RNA Structure and Function

Most cellular RNA molecules are single stranded. They may form secondary structures such as stem-loop and hairpin.

Secondary structure of RNA. (a) stem-loop. (b) hairpin.

The major role of RNA is to participate in protein synthesis, which requires three classes of RNA:

messenger RNA (mRNA)

transfer RNA (tRNA)

ribosomal RNA (rRNA)

Other classes of RNA include

Ribozymes
The RNA molecules with catalytic activity.

Small RNA molecules
RNA interference and other functions.

mRNA and DNA

mRNA is transcribed from DNA, carrying information for protein synthesis. Three consecutive nucleotides in mRNA encode an amino acid or a stop signal for protein synthesis (see Genetic Code). The trinucleotide is know as a codon.

Figure 3-E-3. The sequence relationship of DNA, mRNA and the encoded peptide . The sequence of mRNA is complementary to DNA's template strand, and thus the same as DNA's coding strand, except that T is replaced by U.

Structure of tRNA

The major role of tRNA is to translate mRNA sequence into amino acid sequence. A tRNA molecule consists of 70-80 nucleotides. Its secondary and tertiary structures are shown in Figures 3-C-2 and 3-C-3, respectively. Some nucleotides in tRNA have been modified, such as dihydrouridine (D),pseudouridine (Y), and inosine (I). In dihydrouridine, a hydrogen atom is added to each C5 and C6 of uracil. In pseudouridine, the ribose is attached to C5, instead of the normal N1. Inosine plays an important role in codon recognition. In addition to these modifications, a few nucleosides are methylated.

Figure 3-C-2. The secondary structure of tRNA. Blue color indicates modified nucleotides, with "m" representing "methylated". Anticodon is the trinucleotides complementary to a codon on mRNA.

Figure 3-C-3. The tertiary structure of tRNA. PDB ID = 1TN2.

Ribosome

In prokaryotes, the ribosomal RNA (rRNA) has three types: 23S, 5S, and 16S. In mammals, four types of rRNA have been found : 28S, 5.8S, 5S and 18S. The unit "S" stands for Svedberg, which is a measure of the sedimentation rate. After rRNA molecules are produced in the nucleus, they are transported to the cytoplasm, where they combine with tens of specific proteins to form a ribosome. In prokaryotes, the size of a ribosome is 70S, consisting of two subunits: 50S and 30S. The size of a mammalian ribosome is 80S, comprising a 60S and a 40S subunit. Proteins in the larger subunit are designated as L1, L2, L3, etc. (L = large). In the smaller subunit, proteins are denoted by S1, S2, S3, etc.

Figure 3-C-4. The composition of ribosomes.

During protein synthesis, the ribosome binds to mRNA and tRNA as shown in the following figure. Only the tRNA containing the anticodon which matches mRNA's codon may join the complex.

Figure 3-C-5. The mRNA-ribosome-tRNA complex formed during protein synthesis.

Ribozyme

Ribozymes are the RNA molecules with catalytic activity. They were discovered in early 1980s by Thomas Cech and Sidney Altman who shared the 1989 Nobel Prize in Chemistry.

Small RNA Molecules

Major types of small RNA molecules:

• Small nuclear RNA (snRNA) - involved in mRNA splicing.
• Small nucleolar RNA (snoRNA) - directs the modification of ribosomal RNAs.
• Micro RNA (miRNA) and short interfering RNA (siRNA) - regulate gene expression.

Both miRNA and siRNA are about 20-25 nucleotides long. They are functionally equivalent, but differ in biogenesis. miRNAs are produced from transcripts that form stem-loop structures. In contrast, siRNAs are produced from long double-stranded RNA precursors (reference). These RNAs have been widely used in functional genomics and also have therapeutic potential.

Structure of DNA

The structure of DNA is illustrated by a right handed double helix, with about 10 nucleotide pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C).

Adenine and thymine are connected by two hydrogen bonds (non-covalent) while guanine and cytosine are connected by three.

This structure was first described by James Watson and Francis Crick in 1953.

Exploring a DNA chain

The sugars in the backbone The backbone of DNA is based on a repeated pattern of a sugar group and a phosphate group. The full name of DNA, deoxyribonucleic acid, gives you the name of the sugar present - deoxyribose. Deoxyribose is a modified form of another sugar called ribose. I'm going to give you the structure of that first, because you will need it later anyway. Ribose is the sugar in the backbone of RNA, ribonucleic acid. This diagram misses out the carbon atoms in the ring for clarity. Each of the four corners where there isn't an atom shown has a carbon atom. The heavier lines are coming out of the screen or paper towards you. In other words, you are looking at the molecule from a bit above the plane of the ring. So that's ribose. Deoxyribose, as the name might suggest, is ribose which has lost an oxygen atom - "de-oxy". The only other thing you need to know about deoxyribose (or ribose, for that matter) is how the carbon atoms in the ring are numbered. The carbon atom to the right of the oxygen as we have drawn the ring is given the number 1, and then you work around to the carbon on the CH2OH side group which is number 5. You will notice that each of the numbers has a small dash by it - 3' or 5', for example. If you just had ribose or deoxyribose on its own, that wouldn't be necessary, but in DNA and RNA these sugars are attached to other ring compounds. The carbons in the sugars are given the little dashes so that they can be distinguished from any numbers given to atoms in the other rings. You read 3' or 5' as "3-prime" or "5-prime". Attaching a phosphate group The other repeating part of the DNA backbone is a phosphate group. A phosphate group is attached to the sugar molecule in place of the -OH group on the 5' carbon.
	Note: You may find other versions of this with varying degrees of ionisation. You may find a hydrogen attached instead of having a negative charge on one of the oxygens, or the hydrogen removed from the top -OH group to leave a negative ion there as well. I don't want to get bogged down in this. The version I am using is fine for chemistry purposes, and will make it easy to see how the DNA backbone is put together. We are soon going to simplify all this down anyway!
Attaching a base and making a nucleotide The final piece that we need to add to this structure before we can build a DNA strand is one of four complicated organic bases. In DNA, these bases are cytosine (C), thymine (T), adenine (A) and guanine (G).
	Note: These are called "bases" because that is exactly what they are in chemical terms. They have lone pairs on nitrogens and so can act as electron pair donors (or accept hydrogen ions, if you prefer the simpler definition). This isn't particularly relevant to their function in DNA, but they are always referred to as bases anyway.
These bases attach in place of the -OH group on the 1' carbon atom in the sugar ring. What we have produced is known as a nucleotide. We now need a quick look at the four bases. If you need these in a chemistry exam at this level, the structures will almost certainly be given to you. Here are their structures: The nitrogen and hydrogen atoms shown in blue on each molecule show where these molecules join on to the deoxyribose. In each case, the hydrogen is lost together with the -OH group on the 1' carbon atom of the sugar. This is a condensation reaction - two molecules joining together with the loss of a small one (not necessarily water). For example, here is what the nucleotide containing cytosine would look like:
	Note: I've flipped the cytosine horizontally (compared with the structure of cytosine I've given previously) so that it fits better into the diagram. You must be prepared to rotate or flip these structures if necessary.
Joining the nucleotides into a DNA strand A DNA strand is simply a string of nucleotides joined together. I can show how this happens perfectly well by going back to a simpler diagram and not worrying about the structure of the bases. The phosphate group on one nucleotide links to the 3' carbon atom on the sugar of another one. In the process, a molecule of water is lost - another condensation reaction. . . . and you can continue to add more nucleotides in the same way to build up the DNA chain. Now we can simplify all this down to the bare essentials! Building a DNA chain concentrating on the essentials What matters in DNA is the sequence the four bases take up in the chain. We aren't particularly interested in the backbone, so we can simplify that down. For the moment, we can simplify the precise structures of the bases as well. We can build the chain based on this fairly obvious simplification: There is only one possible point of confusion here - and that relates to how the phosphate group, P, is attached to the sugar ring. Notice that it is joined via two lines with an angle between them. By convention, if you draw lines like this, there is a carbon atom where these two lines join. That is the carbon atom in the CH2 group if you refer back to a previous diagram. If you had tried to attach the phosphate to the ring by a single straight line, that CH2 group would have got lost! Joining up lots of these gives you a part of a DNA chain. The diagram below is a bit from the middle of a chain. Notice that the individual bases have been identified by the first letters of the base names. (A = adenine, etc). Notice also that there are two different sizes of base. Adenine and guanine are bigger because they both have two rings. Cytosine and thymine only have one ring each. If the top of this segment was the end of the chain, then the phosphate group would have an -OH group attached to the spare bond rather than another sugar ring. Similarly, if the bottom of this segment of chain was the end, then the spare bond at the bottom would also be to an -OH group on the deoxyribose ring. Joining the two DNA chains together The importance of "base pairs" Have another look at the diagram we started from: If you look at this carefully, you will see that an adenine on one chain is always paired with a thymine on the second chain. And a guanine on one chain is always paired with a cytosine on the other one. So how exactly does this work? The first thing to notice is that a smaller base is always paired with a bigger one. The effect of this is to keep the two chains at a fixed distance from each other all the way along. But, more than this, the pairing has to be exactly . . . adenine (A) pairs with thymine (T); guanine (G) pairs with cytosine (C). That is because these particular pairs fit exactly to form very effective hydrogen bonds with each other. It is these hydrogen bonds which hold the two chains together. The base pairs fit together as follows. The A-T base pair: The G-C base pair: If you try any other combination of base pairs, they won't fit!
	Note: If the structures confuse you at first sight, it is because the molecules have had to be turned around from the way they have been drawn above in order to make them fit. Be sure that you understand how to do that. As long as you were given the structures of the bases, you could be asked to show how they hydrogen bond - and that would include showing the lone pairs and polarity of the important atoms. If hydrogen bonding worries you, follow this link for detailed explanations. Use the BACK button on your browser to return here later.
A final structure for DNA showing the important bits
	Note: You might have noticed that I have shorten the chains by one base pair compared with the previous diagram. There isn't any sophisticated reason for this. The diagram just got a little bit too big for my normal page width, and it was a lot easier to just chop a bit off the bottom than rework all my previous diagrams to make them slightly smaller! This diagram only represents a tiny bit of a DNA molecule anyway.
Notice that the two chains run in opposite directions, and the right-hand chain is essentially uside-down. You will also notice that I have labelled the ends of these bits of chain with 3' and 5'. If you followed the left-hand chain to its very end at the top, you would have a phosphate group attached to the 5' carbon in the deoxyribose ring. If you followed it all the way to the other end, you would have an -OH group attached to the 3' carbon. In the second chain, the top end has a 3' carbon, and the bottom end a 5'. This 5' and 3' notation becomes important when we start talking about the genetic code and genes. The genetic code in genes is always written in the 5' to 3' direction along a chain.