Enzymes - Have you wondered...

1) How enzymes from thermophilic bacteria is able to remain stable/retain catalytic activity at high temperatures?

2) Why lysosomal enzymes can function at a pH of 5.5 but not at pH of 6.8, even though the numbers are quite close?

Any takers?

Announcement

1) SPA
ANSWERS FOR THE PAST PRACTICALS ARE ON IVLE. GUYS, YOU MAY NEED TO CHECK YOUR EYESIGHT............................................................................................................

2) Enzymes tutorial essay Q
I have received some queries regarding the collection of the Enzymes tutorial essay Q. Just to clarify, I will not be collecting this essay to mark (i.e. not compulsory to hand in) because this Q is rather factual (everything can be found in the lecture notes). But you are still strongly encouraged to attempt the Q so as to test your understanding of the topic. However, if you would like me to mark it, please hand it in to me in the earlier part of next week (Mon/Tues/Wed) as it is my last week in school and I need some time to mark.

3) Plan for next week
I plan to complete the entire ENZYMES TUTORIAL next week so please complete the tutorial and REMEMBER TO BRING IT! Also, a reminder that the practical next week will be a TIME TRIAL (75min) so be prepared for it!

Good luck for your lecture test on Monday! I am expecting you guys to do well for it. Study hard and do me proud! :)

Enzymes worksheet B (temperature) - Q1b

Please be specific in your answer/ note the context of the question (i.e. NAME the enzyme and substrate if the question stem mentions them)

- D: Initially at very low temperature, the enzyme activity (rate of enzymatic reaction) is very low.
- E: This is due to the inactivation of the enzymes, and the low kinetic energies of both the substrate and enzyme molecules, leading to a low frequency of effective collisions between them, and hence reduced rate of formation of enzyme-substrate complexes and products. 

- D: As temperature increases to optimum, the enzyme activity (rate) doubles for every 10C increase in temperature (Q10), and eventually reaches a peak/maximum rate at the optimum temperature (65C). 
- E: Increased temperature increases the kinetic energies of both enzyme and substrate molecules which in turn, increases the frequency of effective collisions between them. As a result, more enzyme-substrate complexes and hence products are formed.

- D: As temperature increases to beyond optimum, the enzyme activity (rate) decreases.
- E: This is due to the excess heat increases the vibrations of atoms within enzyme and disrupts the intramolecular hydrogen bonds, ionic bonds, and hydrophobic/hydrophilic interactions stabilising the secondary and tertiary structures of the enzymes, causing it to unfold and loses its specific 3D configuration/conformation (enzyme denatures). Hence its active site loses its specific shape, causing the substrate to be unable to bind to it. Hence, less enzyme-substrate complexes and products are formed.

P.S. If you have any queries with regards to the 3 MCQs in this enzymes wksheet B, you can ask me under comments here, or during the next tutorial. Note that we will be working on the main enzymes tutorial next week so please complete it over the wkend (treat it as lecture test revision). I aim to finish Enzymes before I leave! Hope you have enjoyed and benefited from my lessons. Don't miss me.. HAHA! See you next week! :)

Nondisjunction in meiosis

http://www.sumanasinc.com/webcontent/animations/content/mistakesmeiosis/mistakesmeiosis.html

This is a very good video on nondisjunction in meiosis. Due to time constraints I don't think i'll be able to play the entire video in class, so please take some time to view it on your own.

P.S. I have created a chatbox on the right! Feel free to chat there. :)

Cell division - terminologies

TYPES OF CHROMOSOME

1) Autosome = a chromosome that is not a sex chromosome. For example, in humans there are 22 pairs of autosomes and 1 pair of sex chromosomes (XX in females or XY in males).

NUMBER OF CHROMOSOMES

2) Aneuploidy = a chromosome abnormality where there is an abnormal number (extra or missing chromosome(s) / +1, +2...etc or -1,-2...etc chromosomes) of chromosomes, due to nondisjunction in mitosis/meiosis I/meiosis II. Eg. Monosomy = presence of only one chromosome (instead of the typical two in humans) from a homologous pair.

3) Polysomy = when a diploid organism has at least one or more chromosome(s) than the normal (diploid) number, due to nondisjunction. Eg. Trisomy = 3 copies instead of 2 copies of a particular chromosome (eg. Trisomy 21 in down syndrome).

NUMBER OF SETS OF CHROMOSOMES

4) Polyploid = cells with more than two paired homologous sets of chromosomes (diploid, 2n). For example, triploid (3n/ cells with 3 times the haploid number of chromosomes/ 3 sets of chromosomes) and tetraploid (4n/ cells with 4 times the haploid number of chromosomes/ 4 sets of chromosomes).

Hope that this is less confusing for you guys now. Since I've already covered most of the terminologies of your SDL on nondisjunction here, i expect all of you to be able to answer most of my questions next week during the tutorial! ;)

Chromosome number and cancer (Cell division tutorial Q8c)

http://www.reuters.com/article/2009/05/20/us-cancer-downs-idUSTRE54J5IN20090520

Cell division tutorial Q15b

The diagram below is the more accurate representation of crossing over as it shows the BREAKING of non-sister chromatids, followed by the EXCHANGE and then the REJOINING of the corresponding sections of genetic material.






The diagram below is the less accurate representation of crossing over as it does not show the exchange taking place. So please don't draw this in your exam scripts.

To help you understand better, below is a pictorial representation of the mechanism of crossing over.

Note that before crossing over, the sister chromatids are genetically identical, for example the chromosome coloured red is homozygous dominant for the 'c' allele (CC) and homozygous dominant for the 'e' allele (EE).

However, after crossing over the sister chromatids are no longer identical, for example the chromosome coloured red is still homozygous dominant for the 'c' allele (CC) but is now heterozygous for the 'e' allele (Ee).

Another diagram to show the products formed after crossing over in meiosis. You should be a pro by now!


If you are clear now about crossing over, please re-attempt MCQ11. Hope you will get it right this time! 


Some tips for MCQ11: 


- Identify/label the pair of homologous chromosomes, and the sister chromatids that are held at the centromere in the diagram. You can use two differently coloured highlighters to help you trace the chromatids from the paternal vs the maternal chromosomes. 


- Has crossing over taken place? How do you know? (Hint: before crossing over, the sister chromatids of a chromosome must be genetically identical/have identical alleles.)


- What are the products formed for this Q? (Note that this question is asking you about the daughter cells formed after MEIOSIS I, and not meiosis II!!! There is a difference, because meiosis I separates the homologous chromosomes while Meiosis II separates the chromatids!) By the way, "segregation of alleles Q from q" means that the separated daughter cell carries only allele Q or allele q (and not both Q and q alleles). 

Let me know if you have any problems (you can raise the Q after tutorial/ leave a comment on the blog). 

We will be working on Cell division SDL worksheet B and Enzymes tutorial/SDL (will probably start with the SDL) next week. I will be collecting the enzyme essay Q to mark as well so remember to do it on foolscap.

Study hard for your test!!! :)

Answers to Cell division tutorial - factual Q

(14di) How does A lead to genetic stability? [2m]

- A (mitosis) sepArates (note the spelling) sister chromatids of a duplicated chromosome to yield two daughter cells with exactly the same number of chromosomes and is genetically identical to the parent cell by having the same alleles/nucleotide sequence.

- No chiasma is formed and no crossing over occurs during A (mitosis), retaining genetic fidelity.


(14dii) How does B lead to genetic variation? [3m]

- During prophase I of B (meiosis), crossing over occurs between homologous chromosomes, resulting in new combinations of alleles on the chromosomes of the gametes.

[independent assortment]
- The arrangement and subsequent sepAration of the homologous chromosomes of each tetrad/bivalent in metaphase I and anaphase I of B (meiosis) respectively is completely independent of the other tetrad/bivalent, producing new combinations of chromosomes in gametes.

[independent assortment]
- The arrangement and subsequent sepAration of the chromatids of each chromosome in metaphase II and anaphase II of B (meiosis) respectively is completely independent of the orientation of other chromosomes, producing new combinations of chromosomes in gametes.


(Q15c) How does meiosis lead to the formation of four haploid nuclei? [2m]

- During anaphase I, homologous chromosomes separate, resulting in two daughter cells, each with a haploid nucleus, at the end of telophase I and cytokinesis.

- During anaphase II, the sister chromatids separate, resulting in four daughter cells altogether, each with a haploid nucleus, at the end of telophase II and cytokinesis.

What is ploidy?

Some of you seem to be confused about what ploidy means. Hope the following helps:

Ploidy = no. of single sets of chromosomes in a cell
- Haploid cells (gametes, for example either the sperm or the egg cell) --> one set of chromosomes (either from father/mother)
- Diploid cells (somatic cells) --> two sets of chromosomes (one set from father/paternal side, one set from mother/maternal side)

KARYOTYPE (number of chromosomes, and what they look like under a light microscope) OF A DIPLOID CELL (below)

P.S.

Please don't forget to refer to the learning outcomes for this topic when you study. Note that when you're describing the behaviour of the chromosomes during mitosis/meiosis, you have to mention the KEY WORDS that have been BOLDED (e.g. "centromere divides") in your lecture notes. :)

Cell division tutorial Q7aiii and Q7b

Q7aiii) How non-kinetochore microtubules help in mitosis (their function had been asked in the A levels bef0re):

The non-kinetochore microtubules from opposite poles slide past and push apart from each other, causing the distance between the poles to increase and hence, elongating the cell.

Animation: http://faculty.plattsburgh.edu/donald.slish/Polar.html

Q7b) Behaviour of chromosomes during mitosis vs meiosis.

Meiosis animation

http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter28/animation__how_meiosis_works.html

Mitosis and Meiosis Lecture Notes Page 1 (Terminologies)

How DNA is packaged
http://www.youtube.com/watch?v=9kQpYdCnU14

Cell structure and function - SDL Wksheet B (Memb transport)

Fluid mosaic model animation:
http://www.stolaf.edu/people/giannini/flashanimat/lipids/membrane%20fluidity.swf

Gramicidin A animation:
http://en.wikipedia.org/wiki/File:Gramicidin_A.gif

Cell structure and function tutorial - Answer to Essay Q

1) The amino acid is taken into the cell by facilitated diffusion or active transport.

2) During protein synthesis by ribosome at the rough ER, the amino acid is added to the growing polypeptide chain, which eventually becomes anchored in the ER membrane.

3) In the ER, the protein may undergo chemical modification such as glycosylation, to form a glycoprotein.

4) ER vesicle carrying the protein buds off from the ER, travels towards the Golgi apparatus and fuses with the cis face of the Golgi apparatus.

5) As the protein travels through the Golgi apparatus through repeated budding and fusion of vesicle, it may undergoes further modification.

6) At the trans face of the Golgi apparatus, the modified protein is sorted and packaged, and eventually enters a Golgi vesicle which buds off from the Golgi apparatus.

7) The Golgi vesicle moves towards the plasma/cell surface membrane and fuse with it.

8) The transmembrane glycoprotein, which contains the radioactive-labeled amino acid, becomes part of the cell surface membrane.

*EXTRA*

For more information about how transmembrane proteins are held in the membrane, you can view this animation: http://www.youtube.com/watch?v=7XTpe7TRQEk

FYI only: Lysosome's role in autolysis

http://www.jci.org/articles/view/11829
A lysosomal protease enters the death scene (2001)

http://www.ncbi.nlm.nih.gov/pubmed/21914490
Lysosomes in cell death (2004)

http://www.ncbi.nlm.nih.gov/pubmed/21914490
Lysosomes and lysosomal cathepsins in cell death (2012)

Interesting read about lysosomes for the layman

http://www.nytimes.com/2009/10/06/science/06cell.html?_r=1

Self-Destructive Behavior in Cells May Hold Key to a Longer Life

"In recent years, scientists have also found evidence of autophagy in preventing a much wider range of diseases. Many disorders, like Alzheimer’s disease, are the result of certain kinds of proteins forming clumps. Lysosomes can devour these clumps before they cause damage, slowing the onset of diseases..."

Cell structure and function

This is a good recap video for the above topic:

http://www.youtube.com/watch?v=LP7xAr2FDFU&feature=related

How a light microscope works - FYI

http://www.microscopemaster.com/brightfield-microscopy.html

"In brightfield microscopy a specimen is placed on the stage of the microscope and incandescent light from the microscope’s light source is aimed at a lens beneath the specimen. This lens is called a condenser.

The condenser usually contains an aperture diaphragm to control and focus light on the specimen; light passes through the specimen and then is collected by an objective lens situated in a turret above the stage.

The objective magnifies the light and transmits it to an oracular lens or eyepiece and into the user’s eyes. Some of the light is absorbed by stains, pigmentation, or dense areas of the sample and this contrast allows you to see the specimen.

For good results with this microscopic technique, the microscope should have a light source that can provide intense illumination necessary at high magnifications and lower light levels for lower magnifications. "

Biological molecules Wksht B - Structured Q2

When checking through your Biological Molecules Tutorial, I found that many of you do not know how to phrase your answer to the above-named question. Since this is an important Q (data analysis Q), I think that it is crucial for you to understand how to phrase your answer. You will be seeing many more of these data analysis Q in future. As such, when you get your worksheets back, please check against your own tutorial worksheet and see that you got the answer below:

Q) DESCRIBE [D] and EXPLAIN [E] the data obtained (you should have two MEANINGFUL observations).

A)
[D1] The ratio of A:T and C:G is 1:1 in BOTH species X and Y.
[E1] This is because according to Chargaff's complementary base pairing rule, Adenine (A) always pairs with Thymine (T), while Cytosine (C) always pairs with Guanine (G).

[D2] In species X, the (C+G) content is 4 times higher than the (A+T) content, whereas in Species Y, both such contents are about the same.
[E2] This is because A and T forms two hydrogen bonds while C and G forms three hydrogen bonds,
making a C-G base pair stronger than a A-T base pair.
Since high temperatures denatures DNA, species Y that lives in a hot spring under high temperatures possesses higher C-G content to ensure stability of its DNA.