IBO 2012 Theory part A Questions 1-12

So lets take a look at one of the problems.

The stop codons are UAA, UAG and UGA.

In a. you see that UAG is in the middle, the same is true about b. and c. In row d. you do not find any stop
codon so it will not result in two polypeptides. In row e. you once again find an UAG in the middle and no stop
codon in f. row
The answer is below:

Lets look at another problem:

What you need to remember is the different number of hydrogen bonds between A-T and G-C pairs, which are
2 and 3, respectively. Then quickly multiply and add respective values and you will come to the answer. Lets
solve c.: you have 8 G-C pairs and 4 A-T pairs, that means there are 8*3+ 4*2= 32 hydrogen bonds. You do the
same with a. and b. and arrange it in the order of increasing melting temperature (which means increasing
number of hydrogen bonds).
The following task is very interesting and I would strongly recommend sketching a small diagram before
attempting to answer the questions:

I am a terrible painter but I tried to make some kind of pathway that represents the abovementioned processes.

a.
b.

c.
d.

Now you are ready to answer the questions.

You see that if Apaf-1 is not released, cell degradation pathway cannot be initiated. This leads you to choose
the answer a.
If there is no Bcl-2, this means that Apaf-1 is always free and not bound to Bcl-2. This in turn allows Apaf-1 to
communicate with cytC of oxidative damage occurs. And this means a cell is destined to degradation and you
are destined to choose answer b.
In this case you are told that Bcl-2 has only membrane-binding domain and cannot bind to Apaf-1, thus, Apaf-1
is again free to initiate death pathway. The answer is b.
Half-life means a period of time during which half of a protein degrades and loses its activity. Therefore if halflife is extended, more Bcl-2s are in the membrane and they can bind more Apaf-1. This means that a bigger
ROS concentration is needed to induce cell degradation and in turn this leads you to choose the answer a.

The original answers are below:

The following problem may look a bit confusing at first if you have never had upper chemistry in your high
school but do not panic as it is not that hard to solve it.

If you think logically, the lower the pH, the more free hydrogen ions (H+) are present in solution and this means
that more hydrogen can bind to amino acids. Conversely, the higher the pH, the less free hydrogen ions you
have and this means that due to thermodynamic laws amino acids tend to release their hydrogen ions into the
solution to neutralise excessive hydroxyl ions (OH).
In order to understand this concept I will try to visually show these relationships. Lets take amino acid alanine
as an example at its ionization state in neutral pH (for future reference, this form of alanine is known as
zwitterion because it has both positive and negative groups giving a molecule an overall negative charge).
There are three possible states an amino acid with neutral side chain can be in a solution (four states for amino
acids with ionisable side chains). For alanine these look like this and depends on pH of a solution:

Now lets consider that we have very acidic solution and very alkaline solution and alanine molecule with no
net charge.

The pK value helps you decide if an amino, carboxyl or side group is protonated or deprotonated at certain pH
values if a solution that you can change.
Now keep in mind, that when polypeptides form, this occurs simultaneously with dehydration reaction, that is,
an amino group of one amino acid joins with carboxyl amino acid and thus neutralizes each other leaving
positive and negative charges at the ends of a polypeptide. Therefore, when calculating overall charged, you
need to take pK value of amino group at N-terminus of the first amino acid and pK value of carboxyl group at
C-terminus of the last amino acid. NB!

Having all this in mind, lets start with Peptide A as an example.

Lets quickly write down pK values from the table of each constituent of Peptide A:
Asp- 3.9 for side chain and 9.78 for amino group
Ala- neutral
Glu- 4.07
Asp- 3.9
Gly- neutral
Ser - neutral
Ser- neutral side group and 2.19 for carboxyl group
No lets proceed to a solution with a pH 1 net charge. When you compare all the above values, you see that they
are all greater than pH 1, that is all pK > pH 1.Therefore the excess of hydrogen ions present in a solution will
bind to side groups and N-terminus as well as C-terminus of a peptide. Thus, we have a net charge of +1

because aspartic acid has a protonated hydroxyl group (-OH) and protonated amino group (-NH3+), a
protonated hydroxyl group (-OH) for glutamate and for another aspartic acid, and a neutral protonated COOH
group for serine.
Lets now look at pH 7. This means that aspartate at N-terminus has its side chain deprotonated because pK 3.9
< pH 7 and also pK 9.78 > pH 7 which tells you that amino group will be protonated (the easiest way to
understand this is to think this way: the lower the pH, the more free hydrogen ions that can attach to the side
chains). Then the glutamate with pK of 4.07 at pH 7 will be deprotonated because a solution of pH has less
hydrogen ions that a solution of pH 1. The same is true about aspartate and serine; they are all be deprotonated
to make a solution less basic. Therefore, the charge of this peptide will be +1 for aspartates amino group,
negative -1 charge for aspartates, glutamates and the second aspartates side chain, and a negative charge for
serines carboxyl group which all make up -4. Adding +1 + (-4) gives you a net charge of -3.
Finally, lets solve the charge is pH 12. This means that all pKs are less than 12 and this means that the solution
is very basic, and side groups give up their hydrogen ions to make a solution less basic. Therefore, you have
deprotonated aspratates side chain (giving you COO- with one negative charge) and neutral -NH2 N-terminus,
also a one negative glutamate (-COO-) and one negative aspartate (-COO-) side chain charge as well as a
negative serines C-terminus with -COO-.
To summarize when solving this kind of problems remember the general rule: if pK > pH, then this shows you
that a solution has lots of hydrogen ions (the lower the pH, the more acidic a solution is) and the group with that
pK will be protonated. Conversely, if pK<pH, this means that a solution is alkaline and a group with that pK
tries to reduce that alkalinity by donating its protein to the solution thus becoming deprotonated. If pK=pH, this
means that an amino acid is neutral (has both positive and negative charges equal in quantity) and this is termed
an isoelectric point.
Taking into account the examples above, try to solve the Peptide B and Peptide C. The answers are below.

As far as question 5.2. is concerned, look at your solved charges and note that pH 12 would not be good as
Peptide B and C have the same charges and at pH 1 peptides differ by only one charge and this may impair their
resolution. Therefore, pH 7 would give you the best resolution.

Another interesting problem is solved below:

In part 8.1. I do not know the right approach to the answer but what I would be focusing on is to think about
different aspects of unique features of these bacteria:
A has a small size so it is less likely that it be repelled, B has a flagellum so it can move and change direction in
response to repulsion, and C has quite a big surface area covered by capsule made of a layer of polysaccharide
or protein which might be charged and thus influences attachment to the substrate. Looking back at the
question, note the word overcome which means some physical efforts. As B bacteria is the only that can move
quite rapidly due to the presence of the flagellum, I would tick box B in the answer sheet.
In part 8.2. you need to remember the functions of flagella and capsule. Bacteria usually adhere to each other by
means of physical appendages and extra-cellular polymeric substances (for example capsule). Having all this in
mind we can say that A (coccus) would form only very very weak bonds with other cells because they do not
have an outer coat and flagella to move (without movement cells will not meet each other). Then my approach
to deciding the strength of forming biofilms between B and C is to think about different sizes of bacteria
because both motility and capsule are important for aggregation. It is obvious that C is bigger than B and this
means that C has a bigger surface area to make contact with other cells as compared to B. Thus bringing all
these facts together we get a sequence of increasing attachment strength as follows A<B<C.

The next question is quite straightforward:

The way you should understand it is to note the phrase no matter what type of bacteria which indicates that all
bacteria have to have that property named i to v. Lipopolysaccharides are found in the outer membrane of
Gram-negative bacteria and if you have Gram-negative bacteria, there are also Gram-positive bacteria which do
not have this property. None of the bacteria have a nuclear envelope as they are prokaryotic. All of the bacteria
have DNA as this is essence for life and reproduction (exception is some RNA viruses, viroids and prions). All
have cytoplasm but this is a bit disputable because cytoplasm is a mixture of cytosol AND organelles and
organelles are defined as membrane-bound structures. Bacteria do not have one but they do have ribosomes
which in turn raise an intense discussion as to whether they should be named with other organelles or they are
unique structures. Lastly, without ribosomes DNA is of no use, therefore, every cell has lots of ribosomes.
The answers are provided below:

I skipped the theory-based questions because if you do not know the certain facts you will not be able to reach a
correct answer and so lets proceed to the questions requiring more of understanding rather than just
knowledge.

So a. may seem correct at first because you have a y-axis named as Net O2 evolution, however, you should
understand that your independent variable is photon flux (or light intensity) and this indicates that it is a
photosynthesis light response curve. That is you are measuring different effects on O2 evolution caused by
changing the levels of photon quanta.
b. is incorrect because saturation is where your graph levels off, that is at the intercept of lines going through
points B and C. Point A is a light compensation point at which use of carbon dioxide is balanced out by the
release of carbon dioxide by respiration.
c. is incorrect as mentioned above because point B is light saturation point.
d. is correct because at saturation point you get the maximal photosynthetic rate (which in this case is measured
by oxygen evolution). The saturation point can be described as the amount of light that is beyond the capability
of the pigments present in plants to absorb. You should have in mind that different plants have different
saturation points, determined by the number and type of pigments in their photosynthetic cells. At higher light
intensities, providing additional light, does not increase photosynthesis as much because some other factors

come into play; most often it is carbon dioxide availability that limits the rate photosynthesis at high light
intensities.
e. is not correct because saturation point does not mean that photosynthesis stops; photosynthetic machinery is
working at its full capacity and other limiting factors should be changed to increase productivity. A negative yintercept represents the rate of respiration, that is the area below A indicates that a plant is USING more of its
resources than PRODUCING it and at that stage a plant growth is markedly slowed. All this leads to correct f.
answer. And for the same reason g. is correct too because all values about light compensation point indicate that
photosynthesis is greater than respiration, in other words, anabolism (synthesizing new materials for growth and
reproduction) is more intensive that catabolism (degrading new materials for respiration).