S. D. V. Stephens

notes / Basic Neuroscience and Geometry of Neuroscience / chapter 1: Neurons and Signalling / From my notebook

N6 The Soma, the Nucleus, and Gene Expression

The soma

  • 20 µm in diameter.
  • Filled with cytosol, a salty, potassium-rich, watery fluid.
  • Separated from the outside by the neuronal membrane.
  • Like all animal cells, it contains organelles.
  • The entire interior (everything EXCEPT the nucleus) is called the cytoplasm of the soma.

The nucleus

“Nucleus”: LOL, it comes from the Latin for “nut,” so we really are all just nuts!

  • Baddie.
  • 5–10 µm in diameter.
  • Contained within a double membrane called the nuclear envelope (LOL), which has pores about 0.1 µm across.
  • Nucleus → chromosomes (“chromies”) → DNA (deoxyribonucleic acid).

The DNA is the same in all your cells; the specific stretches of it that get read are called the genes, and each different cell type uses its own subset of them.

Each chromosome (chromie) contains a double strand of DNA 2 nm in diameter; if we unfolded/unraveled the DNA of all 46 chromosomes and laid it end to end, however, it would measure about 2 m in length.

Genes vary from 0.1 µm to several µm in length.

  • Gene expression: “reading” of DNA.
  • Proteins: products of gene expression.
  • Protein synthesis: occurs in the cytoplasm (where?); other than that, self-explanatory.
  • mRNA (messenger ribonucleic acid): a long molecule that acts as an intermediary between the DNA and the sites that perform protein synthesis (since the DNA NEVER leaves the nucleus).

The assembly of mRNA is called transcription.

The prototypical neuron

A full-page pasted textbook illustration, which the notes title “Prototypical neuron / neural cell,” shows a cutaway of a neuron’s soma among its neighbors. Labeled are the neuronal membrane, the nucleus (whose nuclear pores are marked “pores”), rough ER studded with ribosomes, polyribosomes, the Golgi apparatus, smooth ER, mitochondria, and the axon hillock, where bundles of microtubules run from the soma into the axon.

Transcription

Between protein-coding genes are long stretches of DNA, and we don’t know what they do (mostly). Some regions of this DNA are important for regulating transcription.

At one end of the gene is the promoter, where the RNA-synthesizing enzyme RNA polymerase binds to start the transcription.

Sketch of transcription: a strip of DNA with a promoter block near one end and a terminator block near the other, and below it an RNA polymerase with a strand of RNA trailing behind it; a red double arrow shows the promoter and polymerase binding, a binding regulated by transcription factors.

The promoter and the RNA polymerase bind to each other, and the binding is regulated by special proteins called transcription factors.

A pasted two-panel textbook figure follows. Panel (a) takes a gene through (1) transcription by RNA polymerase, (2) RNA processing into an mRNA transcript, and (3) export from the nucleus through the nuclear pores into the cytoplasm. Panel (b) zooms in on step 2: a gene running from promoter to terminator contains exons 1–3 separated by introns 1–2; the whole gene is transcribed into RNA, and splicing joins the exons into the mRNA. Annotations on the figure label the introns “non-protein coding,” trace each exon down into the finished mRNA, and send that mRNA back into panel (a); beside the export step is scribbled “CRISPR Cas9,” and as the mRNA leaves the nucleus: “I maka da protein!”—Luigi.

  • Introns are non-protein-coding.
  • Exons are protein-coding.

RNA splicing is the process of isolating the exons from the introns and fusing them together. Sometimes, if a different protein is needed, the splicing (alternative splicing) may also remove some exons.

Translation

Proteins are formed from 20 different kinds of amino acids. Picture the mRNA as a little stick figure shouting “Assemble!” at a crowd of amino acids, who answer “O.K.!”, and then BOOM! Protein. This process is called translation.

The study of all that: molecular biology. Mol. bio. is concerned with

Neuronal Genes, Genetic Variation, Mutation, and Engineering

  • The human genome: the entire length of DNA that comprises the genetic information in our chromies. It has already been sequenced (2000s).
  • Gene copy number variations: missing or duplicated genes.
  • Mutations: typographical errors.
  • Single nucleotide polymorphisms: think bear and bare (bad), or benign, like color and colour (no major or recognizable effect).

We live in the “post-genomic era.”

Note. Synthetic DNA???

We genetically modify mice by introducing, deleting, or editing genes and even nucleotides to understand function, with the goal of correcting it. These mice are called knockout mice, knock-in mice, and transgenic mice. Genetic engineering of mice has revolutionized bio.