BLAST

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Genomes and Genes

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35

teria. So the next time you munch on a carrot, you might consider how many

genomes are really in there.

So far, this chapter has neglected viruses. Where do they fit in? By most definitions,

viruses aren’t even alive; they don’t grow or have repair processes. Viruses seem to

break every rule of biology. Some viruses infect prokaryotes and others that parasit-

ize eukaryotes. Viruses come in many different shapes and have wildly different life-

styles. Some have genomes made from RNA instead of DNA, and others have single-

stranded rather than double-stranded genomes.

Genomes and Genes

In general, the genomic structure of prokaryotes is very different from that of eukary-

otes (Figure 2-5). Genomes are organized into chromosomes. Prokaryotes often have

a single circular chromosome, and eukaryotes usually have multiple linear chromo-

somes. People are sometimes surprised to find that genome size and chromosome

number aren’t reflected in organismal complexity. For example, the single-celled

Amoeba dubia has a genome that is about 200 times larger than the human genome.

Although dogs and cats have very similar genome sizes, dogs have twice as many

chromosomes. One rule to keep in mind when thinking about genomic organization

is that genomes of viruses and prokaryotic organisms generally contain little noncod-

ing sequence, whereas the genomes of more complex organisms usually contain a

much higher percentage of noncoding sequence.

Prokaryotic Genes

Prokaryotic genes are relatively simple. They contain a promoter that determines

when the gene is transcribed and a coding region that contains the DNA sequence

for a protein. It is relatively easy to find genes in prokaryotic genomes. Since stop

codons are expected about every 21 triplets (there are three stop codons out of 64

Figure 2-5. Prokaryote and eukaryote cells

Eukaryote

Prokaryote

Chromosome

Nucleus

Prokaryotic gene

Coding sequence

Promoter

Eukaryotic gene

Exon

Promoter

Intron

This is the Title of the Book, eMatter Edition

Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.

36

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Chapter 2: Biological Sequences

total triplet combinations), long open reading frames (ORFs) should be very rare, at

least from an unbiased random model. On average, proteins are 300 amino acids

long, so finding an ORF that is 900 nucleotides long is really unexpected and a pretty

clear signal that the ORF codes for a real protein. Of course, some genes encode

small proteins, and finding these is a bit more difficult.

Eukaryotic Genes

Eukaryotic gene structure is more complicated than prokaryotic gene structure.

Unlike prokaryotic genes, eukaryotic genes are often broken into pieces that are

assembled before they are translated. Like prokaryotes, eukaryotes also have promot-

ers to regulate when genes are turned on, but they are often much larger and may

exist a great distance from the start of translation. In addition, many genes respond

to additional sequences called enhancers and suppressors that aren’t necessarily

upstream of a gene and may be many kilobases away.

In eukaryotes, mRNAs are processed before they are translated (Figure 2-6). Two

kinds of processing are common: splicing and poly-adenylation. Splicing brings

together the coding sequences and throws out the intervening stuff. The sequences

that end up in the mature mRNA are called exons, and the intervening stuff is

called introns. The part of the mRNA that codes for protein is called the coding

sequence (CDS), and the parts at either end are called untranslated regions (UTRs).

The other common post-transcriptional modification is poly-adenylation. In this

process, 50 or more adenine nucleotides are added to the end of the mRNA, which

is called a poly-A tail.

Transcripts

To many people, the most interesting parts of a genome are its genes. However,

genes may account for a small fraction of a genome. In the human genome, for exam-

ple, only 1 to 2 percent of the sequence codes for proteins. So why not just sequence

the proteins? This procedure turns out to be much more difficult than sequencing

nucleotides, but you can sequence the transcripts that code for proteins. Using some

clever molecular biology techniques, it’s possible to separate mRNAs from the rest of

Figure 2-6. Eukaryotic mRNA processing

Primary transcript

Mature transcript

Exon Intron Exon

5' UTR

CDS

3' UTR

ATG Sto p

codon

A A A A A A