Transcript Ch1_2

Biochemistry
阮雪芬
NTU
April 1, 2003
Chapter 1. Introduction
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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
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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
Water
70
1
Inorganic ions
1
20
Sugars and precursors 3
200
Amino acids and
precursors
0.4
100
Nucleotides and
precursors
0.4
200
Lipids and precursors
2
50
Other small molecules
0.2
~200
Macromolecules
22
~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
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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
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
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G: small  reversible
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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
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Products
• Example: DNA and protein
F
How are G values obtained
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G0’ (1.0 M, 25 °C, pH 7.0): Standard free
energy change of a reaction
G
G = G0’ + RT2.303log10 [P]/[R]
K’eq:equilibrium constant
K’eq = [C][D]/[A][B]
G0’ = -RTlnK’eq = -RT2.303log10 K’eq
The Energy Cycle in Life
H3PO4
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 + Pi
• Most ATP synthesis occurs in
chloroplasts and mitochondria
ADT and ATP Structures
What Transports the –p Around the
Cell
ADT + Pi
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
+Pi
How Does ATP Perform Chemical
Work
• AMP + ATP
• Kinase
2ADP
Weak Bonds and Free-energy
Changes
• Covalent bond
X + X  X-X + energy
• Noncovalent bond (weak bonds)
– Ionic bonds: -COO----H3+N– Hydrogen bonds
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-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
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]Vmax/{[S]+Km
Km: A numerical
values that the
affinity of the enzyme
is for its substrate.
The higher the Km, the lower is the
affinity of the enzyme for its substrate.
酵素之一般性質
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催化特性
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催化效率?
基質特異性 (substrate specificity)
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Stereo-specificity
最適氫離子濃度
最適溫度 (Optimum temperature)
共軛因子
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多為維生素
金屬離子
輔酵素: Holoenzyme = Apoenzyme + Coenzym
輔基質 (Cosubstrate): NAD+, NADP+, ATP, CoA
Nomenclature of Enzymes
• -ase: amylase attacks amylose
• -in: pepsin; chymotrypsin; trypsin
• Isoenzyme