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Altius 2,3,4 BB
FLE Exam 2,3,4 Bio/Biochem
Terms in this set (87)
Given a genome content of 50% AT, and assuming random nucleotide variability, the probability of the AUUUA sequence is one in every:
If a genome is 50 % A/T, then it is also 50 % G/C. At each position there is a 1 in 4 (25%) chance of having the necessary base out of the four possible bases.
Why is β-actin used as a loading control in Western blot?
to ensure that the an equal amount of sample is loaded into each lane & to verify that proteins were transferred equally from the electrophoresis gel to the blotting membrane
Where X represents the conjugate base, what pKa is expected to be associated with the smallest H-X bond dissociation energy?
small bond dissociation energy (easily breaks) = weak H-X bond = Strong acid = SMALL pKa
Kw = 10^-14
pKw = 14 = pKa + pKb
Determine net fluid flow across semi-permeable membrane (100mM Na3PO4 on R side, and 200mM NaCl on L side):
formula for osmotic pressure: P = iMRT
i = number of moles (parts) of ions formed per mole of undissolved solute. For a single molecule like sucrose, which does not break apart in solution, i = 1. For the Na3PO4 in Solution A, i = 4.
On the right, there is an osmotic pressure of 4x (bc 4 ions). On the left, there is an osmotic pressure of 2x (bc 2 ions). On the right, there is a molarity of 100mM. On the left, there is a molarity of 200mM.
So there is NO NET FLUID FLOW, because the net effect of osmotic pressure is identical.
The germ cells of a newly discovered diploid organism divide without the DNA replication step that normally occurs prior to meiosis. For this organism, which type of chromosome is found at the metaphase plate during Meiosis I?
In normal conditions, all 46 chromosomes are replicated before meiosis to form DYADS (each chromosome consists of TWO strands of DNA - called a "pair" of sister chromatids). When two homologous dyads pair up during meiosis I, the complex as a whole is called a tetrad/bivalent (4 strands of DNA).
Under the conditions in the question, DNA replication does not occur prior to meiosis so MONADS (each of the 46 chromosomes will only contain ONE strand of DNA - only a "single" sister chromatid)
A student attempts to isolate a solid organic drug compound with a known melting point range of 148-151 °F. An impure sample of this drug is likely to have what melting point range?
Impurities in a solid both DEPRESS the melting point, and BROADEN the range over which the solid melts. (Impurities never increase the temperature at which the solid melts). So a likely melting point range would be 144-150 °F.
The ability of the BBB to regulate flux into and out of the CNS relies heavily on tight junctions. Tight junctions are important in the BBB because:
Tight Junctions seal off the extracellular pathway and require substances to cross the cell membrane, where highly-selective control can be exerted for which molecules do or do not pass through the barrier.
ensure tight associations between cells by stabilizing the cells, but have no clear effect on selective transport
adherens junctions v.s. desmosomes
Adherens junctions form connections between the actin microfilaments of adjacent cells, while desmosomes (made for high stress like skin) form connections between the intermediate filaments. Second, desmosomes look like a patch and occur only at a single location.
Large stores of glycogen in skeletal muscle are critical during prolonged periods of exercise, because:
hydrolysis of ATP is necessary to cock the myosin head, and the binding of ATP to the myosin head is necessary to release the myosin head from the actin filament in preparation for the following contraction cycle
True or False: actin requires ATP for polymerization during muscle contraction
True, Actin monomers (G actin) polymerize to form actin filaments (F actin), but this does not account for the reason why large amounts of ATP are required during exercise
Suppose that for a given cell calcium levels are higher in the extracellular matrix than in the cytosol. If Ca2+ ions enter the cell through ion-specific protein channels, this movement would exemplify what process?
One mole of which lipid (Glycophospholipids, Sphingolipids, Triacylglycerides, or Steroids) will produce the most ATP upon complete oxidative metabolism?
Triacylglycerides bc they are formed when 3 fatty acids are attached to a glycerol backbone. Fatty acids produce the most ATP/carbon of any lipid.
Following ingestion of a meal high in simple carbohydrates, the primary metabolic process at work is:
glycogenesis bc you want to store glucose for the future.
(NOT glycolysis bc it only uses a small amount of glucose before shutting off)
The synthesis of glucagon in pancreatic α-cells is most closely associated with which cellular organelle?
glucagon is a secretory peptide hormone, so it will be translated by ribosomes in the ER
When counting codons, or reading mRNA transcripts generally, it is important to look for the start codon, AUG, first.
This is where translation will begin and it is also the first codon.
The primary mRNA transcript for dystrophin contains 300,000 fewer nucleotides than the DMD gene from which it is transcribed. The primary mRNA transcript is shorter because:
Genes contains large regulatory sequences, such as the promoter region, that are not transcribed. So the primary transcript will always be shorter than the gene itself.
*DON'T include post-transcription processing when answering this question
The average protein is composed of approximately 500 amino acids. This suggests that the average mature mRNA polymer contains approximately:
MORE THAN 1500 nucleotides bc a MATURE mRNA molecule also features additional nucleotides from post-transcriptional processing (untranslated regions on both the 5' and the 3' ends, as well as a poly A tail)
If a woman who is a heterozygous carrier for Duchenne MD has a son with a normal man, what is the probability this son will suffer from Duchenne MD?
50% (XX, xX, XY, xY)
The final electron acceptor during alcohol fermentation in S. cerivisiae (bacterial cell) is acetaldehyde. Is this process analogous to anaerobic respiration in humans?
In humans, when insufficient oxygen is available, glucose undergoes anaerobic fermentation. Pyruvate is reduced and acts as the final electron acceptor. Lactate is the formed in the final step.
[Similar to aerobic respiration, when Oxygen is the final electron acceptor even though water is the final molecule formed.]
What is the intracellular ion concentrations of K+ and Na+ for a resting neuron?
high K+ inside & low Na+ outside
True or false: carbonyl oxygen can act as a hydrogen bond acceptor
(Methane cannot hydrogen bond ever because it has no EN atoms)
The following bacterial cells were grown in a nutritive environment. Following 24 hours of incubation, which bacterial population will include the greatest number of bacteria?
1 cell with a doubling time of 2 hours = 4096 cells in 24hrs
What effect does coordinating a cation (e.g. Zn2+) to a neutral Lewis base have on pKa?
Zn2+ destabilizes the protonated form of the Lewis base. This significantly increases the acidity of any protons attached to the cationic atom of the Lewis base and decreases their associated pKa values.
NADH exhibits a characteristic UV absorbance of 340 nm. This absorbance is the result of photons causing:
NADH absorbs electromagnetic radiation in the UV region as the result of the excitation of pi (π) electrons.
(UV spectroscopy = conjugated systems and transition metal complexes/reactions)
What is a nucleosidase?
an enzyme that cleaves off a nucleoside (a DNA or RNA base attached to a sugar; essentially a nucleotide without phosphate groups)
What are autosomal recessive conditions caused by?
Autosomal recessive conditions result from inheritance patterns. They are not caused by bacterial infections
Autosomal v.s. sex-linked mutations
sex-linked are on sex chromosomes (X or Y)
autosomal are on any other chromosome
What do Short-interfering RNA molecules (siRNAs) do?
interfere with normal mRNA function and have been used successfully in vivo for blocking gene function
siRNA v.s. miRNA
siRNA requires perfect complementarity and will cleave it's target every time. miRNA can bind without being exactly complimentary but will only prevent translation. If the miRNA can bind perfectly it will also cleave the target
Enveloped viruses do not infect cells surrounded by a cell wall. Given this information, an enveloped RNA virus is most likely to infect which host range?
Enveloped viruses can only infect organisms that do not have cell walls.
Animals do not have a wall surrounding their cells. Plants have a cellulose cell wall; bacteria have a peptidoglycan cell wall; and fungi have a chitin cell wall.
Prions are infectious agents composed entirely of protein. In human hosts, prions:
Cannot cause pathology outside the central nervous system.
Although prion infections are usually associated with the consumption of contaminated meat, they can also be inherited and encoded for in a person's DNA.
Prions convert normal proteins of the brain into pathogenic ones. This conversion is exponential and takes years to decades to become pathological
Example of nucleotide sequence of a palindrome:
DNA palindromes read the same from 5'-to-3' on one strand as they do from 5'-to-3' on the complementary strand.
True or False: Ribosomes are composed of both rRNA and proteins
3 types of ROS
H2O2 (hydrogen peroxide)
·OH (hydroxyl radical)
When voltage-gated sodium channels open, Na+ flows into the cell down an electrochemical gradient. Which characteristics most completely describe the thermodynamic properties of sodium influx?
-ΔG, increasing entropy
Sodium is moving down its electrical and concentration gradient. This occurs spontaneously and so it must have a negative ΔG.
Concentration gradient means that the system is displaced from equilibrium. Equilibrium represents an entropy maximum. So if there is movement toward the equilibrium, then entropy is increasing
When testing whether or not the anti-sense oligonucleotide binds and "turns off" the mRNA for Protein X, using a sense-mRNA trial would be useful to demonstrate what?
The sense strand is an excellent negative control as it is structurally and chemically similar to the anti-sense strand without its specific interaction with the Protein X mRNA.
So it would be useful to demonstrate that an inhibitory/stimulatory effect of the anti-sense strand was specific, and not a side effect of adding an oligonucleotide.
Adding the sense mRNA strand did not demonstrate to the researchers that the endogenous mRNA sense strand had not been translated (technically, some sense mRNA not yet bound to the complementary anti-sense mRNA could get translated)
Biologists introduced 35-S into bacteriophage proteins and inoculated cultured bacteria with the labeled phages. From what bacterial centrifugation fraction will the radiolabel be detected?
Viral coat proteins from the extracellular fraction.
35-S will be incorporated into the viral protein, primarily the protein coat. It will not be incorporated into viral nucleic acid, which contains no sulfur.
When bacteriophage viruses infect cells, the protein coat remains outside the cell and the viral nucleic acids are injected into the cell. Thus, the radioactivity would be recovered from the protein coat, which is outside the cell, and not inside the cell.
Researchers added dinitrophenol (DNP) to cultured myocyte mitochondria. If DNP allows facilitated diffusion of protons across the inner mitochondrial membrane without passage through the ATP synthase, what change to ATP levels is expected over time?
Decreasing ATP levels after addition of DNP
During prolonged strenuous exercise, the lactate produced by anaerobic glycolysis is transported to the liver, where it is converted to glucose and metabolized. This process requires the conversion of:
lactate to glucose in the liver
Think of the Cori Cycle
The stimulus frequency applied to the excised mice muscles is intended to mimic:
ACTION POTENTIALS... A muscle contracts and shortens in response to a signal from a somatic motor neuron that generates an action potential in the muscle.
End plate potentials are the depolarizations generated in the muscle itself as a result of the binding of the neurotransmitter.
What is the solubility constant for the dissociation of calcium phosphate is: Ca3(PO4)2(s) ↔ 3Ca^2+(aq) + 2PO4^3-(aq)?
Ksp = [Ca2+]^3 [(PO4)3-]^2
*DOES NOT INCLUDE SOLIDS
What two structural muscle components will produce quantitatively similar twitch myograms?
A single somatic motor neuron innervates a group of muscle fibers called a motor unit. The action potentials delivered by the neuron will be delivered to all the fibers in the motor unit with exactly the same frequency, so the fibers will contract in synchrony. Therefore, a twitch myogram pattern is similar of either a single muscle fiber or all of the fibers associated with a single motor unit.
Do prokaryotes use the formation of mitotic spindles during reproduction?
No, binary fission does not require mitotic spindle formation
During periods of intense skeletal muscle activity, pyruvate is converted to lactic acid and NADH is ___________ (oxidized or reduced) to NAD+
NADH is oxidized to NAD+
What is nondisjunction?
Nondisjunction is the failure of chromosomes to separate during anaphase.
In meiosis, there are two divisions, and the consequences of nondisjunction are different in anaphase I versus anaphase II.
Nondisjunction in anaphase I would cause one cell to have a duplicated copy of both homologues [n+1] and the other cell to have too an aberrant set of chromosomes (aka none) [n-1].
Nondisjunction in anaphase II (after normal meiosis I -> tetrads separate normally) would mean that the 4 resulting cells are [n+1], [n-1], [n], [n]
* Note that nondisjunction during Meiosis II affects only half of the cells
What interaction holds together complementary strands of DNA?
Nucleotide strands are bound together by hydrogen bonds
Phosphorylation is a common mechanism for activating or inactivating an enzyme. Phosphorylation most likely alters enzymatic function because the charge on the phosphate:
Creates a repulsive interaction that causes a conformational change in the enzyme. A repulsive interaction would NOT STABLILIZE a protein structure
An increase in cholesterol has what impact on the plasma membrane?
Increased membrane fluidity at low temperatures and decreased fluidity at high temperatures
Do carbonyls act as electrophiles or nucleophiles in reactions?
Carbonyls are electrophiles in reactions, where the electrophilic carbonyl carbon is attacked by a nucleophile
Do amines act as electrophiles or nucleophiles in reactions?
All amines contain an active lone pair of electrons on the very electronegative nitrogen atom.
Amines act as nucleophiles in all cases, other than protonation to form a quaternary amine.
True or False, thiols and alcohols are both nucleophiles
True, they both act similarly
what are the two MOST common nucleophiles found functioning in enzyme active sites?
alcohols and amines
During prolonged starvation, the human body begins metabolizing structural proteins for energy. Metabolism of structural proteins requires which transition?
Protein metabolism is a catabolic process, breaking larger polymers into monomers. Proteins are NEVER changed into lipids and then metabolized. Proteins are broken down into their amino acids and then fed into various steps of the citric acid cycle.
Inactive osteoclasts feature smooth cell membranes, while activated osteoclasts feature a ruffled cell membrane with numerous invaginations. What is the most plausible purpose for this change in cell membrane morphology?
To increase cell membrane surface area
One of the bone-resorbing enzymes secreted by osteoclasts requires a covalently bound zinc ion to exhibit normal enzyme function. In this scenario, zinc is acting as which of the following?
I. a coenzyme.
II. an allosteric effector.
III. a prosthetic group.
Zinc is an example of a prosthetic group only. Prosthetic groups are non-protein cofactors that are tightly bound to an enzyme and necessary for function.
Coenzymes are organic molecules that are required by an enzyme to function, but are not usually covalently bound. They are differentiated from prosthetic groups because they are loosely bound to the enzyme, whereas prosthetic groups are tightly bound (usually, but not universally, via a covalent bond). While coenzymes are always organic non-protein molecules, prosthetic groups can be either organic or inorganic. Because zinc is covalently bound to the enzyme, it is not "loosely" bound and therefore cannot be classified as a coenzyme.
Allosteric effectors are molecules that bind to an enzyme at a site other than the enzyme's active site and regulate its function. Because allosteric effectors either upregulate or downregulate enzyme function, zinc cannot be an allosteric regulator since the enzyme cannot function without the zinc and enzyme can function without allosteric modulators.
What do vaccines expose the host immune system to?
Vaccines expose the host immune system to viral antigens that are part of the viral capsid. These antigens will induce the production of antibodies in the host.
What physiological process prevents cross-species fertilization among hominids?
Species-specific receptors expressed on the outside of the egg, which are bound by species-specific ligands expressed on the outside of the sperm.
True or False: Eggs fertilized with sperm from another species are always unviable
False. Eggs fertilized with sperm from another species do not always die, if the genetic material is almost identical. An example is the ability of a horse and a donkey to mate and produce a mule.
What is polyspermy?
the fusion of more than one sperm with the egg
Would exhalation of carbon dioxide decrease blood acidity?
Yes, because exhaling carbon dioxide drives the bicarbonate buffer reaction to the left, which consumes H+ ions (blood becomes less acidic)
Would conversion of bicarbonate to carbon dioxide in the blood decrease blood acidity?
Yes, because this is a leftward reaction of the bicarbonate buffer system, which consumes H+ ions (blood becomes less acidic)
Would excretion of protons into the urine by the kidneys decrease blood acidity?
Yes, because this is directly removing H+ ions from the blood
Would release of H3PO4 into the blood stream decrease blood acidity?
No, because the release of phosphoric acid into the blood would directly increase blood acidity. Phosphoric acid will not only dissociate into dihydrogen phosphate and a hydrogen ion, but the resulting dihydrogen phosphate will result in the formation of additional protons
True or false: Blood clotting requires calcium
If a man and a woman, both heterozygous for a mutant autosomal dominant gene HD, have a child, what is the probability the child will develop Huntington's Disease?
75% (HH, Hh, Hh, hh)
Many viruses that invade human hosts have developed the ability to inhibit normal cellular transcription by expressing inhibitor molecules that act in the:
Transcription occurs in the NUCLEOPLASM of the nucleus. RNA polymerase uses the DNA template of the chromosomes to produce a pre-mRNA. The pre-mRNA is then processed to mRNA and moves to the cytoplasm for translation.
Protein-based vaccines stimulate an immune response because they:
contain antigens similar to the antigens found on pathogens
This allows the host immune system to initiate a primary immune response and prepare for a secondary immune response without an actual pathogen infection. AKA Adaptive Immunity
What is the difference between viral vaccines and bacterial vaccines?
viral vaccines contain viral capsid proteins
bacterial vaccines contain surface proteins
What are the common components of a non-specific innate immune response?
recruit inflammatory cytokines and increase blood flow
What amino acid is Q?
What amino acid is N?
What tool is most effective for verifying chromosome fragmentation?
gel electrophoresis bc the migration pattern of DNA on the gel would differ significantly compared to a control with intact chromosomes, making fragmentation easy to visualize
Do human cells undergo transformation?
No, only bacteria undergo transformation (the random assimilation of naked DNA from the environment)
The bond between Ctx and EGFR is most accurately described as an interaction between:
an antibody and an enzyme
Although these are 2 proteins, the best answer choice is the most specific/complete
Pattern of cancer prevalence among an aging population
Sigmoidal curve, bc there is an initial lag phase (very few cancer cases) as the inactivating mutations to tumor suppressor genes accumulate with age and repeated cell divisions. Once a certain threshold is met, then the rate should steadily increase. However, additional accumulations are unlikely to cause additional cancer prevalence once sufficient mutations to cause cancer have already occurred. This suggests a final leveling off in cancer prevalence.
Suppose a novel protein is discovered that is easily incorporated into micelles. This protein is most likely:
an integral membrane protein has both hydrophobic and hydrophilic
Micelles are spheres of amphipathic molecules, usually lipids, with hydrophilic heads on the surface of the sphere and hydrophobic tails pointed into the center of the sphere. Because of this, a protein that can integrate into a micelle must also be amphipathic, featuring both polar and non-polar regions.
Are peripheral membrane proteins found in micelles?
No, most peripheral membrane proteins interact solely with the polar head groups of the membrane, or with the polar regions of other integral proteins, and as such their surface regions are hydrophilic
What macromolecule is capable of acting in vivo as a structural component, a catalyst, and a mediator of cell communication?
Eukaryotic plasma membranes usually contain which of the following?
All of them.
Major Histocompatibility Complex II (MHC-II) proteins are cell surface proteins that function in the immune system to accomplish antigen presentation. Following translation, what organelle is responsible for trafficking these proteins to the cell surface?
Lupus, an autoimmune disease, causes the immune system to target healthy tissue. Lupus most likely leads to the production of:
antibodies against self-proteins, increasing inflammation.
Under normal physiological conditions, double-strand DNA breaks (DSB) are repaired by what mechanism?
What experiment would demonstrate that RPA binds preferentially to ssDNA over dsDNA?
Kd values for RPA binding to ssDNA compared to dsDNA.
Comparing either the association (Ka) or dissociation (Kd) constants would quickly verify which form of DNA the RPA binds more tightly.
During the repair of a DSB in human DNA, which nucleotide polymer is used as the homologous template?
When homologous recombination is used to repair a double-strand break, the template used is the sister chromatid. During this process, the recombination machinery seeks out DNA that compliments the overhangs on each side of the break, and the sister chromatid will have that exact sequence. The sister chromatid is not likely to be damaged in the same region that the broken DNA on the other chromatid, so incorporating DNA from the sister chromatid is an efficient method.
Although the average pKa of the Glu side chain is approximately 4.2, the enolase enzyme contains a glutamate in its active site that is protonated at physiological pH. This Glu residue is protonated because:
The local environment causes the pKa of the Glu side chain to become more basic (increases the pKa), causing the proton on the Glu side chain to remain bound.
A single-cell diploid organism acquires a deleterious point mutation before entering mitosis. If one of the daughter cells reproduces asexually, and the other daughter cell goes through meiosis to produce gametes that fuse with gametes from other individuals, which cell lineage will be most evolutionarily successful?
The sexually-reproducing lineage, because only one-half of the offspring will have the mutation. The point mutation will affect only one set of chromosomes in a diploid organism. Asexual reproduction will transmit the mutation to all progeny, for all subsequent generations. By contrast, sexual reproduction will result in only half the progeny in the first generation inheriting the mutation. These progeny will thrive and produce subsequent generations of mutation-free offspring.
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