CHAPTER 6

THE BIOCHEMICAL
BASIS OF LIFE

ORGANIC CHEMISTRY Organic compounds

are compounds
that contain carbon.
 Organic chemistry is a broad and important branch of Although many organic compounds
chemistry, involving the chemistry of fossil fuels (petroleum are produced by or related to living
and coal), dyes, drugs, paper, ink, paints, plastics, gasoline, organisms, some
rubber tires, food, and clothing. are not.
Organic chemistry is sometimes defined  Organic compounds are compounds that contain carbon,
as the chemistry of carbon and its And organic chemistry is that branch of the science of chemistry
covalent bonds.
that specializes in the study of organic compounds.

CARBON BONDS

o is the primary requisite for all living systems.

The element carbon exists in three forms or allotropes:

o Amorphous carbon - It is the black soot that is formed when a material

containing carbon is burned with insufficient oxygen for it to burn completely.
o Graphite - It is primarily used as a lubricant. although in a form called coke, is used in
the production of steel.
o Diamond - is one of the hardest substances known. Carbon atoms have a valence
of 4; that is, a carbon atom can bond
There are three ways in which carbon atoms can bond to four other atoms.
to each other: single bond, double bond, and triple bond.
CYCLIC COMPOUNDS
 Carbon atoms may link to carbon atoms to close the chain,
funning rings or cyclic compounds.

BIOCHEMISTRY BIOMOLECULES
are usually large
 is the study of biology at the molecular level
molecules (called
and can thus be thought of as the chemistry of life or the
chemistry of living organisms. macromolecules) and
include
 Biochemistry involves the study of the biomolecules that are carbohydrates, lipids,
present within living organisms. proteins, and nucleic
acids

CARBOHYDRATES

 Carbohydrates are biomolecules composed of carbon,

hydrogen, and oxygen in the ratio of 1:2:1.
 Glucose, fructose, sucrose, lactose, maltose, starch, cellulose, and glycogen
are all examples of carbohydrates.

 MONOSACCHARIDES
-The simplest carbohydrates are sugars, and the smallest sugar (or simple sugars)
are called monosaccharides (Greek mono meaning "one"; saccharin meaning "sugar").

 DISACCHARIDES

-are double-ringed sugars that result from the combination of two monosaccharides.

Disaccharides react with water in a process called a hydrolysis reaction, which causes them to
break down into two monosaccharides:
disaccharide + H20 ~ two monosaccharides
sucrose + H20 ~ glucose + fructose
lactose+ H20 ~glucose+ galactose
maltose + H20 ~ glucose + glucose

 POLYSACCHARIDES
-Poly means "many," and in reality; most polysaccharides contain many
monosaccharides-up to hundreds or even thousands of monosaccharides.
-Polysaccharides can be defined as carbohydrates that
contain many monosaccharides. Polysaccharides serve two main functions.

- One is to store energy that can be used when the

external food supply is low.
- The other function of polysaccharides is
to provide a "tough" molecule for structural support and
protection.
LIPIDS
 Lipids constitute an important class of biomolecules.
 Most lipids are insoluble in water but soluble in fat solvents, such
as ether, chloroform, and benzene.
 Lipids are essential constituents of almost all living cells.

 FATTY ACID
- Fatty acids can be thought of as the building blocks of lipids.
- Fatty acids are long-chain carboxylic acids that are insoluble in water.

o FOUR CATEGORIES OF FATTY ACID;

Saturated fatty acid contains only single bonds between
the carbon atoms. The terms saturated,
Monounsaturated fatty acids (such as those found in butter, monounsaturated,
olives, and peanuts) have one double bond in the carbon chain. polyunsaturated
Polyunsaturated fatty acids (such as those found in soybeans, fatty acids, and trans fats are
safflowers, sunflowers, and corn) contain two or more double bonds. often heard in discussions
about human diet.
Trans fats are manufactured by the artificial addition of hydrogen
atoms to unsaturated fats; the process is known as hydrogenation.

Lipids can be classified into the following categories;

Waxes
A wax consists of a saturated fatty acid and a long-chain alcohol.
The waxes that are present in the cell walls of Mycobacterium tuberculosis (the
causative agent of tuberculosis) are responsible for several
interesting characteristics of this bacterium.

Fats and Oils

Fats and oils are the most common types of lipids. Fats and oils are also known as triglycerides
because they are composed of glycerol (a three-carbon alcohol) and three
fatty acids.
Phospholipids There are two types:
Phospholipids contain glycerol, fatty acids, a phosphate glycerophospholipids
group, and an alcohol. (Also called phosphoglycerates) and
sphingolipids. Glycerophospholipids
are the most abundant lipids in cell
membranes. The basic structure of a
cell membrane
is a lipid bilayer, consisting of two
rows of phospholipids,
arranged tail to tail.

Sphingolipids are Glycolipid

phospholipids that Glycolipids are abundant in the brain and myelin sheaths
contain an 18-carbon of nerves. Some glycolipids contain glycerol plus two fatties
alcohol called acids and a monosaccharide.
sphingosine rather than
glycerol. Sphingolipids
are found in the brain
and nerve tissues.

Steroids
Steroids are rather complex, four-ringed structures. Cholesterol is a component
Steroids include cholesterol, bile salts, fat -soluble vitamins, of cell
and steroid hormones. membranes, myelin sheath,
and brain and nerve tissue.
 They act as mediators of Prostaglandins and Leukotrienes
hormones, lower or raise - Prostaglandins and leukotrienes are derived from a
blood pressure, cause fatty acid called arachidonic acid Both have a wide variety
inflammation, and induce
fever. Leukotrienes are
of effects on body chemistry.
produced in - Leukotrienes can produce long-lasting
leukocytes (for which muscle contractions, especially in the lungs, where they
they are named), but also cause asthma-like attacks.
occur in other tissues.
PROTEINS
The complete collection of
 Proteins are among the most essential chemicals in all living proteins
cells, referred to by some scientists as "the substance of life." within a given cell is known as
that cell's proteome. Studies
 Proteins contain carbon, hydrogen,
performed to explore the
oxygen, nitrogen, and
structure and activities of
sometimes sulfur.
proteins are called proteomics.

AMINO ACID STRUCTURES

 A total of 2 3 different amino
~Kids have been found in
proteins-20 primary or naturally occurring
amino acids plus 3 secondary amino acids
(derived from primary amino acids).
 Each amino acid is composed of carbon, hydrogen, oxygen, and nitrogen; three of the
amino acids also have sulfur atoms in the molecule.

NAMES OF AMINO ACID Proteins are

polymers
composed of
amino acids (i.e.,
amino acids are the
building blocks of
proteins).
 The monosaccharides in
carbohydrates are joined
together by glycosidic bonds.
The amino acids in proteins are
joined
together by peptide bonds.
Glycosidic bonds and peptide
bonds are examples
of covalent bonds.
o
PROTEIN STRUCTRES
When water is removed, by dehydration synthesis, amino
acids become linked together by a covalent bond,
referred to as a peptide bond.
When two or more polypeptide chains are bonded
together by hydrogen and disulfide bonds, the resulting
three-dimensional structure is referred to as
a quaternary protein structures.

A dipeptide is formed by bonding two amino acids, whereas the bonding of

amino acids forms a tripeptide. A chain (polymer) consisting of more than
three amino acids is referred to as a polypeptide.
ENZYMES
 Enzymes are protein molecules produced by living cells Examples of Enzymes
as "instructed" by genes on the chromosomes. Catalase Lysozyme
 Enzymes are referred to as biologic catalysts-biologic molecules Coagulase Oxidase
that catalyze metabolic reactions. DNA polymerase Peptidases
DNAse Proteases
 Enzymes are usually named by adding the ending " -ase " to the
Hemolysins RNA polymerase
word, indicating the compound or types of compounds on which an Lipases RNAse
enzyme acts or exerts its effect.

NUCLEUIC ACID
o FUNCTION
- Nucleic acids-DNA and RNA-comprise the fourth
major group of biomolecules in living cells. Nucleic acids contain
Nucleic acids play extremely important roles in a cell;
C, H, 0, N, and P.
 DNA makes up the major portion of chromosomes.
 RNA molecules participate in the conversion of the genetic
code into proteins and other gene products.

o STRUCTURES
 The building blocks of nucleic acids are called
nucleotides, each of which contains three components: a nitrogenous
base, a pentose, and a phosphate group.
 The building blocks of DNA are called DNA
nucleotides, whereas the building blocks of RNA are called RNA nucleotides.
The four types of are two kinds of nucleic acids in RNA in a cell are cells:

 mRNA
The nitrogenous bases adenine, guanine, and cytosine are found in both
 rRNA DNA and RNA. However, thymine is found only in DNA, and uracil is
found only in RNA.
 tRNA

 miRNA

o DNA STRUCTURE
 Within a double-stranded DNA molecule, A in one strand
always bonds with T in the complementary strand, and G in one
strand always bonds with C in the complementary strand. A-T and
G-C are known as base pairs.
 o DNA REPLICATION

 When a cell is preparing to divide, all the DNA The most important enzyme
molecules in the chromosomes of that cell must taking part
duplicate, thereby ensuring that the same genetic in DNA replication
information is passed on to both daughter cells. DNA polymerase
 It occurs by separation of the DNA strands and the (Also known as DNA-dependent
building of complementary strands by the addition DNA polymerase)
of the correct DNA nucleotides
 The point on the molecule were DNA replication
starts is called the replication fork.

o GENE EXPRESSION

The genetic code  A gene contains the instructions (the "recipe" or "blueprint")
contains four "letters" that will enable a cell to make what is known as a gene
(the letters that stand for production (in some cases, more than one gene product).
the four nitrogenous  gene contains the instructions for the production of
bases found in DNA): a particular protein.
"A” for adenine, "G" for
guanine, "C" for
cytosine, and "T" for
thymine.

 The Central Dogma (also known as the "one gene--one

protein hypothesis") states the following: The Central Dogma The term
1. The genetic information contained in one gene of a DNA "dogma” usually refers to a
molecule is used to make one molecule of mRNA by a basic or fundamental doctrinal
process known as transcription. point in religion or philosophy.
2. The genetic information in that mRNA molecule is then Francis Crick's use of the term
"Central Dogma" refers to the
used to make one protein by a process
most fundamental process of
molecular biology-the flow of
genetic information within a
Genes that are expressed at all times are called cell. Although originally
constitutive genes, whereas those that are expressed referred to as the one gene-one
only when the gene products are needed are called protein hypothesis, it is now
known that a particular gene
inducible inducible genes
may code for one or more
proteins.
 o TRANSCRIPTION

 This process is called transcription because the genetic

code from the DNA molecule is transcribed to produce
an mRNA molecule.
 The process by which the information in a single gene
is used to make an mRNA molecule is known as transcription.
 The three-base sequence of the codon determines which
tRNA brings its specific amino acid to the ribosome because the
tRNA molecule contains an anticodon: a three-base sequence
that is complementary to, or attracted to, the codon of the mRNA.

o TRANSLATION (PROTEIN SYNTHESIS)

o
 The three-base sequence of the codon determines
which tRNA brings its specific amino acid to the ribosome
because he tRNA molecule contains an anticodon: a three-base
sequence that is complementary to, or attracted to, the codon
of the mRNA.
 The process message carried by the mRNA, whereby particular
tRNAs bring amino acids to be bound together in the proper
sequence to make a specific protein, is called translation.

The following chart illustrates the sequence of three bases (GGC) in the DNA template
The codons that codes Codons for a particular codon (CCG) in mRNA, which, in turn, attracts
are located particular anticodon GGC) on the tRNA carrying a specific amino acid (proline).
in the
mRNA
molecule,
whereas
anticodon
is located
in tRNA
molecules.