Introduction: Common Terminologies.

Some basic terminologies are brushed through in this section just for reminder’s sake.

The term metabolism describes the many reactions in which organic compounds are synthesized and degraded and useful energy is extracted, stored and used.

The study of the changes in energy during metabolic reactions is called bioenergetics.

The basic thermodynamic principles that apply to energy flow also apply to biochemistry. Thermodynamic considerations can tell us if a reaction is favored, but does not tell us how quickly a reaction will occur. The rates of the normally slow reactions are accelerated by enzymes so much so that enzyme-catalyzed reactions can be up to ×1017 greater than the rate of corresponding unanalyzed reactions!

An enzyme and a small molecule will collide one million times per second. Under these conditions, many enzyme-catalyzed reactions could be achieved if only 1 in about 1000 collisions result in a reaction.

Much of what we now know of biochemistry is attributed to the study of viruses. They are subcellular and consist of a nucleic acid molecule surrounded by a protein coat. Virus nucleic acid can contain as few as three genes or as many as several hundred. Despite their biological importance, viruses are not cells because they cannot carry out independent metabolic reactions; they multiply by hijacking the reproductive machinery of a host cell, making it form new viruses, so they’re genetic parasites.

That is all. Next chapter, water. “We made from water every living thing.” Quran, 21:30.

Introduction: Mass Units and Common Macromolecules- Proteins.

When we discuss molecules and bio polymers we will often refer to their molecular weight or relative molecular mass (Mr) this is the mass of a molecule relative to 1/12 the mass of an atom of carbon isotope -12 (which is exactly 12 atomic mass units. Don’t think too much into it, simply count the atom in the periodic table according to the number of protons it contains).

Now because Mr is a relative quantity, it is dimensionless and has no units associated with its value. The absolute molecular mass of a compound has the same magnitude as the molecular weight, except that it is expressed in units called Daltons; 1 Dalton = 1 atomic mass unit.

The molecular mass is also called the molar mass because it represents the mass, measured in grams, of one mole, which is Avogadro’s constant number = 6.023 × 1023. So 1 mole of an atom or molecule contains 6.023 × 1023 atoms or molecules and that in turn will give us how much the molecule will weigh in grams.

The molecular mass of a typical protein is 38,000 daltons..

The common macromolecules that we shall deal with in the coming chapters are proteins, polysaccharides, nucleic acids and lipids. We shall deal with one in each post:

a-            Proteins.

They are structurally important to the cell since they are the basic components of which the cytoskeleton is made, and functionally important since it is responsible for catalyzing reactions in the form of enzymes, have mobility functions, act as signal molecules for the cell and are part of a complex to form receptors for those signals and pretty much most other complicated functions. Due to these reasons, they are structurally complex as well.

Proteins are large polymers of amino acids joined together throughpeptide bonds to form polypeptides or in other words proteins. This is unclear unless you know what each bolded syllable is.

Amino Acid. Click on link for image credit

First, Amino Acids. Each amino acid consists of a central carbon atom bonded to a;

i-             Carboxylic-acid group (COOH); A carbon atom double-bonded to an oxygen atom and single bonded to a hydroxyl group (O-H).

ii-            Amino group (NH2); This is simply a nitrogen atom single bonded to two hydrogen atoms.

iii-           Hydrogen atom;

iv-           A distinctive side-chain that is unique to each type of amino acid, usually referred to as the “R” group. Thus, amino acids differ only in their side chains.

Amino acids get their name because of the amino group and the carboxylic acid group.

When two amino acids come close together, the hydroxyl group (OH) of the carboxylic-acid, which is polar, attracts a hydrogen atom of the amino group of the other amino acid and in the process, forms and releases a water molecule (See below image). This leads to the formation of a peptide bond which is a covalent bond between the carbon of the carboxylic-acid group of the first amino acid and the nitrogen of the amino group of the second amino acid. When many amino acids are linked together through peptide bonds, they form a polypeptide chain (or proteins).

Formation of a Peptide Bond. Click on image for credit.

Proteins are structurally complex. If you look at one (below), you can only see chaos. This is due to the fact that when amino acids begin to form peptide bonds with one another, they do not line up into a straight linear structure, rather, they begin to spiral and coil due to the interaction of their side chains with one another forming various types of (mostly) hydrogen and (sometimes) sulphur bonds.

The three dimensional shape of a protein is determine largely by the sequence of amino acid residues. This sequence of information is encoded in the gene of the protein and it is important because the protein’s 3-D structure or conformation is what does their jobs.

Many enzymes for instance contain a cleft (groove) called the active site whose function is to catalyze reactions that depend on this structure.

Enzyme with active site (cleft) shown. Click on image for credit.

Substrate is the molecule(s) that require catalysis and when bind with the active site of the enzyme, undergo specific reactions (more on it later).