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Terms in this set (210)
The basic principal behind microscopes is that
magnification leads to better resolution
In _____ microscopy, the light rays that are usually scattered from the object are condensed and used for visualization.
Bright field microscopy and phase contrast microscopy have this in common
the field is bright in both
Unlike electron microscopy, we don't coat objects with heavy metals in light microscopy because
objects inherently absorb light and electron beams are not used in light microscopy
Out of all microscopy types we studied, this is the only one that shows images in 3D
Functions of the cell wall include
resistance to turgor pressure, conferring shape, conferring rigidity
Lipopolysaccharide is present in the cell envelope of
gram negatives only
Gram positive bacteria have ______ strands of peptidoglycan in their cell wall than (as) Gram negative bacteria
This will only appear in Gram negative bacteria cell envelope
o-antigen and lipid A
Bacteria are prokaryotes and so they don't have a true nucleus. They instead have their genetic material packed in the form of ______
These are trace elements required by the cell in small amounts
Cell membranes are _________ structures.
You have isolated a bacterium from the rumen of a cow and wish to know how it transports the sugar "whonose" into the cell. You perform an experiment that shows that whonose is chemically modified during transport. What is the mechanism of "whonose" transport into this cell?
This type of culture media has a defined composition
Which of these are resistant to antibiotics?
endospores and inner layer of biofilms
At the optimal growth conditions of an organism, its _______ are most functional, and its _______ are intact.
________ require a high concentration of salt to grow.
In which stage of bacterial growth are bacteria preparing to grow?
Which of the following is NOT a physical means to control microbes?
Large and/or charged molecules can diffuse through the cell membrane
All forms of transport across the membrane require some form of energy expenditure
If you irradiate a sample with UV rays, then that means you have sterilized your sample
A eutrophic lake could possibly be also devoid of oxygen.
An example of a resistant form of growth that starts by attachment to surfaces is the resistant endospores
On the ocean floor, it is common to find a psychrobarophile.
A strictly aerobic halophile is expected to thrive in animal guts
Compared to light microscopy, electron microscopy can be used to resolve smaller objects
In order to increase the resolution in light microscopy, one can use specimens that are not fixed to the slides.
In the microbial world, all organisms are about the same size.
The smallest distance by which two objects can be separated and still be distinguished
The sudden introduction of large quantities of a previously limited nutrient in an ecosystem
The time it takes for a population to double
The apparent increase in the size of an object
Growth temperature 0-20oC
Growth temperature 40-80oC
pH range 0-5
pH range 5-8
low levels of O2
can grow in either presence or absence of O2
high pressure up to 1000 atm
pH range 9-11
Will not grow in the presence of even the smallest concentration of O2
Phospholipid bilayer + proteins
The attached image shows the process by which bacterial cells form twists in their DNA so that they can pack it in their nucleoid region. The process starts with the DNA in a relaxed state (the circle) and then introduces twists (one of them is shown). Going through this process several times would produce a(an) _____ molecule. Enzymes that increase and decrease this state are known as _______.
In the process of DNA replication shown for the double strand, the _____ is replicated continuously, while the ______ strand is replicated in fragments. This is because the replication enzyme can only work in one direction 5' to 3'
In order to avoid any detrimental scenarios that could occur during DNA replication prior to cell division, the process of replication happens in a _________ manner where each of the daughter cells will receive a double stranded DNA where one strand is old and the other is newly made.
In DNA structure, _____ on one strand binds to ______ on the opposite strand via _____ H-bonds.
C; G; three
In transcription, the sigma factor binds to a gene ______ upstream of transcription start site
In translation, there are 64 possible ______. ______ of them don't code for any amino acids and are used as ______ .
codons; 3; stop codons
Every tRNA molecule has _____ functional regions.
Following DNA transfer, and in cases where the recipient cell needs the uptaken DNA, the received DNA can integrate into the chromosome by a process known as _________
In the figure attached, the cell's own enzymes (shown as scissors) are chopping the incoming viral DNA. The enzymes are not attacking the cell's own DNA. What do we call these enzymes, and how is the cell's own DNA protected?
restriction enzymes; labeling the DNA with methyl groups
Why do cells need to import DNA?
to fix a damaged genome, to use it as food, to adapt to new environments
This level of control of gene expression is the most drastic and least reversible
Imagine the following scenario. A regulatory protein is binding upstream of a gene and is preventing RNA polymerase from binding. This would be an example of regulation of gene expression at the _______ level
RNAses attack a newly made mRNA and prevent it from serving as a template for translation. This is an example of regulating gene expression at the _________ level.
DNA polymerase needs a short primer laid down first before it can start adding nucleotides to the newly-made strand.
RNA molecules are always single stranded
Because in EUKARYOTES transcription occurs in the nucleus and translation occurs in the cytoplasm, the two processes are not coupled.
Most of the functions in the cell are carried out by mRNA
It is common to find thymine (T) in RNA molecules.
For the most part, mRNA codons are the same in different organisms. This means that the genetic code is UNIVERSAL.
There are many reasons for DNA uptake by the cell. However, DNA uptake following conjugation is mainly for increasing the competitiveness of the recipient cell.
In the bacterial world, it is impossible to change gene expression once the mRNA is made.
The term mutation means a change in the nucleotide sequence in the DNA that ALWAYS leads to a change in the protein.
Gene transfer is known to occur between different cells in an environment. There is only one way for this to occur.
The enzyme in replication that does the actual copying
The enzyme in transcription that does the actual copying
The enzyme in replication that unzips the two strands by breaking the H bonds
The enzyme in replication that lays a short RNA primer
The enzyme in replication that removes the short RNA primer
The enzyme in replication that closes the gaps between Okazaki fragments
The template carrying the code to be translated
The housing where the process occurs
The molecules carrying the amino acids
The number of pockets in the ribosomes
The number of ribosomal subunits
The pocket accepting the newly incoming amino acid
The pocket with the uncharged tRNA
The pocket with the growing peptide chain
The region in the tRNA that recognizes the codon on the mRNA
The cell moves towards or away from a chemical by rotating its flagella
Cells work together at high cell density.
Order of Transcription
Sigma factor binds to a region upstream of the gene, the actual copying occurs,Rho binds and RNA polymerase falls off
Order of Replication
Recognition of ori site, Unzipping of the two strands and starting the actual copying, Recognition of ter sites
Order of Translation
The ribosomal subunits sandwich the mRNA, amino acids are added to the growing peptide chain, stop codon in the A site
In the presence of glucose and if the bacterial cell has all enzymes needed for both EMP and ED, which of these pathways would the cell rather go through to metabolize glucose?
What are the products of the ED pathway from 1 glucose?
2 pyruvate+ 1 NADH+ 1 NADPH+ 1 ATP
What are the products of ethanolic fermentation from 2 pyruvates?
2 ethanol+2 CO2
During respiration, which step(s) produce(s) NADH?
PDC and TCA
In a respiring cell, if it runs out of the electron acceptor, it will need to revert to ________ to recycle NADH to NAD.
The proton motive force drives the following process in bacteria:
nutrient uptake, flagellar rotation, ATP biosynthesis
Ammonia oxidizers are organisms that have an ETS in their membrane and they can use NH3 as their electron donor and O2 as their electron acceptor. Based on this information, what kind of process do ammonia oxidizers carry?
From your knowledge about electron donors, which of these do you think could be an electron donor?
H2S, H2, NADH
Water can act as an electron donor to the ETS. But since water is a very stable molecule, energy from light is required to release the electrons from water. What would this make organisms that use water as an electron donor?
In class, Dr. Youssef told us that the majority of lithotrophs use CO2 as their carbon source. What would this make the majority of lithotrophs?
What are the requirements of biosynthesis?
NADPH, ATP, (C,N,H,O)
In amino acid synthesis, the transfer of amino groups between two metabolites is called __________
In biosynthesis of purines and pyrimidine, which of these is made first?
What organism did we talk about that is capable of carrying out oxygenic photosynthesis, CO2 fixation, as well as N2 fixation?
What do Nitrogen fixation and CO2 fixation have in common?
They both are carried out by only a handful of organisms (i.e. they are not widespread processes), They both require a large input of reducing power in the form of NADPH, They both are energy intensive processes
Which of these receive electrons from NADH during fermentation?
Which of the following is a terminal electron acceptor in anaerobic respirations?
sulfate or nitrate
In class we talked about how electron cannot "fly" or "swim" and that for them to move from one substrate to the next they need to be carried on electron carriers. Accordingly, how many forms does an electron carrier have?
In green plants, CO2 is fixed through __________
the Calvin cycle
Nitrogen fixation is found only in a few organisms and is tightly regulated because
nitrogen fixation is energy-intensive
A lithoautotrophic cell produces ATP both by substrate level phosphorylation and oxidative phosphorylation
The minimum number of components in an ETS is 2
There does not exist an anaerobic lithotroph.
Both chemolithotrophs and photolithotrophs use light as their source of energy.
The main reason a cell undergoes fermentation is to make ATP
Chemotrophs organize their light-absorbing pigments (chlorophyls) in the form of antenna complexes to maximize light absorption.
Anabolism or Biosynthesis is defined as the breakdown of large complex molecules into smaller ones to produce energy
Oxygen is a highly oxidized molecule. Accordingly, it can act as an electron donor.
In fermentation all carbon in the original carbon source will eventually be released as CO2
A strictly fermenting cell would also have the enzymes for the PDC (pyruvate dehydrogenase complex) and TCA (tricarboxylic acid or Kreb's cycle) steps of respiration
Key enzyme of CO2 fixation via Calvin cycle
Key enzyme of N2 fixation
Key enzyme of Fatty acid synthesis
Fatty acid synthase
An organism using NADH as the electron source, glucose as the carbon source, and does not require light to grow.
An organism that uses H2 as the electron source, CO2 as the carbon source, and and does not require light to grow.
An organism that uses H2O as the electron source, CO2 as the carbon source, and and requires light to grow.
One of these processes does not employ an ETS: fermentation, respiration, lithotrophy, photosynthesis. Which one?
PDC, TCA, ETS
CO2 fixation using Calvin cycle in Cyanobacteria
Nitrogen fixation in Cyanobacteria
Electron transport systems in prokaryotes
EMP and TCA
The best definition for clade is _______
a group of organisms or species that share a common ancestor
Horizontal gene transfer refers to the transfer of _____ between unrelated species
a piece of DNA containing a gene or a group of genes
Syntrophy refers to ______
symbiotic relationship where both partners depend on one another for the completion of their metabolism
Which set of essential genes are still encoded on the chloroplast genome?
The marker gene most commonly used for constructing phylogenetic trees is _______.
small subunit RNA
What do Firmicutes and Actinobacteria have in common?
both Gram +
Sulfate reducing bacteria belong to the ____ class of Proteobacteria.
Which of these Firmicutes genera form spores upon exposure to unfavorable conditions?
You can expect to find halophilic archaea in all these habitats except _____
The fungal phylum in which morels and truffles can be found is:
Consumers and decomposers break down organic nutrients to inorganic minerals. In an ecosystem, consumers and decomposers are _______.
Bacteria and methanogens are present in the termite gut and aid with wood digestion. What is the relationship of bacteria and methanogens TO EACH OTHER?
In the ocean, phototrophs are present in
neuston and euphotic zone
In soil, who are the major primary producers?
In the anaerobic C cycle, organic C can be converted to CO2 via ______
anaerobic respiration or fermentation
C in the ______ recycles fast
Eutrophic lakes have ____ biochemical oxygen demand (BOD)
_____ is the most oxidized form of nitrogen. Accordingly, it can only be reduced in the N-cycle.
Sulfate (SO4) can act as an electron ______ in the S cycle.
The reservoir of an element is the part of the biosphere that contains significant amounts of that element. A reservoir can be ____
a sink of the element for those processes producing this element, or
a source for the element for those processes using the element
All life forms have DNA as their genetic material, that through the processes of transcription and translation will produce proteins that carry out the function.
Methanogenesis is a process exclusive to the bacterial domain.
In the taxa hierarchy, phylum is at a lower taxonomic level than species.
Carbonate rock is the largest reservoir of N.
In wastewater treatment plants, the relationship between the aerobic hetertrophs and methanogens is endosymbiosis
One expects to find strict anaerobes in the top aerated layers of soil
A symbiotic relationship in which two partners benefit is known as mutualism.
Primary producers 'carry the ecosystem on their shoulders'. They carry out processes like respiration and fermentation
In the aerobic C-cycle, methanogenesis is one of the processes contributing to C element recycling
One of the three forms of S we talked about in the S cycle (H2S, SO4, and elemental S) could either be reduced or oxidized. This form is H2S.
Help keep the H2 concentration down to ensure the completion of wood digestion
Termite gut methanogens
aid in the breakdown of wood to simple nutrients that the termite can absorb
Termite gut bacteria
Help keep the H2 concentration down to ensure the completion of complex plant fiber digestion
aid in the breakdown of complex plant fibers to simple nutrients that the cow can absorb
Rumen bacteria and fungi
provide photosynthesis-rich nutrients (or in other words carry out photosynthesis and CO2 fixation and provide the fixed C to the partner)
Plant in the plant-fungal mycorrhizal interaction, Algae or Cyanobacteria in lichens, Plant in the rhizobium-plant interaction
Protection of the system
Fungus in lichens
Extend to meters away and provide nutrients (especially P)
Fungus in mycorrhizae
Provides fixed nitrogen in the form of NH3
Bacteroid inside the leguminous plant root cells
Uropathogenic E. coli
Boils and exfoliative skin disease
Primary immune response
Generates memory B cells and plasma cells, Antibodies appear in blood days after exposure to antigen, initiated with first disease encounter or vaccination
Secondary immune response
Stored memory B cells are activated to produce antibodies, initiated with a second exposure to antigen or a booster shot, antibodies appear in blood within hours
salty and oily excretions
Lysozymes break down pathogens
Some pathogens evade host immune response by changing their surface antigens
Exotoxins belonging to the superantigen class act by cleaving proteins binding host cells
Opportunistic pathogens cause disease in healthy hosts
T cells can bind to antigens that are free or unbound to MHC proteins
The antibody response following secondary exposure to an antigen is usually very weak
T cells are only part of the cell-mediated but not the humoral immunity
Some complement components can be part of the adaptive immunity
Gram negative bacteria are better at colonizing the skin than Gram positive bacteria
A commensal in one body site might cause disease in another
Healthy humans are not colonized by microorganisms
Which of the following bacteria survive in the acidic environemnt of the stomach and result in gastric ulcers?
Which of the following is likely to cause meningitis?
Which of the following does NOT cause a sexually transmitted infection?
Bordetella pertussis causes what sickness?
Which of the following pathogens is transmitted by a tick and results in a bull-eye rash?
During _____, an immunogen is delibrately introduced in the human body. Following the first encounter with the immunogen, the first antibody to appear in serum is the _____.
immunization or vaccination; IgM
All of these are examples of horizontal transmission of disease EXCEPT
From a parent to an offspring
Which of the following best describes a vector for a disease
an insect or a tick that transmits the pathogen from one host to the next
Out of all the secretion systems we discussed, this one is the most efficient in delivering toxins to the target host cells
When comparing two pathogens, the one with a higher LD50 is
Which region of an antibody binds and is specfic to an antigen?
This immunoglobulin is more common in secretions like breast milk or tears
This refers to the immunogenic part of the pathogen, aka the part of the pathogen that will elicit immune response when introduced in the body.
Following primary encounter with an antigen, what do we call the process of the search for the B cell with the best match to that antigen.
These are secreted by T-cytotoxic cells to poke holes in their target cells
Lactobacillus acidophilus is part of the normal flora of
______ are a series of serum proteins (20 in number) that get activated and punch holes in the membranes of bacteria as part of the innate immune defense
Which of the following is a benefit of commensal microbes to the human host?
prevents colonization by pathogens,makes vitamins, helps digest food
Which of the following body site(s) is/are sterile in healthy individuals?
kidney, bladder, lungs
To avoid being flushed to the acidic stomach, all colonizers of mouth and nose should have the ability to
adhere to surfaces
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