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Nucleic acids

Nucleotides form nucleic acids

Nucleic acids are polymers of the nucleotide monomer and include the central biological molecules DNA (deoxyribonucleic acid), RNA (ribonucleic acid) and ATP (adenosine triphosphate), playing roles in inheritance, protein synthesis and metabolism.

ATP is adenosine triphosphate, a nucleotide involved in metabolism and many biological processes (the molecular energy currency).

A nucleotide is a molecule composed of a pentose sugar, an organic base and at least one phosphate group.



Chemical energy is important in biological processes because it helps maintain the many reactions that go against a natural equilibrium. These include movement of chemicals against a concentration gradient via active transport, enabling enzyme action as ATP acts as a coenzyme, and in certain cells, movement.

As I write this I am absolutely knackered which is juuuuuuuuust hilarious as I am about to cover ATP! Adenosine triphosphate is a small molecule whose constant breaking down and putting back together reactions form the basis of our biological processes which require chemical energy.


ATP

As for many of the different other chemicals that we have covered such as carbohydrates and nucleic acids, these ATP reactions are condensation and hydrolysis. However, here we are not talking about monomers forming polymers or polymers breaking back into monomers. We are talking about adenosine triphosphate breaking down into adenosine diphosphate, inorganic phosphate and energy; and the latter joining back together to make adenosine triphosphate again.


Notice that ATP contains adenine as its organic base, and has 3 phosphates, while ADP has 2 as it has released one in the reaction.

When the hydrolysis of ATP (via the enzyme ATP hydrolase) is coupled to other reactions requiring energy, it enables these processes to take place. The inorganic phosphate released can itself take part in a further phosphorylation reaction with another chemical, often increasing its reactivity.

The condensation of ADP and inorganic phosphate takes place during photosynthesis and respiration, and is catalysed by the enzyme ATP synthase. Because it synthesises ATP. Get it get it.


DNA and RNA

DNA and RNA are key carriers of biological information. For example, DNA may store a gene coding for haemoglobin or insulin, which is then processed by RNA and ribosomes (which are sophisticated machines themselves made of RNA and proteins) to manufacture those proteins.

Both DNA and RNA are nucleic acids (that's the "NA" part of their acronym). They also contain a sugar group of a 5-carbon ring called a pentose. In DNA this is deoxyribose, while in RNA it's ribose. This completes their respective names: deoxyribonucleic acid and ribonucleic acid.

The monomers of these nucleic acid compounds are nucleotides. Aside from the nitrogen-containing base and the pentose, they contain a phosphate group.


As you can see, the nitrogenous base in the DNA nucleotide is one of four options: adenine, guanine, cytosine or thymine.

RNA has thymine switched for uracil, making its base options adenine, guanine, cytosine or uracil.

The bases can be sorted into two categories: purines and pyrimidines depending on their ring structure:




As you can see, adenine and guanine are bigger and have two rings, while thymine and cytosine only have one ring. Uracil is similar to thymine and also pairs with adenine. The presence of uracil instead of thymine occurs in RNA rather than DNA.

To form the DNA or RNA polymer, these nucleotide monomers join together via a condensation reaction which produces a phosphodiester bond.



Starting to look a bit familiar? This is just a small section of what would be a much longer DNA polynucleotide chain. Put two of them together in a double helical fashion, kept together by hydrogen bonds between the two strands, and voilà! we have ourselves a DNA molecule.




As you can see, the base pairings are A-T and G-C. They follow this pairing rule and thus are known as complementary bases. Therefore, if the number of adenine bases were known, the number of thymine bases would be easy to deduce (equal to the number of adenine bases) as well as that of guanine/cytosine bases (total number of bases - adenine - thymine = guanine + cytosine; divided in half equals either the number of guanine bases or that of cytosine bases as they are equal).

These are known as Chargaff's rules and formed the basis for understanding that DNA is the genetic material (rather than proteins). The first rule, discovered through analysing the nucleotide content of DNA, is that the content of purines should equal that of pyrimindes. The second rule states that the amount of adenine, specifically, should equal that of thymine; and that of guanine should equal that of cytosine.

RNA on the other hand does not follow the same complex overall polynucleotide structure as that of the DNA double helix, and is instead a relatively short, single strand of nucleotides - perhaps like the one depicted above with the phosphodiester bond labelled (a trimer)! Except of course, it would contain a uracil (U) instead of a thymine (T).

DNA purification can be carried out routinely by precipitating it.




Alcohol precipitation enables the separation of DNA from solution, following centrifugation. The heavier precipitated material sinks to the bottom (high-speed centrifugation separates contents by density) while the remainder of the solution stays on top. The former is the pellet while the latter is the supernatant. The supernatant can be discarded and the pellet with the precipitated DNA resuspended in a suitable solution for further applications.

Salt (Na+) neutralises the nucleic acids by interacting with the negatively charged DNA, making it less water-soluble and leading to its precipitation out of solution. Ethanol facilitates this interaction.


DNA replication

DNA, of course, replicates. Why? It's a pretty crucial element in the reproduction of living things. For example, a bacterium replicates by splitting itself into 2 (binary fission). The DNA must stay intact and be copied with a high degree of accuracy in order for the two newly formed bacteria to develop and function as their parent - adequately. In multi-cellular organisms such as ourselves, DNA replication occurs as a prelude to cell division.

For such a complex molecule, past scientists have had a challenging time working out the precise mechanism by which DNA replicates. Three hypotheses were made: (for this purpose imagine one DNA molecule)

1. The DNA molecule replicates by providing itself as a template for a brand new shiny DNA molecule, and then remaining its own intact DNA molecule. This is called the conservative replication model.

2. The DNA molecule replicates by providing itself as a template and being modified itself throughout, resulting in 2 new DNA molecules with patches of the old parent DNA molecule combined with patches of brand new material. This is called the dispersive replication model.

3. The DNA molecule replicates by providing each of its strands as a template for 2 new DNA molecules, each having one entire new strand, and one entire old strand from the parent DNA molecule. This is called the semi-conservative replication model.

Here's a visual aid for those who found the above descriptions gibberish:


How does one go about working out which one of these models is the correct one? Well, in the '50s these two chaps by the names of Meselson and Stahl cracked the riddle by carrying out a classic experiment which the examiners are in love with (so learn it well). Such complicated affairs can only be properly depicted by a lovely video. Videos always give the impression that what you are watching, surely, must be a piece of entertainment rather than advanced biology.


Now that we're all clear on the replication model of DNA, let's delve deeper into the details of the process. These are the key steps involved in the semi-conservative replication of DNA:

1. The enzyme DNA helicase unwinds the double helix, causing the hydrogen bonds between the two polynucleotide strands to break.

2. DNA-binding proteins maintain the 2 strands separate during replication.

3. Enzymes called primases attach primers to the exposed strand. Primers are a few nucleotides long and constitute the site where DNA polymerase starts its action.

4. DNA polymerase binds to the aforementioned primer and begins catalysing the reaction between free nucleotides (new) and DNA-bound nucleotides (old). Of course this complies with the principle of complemetarity i.e. A-T, C-G.

5. Because one strand is replicated continuously while the complementary strand is replicated backwards, and hence in fragments (Okazaki fragments) rather than continuously, the resulting DNA fragments must be connected together to form the new strand. New phosphodiester bonds between the sugar-phosphate backbone of DNA are catalysed by the enzyme DNA ligase

Here is a  good video animation of this process.


DNA replication is a critical process to cellular health and sustaining life, so it's no surprise that it is a very efficient process with many checkpoints and enzymes whose job it is to identify errors and correct them. However, with so many millions and billions of replications taking place constantly, some errors - mutations - do creep through and stay in the genome. These happen spontaneously as part of replication, and are random.

Over time, their accumulation becomes significant in contributing to the genetic diversity of a species, and indeed to the evolution of different species. Outcomes of mutation can be advantageous, neutral or deleterious to certain organisms in certain situations. These outcomes are themselves subject to change, producing another layer of diversity that can underpin evolution.


The genetic code



Having already covered the basics of DNA, let's turn our attention to the principles which govern what actually happens to DNA and how this results in life being the way it is!


The Dogma

DNA is a large molecule made up of variable bases (adenine, thymine, cytosine, guanine). The precise sequence and location of these bases determines what structure a second molecule, mRNA (messenger RNA) has once it's "read" the template DNA. In turn, the sequence and location of mRNA bases determines what amino acids will be chosen in the assembly of a given protein that the original DNA encoded for, once it reaches a ribosome and is constructed by tRNA (transfer RNA)


mRNA

mRNA stands for messenger ribonucleic acid. DNA is deoxyribonucleic acid, and the only difference really is in the sugar in the backbone. A more important difference is that mRNA is single-stranded unlike double-stranded DNA. Additionally, instead of the base thymine, mRNA uses uracil. So while adenine pairs up with thymine in DNA, it pairs up with uracil in mRNA. Knowing that, the mRNA derived from this DNA (looking at the top strand) would be as follows:

DNA:    ATGGGTACAAATGC (top strand)
             TACCCATGTTTACG (bottom strand)

mRNA: AUGGGUACAAAUGC (single strand)

As you can see, both the top DNA strand and the mRNA are complementary to the bottom DNA strand (in reality either top or bottom may be read, but for simplicity we only look at the top strand whenever it's given - we assume that is the gene of interest). Therefore the top strand may be called the coding strand (or sense strand) while the bottom is the template strand (or anti-sense strand). It's called template because it's the bit of DNA used to actually build up the mRNA according to. The result? The coding strand of DNA except that T is replaced by U!




How is mRNA read? An amino acid is coded for by 3 bases in a row. These are called triplets. AUG codes for methionine (Met) which happens to be the amino acid which signals that a new gene starts, if at a certain position within the overall code. Therefore it's known as a start codon.


The 3 Secrets of mRNA/DNA

There are 3 key properties of the genetic code which regulate its activity.

1. The genetic code is universal. That's right, the 4 bases are the same in all living things - humans, apples, worms, swans, oak trees, etc.! Moreover, the amino acids coded for by these bases are also completely the same, so AUG codes for the amino acid methionine in all living organisms.

2. The genetic code is non-overlapping, so if you have an mRNA AUGCGA it would be read "AUG", "CGA" and not "AUG", "UGC". The amino acids obtained would be methionine and arginine (Arg).

Tables and diagrams showing you what codes corresponds to what amino acids are widely available and you won't be expected to memorise them.




In addition to the start codon methionine, there are multiple stop codons such as UAG and UGA. These signal where the code can stop its translation into the amino acid sequence.

3. The genetic code is degenerate. That might sound slightly offensive, but bear with! Look above, what do the triplet codes UGU and UGC code for (start reading from the inside out by picking each letter)? They both code for cysteine (Cys). How about CUU, CUA, CUC and CUG? They all code for leucine (Leu). This property of different triplet codes coding for the same amino acid is why the genetic code is termed degenerate.

Additionally, some DNA (and in many organisms most of the DNA) does not actually code for amino acids at all. Some repeats many times over, some has regulatory functions, and some has yet to be cracked in terms of its role in the overall function of the organism.


tRNA (Transfer RNA)

We know DNA is double-stranded and uses A, G, C and T bases, while mRNA is single-stranded and uses U instead of T. What about tRNA? Well, tRNA is a very different soup indeed.



It's clover-shaped and uses the same bases as mRNA. It is single-stranded, and where one part of the strand meets another there are hydrogen bonds between bases just like in DNA except that in DNA there are 2 strands bonded rather than 2 parts of the same strand).

At the top of tRNA as seen above there is an amino acid binding site (P is seen as attached), while at the bottom there is an anticodon - in this case it's GAA. The anticodon is complementary to an mRNA codon (triplet code - in this case it would have to be CUU).


Protein synthesis

Proteins are made up of amino acids linked by peptide bonds, therefore a protein may be referred to as a polypeptide (of course, some proteins such as haemoglobin have extra bits to them). All are encoded for by the information stored in DNA. Let's see how exactly this happens.


Transcription: DNA to mRNA

In a process called transcription, mRNA is formed based on DNA. The bases on the coding strand of DNA are transcribed into a new molecule, mRNA, which is synthesised by the enzyme RNA polymerase



Wanna see more detail?




As you can see, the DNA double helix unwinds, RNA polymerase anneals to the coding strand and recruits freely available bases (A, U, C, G) to build an mRNA strand.


Splicing: pre-mRNA to mRNA

In eukaryotes, genes contain non-coding sequences which must be removed before mRNA is used to produce proteins. These are called introns as opposed to exons which are coding sequences. Splicing therefore is the process of excising (cutting out) introns to be left with mRNA containing purely coding sequence



Translation: mRNA to tRNA

The resulting mRNA finally leaves the nucleus where the above business had been taking place, and arrives in the cytoplasm where the final step takes place. More specifically, in ribosomes. Each mRNA codon is matched against an anticodon on tRNA, which is matched to its respective amino acid. This binds to the next amino acid and so forth, until a polypeptide is made.




Ribosomal RNA (rRNA) is what the ribosome large subunit and small subunits are made of. The rRNA of the large subunit acts as an enzyme, named ribozyme, that catalyses the peptide bond formation between amino acids during translation.






Hence, mRNA provides the codons matched by the tRNA anticodons. In lining up accordingly, the tRNA amino acids are placed in sequence and bound together. This builds the amino acid chain i.e. polypeptide that forms the basis of a new protein. This is its primary structure.

Ok byeeee

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