Chapter 1 The Molecular Logic of Life

Biochemistry explains diverse forms of life in unifying chemical terms.

figure 1-1
Some characteristics of living matter. Chemical complexity; Use energy; Biological reproduction

figure l-2 Diverse living organisms share common chemical features. Same basic structural units (cells) Same kinds of macromolecules (DNA, RNA, proteins)

figurel-3 Monomeric subunits in linear sequences can spell infinitely complex messages

All macromolecules are constructed from a few simple compounds All living organism build molecules from the same kinds of monomeric subunits. The structure of a macromolecules determines specific biological function. Each genus and species is defined by its distinctive set of macromolecules.

Energy production and consumption in metabolism

figure 1-4

Living organisms are not at equilibrium with their surroundings.

figure l-5

The dynamic steady state. A dynamic steady state esults when the rate of appearance of a cellular component is exactly matched by the rate of its

Organisms transform energy and matter from their surrounding

Bioenergetics Universe: system and surroundings System: closed, isolated, open A living organism is an open system.

Living organisms create and maintain their complex, orderly structures using energy extracted from fuels or sunlight.

figure l-6 During metabolic transductions, the randomness of the system plus surroundings (expressed quantitatively as entropy) increases as the potential energy of complex nutrient molecules decreases.

The first law of thermodynamics

In any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change.

The flow of electrons provides energy for organisms

figure 1-7

Sunlight is the ultimate source of all biological energy. Thermonuclear reactions in the sun produce helium from hydrogen and release electromagnetic energy, which is transmitted to the earth as light and converted into chemical energy by plants and some algae and bacteria.

figure l-8

Photosynthetic organisms are the ultimate providers of

figure 1-9

Energy coupling in mechanical and chemical processes.

Free energy (G): the amount of energy available to do work Free Energy Change (G G): is the portion of the total energy change which is available to do work as a reaction proceeds to equilibrium at constant temperature and pressure.

The sign of the free energy change in a process tells us whether that process or its reverse is thermodynamically favorable. G 0 exergonic reaction G 0 endergonic reaction G of a spontaneously reacting system is always negative At equilibrium G G 0

figure l-10

Adenosine triphosphate (ATP). The removal of he terminal phosphoryl of ATP (shaded pink) is highly exergonic, and this reaction is coupled to many endergonic reactions in the cell as in the

Enzymes promote sequences of chemical reactions

gure 1-11

Energy changes during a chemical reaction.

figure l-12

An enzyme increases the rate of a specific chemical eaction.

figure 1-13

A linear metabolic pathway.

figure l-14

ATP is the shared chemical intermediate linking energy- releasing to energy-requiring cell processes.

Metabolism is regulated to achieve balance and economy

figure l-15

Feedback inhibition. Regulation by eedback inhibition in a typical synthetic (anabolic) pathway.

Biological Information Transfer

Genetic continuity is vested in DNA molecules. The structure of DNA allows for its repair and replication with near-perfect fidelity. Changes in the hereditary instructions allow evolution.

figure 1-17

The complementary structure of DNA. Complementarity between the two strands accounts for the accurate replication essential for genetic continuity.

igure 1-18 Role of mutation in evolution. The gradual accumulation of mutations overlong periods of time results in new

figure l-19 The linear sequence in DNA encodes proteins with threedimensional structures.

Noncovalent interactions stabilize three-dimensional structures