best close to the pKa values of their to the pKa values of their acid component.acid component.