Foundation of Biochemistry
Biological and chemical background to biochemistry
Molecular Logic of Life (生命的分子逻辑)
•The Chemical Unity (化学一致性)of Diverse Living Organism
•Energy Production and Consumption in Metabolism
•Biological Information Transfer (生物信息的传递)
Biomolecules (生物分子)
•Chemical Composition (化学成分)
•Three Dimensional Structure (三维结构)
•Chemical Reactivity (化学反应活性)
•Macromelecules and Their Monomeric Subunits (大分子与单体亚基)
一、Biological and chemical background to
biochemistry (生化的生物学和化学基础)
•Living organisms operate within the same physical laws
that apply to all natural processes
•Cell, the units of all living organisms; Nearly all of the
organic compounds (from which living organisms are
constructed) are products of biological activity (生命活动)
•Water is the medium (介质) in which the first cells arose,
and the solvent (溶剂) in which most biochemical
transformations (生化变化) occur.
二、Molecular Logic of Life
Molecules of organisms confirm to all familiar
laws of chemistry (化学规律), they also interact
with each other in accordance with another set
of principles (法则), which we shall refer to
collectively as Molecular Logic of Life
• The Chemical Unity of Diverse Living Organism
生命多样性的化学一致性
1. Living mater has several characteristics (特性)
• Structurally complicated and highly organized
• Extract(吸收), transform(转化), and use energy from
their environment (chemical or sunlight), to build and
maintain their own intricate structures and to do
mechanical, chemical, osmotic, and other types of work
• Capacity for precise self-replication(自我复制) and
self-assembly(自组装), a property that can be regarded
as the quintessence (精髓) of living state
2. Biochemistry seek to explain life in chemical
terms(化学术语)
3. Chemical unity underlines biological diversity
(化学的一致性是生物多样性的基础)
4. All macromolecules(大分子) are constructed
from a few simple compounds
•Energy Production and Consumption in Metabolism
1. Organisms are never at equilibrium (平衡)
with their surroundings
2. Molecular composition reflects a dynamic
steady state (动子学稳态)
3. Organisms exchange energy and matter with
their surroundings
4. Cell and organisms interconvert(转换) different
forms of energy
5. The flow of electrons (电子流动) provides
energy for organisms
6. Energy promotes (推动) sequences of
chemical reactions
7. ATP is the universal carrier (通用载体) of
metabolic energy, linking catabolism and
anabolism
8. Metabolism is regulated to archive balance
and economy
•Biological Information Transfer (生物信息的传递)
1. Genetic continuity is vested (被赋予) in DNA
molecules
Perhaps the most remarkable of all the properties
of living cells and organisms is their ability to
reproduce themselves with nearly perfect fidelity
(保真) for countless generations
2. The structure of DNA allows for its repair
and replication with near-perfect fidelity
Genetic information is encoded in the linear
sequence of four kinds of subunits of DNA.
The double-helical (双螺旋) DNA molecule
contains an internal (内在的) template for
its own replication and repair
3. Changes in hereditary (遗传的) instructions
allow evolution
4. The linear sequence in DNA encodes protein
with three-dimensional structures(三维结构)
DNA
RNA
Protein
folds
Particular three dimensional structure
(Native conformation, 天然构象)
Native conformation is crucial to its function as
either catalyst (催化剂) or structural element
Native conformation is crucial to its function as
either catalyst (催化剂) or structural element
This principle:
The linear sequence of amino acids in a protein
leads to the acquisition of a unique threedimensional structure by a self assembly process
Individual macromolecules with specific affinity
(亲合性) for other macromolecules self-assemble
into supramolecular complexes.
5. Noncovalent (非共价的) interactions stabilize threedimensional structures
Three dimensional biological structures combine the
properties of flexibility () and stability
Noncovalent interactions are also central to the
specificity and catalytic efficiency of enzymes
The formation of oncovalent interactions provides
the energy for self-assembly of macromolecules by
stabilizing native conformation relative to unfolded,
random forms.
Summary :
The physical roots of the biochemical world. We can
now summarize the various principles of the
Molecular Logic of Life:
1. A living cell is a self-contained (控制)， selfassembly, self-adjusting (调节), self-perpetuating (使
自身永存) isothermal (恒温的) system of molecules
that extracts free energy and raw materials from its
environment.
2. The cell carries out many consecutive reactions
promoted by specific catalysts, called enzymes,
which it produces itself.
3. The cell maintains itself in a dynamic steady state,
far from equilibrium with its surroundings.
4. self-replication through many generations is ensured
by the self-repairing, linear information-coding
system.
5. Many weak (noncovalent) interactions, acting
cooperatively, stabilize the three-dimensional
structures of biomolecules and supramolecular
complexes.
6. Stereospecificity (立体专一性) is characteristic
feature of the molecular logic of living cells.
三、Biomolecules
Chemical composition of living mater
1. Living mater is composed mostly of the
lighter elements
2. Biomolecules are compounds of carbon
Molecules containing covalently bonded
carbon backbones are called organic
compounds.
3. Functional groups determine chemical
properties
Three dimensional structure
1. Each cellular component has a
characteristic three-dimensional structure
2. Most biomolecules are asymmetric
3. Interactions between biomolecules are
stereospecific
Chemical reactivity
1. Bond strength is related to the
electronegativities(电负性) of the bonded
atoms
Strengths of bonds common in biomolecules
Types of
bonds
Single bonds
O-H
H-H
P-O
C-H
N-H
C-O
C-C
S-H
C-N
N-O
S-S
Bond dissociation
energy (KJ/mol)
461
435
419
414
389
352
348
339
293
222
214
Types of bonds
Double bonds
C=O
C=N
C=C
P=O
Triple bonds
C C
N N
Bond dissociation
energy (KJ/mol)
712
615
611
502
816
930
Noncovalent bonds or interactions
Hydrogen bonds, Van der waals force,
hydrophilic interaction, hydrophobic
interactions, Ionic interactions: 4-20
2. Five types of chemical transformations occur
in cells
Most cells have the capacity to carry out thousands
of specific, enzyme-catalyzed reactions:
* Transformate of simple nutrients such as
glucose into amino acids, nucleiotides, or lipids
* Extraction of energy from fuels by oxidation
* or polymerization of subunits into
macromolecules
2. Five types of chemical transformations occur
in cells
• Functional group transfer
• Oxidations and reductions
• Rearrangement
• Cleavage (reactions that form or break
carbon-carbon bonds
• Condensation (reactions in which two
molecules condense, with the elimination of a
molecule of water )
Reactions within one category generally occur by similar
mechanism
Macromolecules and their monmeric subunits
1. The major constituents of organisms are
macromolecules
Macromolecules
MW
Proteins
5,000- over millions
Nucleic acids
to several billions
Polysaccharides
to millions
Lipids
750-1,500/individual
2. Monmeric subunits have simple structures
Most larger structures in cells are constructed from 33
organic compounds with molecular weight of 500 or less:
The ABCs of Biochemistry
* 20 amino acids of protein
* 5 nitrogenous bases: uracil, thymine, cytosine, adenine,
quanine
* 2 five-carbon sugars: α- D-ribose, 2-deoxyl-α-D- ribose
* 1 six-carbon sugar: glucose
* 1 phosphoric acid
* 4 components found in many membrane lipids:
Oleic acid (18:1); Palmitic acid (16:0); Choline; Glycerol
Gly
Ala
Leu
, Pro
, Val
Ile
Met
Ser
, Cys
Thr
Asn
, Gln
Phe
Tyr
Trp or Try
Lys
Arg
His
Asp
Glu
Purine, Pu (嘌呤碱）
Pyrimidine, Py (嘧啶碱）
HOH2C
O
OH
H
H
OH
H
OH
H
β-D-ribose
(β-D-核糖)
(D-核糖)
HOH2C
O
H
OH
H
H
OH
(2-D-脱氧核糖)
H
H
β-D-2-deoxyribose
(β-D-2-脱氧核糖)
(油酸)
（棕榈酸）
phosphoric acid:
－O
Choline
H0
Glycerol