POB module 1: homework questions

When scientists want to store single-stranded or double-stranded DNA molecules for a long time, they desiccate the DNA (i.e. remove all the water and store the DNA in dry form). In no more than 280 characters, explain why desiccation will increase the stability of the DNA molecules. Bullet points are fine. (1 pt)

the covalent bonds in the DNA or RNA backbone can be broken down by hydrolysis. removing water from the sample prevents hydrolysis from occurring, preserving intact DNA or RNA strands

Most bacteria do not have cholesterol or equivalent lipids in their plasma membranes, and must therefore modulate membrane fluidity at the level of fatty acid saturation. If such a bacterium has severely impaired ability to desaturate (i.e. introduce double bonds into) its fatty acids, how would you expect its survival in colder environments to compare with that of a bacterium with fully functional desaturation enzymes? Why?

Expect impaired survival (1 pt) because the membrane would solidify or become less liquid or diffusion in the membrane would decrease when the temperature decreased (1 pt))

If you take a culture of budding yeast cells (Saccharomyces cerevisiae), degrade their cell walls using the enzyme zymolyase, and add a large amount of sodium chloride to the medium, the cells shrivel up. However, if you add the DNA-binding dye DAPI instead of sodium chloride, the cells do not shrivel up - moreover, you can use the DAPI to visualize DNA in the nucleus. What can you conclude about the diffusion and hydrophilicity of DAPI, and about osmosis in this context?

If you take a culture of budding yeast cells (Saccharomyces cerevisiae), degrade their cell walls using the enzyme zymolyase, and add a large amount of sodium chloride to the medium, the cells shrivel up. However, if you add the DNA-binding dye DAPI instead of sodium chloride, the cells do not shrivel up - moreover, you can use the DAPI to visualize DNA in the nucleus. What can you conclude about the diffusion and hydrophilicity of DAPI, and about osmosis in this context?

While screening the effects of various compounds on plant cells, you identify a molecule that severely reduces ATP production during photosynthesis, but has no effect on the reduction of NADP+ to NADPH. What is the most likely activity of this molecule in the chloroplast?

It's an uncoupler that collapses the proton gradient in chloroplasts. Anything indicating that electron flow through the photosystems and ETC is unaffected, but the proton gradient is dissipated so protons don't flow through ATP synthase should get the point here.

Saccharomyces cerevisiae, sometimes known as Baker's yeast or Brewer's yeast, is widely used in food and beverage production (e.g. in baking to make bread rise, and to produce alcoholic drinks including beer). S. cerevisiae exhibits a phenomenon known as the Crabtree effect (similar to the Warburg effect in cancer) whereby oxidative phosphorylation is suppressed even when oxygen is available. Briefly explain why this makes S. cerevisiae an idea micro-organism for beer and wine production. (2 pts)

S. cerevisiae will carry out fermentation instead of oxidative phosphorylation (1 pt), producing ethanol and CO2 (just ethanol is fine) even when oxygen is present

You are interested in seeing whether there is cell-to-cell variation in the level of a specific RNA in budding yeast cells: the RNA in question is called Arc1, and contains the sequence 5' GCUGGAACCA 3'. You design a probe to visualize Arc1 RNA in cells: the probe is a fluorescently labeled RNA molecule whose sequence is the reverse complement of Arc1 RNA. What would be the sequence of the RNA that binds to the region shown above? (Write your answer from 5' to 3', and indicate the 5' end) (1 pt)

UGGUUCCAGC

A polar blue dye and a non-polar green dye are added to a 1:1 mixture of oil and water, and the whole mixture is shaken up. The oil is less dense than water. What will the resulting mixture look like when it has had the opportunity to equilibrate, and why? (2 pts)

because oil molecules are hydrophobic, once mixture has equilibrated the oils and water molecules won't mix. the polar water will dissolve the polar blue die while the non polar oil will dissolve the non polar green day. because the oil has a lower density than water the oil will float to the top

You discover a new class of photosynthetic organism with pigments that absorb light at all wavelengths in the visible spectrum except 450-500 nm. What color is this organism? (1 pt)

blue

review free energy change question in HW 3, question 2

check

What would be the effect of each of the following on the movement of electrons through the electron transport chain? Provide a one-sentence rationale for each of your answers A. Rotenone (inhibits complex I) B. Cyanide (inhibits complex IV) C. 2-tert-butyl-4,6-dinitrophenol (a mitochondrial uncoupler) D. Anoxia (the complete absence of oxygen)

decreased but not completely stopped because electrons can enter via complex II, completely stopped because electrons cannot leave the ETC and be transferred to oxygen, unaffected because electrons will still flow through the ETC even though the proton gradient is disrupted, completely stopped bc electrons cannot leave the ETC and be transferred to oxygen

Formamide disrupts hydrogen bonds in aqueous (water-based) solutions. How would you expect formamide to impact the structure of a double-stranded RNA molecule? Briefly (<280 characters) rationalize your answer (2 pts total)

formamide would denature the dsRNA into two single strands because the strands associate via hydrogen bonding. individual RNA strands would remain intact because they are held together via covalent bonds

Sodium dodecyl sulfate (SDS) is an amphipathic chemical commonly used to denature (i.e. unfold) proteins. Based on the structure of SDS below, answer the following questions. (1 pt total) (a) which of the three amino acids below is most likely to bind the hydrophobic tail? (b) Is the SDS tail saturated or unsaturated?

isoleucine is most likely to bond to the hydrophobic tail because it is the most hydrophobic, SDS tail is saturated because there are no double carbon bonds

For each of the two molecules below, indicate how many geometrical isomers or stereoisomers could exist, as directed. Very briefly outline your logic (e.g. 'there are three chiral carbons').

molecule A has 8 stereoisomers because it has three chiral carbons, molecule B has no isomers because the double bond between two carbons prevents the molecule from rotating

As you know, actin is a highly abundant protein in eukaryotic cells; actin forms filaments in the cytoplasm. Will most molecules of Actin be translated by ribosomes in the cytoplasm or ribosomes associated with the rough endoplasmic reticulum (rough ER)?

most of the actin molecules will be translated by free ribosomes in the cytoplasm

A mutant form of an Arabidopsis thaliana plant has defective chlorophyll production, such that the abundance of chlorophyll molecules in chloroplasts is 50% the normal level. The chlorophyll molecules are still close enough for resonance energy transfer to occur. (A) By what fraction would this mutation decrease the overall maximum amount of photosynthesis this plant was capable of? Very briefly rationalize your answer. (B) Next, you identify a second mutation that decreases the abundance of chlorophyll by 90%, reducing the density of chlorophyll molecules such that resonance energy transfer cannot occur. How would this affect the overall maximum amount of photosynthesis this plant was capable of? Very briefly rationalize your answer to this second part.

photosynthesis would be reduced by 50% because the plant can harvest half the normal amount of energy photosynthesis will be reduced to more than 95%. because the resonance energy transfer cannot occur most of the energy captured by the chlorophyll could not be transferred to the reaction center