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--- chapter_06 [2024/08/30 19:30] – [Rethinking familiar old terms in the context of the physical gene] mike
+++ chapter_06 [2025/03/22 07:55] (current) – [Thinking about DNA and genes at scale] mike
@@ Line 1: / Line 1: @@
-<typo fs:x-large>Chapter 06. The physical nature of the gene</typo>
+<-chapter_05|Chapter 05^table_of_contents|Table of Contents^chapter_07|Chapter 07->
-In Chapters 01-06, we defined genes conceptually as units of function and inheritance. In this chapter we will start with a new way to define genes: a physical definition of the gene. Conceptually this is the simplest way to define a gene and it will give us an excuse to briefly review some of the molecular biology that you probably already know. Our focus is not on the details of molecular biology, but on the role of genes in terms of their informational content and on the role of DNA as an informational molecule.
+<typo fs:x-large>Chapter 06. The physical nature of the %%gene%%</typo>
+In Chapters 01-05, we defined genes conceptually as units of function and inheritance. In this chapter we will start with a new way to define genes: a physical definition of the gene. Conceptually this is the simplest way to define a gene and it will give us an excuse to briefly review some of the molecular biology that you probably already know. Our focus is not on the details of molecular biology, but on the role of genes in terms of their informational content and on the role of DNA as an informational molecule.
 ===== Genes are (usually) made of DNA =====
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 {{ :transcription.jpg?400 |}}
 <caption>
-RNA transcription. Unlike with DNA replication, only one of the two strands is used as the template for transcription. The DNA strand that is used as a template is called (not surprisingly) the template strand, and the other DNA strand is called the coding strand. Note that the newly transcribed RNA has the same sequence as the template strand, except that uracil (U) is substituted for thymidine (T) in the RNA. Credit: M. Chao.
+RNA transcription. Unlike with DNA replication, only one of the two strands is used as the template for transcription. The DNA strand that is used as a template is called (not surprisingly) the template strand, and the other DNA strand is called the coding strand. Note that the newly transcribed RNA has the same sequence as the template strand, except that uracil (U) is substituted for thymine (T) in the RNA. Credit: M. Chao.
 </caption>
 </figure>
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 The haploid human genome is approx. 3x10<sup>9</sup> bp in size. This means that the average human chromosome is $\frac{3\times10^9}{23}= 1.3 \times 10^8$ bp, or over one hundred million bp long – that is a very large molecule! Humans and most mammals have about 20,000 genes (which is surprisingly not that many more than Drosophila). This means that on average each human chromosome contains about 1000 genes. Genes are typically 10<sup>3</sup> - 10<sup>4</sup> base pairs in size, although they can be much larger.
-For example, the human dystrophin gene is 2 x 10<sup>6</sup> base pairs. Mutations in dystrophin result in a debilitating disease called Duchenne muscular dystrophy (DMD), which affects humans but also dogs, especially Golden Retrievers. Interestingly, DMD is a sex-linked trait in both humans and dogs - the dystrophin gene is on the $X$ chromosome in both species, and males are affected more than females (Fig. {{ref>Fig6}}. Note that not all of the DNA sequence of a gene may be coding sequence; that is, not all of the DNA sequence of a gene may correspond to codons for amino acids. In fact, most DNA is not gene coding sequence. Most eukaryotic genes (and in rare cases prokaryotic genes) contain DNA sequences called introns; when these intron sequences are transcribed into RNA they are removed from the transcript by a process called splicing (see [[chapter_12|Chapter 12]] for more details). However, the majority of DNA is non-coding sequence in between genes called intergenic regions.
+For example, the human dystrophin gene is 2 x 10<sup>6</sup> base pairs. Mutations in dystrophin result in a debilitating disease called Duchenne muscular dystrophy (DMD), which affects humans but also dogs, especially Golden Retrievers. Interestingly, DMD is a sex-linked trait in both humans and dogs - the dystrophin gene is on the $X$ chromosome in both species, and males are affected more than females (Fig. {{ref>Fig6}}). Note that not all of the DNA sequence of a gene may be coding sequence; that is, not all of the DNA sequence of a gene may correspond to codons for amino acids. In fact, most DNA is not gene coding sequence. Most eukaryotic genes (and in rare cases prokaryotic genes) contain DNA sequences called introns; when these intron sequences are transcribed into RNA they are removed from the transcript by a process called splicing (see [[chapter_12|Chapter 12]] for more details). However, the majority of DNA is non-coding sequence in between genes called intergenic regions.
 <figure Fig6>