why are primers made of RNA strands?

Answer 1

Maybe you're talking about the priming that occurs on the lagging strand of a DNA molecule during synthesis.

Here's more (see paragraphs 3 and 4):

DNA is antiparallel, kinda like a 2 lane highway. One side runs one direction and the opposite complimentary side runs the other way.

Direction is assigned to a strand by referring to it as 5prime to 3prime (5' to 3') The 5' and 3' are in reference to the ribose part of the DNA. 5' refers to the number of the carbon to which the Phosphate (PO4) is attached. 3' refers to a hydroxyl group. (-OH) attached to the 3rd carbon of ribose. Thus ACGT becomes 5'ACGT3' (and the complimentary strand is also 5'ACGT3'.)

DNA is synthesized in a 5' to 3' direction. The enzyme that synthesizes the DNA (DNA polymerase) needs to see the complimentary strand and a 3' hydroxyl to proceed. The strand synthesized without interruption is the leading strand and the strand synthesized in pieces is the lagging strand.

In order to begin the synthesis of one of the lagging strand fragments, an RNA polymerase lays a short temporary piece of RNA down on the DNA strand so that the DNA polymerase can prime off of it. The priming RNA is removed. RNA polymerase doesn't need to see that 3' hydroxyl group from the preceding base like DNA pol does, but DNA pol can use the 3' hydroxyl from the RNA base to prime from.

The 64K question though is how is synthesis achieved all the way to very end of the lagging strand? The secret has to do with the teleomeres.

Answer 2

U could be at the 5' end, and synthesis should involve primase, pyrophosphatase, & DNA polymerase. An Okazaki fragment is a discontinuously made section of the lagging strand at a DNA replication fork. It is involved in DNA synthesis, but synthesis of an Okaziki fragment starts with an RNA primer. You need primer (& primase) to start the fragment, because DNA polymerase can not start strands; it can only add to pre-existing ones. The primer is made of RNA -- that's why you can have a U in it. The U has to be at or near the 5' end, because the rest of the fragment is made of deoxyXTP's and has T, not U. The enzyme primase, which is a special type of RNA polymerase different from regular RNA polymerase, is needed to make the primer. Then DNA polymerase can add to the 3' end of the primer, elongating it. You don't need ligase to make a single Okazaki fragment; you only need ligase to shown individual fragments into a complete strand. Pyrophosphatase is needed to ensure that polynucleotide chain growth is energetically favorable, that is, that the overall ΔG of polymerization is very negative.

B. Either one, pyrophosphatase, DNA polymerase. All nucleic acid (polynucleotide) chains grow 5' to 3' by addition to their 3' ends. Primase is no longer needed, but both pyrophosphatase and DNA polymerase are needed as in A.


2. A. The DNA should look like this:

3' AGGTC...........TGCC 5'
5' TCCAG...........ACGG 3'

B-1. The top strand. The new chain must grow 5' to 3 and left to right, antiparallel to the template, so template must be the top strand.

B-2. U will be on the 5' end. The product must contain U because it is RNA.

B-3. The bottom strand. The sense strand is the one that is not the template, and is the same as the mRNA, except that it has T instead of U.

C-1. The bottom strand. Picture should describe or show one replication fork, not 2 bidirectional forks. Molecule should be a Y shape, with Y horizontal, and opening of Y on the left. New (leading) strand is made continuously, complementary to the top template strand; it grows 5' to 3', antiparallel to the template, left to right. New (lagging) strand is made discontinuously, complementary to the bottom template strand.

C-2. CTGGA. Template strand on bottom contains sequence 5' TCCAG. New complementary lagging strand will contain the sequence 3' AGGTC 5' = CTGGA. (This sequence will be on the 3' end of the Okazaki fragment, not at the beginning, 5' end, which would include RNA primer.)

C-3. The first Okazaki fragment. Each segment (Okazaki fragment) of the lagging strand is made right to left & left-most fragment is made first.

D-1. Neither. The primer 5' AGGTC 3' would not hybridize to any of the sequences shown. It is parallel, not antiparallel, to the left end of the bottom strand. The primer 3' AGGTC 5' would hybridize to the left end of the bottom strand, but it could not act as primer to copy the DNA shown, because chain growth, if any, would occur in the wrong direction. Polymerase always adds to the 3' end of the primer, which is on the left of 3' AGGTC 5'. There is no DNA here to act as template for growth to the left, and no 3' end to build on for growth of primer to the right.

D-2. Neither strand. All synthesis in PCR is continuous. Both strands are completely separated before replication, and the complement to each strand is made separately.

E. Transcription should be different; replication should be the same.
During DNA replication, both strands serve as template, and the entire molecule is replicated. The direction of the fork determines which new strand is made continuously and which is made discontinuously, but the end result is the same, no matter which direction the fork starts from.
During transcription of any section of the DNA, only one strand serves as template. The newly made RNA strand must be antiparallel to the template (transcribed) strand, and the new RNA must grow 5' to 3'. Therefore the direction of transcription determines which strand of the DNA can serve as template. If you reverse the direction of transcription, you reverse which strand can be template. Note that the terms "leading" and "lagging" strands apply only to replication, not to transcription.

Answer 3

There's no why in biology only evolution...

In cells the RNA alternative must have presented an evolutionary advantage to be preferred over DNA priming.

By the way primers used in PCR are DNA.

Answer 4

What Are Primers Made Of