Organic Chemistry

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Burton's Microbiology
for the Health Sciences
Section III.
Chemical and Genetic Aspects of
Microorganisms
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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:
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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).
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
The general structure of
some categories of lipids.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Lipids
Fatty Acids
• Fatty acids are the building blocks of lipids; they are
long-chain carboxylic acids that are insoluble in water.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
Lipids
Fatty Acids
• Fatty acids are the building blocks of lipids; they are
long-chain carboxylic acids that are insoluble in water.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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).
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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).
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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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Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
The Formation of a Dipeptide.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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.
Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins
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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