Question about biology / atoms

[Left Coast]

It means that carbon (C) easily bonds to other atoms to create 3-dimensional shapes.
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...There are an abundance of other elements, which don't do that, and end up looking like:

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Because with h2o, you can never have a 3-dimensional snowflake, because the molecules are not 3-dimensional -they're pancake shaped, two-dimensional. But with 3-dimensional molecules, stacked on top of each other, we can have things like DNA and trees that can grow in every direction -not like flat pieces of paper.

Hydrocarbon - Three-dimensional structures

No no, I meant what did you mean when you said that seems "mystical"?

 

[exchemist]

It means that carbon (C) easily bonds to other atoms to create 3-dimensional shapes.
View attachment 41289

...There are an abundance of other elements, which don't do that, and end up looking like:

View attachment 41290

Because with h2o, you can never have a 3-dimensional snowflake, because the molecules are not 3-dimensional -they're pancake shaped, two-dimensional. But with 3-dimensional molecules, stacked on top of each other, we can have things like DNA and trees that can grow in every direction -not like flat pieces of paper.

Hydrocarbon - Three-dimensional structures

Yes, but as I say this is not unique to carbon. I gave you the example of nitrogen in ammonia. Or how about phosphorus:

 

[Cooky]

Um, look at ice. It is a three dimensional crystal.
.

No it's not. It's a collection of h20, laying all over each other at every angle, all crystalizing into the next, only appearing like one giant crystal to the naked eye.

Ice is nothing like a diamond -- A diamond being a true 3-dimensional crystal.

 

[Cooky]

Yes, but as I say this is not unique to carbon. I gave you the example of nitrogen in ammonia. Or how about phosphorus:

You're right, it's not exclusive to carbon, I don't think I suggested it was. But it's very common with carbon, more than any other element. Isn't it?

 

[exchemist]

You're right, it's not exclusive to carbon, I don't think I suggested it was. But it's very common with carbon, more than any other element. Isn't it?

I wouldn't say so. Nitrogen, phosphorus, silicon, sulphur and heavier elements like tin will form bonds pointing in 3 dimensions. And then you have all the huge variety of transition metal complexes, like this one:

It's really the chain-forming property of carbon that is so special about it.

 

[Cooky]

No no, I meant what did you mean when you said that seems "mystical"?

I think it's mystical that trees can capture such a significant amount of their organic weight from the air. Whereas I thought that wood was made from minerals in the dirt. Turns out that's only a fraction of what a tree is.

Carbon is an amazing element, considering it is gathered from the air, which is a gas.

I like talking about these things.

 

[exchemist]

I think it's mystical that trees can capture such a significant amount of their organic weight from the air. Whereas I thought that wood was made from minerals in the dirt. Turns out that only a fraction of what a tree is.

Carbon is an amazing element, considering it is gathered from the air, which is a gas.

I agree with that. A whole third of the undergraduate chemistry course is carbon chemistry, a.k.a. organic chemistry.

 

[exchemist]

No it's not. It's a collection of h20, laying all over each other at every angle, all crystalizing into the next, only appearing like one giant crystal to the naked eye.

Ice is nothing like a diamond -- A diamond being a true 3-dimensional crystal.

I don't think this is fair. Both ice and diamond are ordered 3 dimensional giant structures. The big difference is that in diamond all the bonds are full strength covalent C-C bonds, whereas in ice the bonds between atoms within each molecule are full strength covalent bonds, but the bonds between molecules are hydrogen bonds, which have only about 10% of the strength.

This is diamond:

This is ice:

They are quite similar, both being based on a tetrahedral bonding of units, the unit being an atom in the case of diamond but an H2O molecule in the case of ice.

 

[Cooky]

I don't think this is fair. Both ice and diamond are ordered 3 dimensional giant structures. The big difference is that in diamond all the bonds are full strength covalent C-C bonds, whereas in ice the bonds between atoms within each molecule are full strength covalent bonds, but the bonds between molecules are hydrogen bonds, which have only about 10% of the strength.

This is diamond:

This is ice:

They are quite similar, both being based on a tetrahedral bonding of units, the unit being an atom in the case of diamond but an H2O molecule in the case of ice.

Then I'm baffled why snowflakes are flat, with 6 arms forming from a hexagon. Can you help me understand why this is?

I was told it had to do with the original shape of the h20 molecule.

 

[Evangelicalhumanist]

@Tambourine hits the nail on the head. The unique thing that makes carbon so suitable for biochemIstry is "catenation": the tendency for carbon to form long chains -C-C-C-C-C.......

Carbon can form 4 bonds, which is more than many elements readily do. It also happens that the bond strength of C-C, C-H and H-H are very similar, and the bond strengths of C-O and C-N are also not dissimilar. This allows carbon to form complicated compounds with H, O and N, involving chains or rings, without there being a strong tendency for them to decompose into something simpler.

Long chain molecules are what you need to build biological structures, such as woody plant tissue (cellulose) or muscle (protein).

The 3D bonding thing is not uncommon. Most elements that can form more than 2 bonds will from compounds in which the atoms are not all in a single line or plane. For instance ammonia (NH3) look like an umbrella with 3 spokes, basically the same as your carbon tetrahedron but with one vertex missing.

See? That's what I meant about science lessons online on RF. Well done, @exchemist

 

[Cooky]

This is ice:

They are quite similar, both being based on a tetrahedral bonding of units, the unit being an atom in the case of diamond but an H2O molecule in the case of ice.

Are you sure that's not a snowflake branching out, rather than a chunk of ice?

 

[Brickjectivity]

To add 2 cents about the production of wood.

That's a tattoo representation of a short piece of a cellulose molecule showing two of its glucose units. In between every two glucose monomers there is a 1,4 glucosidic bond represented by a red heart in the tat. In reality cellulose is generally much longer and may have many more glucose units though the one in the illustration only shows two. Separately a glucose molecule is chemically reactive and sweet. Combined they are no longer so reactive, don't rot as quickly, are difficult or impossible to digest.

The image may also be interpreted to represent starch if you prefer. Starch is different from cellulose only in real life, not in tats. Chemically starch and cellulose aren't the same and don't taste the same.

 

[Polymath257]

I think it's mystical that trees can capture such a significant amount of their organic weight from the air. Whereas I thought that wood was made from minerals in the dirt. Turns out that's only a fraction of what a tree is.

Carbon is an amazing element, considering it is gathered from the air, which is a gas.

I like talking about these things.

Well, one part of this is that we tend to think of air being weightless. In reality, it has quite a bit of mass (and weight).

Here's a fun little exercise: figure out what the mass is of the air in a standard sized room, say an 8' by 10' by 8' room. (For the rest of the world that, sensibly, uses metric, do 2.5m by 3m by 2.5 m).

Most people are surprised by the answer.

 

[Polymath257]

Are you sure that's not a snowflake branching out, rather than a chunk of ice?

Even a snowflake is many times the size of what @exchemist showed in that picture.

So, yes, even in small crystals, the water molecules arrange themselves into a giant three dimensional structure.

Why large crystals take the specific shapes that they do is not a simple thing to figure out simply from the shape of the molecules.

 

[exchemist]

Are you sure that's not a snowflake branching out, rather than a chunk of ice?

No, it's a representation of how the molecules are arranged in the crystal structure. The shape of the resulting crystals, in the commonest form of ice, is hexagonal. There is a description, and a diagram showing how this arises, here: Ice Ih - Wikipedia

The shapes of initial single crystals tend to be one of these:

My understanding of snowflake growth is not at an expert level but my general understanding is that it is something like the following. When a snowflake grows, it tends to grow fastest at the vertices (the edges or points), because at these locations the molecules on the end are exposed and not fully bonded into the structure. This means they are in effect "sticky", having a tendency to grab any passing water molecule and extend the structure that way. There is a description of the process here: What makes a snowflake special?

The effect is the crystals tend to grow outward from the corners of the hexagon, which means they grow faster outward into a plane perpendicular to the main axis of the original crystal than they do in the direction of that axis.

(I offer this explanation a bit nervously as it is decades since I studied this sort of thing and there are probably meteorologists who devote their lives to understanding the precipitation of water in the atmosphere. If anyone knows on the forum knows more about this, I'll be delighted to learn from them.)

 

[exchemist]

See? That's what I meant about science lessons online on RF. Well done, @exchemist

Don't get me started.....Oops, too late!

 

[exchemist]

Well, one part of this is that we tend to think of air being weightless. In reality, it has quite a bit of mass (and weight).

Here's a fun little exercise: figure out what the mass is of the air in a standard sized room, say an 8' by 10' by 8' room. (For the rest of the world that, sensibly, uses metric, do 2.5m by 3m by 2.5 m).

Most people are surprised by the answer.

Let's see....

Volume of air would be 18.75m³.

1 mole of an ideal gas at RTP occupies 24 litres, or 0.024m³. So the room would contain about 700 mol of gas.

A mole of N₂ has a mass of 28g and a mole of O₂ has a mass of 32g (atomic weights of N and O are 14 and 16 respectively).

In air, the mole fraction of N₂ is ~0.8 and of O₂ ~0.2. So say approx 29g per mole of air.

So the mass of air in the room would be 700 x 29g i.e. about 20kg or 44lb......if my arithmetic is sound.

 

[Polymath257]

Let's see....

Volume of air would be 18.75m³.

1 mole of an ideal gas at RTP occupies 24 litres, or 0.024m³. So the room would contain about 700 mol of gas.

A mole of N₂ has a mass of 28g and a mole of O₂ has a mass of 32g (atomic weights of N and O are 14 and 16 respectively).

In air, the mole fraction of N₂ is ~0.8 and of O₂ ~0.2. So say approx 29g per mole of air.

So the mass of air in the room would be 700 x 29g i.e. about 20kg or 44lb......if my arithmetic is sound.

A bit of an under-estimate for the number of moles, but the right order of magnitude!

Most people are surprised that there are 40-50lbs of air in a medium room.

 

[exchemist]

A bit of an under-estimate for the number of moles, but the right order of magnitude!

Most people are surprised that there are 40-50lbs of air in a medium room.

That's interesting. Why is it an underestimate? I thought 24l/mol at RTP was pretty standard.

 

[Polymath257]

That's interesting. Why is it an underestimate? I thought 24l/mol at RTP was pretty standard.

I got 18.75/.024 =781, not 700 moles. So that is off by slightly over 10%