23rd Jul 2014

DNA Replication: The Process

This process is the foundation of who we are—without it, our cells could not reproduce, and we wouldn’t be able to live. I’ll run through the basic process, then let the proteins do the talking for me.

Essentially, in replication, the double helix is unwound in two separate strands by the enzyme helicases, which break the hydrogen bonds between the base pairs. The base pairs are explained, ready to serve as a template for the synthesis of new strands. The place where the helix is being unwound is called the replication fork. The replication fork has a bunch of enzymes swarming all over it, including DNA polymerase which synthesises new nucleotides to whack down like train tracks as the helix unwinds.

However, DNA polymerase can only add new nucleotides in a 5’ to 3’ direction, so one strand is going to get left out. An enzyme can just zip over the top strand and synthesise a matching one since it’s facing the right direction, and it’ll keep going as the strand keeps unwinding because the enzyme is moving left. But the bottom strand has to be synthesised in a 3’ to 5’ direction too, which is in the opposite direction to the way the helix is unwinding, away from the replication fork. So we’ve got these bits constantly being exposed at the fork.

(Image Source)

Instead of synthesising continuously like the top strand, the bottom strand has to be synthesised discontinuously—little bits at a time, starting at the replication fork and moving until they reach the last fragment. These fragments are called Okazaki fragments, and in humans, they’re only made in stretches of 100-200 nucleotides. These fragments then have to be stitched together by an enzyme called ligase, creating one long continuous strand.

Because the bottom strand has to wait for the replication fork to open up a bit before it can start synthesising fragments, the process takes slightly longer—so it’s called the lagging strand, while the top strand is called the leading strand.

Another problem faced by the lagging strand is the creation of RNA. See, DNA polymerase, which synthesises new nucleotides and thus creates the new strands, actually lacks the ability to initiate the process. It can’t start strands out of nothing—it needs to have something to build off of. So, an enzyme called RNA primase is given the job of creating a short, initial stretch of nucleotides. Then DNA polymerase latches on and happily zips off.

In the leading strand, the RNA primase needs to do its job just once, and DNA polymerase chugs along continuously. But in the lagging strand, RNA primase constantly has to create new initial chains of nucleotides—one for each fragment. As you can probably imagine, this is a nightmare—because it means that between every Okazaki fragment, there are bits of RNA, disrupting your DNA strand.

So, before the Okazaki fragments can be stitched together by ligase, these RNA bits have to be removed.

Finally, once all this is done and the lagging strand has been patched up, we have two DNA molecules: each one with one parent strand, and one daughter strand, as per the semi-conservative model. Pretty neat, huh?

Next time: the super-long explanation of the mechanisms behind it all.

Body images sourced from Wikimedia Commons

Further resources: Crash Course: DNA Structure and Replication

23rd Jul 2014

DNA Replication: Meselson and Stahl

In 1958, Meselson and Stahl performed what has been called the most beautiful experiment in biology in order to figure out which model of DNA distribution is correct. It really is dazzlingly simple.

They knew that nitrogen is a key component in DNA—the nucleotides are made up of nitrogen, hence being called “nitrogenous bases”. Almost all of the nitrogen in DNA is nitrogen-14 as it’s the most common isotope in nature. An isotope is an atom that is the same element but has a different numbers of neutrons, making it either heavier or lighter, and sometimes making it unstable and thus radioactive.

image

While nitrogen-14 makes up about 99.6% of all nitrogen, there are some rarer isotopes like the non-radioactive nitrogen-15 (0.04%). It’s rare enough to be distinctive, which is why Meselson and Stahl chose to use it in their experiment.

Firstly, they took E. coli cells (bacteria that usually live in our gut and divide every 20 minutes) and grew them in a medium that contained nitrogen-15 isotopes. This meant that the nitrogenous bases of the E. coli’s DNA was now being made out of the heavier N15 instead of the normal N14. After several generations, until their DNA was saturated with 15N, and there was no 14N left.

As a control, an ultracentrifuge was used to extract DNA from the E. coli. A centrifuge is used to separate material by density, so it separated out the 15N DNA and allowed Meselson and Stahl to see the “level” of density of the 100% 15N DNA in a solution.

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The lighter the sample is, the higher the band will be—the heaviest band, the 100% 15N DNA, will always be the lowest.

Afterwards, the 15N E. coli was placed into an environment that had regular 14N, and they were allowed to divide and reproduce and have all the fun they wanted. After one generation (20 minutes!) DNA was extracted again using the centrifuge—and this time, Meselson and Stahl saw something different. The density of the new DNA molecules had decreased. They realised they were seeing hybrid DNA, containing both the heavier 15N parent strand and lighter 14N daughter strand.

This ruled out the conservative model—if it were correct, they would have seen two distinct bands: one lighter all 14N band, and one heavier all 15N band, because parent and daughter strands stick to their own kind.

But still, at this point, they couldn’t tell whether the DNA molecules were half daughter and half parent like the semi-conservative model suggests, or had bits and pieces distributed throughout like the dispersive model suggests.

So, the E. coli were allowed to replicate again. After another generation, they extracted the DNA yet again with their ultra-cool ultracentrifuge. Now, there were two bands: one heavier band that was still a hybrid (half 15N, half 14N) and one lighter band that was all 14N. If the dispersive model was correct, then we would have seen a band that was neither pure 14N or exactly hybrid—its density would have been somewhere in the middle, since the original 15N would’ve been split (dispersed) randomly among all the strands.

image

(Image Source)

So that had to mean the semiconservative model of DNA replication is correct. When DNA replicates, the resulting molecule is made up of one parent strand and one daughter stand—in this case, one heavier strand and one lighter strand.

If the experiment kept going onto successive generations, we’d see the 14N getting progressively more and more predominant, essentially phasing out the 15N—the opposite of what Meselson and Stahl did at the very beginning to get their E. coli specimens ready.

So to recap: separate DNA out by density, and voila, you’ve proved something that is fundamental to every living being!

Don’t worry if you have no idea how DNA actually physically replicates—that’s coming up next.

Body images sourced from Wikimedia Commons

Further resources: Video from Paul Anderson

22nd Jul 2014

Introduction to DNA Replication

Before you keep reading, it might be helpful right now to duck back and reread my article about nucleic acids.

So: for the next few articles, we’ll be talking about DNA replication, which has to happen in order for cells to grow and divide. Remember when I told you the somatic cell cycle was all about preserving identity? When cells split, they need the exact same DNA as the original cell so they can carry out the same functions perfectly, so all of the original DNA has to make an exact copy of itself.

To do this, the DNA double helix peels apart into two strands, and each strand then serves as a template for new strands to be synthesised. This makes sense—base pairing rules dictate that Adenine must be paired with Thymine, and Guanine with Cytosine. When the double helix splits, the base pairs are exposed and they are able to dictate which nucleotide must be synthesised to match. The “daughter” strands that are produced are exact replicas of the “parent” strands.

This process involves a whole bunch of enzymes, and we’ll go through that in more detail next article.

But for now, let me just ask: what happens to the strands after replication? We’ve got a separated double helix with two parent strands, and two synthesised daughter strands. We know they’ve got to become two double helixes, but are they shuffled around? Which goes where?

In the 1950s, when Watson and Crick first proposed the double helix structure ased on Rosalind Franklin’s data, there were three prevailing theories for how DNA was distributed after replication.

  1. Conservative model: This model suggested that the two parent strands split, served as templates for daughter strands, and then returned to their original pairing with themselves. The two daughter strands, meanwhile, paired up too. So, the parent DNA molecule is “conserved”.
  2. Semi-conservative model: This is the model that Watson and Crick proposed, though they had no evidence. It suggests that each new DNA molecule will have one parent strand and one daughter strand. That is, they don’t return to their original states like in the conservative model; they stay where they are synthesised.
  3. Dispersive model: This model suggests that the DNA is synthesised in short pieces as the double helix unwinds bit by bit. This means that both the parent and daughter molecule have a mixture of old and new parts, dispersed throughout the molecules.

To figure out which model is the correct one, we did what we always do in science when we don’t know the answer: an experiment. Wait with baited breath til the next article, kids.

Body images sourced from Wikimedia Commons

22nd Jul 2014

Photosynthesis: Rubisco, C4 and CAM

Rubisco is the most abundant protein on Earth. It’s used to recognise carbon dioxide in the Calvin Cycle of photosynthesis and fix it to RuBP, so it’s incredibly important to the food chain on Earth—but it’s actually incredibly bad at its job.

It only correctly recognises CO2 about 80% of the time, making the two 3-phosphoglycerate molecules it’s supposed to. This process is called carbon fixation. The other 20% of the time, Rubisco mistakenly grabs up oxygen and attempts to fix it to RuBP, instead producing only one 3-phosphoglycerate and one phosphoglycerate plus a CO2 molecule. This process is called photorespiration. Although Rubisco can make 3-phosphoglycerate with oxygen, it’s far less efficient.

Rubisco does this because carbon dioxide and oxygen are fairly similar-looking molecules, as they both have two oxygens. The percentages above are a rough estimate at 25 degrees Celsius—when the environment is hotter and the ratio of O2 to CO2 in the environment increases, the inefficiency increases too.

To make photosynthesis more efficient, some plants in hot or arid environments have developed alternative methods of carbon fixation, which focus on concentrating carbon dioxide. Plants that just use the Calvin Cycle method are known as C3 method, but while the plants that use specialised methods are called C4 and CAM.

C4

The C4 method is used by plants that live in hot, dry, intense-light conditions, like sugar cane, corn, and tropical grasses. C4 plants aim to keep the concentration of CO2 high and the concentration of O2 low in the chloroplast. They have two special mechanisms that help them do this: a specialised lead anatomy, and a more efficient enzyme to “fix” the CO2 that comes into the chloroplast.

First of all, CO2 molecules that enter through the leaves’ stomata are transported into thin-walled mesophyll cells. Here, the enzyme PEP carboxylase is used to fix CO2 into a temporary 4-carbon compound (hence the name of the method). PEP carboxylase is pretty good at discriminating between CO2 and O2, so we say that it has a high affinity for CO2. Because it can bring in CO2 quicker, the stomata have to be open for less time, and so less water is lost through them.

Then, the mesophyll cells pump the carbon compound across to specialised bundle sheath cells, which have much thicker walls that don’t allow CO2 to leave or O2 to enter. Here, the carbon compound is split into CO2 and a 3-carbon compound, and the Calvin Cycle takes place in the bundle sheath cell’s chloroplast, where CO2 is much more highly concentrated than in the chloroplast of C3 plants. Thus, the CO2 is delivered “directly” to Rubisco, so it basically has less opportunity to screw up.

This process is much more efficient than C3 (from 10 to 120 times more efficient!), but the main drawback is that it costs quite a bit of ATP in order to pump the organic acid into the bundle sheath cells. Because of this, C3 plants often outperform C4 plants if they have sufficient water and sunlight. About 0.4% of plant species use the C2 mechanism.

CAM

CAM plants are even more water efficient than C4 plants, and mainly include succulents like Cacti, as well as some orchids, pinapples, and ferns.

CAM plants keep their stomata closed all day in order to conserve water, but during the night—when there’s no sunlight and the temperature is lower—the stomata open to let CO2 in and let O2 out. But if there’s no sunlight, the light reactions can’t take place and so neither can the Calvin Cycle. Photosynthesis can’t go ahead.

So instead of going straight into the Calvin Cycle, the CO2 that comes in is fixed into an organic acid called malic acid (by PEP carboxylase again), and stored away. Then, in the heat of the day, the stomata close, the acid is broken down, and the CO2 is passed onto Rubisco to be used in photosynthesis. This process all takes place in the same cell, rather than shuttling the CO2 between cells as in C4 plants.

About 10% of plant species use the CAM method.

Body images sourced from Wikimedia Commons

Further resources: C4 plants and CAM plants by the ever-beautiful Khan Academy

21st Jul 2014

GUYS PLEASE IM BLUSHING

21st Jul 2014

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21st Jul 2014
Photosynthesis: Calvin Cycle
You probably know that plants take in carbon dioxide and give out oxygen, but as we saw in the last article, that isn’t a neat exchange, turning O2 into CO2. Rather, oxygen is created as a byproduct of splitting water, and CO2 is consumed by being turned into sugar. This happens in the Calvin Cycle.
In the Calvin Cycle, carbon dioxide, NADPH, and ATP are put in, and a sugar called G3P comes out. There are three steps to create this sugar: carbon fixation, reduction, and regeneration. Note that none of these steps needs direct light!
The first step is carbon fixation. CO2 is taken in from the atmosphere around the plant, added to a 5-carbon sugar called RuBP (ribulose bisphosphate), and thus turned into 3-phosphoglycerate, an organic molecule. This process is catalysed by an enzyme called Rubisco—basically, it recognises CO2 and pairs it with the “CO2 acceptor”, RuBP. For every “turn” of the Calvin Cycle, three CO2 molecules are fixed into two 3-phosphoglycerate molecules.
In the second step, reduction, the cycle takes in 6 NADPH and 6 ATP (from the light reactions) to convert these molecules into glyceraldehyde 3-phosphate (G3P). The “reducing power” of NADPH is used to add electrons to the molecules, and the ATP gives them phosphate groups.
Then in the last stage, regeneration, 3 more ATP molecules are used to turn five molecules of G3P back into RuBP, the CO2 acceptor, so it can be used again at the start of the cycle. What’s leftover—a single G3P—is the output of the cycle. It’s the overall goal of photosynthesis: a sugar molecule that can then be used in cellular respiration to create energy for living cells to use.

So, a roundup of the cycle:
We put in 9 ATP, 6 NADPH, and 3 CO2.
We get out 9 ADP, 6 NADP+, and 1 G3P (plus 3 RuBP molecules).
The ADP and NADP+ are then recycled back to the light reactions, and photosynthesis begins over again.
Body images sourced from Wikimedia Commons
Further resources: 3D video or Video from Crashcourse

Photosynthesis: Calvin Cycle

You probably know that plants take in carbon dioxide and give out oxygen, but as we saw in the last article, that isn’t a neat exchange, turning O2 into CO2. Rather, oxygen is created as a byproduct of splitting water, and CO2 is consumed by being turned into sugar. This happens in the Calvin Cycle.

In the Calvin Cycle, carbon dioxide, NADPH, and ATP are put in, and a sugar called G3P comes out. There are three steps to create this sugar: carbon fixation, reduction, and regeneration. Note that none of these steps needs direct light!

The first step is carbon fixation. CO2 is taken in from the atmosphere around the plant, added to a 5-carbon sugar called RuBP (ribulose bisphosphate), and thus turned into 3-phosphoglycerate, an organic molecule. This process is catalysed by an enzyme called Rubisco—basically, it recognises CO2 and pairs it with the “CO2 acceptor”, RuBP. For every “turn” of the Calvin Cycle, three CO2 molecules are fixed into two 3-phosphoglycerate molecules.

In the second step, reduction, the cycle takes in 6 NADPH and 6 ATP (from the light reactions) to convert these molecules into glyceraldehyde 3-phosphate (G3P). The “reducing power” of NADPH is used to add electrons to the molecules, and the ATP gives them phosphate groups.

Then in the last stage, regeneration, 3 more ATP molecules are used to turn five molecules of G3P back into RuBP, the CO2 acceptor, so it can be used again at the start of the cycle. What’s leftover—a single G3P—is the output of the cycle. It’s the overall goal of photosynthesis: a sugar molecule that can then be used in cellular respiration to create energy for living cells to use.

So, a roundup of the cycle:

  • We put in 9 ATP, 6 NADPH, and 3 CO2.
  • We get out 9 ADP, 6 NADP+, and 1 G3P (plus 3 RuBP molecules).
  • The ADP and NADP+ are then recycled back to the light reactions, and photosynthesis begins over again.

Body images sourced from Wikimedia Commons

Further resources: 3D video or Video from Crashcourse

21st Jul 2014

Photosynthesis: Light Reactions

Photosynthesis is sometimes described as the opposite of cellular respiration, but that’s not really accurate. Quick recap: in cellular respiration, energy is released from sugars when electrons (from hydrogen) are transported through the electron transport chain to an oxygen molecule, where they form water. As these electrons and protons “fall” down the ETC, their energy is harnessed to make ATP.

Photosynthesis, however, reverses the direction of the electron flow. Water is split up and electrons are taken from it. These electrons and their associated hydrogen protons are transferred to carbon dioxide, and they reduce the carbon into a sugar. Sugars are the endgame of photosynthesis; they’re the organic compounds we use to get energy for our bodies. The process of moving the electrons requires energy—which is supplied by light.

This is the equation always quoted when explaining photosynthesis, but it doesn’t do very good job at illustrating the processes going on—the reactants and products don’t actually occur at the same time, like equation suggests.

There are two different stages of photosynthesis: the light reactions (the “photo” part) and the Calvin Cycle (the “synthesis” part). The light reactions take place in the the thylakoid membranes, and the Calvin Cycle takes place in the stroma (the dense fluid inside the chloroplast around the thylakoids). They’re often called the light-dependent reactions and the light-independent reactions, because only the light reaction needs light directly in order to proceed.

Let’s talk about the light reactions first.

Remember that there are two protein complexes in the thylakoid membrane called photosystem II and I. In the heart of each photosystem is a reaction centre: an enzyme that uses light energy to reduce (give electrons to) molecules. The reaction centre is surrounded by light harvesting complexes that transfer light energy from pigments down to the centre.

When a photon of light strikes photosystem II, it excites an electron in a chlorophyll pigment. In this excited state, chlorophyll becomes unstable—it wants to get back to its stable ground state. When the electron “falls” back down to its normal state, its energy excites another pigment, and then that excites another, and so un until the energy reaches the reaction center. Here, the energetic electrons are given to a primary electron carrier called plastoquinone. Plastoquinone then transports these electrons through an electron transport chain into photosystem I.

(Image Source)

Back in PS II, these electrons are replenished by splitting up water into its components: H2O became electrons, protons (hydrogen ions), and oxygen. The oxygen pairs up with another oxygen and is released as O2, a byproduct. The electrons and protons are used to replenish the electrons and protons that are constantly moving onto PS I.

So, back to the electron transport chain. While the electrons get carted into PS I, the protons are being pumped into the hydrogen space. This creates a gradient, which can be used to generate ATP via chemiosmosis—just like in cellular respiration in the mitochondria. But while the mitochondria use it to turn chemical energy into ATP, chloroplasts use it to turn light energy into ATP.

Meanwhile, the electrons in PS I are passed through to the reaction centre, where an electron carrier is waiting for them. A pair of electrons and a hydrogen ion are transferred to NADP+, reducing it to NADPH. This carrier is the endgame of the light reactions. It’s what all this fuss has been about.

After it’s reduced, NADPH+ leaves the photosystems and ventures out into the stroma, ready for the Calvin Cycle, where it will become a sugar.

So, a quick round up: H2O, NADP+ and light go into the light reactions, and O2, ATP and NADPH come out.

However, what I’ve explained above is called non-cyclic electron flow. This is only one of two possible pathway that electrons can travel in the light reactions. The other pathway is called cyclic electron flow.

Cyclic electron flow only uses photosystem I, and it doesn’t give any electrons to NADP+—so it doesn’t create NADPH. Instead, electrons are just passed from PS I through an electron transport chain, causing protons to be pumped across the membrane to create ATP, and then the electrons get put straight back in PS I. The main goal of cyclic electron flow is simply to create a bit more ATP—because the next step, the Calvin Cycle, needs more ATP than NADPH, so the light reactions need to make a bit extra.

Unmarked body images sourced from Wikimedia Commons

Further resources: Video from Sadhela

20th Jul 2014
Photosynthesis: Properties of Light and Chlorophyll
A while back, we talked about how organisms fall into different categories based on what food they eat and how they get it. Humans, for example, are heterotrophs because they get their energy from organic compounds that they didn’t make themselves—another organism did. Autotrophs, however, have special mechanisms to transform energy from the environment into a kind of energy that they can consume. Heterotrophs rely on autotrophs to make their food for them; they’re like the base of the foodchain, supporting everything else.
You’ve probably guessed what kind of autotrophs I’m talking about: plants.
Photosynthesis is the process plants use to convert light energy from the sun into chemical energy that we use in cellular respiration—glucose! Think of a plant’s leaves as solar collector, letting in light, water, and carbon dioxide: the three key ingredients for the photosynthetic process. These are allowed in through little passageways or holes called stomata. Oxygen is produced as a byproduct and is shuttled out via the same route. When the stomata are open, they can also allow the leaf to lose water vapor to the atmosphere—so to prevent plants drying out, the stomata are flanked by guard cells, which control when they open or close.
The leaves of a plant are filled with photosynthetic cells that contain chloroplast, the organelle where photosynthesis takes place. Chloroplasts are filled with stacked-up thylakoid membranes, which contain chlorophyll—pigments used in photosynthesis.

These chlorophyll pigments are actually contained within two light-harvesting protein complexes embedded in the membrane, called photosystem I and photosystem II. Their goal is to capture and pass on light energy. Just so you know, photosystem II is used first and photosystem I is used second; they’re only named I and II because that’s the order they were discovered.
To understand how we can get energy from light, we have to understand a bit about light itself. You know when you pass light through a prism and it’s separated into different colours? Each colour represents a different wavelength of light: red is the longest and violet is the shortest. Colours with shorter wavelengths are more energetic, so, for example, X-Rays and UV light have shorter wavelengths than visible light, which are in turn shorter than radio waves.

When light interacts with matter, it can be either reflected, transmitted, or absorbed. A pigment is a substance that absorbs light. Pigments are usually only good at absorbing only certain wavelengths of light. Black is good at absorbing all visible light and white isn’t—it mostly reflects colours back. There are two chlorophyll pigments (called chlorophyll a, which is the primary pigment, and chlorophyll b) and they’re are good at absorbing most wavelengths of visible light except for green—they reflect green back, which is why most plants are green. Chlorophyll a is most efficient at absorbing red light while chlorophyll b is most efficient at absorbing blue light.

There are also a couple of “accessory pigments” called carotenoids (like xanthophyll and carotene), which help pick up the wavelengths that chlorophyll doesn’t, and also helps protect them from damaging wavelengths.
Photosynthesis depends on chlorophyll capturing light energy, as we’ll see in the next article.
Cool background fact: photosynthesis most likely originated in the infolded regions of the membrane in ancient bacteria. In photosynthetic bacteria today, their membranes are folded in such a way as to act like the theylakoid membranes (remember that bacteria are prokaryotes and don’t have organelles).
Body images sourced from Wikimedia Commons

Photosynthesis: Properties of Light and Chlorophyll

A while back, we talked about how organisms fall into different categories based on what food they eat and how they get it. Humans, for example, are heterotrophs because they get their energy from organic compounds that they didn’t make themselves—another organism did. Autotrophs, however, have special mechanisms to transform energy from the environment into a kind of energy that they can consume. Heterotrophs rely on autotrophs to make their food for them; they’re like the base of the foodchain, supporting everything else.

You’ve probably guessed what kind of autotrophs I’m talking about: plants.

Photosynthesis is the process plants use to convert light energy from the sun into chemical energy that we use in cellular respiration—glucose! Think of a plant’s leaves as solar collector, letting in light, water, and carbon dioxide: the three key ingredients for the photosynthetic process. These are allowed in through little passageways or holes called stomata. Oxygen is produced as a byproduct and is shuttled out via the same route. When the stomata are open, they can also allow the leaf to lose water vapor to the atmosphere—so to prevent plants drying out, the stomata are flanked by guard cells, which control when they open or close.

The leaves of a plant are filled with photosynthetic cells that contain chloroplast, the organelle where photosynthesis takes place. Chloroplasts are filled with stacked-up thylakoid membranes, which contain chlorophyll—pigments used in photosynthesis.

image

These chlorophyll pigments are actually contained within two light-harvesting protein complexes embedded in the membrane, called photosystem I and photosystem II. Their goal is to capture and pass on light energy. Just so you know, photosystem II is used first and photosystem I is used second; they’re only named I and II because that’s the order they were discovered.

To understand how we can get energy from light, we have to understand a bit about light itself. You know when you pass light through a prism and it’s separated into different colours? Each colour represents a different wavelength of light: red is the longest and violet is the shortest. Colours with shorter wavelengths are more energetic, so, for example, X-Rays and UV light have shorter wavelengths than visible light, which are in turn shorter than radio waves.

image

When light interacts with matter, it can be either reflected, transmitted, or absorbed. A pigment is a substance that absorbs light. Pigments are usually only good at absorbing only certain wavelengths of light. Black is good at absorbing all visible light and white isn’t—it mostly reflects colours back. There are two chlorophyll pigments (called chlorophyll a, which is the primary pigment, and chlorophyll b) and they’re are good at absorbing most wavelengths of visible light except for green—they reflect green back, which is why most plants are green. Chlorophyll a is most efficient at absorbing red light while chlorophyll b is most efficient at absorbing blue light.

image

There are also a couple of “accessory pigments” called carotenoids (like xanthophyll and carotene), which help pick up the wavelengths that chlorophyll doesn’t, and also helps protect them from damaging wavelengths.

Photosynthesis depends on chlorophyll capturing light energy, as we’ll see in the next article.

Cool background fact: photosynthesis most likely originated in the infolded regions of the membrane in ancient bacteria. In photosynthetic bacteria today, their membranes are folded in such a way as to act like the theylakoid membranes (remember that bacteria are prokaryotes and don’t have organelles).

Body images sourced from Wikimedia Commons

20th Jul 2014

Anaerobic Respiration and Fermentation

Organisms fall into one of the following groups:

  • Obligate aerobes: require oxygen for cellular respiration and can’t live without it.
  • Facultative anaerobes: make ATP by aerobic respiration if oxygen is present, but can also switch to fermentation or anerobic respiration when it isn’t.
  • Obligate aneorobes: only carries out fermentation or aerobic respiration. Can’t use oxygen—may, in fact, be poisoned by it.

Glycolysis can occur without oxygen, but at some point in aerobic respiration, there’s a point where oxygen is essential to continue on.

The electron transport chain in aerobic respiration uses oxygen as its final electron acceptor, so when oxygen isn’t available, it can’t pass on its electrons. This means it can’t take electrons from NADH and FADH2 because it’s got nothing to give them to, and the whole cycle gets blocked up. Normally, the ETC and the citric acid cycle are intricately linked, because when the ETC oxidises the electron carriers to NAD+ and FAD+, it just passes them back to the citric acid cycle to get recycled all over again. So when oxygen isn’t available and the electron transport train stalls, it stops the citric acid cycle too.

The electron transport chain could use some other atom accept its electrons, like sulfate or nitrate. These aren’t as efficient as oxygen, because they have smaller reduction potentials (i.e., not as good at accepting electrons), but they manage. It just means that fewer ATP are produced in comparison to aerobic respiration.

This process, where oxygen is not the final electron acceptor, is called anaerobic respiration (i.e., without oxygen).

Anaerobic respiration is sometimes used interchangeably with the term fermentation, but there’s a difference. Anaerobic respiration doesn’t use the citric acid cycle (which doesn’t produce oxygen but is an aerobic process), but it still uses the electron transport chain to create a proton gradient across membranes to power ATP synthase.

Fermentation, on the other hand, creates ATP through substrate-level phosphorylation. It doesn’t use the electron transport chain or a proton gradient—it attaches phosphate groups directly to ATP without the help of ATP synthase. Fermentation doesn’t produce much ATP, though. It doesn’t use the citric acid cycle or the ETC—it occurs directly after glycolysis. Remember that glycolysis produces NADH, so fermentation only has one NADH to take an electron from and make energy. Its endgame is actually to oxidise NADH to NAD+ again, because that will allow glycolysis to continue in the absence of oxygen. The hydrogens that are taken from NADH are given to the pyruvate molecules from glycolysis, and one of two things happens: they form either ethanol (alcohol) or lactate, which forms lactic acid.

image

(Image Source)

Humans are not entirely obligate aerobes—fermentation can actually occur in our muscles, forming lactate. When we’re exercising and we can’t get oxygen to our cells quick enough, fermentation occurs, which is what causes muscle fatigue.

Ethanol is formed when a carbon dioxide molecule is removed from pyruvate, and a hydrogen is removed from NADH. The result is NAD+, ethanol, and CO2. The enzyme that facilitates this reaction isn’t found in humans, though, which is a relief or else we’d be walking around drunk all the time.

There are a variety of ways that pyruvate can be broken down to extract energy, but by far the most efficient is aerobic respiration—with oxygen as its final electron acceptor, you just can’t beat the output of dozens of ATP.