Instruction 5-1

Structure and Function of DNA, RNA | Base Pairing Rules | Genetic Engineering | DNA Technology and Recombinant DNA | Adding DNA to Bacterial Genetic Material

Structure and Function of DNA, RNA
CA Biology GR. 9-12. 5.a.

As you know, DNA (deoxyribonucleic acid) is a polymer of four different nucleotides.

Each nucleotide is composed of three parts:

  1. a nitrogen base
     
  2. a five-carbon sugar called deoxyribose
     
  3. a phosphate group (Phosphoric Acid)


These nucleotides differ because they have different bases, which could be any of these:

  1. (A) Adenine - a double-ring base (purine)
     
  2. (T) Thymine - a single-ring base (pyrimidine)
     
  3. (C) Cytosine - a single-ring base (pyrimidine)
     
  4. (G) Guanine - a double-ring base (purine)


Adenine and Guanine are purines, while Thymine and Cytosine are pyrimidines.

Adenine always bonds with Thymine and Cytosine always bonds with Guanine. The reason this happens is that a double-ring base always bonds with a single-ring base.
We will tell you more about "base pairing rules" in our next Instruction.

But for now, just remember -Two strands of these nucleotides, paired by weak hydrogen bonds between the bases,
form the two strands of DNA - the famous DNA double helix.

Short nucleotide sequences are sometimes repeated several million times in genomes of eukaryotic organisms. These sequences are called satellite DNA.

A signal sequence would be the first 20 or so amino acids of a protein destined for secretion from the cells.


The Double Helix
http://www.elmhurst.edu/~chm/vchembook/582dnadoublehelix.html

The two strands of this double helix are not parallel -- they point in opposite directions.

One strand is arranged in the 5' to 3' direction. In other words, it begins with a phosphate group attached to the fifth carbon of the deoxyribose -- the 5' end -- and ends where the phosphate of the next nucleotide would attach -- at the third deoxyribose carbon (3').

The adjacent strand points in the opposite (the 3' to 5') direction.

As you know, DNA needs the help of RNA (ribonucleic acid) to do its work -so it directs the making of it.

Although DNA and RNA are both nucleic acids (polymers of nucleotides), they differ in three main ways:

  1. The sugar in RNA is ribose, not deoxyribose as it is in DNA.
     
  2. In RNA, the nucleotide Thymine is replaced by the nucleotide Uracil.
     
  3. RNA is a single strand and does not form a double helix as DNA does.

A ribozyme is an RNA molecule that functions as an enzyme.


DNA Replication
http://www.eurekascience.com/ICanDoThat/dna_rep.htm 

As you learned in eTAP Biology Instruction 1-4, when a cell needs to make a protein to do something (like digest your lunch), its DNA makes a pattern of it. This is called replication.

But since the DNA can't leave the cell nucleus, it must make a strand of mRNA (messenger RNA) to deliver this pattern to the tRNA (transfer RNA) in the cell's cytoplasm.

Here's how it does it.

First, it "unzips'" the DNA molecule into two separate strands so that each stand can serve as a template (pattern) for the assembly of a new strand.

This results in two identical double-stranded molecules of DNA, each consisting of one single strand of the old DNA and one single strand of the new DNA. This is called semi-conservative replication.

Short nucleotide sequences are sometimes repeated several million times in genomes of eukaryotic organisms. These sequences are called satellite DNA.


The Step-by-Step Process
http://www.bioteach.ubc.ca/TeachingResources/MolecularBiology/DNAReplication.swf 

As we describe the DNA replication process, it might be a good idea to follow it along step by step on the diagram. Note that most of the action unfolds from right to left.

Now here's what happens.

First, an enzyme called helicase (a) unzips the DNA helix and forms a Y-shaped replication fork (j). Next, an enzyme called DNA polymerase (c) moves in the 3' to 5' direction along each template strand. The 3' end of the parental strand is (k) and the 5' end is (l). The new (complement) strand grows in the opposite (5' to 3') direction.

For the 3' to 5' template strand, the DNA polymerase follows readily along the replication fork, quickly assembling a 5' to 3' strand called the leading strand (d).

For the 5' to 3' strand, however, it's slower going. On this strand, the DNA polymerase must move away from the uncoiling replication fork. That's because it assembles nucleotides in the 3' to 5' direction.

Therefore, as the helix is uncoiled, the DNA polymerase can only assemble one short segment at a time before it must return to the replication fork to put together the next segment. These little segments are called Okazaki fragments (g).

The Okazaki segments are connected by DNA ligase (f), and because this stand takes more time to assemble than the leading strand, it is called the lagging strand (e).

The first nucleotides of the leading strand and each Okazaki fragment are initiated by RNA primase (i) and other proteins -- all of which collectively are known as primosome. This primosome initiates each complementary segment with RNA (not DNA) nucleotides which serve as an RNA primer (h) so DNA polymerase can add succeeding nucleotides.

Later, the RNA nucleotides are replaced with the appropriate DNA.

We know that this is a complicated process, so here are the components again:

  1. helicase
     
  2. single strand binding protein
     
  3. DNA polymerase
     
  4. leading strand
     
  5. lagging strand
     
  6. DNA ligase
     
  7. Okazaki fragment
     
  8. RNA primer
     
  9. primase
     
  10. replication fork
     
  11. 3' end of parental strand
     
  12. 5' end of parental strand


Although most of this Instruction has concerned eukaryotic cells, it is interesting to note that a prokaryotic gene 600 nucleotides long can code for a polypeptide chain of about 200 amino acids.


RNA Processing
http://vcell.ndsu.nodak.edu/animations/mrnaprocessing/index.htm  

We went into detail about DNA replication, so now we need to go into detail about RNA processing -- since RNA processing is the next step in protein synthesis.

As you know, when a cell needs to make a protein to do something, its DNA makes a template (pattern) for it. This is called transcription.

But the resulting transcription, which is produced in the cell nucleus, must undergo further processing before it can produce functional RNA molecules for export to the cell's cytosol (cytoplasm). That's because the initial RNA template (pre-mRNA) contains both non-coding sequences of base pairs (introns) and coding sequences (exons).

During RNA processing, the introns are removed and the exons are spliced together. This is what turns pre-mRNA into actual mRNA so it can deliver the DNA's message.

One of the catalysts for this splicing is a type of RNA called small nuclear RNA (snRNA). Together with assemblies of other proteins, these snRNAs are called spliceosomes.

We'll tell you more about all this in the next couple of Instructions.

 

Experiments for Home and Classroom

This web site provides an extremely helpful description of the process of DNA replication. In this activity, students are invited to "role play" by "becoming" various components of the DNA replication process (a DNA molecule, mRNA, various enzymes, etc.). Read the introductory material and then scroll down to "Simulation: Protein Synthesis." (The DNA Replication-Candy Factory analogy on this site is also instructive). Although designed for classroom use, this activity could be performed at home if there are sufficient participants. This is a wonderful activity.
http://www.woodrow.org/teachers/bi/1994/protein_synthesis.html 

For a wonderful Flash animation of the DNA replication process (along with an excellent explanation).
http://www.bioteach.ubc.ca/TeachingResources/MolecularBiology/DNAReplication.swf 

In this activity, students are invited to replicate DNA for themselves. This activity requires Shockwave, although a text version is also available.
http://www.pbs.org/wgbh/aso/tryit/dna/replication.html 

In this activity, students are invited to "Create a DNA fingerprint" and follow a crime all the way from when it's committed till when the culprit is identified. Requires Shockwave.
http://www.pbs.org/wgbh/nova/sheppard/analyze.html 
 

 

Reading List
 
The Double Helix
by
James D. Watson
 

for Students, Parents and Teachers

Now let's do Practice Exercise 5-1 (top).

Next Page:  Base Pairing Rules (top)