Download Organic Chemistry

Burton's Microbiology
for the Health Sciences
Section III.
Chemical and Genetic Aspects of
Microorganisms
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Burton's Microbiology
for the Health Sciences
Chapter 6. Biochemistry: The Chemistry
of Life
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Chapter 6 Outline
• Introduction
• Organic Chemistry
– Carbon Bonds
– Cyclic Compounds
• Biochemistry
– Carbohydrates
– Lipids
– Proteins
– Nucleic Acids
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Introduction
• A microbe can be thought of as a “bag” of chemicals that
interact with each other in a variety of ways; even the
bag itself is composed of chemicals.
• Everything a microorganism is and does is related to
chemistry.
• Organic chemistry is the study of compounds that
contain carbon.
• Inorganic chemistry involves all other chemical
reactions.
• Biochemistry is the chemistry of living cells.
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Organic Chemistry
• Organic compounds contain carbon.
• Organic chemistry is the branch of science that studies
organic compounds.
• Organic compounds are not necessarily related to
living organisms; although some organic compounds
are associated with living organisms, many are not.
• Organic chemistry involves the following chemical
substances. Which ones are not directly related to living
things? fossil fuels, dyes, drugs, paper, ink, paints,
plastics, gasoline, rubber tires, food, and clothing.
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Organic Chemistry
Carbon & Carbon Bonds
• All elements are listed on the periodic table.
• The atomic number indicates the number of protons. This
equals the number of electrons.
• The elemental symbol is 1, 2, or 3 letters, with the first letter
capitalized.
• The atomic weight is the number of protons plus the number of
neutrons
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Organic Chemistry
Carbon Bonds
• Carbon atoms have a valence of 4, meaning that they can
bond to four other atoms.
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Organic Chemistry
Carbon Bonds
• There are 3 ways in which carbon atoms can bond to each
other: single bond, double bond, and triple bond.
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Organic Chemistry
Carbon Bonds
• A covalent bond is one in which a pair of electrons is shared.
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Organic Chemistry
Carbon Bonds
• When atoms of other elements attach to available carbon
bonds, compounds are formed.
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Organic Chemistry
Carbon Bonds
• A series of carbon atoms bonded together is referred to as a
chain.
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Organic Chemistry
Carbon Bonds, cont.
• If only hydrogen atoms are bonded carbon bonds,
hydrocarbons are formed.
• Therefore, a hydrocarbon is an organic molecule that
contains only carbon and hydrogen atoms; some
examples of simple hydrocarbons are shown here:
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Organic Chemistry
Cyclic Compounds
• When carbon atoms link to other carbon atoms to close a
chain, they form rings or cyclic compounds.
• Benzene is a cyclic compound with six carbons and six
hydrogens.
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Biochemistry
• Biochemistry is the study of biology at the molecular
level; it is the chemistry of living organisms.
• Biochemistry involves biomolecules present within living
organisms; biomolecules are usually large molecules
called macromolecules.
• Macromolecules include
• carbohydrates, lipids, proteins, and nucleic acids.
• Other examples: vitamins, enzymes, hormones, and
energy-carrying molecules such as adenosine
triphosphate (ATP).
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Biochemistry, cont.
• Humans obtain their nutrients from the foods they eat.
– Carbohydrates, fats, nucleic acids, and proteins
contained in the foods are digested; their
components are absorbed and carried to every cell in
the body, where they are broken down and
rearranged.
• Microorganisms also absorb their essential nutrients into
the cell.
• The nutrients are then used in metabolic reactions as
sources of energy and as “building blocks” for enzymes,
structural macromolecules, and genetic materials.
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Biochemistry
Carbohydrates
• Carbohydrates are biomolecules composed of carbon,
hydrogen, and oxygen (in the ratio 1:2:1).
• Examples include:
– Glucose, fructose, sucrose, lactose, maltose, starch,
cellulose, and glycogen.
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Biochemistry
Carbohydrates
• Categories of carbohydrates include monosaccharides,
disaccharides, and polysaccharides.
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Carbohydrates
Monosaccharides
• Monosaccharides are the smallest and simplest of the
carbohydrates. Mono means one, referring to the number
of rings in the structure.
– Glucose (C6H12O6) is the most important
monosaccharide in nature; it may occur as a chain or
in alpha or beta ring configurations.
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Carbohydrates
Monosaccharides, cont.
• The main source of energy for body cells is glucose.
– The three forms of glucose are shown above.
– Glucose is carried in the blood to cells where it is oxidized
to produce energy-carrying ATP. ATP is the main energy
source used to drive most metabolic reactions.
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Carbohydrates
Disaccharides
• “Di” means 2; disaccharides are double-ringed sugars
that result from the combination of 2 monosaccharides
(with the removal of a water molecule) – this is known as
a dehydration synthesis reaction.
– Sucrose (table sugar), lactose and maltose, are
examples of disaccharides.
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Carbohydrates
Disaccharides
• Disaccharides
react with water
in a process
called a
hydrolysis
reaction
• This causes them
to break down
into 2
monosaccharides.
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The Dehydration Synthesis
and Hydrolysis of Sucrose
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Carbohydrates
Disaccharides, cont.
• Recall that peptidoglycan
is found in the cell walls
of all members of the
Domain Bacteria
• Peptidoglycan is a
repeating disaccharide
attached by proteins to
form a lattice that
surrounds and protects
the bacterial cell.
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Carbohydrates
Polysaccharides
• The definition of a polysaccharide varies from one reference
book to anothe. In this book, polysaccharides are defined as
carbohydrates that are composed of many monosaccharides.
Most contain hundreds.
– Examples: starch and glycogen
• Polysaccharides serve 2 main functions:
– Storage of energy (e.g., glycogen in animal cells; starch in
plant cells)
– Provide a “tough” molecule for structural support and
protection (e.g., bacterial capsules)
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Carbohydrates
Polysaccharides, cont.
• Polysaccharides are examples of polymers – molecules that
consist of many similar subunits.
• In the presence of the proper enzymes or acids,
polysaccharides may be hydrolyzed or broken down into
disaccharides, and then into monosaccharides.
Hydrolysis of Starch
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Carbohydrates
Polysaccharides, cont.
• Plant and algal cells have cellulose (a polysaccharide) cell
walls to provide support.
• Some protozoa, fungi, and bacteria have enzymes that
can break down cellulose.
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Lipids
• 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 most living cells.
• Lipids can be classified into the following categories:
-Waxes
-Glycolipids
-Fats and oils
-Steroids
-Phospholipids
-Prostoglandins and leukotrienes
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The general structure of
some categories of lipids.
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Lipids
Fatty Acids
• Fatty acids are the building blocks of lipids; they are
long-chain carboxylic acids that are insoluble in water.
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Lipids
Fatty Acids
• Saturated fatty acids contain 1 single bond between
carbon atoms; they are solid at room temperature.
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Lipids
Fatty Acids
• Monounsaturated fatty acids have 1 double bond in the
carbon chain; found in butter, olives, and peanuts.
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Lipids
Fatty Acids
• Fatty acids are the building blocks of lipids; they are
long-chain carboxylic acids that are insoluble in water.
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Lipids
Waxes
• A wax consists of a saturated fatty acid and a long-chain
alcohol.
– Examples: the wax coating on fruits; leaves; skin, fur, and
feathers of animals.
– The cell wall of Mycobacterium tuberculosis (the causative
agent of tuberculosis) contains waxes.
• These waxes protect M. tuberculosis from digestion
following phagocytosis by white blood cells.
• These waxes make M. tuberculosis difficult to stain and
de-stain; explains why M. tuberculosis is acid-fast.
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Lipids
Fats and Oils
• Fats and oils are the most common types of lipids. They are
also known as triglycerides because they are composed of
glycerol and 3 fatty acids.
• Fats are solid at room temperature.
• Oils are liquids at room temperature.
• Most fats come from animal sources (e.g, beef); most oils
come from plant sources (e.g., olive oil).
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Lipids
Phospholipids
• Phospholipids contain glycerol, fatty acids, a phosphate
group, and an alcohol. There are 2 types:
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The Lipid Bilayer Structure
of Cell Membranes
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Lipids
Phospholipids, cont.
• The outer membrane of Gram-negative bacterial cell
walls contains lipoproteins and lipopolysaccharide (LPS).
– LPS consists of a lipid and a polysaccharide portion.
• The cell walls of Gram-positive organisms do not contain
LPS.
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Proteins
• Proteins are the most essential chemicals in all living
cells; considered “the substance of life.”
• Some proteins are the structural components of
membranes, cells and tissues; others are enzymes and
hormones.
• All proteins are polymers of amino acids.
• All proteins contain carbon, hydrogen, oxygen, and
nitrogen (and sometimes sulfur).
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Proteins
Amino Acids
• Amino acids contain carbon, hydrogen, oxygen and nitrogen;
some also have sulfur in the molecule.
• The basic structure of an amino acid is shown here:
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The Formation of a Dipeptide.
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Proteins
Enzymes
• Enzymes are protein molecules produced by living cells.
They are known as biological catalysts - that is, they
catalyze metabolic reactions.
– A catalyst is an agent that speeds up a chemical
reaction without being consumed in the reaction.
• Almost every chemical reaction in a cell requires a
specific enzyme.
• Some protein molecules function as enzymes by
themselves; other proteins, called apoenzymes, only
function when linked with a nonprotein cofactor such as
Ca2+, Fe 2+, Mg 2+, Cu 2+ or a coenzyme.
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Proteins
Enzymes
• Some apoenzymes require vitamin-type compounds
called coenzymes; examples are vitamin C, flavinadenine dinucleotide (FAD), and nicotinamide-adenine
dinucleotide (NAD).
• The combination of an apoenzyme plus a cofactor is
called a holoenzyme (i.e., a whole enzyme).
• Enzymes are usually named by adding the ending “- ase”
to the word. Hemolysins and lysozyme are examples of
enzymes not ending in “ase.”
• The specific molecule on which an enzyme acts is
referred to as that enzyme’s substrate.
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Nucleic Acids
Function
• DNA is the “hereditary
molecule” – the molecule
that contains the genes
and genetic code.
– Information in DNA
must flow to the rest
of the cell for the cell
to function properly
– the flow is
accomplished by
RNA.
• RNA molecules
participate in the
conversion of the genetic
code into proteins and
other gene products.
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Nucleic Acids
Structure
• In addition to the
elements C, H, O, and N,
DNA and RNA also contain
phosphorus, P.
• The building blocks of
nucleic acid polymers
(DNA and RNA) are called
nucleotides.
– Nucleotides are more
complex monomers
than amino acids.
• DNA contains dexoyribose
as its pentose, whereas
RNA contains ribose as it
pentose.
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DNA Structure
• For a double-stranded DNA molecule to form, the
nitrogenous bases on the two separate strands must
bond together.
– A always bonds with T via 2 hydrogen bonds.
– G always bonds with C via 3 hydrogen bonds.
– A-T and G-C are known as “base pairs.”
• The bonding forces of the double-stranded polymer cause
it to assume the shape of a double alpha-helix, similar to
a right-handed spiral staircase.
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Base pairs that occur in doublestranded DNA molecules.
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Double-stranded DNA
molecule, also known
as a double helix.
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DNA Replication
• When a cell is preparing to divide, all
DNA molecules in the chromosomes of
the cell must duplicate, to ensuring that
the same genetic information is passed
on to both daughter cells.
– This is called DNA replication.
– http://youtu.be/hfZ8o9D1tus
• DNA replication occurs by separation of
the 2 DNA strands and the building of
complementary strands by the addition
of the correct DNA nucleotides.
• DNA polymerase is the most important
enzyme required for DNA replication.
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Semiconservative
DNA Replication.
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DNA Replication
Gene Expression
• A gene is a particular
segment of a DNA molecule
or chromosome.
– A gene contains the
blueprint that will enable
a cell to make what is
known as a gene product.
• It is the sequence of the four
nitrogenous bases of DNA
(i.e., A, G, C, and T) that
spell out the instructions for a
particular gene product.
• Most genes code for proteins
• Some code for rRNA and
tRNA.
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DNA Replication
Gene Expression, cont.
• The Central Dogma explains the flow of genetic
information within a cell (proposed by Francis Crick in
1957).
– DNA
mRNA
protein.
– Also known as “one gene – one protein hypothesis.”
– One gene of a DNA molecule is used to make one
molecule of mRNA by a process known as
transcription.
– The genetic information in the mRNA is then used to
make one protein by a process known as translation.
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DNA Replication
Gene Expression, cont.
• The process by which the genetic code within the DNA
molecule is transcribed to produce an mRNA molecule is
called transcription.
– The primary enzyme involved is RNA polymerase.
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DNA Replication
Gene Expression, cont.
• In eucaryotes, transcription occurs within the nucleus; the newly formed
mRNA molecules then travel through the pores of the nuclear membrane
into the cytoplasm, where they are used to produce proteins.
• http://youtu.be/983lhh20rGY
• http://youtu.be/41_Ne5mS2ls
• In procaryotes, transcription occurs in the cytoplasm; ribosomes attach to
the mRNA molecules as they are being transcribed at the DNA – thus both
transcription and translation may occur simultaneously.
• Viral gene expression
• Reverse transcriptase (enzyme that does reverse transcription)
• http://youtu.be/BY35naVuWgY
• Viral replication
• http://youtu.be/StYOdR8hOUU
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DNA Replication
Gene Expression, cont.
• The process of translating the message carried by mRNA,
whereby particular tRNAs bring amino acids to be bound
together in the proper sequence to make a protein, is
called translation.
• The base sequence of the mRNA molecule is read in
groups of 3 bases, called codons.
• The 3-base sequence codon can be read by a
complementary 3-base sequence (the anticodon) on a
tRNA molecule.
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Chart to illustrate the sequence of 3 bases (GGC) in the DNA
template that codes for a particular codon (CCG) in mRNA, which
in turn, attracts a particular anticodon (GGC) on the tRNA
carrying an amino acid (proline).
DNA
mRNA
tRNA
Amino
Template
(Codon)
(Anticodon)
Acid
G
C
G
G
C
G
C
G
C
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Proline
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Translation (protein synthesis)
http://youtu.be/-zb6r1MMTkc
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