[Jazzified]

I have a list of 25 questions to answer.  For the most part I answered all of them and would like to get my answers checked.  I believe they are correct, but would like a second opinion on my answers (my answers are the underlined parts of the sentences).  Here are the questions, followed by the answers I have chosen:

1. The reason cellulose is better suited than starch to be the major component of the plant cell wall is because cellulose molecules form many hydrogen bonds to each other.

2. Polypeptides tend to be the workhorse of the cell.

3. The primary difference between a stem cell and a progenitor cell is stem cells can give rise to many different types of differentiated cells while progenitors can only give rise to one type of differentiated cell.

4. In proteins, hydrogen bonding between the hydrogen (of the amino group) and oxygen (of the carboxylic acid) that are part of the amino acid backbone is primarily responsible for the secondary layer of structure.

5. You are studying a cellular enzyme involved in breaking down fatty acids for energy.  Looking at the R groups of the amino acids, non-polar amino acids would occur in the aprts of the enzyme that interact with the fatty acids.

6. 99 water molecules are required for the synthesis of an amylose polymer that is comprised of 100 glucose monomers.

7. Cysteine, serine, and threonine are examples of polar (uncharged) amino acids.

8. Carbon can combine with 3 hydrogen atoms and 1 hydroxyl group to generate methanol.  Given that oxygen is more electronegative than carbon or hydrogen (carbon and hydrogen electronegativities are very close to equal), polar covalent, nonpolar covalent, and hydrogen bonds are expected to be observed in a container of methanol.

9. If an atom has an atomic mass of 20, the number of electrons that are most likely associated with this atom (assuming the atom has a net charge of zero) is 10.

10. Hydrogen bonds are responsible for the cohesive properties of water.

11. A good example of how form correlates with function is the muscle cells of a long distance runner have lots of mitochondria.

12. The primary difference between Gram positive and Gram negative bacteria is that gram positive has one lipid bilayer in the outer membrane/cell wall while Gram negative has two lipid bilayers.

13. While working with B-galactosidase, an enzyme that catalyzes a reaction that changes the X-gal compound from being essentially colorless to dark blue, you accidentally heat and denature it.  To avoid trouble with your adviser, you attempt to renature the enzyme by slowly cooling it down.  You add X-gal to the cooled enzyme and you get a light blue color instead of the usual dark blue.  The most likely explanation for this is that you have completely renatured the enzyme.

14. A secreted protein has a zip code or sequence that directs it to enter the secretory pathway (ER and Golgi).  What might happen if you artificially added this zip code to a protein that normally functions in the cytoplasm is it would stay in the cytoplasm because the zip code is not the right one for that protein.

15. Based on what is known about the molecular structure of RNA (and how it compares to DNA), it can not be predicted that the 2 RNA strands with complementary sequences should be able to form double stranded duplexes.

16. The following is not a "rule" that drives protein folding: the R groups of oppositely charged amino acids often form ionic bonds (generally on the exterior of the protein).

17. Lipids are a macromolecule that is not a polymer.

18. A short oligonucleotide has the sequence 5'-TATTGGCTA-3'.  The sequence of the complementary piece of DNA is 5'-TAGCCAATA-3'.

19. The following is not one of the primary differences between eukaryotes and prokaryotes: eukaryotes have chloroplasts while prokaryotes have thylakoid membranes.

20. LiCl is a molecule.  Li and Cl atoms are held together by ionic bonds.

21. The octet rule says that atoms tend to gain, lose, or share electrons so as to ahve eight electrons in their outer electron shell.  Given what you know about the chemical formula for the phosphate functional group, you can say that the octet rule is disobeyed in this case.

22. The notion that the more highly ordered molecules are in a substance, the more likely it is to be solid or more firm is exemplified by ice, cellulose, NaCl, saturated fatty acids, and unsaturated trans fats.

23. The pH of a solution is 3.  The molar concentration of the hydroxyl ions in the solution is 10^-11 M.

24. Phosphorus has an atomic number of 15.  5 electrons are likely to be in the valence electron shell.

25. The 3 carbon backbone of a fat molecule is glycerol.

Thank you!

[Yggdrasil]

1. The reason cellulose is better suited than starch to be the major component of the plant cell wall is because cellulose molecules form many hydrogen bonds to each other.

Correct.

2. Polypeptides tend to be the workhorse of the cell.

I would say proteins, but polypeptides is acceptable. (NB: there is a difference between proteins and polypeptides.  While a polypeptide can be a protein a protein is not necessarily a polypeptide.  For example, hemoglobin is a protein, but it a collection of four polypeptides plus four heme groups.  The polypeptides that compose hemoglobin by themselves are non-functional, but when you link them to the hemegroups and assemble them into the correct quaternary structure, they become a functional protein).

3. The primary difference between a stem cell and a progenitor cell is stem cells can give rise to many different types of differentiated cells while progenitors can only give rise to one type of differentiated cell.

Acceptable.  I think there may be differing opinions on the definition of stem cell and progenitor cell, and I think some multipotent cells (cells having the ability to differentiate into a limmited subset of differentiated cells) maybe called progenitor cells.  However, I'm not an expert in this area.

4. In proteins, hydrogen bonding between the hydrogen (of the amino group) and oxygen (of the carboxylic acid) that are part of the amino acid backbone is primarily responsible for the secondary layer of structure.

Correct.

5. You are studying a cellular enzyme involved in breaking down fatty acids for energy.  Looking at the R groups of the amino acids, non-polar amino acids would occur in the aprts of the enzyme that interact with the fatty acids.

Correct.

6. 99 water molecules are required for the synthesis of an amylose polymer that is comprised of 100 glucose monomers.

Correct.

7. Cysteine, serine, and threonine are examples of polar (uncharged) amino acids.

Correct.  Some people consider cysteine to be polar and others do not.  It is a borderline case.

8. Carbon can combine with 3 hydrogen atoms and 1 hydroxyl group to generate methanol.  Given that oxygen is more electronegative than carbon or hydrogen (carbon and hydrogen electronegativities are very close to equal), polar covalent, nonpolar covalent, and hydrogen bonds are expected to be observed in a container of methanol.

Correct.

9. If an atom has an atomic mass of 20, the number of electrons that are most likely associated with this atom (assuming the atom has a net charge of zero) is 10.

Correct, although this principle does not hold for all atoms.

10. Hydrogen bonds are responsible for the cohesive properties of water.

Correct.

11. A good example of how form correlates with function is the muscle cells of a long distance runner have lots of mitochondria.

Sure.

12. The primary difference between Gram positive and Gram negative bacteria is that gram positive has one lipid bilayer in the outer membrane/cell wall while Gram negative has two lipid bilayers.

I don't remember enough microbiology to say its correct, but it sounds right.

13. While working with B-galactosidase, an enzyme that catalyzes a reaction that changes the X-gal compound from being essentially colorless to dark blue, you accidentally heat and denature it.  To avoid trouble with your adviser, you attempt to renature the enzyme by slowly cooling it down.  You add X-gal to the cooled enzyme and you get a light blue color instead of the usual dark blue.  The most likely explanation for this is that you have completely renatured the enzyme.

Why do you get a light blue color instead of a dark blue color?

14. A secreted protein has a zip code or sequence that directs it to enter the secretory pathway (ER and Golgi).  What might happen if you artificially added this zip code to a protein that normally functions in the cytoplasm is it would stay in the cytoplasm because the zip code is not the right one for that protein.

Incorrect.

15. Based on what is known about the molecular structure of RNA (and how it compares to DNA), it can not be predicted that the 2 RNA strands with complementary sequences should be able to form double stranded duplexes.

Why do you think that RNA can't form duplexes while DNA can?

16. The following is not a "rule" that drives protein folding: the R groups of oppositely charged amino acids often form ionic bonds (generally on the exterior of the protein).

What are the other choices?  This one seems like a good "rule."

17. Lipids are a macromolecule that is not a polymer.

Correct.

18. A short oligonucleotide has the sequence 5'-TATTGGCTA-3'.  The sequence of the complementary piece of DNA is 5'-TAGCCAATA-3'.

Correct.

19. The following is not one of the primary differences between eukaryotes and prokaryotes: eukaryotes have chloroplasts while prokaryotes have thylakoid membranes.

Incorrect.  Read up on eukarotes and prokaryotes again.  Specifically about the origins of the word prokaryote and eukaryote.

20. LiCl is a molecule.  Li and Cl atoms are held together by ionic bonds.

Correct.

21. The octet rule says that atoms tend to gain, lose, or share electrons so as to ahve eight electrons in their outer electron shell.  Given what you know about the chemical formula for the phosphate functional group, you can say that the octet rule is disobeyed in this case.

Correct.

22. The notion that the more highly ordered molecules are in a substance, the more likely it is to be solid or more firm is exemplified by ice, cellulose, NaCl, saturated fatty acids, and unsaturated trans fats.

Seems right, but the question seems worded strangely to me.

23. The pH of a solution is 3.  The molar concentration of the hydroxyl ions in the solution is 10^-11 M.

Correct.

24. Phosphorus has an atomic number of 15.  5 electrons are likely to be in the valence electron shell.

Correct.

25. The 3 carbon backbone of a fat molecule is glycerol.

Correct.

[Jazzified]

Thanks!  For the following questions...

13. While working with B-galactosidase, an enzyme that catalyzes a reaction that changes the X-gal compound from being essentially colorless to dark blue, you accidentally heat and denature it.  To avoid trouble with your adviser, you attempt to renature the enzyme by slowly cooling it down.  You add X-gal to the cooled enzyme and you get a light blue color instead of the usual dark blue.  The most likely explanation for this is that you have completely renatured the enzyme.

Why do you get a light blue color instead of a dark blue color?

My other choices for this answer are none of the enzyme polypeptides have renatured correctly; the enzyme is non-functional and some of the enzyme polypeptides have renatured correctly, but not all of them.  Would the answer be the first?

14. A secreted protein has a zip code or sequence that directs it to enter the secretory pathway (ER and Golgi).  What might happen if you artificially added this zip code to a protein that normally functions in the cytoplasm is it would stay in the cytoplasm because the zip code is not the right one for that protein.

Incorrect.

Would the correct answer be it would be come denatured?  The other choice is it would be translated into the ER and get secreted instead of being translated into the cytoplasm.

16. The following is not a "rule" that drives protein folding: the R groups of oppositely charged amino acids often form ionic bonds (generally on the exterior of the protein).

What are the other choices?  This one seems like a good "rule."

The other choices were: nonpolar (or hydrophobic) amino acids are likely to be buried in the interior of the protein, polar amino acids interact with water on the surface of the protein, the R groups of cysteines can form disulfide bridges via hydrogen bonding, and the R groups of polar amino acids can form hydrogen bonds with one another (generally on the exterior of the protein).  Which of these is not a "rule," or does my original answer seem to be the best?

19. The following is not one of the primary differences between eukaryotes and prokaryotes: eukaryotes have chloroplasts while prokaryotes have thylakoid membranes.

Incorrect.  Read up on eukarotes and prokaryotes again.  Specifically about the origins of the word prokaryote and eukaryote.

Out of the given choices, this seemed to be the best one.  The others were eukaryotes have nuclei, prokaryotes have nucleoids; eukaryotes have membrane enclosed organelles, prokaryotes do not; and eukaryotes are quite large, prokaryotes are quite small.  Is my answer still the best one?

22. The notion that the more highly ordered molecules are in a substance, the more likely it is to be solid or more firm is exemplified by ice, cellulose, NaCl, saturated fatty acids, and unsaturated trans fats.

Seems right, but the question seems worded strangely to me.

Is there any way I can check this to be sure?

Thanks for everything!

[Yggdrasil]

My other choices for this answer are none of the enzyme polypeptides have renatured correctly; the enzyme is non-functional and some of the enzyme polypeptides have renatured correctly, but not all of them.  Would the answer be the first?

What would you expect if the first situation were true?  It might be good to go through all of the choices and write out what you would expect to see when you do your x-gal assay.

Would the correct answer be it would be come denatured?  The other choice is it would be translated into the ER and get secreted instead of being translated into the cytoplasm.

Why do you think that a zip code won't function as a zip code if placed on a different protein?

The other choices were: nonpolar (or hydrophobic) amino acids are likely to be buried in the interior of the protein, polar amino acids interact with water on the surface of the protein, the R groups of cysteines can form disulfide bridges via hydrogen bonding, and the R groups of polar amino acids can form hydrogen bonds with one another (generally on the exterior of the protein).  Which of these is not a "rule," or does my original answer seem to be the best?

This one is tricky.  The answer is the one about cysteine.  While it is true that cysteines will form disulfide bridges to stabilize a protein's structure, the disulfide bridges are covalent bonds, not hydrogen bonds.

Out of the given choices, this seemed to be the best one.  The others were eukaryotes have nuclei, prokaryotes have nucleoids; eukaryotes have membrane enclosed organelles, prokaryotes do not; and eukaryotes are quite large, prokaryotes are quite small.  Is my answer still the best one?

Your answer was right.  I missed the "not" part when reading the question.

Is there any way I can check this to be sure?

It's probably fine.

[Jazzified]

My other choices for this answer are none of the enzyme polypeptides have renatured correctly; the enzyme is non-functional and some of the enzyme polypeptides have renatured correctly, but not all of them.  Would the answer be the first?

What would you expect if the first situation were true?  It might be good to go through all of the choices and write out what you would expect to see when you do your x-gal assay.

Okay, I just had a long thought about it.  So the answer would be that "Some of the enzyme polypeptides have renatured correctly, but not all of them" since there is some blue color.  Is this final answer correct?

Would the correct answer be it would be come denatured?  The other choice is it would be translated into the ER and get secreted instead of being translated into the cytoplasm.

Why do you think that a zip code won't function as a zip code if placed on a different protein?

Okay, so for this question, is the answer "it would be translated into the ER and get secreted instead of being translated by the cytoplasm"?  So it is like artificially transferring a nucleus of one type of cell into another cell, and this artificial cell functions in whatever way the inserted nucleus functions (if this makes sense lol)?

[Yggdrasil]

Yes and yes.  In fact, scientists just this past summer did the first experiment where they transfered (or at least claimed to have transfered) the entire genome of one bacterium to another species of bacterium:

http://www.jcvi.org/press/news/news_2007_06_28.php

[Jazzified]

Yes and yes.  In fact, scientists just this past summer did the first experiment where they transfered (or at least claimed to have transfered) the entire genome of one bacterium to another species of bacterium:

http://www.jcvi.org/press/news/news_2007_06_28.php

Thank you so much for all of your help.  I really appreciate it!