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Nucleus basics (pages to 6 th ed.). 1. Structure of DNA: 387-390, fig. 10.10. 2. Components of Chromosomes: origins (p. 547), centromeres(496), genes, telomeres (493):

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nucleus basics pages to 6 th ed
Nucleus basics (pages to 6th ed.)

1. Structure of DNA: 387-390, fig. 10.10

slide5
2. Components of Chromosomes: origins (p. 547), centromeres(496), genes, telomeres (493):
  • 3. Folding of chromosomes: Beads on a string and histones involved, 30 nm solenoid loops, folded loops, mitotic chromosomes: Fig. 12.12 We won’t go into chromatin remodeling by covalent modification of histones or by remodeling complexes.
slide8
4. Chromatin, heterochromatin, euchromatin : 484
  • 5. Replication: Replication is semiconservative, bidirectional, and semidiscontinuous; (550-560), Fig., 13.9-13
  • 6. Eukaryotes have multiple origins of replication; replication occurs in replication units. pp 565-569, Fig. 13.19
slide13
Transcription:

Three main types of RNA’s: mRNA, rRNA, tRNA, plus other small RNA types (421)

3 types of RNA polymerases & their products, use of alpha-amanitin to distinguish between the types. (443; my notes)

Promoters, transcription factors , enhancers, (435), Figs 11.6, 18

RNA processing: 5’ caps, Splicing, 3’ polyA tails, introns, and exons (437), Figs 11.21-23,

Ribosomal RNA- multiple copies of rRNA genes, rRNA formation from a single transcript by nucleolytic processing. (11.12, 14 p. 430)

slide21
Translation:

Large and small ribosomal subunits; Start (met) and stop codons; translation beginning at 5’ end; translation beginning at the amino end, concluding at the COOH end. (455-467)

chapter 12 nucleus
Chapter 12- Nucleus
  • I. Structure and Function of the Nucleus
  • A. Functions: 1) Production, in response to environmental/ internal signals,of RNA; “the control center of the cell”;
  • 2) Ribosome assembly
  • 3) Replication & maintenance of the genome; only molecule that is repaired is DNA.
slide24
B. Structure: Complex, membrane-bound organelle; Approx. 10% of the size of the cell. Membrane prevents the coupling of transcription and translation. Components: (12.1)
transport to and from the nucleus
Transport to and from the nucleus
  • In spite of the fact that it’s a characteristic of “advanced” cells, the nuclear membrane causes problems.
  • Proteins are only made in the cytoplasm; RNA's are made in the nucleus but used in the cyptoplasm; Ribosomes are assembled inside, but used outside. LOTS of proteins are needed in the nucleus- histones, TFs, polymerases of all sorts, etc.
slide29
Karp states that a typical cell, like a growing liver cell (he uses the example of a HeLa cell), has 10,000,000 ribosomes. Every sec it must import 560,000 ribosomal proteins and export 14K ribosomes. Busy, Busy, Busy!
  • Most of this coming and going is through the nuclear pore complex
key parts
Key parts
  • Rings on the cytoplasmic and nuclear sides, with supporting spokes
  • Central transporter- limits diameter to 9 nm, plus FG-domains, limits diffusion to proteins < 40,000
  • About 30 protein types
  • GREAT BIG THING! 15-30X the mass of a ribosome!
  • Cytoplasmic filaments
  • Nuclear basket
getting things in and out
Getting things in and out
  • Simple diffusion of some proteins.
  • Others need signals to enter and leave.
  • The players: Importins alpha and beta; protein with Nuclear Localization Signal (NLS); Ran-GTP; exportin.
slide38

Note that this is a model-”proposed steps”

It’s not really clear how RAN gets back in; it may simply diffuse in. Once in, it is reconverted to RAN-GTP. And, of course, the exportin needs to get back in as well!

slide42

A MAJOR export is mRNA! The splicing complex is involved in export! The Exon Joining Complex binds to TAP, which allows binding to the NPC and export. The EJC and TAP must then get back in.

epigenetics new subject
Epigenetics- new subject
  • What- heritable traits that are not coded by our genes.
  • Methylation of DNA (lowers transcription), and Acetylation of histones (activates) becomes heritable. For example:
  • http://www.ncbi.nlm.nih.gov/pubmed/16391557
  • http://www.ncbi.nlm.nih.gov/pubmed/11368478?dopt=Abstract&holding=npg
slide44

Data came from Swedish region with regular feast and famine conditions.

  • If the Paternal Grandfather was fed too much when he was 9-12, then the children had shorter life expectancy
  • Other studies show effects of starvation and smoking on obesity
slide45

Toxic legacy.In a controversial finding, exposing a pregnant rat to a toxin had health effects for three generations.

J Kaiser Science 2014;343:361-363

Published by AAAS

things to know
Things to Know
  • Nuclear functions
  • Structure of the nucleus, of the nuclear pore complex.
  • Why import/export is important
  • Importin exportin, RAN-GTP/GDP story
  • How splicing, of all things, gets involved in mRNA export.
the quiz
The quiz
  • Nucleus basics- structure of DNA, important terms- histones, nucleosomes, telomeres, splice, cap, tail, triplet codon, three polymerases, transcription, translation
  • Structure of the nuclear pore. Examples of import and exported items
pretend quiz what you might have had on friday
Pretend quiz- what you might have had on Friday

1. What is the complementary DNA sequence from this RNA sequence?

  • 5’A U G A AA C C A G GG C C G3’

2. A polypeptide of _____ Amino acids could be coded for by this mRNA

3. Which end would be the carboxyl end of that polypeptide? (right or left end)

slide49

4. Transcription begins at a(n):

  • Origin b. Promoter c. Enhancer d. Charger

 5. What’s this, and is the cytoplasm up or down?