遺傳 進(jìn)化與生態(tài)學(xué) 5 - Genomes
本期的內(nèi)容是基因組。本文集的這一部分是遺傳、進(jìn)化與生態(tài)學(xué) Genetics, Evolution, and Ecology. 這門課理論上建議在閱讀完文集的第一部分的內(nèi)容之后再開始學(xué)習(xí)，但基礎(chǔ)不足的朋友也可以嘗試閱讀喔~
這一部分的主要內(nèi)容均來(lái)自 Prof. Angela J. Roles 的課程，因此本文集的這一部分均不會(huì)標(biāo)記為原創(chuàng)。但由于文本來(lái)源不清晰，UP主還是一個(gè)字一個(gè)字碼出來(lái)的文章，本文禁止非授權(quán)的轉(zhuǎn)載，謝謝！
Lesson 5: Genomes?
[1] Genomes
Information storage: Genomes
?Cells contain the information to create replicas of themselves
- Replication occurs via processes such as mitosis, meiosis, and binary fission.
- Information is contained in a genome that is inherited by daughter cells.
?Lesson topic: How is that genetic information stored and organized?
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Information storage, transmission, and expression
?Cell replication requires storage and transmission of the info needed to?be a cell
????- Information to make an RNA molecule is stored in nucleic acids (e.g.,?DNA), organized in units labeled genes.?- Note: some viruses store their information only in RNA molecules rather?than as a DNA molecule.
????- Information is transmitted to offspring through reproduction.
?Cell metabolism requires expression of the stored information to create?functional protein or RNAs.
????- Gene expression = the process of transcribing DNA into RNA and?translating RNA into proteins;
????-?Some RNA molecules are functional and are not translated into protein?(e.g., ribosomal RNAs).
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[2] Structural diversity of genomes
?Bacteria, Archaea, and Eukarya
????- Information stored in double-stranded DNA (dsDNA) arranged in linear or?circular molecules;
????- DNA packaged with proteins and super-coiled
?Viruses:
????- Genomes consist of nucleic acids (RNA or DNA);
????- Circular or linear;
????- May be single- or double-stranded (or some of each: Hepadnaviridae,?including hepatitis B).
?Bacteria and Archaea:
????- Genome may consist of one or more circular or linear DNA molecules;
????- May contain additional genes carried on smaller circular (or linear) plasmids?in addition to standard genomic material
?Eukarya:
????- Genome in membrane-bound nucleus;
????- Nuclear genome composed of 2 or more linear DNA molecules;
????- Organelles may have their own circular or linear DNA genomes
?For more info and detail on genome structure in eukaryotes and?prokaryotes: https://www.ncbi.nlm.nih.gov/books/NBK21120/?(Chapter 2 of the text Genomes)
?
[3] Prokarya
Prokaryotic genome structure
?Prokaryotes may have circular?and/or linear chromosomes
?Borrelia burgdorferi (causes Lyme?disease) has 1 main linear?chromosome plus 9 circular?plasmids and 12 linear plasmids.
?Vibrio cholerae (causes cholera)?has 2 circular chromsomes
?Nucleoid?= region of cell where main chromosome is resides
?The genomic material is attached to the plasma membrane;
?the DNA forms looped domains;
?DNA-binding proteins (and other proteins) contribute to packaging of?the DNA into a super-coiled state
????-?Archaean super-coiling proteins resemble those of eukaryotes rather than?bacteria.
[4] Eukarya
Eukaryotes: Membrane-bound nuclei are unique to eukarya; no similar structure has been found in bacteria or archaea.
?(1) Chromosome
Zooming in on chromosome structure:
?Chromosomes consist of?chromatin (DNA and?proteins).
?Chromatids are?super-condensed?chromosomes
????- dsDNA wraps around?histone proteins to form?nucleosomes.
????- Nucleosomes are coiled up?into solenoids (30-nm?fiber).
????- After more coiling, you?have the familiar chromatid?structure.
(2) Chromatin
?Chromosomal structure is part of gene regulation (telling cells which?genes to turn on/off for making proteins)
????- Heterochromatin: highly condensed, not very accessible for transcription
????- Euchromatin: loosely condensed, more accessible for transcription
????- State changes in response to cellular signals or gene activity
?Molecules added to N-terminal tails of histones act as signals
????- Methyl groups repress expression (reduce amount of mRNA produced)
????- Acetyl groups enhance expression (increase amount of mRNA produced)
?
Spatial organization of chromatin
Nucleus of a chicken cell, with chromosomes stained using spectral?karyotyping (“chromosome painting”). You can see exclusive chromosome?territories but homologous chromosomes (e.g., both “1”) in different?locations.
?
Eukaryotic chromosomes
?DNA has been highly?replicated
?Chromatin highly?condensed
?Pair of sister chromatids = one?replicated chromosome
?Centromere: DNA-protein?complex that binds sister?chromatids together; important in?moving chromosomes during?mitosis and meiosis
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Activity
Pause to draw and describe each of the following structures. What is the?ploidy of each? How many copies of the chromosome are present?
????1. One chromatid: One copy of a single set of genes (haploid)
? ??2. A replicated chromosome: Two copies of a single set of genes (haploid)
? ? 3. A pair of homologous chromosomes: Two chromosomes with the same set?of genes (diploid)
? ? 4. A pair of replicated homologous chromosomes: Two copies of two?chromosomes with the same set of genes (diploid)
? ? 5. A pair of sister chromatids: Two copies of a single set of genes (haploid;?same as 2)
? ? 6. Two non-homologous chromosomes: Two different chromosomes,?encoding different sets of genes (different chromosomes shown by color,?position of centromere, size, etc)
(3) Notation
Distinguishing chromosomes
A pair of homologous chromosomes is diploid, with one copy of each chromatid.
Why are there two of them? Where do they?come from?
?Notice how chromosomes carrying?different sets of genes?(heterologous chromosomes) are?distinguished from each?other?--- usually having different sizes?or centromere positions.
?Notice how the two chromosomes?that form a homologous pair are?differentiated, usually by color, to?allow us to distinguish between?maternally and paternally inherited?chromosomes.
(4) Karyotypes
To make a karyotype:
????1.?Collect sample of cells,?induce mitosis;
????2.?Arrest cell division at?metaphase (with?colchicine);
????3.?Lyse the cells;
????4.?Fix and stain the cells?to reveal chromosome?banding patterns;
????5.?Visually pair?homologous?chromosomes by?banding pattern.
Karyotypes and types of chromosomes
?What are somatic chromosomes (or autosomes)?
?What are sex chromosomes?
?What is aneuploidy?
?What is polyploidy?
(5) Genome Sizes
Diversity in chromosome numbers
????Species vary widely in the number of chromosomes in their genome.
?What could cause this kind of diversity?
?Could there be benefits to have more or fewer chromsomes?
?Or could the variation be neutral, not helping or hurting the organism?
?
Condensed eukaryotic chromosomes
Spectral karyotyping:?Fluorescently-labeled DNA?probes specific to each?chromosome are?hybridized to a sample of?DNA.
Allows for easy detection?of structural abnormalities?for diagnosing disease?(such as a chromosome?fragment detached from?its original location).
