Water

An apology

I sincerely apologize for the delay in writing this post. Exams arose and writing for this blog had to be pushed back because, contrary to what you may believe, I have more important matters to deal with! Good news though, I'm back! And I shall keep my promise: let's discuss water - the elixir of life.



Wasser

Many believe that life originated in an environment that was naturally aquaeous. Of course, that means there must have been some water casually lying around somewhere. Despite the fact that most living things are solid objects, they are actually composed of something between 65 and 90% water. The average human body cell is made up of 80% water.

The molecule
When two hydrogen atoms form covalent bonds with an oxygen atom, a molecule of water is formed! A water molecule is actually relatively unreactive but when in the presence of other water molecules, presents some amazing, exclusive features. Water molecules have a bent, shape and are in a trigonal planar. If you consider the lone pairs of electrons on the oxygen atom, the arrangement of all the bonds are actually something close to a tetrahedral. However, the lone pairs each ''add'' an extra 2.5 degrees to the angle size between the lone pair and the hydrogen-oxygen bond because they're closer to the oxygen nucleus. The way I see it, the lone pair has a greater ''weight'' to it and its shorter distance to the oxygen nucleus makes it more influential in relation to the whole molecular shape. In a perfect tetrahedral-shaped molecule (like methane, CH4), the bond angles are 109.5 degrees each. Therefore, in water (which has two lone pairs, remember), the bond angles between the oxygen central atom and each hydrogen atom must be around 104.5 or 105 degrees.



Here's the nitty-gritty maths:

Lone pair = 2.5 degrees
2 x Lone pairs = 2 x 2.5 = 5 degrees
109.5 - 5 = 104.5 degrees or 105 degrees (3sf)

Hydrogen bonding in water

Water molecules are neutral electrically. However, due to the electronegativity of the oxygen and the resulting polarity of the molecule, the oxygen atom has a net negative charge and the hydrogen atom has a net positive charge.

All molecules form vdw forces with each other. But water molecules form hydrogen bonds with each other, the strongest type of intermolecular force I know.





Some substances that dissolve in water are those that form hydrogen bonds which are stronger than the hydrogen bonds that already exist between the water molecules. Other substances, like tablesalt (NaCl), dissolve as a result of having water molecules surround them in a peculiar way (but a way that actually, when you think about it, makes a lot of sense). Here's a beautiful pic:



Oh, and the reason there is a ''2'' in front of the oxygen's delta negative charge is because there are two lone pairs. One lone pair would theoretically cause a single delta negative charge (1).

That's it for now, next time I wanna discuss molecules with a carbonyl group. After hearing a lecture on biochemistry earlier this month, I learnt that carbonyl groups feature very heavily in biochemistry as a general subject. It makes sense to find out a little more about it, right? Until then folks.

Exocytosis

Lipids: fats, oils and steriods

What are lipids?

Lipids are organic molecules. That means they have carbon in them. They also contain oxygen and hydrogen. However, compared to carbohydrates (which also constitutes these three elements), the proportion of oxygen compared to the other elements is considerably less in a lipid.

One thing that characterises lipids from other molecules is the fact that it is insoluble in water. This is why lipids are used in the manufacturing of cell-surface membranes, but we'll get there later.

They are insoluble and so, we can call them hydrophobic. They hate water. However, they are soluble in ethanol (an alcohol) and ether (an...ether). These substances are organic solvents.

Three classifications of lipids exist:
1. Simple lipids e.g. vegetable oils
2. Phospholipids
3. Steroids (what?!)

Why do we need lipids?

Well we need fats for insulation. We are kept warm by layers of fat and this can especially be seen in seals which have thick blubber to deal with the harsh cold winters of the polar regions of Earth.

Plants use lipids to form their waxy cuticles. Wax is a simple lipid. Therefore, plants need lipids for waterproofing (which is what the waxy cuticle does).

Lipids are essential in the formation of cell-surface membranes. This applies to almost all organisms. I think an exception would have to be viruses - they haven't got any cell-surface membranes. I'm not even sure if I would even accept them as living organisms... but we'll look into that another time!

Fats are energy stores. In the short term, we are fuelled by carbohydrates, but the fats are the big ones. They can be burned off very slowly and many animals use it for hibernation.

There are tonnes of other uses too. Trust me.

The test for a lipid

This is really simple. Laughably so. If you add water to a solution of lipid that has been dissolved in ethanol then a cloudy white emulsion is formed as a result.

Fats and oils

Many people often mistake them as being macromolecules. Actually, due to their hydrophobic properties, they tend to cohere together to form massive globular droplets (when I say massive, I mean massive relative to other molecules - for us, they're literally just droplets).

Fats are solids at room temperature.
Oils are liquids at room temperature.

Okay, take a fatty acid. Take an alcohol (say, I don't know, glycerol!). Allow them to react and give off water in a condensation reaction. Esters will be formed and they are the fats and oils. Ester bonds are the (-COO-) linkages between the fatty acid and the glycerol. Of course, you have to take away a molecule of H₂0 away first.

Triglycerides have been formed from the condensation of three glycerol molecules. The ''ide'' comes from the ester bond formation. The ester bonds around the oxygen atom that joins the fatty acid to the glycerol.

Phospholipids

If one of the fatty acid groups in a triglyceride molecule was replaced by a phosphate group and a chloine group was attached to a charged oxygen ion on the phosphate group, then you form what is shown below.

This exists in our cell-surface membranes and a whole stack of them forms the phosopholipid bilayer.

About the cholesterol: it just adds mechanical support amongst the phospholipids.

Steroids

They are made up of complex carbon rings that exist in both plants and animals. Chloesterol is a steroid that gives rise to bile salts and the sex hormones. It, inevitably, exists in mammals. There is another steroid that exists in our skin and is converted to vitamin D through the introduction of ultraviolet rays from the Sun. Steroids have a hydrophillic part and a hydrophobic part. The hydrophilia, in this instance, is caused by the OH group. The lone pairs on the oxygen atom in the hydroxyl group are attracted to the slightly (delta) positive charge on the hydrogen atom of a bent water molecule. The hydrophobic part of the molecule is composed largely of the carbon rings.

Can you spot the hydroxyl groups on both steroids?

Alright, so this has been a modest introduction to a few lipids. I hope you've enjoyed it. Next week, I'm going to look at my most favourite molecule of all time: water.

Exocytosis

Amino acids: the building blocks of life

Okay, so let's move away from DNA and plastids and look at something else: amino acids: the building blocks of life.

The basics: what is an amino acid?

All naturally-occuring proteins are synthesised from the same set of 20 amino acids. Typical amino acids have an amino group (NH₂), a carboxyl group (-COOH), a hydrogen atom (signified by 'H') and a side-chain (R) group. All of these are groups that are attached to the central alpha-carbon atom(C_ɑ). This carbon is known as an asymmetric carbon atom as it has four different atoms or groups attached to it.

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The general structure of an amino acid. The C=O bond is known as a carbonyl bond. Can you spot where the acidic and basic ends of the molecule could potentially be?

Enantiomers

They generally defined as stereoisomers that are mirror images of one another. They are also non-superposable which means that they are not identical. Take a look at your hands. Go on. They are identical non? Well, kinda. They are just the same objects but in opposing mirrored orientations of each other.

If you didn't know what stereoisomers are, they are simply any two molecules that have the same molecular formula and constitution (same sequence of atoms) but are different only in their 3-D arrangement and orientation of atoms.

Here's something funky:

If n is the number of asymmetric carbon atoms then the maximum number of stereoisomers is: 2ⁿ

Okay, so how does this link with amino acids? Well, amino acids with four different groups arranged around the central ɑ-carbon atom are actually able to be in two different orientations. This means that they can attain both the D or L configurations.

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Very handy, ain't it? :P

The 20 standard amino acids

Glycine (Gly, G) has a hydrogen atom as its R group. It is thus the smallest possible amino acid. The atoms that compose the R will undoubtedly affect the chemical and physical properties of the molecule (amino acid) as a whole. Alanine, valine, leucine, isoleucine and methionine have side-chains of differing structures that are hydrophobic and chemically inert, for example.

Phenylalanine, tyrosine and tryptophan are also hydrophobic. The basic amino acids arginine and lysine have positively charged side-chains.





Cysteine and methionine are the only two of the naturally-occuring amino acids that contain the element sulphur. Most amino acids only contain CHON (carbon, hydrogen, oxygen and nitrogen).

As you can see, the R groups of amino acids are very important.
Out of what is known as the 20 standard amino acids, 19 are ɑ-amino acids with a primary amino group and a carboxylic acid group attached to a central carbon atom. The one exception to this general arrangement is proline which is a secondary amino acid and has a secondary amino group. It is actually an ɑ-imino acid.

Amino acids and pH

Firstly, pH is the unit we use to measure the concentration of hydrogen ions in a solution. Acids are acidic because they are proton (hydrogen ion) donors. Bases are basic because they accept protons. Amino acids can do both because of two of the groups on the central carbon: the primary amino group and the carboxyl group. Amino acids are buffers.

Well, that's it then! See you next week where I shall be continuing with biomolecules. Don't forget to send me your feedback at praveenprathapan28@gmail.com.

Exocytosis

Plastids III: The Endosymbiotic Theory

To all who may strongly dislike plastids: this will be the last post about them. Promise!

Endosymbiosis

When two organisms interact in a symbiotic relationship, one can live inside the other. This is an extraordinary biological principle. Obviously the word ''organisms'' would be limited to micro-organsisms (including and especially bacteria) as it would be quite un-endosymbiotic (not a real word!) if a human engulfed another... On the other hand, endosymbiotic relationships without the need to engulf do occur in humans and mammals, but I'm gonna leave that to you to figure out. Email me an answer and the one who gets it right gets to decide a blog topic for me to write within the next few months. Exciting, ain't it? :)

What happens during endosymbiosis?

Let's take a unicellular eukaryotic cell (a single-celled animal cell). Now, if it decides to engulf (but not digest) a friend called cyanobacterium, then the structure inside the animal cell has now got two membranes around it. Obviously these would be the cell-surface membranes of the cyanobacterium and the animal cell.

Cyanobacteria. Scientists theorise that it was these little things that caused the near-extinction of oxygen-intolerant organisms.

Chloroplasts evolved from these structures ages ago. That explains their double membranes (and mitochondria's double membranes too!). However this is just conjecture. According to the endosymbiotic theory, certain organelles started off as free-living bacteria that were engulfed by another cell as endosymbionts. Chloroplasts with two-membrane envelopes are primary plastids and are found in algae that have been here for millions of years. Land plants, have evolved from green chloroplast-containing algae.

A beautiful SEM micrograph of a mitochondrion.
You can see the matrix very clearly here, a rare sight indeed.

Membrane-o-philia

Some plastids like to have more than two membranes surrounding them. Scientists have concluded that this is likely due to multiple endosymbiotic events. If we take a green alga (the consequence of the example I showed you earlier) and make a eukaryotic cell engulf it, we achieve a complex plastid with four membranes. The nucleus of the eukaryote that JUST engulfed is the one that takes charge of the entire structure. What happens to the green agla's nucleus? Well, it becomes a nucleomorph!

A nucleomorph is a small reduced eukaryotic nucleus found in many (but not all) plastids.

Right, I'm going to go into some topics even more closely related to biochemistry (plastids MAY be slightly out of place here, but it's interesting nonetheless!). I'm going to delve into the world of biomolecules next week so stay tuned. As always, do email me your feedback at praveenprathapan28@gmail.com. See ya!

Exocytosis

Plastids II and their evolution

Hello again! Well, I DID say we will continue with the plastids. Let's get cracking shall we? :)

Chromoplasts

Look at a flower. Go on. Do it. See the petals? Pretty colours, eh? Well, they're caused by chromoplasts. ''Chromo'' comes from the Greek word khrōma which translates to colour! Simples!

Chromoplasts are found in colourful things (unsurprisingly!). They are found in flower petals, fruts and structures that have a yellow, orange or red pigmentation.

Lycopene: red (tomatoes)
Xanthophylls: yellow (egg yolk)
Carotene: orange (carrots)

They can form directly from proplastids but can be formed from some chloroplasts. In the same way, chromoplasts can develop into chloroplasts! Pretty neat, eh?

Take a carrot root. Expose it to some light. See if it turns green. It should turn green as a result of chromoplasts (found at the tops of carrot roots) being altered to form chloroplasts which are green in colour. The exposure to light causes the formation of chloroplasts. Personally, I don't really find this surprisng because it is most likely an adaptation that has been evolved into these plants over a long period of time over many generations through the process of natural selection. The plants whose root tips were able to photosynthesise when the plant was upturned (e.g. by an animal) survived as they were able to store and release more energy.

Beautiful, isn't it?

Leucoplasts

To be honest, I have no idea how to say that word. But I DO know that the ''leuco'' comes from the Greek word ''leucos'' which means white. These plastids store a lot of products. A type of leucoplast (as shown on the diagram above) is the amyloplast.

Amyloplasts store starch and are actually pretty huge. They are found in the roots, tubers and seeds of plants. Amyloplasts can convert to chloroplasts when exposed to light. This is quite odd because amyloplasts are actually highly specialised and will need to unspecialise very inconveniently in order to do so. Sometimes, you may find green patches on some raw potatoes. These potatoes have leucoplasts on the outside of them. Whilst the potato was growing, some light must have made contact with these storing leucoplasts.

Amyloplast organelles from a potato cell

The evolution of pastids

These specialised organelles don't come cheap. Chloroplasts, for example, have been accepted as once being bacteria (cyanobacteria, actually) in their own right.

Cyanobacteria have chlorophyll on their outer membranes, giving them a blue/green colour. If a non-green unicellular animal engulfed a cyanobacterium but didn't digest it (as you do), the bacterium would be nurtured like an embryo in a mother. Nurturing would involve the animal cell providing the bacterium with minerals, carbon dioxide and a place to live. This is a dual-beneficial system whereby the animal cell benefits from a supply of sugars (from photosynthsis) and oxygen. They call it love, baby.

Actually, they call it endosymbiosis. :I

Many people also believe that mitochondria formed as a result of an animal cell engulfing (but not digesting) a non-green bacterium. A symbiotic relationship was formed. Awww.


That's all for now! Next time, I'll provide a more thorough explanation of endosymbiosis just because I love you so much. :)

Exocytosis

Plastids

Plastids

Hey everyone, hope you had a wonderful Valentine's day last week! Sorry I forgot to mention it on the day! Anyway, we've been looking at a range of topics situated around the subject DNA. So I'm now going to delve into another topic that has bugged me for very long time. Plastids. Let's get straight to it!

What are they?

They are organelles. That means that they are parts of a cell. They are a type of ''organ'' of a cell, performing a function that is necessary for the overall function of the cell.

They are found in plants. Chloroplasts are plastids. Crazy, but true. Chloroplasts are weird in the sense that they are green (caused by the pigment, chlorophyll) - the only plastids to be of that insane amazing colour. Most plastids do not have a coloured pigment. However, all plastids contain a double-stranded DNA molecule that is free and not encased in a nucleus. The DNA is circular, like that of prokaryotes.

All plastids are able to change from a single type to another one. There are factors that affect the type that it is changed to:
          1. The environment
          2. The stage at which the plastid and cell are in terms of development
          3. The tissue that the plastid's cell resides in

Features of plastids

Plastids display a huge variety of size and structure. The most remarkable thing about them, I believe, is that they display a large array different functions.

Plastids have a common feature: they produce and store substances. Another common feature is that all plastids are derived from a proplastid. These are found in meristematic parts of the organism. Meristematicism refers to the region that contains undifferentiated stem cells - e.g. the active regions or growing points of plants (like in the roots and shoots).

Much like a mitochondrion, plastids all have an envelope that surrounds a matrix. The matrix holds membranes, storage material and droplets containing pigments. The pigment is dependent on the type of plastid. For example, the pigment will be nice and green in a chloroplast.

Remember when I said the DNA wasn't in a nucleus? (don't worry, I was saying the truth!) Basically, the circular DNA is held in nucloids. These are DNA-protein complexes. Nucloids are linked directly to the inner membrane of the matrix.

The number of DNA copies in a nucloid and the number of nucloids are both dependent on the plastid type and its stage of development.

The chloro of the plastids

The chloroplast. The famous king of all the plastids. It is my personal favourite. Why? Because it's green! :D Their primary function is to photosynthesise. This is why they contain the green pigment, chlorophyll.

Chloroplasts have a matrix that is commonly referred to as the stroma. This is surrounded by an envelope (as is a common feature of all plastids). Inside the stroma, there are flattened sacs called thylakoids. These are stacked up to form... stacks. The stacks are called grana.

It is within the thylakoid membrane that the protein-chlorophyll complexes that trap the photons in the light from the sun are embedded.

If this ain't a chloroplast, I give up.

Protoplasts develop into chloroplasts in the presence of light. How much light? I have no idea. But I'll do an experiment, find an answer, and tell you in 5 years! :)

In low levels of light, protoplasts form etioplasts. There are some leaves you see around you that have a yellow colour. These are partly due to the presence of these organelles. The yellow pigment is protochlorophyll. Etioplasts can quickly be converted to chloroplasts through the exposure of light. They have a prolamellar body that is quickly changed into the stroma and thylakoids upon contact with photons.

An etioplast. See the big red thing? That's the ball of tubules that are quickly converted to flat thylakoid membranes as soon as there is an introduction of light.

The transformation of etioplasts to chlroplasts is actually a reversible one. Chloroplasts can thus transform into etioplasts at will.

Right, so I think that's enough brain food for you! Next week, I think I shall continue with this plastid business - there's a lot more in the bigger picture. I'll talk about chromoplasts, leucoplasts and their transformations too. Remember to send in your feedback at praveenprathapan28@gmail.com! So, until then, see ya!

Exocytosis

Onions and crying

Why do onions make you cry?

It's an interesting question. I've always been wondering about it myself for years. It's comforting to know that there is a simple biochemical reason for this strange phenomena. :)

What others might tell you...

People normally say that there is a chemical that is released from an onion that irritates the eyes. This is kinda right... but not quite! There are a few chemical processes that occur naturally first. The chemical released from the onion is not the irritant: it is not the chemical that irratates your eyes.

Let's get to the biochemistry!

Imagine an onion cell with two compartments. One compartment holds the enzymes which are known as alliinases (yeah, it has two ''i''s in it). Imagine that the second compartment, adjacent to the first, holding the sulfur-containing amino acids (AKA amino acid sulfoxides). The name sulfoxide implies that there exists an S-O bond. The difference in electronegativity causes an overall dipole. The oxygen is more electronegative than sulfur.

This is the structure of sulfoxide which is found in a compartment of onion cells. There are two resonance forms pictured above. Resonance is a type of electron delocalisation. This occurs because electrons repel. In a double bond, they move away from each other to make the molecule more stable. In this picture, we can see the two different arrangements of the electrons.

When you cut an onion, the chemicals in the separate compartments are able to mix and form a type of sulfenic acid. This happens because you break the cells open when chopping an onion. The specific name for the acid produced is 1-propenesulfenic acid. Here's the formula:

CH3CH=CHSOH

Right, now something a little weird happens next. Another enzyme called lachrymatory factor synthase (or LFS for short) assures the rearranging of the acid molecule to form propanethial S-oxide. The rearranging, I believe, is what probably causes a decrease in boiling point in the molecule. It probably makes the structure less regular and thus decreases the number and strength of dipole-dipole interactions between the molecules. Temperature can more easily overcome the now weaker intermolecular forces and the boiling point is consequently lowered (the substance becomes more volatile).




Propanethial S-oxide before exposure to LFS enzyme

Right, so what exactly makes us ''cry''?

The gas diffuses through the air and initiates contact with the eye. Three chemicals are formed from the interaction: hydrogen sulfide, propanol and sulfuric acid. The sulfuric acid is dilute but it is in a high enough concentration to cause irritation to the eye. This triggers a sensory neural response which creates a stinging sensation and tear-production by tear glands. Tears are released as a method of flushing out and diluting the sulfuric acid from the eye.

We need sulfuric acid in onions. It sounds quite deadly, but it's true. Without it, onions wouldn't have the nice scent they they have. They would taste nothing like they do now. The same applies to garlic too.

Old wives' tales

Alright, I did promise to do this last week! And I keep my promises. Here are some ways to cut down on crying whilst chopping onions. Decide for yourself which ones really work:

1. Cover your eyes with safety goggles/specs. This provides a barrier against the gas released from
    the onions.
2. Use a fan to blow away the gas.
3. Put a teaspoon in your mouth.
4. Put a piece of bread in your mouth and let it hang there whilst chopping.
5. Wear contact lenses
6. Use a sharp knife (careful when handling sharp objects!)
7. Chill the onions
8. Chop the onion whilst holding it in water. The water becomes acidic due to the reaction between
    water and propanethial S-oxide. However, your hands could slip whilst slicing - so be extra careful.
9. Breathe with your mouth when chopping onions. You will breathe in the gas released by the
    onions.
10. Close your eyes when chopping onions. I'm kidding! That would be suicide.

Well, I hope I have shed some light on an every-day mystery. Now go and impress your mates! I'll be back next week with some more biochemistry as always! Don't forget to send me feedback too! If you are or know anyone doing or is interested in biochemistry, don't hesitate to contact me. I'm nearly always available for any help and discussion on top of other niceties! :)



Exocytosis