BIOCHEMISTRY:
THE CHEMISTRY OF LIFE
INTRODUCTION
 Cells can be thought of as “bags” of
chemicals. Even the bags themselves are
composed of chemicals.
 Most simple procaryotic cells consist of very
large molecules (macromolecules), such as
deoxyribonucleic acid (DNA), ribonucleic
acid (RNA), proteins, lipids, and
polysaccharides, as well as many
combinations of these macromolecules that
combine to make up structures like
capsules, cell walls, cell membranes, and
flagella
 The macromolecules and building blocks
found in cells are collectively referred to as
biological molecules. The building blocks
can be broken down into even smaller
molecules such as water, carbon dioxide,
ammonia, sulfides, and phosphates, which
in turn can be broken down into atoms of
carbon (C), hydrogen (H), oxygen (O),
nitrogen (N), sulfur (S), phosphorus (P)
 Cells contain many large biological
molecules, known as macromolecules.
Macromolecules include DNA, RNA,
proteins, lipids, and polysaccharides.
 Organic chemistry is the study of
compounds that contain carbon
 Inorganic chemistry involves all other
chemical reactions
 Biochemistry is the chemistry of living cells.
 Everything that a cell is and does involves
biochemistry
 Biochemicals make up the structure of a
microorganism, and a multitude of
biochemical reactions take place within the
microorganism.
 The characteristics that distinguish living
organisms from inanimate objects
 Their complex and highly organized
structure
 Their ability to extract, transform and
use energy from their environment
 Their capacity for precise self-
replication and self-assembly
ORGANIC CHEMISTRY
 Organic compounds are compounds that
contain carbon, and organic chemistry is
that branch of the science of chemistry that
specializes in the study of organic
compounds.
 Organic compounds are compounds that
contain carbon. Although many organic
compounds are produced by or related to
living organisms, some are not.
 Organic chemistry is a broad and important
branch of chemistry, involving the chemistry
of fossil fuels (petroleum and coal), dyes,
drugs, paper, ink, paints, plastics, gasoline,
rubber tires, food, and clothing.
CARBON BONDS
 Carbon-carbon bond is a covalent bond
between two carbon atoms. The most
common form is the single bond: a bond
composed of two electrons, one from each
of the two atoms.
 Elements of carbon exist:
 Amorphous carbon is also known as
lampblack, gas black, channel black,
and carbon black.
 Graphite is one of the softest
materials known.
 Diamond is one of the hardest
substances known.
 Carbon atoms have a valence of four,
meaning that a carbon atom can bond to
four other atoms.
 There are three ways in which carbon
atoms can bond to each other: single bond,
double bond, and triple bond.
 Organic chemistry is sometimes defined as
the chemistry of carbon and its covalent
bonds.
 Hydrocarbons are organic compounds that
contain only carbon and hydrogen.
 BIOCHEMISTRY:
THE CHEMISTRY OF LIFE
 When atoms of other elements attach to
available bonds of carbon atoms,
compounds are formed.
CYCLIC COMPOUNDS
 Carbon atoms may link to carbon atoms to
close the chain, forming rings or cyclic
compounds.
BIOCHEMISTRY
 Biochemistry is the study of biology at the
molecular level and can, thus, be thought of
as the chemistry of life or the chemistry of
living organisms.
 Biochemistry involves the study of
biomolecules and can be thought of as both
a branch of chemistry and a branch of
biology.
CARBOHYDRATES
 Carbohydrates are biomolecules composed
of carbon, hydrogen, and oxygen, in the
ratio of 1:2:1, or simply CH2O.
MONOSACCHARIDES
 The simplest carbohydrates are sugars, and
the smallest sugars (or simple sugars) are
called monosaccharides
 Glucose, the main source of energy for
body cells, is found in most sweet fruits and
in blood.
DISACCHARIDES
 Disaccharides (di meaning “two”) are
double-ringed sugars that result from the
combination of two monosaccharides.
 Sucrose, lactose, and maltose are
examples of disaccharides
 The synthesis of a disaccharide from two
monosaccharides by removal of a water
molecule is called a dehydration synthesis
reaction.
 The bond holding the two monosaccharides
together is called a glycosidic bond; it is a
type of covalent bond.
 Disaccharides react with water in a process
called a hydrolysis reaction, which causes
them to break down into two
monosaccharides.
 Bacterial cell walls contain peptidoglycan, a
complex macromolecule consisting of a
repeating disaccharide, attached by
proteins.
 Carbohydrates composed of three
monosaccharides are called trisaccharides.
 Those composed of four are called
tetrasaccharides.
 Those composed of five are called
pentasaccharides and so on, until one
comes to polysaccharides.
 Polysaccharides can be defined as
carbohydrates that contain many
monosaccharides.
 Polysaccharides, such as glycogen, starch,
and cellulose, are examples of polymers—
molecules consisting of many similar
subunits. In the case of polysaccharides,
the repeating subunits are
monosaccharides.
 Bacterial cell walls contain peptidoglycan,
algal cell walls contain cellulose, and fungal
cell walls contain chitin. Peptidoglycan,
cellulose, and chitin are examples of
polysaccharides.
LIPIDS
 BIOCHEMISTRY:
THE CHEMISTRY OF LIFE
 Lipids constitute an important class of
biomolecules.
FATTY ACIDS
 Fatty acids can be thought of as the building
blocks of lipids
 Fatty acids are long-chain carboxylic acids
that are insoluble in water.
 Saturated fatty acids contain only single
bonds between the carbon atoms.
 Monounsaturated fatty acids (such as those
found in butter, olives, and peanuts) have
one double bond in the carbon chain.
 Polyunsaturated fatty acids (such as those
found in soybeans, safflowers, sunflowers,
and corn) contain two or more double
bonds.
 Waxes, fats, oils, phospholipids, glycolipids,
steroids, prostaglandins, and leukotrienes
are all examples of lipids.
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
 Phospholipids contain glycerol, fatty acids, a
phosphate group, and an alcohol.
 Cell membranes consist of a lipid bilayer,
composed of two rows of phospholipids,
arranged tail-to-tail.
 There are two types
 glycerophospholipids (also called
phosphoglycerides)
 sphingolipids.
 Glycerophospholipids are the most
abundant lipids in cell membranes.
 When present in the human bloodstream,
lipids found in the cell walls of Gram-
negative bacteria can cause serious
physiologic conditions in humans, such as
fever and shock.
GLYCOLIPIDS
 Glycolipids are abundant in the brain and in
the myelin sheaths of nerves.
 A person’s blood group (A, B, AB, or O) is
determined by the glycolipids that are
present on the surface of that person’s red
blood cells.
STEROIDS
 Steroids are rather complex, four-ringed
structures.
 Cholesterol is a component of cell
membranes, myelin sheath, and brain and
nerve tissue.
 Steroid hormones include male sex
hormones (testosterone and androsterone)
and female sex hormones (estrogens such
as estradiol and progesterone).
PROSTAGLANDIANS AND
LEUKOTRIENES
 Prostaglandins and leukotrienes are derived
from a fatty acid called arachidonic acid.
 They act as mediators of hormones, lower
or raise blood pressure, cause
inflammation, and induce fever.
 Leukotrienes can produce long-lasting
muscle contractions, especially in the lungs,
where they cause asthma-like attacks
PROTEINS
 BIOCHEMISTRY:
THE CHEMISTRY OF LIFE
 Proteins are among the most essential
chemicals in all living cells, referred to by
some scientists as “the substance of life.”
 Proteins contain carbon, hydrogen, oxygen,
nitrogen, and sometimes sulfur.
 All proteins are polymers of amino acids;
however, they vary widely in the number of
amino acids present and in the sequence of
amino acids as well as their size,
configuration, and functions.
AMINO ACID STRUCTURE
 A total of 23 different amino acids have
been found in proteins, 20 primary or
naturally occurring amino acids plus 3
secondary amino acids (derived from
primary amino acids).
 Proteins are polymers that are composed of
amino acids (i.e., amino acids are the
building blocks of proteins).
 The term essential amino acids is
somewhat misleading, however, in view of
the fact that all of the amino acids are
necessary for protein synthesis.
PROTEIN STRUCTURE
 When water is removed, by dehydration
synthesis, amino acids become linked
together by a covalent bond, referred to as
a peptide bond
 A dipeptide is formed by bonding two amino
acids, whereas the bonding of three amino
acids forms a tripeptide.
 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.
ENZYMES
 Enzymes are protein molecules produced
by living cells as “instructed” by genes on
the chromosomes.
 Enzymes are proteins that function as
biological catalysts, meaning that they
catalyze (speed up) metabolic reactions.
 A catalyst is defined as an agent that
speeds up a chemical reaction without
being consumed in the process.
 Enzymes are usually named by adding the
ending “-ase” to the word, indicating the
compound or types of compounds on which
an enzyme acts or exerts its effect.
NUCLEIC ACIDS
FUNCTIONS
 Nucleic acids—DNA and RNA—comprise
the fourth major group of biomolecules in
living cells. In addition to the elements C, H,
O, and N, DNA and RNA also contain P
(phosphorus)
 Nucleic acids play extremely important roles
in a cell; they are critical to the proper
functioning of a cell. DNA is the “hereditary
molecule”—the molecule that contains the
genes and genetic code.
STRUCTURE
 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; they contain a nitrogenous
base, deoxyribose, and a phosphate group.
The building blocks of RNA are called RNA
nucleotides
 The three types of RNA in a cell are
messenger RNA (mRNA), ribosomal RNA
(rRNA), and transfer RNA (tRNA).
 BIOCHEMISTRY:
THE CHEMISTRY OF LIFE
 The nitrogenous bases adenine, guanine,
and cytosine are found in both DNA and
RNA. However, thymine is found only in
DNA, and uracil is found only in RNA.
DNA STRUCTURE
 Within a double-stranded DNA molecule, A
in one strand always bonds with T in the
complimentary strand, and G in one strand
always bonds with C in the complimentary
strand. A–T and G–C are known as base
pairs.
DNA REPLICATION
 When a cell is preparing to divide, all the
DNA molecules in the chromosomes of that
cell must duplicate, thereby ensuring that
the same genetic information is passed on
to both daughter cells.
 The most important enzyme taking part in
DNA replication is DNA polymerase (DNA-
dependent DNA polymerase).
 Francis Crick provided this method of
visualizing what happens during DNA
replication.
 First, remember that DNA is a
double-stranded molecule. Think of
it as a hand within a glove. When the
hand is removed from the glove, a
new glove is formed around the
hand. Simultaneously, a new hand is
formed within the glove. What you
end up with are two gloved hands,
each of which is identical to the
original gloved hand
 The most important enzyme required for
DNA replication is DNA polymerase (also
known as DNAdependent DNA
polymerase).
GENE EXPRESSION
 gene is a particular segment of a DNA
molecule or chromosome.
 A gene contains the instructions (the
“recipe” or “blueprint”) that will enable a cell
to make what is known as a gene product
(in some cases, more than one gene
product).
 The genetic code contains four “letters” (the
letters that stand for the four nitrogenous
bases found in DNA): “A” for adenine, “G”
for guanine, “C” for cytosine, and “T” for
thymine.
 The Central Dogma. It was Francis Crick
who, in 1957, proposed what is referred to
as the Central Dogma to explain the flow of
genetic information within a cell:
 The genetic information contained in
one gene of a DNA molecule is used
to make one molecule of mRNA by a
process known as transcription
 The genetic information in that
mRNA molecule is then used to
make one protein by a process
known as translation.
 Genes that are expressed always are called
constitutive genes, whereas those that are
expressed only when the gene products are
needed are called inducible genes.
 Transcription. When a cell is stimulated (by
need) to produce a particular protein, the
DNA of the appropriate gene is activated to
unwind temporarily from its helical
configuration.
 The process by which the information in a
single gene is used to make an mRNA
molecule is known as transcription.
 The primary enzyme involved in
transcription is called RNA polymerase
(DNA-dependent RNA polymerase).
 In eucaryotes, transcription occurs within
the nucleus. The newly formed mRNA
molecules then travel through the pores of
the nuclear membrane, out into the
cytoplasm, where they take up positions on
the protein “assembly line.”
 BIOCHEMISTRY:
THE CHEMISTRY OF LIFE
 In procaryotes, transcription occurs in the
cytoplasm. Ribosomes attach to the mRNA
molecules as they are being transcribed at the
DNA; thus, transcription and translation
(protein synthesis) may occur simultaneously.
 Translation (Protein Synthesis). The base
sequence of the mRNA molecule is read or
interpreted in groups of three bases, called
codons
 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.
 Codons are located on mRNA molecules,
whereas anticodons are located on tRNA
molecules.
 The process by which the genetic information
within an mRNA molecule is used to make a
specific protein is called translation. Translation
occurs at a ribosome.