Summary; Microbiology a clinical approach
Part I: Foundations
Chapter 1: What is microbiology and why does it matter?
Hans Zinsser: early pioneer in microbiology and infectious disease; Microbiology is still very important
o Infectious diseases after natural disasters (Katrina) hard to deal with than the physical elements
of the disaster
Bacillus anthracis inhalation anthrax
- Very deadly
- Potential weapon for bioterrorists Deadly pneumonia on massive scale
Mycobacterium tuberculosis tuberculosis
- Contagious and is expelled in the air with each cough expelled for a far distance and hang in the air for a
relatively long period
- Easily exposed to other people an infected patient has contact with
o Example: waiting room in hospital; Ill or immunocompromised people
- Estimation: some respiratory diseases could be moved around the world in less than 48 hours.
Diarrhea and vomiting with abdominal pain signs of food poisoning
- But blood in stool, anemia and renal failure indicate Escheria coli a enterohemorrhagic bacteria
o Found in improperly processed ground beef (hamburger), but also in water (feces) and milk (cow)
- Bacterial hemorrhagic diseases is a problem caused by the high volume of food production and has resulted
in significant changes in the beef industry
MRSA: nosocomial (hospital acquired) infection with Staphylococcus aureus bacterium antibiotic methicillin
resistant
Epidemic fever; Group A streptococcal pathogens normally found on the skin
- Washing hands before delivering babies decrease of deaths of mothers
- Important for hospital hygiene (Ignaz Semmelweis)
Typhoid fever
- People can become carriers but can pass on the infection to others (Mary the Cook)
Influenza: viral disease
- Numerous strains of this virus and some are very destructive
- Three severe epidemics; the worst in 1918: Spanish flu 30-50 million died in 1 year
- Potential for genes from the virus that infects humans to combine with genes of a type of influenza virus in
birds (avian influenza) result could be a pandemic
-
19th century:
- Tuberculosis and other pulmonary infections were the scourges of the worlds
- Leading cause of premature death
Although causes were discovered little that could stop or prevent them
Golden age of microbiology: when microbes were directly associated with the diseases they caused and was
followed by advances in public health that lessened the number of deaths resulting from infection
20th century:
, - Structure, physiology and genetics of microbes links between microbial properties and disease
- Discovery of penicillin (1929) and sulfonamide drugs (1936)
- Increased knowledge on molecular level
- Development of vaccines and antibiotics and better sanitation methods
21st century:
- Diseases are reappearing and resistance to treatments is growing
- New diseases are emerging and organisms that were thought to be harmless are now being found to cause
disease in certain circumstances
- Potential for bioterrorism
Virulence; the potential to cause disease among human pathogens
- Categorization of pathogenic microorganisms based on their degree of virulence
Tiny fraction of microbes are involved in disease smaller amount are human pathogens
Microbial flora: bacteria and some fungi naturally colonization of the skin and the mucosal surfaces
- Harmless and some cases provide important products (vitamins)
In some circumstances pathogenic (mildly virulent)
Yersinia pestis; Y. pestis causes bubonic plague
- Highly virulent, Disease comes on suddenly with great severity and very deadly
Basic aspects of how pathogens can cause disease: Three perspectives
1. Epidemiology; the study of factors determining the frequency and distribution of disease
2. Pathogenesis; the study of how disease develops
3. Host defense
Epidemiology:
- Pathogens must accomplish five tasks to successfully cause disease
1. Get into the body or the cell
2. Be able to stay in
3. Defeat the host defenses
4. Cause damage to the host
5. Must be able to be transmitted to a new host so that the infection will continue
- Pathogen is looked at from this perspective and classified with regard to transmission
o Air, food, water, insect vectors or person-to-person contact
- Epidemic outbreaks of diseases are fostered by factors such as poor socioeconomic conditions, ignorance of
the cause of infection, natural disasters, and poor hygiene.
- Current pandemic: AIDS caused by HIV infection
Pathogenesis:
- Virulence factors are required for the organism to persists in the host, cause disease and escape the host
defenses so that infection can continue
- Variety of methods to damage host cells and tissues
o Digestive enzymes and toxins
o Production of viral particles death of infected cell
o Overcompensating host defense fever, pain and swelling (inflammation)
Too severe can damage the host
- Symptoms are associated with the particular organs that are involved in the infection
Host defense:
, - Pathogen uses multiple methods to survive and thrive, while the host defense (immune system) becomes
involved immediately in an attempt to kill or expel the pathogens outcome depends much on success of
immune system
o Host defense failure Acquired Immunodeficiency syndrome (AIDS)
- Two basic types of defense against infection:
o Innate immune response
Nonspecific, first line of defense
o Adaptive immune response:
Specific, second line of defense, immunological memory
- Pathogen; must find a way to defeat, evade or hide from these potent defenses
o Attack defending cells, changes looks, hide in defending cells
Treatment: antibiotics, disinfectants and antiseptics
- Antibiotics; must kill the disease-causing microorganism but not harm the patient penicillin
o Prevents formation of peptidoglycan in the bacterial cell wall (not in humans)
- Antiseptics; a chemical substance that can be used on tissues to control the growth of microorganisms
- Difficult for viruses; intracellular parasites that reside in our cells only treatment is killing the infected cell
or preventing invading the host cell
- Most important; health measures and immunization
Some organisms are beneficial;
- recycling vital elements (Nitrogen), Interact with animals, plants and the environment (carbon, nitrogen,
oxygen and sulfur), bacteria and fungi (decompose organic waste and dead plants and animals CO2) –
- Bioremediation and recycling
- Recycle water during sewage treatment
- Organisms use the toxic waste as a source of energy, and in the process they decontaminate it.
Insect control:
- Control pests all of which can damage crops used for food pest control is safer than old methods.
Biotechnology:
- Drugs are mass-produced in genetically engineered bacteria.
Chapter 2: Fundamental chemistry for microbiology
Tissues are organized in the following sequence; atoms molecules cells tissues
- Tissues are the basis of organ structures, but the infectious processes are usually found at the level of cells
and tissues
Atoms are composed of;
- Protons; core and positive charged atomic number
- Neutrons; core and no charge atomic weight is protons + neutrons
- Electrons; shells and negative charge number of protons
Shells are more stable if they are full of electrons, if an electron shells is not full unstable and capable of bonding
to make it full
- Basis for ionic bonding
o Sodium (11): unstable loses an electron becomes positive = cation
o Chlorine (17): unstable gains an electron becomes negative = anion
- Sodium and chlorine combined share electrons electrical charges changes and they become ions
- Opposing charges of these cations and anions are attracted two ions form an ionic bond
Covalent bonds:
- Seen in biological molecules
- Sharing of a pair of electrons (1 = single, 2 = double)
- Covalent bonds can have polarity which can be viewed as the equality of sharing that occurs
, o Nonpolar covalent bond; the sharing of electrons between two atoms is equal and in this case, the
bonds are electrically neutral
o Polar covalent bond; if sharing is unequal there can be a polarity, which results in a weak electrical
charge H20
- Because of sharing, no need to move electrons only bring the outer shells closer together.
Carbon (6): basis for biological life on this planet
- Carbon needs four more electrons to fill the shell bonding to other atoms
- Binding with hydrogen
- Carbon’s ability to bond covalently with other atoms makes it useful for building biological molecules
carbohydrates, lipids, proteins and nucleic acids
Hydrogen bonds:
- Chemical bonds between and within molecular structures give molecules shape
- Form because of the polarity of molecules seen in covalent bonding
- Water molecules become attracted because of polarity positive and negative side
- Water becomes fluid and when the temperature is lowed, the breaking and rejoining slows down and the
water becomes ice opposite with heating
Water properties:
1. Solubility; molecules can dissolve in water
2. Reactivity; can help in dehydration synthesis and hydrolysis
3. Heat capacity; can absorb heat that is given off by other chemical reactions
Acid; donor that donated hydrogen ions to a solution
Basic; hydroxyl ion, can neutralize H+ ions alkaline
- pH = definition of the acidity or alkalinity of a solution 0 = most acidic, 14 = most alkine, 7 = neutral
(water)
4 categories of biological molecules
- Carbohydrates
o Most easily used source of energy
o Contain; carbon, oxygen and hydrogen
o Three major categories based on how many building blocks are involve
Monosaccharide; smallest type and is the building block used to make larger carbohydrates
Disaccharide; two monosaccharide building blocks together
Polysaccharides; many monosaccharides together storage form and holds most energy
o Monosaccharide; consists of a carbon chain with several functional groups attached to it (Glucose)
- Lipids
o Fats
Lipids that contain the three-carbon molecule glycerol and one or more fatty acids
Saturated or unsaturated depending on how many hydrogen atoms are attached to pairs
of carbons in the tails; unsaturated is double bonds
o Phospholipids and glycolipids
Lipids that have other molecules attached to them, such as carbohydrate or phosphate
Phospholipids is the foundation of the cell’s plasma membrane phosphate end is
hydrophilic, and opposing end is hydrophobic
o Steroids
Cholesterol, which is insoluble in water and is found in the cell membrane of some
eukaryotic cells and also in the bacterium Mycoplasma.
o Relative insoluble in water, useful as elements of cellular structure plasma membrane
o Used as energy sources, and some contain more energy than carbohydrates
o Contain more hydrogen and less oxygen
- Proteins
, o Properties of proteins:
3D molecule structure is related to function
Made up of amino acid building blocks carbon structures, one amino group and one
carboxyl group
Involved in the formation of a peptide bond
Made up of long sequences of linked amino acids peptides
Some can form disulfide bridges folding of the protein
o Protein structure: breakdown of 3D structures in four levels
Primary level; sequence of the amino acids in the polypeptide chain
Secondary level; folding or coiling of the polypeptide (helix or a pleated sheet form)
Tertiary level; folding of the chain upon itself disulfide bridges
Quaternary structure; very large proteins for which more than one polypeptide is joined
o Types of protein:
Structural proteins and enzymes are the most important
Structural proteins; contribute to cellular structures to maintain cell shape
o Involved in motility with flagella
Enzymatic proteins; cellular functions such as metabolism
o Buildup or breakdown of organic molecules enzymatic reactions depend
on the energy of activation
o Enzymes lower the needed energy
- Nucleic acids
o Involved in cellular information and function as energy molecules
o Two types of informational molecules DNA and RNA
Adenine and guanine; purines double-ring structures
Thymine and cytosine; pyrimidines single-ring structures
o Structure of Nucleic Acids
Long polymeric structures in which nucleotides are linked together
Backbone; phosphates and sugars
5’end and 3’end on 3’end nucleotides can link
Cells and most viruses; Double-stranded DNA (antiparallel)
Complementary base pairing between A-T and C-G
Twisted in double-helix
RNA = single-chain molecule
Uracil instead of Thymine
Complementary base pairing between DNA and RNA transcription
All use carbon as primary building block and are naturally occurring.
- All living organisms require energy, and large organic molecule can provide this energy harvest energy in
organic molecules by breaking the chemical bonds. energy can be used to form ATP (used for cellular
work)
ATP:
- Energy is required for all the processes in the cell protein synthesis
- Major energy molecule in biological systems is ATP
o Bonds between phosphates are high-energy bonds broken down yield energy
- Phosphate is removed from ATP ADP; energy production
o ADP can be recycled by phosphatases requires energy
- Phosphate from ADP can be removed AMP; also energy yielded but less
Chapter 3: Essentials of Metabolism
Metabolism; involves catabolism (break down of molecules, and energy release) and anabolism (energy used to build
molecules) regulated
, - The chemical processes that go on inside any living organism. pathogens require energy to live, required
trough catabolism: Energy in an organism is linked to growth better metabolism, better growth more
successful pathogens in causing disease.
Carbon and energy are required for growth; two ways
- Autotrophy; self feeding, obtain carbon atoms from inorganic sources such as CO2 in the environment
o Photoautotrophs; use sunlight as a source of energy
o Chemoautotrophs; obtain energy from chemical reactions involving inorganic substances such as
nitrates and sulfates
- Heterotrophy; other feeding, obtain carbon atoms from organic molecules present in other organisms
(humans)
o Photoheterotrophs; obtain energy from sunlight and convert it to chemical energy
o Chemoheterotrophs; obtain energy by breaking down organic compounds nearly all infectious
organisms
All catabolic pathways involve electron transfer
- Oxidation and reduction reactions always occur together; redox reaction (oxygen final acceptor electrons
= aerobic)
o Oxidation; chemical reaction in which an atom, ion or molecule loses one or more electrons
o Reduction; chemical reaction in which an atom, ion or molecule gains one or more electrons
- When a substance is oxidized it loses electrons and when a substance is reduced it gains electrons
Respiration;
- Macroscopic level; the exchange of CO2 and O2 in the lungs
- Cellular level; describes catabolic processes aerobic respiration (metabolism uses oxygen),and anaerobic
respiration (without oxygen)
o Determines the amount of ATP that the micro-organism produces.
Anaerobic cellular respiration; glycolysis 2 ATP/glucose molecule
Aerobic cellular respiration; Krebs cycle and electron transport 38 ATP/glucose molecule
Microorganism Faster growth
o Some micro-organisms can use anaerobic or aerobic cellular respiration facultative anaerobes
Grow well in the presence of oxygen and can still grow a little in the absence of oxygen
many pathogens
Oxidation of glucose (aerobic respiration): Glucose + 6O2 6CO2 + 6 water + energy (reactants/substrates
products)
Chemical pathways; the product of one reaction serves as the substrate for the next reaction mediated by
enzymes; facilitate or promote the running of certain reactions under physiological conditions and are required for
the reactions to proceed at an appropriate speed.
Enzymes are found in all living organisms’ protein and shape (3D) is related to function
- Enzymes act as catalysts; help get reactions started and help them to proceed, but are not itself changed in
any way by the reactions.
- Enzymes Chemical reaction; lowering the energy of activation (energy required to start reaction) in
metabolism
- Active site; site on the enzyme where the enzymatic activity takes place substrate fits into the enzyme
o Enzyme and substrate interact at active site and form; enzyme-substrate complex
- Changes in the substrate molecule lead to the formation of the product of the reaction.
- Enzymes are highly specific catalyzes only one type of reaction and most enzymes react with only one
substrate
o Some react with more than one substrate but work in a particular type of reaction
,Apoenzymes; enzymes that require the help of some other substance before they can react with substrate active
site does not fit the enzyme’s substrate; change shape because of helper
- Cofactor; when the helper substance is an inorganic ion (magnesium, zinc or manganese)
- Coenzyme; when the helper substance is a nonprotein organic molecule
Carrier molecules; carry hydrogen atoms or electrons in redox reactions metabolic reactions
- Coenzymes or cofactors can be carrier molecules
- When a carrier molecule receives either hydrogen atoms or electrons it becomes reduces releases them it
becomes oxidized
o Coenzyme carrier molecules in biological reactions; FAD and NAD+ Vitamins
FAD: 2 hydrogen atoms and 2 electrons Reduced form; FADH2
NAD: hydrogen atom and electron Reduced form; NADH
Necessary to regulate enzyme activity 2 ways;
- Competitive inhibition:
o An inhibitor molecule, similar in structure to the substrate for a given enzyme, competes with the
substrate to the enzyme’s active site
o Reversible and depends on the relative numbers of inhibitor molecules and substrate molecules
present
- Allosteric inhibition:
o Involves inhibitor molecules, but the molecules do not block the active site, but bind to another part
of the enzyme, called the allosteric site
o After binding to the allosteric site, the 3D structure of the enzyme changes in such way that the
active site changes and the substrate can no longer fit.
o Some bind reversible and so can unbind and allow activity to resume some are permanently
disabled
Example; lead and mercury and other heavy metals
Feedback inhibition; regulatory mechanism for enzymatic activity and is used in many metabolic pathways.
- Final product in a pathway accumulates and begins to bind to and inactivate the enzyme that catalyzes the
first reaction of the pathway
- Reversible and when the level of end product decreases, the inhibition stops.
Three major factors that affect enzyme activity
- Temperature: high temperatures can break the hydrogen bonds that hold the enzyme in its shape, and
change in structure can inhibit enzyme activity minor increases in temperature can help reactions occur
more rapidly.
o Lower temperatures slow the metabolic reactions and slow the growth of orgnaisms
- pH: alter the electrical charges in the enzyme molecules, changes inhibit the molecules ability to bind to its
substrate
o Very high or very low pH can denature the enzyme
- Concentration of substrate, product and enzyme: smaller number of enzyme molecules available, the
smaller the number of substrate molecules that can bind to enzyme at any instant, and so the slower the
reaction.
Catabolism; the breakdown of large molecules into smaller ones.
- Fueling reactions; make energy available to an organism
- Nutrient molecules in the food can be processed in several ways to release energy that is then stored in
high-energy bonds of ATP and other energy molecules.
o Glycolysis, the Krebs cycle and electron transport chain
Glycolysis:
- Catabolic pathway used by most organisms
, - Carbohydrate (glucose) is broken down through a series of steps that result in the production of 2 ATP for
each molecule of glucose involved
o Occurs in cytoplasm and does not require oxygen
During glycolysis:
- Phosphate groups are removed from ATP and transferred to substrates phosphorylation and makes the
substrates more energetic
o Increase in energy is required to start the glycolytic pathway
- 6-carbon glucose molecules broken down in half; 3-carbon molecules (pyruvate) processed into Krebs
cycle or into fermentation pathways
- Two electrons are transferred to the carrier molecule NAD+, converting it to NADH carries the electrons
to electron-acceptor molecules
- 4 ATP molecules are produced in glycolysis net gain of 2 ATP molecules (first steps consume 2 ATPs)
- Recycling of ATP: ATP ADP + P + energy released; ADP + P + energy ATP
The Krebs cycle:
- Catabolic pathway seen in aerobic cellular respiration in which the pyruvate produced in glycolysis is
metabolized further (TCA or citric acid cycle)
- Cycle accepts only two-carbon molecules (pyruvate contains 3 modified) removal of one carbon
molecule in the form of CO2 (involving the carrier molecule NAD+ and the addition of a molecule called
coenzyme A (CoA) to form acetyl-CoA
- Sequence of reactions in which hydrogen atoms are removed and their electrons are transferred to
coenzyme carrier molecules
- CO2 is given off during this cycle, and each step in the cycle is controlled by a specific enzyme
- Three important things during the cycle:
o Carbon is oxidized to CO2
o Electrons are transferred to coenzyme carrier molecules that take the electrons to the electron
transport chain
o Energy is captured and stored when ADP is converted to ATP
The electron Transport chain:
- Cellular process in which electrons are transferred to a final electron acceptor
o In aerobic metabolism (oxygen), in anaerobic metabolism (some inorganic oxygen-containing
molecule)
- During electron transport, hydrogen atoms are transferred to NAD+ carrier molecules, which transfer the
hydrogen atoms to proteins precise arrangement in the microbial cell membrane or in the inner
membrane of the mitochondria in eukaryotic cells
- Involves oxidation and reduction reactions
- When oxygen is the final electron acceptor in the chain it becomes reduced to the final form found in the
H2O molecule
- Differs between organisms, some use more than one type
- During anaerobic metabolism the electron transport chain keeps the Krebs cycle turning by being a place for
the reduced carrier molecule NADH to drop off electrons.
- Energy is released via a process called chemiosmosis
Chemiosmosis:
- Protons are pumped out of the cell during electron transfer
- In eukaryotic cells chemiosmosis occurs in the mitochondria, protons are pumped into the intermembrane
space
- In prokaryotic cells protons are pumped across the plasma membrane
- Difference in proton concentration concentration gradient; proton motive force
o Region of high concentration to low concentration protons move from outside the cell, the cell in
Movement through specialized proteins embedded in the membrane energy is released
and used to form ATP
