LO5: Describe Microbial Physiology and Genetics

Microbial Physiology

Is the study of the life-support processes of microbes, which involves a large number of complex biochemical reactions known as metabolism. 

Components of Microbial Physiology

• Metabolism and energy production (known as catabolism) or the use of energy (known as anabolism). 

• The catabolic pathways through aerobic respiration (bacteria) and anaerobic fermentation (yeast). 

• The anabolic pathways through photosynthesis (cyanobacteria) and chemosynthesis (most bacteria).  

• The role of metabolism and enzymes in energy production. 

Cell Requirements

• Energy to divide or reproduce.  The energy comes from metabolism or chemical reactions that place in the cell.

• Enzymes to regulate and speed up these chemical reactions.

• Oxygen, which must be correct for balanced growth, for example, aerobic bacteria (available oxygen) versus anaerobic bacteria (limited oxygen). 

• Other required nutrients include nitrogen, phosphorus and sulfur, magnesium, potassium and other lesser elements (calcium, iron).

Bacteria requirements

Bacteria, like all living organisms, require nutrients (food in the form of glucose) for metabolic purposes and cell division. They grow best in an environment that satisfies these requirements.  Bacteria must manufacture the required nutrients for successful growth.  This is how bacteria thrive and survive. Nutrients can be in the form of carbon, nitrogen and other elements. 

4 Nutritional Categories

1. Source of Carbon:

• Heterotrophy

• Autotrophy

2. Source of Energy:

• Phototrophy

• Chemotrophy

Requirements for Binary Fission

• Certain nutritional requirements in order for them to live, grow, reproduce, repair etc.

• Water, which is the absolute necessity, as this is where oxygen and hydrogen comes from.

• Foods to supply energy and nutrient chemicals in the form of carbon (carbohydrates or glucose, proteins) to build cell components.

Heterotrophs

• Are also known as other feeders.  The nutrients needed for growth and reproduction have been made by other sources.

• Are organisms that feed on organic compounds (contain carbon such as carbs, fats, proteins) from the environment, other than CO2 at the basic level, as their carbon source. 

• Use these compounds to build cellular materials and energy. 

• Include humans, animals, protozoa, saprophytic fungi and bacteria, parasitic fungi and bacteria, most bacteria. 

Where do humans get carbon?

They use carbohydrates and fats as their carbon source.

Examples of Heterotrophs

• Protozoa

• Saprophytic fungi that inhabit dead wood

• Parasitic fungi that feed on the living (ringworm and athletes foot)

• Saprophytic bacteria that live in the soil and feed on dead decaying organic matter

• Parasitic bacteria that feed on organic matter like human tissues

• Bacteria found in polluted water (chlamydia)

• Animals

Autotrophs

• Are also known as self-feeders

• Are self sufficient.

• Provide themselves with the food they need for growth and reproduction.

• Use CO2 as their sole source of carbon to build cellular materials.

• Use inorganic compounds (lack carbon) for nutrients and synthesis.

• Are free-living, non-parasitic bacteria.

• Include plants, algae, and certain bacteria such as Cyanobacteria.  Plants take in CO2 and release O2 for Heterotrophs.

Examples of Autotrophs

• Cyanobacteria

• Plants

• Algae

• Chemosynthetic bacteria

• Photosynthetic protists

Heterotrophs VS Autotrophs

• Carbon sources, water being the absolute, are the primary requisite for all living systems.

• Bacteria eat other organisms.

• Cyanobacteria can make their own food.

• Heterotrophs release CO2 into the environment for autotrophs

• Autotrophs take in CO2 from the environment and release O2 for Heterotrophs.

Phototrophs

• Use light as an energy source by a process called photosynthesis, which converts light energy into chemical energy.  On land, green plants use the energy from the sun to make food.

• Include plants, algae and certain bacteria called cyanobacteria.

Chemotrophs

• Can use either inorganic or organic chemicals as an energy source. Energy comes from chemical reactions, cell membrane for bacteria and mitochondrion in eucaryotic cells. 

• Include Bacteria, Protozoa, and Fungi

Chemosynthetic Bacteria

• In the deep sea hydrothermal vent sites, where the sun’s rays never reach, bacteria make food from chemicals, which is a process called chemosynthesis. 

• From bacteria to tubeworms, they are the only complex ecosystem known to live on energy from chemicals rather than energy from the sun.

Tube worms

• Grow near the boundary of where the hot vent fluid mixes with the cold seawater. 

• Can grow over 2.4 meters (8 feet tall). 

• Lack a mouth or stomach and instead have billions of symbiotic bacteria living in their red plumes.

• Help collect chemicals that the bacteria need from the water, and the bacteria convert it into sugars that the tubeworm can use for energy. 

• Archaea, an ancient life form, was recently was found at vent sites.

Ecology

• Is the study of the interactions between living organisms and the nonliving world around them.

• Interrelationships among the different nutritional categories are of prime importance in the functioning of the ecosystem.

• The terms relating to the energy source can be combined with the terms relating to the carbon source. See examples below.

Chemoautotrophs

• Use chemicals as a energy source and CO2 as a carbon source. 

• Are Gram-negative bacteria that can extract energy from minerals, by oxidizing the chemicals in the minerals  for example copper. 

• Are iron-oxidizing bacteria live in freshwater ponds that contain a high concentration of iron salts.  The iron bacteria oxidize the iron in the salts to obtain energy.

Chemoheterotrophs

• Include most bacteria, and all fungi, all protozoa and all animals.

• This indicates that the energy source is chemical reactions and the carbon source is organic compounds such as carbohydrates, fat etc.

• Dead plants and animals are recycled by certain bacteria and fungi (chemoheterotrophs) into nutrients returned to the soil, water and air for the phototrophs and the chemotrophs.

Photoautotrophs

• Include cyanobacteria, plants, algae, purple and green sulfur bacteria (light self-feeders), because they use light energy and CO₂ (carbon) to synthesize food.

• For example, plants (photoautotrophs) produce food and oxygen for humans and animals (chemoheterotrophs).

Photoheterotrophs

• Use light as an energy source and organic compounds other than CO2 for a carbon source. 

• Include purple non-sulfur bacteria growing in a hot spring run-off channel.

Metabolism

• Refers to all chemical reactions that occur within any cell, microbe, or human. 

• Proceeds in many directions simultaneously, like a revolving door breaking down some materials and building others.

• Is enhanced and regulated by enzymes. The cell can only perform a certain metabolic reaction if it possesses the right enzyme, similar to a lock and key.  For chemical reactions (metabolism) to take place at a faster rate, living cells must have an adequate supply of enzymes.

Enzymes

• Are also known as biological catalysts.

• Are protein molecules that either cause a metabolic reaction to occur or speed up the rate of chemical reactions at certain temperatures without being used up in the process.  

• Are responsible for hundreds of thousands of chemical reactions.

• Play a key role in metabolism because they lower the amount of energy required for reactions to take place.

• Are reusable, but eventually get used up and new ones must be made.  Once chemical reactions take place, the enzyme is released to participate in another reaction.

• Are specific in that they only speed up one particular chemical reaction.

Endoenzymes

• Are produced within a cell that remain within the cell to catalyze reactions.

• Are used to digest materials that the white blood cells known as phagocytes, have ingested.

Exoenzymes

• Are produced within a cell and then released outside of the cell to catalyze extracellular reactions.

• For example, cellulase secreted by saprophytic fungi to digest or break down cellulose in the external environment.

• Include lysozyme, found in human tears and saliva, which digests the cell walls of gram positive-bacteria.

Optimal Conditions for Enzymes

• pH - extreme acidity.

• Temperature - heat can denature enzymes by breaking bonds.

• Concentration - of enzyme and/or substrate (chemical substance that is changed by the enzyme) maybe to too high to too low.

• Inhibitors - for example heavy metals like lead, zinc, mercury and arsenic.

Energy

• Is the end result of the metabolic reactions that take place in a cell.

• Is required not only for metabolic reactions, but also for growth, repair, reproduction, sporulation, and movement of the organism as well as release of waste products, building DNA and enzymes. 

• Is temporarily stored in high energy bonds in the form of ATP molecules (adenosine triphosphate) until the cell requires it. ATP molecules are the major energy-storing or energy-carrying molecules in a cell. ATP molecules are found in all cells because they are used to transfer energy from energy-yielding molecules, like glucose to energy-requiring reactions. 

• Can be temporarily stored in the form of ATP molecules until the cell requires it. As it is being used up, it must be rebuilt using energy from glucose  which is the favorite food of cells or lipids.

Energy (Procaryotic/Bacteria)

Needed for cellular functions is provided by ATP molecules, which are formed in the cell membrane of bacteria via cellular respiration.

Energy (Eucaryotic)

Needed for cellular functions is provided by ATP molecules, which are formed in the mitochondrion via cellular respiration.

Catabolism

• Is the process by which energy is released when materials are broken down.

• Is released in small amounts as the cell needs it in a sequence of catabolic (releases energy) and anabolic reactions (uses energy).  The energy produced in a catabolic reaction is used to drive an anabolic reaction.

• Is the metabolic breakdown of organic compounds (contain carbon and hydrogen).

• Involves the breaking of chemical bonds or stored energy, therefore energy is released.

• Means that larger molecules are broken down into smaller molecules.

Organic Compounds

Nutrients such as carbohydrates, fats, proteins, nucleic acid, that result in the production of energy and smaller molecules.

Examples of Catabolism

• The breakdown of red blood cells in the liver.

• Cells breaking down sugar or glucose into carbon dioxide and water.

• The break down of glucose by bacteria is the key source of energy for ATP (high energy) production.

• This process is similar in many living things such as plants, animals and humans.

Catabolic Biochemical Pathways

• Is a series of linked biochemical reactions that occur in a stepwise manner, leading from a starting material to an end product.

• Glucose is the favorite food or nutrient of cells, including microbes.  Nutrients are energy sources and chemical bonds are stored energy.

• Generate or release energy by breaking down glucose, the favorite food.

• How the glucose is used by the cell, depends on the organism (yeast or bacteria), it’s available nutrients or energy sources and types of enzymes it can produce.

• The pathway used depends on the metabolic machinery present in the bacterial cell.

• The end product depends on the species of the organism (for example, yeast or bacteria) and on the sugar used as the source of carbohydrate.

Two processes by which glucose is catabolized

• Aerobic Respiration or how humans  and cells take in oxygen.

• Fermentation of glucose or the process to make beer and wine.

Fermentation of Bacteria

Can lead to dental caries

Fermentation of yeasts

Leavens bread

Aerobic respiration

• Is the process by which living cells take in oxygen, and oxidize or consume organic substances, in other words breathing using oxygen. 

• Takes place in the presence of oxygen.

3 Phases of Aerobic Respiration

Glycolysis, Krebs cycle, and Electron transport system (ETC)

Glycolysis

No oxygen, 2ATP, takes place in the cytoplasm in both eucaryotic/procaryotic cells.

Krebs Cycle

Oxygen, 2ATP, takes place in mitochondrion in eucaryotic cells and the inner surface of the cell membrane in procaryotic cells.

Electron Transport System

Oxygen, 32 to 34 ATP. Procaryotic cells yield 36 ATP.  Eucaryotic cells yield 38 ATP.

Aerobic Respiration in Humans

• Oxygen from the environment flows into the body and carbon dioxide is released.

• This oxygen flow goes from the lungs,  into the bloodstream, and then into the cells.

• Red blood cells carry oxygen to tissues of the body.

• Humans get oxygen from the plants.  Humans give back CO2 to the plants.

• Is the pathway taken by humans and infectious bacteria, because they require oxygen and high energy to sustain life.

• Takes huge amounts of energy, and generates 36-38 ATP

Aerobic Respiration in Cells

• Is a chemical reaction whereby organic compounds such as glucose, are converted into energy for the cell, using oxygen from the environment.  The by-products of carbon-dioxide and water are released back into the environment.

• Includes the breakdown of glucose to pyruvic acid using oxygen, then it’s released as carbon dioxide and water and energy in the form of ATP molecules.

• Is continued further through a series of reactions (Krebs cycle and electron transport system) that yield high energy in the form of ATP molecules (36-38 ATP in total).

• Aerobes and facultative anaerobes are more efficient in energy production than anaerobes.

Fermentation of Glucose

• Is an anaerobic process that takes place in the absence of oxygen.  The reactions produce very little energy, so are not efficient ways to catabolize glucose.

• Usually involves the breakdown of glucose (sugar) with end products of lactic acid and ethyl alcohols and CO2.

First Step of Glucose Fermentation

Glycolysis, (breakdown of glucose to pyruvic acid) which involves no oxygen and produces very little energy. 

Second Step of Glucose Fermentation

• The conversion of pyruvic acid to an end product, which depends on the specific organism involved.

• By certain gram positive-bacteria called lactic acid bacteria (S. mutans), involves the end products of pyruvic acid to lactic acid resulting in dental caries.  Examples include making buttermilk from milk.

• By certain yeasts and bacteria,  involves the end product of pyruvic acid to ethyl alcohol and CO2.  An example is the making of beer and wine and bread.

Examples of Glucose Fermentation

• The lack of oxygen in human muscles during exertion, which produces lactic acid, which is a waste product and results in soreness.

• Lactic acid bacteria break down the carbohydrates in cucumbers and cabbage to make pickles and sauerkraut. Is a slow process that produces very little energy or ATP (2 ATP).

• Milk and the presence of lactobacillus and streptococcus bacteria, to produce yogurt.

• Milk and adding a curdling agent, to produce cheese.

• The case in Japan of a presumed alcoholic. The yeast in his body fermented carbohydrates. Upon eating carbohydrates such as pasta or sugar, he appeared drunk. Candida albicans in the intestine is normal flora, but it can mutate to a fermenting yeast.

Aerobic Respiration VS Fermentation

• Aerobic respiration rather than fermentation is the better choice, because it releases many ATP molecules (36-38).

• Some organisms can only thrive in oxygen free environments, so must use the fermentation pathway, which releases very few or only 2 ATP molecules.

Microbe Energy Requirements

Most microbes, especially infectious bacteria, require huge amounts of energy to sustain life, for example for growth, repair, and movement, release of waste products, building DNA and enzymes and reproduction.

Anabolism

• Is the process by which carbohydrates or glucose (through photosynthesis or catabolism) and proteins (through DNA and RNA) are synthesized or built in the cell.

• Is the chemical bonds being formed, therefore energy is required.  Chemical bonds = stored energy.  Smaller molecules are bonded together to create larger molecules.

• Uses energy for building protoplasmic materials needed for growth and maintenance and other cellular functions.

• Energy comes from sun via photosynthesis or from catabolism via respiration and ATP molecule production or chemosynthesis.

• Includes the synthesis of enzymes and proteins within a cell.  Cooking destroys enzymes required for healthy cell building.

What is Anabolism needed for?

• Need to increase your anabolic state to build muscle.

• Need to decrease your catabolic state to break down of muscle. 

Connecting Anabolism and Catabolism

• Energy released during catabolic reactions is used to drive anabolic reactions. Both reactions require the action of enzymes.

• Energy released during catabolism cannot drive anabolic reactions unless it is transferred to special molecules called ATP molecules (adenosine triphosphate, which acts like the fuel).

• The cell would die without a supply of ATP. 

Adenosine Triphosphate (ATP)

• The ATP molecules act like a portable battery moving to parts of the cell where energy is required. 

• ATP is not stored in the cell like enzymes are, because they take up too much room.

• As it is being used up, it must be resynthesized using energy from glucose or lipids.

• The energy that is stored in glucose or lipids is later released to reform ATP. 

• The energy stored in glucose is like money in the bank. 

• The energy stored in ATP molecules is like money in your pocket to use at will.

• ATP molecules supply energy for binary fission, spore formation, protein synthesis, carbohydrate break down etc. 

Anabolic Biochemical Pathways

Photosynthesis/Chemosynthesis are the two anabolic pathways that use energy to build glucose.  In many bacteria, energy comes from the sun through photosynthesis, but in several species, energy is derived from chemical reactions through chemosynthesis.

Photosynthesis

• Is the process that traps sunlight and converts it into energy and carbohydrates (glucose) which can then be converted into more energy through Aerobic Respiration. 

• Light energy is converted to chemical energy, which is then used to synthesize organic compounds from CO2.

• Is the opposite of aerobic respiration.  Water plus CO2 = glucose and oxygen.  In aerobic respiration glucose plus oxygen = water and CO2

Where does photosynthesis occur?

• Takes place in organisms that have chlorophyll, that serve to trap light energy. 

• This is the energy source used for algae, cyanobacteria, and plants, which use light, CO2 and water to build glucose.

Photosynthesis by product

Oxygen. The exception is purple/green sulfur bacteria, by product is sulfur. They do not produce oxygen.

Chemosynthesis

Is the process by which energy is derived from chemical reaction. 

Chemosynthesis by product

One of them is sulfur.  Sulfur oxidizing bacteria found at vent sites at the bottom of the ocean.

Chemosynthesis examples

• Archaeans that produce methane gas instead of oxygen and use C02 for energy.

• Humans, most bacteria, protozoa, fungi and animals that use organic compounds for energy.

• Tubeworms and their bacteria.  Their survival depends on a symbiotic relationship with the billions of bacteria that live inside of them.  These bacteria convert the chemicals that shoot out of the hydrothermal vents into food for the worm.  This chemical-based food-making process is referred to as chemosynthesis. 

Energy production bacteria VS humans

• In bacteria, energy is produced on the cell membrane.

• In humans, energy is produced in the mitochondria.

Summary of Anabolism, Catabolism Photosynthesis, and Chemosynthesis

• Metabolic reactions within any cell either produce energy or utilize it. 

• Energy production is termed catabolism and utilizing energy is termed anabolism.

• Catabolism can take 2 pathways; fermentation (no oxygen) or respiration (with oxygen).

• Both pathways use carbohydrates or glucose as their energy source, and convert it to pyruvic acid. 

• Respiration with oxygen produces the highest amount of energy or ATP.  Therefore, infectious bacteria would take this route, as they require more energy than it takes to make wine, which is a fermentation process.

• The energy required by anabolism either comes from the sun through photosynthesis or from catabolism via Chemosynthesis or respiration and ATP molecule production.

• Plants, cyanobacteria and algae use photosynthesis, but humans and most bacteria use chemical reactions.

Purpose of Anabolism and Catabolism

Catabolism, (aerobic respiration, fermentation) and Anabolism (photosynthesis and chemosynthesis) provide microbes (as well as humans and plants) with the energy they need for existence and maintenance.

Photosynthesis VS Aerobic Respiration

Photosynthesis: produces food, stores energy, uses water, uses CO2, releases O2, occurs in sunlight

Aerobic Respiration: uses food, releases energy, produces water, produces CO2, uses O2, occurs in daylight or dark

Genes

The fundamental units of heredity that direct all functions of the cell. 

Bacterial Genetics

Is the study of heredity in bacterial cells. Virtually all microbial traits are controlled or influenced by heredity. 

Inherited traits of bacteria

• Their shape and structural features (capsules, flagella, pili), their metabolism, their ability to move or behave and interact with other organisms, possibly causing disease. Individual organisms transmit these physical traits/characteristics to their offspring through genes. 

• For example, the cell can’t produce flagella unless it possesses the gene to make flagella.

• Because there is only one chromosome to replicate just before cellular division, identical traits of a species are passed on from the parent to the daughter cells. 

Bacteria DNA

• Possess one chromosome (DNA molecule) in the form of a circular strand of genes. 

• There is only one chromosome to replicate so identical traits of a species are passed on from the parent to the daughter cells.

Human genetics

Is the study of heredity in human cells.

Human Inherited Traits

• Bacteria pass on their traits such as the presence of flagella, or certain enzymes  much the same way as human cells.

• Humans have 46 chromosomes and thousands of genes and pass on their physical traits such as eye, hair or skin color to their children.

Why have bacteria been successful?

They have been around the longest (3.5 billion years) versus humans (100,000 years). Because of their diverse genes, bacteria can survive anywhere from snow to boiling water. Their numbers are huge; a pinch of soil has more bacteria than all the people in the US today. Every half hour a new generation appears.

Genetic Engineering

• This field involves the introduction of new genes into cells. When the cells replicate, they are coded with the new genes.

• An array of techniques has been developed to transfer eucaryotic genes, particularly human genes, into other easily cultured cells to facilitate the production of important gene products (mostly proteins).

Plasmids

A molecule of DNA that can function and replicate while physically separate from the bacteria chromosome. Frequently used as vehicles for inserting genes into cells.

Genetically Engineered Microbes

• Can be used to clean up the environment (toxic waste). 

• For example, a soil bacteria can break down oil, but can’t live in salt water. Insert this gene into marine bacteria and now this bacteria can clean up oil spills at sea.

Genetic Engineering Benefits

There are many industrial and medical benefits.  Genetically engineered bacteria (made in labs), are used to produce insulin (using E.coli), interferon and materials for vaccines. The Hepatitis B vaccine is made from genetically engineered yeasts.

Gene Therapy

Genes are becoming play things. Let’s insert them and see what happens.

Gene Therapy of Human Diseases

Involves the insertion of a normal gene into cells to correct a specific genetic or acquired disorder that is being caused by a defective gene. 

Viruses in Gene Therapy

• Viruses are currently being used as vectors to insert normal genes into cells that contain abnormal genes. 

• Specific viruses are selected to target the DNA of specific cells. 

• For example, a virus capable of infecting liver cells, is used to insert a therapeutic gene in the DNA of the liver cells. 

Future of Gene Therapy

Genes may someday be regularly prescribed as drugs in the treatment of diseases for example autoimmune diseases, cystic fibrosis, heart disease.

Genotype

A complete set of genetic material.

Phenotype

The set of observable characteristics/traits of an organism.

Gene Mutations

The DNA of any gene on the chromosome is subject to accidental alteration, which alters the gene code and changes the trait controlled by that gene. This change in the DNA is transmissible to the daughter cells of each succeeding generation. 

Gene Mutation Causes

This could be the result of a stressful environment, spontaneous or random mutations that occur naturally.

Gene Mutation Benefits/Harms

• Can be beneficial to the cell, for example resistance to antibiotics, in which case the cell survives and becomes more pathogenic.

• Can be harmful or lethal to the cell, in which case the cell is harmed or dies as a result of the production of nonfunctional enzymes. 

Silent Gene Mutations

They have no effect on the cell. Some of these changes include cell shape, nutritional needs, virulence and drug resistance.

Mutagens

Physical and chemical agents that cause an increased mutation rate. In the research laboratory, x-rays, ultraviolet lights and radioactive and chemical substances are used to increase the mutation rate of bacteria to develop vaccines or medical research. 

Conjugation

In addition to mutation, bacteria can pass along their genetic information by this process using the sex pilus.

Other ways bacteria acquire new genetic information

Lysogenic conversion, Transduction, and Transformation

Lysogenic Conversion

Involves bacteriophages and the acquisition of new viral genes

Transduction

Involves bacteriophages and the acquisition of new bacterial genes

Transformation

Involves the uptake of DNA fragments (“naked DNA”) from its environment