chromosome – AP Biology

the blueprint of life [10]: eukaryotic structure of DNA 3

let’s go over the terms again. Make sure you all know what they mean.

•Nucleus: 细胞核; Nucleolus: 核仁; Nucleoid: 类核

• Mitosis: 有丝分裂; Meiosis: 减数分裂

Interphase: 分裂间期; Prophase: 分裂前期; Metaphase: 分裂中期; Anaphase: 分裂后期; Telophase: 分裂末期

• Histone: 组蛋白

• Nucleosome: 核小体

•Chromosome: 染色体; Chromatin: 染色质; eu- 真染色质; hetero- 异染色质

Sister chromotid 姐妹染色单体;
mitotic spindle 纺锤体
spindle microtubule纺锤丝

• Centromere: 中心粒; Telomere: 端粒

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The familiar picture of a chromosome is actually that of the most highly condensed state at mitosis(which we reviewed in the blueprint of life [8]: eukaryotic structure of DNA 1(chromatin structure)).

As the daughter chromosomes are pulled apart by the mitotic spindle at cell division, the fragile centimeters-long chromosomal DNA would certainly be sheared by the forces generated, were it not in this highly compact state.

picture above is from Instant Notes in Molecular Biology

As we can see from the picture, the chromosomal loops fan out from a central scaffold or nuclear matrix region consisting of protein(which we talked about last section). One possibility is that consecutive loops may trace a helical path along the length of the chromosome.
The centromere is the constricted region where the two sister chromatids are joined in the metaphase chromosome. This is the site of assembly of the kinetochore, a protein complex which attaches to the microtubules of the mitotic spindle.

(The microtubules act to separate the chromotids at anaphase)

The DNA of the centromere has been shown in yeast to consist merely of a short AT-rich sequence of 88 bp, flanked by two very short conserved regions, although in mammalian cells, centromeres seem to consist of rather longer sequences, and are flanked by a large quantity of repeated DNA, known as satellite DNA.

Telomeres are specialized DNA sequence that form the ends of the linear DNA molecules of the eukaryotic chromosomes. A telomoere consists of up to hundreds of copies of a short repeated sequence(5′-TTAGGG-3′ in humans), which is synthesized by the enzyme telomerase in a mechanism independent of normal DNA replication.

The telomeric DNA forms a special secondary structure, the function of which is to protect the ends of the chromosome proper from degradation.(Independent synthesis of the telomere acts to counteract the gradual shortening of the chromosome resulting from the inability of normal replication to copy the very end of a linear DNA molecule—we will talk about this when reaching DNA replication)

Interphase chromosome

In interphase(S phase, to be exact), the genes on the chromosomes are being transcribed and DNA replication takes place. During this time, the chromosmes adopt a much more diffuse structure and cannot be visualized individually. It is believed, however, that the chromosomal loops are still present, attached to the nuclear matrix.

The blueprint of life [9]: eukaryotic structure of DNA 2(nucleosome)

Eukaryotic chromosome is packaged in hierarchical levels, mediated by various proteins.

DNA duplex→Nucleosome → Chromatin →Chromosome

We talked about DNA duplex and chromatin; now it’s time to meet the basic unit of chromatin structure–nucleosome.

Definition: nucleosome is the chromatin subunit that consists of DNAand a set of eight histone core proteins(complex of (H2A)₂(H2B)₂(H3)₂(H4)₂, →octamer. More loosely with one molecule of H1 )

Comparison

The proteins protect the DNA from the action of micrococcal nuclease.

Micrococcal Nuclease is an endo–exonuclease that preferentially digests single-stranded nucleic acids The enzyme is also active against double-stranded DNA and RNA and all sequences will be ultimately cleaved.(wikipedia)

Digestion with nuclease leads to the loss of H1, yielding a very resistant structure consisting of 146 bp of DNA associated very tightly with the histone octamer. The structure, known as the nucleosome core, is structurally very similar whatever the source of the chromatin.

Adjacent nucleosome is connected by a varied length (10-100 bp, average 55bp)of DNA, called “linker DNA”

One molecule of linker histone H1 binds to the linker DNA between nucleosome.

H1 also acts to stabilize the point at which the DNA enters and leaves the nulceosome core.

↑Chromatins at different packaging levels

30 nm chromatin fiber: condensed form

10 nm chromatin fiber : less-condensed form, like a thread of beads

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Summary of Nucleosome Structure:

NUCLEOSOME STRUCTURE, image from bricker.tcnj.edu

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Higher Order Structure

The organization of chromatin at the highest level seems rather similar to that of prokaryotic DNA(see THE BLUEPRINT OF LIFE [7]: PROKARYOTIC CHROMOSOME STRUCTURE OF DNA). Even the size of the loops is approximately the same, up to aorund 100 kb of DNA, although there are many more loops in a eukaryotic chromosome.

The loops are constrained by interaction with a protein complex known as the nuclear matrix. The DNA in the loops is in the form of 30 nm fiber, and the loops form an array about 300 nm across.

”Solenoid model “of 30-nm chromatin fiber

6 nucleosomes per turn

“Zigzag model” of 30-nm chromatin fiber

6 nucleosomes per turn, longer linker DNA may be required

HIGHER ORDER STRUCTURE, shown by prof. Dong

Genetics [9] Reproduction 2: Meiosis

During the process of reducing the number of chromosomes by half, the combination of alleles are rearranged to give recombinant gametes. Two distinct processes are involved. These are independent assortment of chromosomes and crossing-over.

Meiosis involves twosuccessive divisions, resulting in producing four cells, each containing half the number of chromosomes of the mother cell. There is NO replication between the two divisions.

We call the two divisions meiosis I and meiosis II, as in Chinese 减数第一次分裂 and 减数第二次分裂. Here we will introduce more of meiosis than meets in high school textbooks.

Meiosis I

meiosis I is divided into prophase, metaphase, anaphase and telophase. Although they have the same names as the four phases in typical mitosis, behavior of chromosomes in these four phases in meiosis is very different from that in mitosis.

In prophase each chromosome pairs with its homolog (copy of the same chromosome inherited from the other parent). The paired chromosomes are called bivalents. Each pair is held together by chiasmata(plural of chiasma). The exchange of genetic material is known as crossing-over.

A chiasma (plural: chiasmata), in genetics, is thought to be the point where two homologous non-sisterchromatids exchange genetic material during chromosomal crossover during meiosis (sister chromatids also form chiasmata between each other, but because their genetic material is identical, it does not cause any change in the resulting daughter cells). (from wikipedia)

Prophase of meiosis is subdivided into five stages: leptotene, zygotene, pachytene, diplotene, and diakinesis.
In leptotene(literal translation:thin threads), the chromatin is seen to condense into very long thin strands, that appear tangled in the nucleus. As prophase proceeds chromosomes become shorter and thicker.
At zygotene(literal translation: yoked/linked threads), homologous chromosomes are seen as partially paired structures. They are still very elongated at this stage and chromosome pairs may overlap or interwine.
By patchytene(thick threads), pairing is complete, though it still isn’t possible identify clearly the individual chromatids in each bivalent.
As the homologous chromosomes begin to separate, transition from patchytene to diplotene(double threads) occurs.

This process begins at the centromeres and the bivalents are seen to be held together by chiasma.

The nuclear membrane and the nucleolus breaks down.

The four chromatids in each bivalent become identifiable and individual chiasma clearly to be identified.

Chromosomes carrying on condensing, the cell moves into diakinesis(moving apart), the final subdivision of prophase I.

The scheme below shows the five stages in prophase in a simple way:

At metaphase I the nuclear envelope breaks down, the bivalents lie across the equator of the cell with their centromeres attached to the microtbules←similar to the spindle in mitosis.

The dynamic action of the spindle causes one member of each homologous cell to move to the opposite poles of the cell.

↑WHY wouldn’t the action of the spindle tear apart the sister chromatids?

BECAUSE at metaphase the sister chromatids are held together by proteins called cohesions, which holds chiasmata in place and so holds the chromosomes together.

At anaphase I the cohesions in the chromosome arms are cut, allowing the homologs to separate.

In telophase I, two neclei form around the segregating chromosomes and a degree of chromosome decondensation is observed.

Meiosis II

The process of meiosis II closely resembles that of the typical mitosis.

In prophase II the chromosomes are seen to recondense within the two nuclei. At metaphase II, the nuclear membrane breaks down and chromosoms rearranged at the equator , the centromere splits and…At anaphase II and telophase II,the initial dipliod cell has divided into four…we already knew these in high school.

What we didn’t know in high school is that each of the four haploid cells has a different genotype. And in many instances the group of four haploid cells may remain together and is known as a tetrad.

SUMMARY OF MEIOSIS

the blueprint of life [8]: eukaryotic structure of DNA 1(chromatin)

• Mitosis: 有丝分裂; Meiosis: 减数分裂

Interphase: 分裂间期; Prophase: 分裂前期; Metaphase: 分裂中期; Anaphase: 分裂后期; Telophase: 分裂末期

• Histone: 组蛋白 hhistidine 组氨酸

• Nucleosome: 核小体

•Chromosome: 染色体; Chromatin: 染色质; eu- 真染色质; hetero- 异染色质

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The total length of DNA in a eukaryotic cell depends on the species, but it can be thousands of times as much as in a prokaryotic genome.

Eukaryotic chromosome is made up of a number of discrete bodies called chromosomes. The DNA in each chromosome is believed to be a single linear molecule, which can be up to several centimeters long.

All these each contain a long linear DNA molecules, which must be packaged into the nucleus, a space of approximately the same volume as a bacterial cell

SO, much longer DNA chains packaged into a space of the same volume as a bacterial cell? → for example, 2 cm of DNA length versus ~10 µm of cell size for fruit fly; most condensed form of human chromosome is about ~2 µm long = 10,000× packing ratio

the obvious result is in their most highly condensed forms, the chromosomes have an enormously high DNA concentration: perhaps 200 mg/ml.!

The feat of packing is accomplished by the formation of a highly organized complex of DNA and protein, known as the chromatin, a nucleoprotein complex. (←our hero today, has finally showed up.)

Chromosomes greatly alter their level of compectness as cells progress through the cell cycle, vary between highly condensed chromosomes at metaphase(just before the cell division), and very much more diffuse structures in interphase.(This implies the existence of different levels of organization of chromatin)

More than 50% of the mass of chromatin is protein. Most of the protein in eukaryotic chromatin consists of histones, of which there are five families: H2A, H2B, H3 and H4, known as the core histones, and H1.

The core histones are small proteins, with masses between 10 and 20 kDa, and H1 histones are a little larger at around 23 kDa.

The unified atomic mass unit (symbol: u) or dalton (symbol: Da) is the standard unit that is used for indicating mass on an atomic or molecular scale (atomic mass). One dalton is approximately the mass of a nucleon and is equivalent to 1 g/mol.^[1] It is defined as one twelfth of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state,^[2] and has a value of 1.660538921(73)×10⁻²⁷ kg.^[3]

All histones proteins a large positive charge; between 20 and 30% of their sequences consist of the basic amino acids, lysine and arginine. This means that histones will bind very strongly to the negatively charged DNA in forming chromation.

amino acids in English?

Members of the same histone class(family) are very highly conserved between relatively unrelated species, for example between plants and animals, which testifies to their crucial role in the chromation.

Within a given species, there are normally a number of closely similar variants of a particular class, which may be expressed in different tissues, and at different stages in development.

There is not much similarity in sequence between the different histone classes, but structural studies have shown that the classes so share a similar tertiary structure, suggesting that all hisotnes are ultimately evolutionarily related.

H1 histones are somewhat distinct from the other histone classes in a number of ways; in addition to their larger size, there is more variation in H1 sequences both between and within species than in other classes. Histone H1 is more easily extracted from bulk chromatin, and seems to be present in roughly half the quantity of the other classes, of which there are very similar amounts.

Next section we will cover the distinct role of histone Hi in chromatin structure.

the blueprint of life [7]: prokaryotic chromosome structure of DNA

First, let’s make sure the anatomy of prokaryotes are familiar to us:

Prokaryotes are the simplest living cells, typically 1~10μm in diameter, and are found in all environmental niches from the guts of the animals to acidic hot springs.

They are bounded by a cell (plasma)membrane comprising a lipid bilayer, in which are embeded proteins that allow the exit and entry of small molecules.
Most prokaryotes also have a rigid cell wall outside the plasma membrane, which prevents the cell from swelling or shrinking in environments where osmolarity differs significantly from that inside the cell.
Sometimes the cell wall is surrounded by an (often) polysaccharide envelope called capsule.
The cell interior (cytoplasm or cytosol) usually contains a single, circular chromosome compacted into a nucleoid and attached to the membrane.
There are no distinct subcelluar organelles in prokaryotes as in eukaryotes(except for the ribosomes核糖体).
The surface of a prokaryote may carry pili, which allow the prokaryote to attach to other cells and surfaces. Some prokaryotes also carry flagella, whose rotating motion allows the cell to swim.

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To talk about prokaryotic chromosome structure, we use E. coli (大肠杆菌)as the example.

E. coli chromosome contains a single supercoiled circular DNA molecule of length 4.6 million bp.
E. coli chromosome is highly folded: 1500 µm of DNA length versus ~1 µm of cell size, forming a structure called the nucleoid.
The nucleoid has a very high DNA concentration, perhaps 30~50 mg/ml, as well as containing all the proteins associated with DNA, such as polyerases, repressors(a protein that is determined by a regulatory gene, binds to a genetic operator, and inhibits the initiation of transcription of messenger RNA), etc.

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DNA domains (loops)

Remember this famous electron micrograph of an E. coli cell we showed before? The cell was carefully lysed, all the proteins removed and then, it was spread on an EM grid to reveal all of its DNA.

Several of such experiments revealed one level of organization of the nucleoid.

The DNA consists of 50~100 domains or loops, about 50~100 kb in size (kb: kilobase, a unit of measure of the length of a nucleic-acid chain that equals one thousand base pairs).
The ends of the loops are constrained by binding to a structure which probably consists of proteins attached to part of the cell membrane.
Not known whether the loops are static or dynamic, but one model suggests that the DNA may spool(wind) through sites of polyerase or other enzymic action at the base of the loops.

E coli DNA instant notes

image above is from”Instant Notes in Molecular Biology”

Supercoiling of the genome

The E. coli chromosome as a whole is negatively supercoiled, although there is some evidence that indicates individual domains may be supercoiled independently. Electron micrographs indicate that some domains may not be supercoiled, perhaps because the DNA has become broken in one strand, where other domains clearly do contain supercoils.

The domains may be topologically independent. There is, however, no real biochemical evidence for major differences in the level of supercoiling in different regions of the chromosome in vivo

DNA-binding proteins

The looped DNA domains of the chromosome are constrained further by inter-action with a number of DNA-binding proteins.

The most abundant of these are protein HU, a small basic (+charged) dimeric protein, which binds DNA non-specifically by the wrapping of the DNA aorund the protein.

And H-NS (formerly known as the protein H1), a monomeric neutral protein, which also binds DNA non-specifically in terms of sequence, but seems to have a preference for regions of DNA which are intrinsically bent.

These proteins are sometimes known as histone-like proteins, and have the effect of compacting the DNA, which is essential for the packaging of the DNA into the nucleoid, and of stabilizing and constraining the supercoiling of the chromosome.

the blueprint of life [6]: Chromosomal Structure of DNA 1

vocabulary

•Nucleus: 细胞核; Nucleolus: 核仁; Nucleoid: 类核

• Mitosis: 有丝分裂; Meiosis: 减数分裂

Interphase: 分裂间期; Prophase: 分裂前期; Metaphase: 分裂中期; Anaphase: 分裂后期; Telophase: 分裂末期

• Histone: 组蛋白

• Nucleosome: 核小体

•Chromosome: 染色体; Chromatin: 染色质; eu- 真染色质; hetero- 异染色质

• Centromere: 中心粒; Telomere: 端粒

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WHAT is chromosome:

Structure containing the genes of a cell and made of a single DNA molecule and its associated proteins.

CHROMOSOMES OF EUKARYOTES, shown by prof. Dong

HOW long is DNA in an chromosome
HOW LONG IS DNA, shown by prof. Dong.

→A chromosome is too long to fit into a cell without compaction.

WHY is DNA packed into chromosomes

Chromosome is a compact form of the DNA that readily fits inside the cell
To protect DNA from damage
DNA in a chromosome can be transmitted efficiently to both daughter cells during cell division
Chromosome confers an overall organization to each molecule of DNA, which regulates gene expression as well as recombination

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Diversity of chromosomes

in terms of:

Shape: circular or linear
Number: species-specific

eg. -fruitfly 8; -human 46; -horse 64; -dog 78; -chicken 78

-maize 20; -rice 24; -wheat 42

Copy number: haploid单倍体, diploid双倍体, polyploid 多倍体

Overall structure: highly different between prokaryotes 原核生物and eukaryotes真核生物

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Next section we will first talk about prokaryotic chromosome structure of DNA.