City College of San Francisco Microbiology 12

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Chemical Principles

( Or, why do I have to study chemistry? I thought I was taking microbiology?!)

You will soon discover that it is impossible to get through microbiology without a background in chemistry. Here's a few good reasons why:

We need an understanding of the chemical make-up of microbes, their metabolism and the chemicals they synthesize. Microbes produce a vast array of chemicals that are actually beneficial to us and the environment. Here's a few examples:

• E. coli synthesize vitamin K which is necessary factor in the blood clotting pathway.
• Various microbial fermentation products are of economic and medical value (production of foodstuffs, and medicines)
• Numerous microbes naturally synthesize antibiotics
• Cyanobacteria are important contributors to the earth's oxygen
• Microbes take part in many chemical processes that are vital for the recycling of elements in the environment

We also need to understand the chemicals and molecules which allow microbes to cause infection an disease. For example:

• Toxins are produced by various pathogens. If we understand the make-up of the toxin we can perhaps inactivate or neutralize it.
• Cell or tissue-harming enzymes
• Molecules which allow microbes to attach an/or enter cells
• Molecules and structures of microbes that are exposed to the immune system can be potential targets of vaccines

Certain metabolic pathways or molecules can be unique to microbes and can serve as selective targets for antibiotics or other antimicrobial drugs. For example:

• The peptidoglycan cell wall and its synthesis is unique to certai bacteria
• The protease enzyme of HIV is unique to the virus and can be blocked by specific inhibitors.

Microbial metabolism is being increasingly exploited by the field of genetic engineering in order to make useful products in an efficient manner.

ATOM

• Smallest unit of an element that retains the properties of that element.
• Atoms consist of three components: neutrons and protons (in the nucleus) and electrons which orbit about the nucleus in specific orbits or shells.
• The maximum number of electrons in each orbit is constant.
• The number of electrons in the outermost orbit of an atom determines its chemical characteristics
• An atom is most stable when its outermost shell is filled. An unstable atom seeks to fill its outermost shell with electrons.

COMPOUND

• Two or more atoms, either of the same or different elements, form a stable union by a chemical bond.
• Each compound has its own unique chemical characteristics
• A molecule is the smallest unit of a compound that retains its characteristics. For example, a water molecule is also a compound.
• Functional groups of organic compounds: characteristic groups of atoms responsible for most of the properties of organic compounds. These allow us to classify organic compounds into groups. For example:
  • R-OH ( alcohols)
  • R- OOH (organic acids)
  • H2N-R-COOH (amino acids)*
  • R- -SH (sulfhydryl)

* Note: many molecules contain more than one type of functional group

CHEMICAL BONDS

Associations between atoms that give them stability are called bonds. Bonds range in their degree of strength and play a key role in the formation and function of key biological molecules.

Strong bonds: are very stable Strong bonds are needed by living organisms to form STABLE STRUCTURES that are not easily damaged by heat, pressure, changes and pH.

Covalent bonds are strong bonds that form when atoms share electrons so as to FILL each other's outermost electron shells . Such bonds are highly stable and help maintain the complexity of structure of large biological molecules. For example, covalent bonds form between a sugar and a phosphate group form the backbone of the DNA molecule.

Covalent bonds are either:

• nonpolar:electrons are distributed equally between atoms
• polar: bonds are formed asymmetrically in a molecule creating an uneven distribution of shared electrons. The atoms have partial negative and positive charges. This occurs in water molecules.

Ionic bonds are still relatively strong bonds but weaker than covalent bonds. Ionic bonds form when atoms DONATE or RECEIVE electrons to or from other atoms to FILL their outermost electron orbits. Such bonds form between two ions by attraction of opposite charges rather like the poles of magnets.

• an atom that has a net charge is called an ion
• atoms that lose electrons (electron donors) are positively charged cations; e.g. Na⁺
• atoms that gain electrons (electron acceptors) are negatively charged anions; e.g. Cl^-.

Hydrophobic associations are not true bonds . When surrounded by hydrophilic molecules, such as water, hydrophobic molecules are repelled and associate with each other. For example, the lipid bilayer of cell membranes is pushed to the interior of the membrane and away from water. Similarly, hydrophobic regions of proteins will face away from hydrophilic molecules.

Hydrogen bonds

• Strong bonds are relatively inflexible, so weak bonds, such as hydrogen bonds. fulfill this purpose.
• Hydrogen bonds act as weak bridges or stabilizing attractive forces between or within molecules. Hydrogen bonds are very important in living systems, allowing flexibility while maintaining conformation.
• They exist when a hydrogen covalently bonded to an oxygen or nitrogen atom is attracted to another hydrogen or nitrogen within a polar molecule.
• Hydrogen bonds between DNA base pairs collectively stabilize the DNA double helix, but are relatively easy to disrupt when it is necessary to replicate to DNA.
• hydrogen bonds help give many proteins structure and conformation. This is particularly critical in the case of enzymes as their shape, particularly of the active site, dictates their function. If a protein is denatured by heat or chemical means it will lose its shape but more importantly it will loose its activity.

Water and its properties

• One of the most abundant inorganic compounds vital for living organisms. On average about 70% of cell content is water.
• Water is a polar molecule. Polarity gives water properties useful for living cells:
  • It acts as a solvent; many other polar molecules such as salts (dissociate into ions in water ("like dissolves like")
  • Owing to its many hydrogen bonds,water maintains a relatively constant temperature and protects cells from harmful temperature variations. 
• Water is essential for most biochemical reactions including: Dehydration synthesis (condensation). Water is released when 2 organic molecules join together to make a polymer (e.g., joining of sugars to make starch). Hydrolysis; water is added to break a bond between 2 or more molecules. This occurs in many of the decomposition reactions of digestion.

MAJOR BIOLOGICAL MOLECULES

For a review of the following important macromolecules click here

For the following discussion, the emphasis will be on relevance to microbiological systems.

CARBOHYDRATES

A diverse group of compounds including sugars and starches. The fermentation products of various sugars are very useful in bacterial identification. Sugars are components of the following structures or molecules in living systems:

• Deoxyribose in DNA
• Ribose in RNA and ATP
• Bacterial cell walls (NAG, NAM,)
• Chains of O-polysaccharides extend from the LPS coat of gram negative bacteria
• Bacterial capsules
• Receptors/markers on cell surfaces

Carbohydrate structure

All carbohydrates contain C, H, and O atoms. Hydrogen and oxygen occur in 2:1 ratio in simple sugars. For example, glucose = C₆H₁₂ O₆. General formula for CHOs is (CH₂O)n. Where n = 3 or more units.

Carbohydrates are divided into 3 groups based on size:

• monosaccharides (3-7 carbons)
• disaccharides: 2 monosaccharides bonded by dehydration synthesis.
• polysaccharides: 8 or more monosaccharides

LIPIDS

In living systems lipids are essential components of cell walls and membranes.

Types of lipids and their structure:

• Lipids are nonpolar, hydrophobic molecules.
• Simple lipids (fats) consist of a molecule of glycerol + 3 fatty acids joined by an ester linkage.
• The cell walls of Archaea have unusual lipids in that they are connected by ether linkages. These bonds contribute to the ability of many of the Archaea to live in extremely harsh environments
• Saturated fats (usually animal) have only single bonds between carbons in the fatty acid chains and contain a maximum number of hydrogens.
• Unsaturated fats (usually plant-derived) have one or more double bonds, which permit flexibility
• Phospholipids are essential components of cell membranes and are amphipathic containing both nonpolar and polar regions. They consist of glycerol, two fatty acids and a phosphate group.
• Sterols are important components of plasma membranes of animal cells and a group of bacteria called Mycoplasma . Sterols all contain a characteristic 4- ring carbon system.
• Mycolic acid of mycobacteria comprises a thick, waxy material which comprises up to 60% of stheir cell walls. This lipid barrier contributes to slow generation times and to the pathogenesis of these bacteria.

PROTEINS

Proteins are major components of the following biochemical molecules or structures and account for up to 50% or more of a cells dry weight.

Structural proteins:

• part of cell membranes forming receptors and channels (e.g. porins of gram negative cells)
• microtubules and filaments form the cytoskeleton of eukaryotic cells; allow cell signaling, membrane transport, contraction and movement of cells

Functional or secreted proteins include:

• enzymes
• hormones
• antibodies
• exotoxins of microbes
• bacteriocins

Conjugated proteins:

Proteins that are chemically joined to other compounds. For example, glycoproteins often exist on surface of microbes and can be important in stimulating immune responses.

Prions are unusual agents of disease

The term prion stands for "Proteinaceous infectious agent." The scientific community has grown more accepting of the proposal that abnormally folded proteins can somehow be transmitted and cause a group of diseases known as spongiform encephalopathies. We will consider prions in a later lecture.

Protein structure

About 20 amino acids occur naturally and can be arranged in any order to make up a unique polypeptide.

Peptide bonds form, via condensation, between the amino group (-NH₂) of one amino acid and the carboxyl group (COOH) of another.

There are four levels of protein structure:

• primary: linear amino acid sequence (does not reflect folding)
• secondary: a-helix or B-pleated sheets (coils or folding)
• tertiary: 3-D structure
• quaternary: 2 or more polypeptide chains (such as found in hemoglobin)

Protein folding is typically maintained by hydrogen and disulfide bonds. If such bonds are broken the protein may be denatured.

NUCLEIC ACIDS

Nucleic acids include the molecules DNA and RNA which comprise the genetic material of living cells that carry the instructions for making functional proteins.

Typically the flow of genetic information moves from DNA to RNA to protein. However, certain exceptions to this rule exist in the microbial world. For example, retroviruses possess RNA as their genetic instructions and reverse transcribe it into a DNA form. Prion agents possess no known nucleic acid at all, yet seemingly have the ability to replicate.

Structure:

• Nucleotides consist of a pentose sugar + phosphate group+ nitrogenous base
• Nitrogenous bases are either pyrimidines or purines. Pyrimidines include thymine and cytosine. Purines include adenine and guanine.
• DNA consists of 2 strands of nucleotides wound in a double helix in antiparallel array. Complementary base pairs are held together by hydrogen bonds between A ..T and C...G

Hydrogen bonding between A-T base pairs	Hydrogen bonding between G-C base pairs

RNA is typically single-stranded and differs from DNA in that it contains ribose and the nitrogenous base called uracil.

The three major forms of RNA are:

• Messenger RNA (mRNA): carries genetic instructions from DNA that will be translated into protein.
• Ribosomal RNA (rRNA): as part of a ribosome, assists in translating mRNA into protein. rRNA sequences are remarkably conserved and are important in understanding the evolutionary relatedness between microbes. rRNA sequences or genes are increasingly being used to classify microbes into groups.
• Transfer RNA molecules act to "taxi " amino acids to the site of protein synthesis.

ADENOSINE TRIPHOSPHATE

• ATP is the major energy-carrying molecule of living cells, storing and releasing chemical energy for cellular activities as needed.
• ATP consists of of the sugar ribose, adenine (a nitrogenous base) and 3 phosphate groups
• Synthesized in mitochondria, chloroplasts, and on the inner cell membrane of bacteria.