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State three harmful effects and four beneficial effects associated with the activities of microorganisms.
- harmful - spoilage of food, cause infectious diseases in humans, agricultural loss as a result of infectious diseases
- beneficial - food production, energy production, cleaning up the environment, sustaining agriculture, production of natural gene products
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Define microbiota and microbiome. ***
- microbiota = refers to all the microorganisms that live in a particular environment
- microbiome = the entire collection of genes found in all of the microbes associated with a particular host
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Briefly describe two different beneficial things the human microbiome does for the normal function of our body. ***
- regulation of host metabolism
- regulation of host immune response
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State several diseases associated with a change in our "normal" microbiota. ***
- diabetes
- nonalcoholic fatty liver disease
- hypertension
- obesity
- gastric ulcers
- colon cancer
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List and recognize a description of each of the 5 basic groups of microbes.
- bacteria - reproduce by binary fission
- fungi - yeasts and molds
- viruses - need a host organism to survive
- protozoa - lack a cell wall
- algae - carry out photosynthesis
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Briefly describe why, in terms of differences in cell size, a eukaryotic cell is structurally more complex and compartmentalized than a cell that is prokaryotic.
- since prokaryotic cells are very small, they have a larger surface to volume ratio
- eukaryotic cells have a smaller surface to volume ratio so they have more compartments/membranes in order to increase the ratio
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Briefly state why viruses are not considered as prokaryotic nor eukaryotic.
they are acellular, do not grow/divide or have independent metabolism carried out, need a host cell to survive and reproduce
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Define phylogeny
the evolutionary relationships between organisms
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Name the 3 Domains of the 3 Domain system of classification and recognize a description of each.
- bacteria - prokaryotic cells, membranes of fatty acid chains, cell walls made of peptidoglycan
- archaea - prokaryotic cells, membranes made of branched hydrocarbon chains, no peptidoglycan in cell walls, live in extreme environments
- eukarya - eukaryotic cells, membranes made of fatty acid chains, if there are cell walls they are not made of peptidoglycan
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Name the four kingdoms of the Domain Eukarya and recognize a description of each.
- protista - simple, unicellular, eukaryotic
- animalia - multicellular, eukaryotes, lack cell walls, no photosynthesis, ingestion of nutrients
- fungi - unicellular or multicellular, eukaryotes, cell walls not organized into tissues, absorption of nutrients
- plantae - plants, multicellular, eukaryotic, photosynthesis + absorption of nutrients
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Define horizontal gene transfer
- the transfer of genes between relatives instead of from parent to offspring (which is vertical)
- allows for the spread of genetic elements
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*List the three basic shapes of bacteria.
coccus, bacillus, spiral
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*List and describe 5 different arrangements of cocci.
- diplococcus
- streptococcus
- tetrad
- sarcina
- staphylococcus
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Define and give the abbreviation for the metric unit of length termed micrometer and state the average size of a coccus-shaped bacterium and a rod-shaped bacterium.
- um (10^-6)
- coccus = 0.5 - 1 um
- bacillus = 1-4 um long, 0.5-1 um wide
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List and describe 3 different arrangements of bacilli.
- bacillus - single oval shaped bacilli
- streptobacillus - chain of bacillus
- coccobacillus - oval and similar to coccus
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*List and describe 3 different spiral forms of bacteria.
- vibrio - curved rod or comma shaped
- spirillium - thick, rigid spiral
- spirochete - thin, flexible spiral
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*State the chemical composition and major function of the cytoplasmic membrane in bacteria.
- phospholipid bilayer
- major function is to decide what goes in and out of the cell by being selectively permeable
-
Briefly describe the fluid phospholipid bilayer arrangement of biological membranes.
double layer of fatty acids with polar heads facing outwards and non-polar tails facing inwards, presence of sterols along the membrane as well as diff membrane proteins
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State the net flow of water when a cell is placed in an isotonic, hypertonic, or hypotonic environment and relate this to the solute concentration.
- isotonic - equal flow both ways
- hypertonic - water flows out of the cell
- hypotonic - water flows into the cell
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Define passive diffusion
movement of molecules of areas of higher concentration to lower concetration, down the gradient, no energy or transport proteins needed
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Define osmosis
diffusion of water molecules across the membrane from an area of higher water concentration to an area of lower water concentration
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Define facilitated diffusion
transport of substances down a concentration gradient with the help of transport proteins
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Define transport through channel proteins
transport of water or certain ions down a gradient
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Define transport through uniporter
helps to transport proteins from one side of the membrane to the other
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Define active transport
movement of molecules against the concentration gradient, uses both transport proteins and metabolic energy
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Define transport through antiporter
- transport two molecules, each in opposite directions
- one molecule moves down the gradient
- the other molecule moves against the gradient
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Define transport through symporter
simultraneously transporting two substances across the membrane in the same direction
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Define the ABC transport system
- ATP-binding casette system
- periplasmic-binding protein picks up substance and delivers it to the transport protein, which then moves it across the membrane
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Define group translocation
substance is chemically altered during transport, once inside it remains inside the cell
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*State how the antibiotic polymyxin and disinfectants such as orthophenylphenol, chlorhexidine, hexachlorophene, zephiran, and alcohol affect bacteria.
they do this by altering the microbial cytoplasmic membrane and causing leakage of cellular needs
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*Define binary fission and geometric progression and relate this to bacteria being able to astronomically increase their numbers in a relatively short period of time.
- binary fission - when one bacterium splits into two
- geometric progression - the doubling of a population every generation time as a result of binary fission
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Briefly describe the process of binary fission in bacteria, stating the functions of Par proteins, the divisome, and FtsZ proteins.
- binary fission is when one bacterium splits into two
- par proteins separate chromosomes to opposite sides of the cell during division
- divisome is the apparatus that divides the cell
- FtsZ proteins form a constricting ring at the division site and direct inward growth of the cell wall
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State the 3 parts of a peptidoglycan monomer and state the function of peptidoglycan in bacteria.
NAM sugar + NAG sugar + pentapeptide bonded to NAM
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**Briefly describe how bacteria synthesize peptidoglycan, indicating the roles of autolysins, bactoprenols, transglycosylases, and transpeptidases.
- autolysins break the glycosidic bonds between monomers and the peptide cross-links, creating a breakage in the chain
- bactoprenols transport the monomers (which are made in the cytosol) across the membrane and insert them into the break in the chain
- transglycosylases create the glycosidic bonds between the new monomers and existing monomers to link them together
- transpeptidases reform the cross-links between the peptides, creating a strong cell wall
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*Briefly describe how antibiotics such as penicillins, cephalosporins, and vancomycin affect bacteria and relate this to their cell wall synthesis.
they interfere with the enzymes responsible for the synthesis of peptidoglycan, which weakens the cell wall, and causes bacterial lysis because of the osmotic pressure
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How do penicillins and cephalosporins specifically inhibit peptidoglycan synthesis?
- they bind to transpeptidases and prevent them from re-forming cross-links, which weakens the cell wall
- eventually, the bacteria will burst due to osmotic lysis
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*State what color Gram-positive bacteria stain after Gram staining.
- purple
- retains the initial dye crystal violet
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*State what color Gram-negative bacteria stain after Gram staining.
- pink
- decolorize during gram stain procedure, pick up counterstain safranin
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State what color acid-fast bacteria stain after acid-fast staining.
- red
- resist decolorization with an acid-alcohol mixture during the acid-fast stain procedure
- retain the initial dye carbolfuchsin
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**Describe the composition of a Gram-positive cell wall and indicate the possible beneficial functions to the bacterium of peptidoglycan, teichoic acids, and surface proteins.
- composition: very thick peptidoglycan, teichoic and lipteichoic acids interwoven in cell wall, surface proteins on outer surface
- peptidoglycan - prevents osmotic lysis
- teichoic acids - help make the wall stronger
- surface proteins - can function as enzymes or adhesins
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*Briefly describe how PAMPs of the Gram-positive cell wall can promote inflammation.
- PAMPs bind to PRRs located on macrophages
- this triggers innate immune defenses (inflammation, fever, phagocytosis)
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*State the function of bacterial adhesins, secretion systems, and invasins.
- adhesins - enable bacterium to intimately adhere to host cells to colonize them and resist flushing
- secretion systems - enable the bacterium to directly inject bacterial effector molecules into the cytoplasm of the host cell to alter its cellular machinery or cellular communication to the benefit of the bacteria.
- invasins - enable a bacterium to enter a host cell
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*What is an antigen?
- a molecular shape that reacts with antibody molecules and antigen receptors on lymphocytes to initiate an adaptive immune response
- it is recognized as a foreign molecule
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*What is an epitope?
- the actual part of the antigen that reacts with antibodies and receptors on B lymphocytes and T lymphocytes
- 5-15 amino acids with a unique shape
- a single antigen can have hundreds of epitopes, and our body makes an antibody for each one
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*Briefly describe how opsonizing antibodies can promote phagocytosis and how antibodies made against cell wall adhesins can block colonization.
- opsonizing antibodies stick the bacteria to a phagocyte so it can be engulfed
- antibodies can also be made against adhesins and they bind to the bacterial cell wall before it can bind to the host cell and prevents it from doing so
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**Describe the composition of a Gram-negative cell wall and indicate the possible beneficial functions to the bacterium of peptidoglycan, the outer membrane, lipopolysaccharides, porins, and surface proteins.
- composition:
- petidoglycan - prevents osmotic lysis
- outer membrane - semipermeable, prevents toxins from entering, can form vesicles for quorom signaling
- lipopolysaccharides - adds strength
- porins - function as channels for entry/exit of molecules
- surface proteins - can serve as adhesins, secretion systems or invasins
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*Briefly describe how LPS and other PAMPs of the Gram-negative cell wall can promote inflammation.
the PAMPs can be recognized by PRRs on macrophages, which triggers the release of cytokines, which initiates inflammation
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Define periplasm.
the gelatinous material between the peptidoglycan and cytoplasmic membrane
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What is cystitis, urethritis, and pyelonephritis
- cystitis - inflammation of bladder
- urethritis - inflammation of urethra
- pyelonephritis - inflammation of the kidneys
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Name 4 risk factors for UTIs
- having sexual intercourse (for women)
- being pregnant
- having diabetes mellitus
- insertion of urinary catheters (most common)
- being immunosuppressed
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Name the most common bacterium to cause UTIs; name at least 3 other bacteria that commonly cause UTIs.
- most common = E. coli
- 3 others = Klebsiella pneumoniae, Proteus mirabilis, Enterococcus species., and Pseudomonas aeruginosa
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Name at least 3 common symptoms of UTIs.
- painful/uncomfortable urination
- urgency to urinate
- increased freq of urination
- back pain
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What infection does Escherichia coli usually cause?
Urinary Tract Infections (UTIs)
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Describe Escherichia coli
- moderately sized
- gram-negative bacillus
- flagella over entire surface
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Describe Enterococcus
- gram-positive cocci
- usually in pairs or chains
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What infections does Enterococcus usually cause?
- UTIs
- bacteremia (bacteria in the bloodstream)
- nosocomial infections (acquired in the hospital)
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**Describe the composition of an acid-fast cell wall and indicate the beneficial function to the bacterium of peptidoglycan, arabinogalactin, mycolic acid, and porins.
- composition - thin, inner layer of peptidoglycan
- arabinogalactin - adds strength
- mycolic acid - impede entry of chemicals into membrane
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Describe Mycobacterium tuberculosis and what infection it causes
- acid-fast bacterium
- obligate aerobe
- tuberculosis
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What are exoenzymes?
- enzymes that function outside of the cell
- they hydrolyze macromolecules into smaller molecules so they can be transported across the membrane
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What are endoenzymes?
- enzymes that function within a cell
- chemical reactions in cytoplasm fall under this
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Define cytosol
refers to the liquid portion of the cytoplasm
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State the primary function of the bacterial cytoplasm.
the site of most bacterial metabolism
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Define metabolism
all of the organized chemical reactions an organism carries out
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Define catabolic reaction
reaction that breaks molecules down into its building blocks for other more complex use
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Define anabolic reaction
reaction that synthesizes molecules from smaller building blocks
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Define genome
the sum of an organism's genetic material
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Describe the composition of the bacterial chromosome.
- made of 80% water
- cytosol
- nucleic acids, amino acids, DNA
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*Name the enzymes that enables bacterial DNA to become circular, supercoiled, and unwind during DNA replication.
DNA topoisomerases
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*Briefly describe the process of DNA replication.
- helicases unwind the double stranded DNA
- single stranded binding proteins keep the DNA from zipping back up
- topoisomerase relieves stress
- DNA polymerase produces new complementary strand
- DNA ligase joins DNA fragments together
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What is the function of DNA polymerase III in bacterial DNA replication?
replaces the primase and adds DNA nucleotides to the RNA primer
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What is the function of DNA helicase in bacterial DNA replication?
unwind the double stranded DNA
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What is the function of primase in bacterial DNA replication?
- joins RNA nucleotides without needing a preexisting strand of nucleic acid
- first adds several complementary RNA nucleotides opposite the DNA nucleotides on the parent strand
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What is the function of DNA ligase in bacterial DNA replication?
links together the DNA fragments
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*State the function of DNA
contains genetic instructions for the cell
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*In terms of protein synthesis, briefly describe the process of transcription and translation.
DNA is transcribed into mRNA which is then translated into a protein with the help of rRNA and tRNA
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*Briefly state how the following antibacterial chemotherapeutic agents affect bacteria:
a. fluoroquinolones (norfloxacin, lomefloxacin, fleroxacin, ciprofloxacin, enoxacin, trovafloxacin, etc.)
b. trimethoprim and sulfamethoxazole
- flouroquinolones - inhibit topoisomerases, which are needed for bacterial nucleic acid synthesis
- trimethoprim + sulfamethoxazole - nlock enzymes in pathway for tetrahydrofolic acid (needed for bacteria to make nucelotide bases)
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*Describe plasmids and indicate their possible benefit to bacteria
- Small molecules of double stranded, helical, non-chromosomal DNA not essential for normal bacterial growth
- can help with antibiotic resistance
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*Function of transposons
Small pieces of DNA that encode enzymes that can cut a segment of DNA out of one molecule and insert it into another DNA molecule
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Function of integrons
transposons that carry multiple gene clusters/cassettes that move as a unit from one piece of DNA to another
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Function of episome
- plasmids that can insert themselves into a host cell's chromosome and have their replication be regulated by the chromosome
- usually plasmids replicate independently of the cell's chromosome
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Function of *conjugative plasmid
contains genes coding for proteins involved in DNA transfer + formation of mating pairs
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*State the most common way plasmids are transmitted from one bacterium to another.
conjugation
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*Define horizontal gene transfer.
- The ability of bacteria to adapt to new environments as a part of bacterial evolution
- usually a transfer of genes between relatives of bacteria
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Describe the structure and chemical composition of bacterial ribosomes and state their function.
- ribosomes are made of 30S and 50S subunits
- made of rRNA and proteins
- function = protein synthesis
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In terms of protein synthesis, briefly describe the process of transcription and translation.
- transcription - when mRNA is synthesized from complementary DNA sequence
- translation - tRNAs bring in specific amino acids to form polypeptide chain
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State, in a general sense, how antibiotics like tetracyclines affect bacterial growth
- they bind to the 30S subunit
- prevents tRNA from binding to the A site of the ribosome
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How do antibiotics like macrolides affect bacterial growth
- bind to 50S subunit
- prevent the enzyme peptidyltransferase from forming peptide bonds between amino acids
- this inhibits elongation of the protein
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Name 2 common genera of bacteria capable of producing endospores and state which is an obligate anaerobe.
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*Briefly discuss the function of a bacterial endospore.
serves as a resistant, dominant survival form of the organism
-
Describe the structure of a bacterial endospore.
multiple layers of resistant coats (cortex, spore coat, sometimes an exosporium) surrounding nucleoid, ribosomes, RNA molecules and enzymes
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*Define sporulation and germination.
- sporulation - process where under conditions of starvation, a single endospore forms within some of the bacteria
- germination - process that triggers endospore to grow
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Name three infections that may be transmitted to humans by endospores.
- anthrax
- tetanus
- botulism
- gas gangrene
- pseudomembranous colitis
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*State the chemical composition and 2 common functions of a bacterial glycocalyx.
- composition - a viscuous polysaccharide or polypeptide slime
- 2 functions - allows bacteria to resist phagocytic engulfment & adhere to environmental surfaces, colonize, and resist flushing
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*Briefly describe the following steps in phagocytosis: unenhanced attachment
PAMPs are recognized by endocytic PRRs
-
*Briefly describe the following steps in phagocytosis: enhanced attachment
when microbes attach to phagocytes with the help of opsonizing antibodies (IgG/C3b/C4b
-
*Briefly describe the following steps in phagocytosis: engulfment
polymerization and depolymerization of actin filaments send pseudopods out to engulf the microbe and place it in a vesicle called a phagosome
-
*Briefly describe the following steps in phagocytosis: destruction
lysosomes containing digestive enzymes and microbicidal chemicals fuse with the phagosome containing the ingested microbe and the microbe is destroyed
-
*Briefly describe how a capsule might initially enable some bacteria to resist being phagocytosed by white blood cells.
- the capsule may cover up the PAMPs on the bacteria
- it can also cover up the C3b sometimes and prevent contact with the phagocyte receptor
-
*Briefly describe how opsonizing antibodies made against bacterial capsules help protect the body.
- the opsonizing antibodies can make antibodies against the actual capsule instead of the bacteria
- this helps destroy the bacteria through phagocytosis and protects the body
-
*Define biofilm
groups of bacteria attached to a surface and enclosed in a common secreted adhesive matrix
-
state at least 3 advantages of biofilm formation to bacteria.
- resist attacks by antibiotics
- adhere to surfaces + resist flushing
- resist phagocytes + attacks by the body
- trap nutrients
- communicate w/other bacteria in the biofilm
-
Describe the basic structure of a bacterial flagellum and state its function.
- 3 parts - flagellum, hook, basal body
- function is for locomotion / to keep bacteria in optimum environment via taxis
-
State what provides the energy for bacterial flagellar rotation.
the proton motive force provides this energy
-
Define the following flagellar arrangements: monotrichous
single flagellum at one pole
-
Define the following flagellar arrangements: lophotrichous
2 or more flagella at one or both poles
-
Define the following flagellar arrangements: amphitrichous
single flagellum at one end of organism
-
Define the following flagellar arrangements: peritrichous
flagella over the entire surface
-
Define the following flagellar arrangements: axial filaments
internal flagella (only found in spirochetes)
-
Define taxis.
a motile response to an environmental stimulus
-
Compare and contrast how bacteria with peritrichous flagella and bacteria with polar flagella carry out taxis.
- peritrichous - rotate counterclockwise/left and clockwise/right
- polar - rotate counterclockwise/forward and clockwise/backwards
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*State how bacterial flagella may play a role in the initiation of innate immune defenses.
flagellin protein acts as a PAMP for PRRs, which can initiate inflammatory response
-
*Briefly describe how bacterial flagella and chemotaxis may play a role in the Pathogenicity of some bacteria.
- their motility allows the to move through mucus and get to places other bacteria may not be able to
- spirochetes can penetrate host mucous membranes and enter lymphocytes + bloodstream
-
*Briefly describe how antibodies made against bacterial flagella can immobilize bacteria and/or promote phagocytosis.
- they can stick bacteria to phagocytes so they can be destroyed
- they can also arrest the organism's movement, blocking its ability to spread
-
*State the chemical composition, structure, and function of the short adhesion pili of bacteria.
- composition - short protein shafts with an adhesive tip at the ends
- function - enable bacteria to colonize cells and resist flushing
-
*Briefly describe how antibodies made against the adhesive tip of bacterial pili may block colonization and/or promote phagocytosis.
- the anitbodies can bind to the adhesive tips before they bind to the host cell, preventing it from colonizing
- the antibodies can also stick the bacterium to a phagocyte = opsonization
-
State the function of a bacterial conjugation (sex) pilus.
helps form mating pairs to exchange genetic info between bacteria via conjugation
-
*Define bacterial conjugation.
the transfer of genetic material between bacterial cells through direct cell-to-cell contact
-
*State how the ability to change the shape of the adhesive tip of its pili could be an advantage to a bacterium.
this is an advantage because it can allow the bacterium to bind to various host cells AND evade immune defenses/antibodies
-
*Briefly describe twitching motility induced by type IV pili.
extension and retraction of the pili allow the bacterium to drag itself along a solid surface
-
What PAMPs are associated with gram-positive bacteria
- peptidoglycan
- teichoic + lipoteichoic acids
-
What PAMPs are associated with gram-negative bacteria
-
What PAMPs are associated with acid-fast bacteria
- peptidoglycan
- arabinogalactan
- mycolic acid
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