3636 Chapter 06

Burton's Microbiology for the Health SciencesSection III. Chemical and Genetic Aspects of Microorganisms

Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Burton's Microbiology for the Health SciencesChapter 6. Biochemistry: The Chemistry of Life


Chapter 6 Outline Introduction Organic Chemistry Carbon Bonds Cyclic Compounds

Biochemistry Carbohydrates Lipids

Proteins Nucleic AcidsCopyright 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.


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 fossil fuels, dyes, drugs, paper, ink, paints, plastics, gasoline, rubber tires, food, and clothing.


Organic ChemistryCarbon Bonds Carbon atoms have a valence of 4, meaning that they can bond to four other atoms. There are 3 ways in which carbon atoms can bond to each other: single bond, double bond, and triple bond. A covalent bond is one in which a pair of electrons is shared.

When atoms of other elements attach to available carbon bonds, compounds are formed. 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 to the available 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:


Organic ChemistryCyclic 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.

The benzene ring.


Biochemistry Biochemistry is the study of biology at the molecular level; it is the chemistry of living organisms. Biochemistry involves the study of biomolecules present within living organisms; biomolecules in living organisms 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 by various means. 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

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. Categories of carbohydrates include monosaccharides, disaccharides, and polysaccharides.


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. Monosaccharides contain from 2 to 9 carbon atoms most contain 5 to 6. A 3 carbon monosaccharide is called a triose; a 4 carbon one is a tetrose; a 5 carbon one is a pentose; a 6 carbon one is a hexose; a 7 carbon is a heptose; and so on.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

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

CarbohydratesDisaccharides 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. Disaccharides react with water in a process called a hydrolysis reaction, which causes them to break down into 2 monosaccharides.


The Dehydration Synthesis and Hydrolysis of Sucrose


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. Carbohydrates composed of 3 monosaccharides are called trisaccharides; those composed of 4 are called tetrasaccharides; those composed of 5 are called pentasaccharides, and so on until we come to polysaccharides.


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)


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


Carbohydrates

Polysaccharides, cont. Some bacteria produce polysaccharide capsules for protection from phagocytes. 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. When polysaccharides combine with other chemical groups (amines, lipids and amino acids), complex macromolecules are formed. For example, chitin, the main component of the hard outer covering of insects, spiders, and crabs and found in the cell walls of fungi.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

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 -Fats and oils -Phospholipids -Glycolipids -Steroids -Prostoglandins and leukotrienesCopyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

The general structure of some categories of lipids.


Lipids

Fatty Acids Fatty acids are the building blocks of lipids; they are long-chain carboxylic acids that are insoluble in water. Saturated fatty acids contain 1 single bond between carbon atoms; they are solid at room temperature. Monounsaturated fatty acids have 1 double bond in the carbon chain; found in butter, olives, and peanuts.

Polyunsaturated fatty acids contain 2 or more double bonds; found in soybeans, safflowers, and corn. Essential fatty acids cannot be synthesized in the human body and must be provided in the diet.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 acidfast.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. Most fats come from animal sources (e.g, beef); most oils come from plant sources (e.g., olive oil).


Lipids

Phospholipids Phospholipids contain glycerol, fatty acids, a phosphate group, and an alcohol. There are 2 types: Glycerophospholipids (also known as phosphoglycerides) Sphingolipids Glycerophospholipids are the most abundant lipids in cell membranes. A cell membrane is a lipid bilayer, consisting of 2 rows of phospholipids, arranged tail-to-tail.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

The Lipid Bilayer Structure of Cell Membranes


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. Lecithins and cephalins are glycerophospholipids found in brain and nerve tissues, as well as egg yolks. Sphingolipids are phospholipids that contain sphingosine rather than glycerol. Sphingolipids are found in brain and nerve tissues. Sphingomyelin is one of the most abundant sphingolipids, and makes up the myelin sheath that coats nerve cells.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Lipids

Glycolipids, Steroids, Prostaglandins, and Leukotrienes Glycolipids are abundant in the brain and in the myelin sheath of nerves. Steroids are complex, 4-ringed structures; examples are cholesterol, bile salts, steroid hormones, and fat-soluble vitamins (A, D, E and K). Prostaglandins and leukotrienes are derived from a fatty acid called arachidonic acid. Both have a wide variety of effects on body chemistry such as controlling blood pressure or hormones; leukotrienes can produce long-lasting muscle contractions.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).


Proteins

Amino Acids Amino acids contain carbon, hydrogen, oxygen and nitrogen; some also have sulfur in the molecule. Humans can synthesize certain amino acids, but not others. The thousands of different proteins in the human body are composed of a wide variety of amino acids in various quantities and arrangements. The basic structure of an amino acid is shown here:

Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Proteins

Protein Structure Amino acids are linked together to form proteins via covalent bonds referred to as peptide bonds; there are dipeptides, tripeptides, and polypeptides.

The linear sequence of amino acids is referred to as the primary protein structure. The twisting or coiling of the chain of amino acids is referred to as the secondary protein structure. The folding or entwining of the chain is the tertiary protein structure. The bonding of 2 or more polypeptide chains is known as the quaternary protein structure.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

The Formation of a Dipeptide.


Protein StructureA. Primary Structure B. Secondary Structure C. Tertiary (globular) Structure D. Quaternary StructureCopyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

ProteinsEnzymes Enzymes are specialized 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

ProteinsEnzymes 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 enzymes substrate.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Nucleic AcidsFunction DNA and RNA comprise the 4th major group of biomolecules in living cells. DNA and RNA are critical to proper functioning of a cell. 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 AcidsStructure In addition to the elements C, H, O, and N, DNA and RNA also contain phosphorus, P.

The building blocks of nucleic acid polymers are called nucleotides. Nucleotides are more complex monomers than amino acids. The building blocks of DNA are called DNA nucleotides. The building blocks of RNA are called RNA nucleotides.

DNA contains dexoyribose as its pentose, whereas RNA contains ribose as it pentose.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Two nucleotides, each consisting of a nitrogenous base (A or T), a five-carbon sugar (S), and a phosphate group (P)


Nucleic Acids

Structure, cont. There are 3 types of RNA, named for their function: Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA) The 5 nitrogenous bases in nucleic acids are: adenine (A), guanine (G), thymine (T), cytosine (C) and uracil (U). A and G are purines; T, C and U are pyrimidines. Thymine is found in DNA but not in RNA. Uracil is found in RNA, but not in DNA. The other 3 bases are found in both.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

The Pyrimidines and Purines Found in DNA and RNA.


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.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

Base pairs that occur in doublestranded DNA molecules.


A section of a nucleic acid polymer.


Double-stranded DNA molecule, also known as a double helix.


DNA Replication When a cell is preparing to divide, all DNA molecules in the chromosomes of the cell must duplicate, thereby ensuring that the same genetic information is passed on to both daughter cells. This is called DNA replication. 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 (also known as DNA-dependent DNA polymerase) is the most important enzyme required for DNA replication.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

DNA Replication.


DNA ReplicationGene 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. Although most genes code for proteins, some code for rRNA and tRNA. Some genes code for more than one gene product.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

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. All genes on a chromosome are not being expressed at any given time. It would not be logical for a cell to produce a particular enzyme if it was not needed. Genes that are only expressed when the gene products are needed are called inducible genes.

Genes that are expressed at all times are called constitutive genes. 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.Copyright 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

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. 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.


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.


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 Template

mRNA (Codon)

tRNA (Anticodon)

Amino Acid

GG C

CC G

GG C Proline


Translation (protein synthesis).


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3636 Chapter 06