Clue to previous blogpost "Enzymes...have you wondered"

Click to enlarge

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

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

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.

Clarification

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