What is Biochemistry?

Today we will try to define what is the scope of study of biochemistry. As the name implies, biochemistry involves the study of the chemistry of biological processes. In other words, we are interested in knowing at the molecular and atomic level why biological systems (living organisms) behave the way they do.

Having said that, we have to understand clearly what a living organism is, and how it differs from innanimate matter. In a very simple way, we can define a living organism as something that:

• Has goals. Usually, we will see that the final goal is to self-perpetuate. Bateria, despite their size and lack of brain, move around until they find a spot that will make them grow larger. Rocks, on the other hand, sit there...
• Can extract and use energy from their environment. Again, if we think of bacteria, they move around. To do this, they have to burn energy, because many times they have to go against the flow. They get this energy from nutrients, which they have to 'capture' and 'eat'. Again, a rock sitting on a clif can only fall, and loose energy (potential energy), but never gain energy...
• Can order matter at the microscopic level. In most living systems, everything has a certain, required, order. For example, every bacteria has a cell membrane. The cell membrane has certain components, and they are arranged in a certain manner. No matter how hard you try, the membrane on a certain cell will look pretty much like the membrane on another cell, and the molecular order will be the same.
• Can grow and develop. Bacteria just don't pop-up in their full size. They develop from other bacteria, and go through cycles, the same way that we are born and age.
• Can reproduce or self-perpetuate. Probably the most defining characteristic of living entities is that they can self-replicate. Most of the elements in a cell can be made by the same cell, and this will occur at all leves: aminoacids, nucleic acids, etc., that form the cell are also made by the machinery present in the cell. The final result of this is the self-replication of the whole cell, which we call reproduction.
• Can order the environment around them. Just look around you...

• Only a small number of atoms in the atomic table are used (C, N, O, H are the most, S and P come second, and then we have some metals).
• These atoms form molecules in a relatively small number of arrangements (amino acids, nucleic acids, carbohydrates, fatty acids).
• These molecules form even larger molecules by repeating their patterns in very simple ways (proteins, DNA, RNA, polysaccharides, lipids).
• Some of these larger macromolecules have all the information needed to prepare smaller blocks using the basic atoms, as well as themselves.
• The machinery needed for all this is self-perpetuating.

If you think a bit, all this ordering means that living systems fight equilibrium! A system that reaches equilibrium looses order. Thus, if we want to keep order in a biochemical system we will always have to move it away from equilibrium.

Dimenssions, times, and energies

In order to study biochemistry, we have to get used to certain usints of lenght, energy, and time.

1. What scale of length is appropriate for describing living things. It depends at what level you are looking.

What is the appropriate length scale when looking at a whole organism? How about feet? Contrast to measuring your height in cm or in miles! (I am 180 cm or 0.0011 mile high. Why aren't those units as 'nice' as feet?). How big is a single cell? A red blood cell is about 7 micrometers, a bacterium is about 3 micrometers, where 1 MICROMETER = 10^-6 M = 0.000001 M:

A virus? (About 0.1 micrometer)

A protein? (About 0.01 micrometer)

A bond? (0.0001 micrometer)

Oops! Maybe we need a more convenient unit of measure when things get so small. How about the ANGSTROM? 1 ANGSTROM = 1 X 10^-8 cm, and 1 micrometer = 10,000 ANGSTROMS

In terms of Angstroms:

A virus is 1000 A

A protein 100 A

A chemical bond, about 1 A

milli - 10^-3
micro - 10^-6
nano - 10^-9
pico - 10^-12

Some common biolgical events and their characteristic time:

Primary event in vision - picosencond

Hinge motion in protein - nanosecond

Unwinding part of a helix - microsecond

Enzyme-catalyzed reaction - millisecond (binding, reaction, release of product)

Synthesize a protein - 1 second

Reproduce a bacterium - 1000 seconds

We will almost always use the kilocalorie (kcal). The kcal is the same as one dietary calorie. One kcal is the energy needed to heat one kg of water by one degree centigrade. Usually we will see kcal/mole - in other words, the same energy contribution, but multiplied by Avogadro's number (6.02 X 10²³). Some common energies:

• Random thermal energy (energy in one degree of freedom at room temperature) - 0.6 kcal/mole
• A chemical bond - 100 to 300 kcal/mole
• A hydrogen bond - 5 kcal/mole
• Chemical energy 'stored' in ATP - 12 kcal/mole

If you consider all the points we mentioned at the begining, and you think of the type of chemistry that is required to them, you will arrive to the following conclusion: In order to understand how living organisms order their environment, consume and transform energy, and fight equilibrium, you will need Physical Chemistry. To understand how all these processes occur at the molecular and atomic level, you will need concepts from Organic Chemistry.

Therefore, in our next lectures we will review some basic concepts of Physical Chemistry and Organic Chemistry...