Exam 1 (Lect. Qs 1-5) Flashcards
Which of the following structures is found only in Bacteria?
a. cell well
b. flagellum
c. cell membrane
d. nucleus
e. lipopolysaccharide
lipopolysaccharide
which of the following statements about viruses is true?
viruses that infect bacteria cannot infect humans
what are prions?
infectious proteins with no nucleic acid
taken together, the experiments of Pasteur, Tyndall, and Koch demonstrated that….
as long as no living organisms enter a solution, it can be kept sterile indefinitely
there is much interest using bacteriophages to kill the bacteria that cause infectious diseases in humans. which of the following is a valid concern about such therapy?
the virus preparation might be contaminated with a few live bacterial cells
viroids are…
small pieces of RNA without a protein coat
archaea have…
a cell membrane
in Pasteur’s famous experiment that finally disproved spontaneous generation, bacteria grew …
only in media that came in contact with other bacteria
Tyndall repeated the same experiment, but got different results; this was because…
the media he was trying to sterilize contained endospores
which of the following is currently (2008) believed to be a major difference between prokaryotes and eukaryotes
eukaryotes have a nucleus surrounded by a nuclear membrane
which of the following entities make more copies of itself by acting as a template for protein folding?
prion
single-celled photosynthetic organism with nuclei and without cell walls are…
algae
which of the following statements about bacteriophage is correct?
they have a protein coat
how do prions cause disease like mad cow disease?
they act as a template to misfold native proteins
the 3 main branches in the phylogenetic “tree” of life are…
bacteria, archaea, and eukaryotes
which of the following is a hallmark of protozoa, but NOT of bacteria?
endocytosis to engulf nutrients
these viruses infect the bacterium Escherichia coli. which of the following MUST also be true?
they cannot infect humans
prions are infections agents that contain …
protein only
we said in an early lecture that science should be “predictive”. what does this mean?
if you change a variable in an experiment, you know how the results will change
which of the following correctly describes comparisons between Bacteria, Eukaryotes, and Archaea?
only Bacteria have peptidoglycan in their cell structures
last semester, when he was working with bacteriophage in the lab, a student came to me and said his doctor had told him he had a viral infection. he was pretty sure he had acquired the infection from the bacteriophage he was working with in lab. What would you have told him?
Bacteriophage can’t infect humans
why did early attempts to repeat Louis Pasteur’s pasteurization experiments fail?
in 1870 scientists were unaware of any life forms that could survive by boiling water
which of the following best describes the bacterial cytoskeleton?
a helical protein fiber extending from one pole of the bacterial cell to the other
the pictures shown here represent the same organism at different stages in its life cycle. what is the organism?
a type of fungus
a structure that is 50 nanometers in diameter and is composed only of protein, RNA and lipid would most likely be an example of which of the following?
an enveloped virus
which of the following is something that Pasteur could have concluded logically after his swan necked flask experiment?
boiling destroys microbes in broth, and they do not regrow from air
saying that microbes are “diffusion limited” is the same as saying that they..
lack an organized intracellular transport system
what are Archaea?
a kingdom of Prokaryotes that lack peptidoglycan
what is the organism that is depicted in the micrograph at the right?
a protozoan
you have discovered a new organism that is about 200 nm across its largest dimension. it contains DNA, RNA, protein and lipid. it can replicate its DNA, but requires a host cell in which to do that. it appears to have no ATP generating mechanism. what is it? why?
a prokaryote because of its composition
which of the following was true of Pasteur’s famous swan-necked flask experiment?
when a different source of organisms was used, the results were different
the fact that bacteria lack an endomembrane system explains their…
small size
you are examining an organism under the microscope. it is about 15 micrometers in diameter. a chemical analysis shows that it contains DNA, RNA and protein as well as other macromolecules. you grow it on a petri dish to get a pure culture, but this time when you look at under the microscope it consists of filaments 100 micrometers long and 8 micrometers wide. explain this
you are looking at a fungal culture
we mentioned that viroids can infect and kill plant cells. how?
they inhibit protein synthesis by the plant cell
modern biology considers that the 3 kingdoms of life are…
archaea, bacteria, eukaryotes
you inoculate a pure culture onto a petri dish, but when you look at the culture after it has grown, you find both the organisms shown at the right. what is the best explanation for this
your pure culture was a fungus
Eureka! you have discovered a new organism! you decide to analyze it chemically. finding which of the following would mean that your new organism CANNOT be a virus?
NADH
how do prions cause infectious diseases?
they misfold, then cause other proteins to misfold, eventually damaging host cells
Which of the following is NOT caused by hydrogen bonding?
A. protein alpha helices
B. ice floats in water
C. DNA double helix
D. NaCl dissolves in water
E. Hydronium ions form in water
hydronium ions form in water
Van der Waals (hydrophobic) interactions occur when…
a random charge fluctuation sets up a transient dipole in a non-ionic molecule
two molecules with polar covalent bonds are attracted to each other. the resulting bond could be a …
hydrogen bond
weak bonds are caused by …
charge interactions
why is it important that most intermolecular interactions in cells are weak bonds?
they are mores easily reversible
what happens when water hydrates itself?
H30+ and OH- ions form
to have a dipole moment (to be polar) a molecule must…
have a bond in which one atom has a substantially higher electronegativity than the other
which of the following CANNOT participate in hydrogen bond formation?
A. C in C=O
B. H in N-H
C. N in N-H
D. H in C-H
E. O in O-H
the H in C-H
the pH inside a bacterial cell is 7. the pH outside is 6. what is the size of the H+ gradient?
there are 10 times as many protons outside cell than inside
which of the following serve as a hydrogen bond donor?
A. H in N-H bond
B. H in B-H
C. H in C-H
D. O in C=O
E. O in P=O
H in N-H
weak bonds are caused by …
charge interactions
a C-C bond in molecule A undergoes random charge fluctuation. as molecule A comes close to a C-C bond in molecule B, what will happen to molecule B?
a dipole will be induced, which will weakly attract molecule B to molecule A
the hydrophobic effect is used to explain …
how micelles form in an aqueous environment
which of the following pairs of atoms may be involved in hydrogen-bond formation, either as donor or acceptor?
A. C-H
B. P=O
C. C=C
D. S-H
E. Na-Cl
P=O
a difference between strong bonds and weak bonds is that …
weak bonds involve charge attraction between two molecules or within a large molecule
proteins with the amino acid valine on their surface often stick together when placed in water. why?
due to the hydrophobic effect, water forms a network of H-bonds around collected valines
the pH of bacterial cytoplasm is 7, and the pH of the environment where the bacterium is growing is 5. how much difference is there in the H+ concentration between the inside and outside of the bacterial cell?
the outside of the cell has 100 times as many protons as the inside
which of the following statements is true about polar covalent bonds?
electrons in a P.C.B spend more time around one of the bond atoms than the other
what advantage is it for biological systems to use hundreds of weak bonds rather than one strong bond to hold molecules together?
weak bonds can be broken with less energy input than strong bonds
which of the following is a consequence of water forming hydrogen bond networks?
A. water dissolves polar molecules and ions easily
B. hydrophobic molecules form micelles in water
C. water evaporates more easily than most other solvents
D. water consists of mostly H3O+ and OH- ions
E. the hydrophobic effect only occurs in the absence of water
water dissolves polar molecules and ions easily
an acidiphilic bacterium lives in an environment with an external pH of 3. there are approximately….
10,000 times as many H+ outside than inside the cell
which of the following could be a hydrogen acceptor?
A. C in C-H
B. N in C-N
C. P in P-O
D. N in N-O
E. H in C-H
N in C-N
what makes a biological strong bond strong?
electron sharing between atoms in bond
how can the R-group of isoleucine interact with the R-group of valine?
a temporary dipole in isoleucine’s R-group can induce another dipole in leucine’s
which of the following is a consequence of the unique structure of water molecules?
A. water interacts with the fatty acid groups of phospholipids
B. the density of solid water is greater than that of the liquid water
C. there are a small number of ions even in pure water
D. water evaporates more easily than other molecules with the same mass
E. as water is heated, more hydrogen bonds form between water molecules
there are a small number of ions even in pure water
two molecules are composed of the same atoms, but the molecules have different molecular weights. this can be explained by the existence of …
isotopes
in a biological context, which of the following describes a strong bond?
A. all biological bonds are strong, otherwise the cell would disintegrate
B. an attraction between molecules with multiple charges
C. any molecular interaction that requires energy input to break apart
D. many hydrophobic interactions between lipid tails in the cell membrane
E. electron sharing between atoms with an electronegativity difference less than 1.6
electron sharing between atoms with an electronegativity difference less than 1.6
which of following is most important in formation of micelles from a collection of phospholipids? why?
the hydrophobic effect, since without water the micelle will fall apart
in order to make ATP, a bacterium needs a change in pH of about 2. assume ions can pass through porins freely, if the bacterium is growing in a neutral solution, what must be the proton concentration in the bacterial cytoplasm
10^-9 molar
what can you say bout the element Phosphorous from its entry in the periodic table?
with a full outer energy shell it would be a (-3) ion
the amino acid depicted at the right can participate in what sort of tertiary interactions?
van der waals interactions
which of the following is NOT a description of the hydrophobic effect? (picture provided)
a transient interaction between temporary dipoles
enzyme X has the amino acid threonine in its active site. a mutation that replaced threonine with valine would likely have what effect on enzyme X?
it would cause the active site to become partially denatured
we can’t digest cellulose, though bacteria can, because…
we cant digest beta-glycosidic bonds, but bacteria can
nucleic acids are put together from their monomers, nucleotides, with _____ bonds
phosphodiester
rank the following lipids in order from most solid to least solid at room temperature:
1) saturated lipids
2) cis-unsaturated lipids
3) trans-unsaturated lipids
most solid (1)>(3)>(2) least solid
what is wrong with the model of a nucleic acid molecule? (look at picture on key)
model is not antiparallel
which of the following is NOT true of cellulose?
A. it has intramolecular H-bonds
B. it is branched
C. it is linked Beta-1,4
D. it contains just one glucose isomer
E. it is considered biodegradable, even though humans can’t digest it
it is branched (glycogen is)
bacteria can vary the lipids they use in their membrane, depending on the temperature. the goal is to keep the membrane from melting, but not allowing it to get solid that proteins cant move around. how would the membrane of a psychrotroph growing at 28 celcius compare to the membrane of the same organism growing at 5 celcius
it would have more cis-unsaturated lipids at 5 celcius
amphipathic phospholipids form a membrane bilayer if placed in water. what would happen if the membrane were placed in a nonpolar solvent?
the bilayer would fall apart and form a thin monolayer on top of the solvent
AND
it would turn inside out
in a protein tertiary structure, the side chains of the amino acids valine and isoleucine could interact by …
van der waals interactions
which of the following does NOT involve H-bonding?
A. ice floats in water
B. DNA forms double helix
C. lipids form from fatty acids and glycerol
D. evaporation of sweat cools your body
E. water striders can walk on surface of pond
lipids form from fatty acids and glycerol
which of the following describes hydrophobic effect?
hydrogen bonding of water around hydrophobic molecules
in a protein alpha helix, hydrogen bonds form between…
atoms in the peptide bonds that join amino acids together
a great deal of the structure of a bacterium is composed of carbohydrates. which of the following structures does NOT involve carbohydrates?
carboxysomes
a nucleic acid polymer is formed by …
phosphodiester bonds between 5’ and 3’ carbon atoms
which of the following lipids would be the most fluid at room temperature?
lipids with 3 cis-unsaturated fatty acids
which of the following amino acids does NOT have D- and L- sterioisomers: phenylalanine, glycine, glutamate, valine, lysine
glycine
alpha helices and beta pleated sheets …
are both considered to be protein secondary structures
why is it important to understand that glycosidic bonds can have both alpha and beta anomers?
it is much harder to digest beta-glycosidic bonds; only bacteria can do it
this is the structure of DNA synthesis inhibitor and antiviral drug AZT. how does AZT interfere with the structure of nucleic acids so much that it can be used as an antiviral?
its 3’ end cannot participate in a dehydration synthesis reaction
condensation reactions…
usually require energy input
how is H-bonding involved in the structure of cellular lipid molecules?
H-bonding is not involved in the structure of a lipid molecule
which of the following is true about a condensation reaction?
it generally requires energy input
what is a disulfide bond?
a covalent bond that is involved in forming protein tertiary structures
in which of the following polymers would you find alpha glycosidic bonds?
starch
which of following is correct referencing to a hydrolysis reaction?
carrying it out releases energy
beta sheets…
involve peptide bond amino groups as H-bond donors
we know that trans-unsaturated fatty acids contribute to heart disease, but they were formerly in widespread use in the food industry. what was the advantage in using them?
they could be synthesized cheaply by heating cholesterol-free natural oils
which of following would NOT require enzyme catalysis?
folding of a protein into an alpha helix
it is important for a bacterium to keep its membranes from either melting or solidifying as the temperature of the environment changes. membranes of psychrophilic bacteria must therefore have more ____ than membranes of mesophiles
cis-unsaturated lipids
what is currently our best description of a biological membrane?
about 50% protein with phospholipids grouped in mobile rafts between the proteins
which of following is true about weak bonds in protein tertiary structure?
it is important for protein function that they can form and break spontaneously
how does starch compare to cellulose?
starch has fewer hydrogen bonds in its structure than cellulose does
compared to a mesophile, a psychrophile should have
more cis-unsaturated lipids
which of following reactions involves a net release of energy?
making glucose from starch
a phosphodiester bond is important in the structure of…
RNA
what type of microscope views a specimen with light reflected from the specimen rather than passed through the specimen?
dark field
what type of microscope would you use to examine a biofilm that was 2mm thick?
confocal scanning laser
what type of microscope measures electric current passing through a probe rather than using any part of the electromagnetic spectrum?
atomic force
what is the main difference between negative stain and positive stain?
a negative stain is not charged, and stains the background rather than the cell
which type of microscope uses special prisms to make a thin specimen appear pseudo-3-dimensional?
differential interference contrast
what is the main advantage of using an electron beam rather than light to illuminate a specimen?
electrons have a shorter wavelength than light
what is the best technique to use if you wish to count the relative numbers of two different bacterial species on the same slide?
flourescence microscope, with fluorescent antibody stain
which type of microscopy would be most suitable for examining the 3D appearance of magnetosomes inside a bacterial cell?
cryo electron tomography
why cant live bacteria be seen well with a bright field microscope?
the contrast achieved by bright field microscopy is too low
which of following microscopes depends on interference of illuminating waves that pass through internal cellular structures that have a different refractive index?
phase contrast microscope
the important feature of a confocal scanning laser microscope is…
a pinhole that blocks light from all but one plane of a thick specimen
a negative stain is best used to view ____ structures
uncharged
one way to enhance contrast under a microscope without enhancing resolution is to…
use a simple stain
in order to view this specimen, a special technique must be used; why?
this technique must be used to view individual cells
an atomic force “microscopic” is different enough that some people don’t consider it a microscope at all. what is so different about it, compared to other microscope types?
there is no true magnifications system; just a sensitive electrical probe and amplifier
how can the contrast of a microscopic image be improved?
by staining the specimen
these bacteria are about 0.1 micrometers in diameter. how is it that we can see them?
we are illuminating them obliquely and viewing the reflected light
both phase contrast and Nomarski microscopy are based on what optical principal?
passing through a specimen alters the spacing of the peaks in a light wave
this microscope is especially useful for viewing biofilms and other thick specimens. a movable pinhole contributes to the clarity and focus of the image
confocal scanning laser microscope
which type of microscope is best for examining unstained protozoal cells?
differential interference microscope
which type of microscope is the best to use for viewing virueses attached to human host cells?
scanning electron microscope
cryo electron tomography is most useful for..
obtaining a 3D view of internal cellular structures
the acid-fast stain is an example of a differential stain. what makes it “differential”?
it stains special bacterial structures called differentials that are present in some cells AND it uses two stains, along with a solvent that removes stain from some cells but not all
a phase contrast microscope involves the use of which of the following hardware items?
an annular diaphragm and an etched glass plate
for what purpose would you use a negative stain?
to stain the background around uncharged structures
a positive diagnosis for a particular disease is made by examining a throat swab stained with the Acid-Fast stain. what organism is causing this disease?
mycobacterium
the contrast of a specimen viewed by light microscopy can be improved by ..
blocking directly transmitted light
viewing a thick specimen, such as a bacterial biofilm, would likely require which of the following?
a movable pinhole
the bacteria that cause whooping cough are very tiny. you’re trying to examine a specimen from a patient to see if these bacterium might be present, but you’re having a trouble seeing them. what could you do to get a better view?
use a dark-field plate over the condenser to block direct illumination
how can you improve the resolution of a light microscope?
have the light pass through a medium with a refractive index <1
which of the following microscopes depends on the phenomenon of photon drag to differentiate between structures with different refractive index?
phase contrast
which staining technique is correctly matched with a microscope technique for which that stain would typically be used?
acid fast stain and bright field microscopy
a major difference between Gram negative and Gram positive cell walls is …
gram positive walls are crosslinked via a pentaglycine interbridge
the purpose of osmoprotectants accumulating within bacterial cells is to ..
prevent the cytoplasm from shriveling up in hyperosmotic environments
the PMF is used directly for all of the following EXCEPT…
A. flagellar rotation
B. transport through major facilitator (MFS) transporters
C. transport of water through aquaporins
D. ATP synthesis via chemiosmosis
E. transport of amino acid glutamate into the cell
transport of water through aquaporins
in an environment that was isotonic to the cell’s cytoplasm, what effect would penicillin have on logarithmic phase Gram negative rod shaped cells?
the cells would lose their rod shape
what would happen to Mycoplasma cells placed in a solution that was hypotonic with respect to the cytoplasm of the cells?
they would lyse
which of the following transporters requires an ion gradient, not just a membrane potential, in order to move molecules across a membrane?
major facilitator (MFS) symport
How does an amino acid get through the Gram negative outer membrane?
through special facilitated diffusion channels
what part of bacterial cells is called “endotoxin” because of its toxic effects in vertebrates?
lipopolysaccharide
which of following is NOT involved in the formation of a proton motive force (PMF) in bacteria?
a charge separation (voltage gradient) across the cell membrane
is a blood infection with Gram negative or Gram positive cells more dangerous? why ?
G-, because of toxic shock induced by LPS “endotoxin”
Mycolic acids cause mycobacteria to …
resist chemical damage
if a Gram positive bacterium is placed in a solution that is hypotonic with respect to its cytoplasm, how will it survive?
it has a cell wall
LPS is highly toxic to mammals. what feature of LPS make it so unusual compared to other molecules in its class?
it has a lipid that is not based on a glycerol backbone
what is the unique feature of the Mycobacterial cell wall?
it contains a thick layer of very dense lipids
when a Gram positive bacterial cell is placed in a hyperosmotic environment, what happens?
water flows out of the cell through passive diffusion carriers
a typical bacterial cell is growing in a typical culture. it is using the ATP synthase to make ATP. then a scientist adds a chemical to its membrane that permits protons to flow freely across the lipid bilayer. will the bacteria still be able to use its ATP synthase?
no. without a proton gradient, there is no PMF, and no PMF means no ATP synthase
we said that membranes are semi-permeable. which of following can pass freely through the membrane without the use of transport proteins?
small non-polar molecules
what will happen when cells of the bacterium Mycoplasma are placed in distilled water?
they will lyse
some bacteria have mycolic acids in their outer membrane. what property does the mycolic acid give these bacteria?
resistance to chemical disinfectants
some bacterial cells can synthesize osmoprotectants to avoid _______
plasmolysis in a hypertonic environment
most, though not all, bacteria have an electron transport chain. why?
to create a proton gradient
a former student of mine now works as a microbiologist for a company that makes medical implants. his company was thinking of using cell mass as a surrogate measurement for endotoxin concentration. my student wondered whether this was a good idea, and he called to ask me about it. what do you think? was it a good idea?
no. not all bacteria have endotoxin. mass wouldn’t tell you if they have it or not
bacterially synthesized osmoprotectants are most useful to prevent ___ in a ____ environment
plasmolysis ; hypertonic
is it possible for a bacterium to have a PMF if the bacterium is in an isotonic environment?
yes. individual ions can still form charge and concentration gradients even though the overall ion concentration is isotonic
what is the feature of the Mycobacterial cell envelope that is not found in other bacteria?
it contains a thick layer of very dense lipids in its outer membrane
if a typical (non-halophilic) bacterial cell is placed in a hypertonic environment…
it will undergo plasmolysis
which of following is a unique molecule in the Gram positive cell envelope (envelope = wall + membranes))?
lipoteichoic acid
you stain a slide of Mycobacterium according to the Gram stain procedure. what will you see under a bright-field microscope?
it has a very hydrophobic substance in its outer membrane, so it will not stain
cytoplasm in normal cells typically has about 15mM [Na+]. if you placed typical cells in a solution with 150mM [Na+], what would happen?
water would rapidly leave the cells
what is the function of the LPS that is a part of some bacterial cell envelopes?
it is an additional permeability barrier
