I'd better get on to studying for SCIE1106 (Molecular Biology of the Cell), because that unit is quite tricky. I'm not going to finish going through all of the CHEM1004 stuff, since the rest is either basic stuff that you should know before (like the structure of an atom and bonding) or stuff that requires diagrams to explain properly.
So now I'm onto the beginning lectures of SCIE1106. I can't believe that we only had four lectures with that guy- he covered so much content that it felt more like 6 lectures. Anyhow...
The first two lectures went from telling us what an atom is to explaining the basic properties of proteins, carbohydrates and lipids. (Yup, I told you that these lectures probably covered way too much...) These are topics that I've covered before, so let's take a look at the content of the next two lectures.
First up: similarities and differences between eukaryotic and prokaryotic cells!
Eukaryotic and prokaryotic cells are similar in that they all use more or less the same molecules, carry out the same basic chemistry and carry information in their DNA. However, they have several important differences.
The main distinguishing difference between eukaryotic cells and prokaryotic cells is that prokaryotic cells do not have a nucleus, whereas eukaryotic cells do (well, mature red blood cells don't, but they're pretty much the only exception). Eukaryotic cells store their linear DNA in the nucleus, whereas prokaryotic circular DNA just floats around in the cytosol. In fact, aside from not having a nucleus, prokaryotic cells generally do not have any organelles at all, whereas eukaryotic cells have several membrane-bound organelles which carry out various functions in the cell. Another difference is that while both cells have ribosomes, eukaryotic cells have larger ribosomes than prokaryotic cells.
Cells can derive energy from different sources. Organotrophic cells derive energy from organic molecules, phototrophic cells derive energy from light whereas lithotrophic cells derive energy from inorganic molecules.
Organelles
As mentioned above, eukaryotic cells have many different organelles- different membrane-enclosed structures where various processes take place. I've already written a bit about membranes in an earlier post- I might write another one later more specific to the content of this unit.
Nucleus
The nucleus is the place where most of the eukaryotic DNA is stored. Some of the DNA is present as heterochromatin, which is highly condensed throughout the entire cell cycle, while the rest is present as euchromatin, which is not condensed until mitosis. The nucleus has a double membrane which is continuous with the membrane of the endoplasmic reticulum. The membrane has several pores through which substances can pass through. Within the nucleus, there is a structure called the nucleolus, in which ribosomes are produced.
Ribosomes
Ribosomes are packages of protein and ribosomal RNA (rRNA) found in the cytosol and endoplasmic reticulum. They are the site of protein synthesis and are made up of two subunits: a small and a large subunit. Eukaryotic ribosomes are larger than prokaryotic ribosomes- eukaryotic ribosomes are 80S while prokaryotic ribosomes are 70S. (Sorry, I can't remember exactly what the "S" was meant to stand for right now, aside from that it's a form of measurement. Something to do with sedimentation or something like that.) Ribosomes located within the mitochondria and chloroplasts are also 70S (it has been hypothesised that mitochondria and chloroplasts were originally bacteria that were engulfed by eukaryotic cells).
Mitochondria
Mitochondria are often referred to as "the powerhouse of the cell," as they produce ATP (adenosine triphosphate), a form of energy that the cell can use. (One common misconception is that mitochondria produce energy. They do not produce energy, as that would be breaking the law of conservation of energy. Mitochondria simply convert energy to a form that can be used by the cell.) Mitochondria, like the nucleus, have two membranes: a smooth outer membrane that is permeable to small ions and molecules, and a folded inner membrane which is impermeable and has transport proteins to carry solutes across. The folds of the inner membrane are also known as "cristae," and they are where ATP synthesis takes place.
Aside from having their own 70S ribosomes, mitochondria also have their own DNA. They also have their own RNA as well. This DNA codes for enzymes required for the reactions that produce energy.
Energy production is quite a complex process. It starts in the cytosol, where carbohydrates and some amino acids are oxidised to form pyruvate. This process, known as glycolysis, generates some energy molecules. Pyruvate can then enter the mitochondria, along with fatty acids. Both pyruvate and fatty acids are then converted to acetyl CoA (which is essentially an acetyl group attached to coenzyme A).
In the mitochondria, acetyl CoA is repeatedly oxidised in a cycle known as the citric acid cycle. (Some amino acids can also enter this cycle directly.) CO2 is produced in this cycle, and the mobile electron carriers NAD+ and FADH are reduced to NADH and FADH2, respectively. (I mentioned these electron carriers in an earlier post for CHEM1004.)
NADH and FADH2 carry electrons to the electron transport chain (ETC), located in the inner membrane of the mitochondria. Electrons from NADH first enters Complex I (NADH dehydrogenase complex) of the ETC, are carried by ubiquinone (Q) to Complex III (Cytochrome b-c1 complex), are carried by cytochrome c (c) to Complex IV (cytochrome oxidase complex), where they finally reduce oxygen to form water. (This is why oxygen is required for aerobic respiration in the mitochondria- if insufficient oxygen is present, the cell makes do with energy produced from glycolysis.) The energy released when these high-energy electrons travel through the ETC transports protons into the space between the two mitochondrial membranes. This generates a proton gradient as there are more protons in the inner membrane space than in the mitochondrial matrix. The protons move through ATP synthase to get back to the matrix. As they move through ATP synthase, ATP is produced.
Electrons from FADH2 travel through the ETC in the same way, but instead of entering Complex I, they enter Complex II (succinate dehydrogenase). Ubiquinone then takes these electrons to Complex III.
Chloroplasts
Chloroplasts are organelles only found in plant cells. Like mitochondria, they are also likely to have originated from prokaryotic organisms that were taken up into eukaryotic cells. They also have their own DNA, RNA and 70S ribosomes.
Chloroplasts are sites of photosynthesis, or converting light energy into a form that can be used by the cell. They do this by harvesting light and producing carbohydrates.
Chloroplasts, like mitochondria and the nucleus, have double membranes. The two membranes have similar properties to that of the mitochondria: the outer membrane is smooth and permeable to small molecules whereas the inner membrane is impermeable and has transporters to transport solutes across it.
The inside of chloroplasts contains stacks of thylakoids, which are formed by the folded internal membrane. These stacks are also known as grana, and they are where light is harvested. The lumen is the space between thylakoids in a granum. The stroma is essentially the rest of the inside of the chloroplast.
Now it's time to look at how chloroplasts harvest light! This should be a challenge seeing as I didn't really learn it that well the first time. At least now that I understand ATP synthesis, it shouldn't be too hard, right? Right?? Well, we shall see...
The thylakoid membranes contain special pigments that can collect light. This light energy is converted to NADPH and ATP, though unfortunately the slides don't go into too much detail into how they do this. I did find a good website though- http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/LightReactions.html.
The understanding I have is that the electron transport chain in chloroplasts has two "photosystems" called I and II. These have antenna pigments that can collect light (as I mentioned above). When Photosystem II absorbs a photon of light, it removes an electron from a molecule called P680. located inside Photosystem II. After an electron has been removed, P680 is electronegative enough to pick up electrons from water in the lumen. These electrons are picked up by plastoquinone (PQ) to the cytochrome b6/f complex. Electrons provide this complex with energy to transport protons from the stroma to the lumen, creating a proton gradient. Electrons at the cytochrome b6/f complex are then picked up by plastocyanin (PC) to Photosystem I. The electrons then pass through ferredoxin (Fd) before ultimately reducing NADP+ to NADPH. Additionally, the protons from the proton gradient that was formed earlier power ATP synthase as they move back into the stroma- just like ATP synthase in the mitochondria.
Sorry if that was overly confusing :(
After NADPH and ATP are produced, they can power the synthesis of carbohydrates from atmospheric CO2. This process, known as the Calvin cycle, takes place in the stroma of chloroplasts. Rubisco, which is apparently the most abundant enzyme in the world, catalyses the first step of this process. Fortunately, we don't need to go into much detail about this for now.
Endoplasmic Reticulum
The endoplasmic reticulum is a network of sacs and tubules that extends throughout the cytosol. It can be divided into two sections: the rough endoplasmic reticulum, which contains ribosomes for protein synthesis, and the smooth endoplasmic reticulum, where lipids are produced. The cisternae (tubules) of the rough endoplasmic reticulum are parallel and flat, whereas the cisternae of the smooth endoplasmic reticulum are tubular and branching in comparison.
Golgi Apparatus
The Golgi apparatus is a specialised section of the endoplasmic reticulum in which proteins are modified before being packaged and sent to different locations. The cis face of the Golgi apparatus is adjacent to the rest of the endoplasmic reticulum, whereas the trans face faces towards the cell membrane. The most common modification that takes place within the Golgi apparatus is the addition of carbohydrates to form glycoproteins (i.e. proteins with carbohydrate chains added).
Vacuoles
Vacuoles are seen mainly in plant cells, though if I remember correctly animal cells may have some smaller vacuoles as well. They have many functions, including degradation, detoxification and storage.
Peroxisomes
Peroxisomes are small organelles containing oxidation enzymes. They perform detoxification functions in both animal and plant cells. In plants, peroxisomes are also sites of photorespiration (carbon recycling) and conversion of stored fats into sucrose.
Cytoskeleton
The cytoskeleton is a topic that I have already covered in an earlier post, though again I may write another post more relevant to this unit.
Phew! I'm going to go rollerblading now!
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