Rexx18
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Pretty much finished revising for the AQA AS bio exam next Monday, just have a few general questions and would appreciate any answers.

1. When testing for non-reducing sugars, you add dilute HCl to hydrolyse it into monosaccharides, but why is there a need of neutralising it with NaHCO3 after?

2. In the quaternary protein structure, what type of bonds hold the different polypeptide chains together? Is it ionic, hydrogen or both and could disulphide bridges possibly form between different polypeptides?

3. What causes DNA to twist exactly, why can it not form a straight ladder structure (in terms of structure, not function)?

4. When preparing a temporary mount, what exactly is the importance of the water drop at the first step?

5. Could a species of bacteria possibly be resistant to an antibiotic if it doesn't have any plasmids, i.e., can you find the genes for antibiotic resistance within the circular DNA loop?

6. Might sound like a stupid question, but the inside of a channel protein is either positive or negative, depending on what sort of ions it wants to allow to pass. Let's say the inside is negative, meaning that positive ions will go through. If an ion is travelling very slowly, i.e., not fast enough, is it possible for it to become 'stuck' inside of the channel protein due to the opposite charges attracting?

7. Why do antibiotics interfere with bacteria's metabolic reactions but not our own?

8. Why are treacheal cartilages C-shaped and not a complete circle?

9. In emphysemia, the elastin is broken down and lungs can't recoil as well. What does recoil mean in this context and why is it important?

10. My textbook says that lipase enzymes hydrolyse lipids into monoglycerides and fatty acids, whereas the internet says into glycerol and fatty acids. Which one does happen or would both happen?

11. Probably outside of spec, but why is fructose absorbed by facilitated diffusion, rather than by co-transport like glucose and galactose?

12. When talking about the Bohr effect, is it the pCO2 that decreases affinity for oxygen or is it the formation of carbonic acid (therefore the decrease in pH)?

13. In the phloem, assimilates move downwards due to the difference in hydrostatic pressure. How do other organic substances move upwards?

14. What is the role of rRNA?

15. Suppose you have 3 alleles for a single gene. Normally, the 2 alleles are found on the same locus on both chromosomes, where 1 of the alleles is on one chromosome and the other allele is on the other chromosome. If you have more than 2 alleles, e.g., 3, where can you find the 3rd one?

16. Do mutagenic agents increase the chance or probability of a mutation?
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OxFossil
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I'll have a go at some of the DNA-related questions:

3. I don't think there is any reason, in principle, why a straight ladder-type structure would not work. The helix forms for energetic reasons. Key factors include - the hydrophobic bases try to minimise contact with water molecules, whilst the hydrophilic sugar-phosphates are happier on the outside of the chain. To minimise water contact, the bases tend to contract together, but this is constrained by the allowable bond angles in the sugar-phosphate chains - they cannot be forced beyond a certain point, so you end up with a twisted ladder effect.

14. As you know, rRNA forms the largest part of the ribosome, which is a complex of rRNA and several enzymes, and the site where mRNA and tRNA come together and proteins are constructed. The assembly process is extremely complicated. Crucial functions of the rRNA molecule include "checking" the matching of mRNA and tRNA codons to ensure that translation is accurate and bringing together the incoming tRNA with the the tRNA that is at the end of the growing peptide chain. Evidentally, the RNA nature of the ribosome is essential, since rRNA is highly conserved in evolution. Incidentally, the difference between prokaryote rRNA and eukaryote rRNA is one way in which some antibiotics work - they disrupt prokaryote rRNA that is found in bacterial infection whilst having no effect on our host cells' rRNA (your question 7)

15. Not quite sure what you mean here. Obviously, if there is just one locus for a gene in a genome, then it will be present only in as many copies as there are homologous chromosomes to carry it. e.g. in humans, there would be two copies. You couldn't have three different alleles present in a diploid organism if there was just a single locus for that gene. However, if there are multiple loci, or when you have multiple repeated sequences, then you could have more variation. Whether this counts as 3 (or more) "alleles" depends in part on the origin of the repeat (copy number variation is an interesting area of research), but in general, you should assume that diploid organisms carry only a maximum of two alleles.

16. Short answer - yes. Obviously, not all mutagens bring this about in the same way. Some break DNA, others cause base insertions, deletions or substitutions, others frame-shift reading errors etc. James Shapiro has argued controversially that organisms have adapted to induce mutagenesis in themselves when they "need" new variation (such as at times of starvation) - a process he calls "natural genetic engineering)
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OxFossil
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5. Also, yes. There is a spontaneous point mutation rate in all replication, which is low - and the repair system is generally extremely efficient. However, bacteria reproduce at such a rate that even at extremely low mutation rates, resistant lines emerge. (As I indicated above, Shapiro also suggests that bacteria sometimes "deliberately" mutate at loci that are more likely to generate useful variation - but this is highly contentious)
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Rexx18
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(Original post by OxFossil)
I'll have a go at some of the DNA-related questions:

3. I don't think there is any reason, in principle, why a straight ladder-type structure would not work. The helix forms for energetic reasons. Key factors include - the hydrophobic bases try to minimise contact with water molecules, whilst the hydrophilic sugar-phosphates are happier on the outside of the chain. To minimise water contact, the bases tend to contract together, but this is constrained by the allowable bond angles in the sugar-phosphate chains - they cannot be forced beyond a certain point, so you end up with a twisted ladder effect.

14. As you know, rRNA forms the largest part of the ribosome, which is a complex of rRNA and several enzymes, and the site where mRNA and tRNA come together and proteins are constructed. The assembly process is extremely complicated. Crucial functions of the rRNA molecule include "checking" the matching of mRNA and tRNA codons to ensure that translation is accurate and bringing together the incoming tRNA with the the tRNA that is at the end of the growing peptide chain. Evidentally, the RNA nature of the ribosome is essential, since rRNA is highly conserved in evolution. Incidentally, the difference between prokaryote rRNA and eukaryote rRNA is one way in which some antibiotics work - they disrupt prokaryote rRNA that is found in bacterial infection whilst having no effect on our host cells' rRNA (your question 7)

15. Not quite sure what you mean here. Obviously, if there is just one locus for a gene in a genome, then it will be present only in as many copies as there are homologous chromosomes to carry it. e.g. in humans, there would be two copies. You couldn't have three different alleles present in a diploid organism if there was just a single locus for that gene. However, if there are multiple loci, or when you have multiple repeated sequences, then you could have more variation. Whether this counts as 3 (or more) "alleles" depends in part on the origin of the repeat (copy number variation is an interesting area of research), but in general, you should assume that diploid organisms carry only a maximum of two alleles.

16. Short answer - yes. Obviously, not all mutagens bring this about in the same way. Some break DNA, others cause base insertions, deletions or substitutions, others frame-shift reading errors etc. James Shapiro has argued controversially that organisms have adapted to induce mutagenesis in themselves when they "need" new variation (such as at times of starvation) - a process he calls "natural genetic engineering)
Thanks a lot for your in-depth answers, especially 14. With 16, I rather meant chance or probability, I remember our teacher telling us to use one of those words in the exam since they mean different things, but I found the answer, it's probability the exam wants.
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OxFossil
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(Original post by Rexx18)
Thanks a lot for your in-depth answers, especially 14. With 16, I rather meant chance or probability, I remember our teacher telling us to use one of those words in the exam since they mean different things, but I found the answer, it's probability the exam wants.
OK, thanks. Your point about the exam board requirement prompts me to say that my answers take no account at all of what any exam board or requirement might need to hear. Meanwhile, on your 8 and 9, it's not my field, but I would say:

The trachea requires some reinforcement and stiffening to guard against collapse (its easy to imagine circumstances in which simply tilting one's head forward onto one's chest would otherwise lead to its occlusion) The ventral (front) aspect is a better choice than the rear (dorsal) aspect for reinforcement perhaps partly because the front is less protected from external assault but mainly because the dorsal aspect runs alongside the oesophagus ( you can easily deduce why that side needs some flexibility)

The lungs benefit from elastin because breathing involves repeated cycles of inflation and deflation. With an entirely passive material, you would need to expend energy on both parts of the cycle, whereas with a material that naturally recoils, energy is only needed on the expansion part of the cycle. Imagine a balloon versus a paper bag - overall, the energy needed to overcome this elastic resistance on inspiration must be less than that required to inflate and deflate a passive material. You can observe this in someone with severe emphysema - the work they are having to put in simply to maintain their breathing is obvious and heartbreaking to see (although this may be also down to the need to maintain a high respiration rate due to the loss of effective exchange surface, this is in turn partly caused by loss of elasticity)
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Rexx18
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(Original post by OxFossil)
OK, thanks. Your point about the exam board requirement prompts me to say that my answers take no account at all of what any exam board or requirement might need to hear. Meanwhile, on your 8 and 9, it's not my field, but I would say:

The trachea requires some reinforcement and stiffening to guard against collapse (its easy to imagine circumstances in which simply tilting one's head forward onto one's chest would otherwise lead to its occlusion) The ventral (front) aspect is a better choice than the rear (dorsal) aspect for reinforcement perhaps partly because the front is less protected from external assault but mainly because the dorsal aspect runs alongside the oesophagus ( you can easily deduce why that side needs some flexibility)

The lungs benefit from elastin because breathing involves repeated cycles of inflation and deflation. With an entirely passive material, you would need to expend energy on both parts of the cycle, whereas with a material that naturally recoils, energy is only needed on the expansion part of the cycle. Imagine a balloon versus a paper bag - overall, the energy needed to overcome this elastic resistance on inspiration must be less than that required to inflate and deflate a passive material. You can observe this in someone with severe emphysema - the work they are having to put in simply to maintain their breathing is obvious and heartbreaking to see.
Alright, thank you again for the answers.
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