Biochemistry 阮雪芬NTU April 1, 2003

Chapter 1. Introduction History What is biochemistry Biochemistry and life Biochemical Energy Transfer of Information from DNA to Protein

History Life: 150 years ago Biochemistry: 60 years ago

What is Biochemistry ?

Definition The science that is concerned with the structures, interactions, and transformations of biological molecules The chemistry of life

Biochemistry can be subdivided three principal areas Structural chemistry Metabolism The chemistry of processes and substances that store and transmit biological information (molecular genetics)

Biochemistry and Life The cell is the fundamental unit of life Prokaryotes and eukaryotes Eukaryotic cells –animal cells –plant cells (chloroplasts and cell walls)

Biochemistry and Life Cells are composed of: –Small molecules –Macromolecules –organelles

Biochemistry and Life Percent of Total Cell Weight Number of Types of Each Molecules Water701 Inorganic ions120 Sugars and precursors3200 Amino acids and precursors Nucleotides and precursors Lipids and precursors250 Other small molecules0.2~200 Macromolecules22~5000 The Approximate Chemical Composition of Bacterial Cell

Biochemistry and Life Expect for water, most of the molecules found in the cell are macromolecules, can be classified into four different categories: –Lipids –Carbohydrates –Proteins –Nucleic acids

Biochemistry and Life Lipids are primarily hydrocarbon structures Carbohydrates, like lipids, contain a carbon backbone, but they also contain many polar hydroxyl (-OH) groups and therefore very soluble in water. Proteins are the most complex macromolecules in the cell. They are composed of linear polymers called polypeptides, which contain amino acids connected by peptide bonds.

Lipid Structure

Carbohydrates Structure

Biochemistry and Life Each amino acid contains a central carbon atom attached to four substituents –A carboxyl group –An amino group –A hydrogen atom –An R group Nucleic acids are the large macromolecules in the cells. They are very long linear polymers, called polynucleotides, composed of nucleotides.

Amino Acids Structures

Biochemistry and Life A nucleotide contains : –A five-carbon sugar molecules –One or more phosphate groups –A nitrogenous base DNA: A, T, G, C RNA: A, U, G,C

DNA Contain Four Bases RNA

Covalent Structure of DNA

Watson-Crick base pairs

The Double Helix

Ch.1 Chemistry, Energy, and Metabolism

Introduction Metabolic reactions and metabolism Energy Entropy G = H – T S Chemical equilibrium point G: small  reversible G: large  one direction

Introduction A B C D E F Products Whenever the overall chemical process of a metabolic pathway has to be reversed, the reverse pathway is not exactly the same as the forward pathway-some of the reactions are different in the two directions.

Why is this metabolic strategy used in the cell A B C D E F Products Example: DNA and protein

How are G values obtained G 0’ (1.0 M, 25 °C, pH 7.0): Standard free energy change of a reaction G G = G 0’ + RT2.303log 10 [P]/[R] K’ eq :equilibrium constant K’ eq = [C][D]/[A][B] G 0’ = -RTlnK’eq = -RT2.303log10 K’ eq

The Energy Cycle in Life

H 3 PO 4

Biochemical Energy Biochemical Energy All cellular functions re quire energy. The most-important chemical form of energy in most cells is ATP, adenosine 5’-triphosphate. ATP ADP + P i Most ATP synthesis occurs in chloroplasts and mitochondria

ADT and ATP Structures

What Transports the –p Around the Cell ADT + P i ATP + H2O +energy

How Does ATP Perform Chemical Work Coupled reactions Reaction 1: XOH + AMP-p-p  X-p + AMP-p Reaction 2: X-p + YH  X-Y + AMP-p Sum: XOH + YH + AMP-p-p  X-Y + AMP-p +P i

How Does ATP Perform Chemical Work AMP + ATP 2ADP Kinase

Weak Bonds and Free-energy Changes Covalent bond X + X  X-X + energy Noncovalent bond (weak bonds) –Ionic bonds: -COO - ---H 3 + N- –Hydrogen bonds -O-H---O- -O-H---N- -N-H---O- -N-H---N- –Van der Waals attractions

Ch.2 Enzymes

e. g., Hexokinase: proved by X-ray

S the enzyme by binding to the enzyme. The reaction gradually diminishes in rate with time; this is due to accumulation of product, which inhibit S the enzyme by binding to the enzyme.

Michaelis-Menten equation: V = [S]V max /{[S]+K m K m : A numerical values that the affinity of the enzyme is for its substrate.

The higher the K m, the lower is the affinity of the enzyme for its substrate.

酵素之一般性質 催化特性 – 催化效率 ? 基質特異性 (substrate specificity) –Stereo-specificity 最適氫離子濃度 最適溫度 (Optimum temperature) 共軛因子 – 金屬離子 – 輔酵素 : Holoenzyme = Apoenzyme + Coenzym – 輔基質 (Cosubstrate): NAD +, NADP +, ATP, CoA 多為維生素

Nomenclature of Enzymes -ase: amylase attacks amylose -in: pepsin; chymotrypsin; trypsin Isoenzyme