Structures and Functions – RNA Basics

by Kevin Ahern, PhD

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    00:01 So RNA has many functions and some of these functions include the following.

    00:04 Obviously, we have discussed in other presentations, the synthesis of proteins and this includes the various most common types of RNA: the transfer RNA, the ribosomal RNA and the messenger RNA.

    00:16 RNA, as I noted, is the genetic material for certain RNA containing viruses.

    00:22 RNA has been found to catalyze reactions in some cases and this type of the RNA has the name of a ribozyme.

    00:29 RNA is also, more recently described as, being able to control gene expression and these tiny little RNAs called miRNA and siRNA participate in a process we described as RNA interference.

    00:44 And last RNAs participate in the processing of yet even another RNAs.

    00:48 And these are called small nucleolar RNAs or snoRNAs, as we shall see.

    00:54 Now RNA of course has a structure that comes from the nucleotides comprising it and the nucleotides are ribonucleotides, A,U,C, and G.

    01:05 The RNA strands are a little bit different from DNA strands and the RNAs are usually present in a single stranded form, although, some viruses have a double stranded nature.

    01:16 The single stranded form of RNA can pair with itself in many cases.

    01:22 And one of the reasons this is more commonly happening with RNA than it is with for example a single stranded DNA, is that in RNA a base pair between G and U is somewhat stable. A GT base pair in DNA is not stable.

    01:36 Watson and Crick were credited with discovering the B form of DNA which you can see on the right side of this slide.

    01:42 Rosalind Franklin whose data they borrowed discovered the A form of DNA that you see on the left.

    01:48 Now the reason I am showing you these two slides is that RNA also has some specific configurations that it makes.

    01:56 The A form of DNA and the B form of DNA, though they look very similar are not the same.

    02:01 The B form of DNA you see in the bases aligned and what's look like a stereotype fashion on the right.

    02:06 But in the A form those bases are not flat.

    02:10 Now turns out that the A form of DNA is also the form that DNA-RNA duplexes form and it's also the form that RNA-RNA duplexes form. So for our purposes the A form will be the more relevant structure to be thinking about with respect to the structure of RNA when it is in a duplex.

    02:31 Now I wanna illustrate one of the common types of self paring things that RNA molecules can do and this depends on the sequences of course.

    02:40 So we see on the screen a sequence of a single strand of RNA.

    02:44 Now the bases in this RNA actually are able to form complementary pairs with each other and you can see this in the red nucleotides that I have marked here.

    02:54 What happens with this RNA is that these nucleotides can find each other very readily and when they do they form what's called a stem-loop structure.

    03:03 This stem-loop structure arises from the fact that there is an invert repeat of those nucleotides.

    03:10 And that invert repeat of those nucleotides allows for a pairing structure such as we see.

    03:15 We call this structure a stem-loop and it's sometimes also called a hairpin.

    03:19 A stem-loop has obviously a loop at the top and a stem at the bottom.

    03:26 Now we see this self-pairing nature of RNA in many different forms of RNA.

    03:32 Here is actually a ribozyme, a catalytic RNA, and you can see that it has extensive sets of structures or base pairings within itself.

    03:41 These types of base pairings are referred to as secondary structures.

    03:45 So the stem-loops are examples that we can see very simply in this figure and we can also see that there are stems that have mismatches within them.

    03:55 So it's not like everything is perfectly paired and not like everything has to be perfectly paired in order to give this structure.

    04:02 There are also unpaired regions within a molecule, as you can see here.

    04:06 And last there are stems that have bulges and bulges arise where there portions that pair and then inserts, as you can see in the bottom sequence, that don't fit into the overall structure.

    04:20 Now we have seen before in another presentation that the various ribosomal RNAs have secondary structure as well and these of course arise from the self pairing that you see here.

    04:31 It's though that these secondary structures of the small ribosomal RNAs are important for the binding of proteins in the ribosome and to give those proteins and the structure that the ribosome ultimately has.

    04:46 Now we also have seen in another presentation the structure of transfer RNAs and the transfer RNAs have this internal base pairing sequence that we have seen here.

    04:58 In last we have also seen the larger ribosomal RNAs whose sequence is so large we can't show you the individual nucleotides very clearly. But in the figure on the right you can get an idea of all the stems and stem-loops and mismatches and so forth that are appearing in that molecule.

    About the Lecture

    The lecture Structures and Functions – RNA Basics by Kevin Ahern, PhD is from the course RNA and the Genetic Code.

    Included Quiz Questions

    1. tRNA contains codons
    2. Three forms are used in translation
    3. Some forms of RNA catalyze reactions
    4. RNA is sometimes used as genetic material
    1. It has more possibilities than DNA due to G-U base pairs
    2. It cannot have duplexes within one strand
    3. It causes ribosomes to come apart at the end of translation
    4. It is in the B form when it is a duplex
    1. They have many chemically modified bases
    2. They resemble rRNAs in structure
    3. They have an amino acid attached at their 5’ ends
    4. They have 5’ ends terminating in CCA

    Author of lecture Structures and Functions – RNA Basics

     Kevin Ahern, PhD

    Kevin Ahern, PhD

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