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OK biol clan this is where you revise.
Any queries that relate directly to questions you come across in the trial exams are to be posted below. Please indicate which exam, year and question number you are referring to. It will make things a lot easier for me.
You can also ask general questions about the exam as well.
I suggest you also check out what was posted under biol 4 exam revision from last year's class.

Found this website that has fantastic diagrams in relation to DNA. Worth looking at if anyone's forgotten what we did at the beginning of the semester
http://www.genome.gov/glossary.cfm

This may be a bit late, but found some really good animations on this website; http://www.maxanim.com/genetics/index.htm... just helped me clear up a few things!

Q.hi voj, im just doing revision at the moment. can you please give me a definition of the sanger method? All i know is that it's a method of DNA sequencing
A. yep that is right. it involves the chain termination method of sequencing which I have described in the course notes. So go back over this. Although you do not really need to know the fine detail in the method, it is useful to have an overview of the process and importantly the purpose, which is to determine the actual sequence of nucleotides in a sample of DNA. VM

Q.when it comes to transcription and translation how much detail should we know?
A. In as much detail as possible. you should know each of these processes, where they occur, what their purpose is and what molecules are involved. VM

Q. in the study design it says 'eukaryote chromosomes' and 'prokaryote chromosomes' what is this? is it just the structure of the cells?
A. You are expected to know how genetic material is arranged in cells, whether prokaryotic (bacteria) or eukaryotic. In bacteria there is a single chromosome (usually circular) that contains the bacterial genes. In addition, bacteria can also have an extra circular piece of DNA called a plasmid that also contain genes and replicates independently to that of the bacterium's chromosomal DNA . In eukaryotic cells/organisms DNA is arranged in chromosomes (linear) found in the nucleus that is combined with proteins and forms a condensed material called chromatin. Only during mitosis and meiosis do the chromosomes become distinct and appear in the shape we are all familiar with. You should also remember that mitochondria contain their own circular DNA as well. VM

Q. is the cell cycle the same as mitosis?
A. Not quite. The cell cycle represents the life of a cell. The coure notes has a diagram that you need to be familiar with. Mitosis is part of the cell cycle (only a small part in terms of time). You need to know that cells spend most of their time in interphase and then carry out mitosis as part of their cycle. Interphase consists of 3 stages: G1, S and G2. Know what happens in each of these too. One way to look at it is that a cell is either in interphase or undergoing mitosis. VM

Q. What is a good definition of an INDEX FOSSIL and are they different from indicator fossils?
A. First of all they are the same thing. Index fossils allow for relative dating of a sedimentary layer. A good index fossil is one that represents a species that is known to have only lived for a short geological time period. And therefore its presence in a layer of rock allows the dating of that layer. A useful index fossil is also geographically widespread, common and easy to identify. VM

Q. Is it okay to say a HOMOZYGOUS RECESSIVE /DOMINANT INDIVIDUAL OR GENOTYPE? ( I know you cant say recessive allele etc)
A. I am not sure what you are exactly querying. What you write will depend largely on the question that is being asked. There is no problem in referring to an individual as homozygous recessive or dominant. The genotype if written automatically denotes what an individual is phenotypically. If they are Bb, then they are heterozygous for that partciular gene and will show the dominant characteristic. And you are spot on with the last comment, alleles should never be referred to as dominant or recessive. VM

Q. What is a good experimental set up to show that a trait is genetically inherited and not environmentally inherited, possible using the fact that one plant grew taller in one farm than another.
A. There isn't one answer to this as it will depend on the exact question being asked. But as a general rule, you need to have two LARGE groups of genetically identical plants. If each group is subjected to only one different enviornmental condition and one group grows tall and the other grows short, you can conclude that that environment factor has influenced the phenotype (cannot be genetic as they are identical). All other conditions would need to have been kept the same. I guess if you wanted to do it the other way around, then you would need two large groups of plants, each in exactly the same environment. The only thing that is different is their genetic make up. If one grows taller than the other than you might suggest that is likely to be due to genetics. VM


Q.How should we set out genotypic and phenotypic ratios? e.g., 1RR : 2Rr : 1rr OR 1/4RR : 1/2Rr : 1/4rr ? and should probability and chance be written as a fraction or percentage?
A. Your knowledge of biology is what is being assessed, not mathematics. either of the options you have written should be acceptable for the genotypic ratios. If a questions specifically says "what is the probability...?" then write it as a fraction out of 1 for safety. If a question says "what is the likelihood or chance...?" then it shouldn't matter, use a percentage or a fraction or a statement like 1 in 4. VM

Q.Does pre-RNA stand for preliminary mRNA or primary mRNA ?
A. Actually, to be strictly accurate, neither. You would not be expected to write fully what "pre-" represents in the exam. Writing pre-mRNA is sufficient and as long you know its role in gene expression that is all that matters. ie, it is immature mRNA that will be modified through the removal of introns (or something like this). So, pre stands for precursor mRNA, sometimes called primary mRNA, and preliminary mRNA is probably the least accurate term to use. Typical biology it is easy to bandy around terms and become slack in using the "correct" term. The only thing you need to be able to write fully, if required, would be messenger or transfer RNA. VM

Q.Does the term 'transfection' only apply to viral vectors or all prokaryotes (e.g. bacteria) in terms to organisms having genes inserted?
A. My understanding is that transfection is a general term referrring to the insertion of foreign DNA into a recipient organism without using viral vectors. Though, I don't think this is a term VCAA has used before. But the term transformation is important, which is the same process but more specifically refers to modifying prokaryotes and non-animal eukaryotes with non-viral methods. We would not refer to us humans as being transformed. Be familiar with the fact that there are different gene delivery methods, such a viral methods and non-viral methods (gene guns, liposomes etc). VM

Q.what is heat shock and do we need to know about it?
A. Okay, this is a specific part of the procedure when transforming bacteria. As part of trying to get bacteria to take up a recombinant plasmid, the bacteria are exposed to a cold environment and then suddenly to a warm environment which aids in the uptake of the plasmid. I think its in this direction. But really you shouldn't be asked about something as specific as this. Know that not all bacteria will take up a recombinant plasmid, only some do (these bacteria are referred to as competent) and those that do are the only ones that become transformed, hence the need of including an antibiotic resistance gene on the recombinant plasmid so that transformed bacteria can be distinguished from those that aren't. VM

Q.VCAA 2006 multiple choice question 8: SSWW x ssww, the answer said that there would be approximately equal numbers of S_W_ individuals and ssww individuals. how is that correct? (genes are unlinked)
Please answer soon! as in, before 9am on monday!
A. You are trying to be funny, aren't you? Is this soon enough? within the hour! :-) give me a moment now as I have to read the VCAA exam first. Okay, the answer is clearly D, no question about it. I think this is where you may have misread the question. Even though initially the genotypes are written in a way that represent non-linked, the information says that "they performed a number of test crosses to see if the chromosomes were linked". And the question is about what sort of results would you get if the two genes were linked and close together. Now, if they are close together you wouldn't expect many recombinant phenotypes and you would definitely expect the two parental phenotypes (long and straight, short and wavy) to be similar in number (irrespective of how far apart the two genes are on the chromosome). Remember the theoretical ratio of 1:0:0:1. Options A and B involve more of a recombinant phenotype which cannot be true and option C involves a recombinant phenotype being equal to parental, also not true. D is the only one that has parental phenotypes and in roughly equal numbers. VM
Thanks Voj! Very prompt and useful. I actually didn't read the question wrong about being linked, i just wrote it wrong here. What i failed to notice was thats its a TEST CROSS rather than an F1 cross. My bad. I will say it again, reading the question info carefully is paramount. VM
P.S Not to knock your teaching methods which are for the most part superb, but i think in all of your course notes you wrote 'complimentary' instead of 'complementary' when referring to base pairs. So unless you mean the bases were saying nice things to each other, you might want to revise that. :D
Well only took you 4 months to tell me. I appreciate you letting me know though. And yes you should be knocking me (so to speak) even my typing and proofreading. Everyone makes mistakes. But we can only improve if we are aware of them. But it is funny that I have done that. Although, I would think that you would still get the marks if you made that mistake, as in a biological sense you are not being ambiguous really. Off course, you should always spell biological words correctly anyway. VM
Q.How does RNA processing affect gene expression? I understand there is splicing involved in transforming pre-mRNA into mature mRNA, but what could vary in this process?alternate_splicing.png
A. Ah yes. Alternate splicing of the pre-mRNA can have a dramatic effect on the end product, which is off course the polypeptide that is produced. Remember gene expression is about how the DNA sequence is expressed in the form of a polypeptide (protein) produced by the cell. Introns get removed leaving behind exons. Depending on which part of the pre-mRNA is removed and which is kept, the same gene can result in different polypeptides being produced. I will create a diagram to help show this. Give me a little time to do this. VM

- Thanks for the diagram voj, it helps a lot. But still confused as to why different introns would be removed for the same gene? Isn't this all predetermined? Or are you saying that the varying polypeptide depends on which areas the pre-mRNA has been spliced?
Yep the last comment is exactly what I mean. somehow the cell is able to regulate which bits get removed and which don't based on the cell's needs. You don't know to a lot here just know that it can happen. VM

Q. In Stav 2009 exam, Q17 of multiple choice, there is reference to 'homologous amino acids'. What does this mean?
A. I don't have the trial exams with me but I will try and give you some explanation now. If need be I will update my response tomorrow when I can look at the exam. I really wouldn't expect VCAA to be asking you about homologous amino acids. All I know is that sometimes when a mutation occurs (substitution) and a different amino acid gets put in the polypeptide (replacing the one that was previously there), the protein can still pretty much function the same way because the "new" amino acid has similar chemical properties to the "old" one. In this case these two amino acids are said to be homologous. VM
i think this question is asking about the conservation of genes and crucial DNA sequences and how mutations will affect the polypeptide produced. In this case homologous amino acids refers to the similarity in amino acid sequences between related species in 4 different areas of an enzyme amino acid sequence to highlight that the highest degree of similarity will occur in the active site of the enzyme (which in this case is area 3, as it has 78% homologous amino acids) because it is the most crucial part of the enzyme protein. OK fair enough, I will check tomorrow. Yep, the comment above is spot on. The question doesn't require you to really know the meaning of homologous amino acids as they tell you the %s represent the no. of amino acids that are the same. Personally, I think they are using the term incorrectly in this question. VM

Q. What does mRNA longevity refer to? Is that how long the mRNA strand can survive from in the cell in between the nucleus and the ribosome?
A. Spot on. Like other chemical molecules, mRNA will only remain intact for a certain amount of time before it is broken down. The longer it can remain intact the more often it will be able to attach to a ribosome and make the polypeptide that it is coding for. VM

Q.2007 VCAA exam, multiple choice question 13: apoptosis can involve the death of perfectly healthy cells. Can it? Is that like in embryo development?
A. absolutely, and yes, that is what happens during embryonic development to form different structures (eg digits). There is nothing wrong with the cells, they are just programmed to die at that stage of development. VM

Q. vcaa 2008 mcq 10. in regard to option B. why is the mitochondrial DNA not affected by the environment? is only nuclear DNA affected by the environment?
A. This was a bit of a tough question because it was easy to pick other options. Regulation of gene expression is more open to "environmental influences" for nuclear DNA because of the way it is packaged. Remember a gene is by default in the off position and to be turned on has to be exposed, histone proteins unraveled, etc. mtDNA is just a single circular piece and the genes are probably less susceptible to environmental triggers. The key was to recognise option A is the most likely answer. Something to keep in mind for any question about mtDNA and human origins is that mtDNA evidence (differences among populations) suggests humans arose out of Africa. VM

Q.why is the use or making of tools not the first evidence of human cultural evolution? how are we to know that burial ceremonies were?
A. This is a bit of a dodgy one. You have obviously come across it in an exam, I assume a VCAA one, so put it in the memory banks. With these sorts of questions the advice I have is to read options carefully and remember that you may need to choose the best alternative. I can only hope that VCAA have written questions that are clear cut when it comes to cultural and technological evolution. Do not worry about it because everyone will be in the same boat as you. VM

Q.in CSE 2009 mc Q 24 skull 4 is said to be more closely related to human than skull 1, even though skull 1 has smaller teeth. why is this so?
A. I can't answer this one unless I look at the actual question, so I will answer it as soon as get into school tomorrow. VM
A. Yes skull 1 and 4 are similar but I think the key feature is that skull 4 has a flatter face and less pronounced brow ridges. When looking at skulls look at several features to help you make distinctions. I am pretty sure VCAA has always had images that have been clear cut in the exams, so I would expect them to continue to do this. VM


Q.in CSE 2009 mc Q3 why are there 21 homologous pairs? is it because chromosomes 21 are a homologous triplet, not pair?
A. Yes, I am familiar with this question and I agree with your reasoning. Like quite a few of the questions in the trial exams, I think it is a poorly constructed question. There are so many other better ways to test your understanding of the term "homologous pairs". VM

Q.also in CSE 2009 exam, question 6b: if diverse environments lead to different species evolving, is it divergent evolution or adaptive radiation? what's the difference? (sorry to inundate you with questions so soon to the exam and late at night btw)
A. OK, these two terms can be confused. In this question if you wrote divergent evolution or adaptive radiation you would get the mark. Divergent evolution is the general term for divergence from a common ancestor. Adaptive radiation is an example of divergent evolution whereby there are a number of different species that arise due to the utlisiation of different available niches each requiring certain suitable characteristics to survive. VM

Q.last question (for tonight): will we be penalized for giving answers that are too long? and not concise enough?
A. No. As long as you somewhere in your answer have included the relevant points (that have been assigned as getting a mark) and you haven't contradicted yourself anywhere. Having assessed biol exams, just having a key point or even just a key term will get you the mark. How you get across these key points doesn't matter. It is not an English exam. I guess the more you write the more opportunity you are creating for making a mistake or contradicting yourself. Though, if you know your stuff (like you do) this will not an issue. VM

Q.out of africa hypothesis - why does increased mtDNA variation in African populations support this hypothesis? and why is there increased variation there and less in populations that moved elsewhere? would the mutations accumulate in the same way regardless of the populations location? im so very confused
A. Yes it is confusing. Look at this way, if populations around the planet didn't differ in their mtDNA variation it would suggest that each population has arisen from their own localised ansestor about the same time ago (multiregional hypothesis). The fact that their is more variation in Africa suggests that more time has gone by since their common ancestor, hence the notion that humans began there. The other populations have come about through migration out of Africa at a later time and therefore these lineages haven't been around as long, hence less time for mtDNA differences to accumulate, thus less variation within these populations. VM

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