Protein Synthesis is what we call this and there are some beautiful steps along the way. DNA unravels a little bit and some enzymes read the unraveled piece and start assembling the instructions (each instruction is a codon of three DNA nucleic acids) in another molecule, similar to DNA, called RNA. Both are nucleic acids but there are slight differences. For our discussion here, the big difference is that it is a single stranded molecule. This molecule carries the the code transcibed from DNA for one protein. The RNA that carries this code is called messenger RNA or mRNA for short.

The DNA RNA connection

The RNA assembly process is called transcription.
Another structure, a Ribosome, reads the mRNA containing the codons  from DNA and assembles the protein molecule by molecule, a process called translation. Another very short piece of RNA carries one amino acid, the protein building block. It also has some recognition molecules so the Ribosome know which kind it is and how to stick it in the growing protein chain. This little guy is call called transfer RNA, tRNA, transferring an amino acid onto the emerging protein.

The Ribosome, itself, contains Ribosomal RNA, rRNA. rRNA is heavily involved  in the translation. It is made in two parts. The mRNA is run through these two parts and read codon by codon. The rRNA grabs the tRNA molecule, and sticks its amino acid onto the end of protein in progress.

There it is. DNA has the code. Enzymes transcibe this code onto mRNA, the messenger. The messenger is translated by the Ribosome, rRNA, into the protein. Assembling it from pieces carried by the translation RNA, tRNA.

There are other kinds of RNA but I’ll save those for another time.

Introns are spliced away as part of the process of translating DNA into protein.

In the 1970′s,  it became apparent that the majority of our DNA didn’t code for genes. As a matter of fact, less than 5% of our DNA carries the instructions that build and operate us. Some of this DNA is between the coding DNA (genes) and much is intermingled with in the genes. In 1972, Susumu Ohno coined the term “Junk DNA”. And it stuck. Even though today we are discovering new functionality in this this junk we still call it that. We note that a number of species have much more DNA than humans, yet not nearly the complexity. Salamanders, for example have more than thirty times as much DNA as humans. Who’s more complicated?
When it comes time to translating the instructions in DNA into a protein, the RNA that carries the the instructions also contains some of this “junk” that it got during the DNA to RNA transcription.
Genes are made of sequences of DNA, that code for proteins. Yet there are portions of the genes that are skipped over, the junk. So we refer to the parts that carry protein information as exons. Interleaved with  the exons are the introns, the parts that get spliced out when the DNA instructions are translated into proteins. All this intron and exon stuff is made of the same for coding molecules of DNA yet the translation mechanisms are smart enough to weed out the introns, leaving only the exons to define the protein.
Here’s the amazing thing. Humans gene have an average of seven or eight introns per gene.  Some have more than hundred and only a fraction of genes have no introns at all.  Not only are there lots of intron but they are big. A gene’s introns can contain easily contain ten times as many DNA molecules as the exon, the part the translates to a protein.  TEN TIMES THE SIZE.
That’s not the end of the story. Remember that I mentioned how relatively few genes are needed to create and operate us? Like twenty five thousand or so genes describe all the mechanism we have from simple cell metabolism up to things like blood, heart beating and thinking deep thoughts. Well, introns play a role in fashioning variations on the proteins that drive us.
And that’s another story…

Mitochondrion - The Powerhouse

Perhaps early on in evolution the mitochonrion was a separate bacteria, it’s about the right size. As the eukaryotes evolved these guys became incorporated into the cell and were relegated to a specific task: the conversion of sugar into an immediately available source of energy. This conversion required the presence of oxygen, which was not available until plants started converting sunlight to sugars and oxygen. So, mitochondria take sugars and oxygen, aerobic conversion, and convert them to energy, carbon dioxide and water. Lots of energy. There can be from a few to thousands of these guys in each cell. They have a large surface area of folded membrane which where an important part of the energy extraction takes place.
In earlier cells, bacteria and the like, conversion of sugar to energy was rather inefficient.  They were around before oxygen was available. They converted sugar to energy without oxygen, anaerobic conversion.
Her are a couple of tidbits.

1. Mitochondria have their own DNA instruction set. We call it mtDNA. It is separate from the DNA that came from your parents.
2. So here is another little tidbit. When an egg (ovum) is fertilized, the sperm only donates DNA to the operation. Everything else is supplied by the ovum. So everybody has mitochondria donated by mom only – thanks mom! This has consequence in everything from forensics to genetic archeology.

Flow of information in the cell

1. DNA carries the instruction set.
2. The instructions are transcribed into RNA
3. RNA also translates those instructions into proteins.
4. Proteins do the work of life.

The idea is that one gene creates one protein.  This idea was postulated in the early 1940′s by a couple of scientists, Beadle and Tatum, looking at enzymes (which are a kind of protein). As a matter of fact, we can define a gene as the set of nucleotides (remember my snippet on The Code earlier?) that carry the instructions to build one protein. We call the genetic instruction set,  the genotype.
The Central Dogma then is a description of information flow in living systems and it holds for all cells from symple bacteria to the most complex cells in us humans. It’s not the whole story but it’s a good working hypothesis.
There are questions this doesn’t answer, like what starts and stops the flow of information for a particular gene? How do some viruses corrupt this machinery? How does cancer work? How do only twenty five thousand genes encode all the instructions necessary to build and operate a human being?
Well, these are teasers for another snippet.

The cell cycle is nearly always shown in this clockwise circular diagram

We like to break things up into stages or phases. So, we do this with the cell and call it the cell cycle. And it is a cycle. The end, if you could call it that, of one cell cycle is the beginning of the next.
So we start with the creation of a brand new cell. This guy is usually a bit wornout and spends the first part of its life building up fuel supplies and beefing up. We call this a gap, G1. Nothing much novel is going on, just doing its function and building up reserves for the next cycle.
This is pretty intricate. The  cell is going to create copies of all its chromosomes and other important parts. This takes a lot of energy. We call this phase synthesis, S.
This is pretty exhausting, so the cell goes into another building up and bulking up phase. This, too, is called a gap, G2.
Finally, with much duplication of parts and chromosomes, the cell enters a phase where it divides. This is a wonderfully choreographed and complex event. The end result of this is the cell splits in two and, presto, two new cells. This phase is called the mitotic or M phase.
Guess what? We now have two new but exhausted cells and they start over in the G1 phase.
Of course, I haven’t told the whole story! I’m not going to. A lot enzymes and external factors come into play in controlling the cell cycle. And, there is variation the of cell cycle called meiosis. But that only happens to germ cells, sperm and eggs. Very important stuff but another story…

On the left is a normal cell. On the right is one undergoing apoptosis.

When a cell commits this kind of suicide, it goes through a ritual. It packs up its contents into smaller structures enclosed in membrane and spews these off to be be taken care of by surrounding cells or other system mechanisms. This is a polite thing. No muss no fuss just some trash bagsto be disposed of. Neat.
Sometime cells evicerate spewing their contents willy nilly. Cell necrosis. In an organism, this can cause inflammation and untowards immune reactions.
So why would a cell commit suicide?

• During embryogenesis and the early years of life we make a lot more cells than we need. For example webbing between fingers and brain neurons. As development continues the excess cells are signaled to go away.
• Sometimes a cell detects damage to itself. Unrecoverable damage. In that case, it will voluntarily self destruct.
• Through out our life time, the body regulates tissue cell populations and cell reproduction.

Death is as important as life in the cell cycle.  There are twenty or more genes involved in apoptosis. Some to initiate the process others to do the packaging.

Bacteria are prokayrotes

Some cells are very organized. They have separate compartments for the the instruction set (the nucleus) the powerhouse (mitochondria), and protein machinery (ribosomes). Some cells are not so structurally organized. Everything is kind of mixed and mashed together.
Organized cells, we call eukaryotes, have DNA that comes in strands of pairs, we like to count and call chromosomes, all our plants and animals (and us) are made of of eukaryotic cells.  Less organized cells have DNA in a big ring. Bacteria, both friend and foe, come in this variety. They’re called prokaryotes. These guys are typically much smaller than eukaryotic cells.

Eukaryotic Cells

Another way of categorizing cells is by what they eat.  Some cells do quite well living off nonliving things, autotrophs. Plants (eukaryotic)use cholophyll to convert sunlight to energy. Some bacteria (prokaryotic)use chemical energy. Heterotrophs (prokaryotes and eukaryotes) eat other living things.

• The cell membrane separates the outside world from the internal workings of the cell. It builds channels, protein tubes, through membrane to transport some kinds of nutrient and signal molecules Some of them are like gates and open or close the gate base upon the needs of the cell.  Some are more passive, only allowing molecules that have certain geometries.
• In a bigger way, hair, feathers and finger nails are all composed of proteins.
• They decorate their external membrane with proteins  to recognize other cells as friend or foe.
• Reactions are catalysed by proteins called enzymes. Some reactions inside a cell would take so long the cell would die before the reaction takes place. Other reactions can take so much energy to complete the cell would burn up in the attempt.

p53 an amazing multifaceted protein

You might expect that the reactions catalyzed by proteins would be  pretty sophisticated chemical events. And, they are. Yet the crucial part of many reactions is the proximity of the molecules that react. Here is where things go mechanical on us. Suppose we have two molecules we want to stick together. Well, we just might have a complicated protein that has a couple of notches or grooves where a molecule might fit nice and snug.  One the right molecule finds that notch it fits in and the protein latches on to it. Now the second molecule finds it cubby hole in the protein and it gets latched down. With these tow molecules in place, the protein takes on new properties and changes shape. The shape it changes to shifts the two molecules together where they plug in or attach. Pretty amazing a little bit of chemistry, a good fit and a shape shifting protein eliminates a lot of the energy and speeds up the process of hooking two molecules together.
There are lots of variation on the enzyme reaction. But the idea is the same – to lower the energy it takes to facilitate a chemical reaction. And, this happens continuously in every cell.
Go figure.

The Spiral DNA Molecule

Pretty reasonable thinking. That is until James Watson and Francis Crick, and  Maurice Wilkins and Rosalind Franklin in the UK elucidated the structure of the chromosome in 1953. They found that it is composed of DNA: a series of  nucleic acids, phosphates and sugars, called nucleotides. There are four kinds of nucleotides in the structure.

But how can four nucleotides code for twenty plus amino acids? Well, with four nucleotides you need at least three in any combination to code for the amino acids. Any combination of two give us only sixteen codes. Three gives us sixty four. Nature likes things simple. In the 1960′s, the instructions for life were decoded. Indeed it turned out to be three nucleotide combination’s, no need for more, can’t have any less. That’s all that are necessary. These are called triplets or a codons.

Humans have twenty three chromosome pairs. They contain several billion nucleotides, our genetic code. This turns out to be  way more than enough to encode the twenty five thousand, or so, proteins. The instructions for life.