Exam 1 Flashcards
What is the benefit of being small?
Better chemical exchange wit the environment thus allowing faster growth
What is LUCA?
The last universal common ancestor.
-DNA as genetic material.
-RNA and protein to catalyze reaction
-lipid cell membrane
-two major branches—> bacteria
—> archaea and eukarya
What is the human microbiome?
Microbes that live in and on a human
Why can’t Kochs postulates describe the relationship between all microbes and disease?
Because most microbes cannot be cultured in a lab
What is bioremediation?
The use of microbes to clean up polluted environments
Why are microbes used for bioremediation?
They are able to degrade pollutants because of their metabolism via the biochemical pathways
What is the traditional way of distinguishing prokaryotes and why is it not ideal?
Through the similarities of genome sequence and phenotypes.
-Not all microbes can be cultured in a lab which makes it hard to categorize based on phenotype.
How are prokaryotes classified using OTU?
Classify proteins solely based on DNA sequence information
What is the 16s-rRNA?
encodes the ribosomal RNA
-located in the small subunit of prokaryotes
Cyanobacteria Characteristics
-Oxygenic photosynthesis
-original producer of atmospheric O2
-Produce half of the atmospheric O2
-unicellular and filamentous
-ancestor of chloroplast
Proteobacteria(gram negative)
Alpha- bacteria that live with plants
Beta- include pathogens
Gamma- include enterobacteria, vibrios, and psuedomonads
Epsilon- include helicobacter and pylori
Firmicutes
-Low GC content in genomes
-gram positive phylum but include mycoplasmas
- include endospore forming bacteria, include bacilli and clostridium classes
-include yogurt and cheese bacteria (lactobacillus)
Bacteroidetes
-may be oblige aerobes, facultative anaerobes, or obligate anaerobes
-include the genus bacteroides, which play a major component in the human gut microbiota
Actinobacteria (gram positive)
-high GC content in genomes
-include Streptomycin genus
-soil bacteria
-filamentous
-many species of streptomycin produce antibiotics
Example of Archaea Phyla
Crenarchaeota
-include thermoacidophiles that live in hot springs and prefer pH as low as 2.0
- Many metabolize sulfur
- Many live in the ocean in non extreme conditions
Example of Archaea Phyla
Euryarchaeota
-include methanogens(methane producers) and extreme halophiles( grow in high salt conditions)
In what phylum is streptomycin found in?
Actinobacteria
Define the 4 levels of protein structure
-Primary structure: the linear amino acid sequence
-Secondary structure: a repeating structure due to hydrogen bonds between amino acid side chains; a helix or b sheet
-Tertiary structure: the 3-dimensional structure or “fold”of the protein; depends on hydrogen bonds, electrical charges, and hydrophobic interactions between amino acid side chains; critical for protein function
-Quaternary structure: 2 or more independently-folded polypeptides together in a complex; often held together with disulfide bonds
What is transcription?
The synthesis of RNA from a DNA template by RNA Polymerase
Who are the main players in transcription? Of the players you mentioned,
indicate which ones are enzymes and which ones are regions on DNA or RNA.
RNA polymerase binds to the promoter also known as the transcription site (+1)
-In bacteria the promoter is the -35 and -10 region.
What is translation? Who are the players and how is it initiated?
-Process of mRNA—–> proteins
-Ribosomes, tRNA, amino acids, mRNA
-Ribosome binds to the shine delgarno sequence(ribosome binding site)
What is replication? Where does it begin? who catalyzes the reaction?
-Process of duplicating a DNA molecule
-origin of replication
-DNA polymerase catalyzes the reaction
What is recombination?
Genetic exchange between two different DNA molecules or different regions of the DNA molecule.
When does replication need to occur?
Cells must replicate their DNA before dividing. The new daughter cells must receive a copy of the genome
What are the two main electron microscopy?
TEM: make thin slices of the specimen so electrons can pass through
SEM: produces a 3D image
What does polymyxin disrupt?
Disrupts the structure of the cell membrane
What is passive transport?
Relies on diffusion, does not use energy
What is active transport?
-Requires energy
-mediates the entry of all nutrients
Bacterial vs Archaeal Cell Membrane
Bacterial cells are phospholipid (glycerol esters). In contrast, archael cell membranes;
-May or may not have phosphate(may not be phospholipid)
-are glycerol ethers
-may be lipid monolayers with diglycerol tetraethers
What is the role of the bacterial cell wall?
-Determines shape of bacteria and protects from osmotic stress
What is the bacterial cell wall made of?
-made of murein (peptidoglycan)
What enzyme can digest murein?
Lysozyme
what antibiotics can inhibit the synthesis of murein?
Penecillin and cephalosporins
What is an isotonic environment?
Salt concentration outside and inside cell are the same
What is a hypotonic environment?
Salt concentration outside the cell is less than inside the cell.
-water flows in causing cell to swell and burst
What is a hypertonic condition?
Salt concentration outside the cell is more than inside the cell.
-water flows out of cell causing the cell to shrink
What happens to a bacterial cell treated with lysozyme placed in a hypotonic condition?
-it will lose its shape and then will burst
What happens to a bacterial cell treated with lysozyme placed in isotonic solution?
-it will lose its shape but nothing would occur to it
What are some characteristics of a gram negative bacteria?
-thin cell wall
-outer membrane
-periplasm
-LPS
-Porins
What is LPS?
The outer leaflet of the outer membrane of gram negative bacteria
-has 3 components: Lipid A, core polysaccharide, O antigen
What are porins?
Special channels in the outer membrane of gram negative bacteria
-Diffusion of hydrophilic nutrients
What are acid fast bacteria and what makes them different?
-bacteria in the mycobacteria genus
-have a thick waxy layer of mycolic acid that protects them from disinfectants and acid
- grow slowly due to the lipid layers that slow the entry of nutrients in the cell and require a lot of energy to synthesize
What are mycoplasmas?
Bacteria that lack a cell wall
What is a capsule?
Layer of slime usually made of polysaccharides
-retains water which keeps cell from drying
-helps cells adhere to surfaces
What type of motility do pili do?
Twitching
What is the purpose of pili?
- conjugation( transfer of DNA material)
-fimbriae
—>attachment
—->twitching motility
What are nucleoids and its characteristics?
Nucleoids are where prokaryotes have their nucleus instead of a nucleus.
-its highly supercoiled, condensed, and compacted
-DNA gyrase adds negative supercoils
What antibiotic inhibits DNA gyrase?
Quinolone
What antibiotic inhibits RNA polymerase?
Rifampin
Which antibiotics target ribosome synthesis?
aminoglycosides, tetracyclines, chloramphenicols, erythromycin
Distinguish between soluble and membrane proteins
cell lysis and high speed centrifugation
Test whether protein is located in the cytoplasm
GFP fusion
Test whether protein is in the periplasm
spheroplast formation and centrifugation
Blue PhoA
protein in the periplasm
White PhoA
protein in the cytoplasm
You are studying protein Y in E. coli. You perform spheroplasting and centrifugation and obtain that its in the pellet. If you fused PhoA to the C-terminus of Protein Y, can you predict the color of E.coli expressing this fusion?
You wouldn’t be able to determine the color because the c-terminus in the membrane can be facing the cytoplasm or periplasm.
How are non culturable microbes studied?
using FISH(fluorescent in situ hybridization) which uses fluorescently-labeled DNA probes which hybridize to specific DNA sequences in cells. Also by using fluorescent antibody probe that uses antibodies to identify proteins that are specific to a bacteria.
Minimal medium
A defined medium that has only specific chemical compounds needed for growth
Rich/complex
Abundance of nutrients
-precise chemical composition is unknown
What is the lag phase?
cells are metabolically active but are not growing at full speed during adjustment to new medium
What affects the lag phase?
-number of cells inoculated
-age/growth of cells in inoculation
-anything else that affects metabolism such as type of media or bacteria
What is occurs in the log phase?
-cells are growing at a maximal constant rate
- cells double in one generation time
What affects the log phase?
-anything that affects metabolic rate
What is the stationary phase?
Growth rate is slowed down due to limited nutrients, amount of space, and buildup of waste
How many endospores can be produced by one bacteria?
One
Which bacteria can form endospores?
Firmicutes
—-> Bacillus and Clostridium
Why do bacteria form endospores?
For survival but once there is favorable conditions they are able to germinate again
What is quorum sensing?
Bacteria communicating with one another via secreted molecules called autoinducers.
How does quorum sensing work?
-when a sufficiently high concentration of autoinducer is present, the
autoinducer binds to the LuxR protein, activating LuxR
-active LuxR turns on expression of the lux operon, which encodes the
gene for luciferase (the enzyme that produces light).
What is biofilm?
a community of bacterial cells attached to a
surface by means of exopolymeric substances
Are biofilm bacterial cells planktonic or sessile?
Sessile
Why are biofilms important?
-They trap nutrients for cell growth
-increase antibiotic resistance of bacteria
How are biofilms formed?
-loose attachment to surface
-a stable attachment to the surface via formation of micro colonies
-secretion of exopolymeric matrix that encases the bacteria
Where are biofilms found?
-teeth cavities
-hospital tubes
How do bacteria choose whether to form biofilms?
High levels of cyclic-di-GMP in cells favor biofilm formation
Two ways bacteria become antibiotic resistant
-Mutation in DNA gyrase
-Receiving indole from charitable neighbor
Barophiles
Grow faster at higher atmospheric pressure
Psychrophile
Grow at low temperatures ——-> 5 degrees Celsius
Mesophiles
Live in normal conditions—-> 37 degrees Celsius
Connection between biofilms and increase of heart attacks
Stress—->norepinephrine——>increase in iron in blood——>dispersal of biofilm in plaque——>rupture of plaque from artery wall—->blood clots——>heart attack ot stroke
