DNA: the molecular goddess

WOOPS! It's been a while (sick kids, getting my garden in, taxes, etc.) but not as long as I'd intended. I found I had posted this on my other blog, Over the Dither and Through the Words. Well, here it is now and I'm getting my next post prepared. Enjoy!

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In my last post on cell structure, we took a look at cell membranes which are made of a phospholipid bilayer. They protect the cell and cell organelles from the outside environment while letting a few players in and out to do their job. But what is it that membranes protect? Primarily, DNA (short for DeoxyriboNucleic Acid), a molecule that can make copies of itself. How DNA works was the next thing that blew my mind in biology, and pretty much cemented what I wanted to study.

DNA is the ultimate celebrity superstar of molecules. It’s the subject of many a science fiction story, volumes of textbooks and encyclopedias, various t-shirts, jewelry, and a scarf I want to knit someday. Everyone has heard of it, knows what it looks like, and knows that it carries our genes. If DNA is news to you, then you are probably fairly young or you’ve been living under a rock.

So how does this double helix encode our genes? You might think of a gene as that bit of information which gives us our eye color, makes us tall or short, shapes our nose, and gives us ADD (or not). While many of these things can be traced to a single gene, the more accurate definition of a gene is a sequence of DNA which gives instructions to put together a protein.

DNA has an alphabet of four letters, called nucleotides, nucleobases or bases for short. These nucleotides can fit together in two matching pairs called base pairs. The base pairs make up the rungs of the twisted ladder structure of DNA, with the sides being the twinned backbones of the macromolecule. The base pairs connect to each other across the rung, matching molecular shapes in the middle to make a light bond which can be zipped or unzipped. On one side of the ladder is the complementary template, and on the other is the actual code that creates a protein when transcribed.

These four nucleobases of DNA are Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). A pairs up with T, and C pairs up with G. Ever watched the eugenics dystopian movie Gattaca? It's title refers to the bases of DNA.

Three of these bases together make a word, called a codon. This codon represents an amino acid. The twenty amino acids are the building blocks of proteins. There are also codons which say stop and start. This dictionary of codons which can be translated into amino acids, or stop and start is calledthe genetic code. How we got this genetic code is one of those mysteries that we still haven’t solved.

When making a protein, DNA is unzipped by certain enzymes, and a copy of it is made. This copy isn’t DNA, but RNA – a single strand instead of a double strand. Instead of Thymine, RNA uses a base called Uracil which still pairs with Adenine. Once the sequence of RNA is copied from the DNA (beginning at the start codons and ending at the stop codons), it is moved to a part of the cell where the protein can be built. This special sequence of RNA is called messenger RNA, or mRNA.

A DNA molecule being unzipped, transcribed, and it's mRNA template going on to a ribosome as a molecular blueprint for building a protein out of amino acids.

Another form of RNA is transfer RNA, or tRNA. tRNA is connected to an amino acid and has an anti-codon which has the three bases matching the codon for the amino acid. The mRNA goes to a ribosome, which is kind of a molecular reader. There can be up to 10 million ribosomes in a single cell. As the mRNA clicks through the ribosome, tRNAs connect to the proper mRNA codon, and then their amino acids are bound together. In this way, the long protein chain is created.

DNA doesn’t just code for proteins. In fact, only about 1.5% of the human genome represents protein sequences. It also has regulatory sequences, which control what proteins are made and how much and structural sequences for the chromosomes. And there can be a lot of repetitive DNA which doesn’t appear to do anything, though we can’t be positive about that right now. All of these can affect our genes and how they're expressed - in other words, what kind of inborn traits we have. But some of it does appear to be fossils of a type: broken copies of sequences we use or perhaps ones we no longer use. It’s this extra DNA which is another proof that species, including humans, have evolved over time. In the human genome, there are over 3 billion base pairs with approximately 23,000 protein coding genes. We are still exploring what each of those genes do.

So, cell membranes and DNA were the two sirens that pulled me into biology. Before I go any further into the other cool molecules, I think it's a good idea to get the lay of the land. In my next post on cell structure we'll take a brief look at a whole animal cell and get a simple description of each of the cell organelles.

How cell membranes patch holes

Cell membranes of our muscle cells can get ripped when we exercise. Ack! But don't shy away from the gym or the great outdoors. Of course our cells have a way to repair the tiny holes. It happens all the time. But we haven't been quite sure how things got patched up. In this article, scientists were actually able to observe the repair of cell membranes of living cells in a living organism. To do this, they used a zebrafish embryo, which is tiny and mostly transparent. They tagged proteins with florescent proteins (a cool technique for seeing molecules which I'll blog about someday) which the researchers knew were involved in repair. Then they burned holes in the cell membrane with a laser and watched what happened under a microscope. Holes in a cell membrane with a laser - wow.

This was done by Prof. Uwe Strähle and Dr. Urmas Roostalu from Karlsruhe Institute of Technology (KIT) and Heidelberg University. Read more about what they observed in the article from Science Daily.

Cell membranes: way cooler than the wall of China

Cell membranes are one of the tiny wonders of the world. More than just a barrier, they selectively keep things out or let things in to the cell. They have components which identify the cells they protect, receive signals that change what the cell is doing, and send out signals as well.

But what is more amazing is that they are self assembling. If you have a test tube with the molecules that make up a cell membrane mixed evenly in water, you'll find that they quickly form up into spheres of cell membrane. It's one of those things that is both simple and complex. I still have to admit to being a bit awed by them.

The main ingredients of a cell membrane are phosphoglycerides (more commonly known as phosphlipids). There are several versions, but their main construction is a single phosphate head and two fatty acid tails. The phosphate head likes to be around water and mixes with it regularly. The fatty acids are basically oil, and try to avoid water. When you mix these molecules up randomly in water, they come together in a double layered sheet of molecules with the water loving phosphate heads spread out on the outside and the water avoiding tails bunched up on the inside. Beautiful!

Only small molecules such as water, carbon dioxide, and oxygen can pass through membranes made of just phospholipids. These substances enter or exit the cell by diffusion, which basically means things bumping around each other enough that they get spread out evenly. Laws of probability and all that. But cells may need to ingest large molecules such as sugars and proteins. And they may want to keep a concentration of some substances higher or lower in the cell than its surrounding environment.

For this, there are proteins that imbed themselves all the way through the membrane, called integral proteins. Some of these proteins are just pores that certain molecules can fit through. This is how glucose enters the cell. A cell is constantly breaking down glucose to create energy, so there is usually less glucose in the cell than outside of it (the cell is always breaking down glucose to create energy), so it naturally diffuses into the cell. But because a glucose molecule is so big, it must move through the transport proteins in the membrane. No energy is needed to let these kinds of molecules pass.

But some proteins are pumps that actively move molecules in or out. A good example of this are the mineral salts that plants need. These minerals are in a lower concentration in the soil or water than in the cell. To absorb the minerals, the plant cell must use active pumps to keep a higher concentration.

Other integral proteins receive signals which don't have to enter the cell to affect it. These special signal molecules will change the shape of the protein when they attach to it. On the inside of the cell, this shape change starts a chain reaction which causes the cell to either start producing something, stop producing something, or in the case of muscle cells, to change shape.

Some proteins might be stuck to just the surface or partway through a membrane. These peripheral can act as identifiers. In blood cells, surface proteins determine the blood type.

There is a lot more to cell membranes, far more than can be covered in one post or even a series of posts. They are an essential component of all biological life, as important as DNA. Not only do they protect the cell from the outer environment, they protect the cells organelles and store molecules that they don't want to use yet. They can store things for later use, which would otherwise be quickly metabolized in the cell's cytoplasm.

We are learning from these natural technologies. Scientists have now created artificial membranes, an important step to creating artificial life forms. This could have applications in medicine, building, convenience, and many other things (some of them admittedly scary but that's another post). Other technologies which take their cue from the cell membranes are the liposomes found in our face lotions.  Another possible technology  is protecting buildings. While we'll still face pitfalls and dangers, I firmly believe that learning from nature and protecting it, rather than trying to circumnavigate it will propel us into a better world.