(Some of this is review)

Eukaryotes possess a nucleus. The nucleus is where genetic information is stored.

Prokaryotes lack in nucleus.

Prokaryotes typically have 2000-3000 genes. These are circular chromosomes.

Eukaryotes have an order of magnitude more genes. These are on linear chromosomes.

Humans and fruit flies both have an estimated 50,000 to 100,000 genes. You do not have to be an advanced eukaryote to have a lot of genes.

In eukaryotes the most common organelle is the mitochondrion, which is responsible for generating energy by oxidation. Glucose and oxygen are used to make ATP.

Oxidation is giving up electrons. Reduction is taking on electrons (the atom or molecule becomes more negative, thus, is reduced). When a substance is oxidized it often involves giving up electrons to oxygen.

In plants the energy-producing organelle is the chloroplast which carries out photosynthesis. In photosynthesis sunlight is absorbed by the green pigment chlorophyll. Sugars are made in this process. See fig. 11.3.

Higher organisms have multiple chromosomes. In the middle region is the centromere. At cell division microtubules attach to the centromeres and drag the two sets of chromosomes apart.

The end structure of the chromosome is the telomere. See fig. 11.4.

A telomere consists of a six base pair sequence repeated about 2,000 times.

Whenever DNA molecules are replicated the process starts with a primer made of RNA. A linear chromosome is shortened by one primer each time it is replicated as shown in fig. 11.5. The part of the original DNA base-paired to the primer does not get replicated in the new DNA because the new portion is an RNA primer not DNA. See fig. 11.5.

Telomerase helps cancel this loss by adding six base pair sequences at each division.

The cell with a single set of chromosomes is called haploid. This is one reason that mutations in bacteria can easily result in phenotypic changes, ie antibiotic resistance.

The cell with a duplicate copy of their chromosomes is called diploid. Eukaryotes have two copies and are diploid. If one is mutated the other can still work.

If unfolded, a chromosome can be up to one cm long. These must fit into a cell nucleus which is five microns or less in diameter. This represents a 2000 fold shortening. How is this shortening done? It is done similarly to packing clothes into a bag or suitcase for a trip.

DNA coils around histones, which are positively charged proteins that neutralize the negative charge of DNA. Under a microscope, DNA plus histone can be seen and is called chromatin.

Each 200 base pairs of DNA is wrapped around 9 histones to form a nucleosome as shown in figure 11.7.

The chain of nucleosomes is coiled further into a large helix (not shown in fig. 11.8).

These are further super-coiled. See fig. 11.8.

Chromosomes visible under a microscope (the photos you see in a textbook) are condensed and dividing or about to divide. During typical cell operations the DNA is more spread out in the nucleus as chromatin.

Almost all bacterial DNA is unique and not repeated sequences.

In eukaryotes, there's much repetition.

Figure 11.10 shows a stylized eukaryotic chromosome.

Humans have about 65 percent unique DNA, another 25 percent is moderately repetitive sequences and another 10 percent is highly repetitive sequences. See fig. 11.10.

Other species vary in their ratios of these.

Moderately repetitive sequences: some of this is functional as multiple genes for rRNA and tRNA. Some is of no use, however.

Highly repetitive sequences: There may be hundreds of thousands to millions of copies of these. They are of no known use.

The Alu element is a 300 base pair sequence scattered throughout human DNA. We have 300,000 to 500,000 copies of this. It is of no known use, like having an old car on blocks in your yard.

These are defective duplicate copies of genuine genes. These have only one or two copies. They contain various defects which prevents them from being expressed. They are useless.

Actual genes are often interrupted with non-coding DNA known as introns. The actual coding sequences are called exons. See figure 11.11. In higher eukaryotes, most genes have introns and they may be longer than the exons.

Eukaryotes have about 10-20 times as many genes as bacterial cells.

There is a different RNA polymerase to make RNA from different parts of the gene DNA:

RNA

I Used on housekeeping genes which code for large ribosomal RNA (rRNA).

II Used on genes which code for protein.

III Used on housekeeping genes which code for tRNA and small ribosomal RNA.

rRNA and tRNA are needed all the time and are made by housekeeping genes.

Making proteins is a different story. In this case RNA polymerase II is regulated by proteins call transcription factors that bind to specific sequences on the DNA. The sequences are promoters and enhancers. See figures 11.12 and 11.13.

Promoters are found in front of all genes. See fig. 11.12.

Enhancers are involved in gene regulation, especially during development or in making proteins for different cell types. Enhancers enhance the rate of transcription by binding to transcription factors. An enhancer switches a gene on. It may be a distance away from the actual gene. See figure 11.13.

They need to get into the nucleus and respond to stimulus signals so the gene can be turned on. An example is MyoD (fig. 11.14) which switches on a number genes in muscle cells. It is not used in other cell types.

The RNA molecule resulting from transcription is a primary transcript. See figure 11.15. It can have a lot of exons and introns, as did the DNA. The introns need to be removed and the exons joined end-to-end.

A cap is added to the RNA by a capping enzyme. The cap is GMP. See figure 11.16. GMP = guanosine monophosphate.

A poly-A tail is also added. See figure 11.17. A = adenine.

Splicing out the introns is done by a special complex of proteins and small RNA molecules called a spliceosome. See figure 11.18. The spliceosome recognizes both ends of an intron and binds to it. This makes the DNA loop around. The proteins plus small nuclear RNA are responsible for RNA splicing and are called Snurps. See figures 11.18, 11.19. Splicing must be accurate to within a single base pair.

See figure 11.20 for an overall view.

These are for using different splice sites on an mRNA which allow more than one possible protein to be made from a single gene. Some of these methods are used in higher eukaryotes. You not have to know the details of this.

Insertion or deletion of uridine. See fig. 11.26.

Once the mRNA Is finally modified, introns removed and cap and tail added, the mRNA can move out of the nucleus through nuclear pores which are surrounded by proteins.

Much of this is review. you had more detail in chapter 7.

Initiation factors are required to complete the ribosome assembly plus the tRNA and mRNA and correct order. See figures 11.29, 11.30.

There is an initiator tRNA that brings the first amino acid in. Eukaryotic mRNA does not have an S-D sequence as do prokaryotes. Instead, it is recognized by the special cap structure at the five-prime end.

Cap binding protein binds to the cap of the mRNA and turns over the mRNA to the small ribosomal subunit. The first AUG codon of the mRNA is recognized to start protein synthesis. The incoming amino acids are bound to the polypeptide chain similarly to bacteria. Eukaryotes make only a single protein type per mRNA. Prokaryotes can make multiple proteins because they can have several start locations in the mRNA nucleotide chain.

Once the ribosome reaches the stop codon it disassembles. A protein called a release factor recognizes the stop codon and controls the disassembly of the new protein, the two ribosomal subunits and the mRNA. See figure 11.31.