Download Speaking the Language

Getting Started. Speaking the
Language and Walking the Landscape
To know biochemistry is to communicate in the language of the
science. Communication is absolutely essential in silent thought and
spoken words. Words conjure up images that stay with you. Correct
answers on exams will depend on how well you interpret what is being
asked. Simply put, If you don’t understand the question, you won’t know
the answer. The language of biochemistry must not be a foreign
language to you. Biochemical terms for the most part are taken from
organic chemistry, but many are unique to the science itself. For example
proteins, carbohydrates, nucleic acids, etc. have their own descriptors
that convey specific meanings. It is not necessary that you memorize the
exact wording of the definitions, only the meaning and unique concept,
structure, reaction, etc. they are meant to convey.
Metabolites, Macromolecules and Molecular Complexes:
Small molecules such as amino acids, monosaccharides, fatty acids, and
nucleotides are common in living systems. Such substances are referred to as
“metabolites”, implying they are primed for chemical change. It is, however, the giant
molecules with molecular weights in the hundreds of thousands that sets biochemistry
apart from anything you experienced in organic chemistry. DNA, for example, represents
two intertwined chains with a molecular weight in the millions (click 1). LDL likewise is a
giant complex composed of lipid and proteins (click 1) and ATP synthase is a huge
assembly of proteins that is composed of more than 20 different proteins in the
mitochondria (click 1). Thus, biochemistry runs the gamut of molecules from the very tiny
to giant molecular assemblies.
ATP Synthase
DNA
LDL Particle
Structure vs Function: Structure plays a preeminent role in the function of biomolecules. A
simple amino acid, for example has 3 important structural features linked to its function: (1)
a –COOH group, a –NH3 group, and a variable R group (click 1). The carboxyl and amino
group are designed to joins amino acids together in peptide bonds (click 1). Amino acids
therefore are designed to “polymerize”, i.e., unite with one another to form macromolecules
built from smaller defined units. Similarly, carbohydrates join to one another through acetal
bonds, which in biochemistry are call glycosidic bonds (click 1). The lesson here is to see
how these orgainic principles of bonding carry over to biochemistry and the structure of
biomolecules.
H
R
C
H
COOH
R’ C
NH2
H
COOH
NH2
C
OH
OH
HO
OH
OH
COOH
CH2OH
O
OH
OH
C
R’
CH2OH
O
O
CO-NH
NH2
CH2OH
CH2OH
HO
R
H
OH
O
O
HO
OH
OH
OH
OH
Little Begets Big
The assembly of larger biomolecules is based on a simple repeat pattern.
Proteins, polysaccharides, membrane lipids, RNA and DNA are built from simpler
molecules. This organizing principle should not be overlooked. To help you see the
importance of modular design, consider the various stages of molecular assembly for
each category of biomolecules (click 1)
Building Block
First Stage
Second Stage
Final Stage
Amino acids
Peptides
Polypeptides
Proteins
Monosaccharides
Fatty acids
Mononucleotides
Disaccharides
Monoacylglycerols
Dinucleotides
Oligosaccharides
Diacylglycerols
Oligonucleotides
Polysaccharides
Triacylglycerols
Polynucleotides
Each stage can be represented by a stable set of molecules. For example, common
disaccharides include sucrose, maltose, lactose; common peptides are oxytocin,
vasopressin, growth hormone; common polypeptides include insulin, glucagon.
What’s in a Name
Nomenclature is important in any science. Names given to compounds,
complexes, reactions, etc. have a rationale basis and it will up to you to spot the reason
behind the name. Lets start with the word “glycan”. A glycan is literally any
carbohydrate. It can be a simple substance or a complex. A “proteoglycan” is thus a
protein with a carbohydrate appendage. If the appendage is small and the protein is
the major component, its called a glycoprotein with emphasis on the word “protein”. The
amino acid “glycine” derives its name because of its sweet taste, like a carbohydrate,
i.e., a glycan. All of these terms come from a simple root word.
Another important root word is “glycer” as in glycerol. Glycerol is a 3-carbon
trihydroxy alcohol that is a major building block of lipids (click 1). The alcohol groups
serve as attachment points for fatty acids. From this simple stem compound come
compounds such as the “acylglycerophophates, glycerate, monoacylglycerols, etc (click
1).
O
O
CH2OH
H-C-OH
CH2OH
D-glycerol
H2-C-O-C-R
H-C-OH
CH2OH
Monoacylglycerol
H2-C-O-C-R
H-C-OH
CH2OPO3H
Monoacylglycerophosphate
COOH
H-C-OH
CH2OH
D-glycerate
It would be virtually impossible to list names, prefixes, abbreviations, etc. of all
the biomolecules. The impact of this lesson, however, is to alert you to how names give
important clues to the structural features of molecules. Below are common chemical
prefixes that wind their way into biochemical terminology (click 1).
Acyl: implying a fatty acid attached
Alpha: implying the first carbon from a carboxyl group
Aceto: implying an acetyl group
Amido: implying an amide group in the molecule
Beta: implying the second carbon from a carbonyl group
Glyco: implying a carbohydrate appendage
Methyl or meth: implying a CH3- group:
As you study your lessons
pay close attention to the
names and see if you can
determine why the molecule
is so-called. This is one way
to prepare for exams where
the question may assume that
you are familiar with the
compound being asked.
Phospho: Implying a phosphate group
Thio: Implying a sulfur group
Mono, di, tri, oligo, poly: implying one, two, three, several, many units
Tetra, penta, hexa, hepta, octa: implying 4, 5, 6 and 7 units
Homo: implying sameness in two or more components
Hetero: implying a difference in two or more components
Test and Extend Your Knowledge of Terminology
Q. What structural features would you expect to see in the amino acid “methionine”?
A: The name implies the presence of a sulfur atom (thio) and a methyl group
Q: What structural difference exists between a “heteropolysaccharide” and a
“homopolysaccharide?
A: Hetero would be expected to be composed of more than one type of sugar unit; homo
would have all units the same.
Q: Hydrolysis is a term in biochemistry that is used to signify the breaking down of a
compound by inserting a water molecule across the bonding atoms. What would be the
hydrolysis products of a polysaccharide? A protein? DNA? RNA? Triacylglycerol?
A: Polysaccharide = monosaccharides. Protein = amino acids. DNA = deoxyribose,
phosphate, and a base. Triacylglycerol = glycerol and 3 fatty acids.
Q: Assume you have a protein that is classified as a “homopolymer”. The hydrolysis of all
the peptide bonds in this protein would yield how many types of amino acids.
A: One
Q: Can one observe the principle of modular design in a simple molecule as opposed to a
complex structure like a protein?
A: Yes. Cholesterol is a simple molecule in that it cannot be separated from or hydrolyzed
into smaller molecules. Cholesterol, however, is built entirely from isoprene units that
polymerize during the synthesis process.