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INTRODUCTION to BIOCHEMISTRY

LIVING THINGS
- composed of lifeless molecules
- these molecules conform to all the physical and chemical laws that describe the behaviour of the
inanimate matter
The IDENTIFYING CHARACTERISTICS of LIVING MATTER
1. Living organisms
- complicated and highly organized
- cells possess intricate internal structure containing many kinds of complex molecules
2. Each component part of a living organism have specific purpose or function
- macroscopic structures
- chemical compounds in the cell
3. Living organisms
- capacity to extract and transform energy from the environment build and maintain intricate structure
from simple raw materials
- carry out other forms of purposeful work (ex: locomotion)
4. Capacity for precise self-replication
BIOCHEMISTRY and the LIVING STATE
A. Question
- why does living matter radically differ from non-living matter since both of them consists of inanimate
molecules
B. Goal of the Science of Biochemistry
- determine how the collections of inanimate molecules found in living organisms interact with each
other to constitute, maintain, and perpetuate the living state
BIOMOLECULES
A. Chemical Components of Living Organisms
- organic compounds of carbon which is reduced or hydrogenated
- many organic molecules also contain nitrogen
B. E. coli
- contains 5000 different kinds of compounds
- 3000 different kinds of proteins
- 1000 different kinds of nucleic acids
C. Macromolecules
- comprise most of the organic matter in living cells
- very large molecular weights
- proteins, nucleic acids, polymer substances (starch, cellulose)
D. Humans
- > 100,000 different kinds of proteins
- none of the E. coli protein molecules is identical with any of the human molecules
E. Cell Macromolecules
- composed of simple, small building-block molecules strung together in long chains
- thousands of different macromolecules are constructed from few simple building-block molecules
1st Axiom:

There is an underlying simplicity in the molecular organization of the cell

- building-block biomolecules are identical in all species

2nd Axiom:

All living organisms have a common ancestor

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- each organism has its own sets of nucleic acids and proteins
3rd Axiom:

The identity of each species of organisms is preserved by its possession of

characteristic sets of nucleic acids and proteins

- from the functional versatility of the building-block biomolecules

4th Axiom:

Principle of molecular economy in living organisms

- living cells contain the simplest possible molecules in the least
number of different types, just sufficient to endow them the
attribute of life and with specie identity, under environmental
conditions in which they exist

ENERGY TRANSFORMATIONS in LIVING CELLS

A. 2nd Law of Thermodynamics (branch of physics dealing with energy and its transformations)
- all physical and chemical processes always proceed with an increase in the disorder or randomness in
the environment (entropy)
B. 1st Law of Thermodynamics
- energy can neither be created nor destroyed
- living organisms cannot consume or use-up energy only transform one form of energy to another
1. Ex: heat
2. Environment
- source of free energy
- source of raw materials
5th Axiom:

Living organisms create and maintain their essential orderliness at the expense
of their environment, which they cause to become more disordered and random

C. In Thermodynamic Language
1. Living Organisms are Open Systems
- exchange both energy and matter with their environment and transform it not in
equilibrium with the environment
2. Living Organisms are in Steady State (the Condition of an Open System)
transfer rate of matter and energy
from the environment into the
system

transfer rate of matter and energy

out of the system

the cell is a non-equilibrium open system

3. Living Cell
- isothermal
- no significant difference in pressure between parts of the cell
- unable to use heat as a source of energy (heat can do work at constant pressure only if it passes
from a zone of high temperature to zone of low temperature)
6th Axiom:

Living cells function as isothermal chemical engines

- energy absorbed from the environment is transformed into chemical
energy to carry out chemical works at essentially constant
temperature

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CHEMICAL REACTIONS in LIVING CELLS
A. Enzyme Catalyzed Reactions
- 100% yield
- no by products
1. Specificity
- one enzyme for one specific reaction
- no effect on other chemical reactions
carry out many different chemical reactions simultaneously
2. Chemical Reactions
- sequences of consecutive reactions
- the product of the 1st reaction becomes the substrate of the 2nd reaction
- connected into networks of converging or diverging pathways (linked by common
intermediates)
- sequential reactions makes the transfer of chemical energy possible
7th Axiom:

The specificity of molecular interactions in cells results from the

structural complimentarity of the interacting molecules
- lock and key complimentarity between enzymes and substrates

B. Divisions of Living Cells According to Type of Energy They Derive from the Environment
1. Photosynthetic Cell
- sunlight as main source of energy
- radiant energy absorbed by chlorophyll chemical energy
2. Heterotrophic Cells
- energy from highly reduced, energy-rich organic molecules
- ex: glucose CO2 + H2O
C. ATP - major carrier of chemical energy
- as it transfers energy to other molecule, it losses its terminal PO4 group ADP

D. ADP - discharged or energy poor

- accept chemical energy by regaining PO4 group
ATP biosynthesis of cell components

ADP energy from environment

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8th Axiom:

Consecutively linked sequences of enzyme catalyzed reactions provide the means for
transferring chemical energy from energy-yielding to energy-requiring processes

SELF-REGULATION of CELL REACTIONS

A. Linkage of Enzyme-Catalyzed Reactions into Consecutive Sequences
regulation of metabolism with self-adjusting properties
- over accumulation of an end-product of metabolism inhibit the rate limiting step (feedback
inhibition)
B. Living Cells also Regulate the Synthesis of Catalysts
9th Axiom:

Cells are capable of regulating their metabolic reactions and the biosynthesis of their
enzymes to achieve maximum efficiency and economy

SELF-REPLICATION of LIVING ORGANISMS

A. 3 Features:
1. Some organisms are so immensely complex that the amount of genetic information transmitted seems
out of proportion to the minute size of the cells that must carry it
- genetic information is present in the chromosome coded through specific sequences of
nucleotide building-blocks in a very amount of DNA
10th Axiom:

The symbols in which the genetic information is coded in DNA are

submolecular in dimension

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2. Extraordinary stability of genetic information stored in DNA
a. Structural Complementarity
- one DNA strand serves as the template for the enzymatic replication of a structurally
complimentary DNA strand

b. DNA Breaks
- may occur even in normal cells
- quickly and automatically repaired by specific enzymes
c. Errors of Mutation
- infrequent
- not always deleterious
- may allow specie of organism to change its identity for adoption in the course of
evolution
3. Genetic information is encoded in the form of a specific sequence of 4 different nucleotide buildingblocks in the linear DNA molecule
- the one-dimensional information of DNA is translated to 3-dimensional macromolecular and
supramolecular components of living cells by translation of DNA structure into protein
structure
The MOLECULAR LOGIC of the LIVING STATE
- a living cell is a self-assembling, self-regulating, self-replicating, isothermal open system of organic
molecules operating on the principle of maximum economy of parts and processes; it promotes many
consecutively linked organic reactions for the transfer of energy and for the synthesis of its own components
by means of organic catalysts that it produces itself