Clarification: Events at the rER (synthesized protein will end up in the rER lumen and later bud off in an ER vesicle)

- protein synthesis
- folding of protein
- chemical modification of protein (FURTHER chemical modification will occur in the GA later)

Lysosome vs Peroxisome

http://sln.fi.edu/qa97/biology/cells/cell7.html

"Peroxisomes contain oxidative enzymes. They are similar to lysosomes. Their enzymes have two functions; to convert fats to carbohydrates and to detoxify potentially harmful molecules which form in the cell.

Peroxisomes, in contrast to lysosomes, are produced only on the smooth ER system. They are found in the cytoplasm of many eukaryotic cells as well as prokaryotic cells, microorganisms, and plant cells.

The enzymes of peroxisomes remove hydrogen atoms from small molecules and joins them to oxygen creating hydrogen peroxide (toxic), which is later neutralised by a peroxisomal enzyme, catalase. In the liver this method is used to break down molecules of alcohol into substances that can be eliminated from the body. "

Clarification - primary vs secondary lysosomes

1) Origin of Primary lysosomes (page 17 of your notes I believe)

In your cell structure and function lecture notes, under the section on Lysosomes, it states that primary lysosomes bud off from the Golgi Apparatus OR Endoplasmic Reticulum.

Note that primary lysosomes largely originate from the GA, that is why we have emphasized this during the lecture/tutorial. In some cases, primary lysosomes can bud off the ER but you do not need to know this in detail.

Even if you mention just GA alone, it is still correct. :)

2) Primary vs Secondary lysosomes (tutorial structured Q1d)

- Primary lysosome are formed from the GA while the secondary lysosome is formed by the fusion of the primary lysosome and an endocytotic/phagocytotic vesicle.

- The primary lysosome does not release its contents out of the cell but the secondary lysosome may release useful products (which will serve as building blocks of new materials) into the cytoplasm of the cell via facilitated diffusion, or release waste products/products that cannot be digested out of the cell via exocytosis.

You can view a good diagram of primary and secondary lysosomes here: http://biology.kenyon.edu/HHMI/Biol113/lysosomes.htm

Cell structure and function (cell membrane) - SDL Wksheet A

Video of facilitated diffusion:
http://www.youtube.com/watch?v=I4123hUU8xo&list=FL-cFTJ8NxBjonnjuwSQgSsw&index=26&feature=plpp_video

Video of active transport:
http://www.youtube.com/watch?v=yz7EHJFDEJs&feature=autoplay&list=FL-cFTJ8NxBjonnjuwSQgSsw&lf=plpp_video&playnext=1

Query about cell membranes: Can water diffuse through the lipid bilayer?

Water, though small, is a hydrophilic molecule. Hence it cannot diffuse through the hydrophobic interior of the lipid bilayer. Aquaporin channels are required for water to pass through the lipid bilayer.

FYI: You can read about the experimental discovery of aquaporin in the links below:

http://www.ncbi.nlm.nih.gov/pubmed/11773613

http://www.bing.com/images/search?q=aquaporin+oocyte&view=detail&id=2BE08C8AEE232A3B3F05FE97719A64215101C3BE&first=0&FORM=IDFRIR

Reminder

HOMEWORK this weekend (besides studying VERY HARD for your lecture test on Monday :p):

1) For the current tutorial worksheet on Cell Structure, please copy out (since you should have already done it) your essay question (there's only one essay question, on the last page) onto a piece of foolscap for me to mark. Hand it in to your Bio reps and Bio reps, please put it in my *new* pigeonhole (labelled with my name) by 5pm the coming Monday.

I believe this is crucial as alot of students do badly in essays as they not know how to phrase their answers. As such, all essays (in future) must be done on a piece of foolscap and handed in for me to mark.

2) After the lecture test on Monday, I will be collecting your tutorial worksheets on Biological Molecules (carbo, lipids, protein tutorial worksheet + SDL worksheet B on nucleic acids) during our tutorial class next week. So please remember to bring them to school.

This is because all of you are new to the rigours of JC life, so I want to check that you are keeping up well with the course (and understand what is expected of you). :)

Good luck for your test!

Cell structure and function tutorial - origin of mitochondria and chloroplasts

Q1) How does the presence of double-membranes in these two organelles serve as evidence that these two organelles actually existed as free -living bacteria centuries ago?

A1) - The ancestor eukoryotic cells engulfed bacteria by phagocytosis/endocytosis, and the bacteria eventually became the mitochondria or chloroplast.
- Hence, the outer membrane is derived from the eukaryotic cell and the inner membrane is derived from the bacteria.

FYI only: This theory is actually named the "endosymbiotic theory", but you are not required to know it. You can watch an animation of the theory here: http://www.youtube.com/watch?v=EgaGh9-mFnQ

Note: Please do not be confused, prokaryotes (i.e. bacteria) have only one cell membrane. You will learn more about its structure in the later topics.


Q2) How does linear DNA (in eukaryotes) and circular DNA (in prokaryotes, mitochondria, and chloroplasts) look like under the electron microscope (EM)?

A2) Linear DNA (above) and circular DNA (below), in a relaxed state.

Cell structure and function (cell membrane) - SDL Wksheet A

Endocytosis vs Exocytosis (opposite processes)
http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120068/bio02.swf::Endocytosis%20and%20Exocytosis

http://www.youtube.com/watch?v=K7yku3sa4Y8&list=FL-cFTJ8NxBjonnjuwSQgSsw&index=52&feature=plpp_video

Endocytosis
- Definition: Cellular uptake of biological molecules (eg. proteins) and particulate matter via formation of new vesicles (called endosomes in general) from the plasma membrane.

- Importance: This is required as most substances required by the cells cannot pass through the plasma membrane.

- Types:

(i) Phagocytosis ("cellular eating") - process of engulfing solid particles (eg. bacteria, food) by the cell membrane to form a phagocytic vacuole/ phagosome by phagocytic cells (eg. white blood cells). The resulting phagosome subsequently fuses with primary lysosomes to form secondary lysosomes. Hydrolases present in lysosomes hydrolyse the solid particles and the nutrients released will then diffuse out into the cytosol for use in other metabolic processes.

(ii) Pinocytosis ("cellular drinking") - non-specific process where a cell creates a pinocytic vacuole around a droplet of extracellular fluid and brings it into the cell. The resulting pinocytic vesicle/ pinocytic vacuole subsequently fuses with primary lysosomes to form secondary lysosomes. Hydrolases present in lysosomes hydrolyse the particles and the nutrients released will then diffuse out into the cytosol for use in other metabolic processes.

(iii) Receptor-mediated endocytosis - Specific binding of extracellular substances (eg. LDL) to protein receptors (eg. LDL receptor) on the cell surface membrane, triggering the formation of a vesicle, and the subsequent internalising of the substances.

Cell structure and function tutorial - identifying rER vs sER

rER: granular (due to presence of ribosomes on its surface), more regular, flattened cisternae, continuous with outer membrane of nuclear envelope

sER: non-granular, less regular, tubular (more "rounded") cisternae

Cell structure and function tutorial - Ribosomes

Location of ribosomes
- Eukaryotic ribosomes in the cell are found in the cytosol as either free ribosomes, or ER-bound ribosomes. As the bound ribosomes are bound to the ER, the proteins made by the bound ribosomes are fed into the lumen of the ER where it can be modified (eg. glycosylation) (picture below).
- Modification of proteins helps it to fold properly or targets it to the correct location in the cell. Further modification of proteins occur in the GA.


- Both free and bound ribosomes function to carry out protein synthesis. The difference is that the proteins made by the free ribosomes are for more "localised" use whereas the proteins made by the bound ribosomes are usually transported to other parts of the cell (eg. inserted into the membrane), or secreted out of the cell for use.
- Ribosomes may be found as polyribosomes/polysomes (complex of mRNA with many ribosomes - to increase rate of translation/proteins synthesis) (picture below).

Types of ribosomes
- Ribosomes are made up of a small subunit and a large subunit.
- There are 2 types of ribosomes, 70S and 80S. 80S ribosomes are bigger than 70S ribosomes. "S" refers to Svedberg, a unit of sedimentation coefficient used for centrifugation. Prokaryotic cells (bacteria), mitochondria and chloroplasts have only 70S ribosomes, while eukaryotic cells (include plant and animal cells) have 80S ribosomes (in their cytosol) PLUS 70S ribosomes (in their mitochondria/chloroplasts).

Synthesis of ribosomal subunits (a little complex; you may draw out the process to improve understanding)
- Ribosomal subunits (both small and large) are composed of rRNA and proteins.
- rRNA is synthesised by the nucleolus. Newly-synthesized rRNA remains in the nucleolus to wait to be assembled with the ribosomal proteins (aka the protein component of ribosome).
- The ribosomal proteins (like other proteins) are synthesised by the ribosomes in the cytoplasm. Once made, they will be imported into the nucleus (through the nuclear pore; import regulated by the nuclear pore complex of proteins) to the nucleolus where it is assembled with the rRNA. Hence, assembly of ribosomal subunits (picture below) is carried out by the nucleolus. Once assembled, the ribosomal subunits are then exported out of the nucleus and into the cytoplasm.

Practical: Videos for use of a microscope

Using:
http://www.youtube.com/watch?v=X-w98KA8UqU&list=FL-cFTJ8NxBjonnjuwSQgSsw&index=10&feature=plpp_video

Focusing:
http://www.youtube.com/watch?v=scEhgAiazzU&feature=autoplay&list=FL-cFTJ8NxBjonnjuwSQgSsw&lf=plpp_video&playnext=1

Wet mount:
http://www.youtube.com/watch?v=jjevU-XMVzU&list=FL-cFTJ8NxBjonnjuwSQgSsw&index=13&feature=plpp_video

Clarification

1) Chloroplast is bound by a double membrane but it has another set of membrane inside of it called the thylakoid membrane.

Biology Flashcards for your smartphone

Revision flash cards, courtesy of Mr Chee!

1) Go to app store, search for "iflashcards".
2) After downloading, go to "card management" --> "browse cards by account" --> search for "frozespot171".
3) Proceed to view and save cards.

Terminologies

Dear all,

I understand that some of you may be confused about the terminologies polar/nonpolar/hydrophilic/hydrophobic. These terminologies are probably more Chemistry-based than Biology-based so I may not be an expert in this, but let me try my best to clarify these terms. I think you will learn more about these terms in Chemistry so maybe you will have a better idea then. The examples I have used below are from Wikipedia.

Polarity is dependent on (1) the difference in electronegativity between atoms in a compound and (2) the asymmetry of the compound's structure.

(1) The main reason why a molecule is POLAR is due to the presence of a large electronegativity difference between its atoms. This leads to unequal sharing of electrons in a covalent bond.

For example, water (H2O) is a polar molecule due to the unequal sharing of electrons between oxygen and hydrogen, as oxygen is more electronegative than hydrogen and will hence pull shared electrons towards itself more. Due to the polar nature of the water molecule itself, polar molecules are generally able to dissolve in water. Hence, polar and nonpolar molecules are also called hydrophilic and hydrophobic molecules, respectively.

On the contrary, oxygen (O2) is a nonpolar molecule as the oxygen atoms are of equal electronegativity. Methane (CH4) is also a nonpolar molecule because carbon shares the electrons with hydrogen almost equally.

(2) The shape (you can google "VSEPR" to see all the possible shapes of molecules) of the molecule also determines whether a molecule is polar or nonpolar. A molecule is POLAR if there is asymmetrical arrangement of polar covalent bonds.

A phosphate group (PO4) has a tetrahedral (asymmetrical) shape, so there is an imbalance between the 4 oxygens and creates and stronger pull to one side of the molecule and hence making it polar.

On the contrary, boron trifluoride molecule (BF3) has a trigonal planar (symmetrical) arrangement of three polar bonds at 120°. This results in a more equal distribution of electrons in the molecule so it is nonpolar.

Hope this helps.

FYI: Scientists that have contributed to the discovery of DNA structure (in chronological order)

1) Edwin Chargaff

- discovered complementary base pairing in DNA

2) Rosalind Franklin

- Used Xray diffraction to find the dimensions of DNA

3) Watson and Crick

- Proposed correctly the structure of DNA, based on the dimensions proposed by Rosalind Franklin

Announcement

Dear all,

Please note that I will be collecting all your tutorial worksheets (including worksheet B) for the whole topic of Biological molecules (Carbohydrates, Lipids, Proteins, Nucleic acids) to check after the holidays, once we are done with going through the tutorial. So please remember to bring ALL your tutorial worksheets to class after the March holidays.

This march holidays, please revise for your lecture test, start on your tutorial worksheet for the next topic on Cell Structure and Function, and read your lab protocol on Microscopy (there's ALOT to read for the next lab session so please read up in advance).

Enjoy the holidays! :)

Miss Teong

Biological molecules Wksht B - Structured Q1d (DNA vs alpha-helix)

1) The monomers in DNA are deoxyribonucleotides but the monomers of alpha-helix are amino acids.

2) The bonds between monomers in DNA are phosphodiester bonds whereas the bonding between monomers in alpha-helix are peptide bonds.

3) There are only 4 types of monomers in DNA, but 20 possible monomers in alpha-helix.

4) DNA is a double helical structure while alpha-helix is made of single helical structure.

5) Intermolecular hydrogen bonding and hydrophobic interaction between stacked bases stabilise the 3-dimensional structure in DNA, but only intramolecular hydrogen bonding stabilise the structure of the alpha-helix.

Graph drawing for lab: Sample of line of best fit

Line/curve of best fit best represents the data on a scatter plot. It may pass through none, some, or all of the points. Try to balance the number of points above and below the line.

Biological molecules wksht B: Structured Q1c (Why does DNA run antiparallel?)

1) Each complementary base pair can only fit together within a double helix if the two strands are antiparallel.

2) Such precise orientation of the bases will then allow hydrogen bonds to form between the bases, hence stabilizing the structure of DNA.

Biological molecules wksht A: Polynucleotide formation

Please note that:

1) The raw material needed is a nucleoside TRIphosphate. But the monomer that is eventually making up the polynucleotide chain (polymer) is a nucleotide (aka nucleoside MONOphosphate).

2) This is NOT a condensation reaction as NO water molecule is evolved. Instead, pyrophosphate is evolved.

Biological molecules tutorial: Protein structure (key points covered)

1) Primary structure
- number, type, and sequence of amino acids
- held together by peptide bonds
- determines the type of bonding possible in secondary/tertiary/quaternary structure

2) Secondary structure (alpha-helix or beta-pleated sheet)
- folding and coiling of polypeptide backbone
- hydrogen bonds
- between neighbouring amino acids at peptide bond regions

3) Tertiary structure
- further coiling and folding to form a compact three-dimensional globular structure
- all four types of intramolecular bonding possible (hydrogen bonds, disulfide bridges, ionic bonds, hydrophobic/hydrophilic interactions)
- between R groups of amino acids

4) Quaternary structure
- aggregation of 2 or more extensively coiled polypeptide chains
- held together by four possible types of intermolecular bonds (hydrogen bonds, disulfide bridges, ionic bonds, hydrophobic/hydrophilic interactions)