Chapter 4. DNA, Chromosomes, and Genomes
Structure and Function of DNA Highlights
*A DNA Molecule Consists of Two Complementary Chains of Nucleotides *The Structure of DNA Provides a Mechanism for Heredity *In Eukaryotes, DNA Is Enclosed in a Cell Nucleus
Chromatin Loops
-formed from 30nm fibers that are attached to a protein scaffold (SARs) -range from 1 to 4 million bp
Structural organization of the nucleosome
A nucleosome contains a protein core made of eight histone molecules.
The Nucleus
A part of the cell containing DNA and RNA
Nucleosome Sliding
A way to alter chromatin structure A Chromatin remodeling complex. By using the energy of ATP hydrolysis to move DNA relative to the core, the protein complex changes the structure of a nucleosome temporarily, making the DNA less tightly bound to the histone core.
Genome
All the genetic information in an organism; All of an organism's chromosomes. It specifies all the RNA molecules and proteins that the organism will ever synthesize.
heterochromatin and euchromatin
Clusters of DNA, RNA, and proteins in the nucleus of a cell tightly coiled around histones
Nucleosomes
DNA coiled around histones (proteins that help organize and pack DNA)
Epigenetic inheritance
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.
The Global Structure Of Chromosomes Highlights
*Chromosomes Are Folded into Large Loops of Chromatin *Polytene Chromosomes Are Uniquely Useful for Visualizing Chromatin Structures *There Are Multiple Forms of Chromatin *Chromatin Loops Decondense When the Genes Within Them Are Expressed *Chromatin Can Move to Specific Sites Within the Nucleus to Alter Gene Expression
Chromosomal DNA And Its Packaging In The Chromatin Fiber Highlights
*Eukaryotic DNA Is Packaged into a Set of Chromosomes *Chromosomes Contain Long Strings of Genes *The Nucleotide Sequence of the Human Genome Shows How Our Genes Are Arranged *Each DNA Molecule That Forms a Linear Chromosome Must Contain a Centromere, Two Telomeres, and Replication Origins *DNA Molecules Are Highly Condensed in Chromosomes *Nucleosomes Are a Basic Unit of Eukaryotic Chromosome Structure *The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged *Nucleosomes Have a Dynamic Structure, and Are Frequently Subjected to Changes Catalyzed by ATP-Dependent Chromatin Remodeling Complexes *Nucleosomes Are Usually Packed Together into a Compact Chromatin Fiber
Chromatin Structure and Function Highlights
*Heterochromatin Is Highly Organized and Restricts Gene Expression *The Heterochromatic State Is Self Propagating *Chromatin Acquires Additional Variety Through the Site-Specific Insertion of a Small Set of Histone Variants *Covalent Modifications and Histone Variants Act in Concert to Control Chromosome Functions *A Complex of Reader and Writer Proteins Can Spread Specific Chromatin Modifications Along a Chromosome *The Chromatin in Centromeres Reveals How Histone Variants Can Create Special Structures *Some Chromatin Structures Can Be Directly Inherited *Experiments with Frog Embryos Suggest that both Activating and Repressive Chromatin Structures Can Be Inherited Epigenetically *Chromatin Structures Are Important for Eukaryotic Chromosome Function
Complementary base pairs in the DNA double helix.
A consequence of DNA's structure and base-pairing requirements is that each strand of a DNA molecule contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand. The shapes and chemical structures of the bases allow hydrogen bonds to form efficiently only between A and T and between G and C, because atoms that are able to form hydrogen bonds can then be brought close together without distorting the double helix. As indicated, two hydrogen bonds form between A and T, while three form between G and C. The bases can pair in this way only if the two polynucleotide chains that contain them are antiparallel to each other.
Chromosomal DNA And Its Packaging In The Chromatin Fiber Summary
A gene is a nucleotide sequence in a DNA molecule that acts as a functional unit for the production of a protein, a structural RNA, or a catalytic or regulatory RNA molecule. In eukaryotes, protein-coding genes are usually composed of a string of alternating introns and exons associated with regulatory regions of DNA. A chromosome is formed from a single, enormously long DNA molecule that contains a linear array of many genes, bound to a large set of proteins. The human genome contains 3.2 × 109 DNA nucleotide pairs, divided between 22 different autosomes (present in two copies each) and 2 sex chromosomes. Only a small percentage of this DNA codes for proteins or functional RNA molecules. A chromosomal DNA molecule also contains three other types of important nucleotide sequences: replication origins and telomeres allow the DNA molecule to be efficiently replicated, while a centromere attaches the sister DNA molecules to the mitotic spindle, ensuring their accurate segregation to daughter cells during the M phase of the cell cycle. The DNA in eukaryotes is tightly bound to an equal mass of histones, which form repeated arrays of DNA-protein particles called nucleosomes. The nucleosome is composed of an octameric core of histone proteins around which the DNA double helix is wrapped. Nucleosomes are spaced at intervals of about 200 nucleotide pairs, and they are usually packed together (with the aid of histone H1 molecules) into quasi-regular arrays to form a 30-nm chromatin fiber. Even though compact, the structure of chromatin must be highly dynamic to allow access to the DNA. There is some spontaneous DNA unwrapping and rewrapping in the nucleosome itself; however, the general strategy for reversibly changing local chromatin structure features ATP-driven chromatin remodeling complexes. Cells contain a large set of such complexes, which are targeted to specific regions of chromatin at appropriate times. The remodeling complexes collaborate with histone chaperones to allow nucleosome cores to be repositioned, reconstituted with different histones, or completely removed to expose the underlying DNA.
Nucleosome
Bead-like structure in eukaryotic chromatin, composed of a short length of DNA wrapped around a core of histone proteins
DNA as a template for its own duplication.
Because the nucleotide A successfully pairs only with T, and G pairs with C, each strand of DNA can act as a template to specify the sequence of nucleotides in its complementary strand. In this way, double-helical DNA can be copied precisely, with each parental DNA helix producing two identical daughter DNA helices. The ability of each strand of a DNA molecule to act as a template for producing a complementary strand enables a cell to copy, or replicate, its genome before passing it on to its descendants.
Covalent Modifications of Chromatin
Chromatin state determined by covalent modification of histones -> acetylation or methylation of lysines and phosphorylation of serines
The Global Structure Of Chromosomes Summary
Chromosomes are generally decondensed during interphase, so that the details of their structure are difficult to visualize. Notable exceptions are the specialized lampbrush chromosomes of vertebrate oocytes and the polytene chromosomes in the giant secretory cells of insects. Studies of these two types of interphase chromosomes suggest that each long DNA molecule in a chromosome is divided into a large number of discrete domains organized as loops of chromatin that are compacted by further folding. When genes contained in a loop are expressed, the loop unfolds and allows the cell's machinery access to the DNA. Interphase chromosomes occupy discrete territories in the cell nucleus; that is, they are not extensively intertwined. Euchromatin makes up most of interphase chromosomes and, when not being transcribed, it probably exists as tightly folded fibers of compacted nucleosomes. However, euchromatin is interrupted by stretches of heterochromatin, in which the nucleosomes are subjected to additional packing that usually renders the DNA resistant to gene expression. Heterochromatin exists in several forms, some of which are found in large blocks in and around centromeres and near telomeres. But heterochromatin is also present at many other positions on chromosomes, where it can serve to help regulat developmentally important genes. The interior of the nucleus is highly dynamic, with heterochromatin often positioned near the nuclear envelope and loops of chromatin moving away from their chromosome territory when genes are very highly expressed. This reflects the existence of nuclear subcompartments, where different sets of biochemical reactions are facilitated by an increased concentration of selected proteins and RNAs. The components involved in forming a subcompartment can self-assemble into discrete organelles such as nucleoli or Cajal bodies; they can also be tethered to fixed structures such as the nuclear envelope. During mitosis, gene expression shuts down and all chromosomes adopt a highly condensed conformation in a process that begins early in M phase to package the two DNA molecules of each replicated chromosome as two separately folded chromatids. The condensation is accompanied by histone modifications that facilitate chromatin packing, but satisfactory completion of this orderly process, which reduces the end-to-end distance of each DNA molecule from its interphase length by an additional factor of ten, requires additional proteins.
Chromosomes
Consists of a single, enormously long linear DNA molecule along with the proteins that fold and pack the fine DNA thread into a more compact structure. - They are what carry genes—the functional units of heredity. Threadlike structures made of DNA molecules that contain the genes
Deoxyribonucleic acid (DNA)
DNA Molecule consists of two long polynucleotide chains composed of four types of nucleotide subunits. Each of these chains is known as a DNA chain, or a DNA strand. The chains run antiparallel to each other, and hydrogen bonds between the base portions of the nucleotides hold the two chains together. Nucleotides are composed of a five-carbon sugar to which are attached one or more phosphate groups and a nitrogen containing base.
The three-dimensional structure of DNA
DNA double helix—arises from the chemical and structural features of its two polynucleotide chains. Because these two chains are held together by hydrogen-bonding between the bases on the different strands, all the bases are on the inside of the double helix, and the sugar-phosphate backbones are on the outside A always pairs with T, and G with C . This complementary base-pairing enables the base pairs to be packed in the energetically most favorable arrangement in the interior of the double helix. In this arrangement, each base pair is of similar width, thus holding the sugar-phosphate backbones a constant distance apart along the DNA molecule. The members of each base pair can fit together within the double helix only if the two strands of the helix are antiparallel—that is, only if the polarity of one strand is oriented opposite to that of the other strand.
DNA and its building blocks
DNA is made of four types of nucleotides, which are linked covalently into a polynucleotide chain (a DNA strand) with a sugar-phosphate backbone from which the bases (A, C, G, and T) extend. A DNA molecule is composed of two antiparallel DNA strands held together by hydrogen bonds between the paired bases. The arrowheads at the ends of the DNA strands indicate the polarities of the two strands.
The Key Components of Chromosomes: • Multiple origins of replication • One centromere • Two telomeres (All are nucleotide/DNA sequences)
Each chromosome operates as a distinct structural unit: for a copy to be passed on to each daughter cell at division, each chromosome must be able to replicate, and the newly replicated copies must subsequently be separated and partitioned correctly into the two daughter cells. These basic functions are controlled by three types of specialized nucleotide sequences in the DNA, each of which binds specific proteins that guide the machinery that replicates and segregates chromosomes
epigenetic inheritance
Epigenetic inheritance plays a central part in the creation of multicellular organisms. Their differentiated cell types become established during development, and persist thereafter even through repeated cell-division cycles. The daughters of a liver cell persist as liver cells, those of an epidermal cell as epidermal cells, and so on, even though they all contain the same genome; and this is because distinctive patterns of gene expression are passed on faithfully from parent cell to daughter cell. Chromatin structure has a role in this epigenetic transmission of information from one cell generation to the next.
Structure and Function of DNA Summary
Genetic information is carried in the linear sequence of nucleotides in DNA. Each molecule of DNA is a double helix formed from two complementary antiparallel strands of nucleotides held together by hydrogen bonds between G-C and A-T base pairs. Duplication of the genetic information occurs by the use of one DNA strand as a template for the formation of a complementary strand. The genetic information stored in an organism's DNA contains the instructions for all the RNA molecules and proteins that the organism will ever synthesize and is said to comprise its genome. In eukaryotes, DNA is contained in the cell nucleus, a large membrane-bound compartment.
CHROMATIN STRUCTURE AND FUNCTION
Having described how DNA is packaged into nucleosomes to create a chromatin fiber, we now turn to the mechanisms that create different chromatin structures in different regions of a cell's genome. Certain types of chromatin structure can be inherited; that is, the structure can be directly passed down from a cell to its descendants. Because the cell memory that results is based on an inherited chromatin structure rather than on a change in DNA sequence, this is a form of epigenetic inheritance. Here, we are concerned with only one, that based on chromatin structure. We begin this section by reviewing the observations that first demonstrated that chromatin structures can be inherited. We then describe some of the chemistry that makes this possible— the covalent modification of histones in nucleosomes. These modifications have many functions, inasmuch as they serve as recognition sites for protein domains that link specific protein complexes to different regions of chromatin. Histones thereby have effects on gene expression, as well as on many other DNA-linked processes. Through such mechanisms, chromatin structure plays an important role in the development, growth, and maintenance of all eukaryotic organisms, including ourselves.
THE GLOBAL STRUCTURE OF CHROMOSOMES
Having discussed the DNA and protein molecules from which the chromatin fiber is made, we now turn to the organization of the chromosome on a more global scale and the way in which its various domains are arranged in space. As a 30-nm fiber, a typical human chromosome would still be 0.1 cm in length and able tospan the nucleus more than 100 times. Although the molecular details are still largely a mystery, this higher-order packaging almost certainly involves the folding of the chromatin into a series of loops and coils. This chromatin packing is fluid, frequently changing in response to the needs of the cell.
Nucleotides in DNA
In the case of the nucleotides in DNA, the sugar is deoxyribose attached to a single phosphate group (hence the name deoxyribonucleic acid), and the base may be either adenine (A), cytosine (C), guanine (G), or thymine (T) The nucleotides are covalently linked together in a chain through the sugars and phosphates, which thus form a "backbone" of alternating sugar-phosphate-sugar-phosphate. These same symbols (A, C, G, and T) are commonly used to denote either the four bases or the four entire nucleotides—that is, the bases with their attached sugar and phosphate groups. The way in which the nucleotides are linked together gives a DNA strand a chemical polarity. This polarity in a DNA chain is indicated by referring to one end as the 3ʹ end and the other as the 5ʹ end, names derived from the orientation of the deoxyribose sugar.
Chromatin Structure and Function Summary
In the chromosomes of eukaryotes, DNA is uniformly assembled into nucleosomes, but a variety of different chromatin structures is possible. This variety is based on a large set of reversible covalent modifications of the four histones in the nucleosome core. These modifications include the mono-, di-, and trimethylation of many different lysine side chains, an important reaction that is incompatible with the acetylation that can occur on the same lysines. Specific combinations of the modifications mark many nucleosomes, governing their interactions with other proteins. These marks are read when protein modules that are part of a larger protein complex bind to the modified nucleosomes in a region of chromatin. These reader proteins then attract additional proteins that perform various functions. Some reader protein complexes contain a histone-modifying enzyme, such as a histone lysine methylase, that "writes" the same mark that the reader recognizes. A reader-writer-remodeling complex of this type can spread a specific form of chromatin along a chromosome. In particular, large regions of condensed heterochromatin are thought to be formed in this way. Heterochromatin is commonly found around centromeres and near telomeres, but it is also present at many other positions in chromosomes. The tight packaging of DNA into heterochromatin usually silences the genes within it. The phenomenon of position effect variegation provides strong evidence for the inheritance of condensed states of chromatin from one cell generation to the next. A similar mechanism appears to be responsible for maintaining the specialized chromatin at centromeres. More generally, the ability to propagate specific chromatin structures across cell generations makes possible an epigenetic cell memory process that plays a role in maintaining the set of different cell states required by complex multicellular organisms.
Chromatin
Is a complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells. Divided into 2 groups: The histones and the non-histone chromosomal proteins, which bind to the DNA to form eukaryotic chromosomes, each contributing about the same mass to a chromosome as the DNA.
THE STRUCTURE AND FUNCTION OF DNA
Life depends on the ability of cells to store, retrieve, and translate the genetic instructions required to make and maintain a living organism. This hereditary information is passed on from a cell to its daughter cells at cell division, and from one generation of an organism to the next through the organism's reproductive cells. The instructions are stored within every living cell as its genes, the information-containing elements that determine the characteristics of a species as a whole and of the individuals within it. We begin this chapter by describing the structure of DNA. We see how, despite its chemical simplicity, the structure and chemical properties of DNA make it ideally suited as the raw material of genes. We then consider how the many proteins in chromosomes arrange and package this DNA. The packing has to be done in an orderly fashion so that the chromosomes can be replicated and apportioned correctly between the two daughter cells at each cell division. And it must also allow access to chromosomal DNA, both for the enzymes that repair DNA damage and for the specialized proteins that direct the expression of its many genes.
DNA replication Origin
One type of nucleotide/DNA sequence that acts as the location at which duplication of the DNA begins. Eukaryotic chromosomes contain many origins of replication to ensure that the entire chromosome can be replicated rapidly
Gene Expression
Process through which a cell converts the nucleotide sequence of a gene first into the nucleotide sequence of an RNA molecule, and then into the amino acid sequence of a protein. (The conversion of the information encoded in a gene first into messenger RNA and then to a protein)
Covalent Modifications: The Histone Code
The amino acid side chains of the four histones in the nucleosome core are subjected to a remarkable variety of covalent modifications, including the acetylation of lysines, the mono-, di-, and trimethylation of lysines, and the phosphorylation of serines Image: Trimethylation of lysine 9 attracts a protein called heterochromatin-specific protein 1 (HP1)
CHROMOSOMAL DNA AND ITS PACKAGING IN THE CHROMATIN FIBER
The most important function of DNA is to carry genes, the information that specifies all the RNA molecules and proteins that make up an organism— including information about when, in what types of cells, and in what quantity each RNA molecule and protein is to be made. The nuclear DNA of eukaryotes is divided up into chromosomes, and in this section we see how genes are typically arranged on each chromosome. In addition, we describe the specialized DNA sequences that are required for a chromosome to be accurately duplicated as a separate entity and passed on from one generation to the next. We also confront the serious challenge of DNA packaging. If the double helices comprising all 46 chromosomes in a human cell could be laid end to end, they would reach approximately 2 meters; yet the nucleus, which contains the DNA, is only about 6 μm in diameter.
A simplified view of the eukaryotic cell cycle
To form a functional chromosome, a DNA molecule must be able to do more than simply carry genes: - It must be able to replicate, and the replicated copies must be separated and reliably partitioned into daughter cells at each cell division. This process occurs through an ordered series of stages, collectively known as the cell cycle.
Histones
are responsible for the first and most basic level of chromosome packing, the nucleosome, a protein-DNA complex
Condensins
protein complex that helps configure duplicated chromosomes for segregation by making them more compact
The Code-Reader Complex
• Combinations of covalent modifications of histones (the histone code) -> signals how chromosome should be packaged • Regulatory proteins bind specific "tags" together with code-reader complex • The code-reader complex recruits additional proteins -> carryout biological functions dictated by specific code
Gene Arrangement
• Very little of the human genome actually codes for proteins • Transposable elements make up much of our DNA; Short mobile DNA segments • Exons = Sequences of DNA that actually code for protein • Introns = Non-coding sequences in between
Packaging of Nucleosomes into 30 nm Fiber
•Tetranucleosome structure is a zigzag model for stacking of nucleosomes • A larger linker histone (H1) assists in stacking
