HOW IS GENETIC INFORMATION USED:

DNA and RNA are nucleic acids.

DNA is used to make messenger RNA.

DNA ---> mRNA is called transcription.

Briefly, what happens in transcription is shown in Figure 6.1:

The double stranded DNA strands are pulled apart and an RNA strand is made from the single exposed template strand of DNA.

This mRNA has a sequence of nucleotides which is complementary to that of the DNA template strand.

THE CHEMICAL DIFFERENCE BETWEEN DNA AND RNA:

DNA is deoxyribonucleic acid.

RNA is ribonucleic acid.

Three differences between DNA and RNA:

1. In DNA the sugar is deoxyribose which lacks an oxygen that the two-carbon position.

In RNA the sugar is ribose which has an oxygen at the two-carbon position. See Figure 6.2.

2. The second difference is that RNA has the pyrimidine base, uracil (U), which replaces the base thymine (T) of DNA.

One can say the genetic alphabet has five letters: A, C, G, T and U.

3. The third difference is that DNA is a double strand and RNA is a single strand.

The sequence of the RNA molecule is identical to the other strand of DNA (the non-template strand) except for U instead of T. This DNA strand is typically not used to make RNA. The DNA template strand has special promotor regions that bind proteins to turn the genes on to make RNA.

HOW MUCH DNA OF THE CHROMOSOME IS USED TO MAKE RNA:

In a bacterial cell about 30 percent of the genes are used at a particular time.

In higher organisms the number used at any one time is much smaller.

Each mRNA molecule carries the information from a short segment of a chromosome.

MESSENGER RNA IS MADE BY RNA POLYMERASE.

This enzyme binds to the DNA and opens the double helix. It then makes the mRNA. See Figure 6.4.

The sigma subunit of RNA polymerase recognizes two sites on the promoter strand of DNA. This promotor strand is upstream of the actual DNA sequence coding for the gene.

Once bound, the sigma subunit then drops off and the RNA polymerase makes the mRNA. See Figure 6.7.

A terminator sequence of DNA with a hairpin turn exists beyond the gene sequence. This area is called a "stem and loop." When RNA polymerase reaches the stem and loop it pauses. This provides an opportunity for termination. Pauses are longer at a string of "A"s and "U"s. See Figure 6.10. This area is weak and the RNA and DNA fall off. A to U is just two hydrogen bonds, rather than three, resulting in a weaker strand in this region.

HOW DOES THE CELL KNOW WHICH GENES TO TURN ON?

How does the cell know when to use the promoter region and start the gene?

Some genes are housekeeping genes and are switched on all the time. They always bind the sigma unit of RNA polymerase.

Genes which are needed only part of the time need gene activator proteins to help get the RNA polymerase to bind. These gene activator proteins work as a control mechanism to turn genes on or off.

Higher organisms like us have many specialized cells which have different sets of genes that are turned on or turned off. Our genes have multiple activator proteins known as transcription factors (see Chapter 11).

BACTERIAL GENES WILL BE USED IN THE FOLLOWING EXAMPLES. OUR GENES ARE CONTROLLED SIMILARLY AND THIS IS DISCUSSED IN CHAPTER 11.

An activator protein will bind the promoter site of a gene. This makes the site more amenable to the sigma subunit of mRNA polymerase.

But what activates the activator protein?

Typically something in the environment, an outside influence as far as the cell is concerned, activates the activator protein. An example is shown in Figure 6.12.

E. coli bacteria can use the sugar maltose as an energy source. In this case maltose is the outside influence. When maltose comes into the bacterial cell it binds to the activator protein MalT. This causes the MalT protein to change shape. The shape of proteins is called conformation and changing shape is critical in countless biological processes.

The active form of MalT can now bind to DNA at the promoter site. The door is now open for RNA polymerase to bind to the promoter site and start making mRNA.

NEGATIVE REGULATION

Activator proteins help turn genes on. Repressor proteins help turn genes off. They bind to a DNA segment called the operator. This blocks the binding of RNA polymerase simply by getting in the way.

An example of this is the lactose repressor, again in E. coli. When lactose is around, the LacI protein, which is the repressor protein, sits on its operator site and the gene cannot turn on (Fig 6-13). If lactose comes into the environment it binds to LacI, changing its shape so that it falls off the DNA. The RNA polymerase can now bind. The gene for choosing lactose has been switched on by bringing in lactose to knock off the repressor protein.

REGULATOR PROTEINS BIND SMALL MOLECULES

The small molecules are called signal molecules. Nutrients such as lactose and maltose are examples of signal molecules in bacteria.

MOST REGULATOR PROTEINS CHANGE SHAPE

This changing of shape is called conformation. Proteins that change shape by the binding of a signal molecule are called allosteric proteins.

MOST REGULATOR PROTEINS HAVE TWO TO FOUR SUBUNITS

You don't have to know this section.

GLOBAL CONTROL PROTEINS

We have talked about regulator proteins to turn on or turn off single genes. Global regulator proteins control expression of many genes in response to the same signal.

An example of this is the Crp protein. The signal molecule for the Crp protein is cyclic AMP (cAMP). See Figure 6.18. cAMP changes the shape of Crp and makes active. When a bacterial cell has run out of glucose the amount of cyclic AMP in the bacterial cell increases and can activate Crp. Crp is the activator for switching on the genes for making maltose, lactose, and alternative nutrients to glucose.

Cyclic AMP is an example of a regulatory nucleotide.

THE OPERON MODEL FOR GENE REGULATION

A cluster of genes switched on together by being transcribed from the same promoter is known as an operon. Bacterial cells use this system often. Higher organisms such as ourselves do not. Our genes are regulated one at a time. However, our genes are regulated by binding of control proteins, both global and specific, in front of the gene, as we described earlier. This we have in common with bacteria.

Let's look at the example of the lac operon. It consists of three genes: lacZ, lacY, and lacA. Switching these genes on depends on two regulator proteins, LacI and Crp. See Figure 6.21. There different combinations of Crp and lacI binding; see table, page 59. Only when the activator protein, Crp, is bound to the activator site and the LacI repressor protein is not bound, can RNA polymerase bind and make mRNA.

ANTISENSE RNA

You don't need to know this. This is RNA made from the non-template strand of DNA, and is complementary to the RNA molecule that makes protein.

Antisense RNA is only occasionally used in gene regulation. You can see that if anti-sense RNA is made, it will base pair with the mRNA. This prevents the mRNA from making protein. Anti-sense RNA is being tested experimentally to suppress cancer.

QUORUM SENSING

You don't need to know this.

Light-emitting bacteria in the sea make a signal molecule called Lux1 which can freely enter and exit cells. This molecule is called an auto-inducer. If enough bacteria are around, the auto-inducer goes into the bacteria rather than floating off to sea. It binds to the LuxR regulator proteins that bind to a promoter site to turn on the Lux gene to make luciferase, which is responsible for light emission (Fig 6-23). The light emission attracts fish, which gobble up the bacteria. The fish intestines are a good living environment for Vibrio fischeri bacteria.