Biology Frequently Missed Questions
How many moles of NADH and FADH2 will be produced when one mole of Pyruvate is being completely oxidized to CO2?
4 NADH (1 NADH at PDH + 3 NADH in Krebs) 1 FADH2 (in krebs)
Which of the following molecules can your cells use as a precursor for glucose synthesis? (answer yes or no) (5 pts) - Acetyl-CoA - Malate - triacylglycerol - Fatty Acid - Fructose 6-phosphate
Acetyl-CoA __no___ - Malate __yes__ - triacylglycerol __yes__ - Fatty Acid __no___ - Fructose 6-phosphate__ yes__
Would the 4 bases found within a single tRNA molecule obey Chargaff's Rule? Why?
Chargaff's rule only applies to double-stranded molecules; DNA. tRNA is a single stranded molecule
How might you use PCR to test for HIV? Be very specific how mught you design the test
Design primers that bind viral DNA in the nucleus and have it amplify the HIV DNA **getting a product from the PCR would be the test
Decades ago, there was a hypothesis called the 'one gene, one protein hypothesis' which is now known as the 'one gene, one polypeptide hypothesis'. Based on your knowledge of biology, why was this revision necessary? Describe an exception to the new version?
Most proteins are composed of more than one polypeptide. Exception - alternative splicing of introns results in more than one polypeptide per gene
Describe glycolysis in terms of phosphate groups. Explain the different roles of phosphate groups in different stages of glycolysis. Be as specific as possible. Include in your answer, the origin and destination of each phosphate.
Overall 4 phosphates are attached to 4 of the 6 carbons originating from glucose. The first 2 phosphates come from ATP while the second 2 phosphates come from inorganic phosphates (Pi). The 4 phosphates are then transferred to ADP to make 4 ATP
In 1935, Albert Szent-Gyorgi showed that the production of CO2 by the a cell extract (which includes active enzymes) increased when succinate was added. For every mole of succinate added, many more moles of CO2 were produced. Explain this effect in terms of the known catabolic pathways.
Succinate is an intermediate in the citric acid cycle that is not consumed, but is regenerated by the operation of the cycle. Its addition to an extract allows the citric acid cycle to operating at a faster rate, oxidizing acetyl-CoA to CO2.
In epinephrine/adrenaline signaling, describe three separate roles of nucleotides or nucleosides outside of the nucleus.
When epinephrine binds to its receptor on a muscle cell (a type of G protein coupled receptor) it triggers a signal transduction cascade involving the production of the second messenger molecule Cyclic AMP (cAMP)
Two major conclusions of the Ribonuclease A experiments regarding protein folding are i) the primary structure of a protein contains the information necessary for the 3D structure, and ii) Cooperative folding. What experimental results led to these conclusions? Describe the portion of the experiment and relevant results that led to each of these conclusions, and why this is a logical conclusion.
i) after the protein was denatured, it returned to its native structure when denaturing agents were removed. ii) allowing disulfide bonds to form but not H bonds (disrupted by Urea) results in incorrect disulfide bonds.
What is the general chemical formula of a monosaccharide?How does this compare to amino acids?
monosaccharides = CnH20n Amino acids do not have one chemical formula, but all have at least one C, >1 H, at least 2 O and must include N. two amino acids also require S
You suspect that your friend has inhaled a radioactive isotope of oxygen (18O2). Minutes after inhalation, what molecule(s) do you expect the 18O to be part of? Why?
the O2 is converted to H2O in complex 4 of the mitochondria
Explain how changing a single nucleotide within a gene can have the following result. (i) A peptide with a single amino acid different. (ii) A peptide with the same primary sequence only at the N terminal end. The C terminus has a completely different primary sequence. (iii) Much less of the protein made, but protein structure is unchanged (iv) no change
(i) changes AA one codon into another (ii)frameshift mutation - either add or subtract one nucleotide within the coding region, changing every subsequent codon (iii)must have changed something in the regulatory region (iv) may have changed one codon to another, but with the same AA resulting. or it was in an intron or other non-coding region of a gene.
Which of the following is not a potential point of regulation of gene expression? (3 pts) (i) The level of transcription (ii) The level of processing mRNA (iii) The level of mRNA stability (iv) The level of translation (v) All of the above are potential points of gene regulation.
(v) All of the above are potential points of gene regulation
Which of the statements below about the citric acid cycle is false? (3 pts) (i) CO2 is released during operation of the cycle. (ii) The cycle takes place largely in the mitochondrial matrix. (iii) Some amino acids can be converted into intermediates of the cycle (iv)The cycle requires NADH and FAD2. (v) Inhibit mitochondrial ATP synthesis (iv) The cycle does not operate under anaerobic conditions.
(v) Inhibit mitochondrial ATP synthesis
What is the difference between LB and M9-Glucose media? When/why was either used ?
-LB was very media rich and ensured the growth of the bacteria/cells -M9-glucose media allowed for minimal growth of the bacteria/cells -Both were used as means of controlling the experiment (positive and negative controls)
The gates responsible for returning to resting potential...
-both the voltage-gated K and Na channels Resting potential is established because only leak K+ channels are open
Why do you think that kidney's are affected by diabetes/high blood pressure?
-glomerialus and bowman's capsule can be damaged if the blood pressure is too high for too long -extra sugar in the blood is very reactive and can bind to proteins unenzymatically inhibiting protein function
How did the "binary pattern of polar and nonpolar residues " assure that the protein would be globular? Why was it important that the proteins would be globular?
-hydrophobic effect -because they wanted to create enzymes (enzymes are globular and compact so they can interact)
What is the boundary stopping us from curing HIV? Knowing this, how might we go about finding a cure?
-the latent reservoir -SHOCK AND KILL SRATEGY; wake up latent viral reservoir then kill the infected cells GENE EDITING; editing T-cell receptor genes; edit them to make a similar change to those who are resistant to HIV (changing the CCR5; second receptor via CRISPR) DUAL ANTIBODY TREATMENT transfusions of antibodies after infection GENE EDITING of HIV CRISPR would modify HIV genes to stop them or add stop codons where they don't belong
Dosage compensation is necessary due to unequal gene dosage for X-linked genes. Briefly describe the three different dosage compensation strategies.
1. condense and deactivate one X chromosome in females (or all but one X chromosome) 2. double transcription on the X chromosome of males. 3. reduce transcription by half on both X chromosomes in females.
How might you use a Western Blot test for HIV ?
1.) ELISA- looks for antibodies, if positive Western Blot is preformed 2.) Western Blot- uses antibodies which bind to HIV and looks for HIV proteins
Describe the life cycle of HIV
1.) fusion of the HIV cell to the host cell surface 2) HIV RNA, reverse transcriptase, integrase and other viral proteins enter the cell 3) viral DNA is formed via reverse transcriptase 4) viral DNA is transported across the membrane/ nucleus and integrates into the host cell 5) New viral RNA and proteins move to cell surface and new, immature, HIV forms 6) the virus matures by protease, releasing individual proteins
What is an Operon? Why do prokaryotes have operons but eukaryotes do not? Be specific.
An operon is a collection of genes all under the control of the same promotor. Eukaryotes do not have operons, each gene is made on individual mRNA each with their own promotor. (polycistronic mRNA) They don't need operons because Eukaryotes use other means of gene regulation; for example histone modification and alternate splicing.
How would kidney function differ if the nephron is shorter/longer w/o a loop?
Aquaporins are present in the first ascention (into the cortex) it moves down to a saltier region as water leaves via osmosis -after the loop of henle; the ascention back upwards becomes less concentrated and the salt is actively transported outwards into the blood -the loop is necessary because the structure is vital in the function of filtration
DNA Polymerase
DNA dependent DNA Polymerase
Primase
DNA dependent RNA Polymerase
Compare and contrast the structure and/or function of a telomere and a poly(A) tail. Briefly describe 2 significant similarities and 2 differences.
DNA vs. RNA Double stranded vs. single Both are non-coding sequences Both serve to protect the ends from degradation Both get shorter over time
You are tasked with producing a drug that disables the function of a specific cell receptor protein. In general terms, explain the approach that you would take to develop such a drug
Design a drug (using non-competitive inhibitors- usually easier) that binds to the receptor protein on the cell. This inhibits the substrate from binding, inhibiting the function of the receptor protein
Explain why errors in transcription are not as potentially harmful as errors in DNA replication.
Errors in Transcription have several opportunities to be fixed, it could be spliced out during the formation of the mature mRNA or the mistake could be fixed right away by utilizing the exonuclease function of RNA polymerase, before even finishing the transcript. A mistake during replication of DNA could potentially be passed on to other cells during mitosis, potentially hindering protein function and damaging certain aspects of the organism as a whole. In conclusion, errors in transcription only cause temporary errors in translation. Errors in DNA replication could affect new daughter cells and future generations
What types of organisms produce cyclins? Under what conditions would they be producing a specific cyclin? Be specific.
Eukaryotes use cyclins to regulate the cell cycle. Cyclins are regulatory proteins that bind to, activate, and determine the specificity of cyclin dependent kinases. They help control the cell cycle by regulating CDKs, which in turn regulate the structure and function of many other proteins.
Sex determination pathways for most Eukaryotes involve alternative splicing of the transcript for the gene Doublesex. How can the same transcript can be spliced one way in one sex and a different way in the other sex (how is the alternative splicing made possible)?
If a protein binds to the intron/exon boundary and interferes with the splicing enzymes, then a specific intron will not be removed from the transcript.
You have engineered a new transcription factor to replace CAP in regulating the Lac Operon. Rather than using cAMP as a ligand, it uses glucose. Describe how you would want this new protein to function, if it were to perform the same function as CAP. Describe the changes in structure and function upon ligand binding.
If glucose were the ligand regulating the structure and function of CAP, then when glucose is bound to CAP, the resulting conformational change should result in DNA binding and increased transcription.
Ethanol is a high energy molecule - which is why heavy alcohol consumption can contribute to obesity and fatty liver disease. How is it that consuming large quantities of ethanol can result in low blood glucose levels the next day? Be specific.
In ethanol metabolism in the liver the ratio of NAD+ and NADH is increased from 4: 1 to 2:1 which slows the rate of carbohydrate catabolism. In turn, the release of glucose into the blood stream is much slower resulting in swelled blood vessels which contributes to feelings of lethargy
When a coding strand of eukaryotic DNA (single strand) is hybridized to the mRNA it encodes, the hybrid molecule contain loops of single-stranded DNA. What specifically are these loops?
Introns
During the course of an Action Potential. the membrane charge rapidly rises and then falls. What event(s) cause the fall?
K+ flows out of the cell causing the membrane potential to drop/fall after the Na+ channel closes- repolarization
Lactose, Lactate, NADH, Oxaloacetate, Pyruvate, Acetyl-CoA (note '>' indicates 'greater than')
Lactose > Lactate > Oxaloacetate > Pyruvate > Acetyl-CoA > NADH
Explain the logic that T.H. Morgan used in his experiments that showed that chromosomes were the material of heredity.
Morgan followed the inheritance of the white vs. red eye traits and found them to precisely follow the inheritance of the X chromosome
Telomerase is an
RNA dependent DNA polymerase
The human disease beriberi is caused by a deficiency of thiamine in the diet. People with severe beriberi have higher than normal levels of pyruvate in their blood and urine. Thiamine is is a precursor for the cofactor thiamine pyrophosphate (TPP) which is required for proper function of the pyruvate dehydrogenase complex. Based on your knowledge of metabolism and energy production, what diet recommendations would you give to someone with beriberi? Why? (other than thiamine, what should they eat, and what should they avoid eating?)
Since PDH is not functioning properly, then pyruvate cannot be converted to Acetyl-CoA properly. A diet that could provide Acetyl-CoA BUT NOT FROM PDH, would include a diet higher in fatty acids, and lower in carbohydrates.
You have copied the coding region of the human gene for insulin and put it into the genome of E. coli, under the control of the regulatory region of the lac operon. You successfully make the protein product but the newly made insulin, is unfortunately not functional. Explain a likely reason why this may have occurred? be specific
Since the genetic code is universal. the same protein is expected to be made. Insulin is made in a larger, inactive form that needs to be modified to become active. The enzymes required for activation would not be present in a bacteria. The gene may have contained introns.
Which nitrogenous base will only temporarily be found in a double helix?
Uracil because if uracil was a base in DNA you wouldn't be able to tell if there was a mutation
The catabolism of what type of biomolecule(s) necessitates the production of urea in mammals?
amino acid catabolism produces ammonia which is detoxified through the synthesis of urea
Explain why denatured proteins tend to be insoluble while the properly folded version is soluble?
denatured proteins tend to bind together due to the exposed hydrophobic regions, resulting in an insoluble mass
A major conclusion of the De Novo Protein Synthesis paper was that several novel genes (out of millions) produced new proteins which replaced the function of the deleted gene (knock-out). List two hypotheses that the authors considered and rejected. What experimental evidence allowed to reject these hypotheses.(5 pts ea)
hypothesis 1: hypothesis 2:
Which of the following statements about the 5′ cap of mRNA is false? (3 pts) (i) It protects mRNA from being digested by enzymes. (ii) It is added to the pre-mRNA during transcription. (iii) It is a chemical modification of GTP. (iv) It assists in transport of mRNA from the nucleus to the cytoplasm. (v) All of the above are true; none is false.
iv) it assists in the transport of mRNA from nucleus to cytoplasm
How many total ATP can eventually be produced from ONE molecule of AcetylCoA? Explain your reasoning or show your work.
one Acetyl-CoA can make 3 NADH and 1 FADH2, which is (3 x 1.5 ATP) + 1.5 ATP) + 1 GTP/ATP = 10 ATP
The addition of methyl groups (CH3) to DNA bases, can change gene expression. Describe how DNA methylation of a regulatory region of one gene might decrease gene expression but methylation of another gene can increase expression. be specific
the additional of methyl groups to DNA bases will change their shape and can prevent protein binding. Methylating a site used by a positive transcription factor will reduce gene expression. Methylating a site used by a negative transcription factor will increase gene expression.
What part(s) of a peptide participate in the bonds holding an α-helix together? How distant are these in the peptide primary structure?
the bonds that hold the helices together in secondary structure are hydrogen bonds, every fourth residue in primary structure a hydrogen bond will form
During which phase(s) of the cell cycle are chromosomes composed of two chromatids? Include any relevant stages of the cell cycle, including mitosis, in your answer
the end of S, G2, and mitosis up to anaphase
Some bacteria that are resistant to an antibiotic sometimes appear spontaneously among different types of bacteria that are resistant. Based on your knowledge of biology, what might explain this observation?
the most likely explanation is that those that become 'spontaneously' resistant have received DNA (transformation) from those nearby bacteria that are already resistant.