Cell Chpt 4: DNA, Chromosomes & Genomes

Question 1

What did painstaking observations of cells and embryos in the late nineteenth century lead to regarding hereditary information?

Answer 1

hereditary information is carried on chromosomes—threadlike structures in the nucleus of a eukaryotic cell that become visible by light microscopy as the cell begins to divide

Question 2

Later, when biochemical analysis became possible, chromosomes were found to consist of what?

Answer 2

Deoxyribonucleic acid (DNA) and protein, with both being present in roughly the same amounts.

Question 3

During this time what was DNA thought to be?

Answer 3

For many decades, the DNA was thought to be merely a structural element.

Question 4

Describe the first experimental demonstration that DNA is the genetic material

Answer 4

These experiments, carried out in the 1920s and 1940s, showed that adding purified DNA to a bacterium changed the bacterium’s properties and that this change was faithfully passed
on to subsequent generations. Two closely related strains of the bacterium Streptococcus pneumoniae differ from each other in both their appearance under the microscope and their pathogenicity. One strain appears smooth (S) and causes death when injected into mice, and the other appears rough (R) and is nonlethal. An initial experiment shows that some substance present in the S strain can change (or transform) the R strain into the S strain and that this change is inherited by subsequent generations of bacteria. This experiment, in which the R strain has been incubated with various classes of biological molecules purified from the S strain, identifies the active substance as DNA.

Question 5

Describe the structure of DNA molecules

Answer 5

A deoxyribonucleic acid (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

Question 6

How are nucleotides composed?

Answer 6

Nucleotides are composed of a five-carbon sugar to which are attached one or more phosphate groups and a nitrogen-containing base. 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).

Question 7

What is meant by the ‘backbone’ of DNA?

Answer 7

The nucleotides are covalently linked together in a chain through the sugars and phosphates, which thus form a “back- bone” of alternating sugar–phosphate–sugar–phosphate. Because only the base differs in each of the four types of nucleotide subunit, each polynucleotide chain in DNA is analogous to a sugar-phosphate necklace (the backbone), from which hang the four types of beads (the bases A, C, G, and T).

Question 8

How does the way in which the nucleotides are linked together gives a DNA strand a chemical polarity?

Answer 8

If we think of each sugar as a block with a protruding knob (the 5ʹ phosphate) on one side and a hole (the 3ʹ hydroxyl) on the other, each completed chain, formed by interlocking knobs with holes, will have all of its subunits lined up in the same orientation. Moreover, the two ends of the chain will be easily distinguishable, as one has a hole (the 3ʹ hydroxyl) and the other a knob (the 5ʹ phosphate) at its terminus. 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.

Question 9

Why are all of the bases on the inside of the double helix?

Answer 9

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.

Question 10

How are the two strands of the double helix kept equidistant?

Answer 10

In each case, a bulkier two-ring base (a purine; A,G) is paired with a single-ring base (a pyrimidine; T,C): A always pairs with T, and G with C. This complementary base-pairing enables the base pairs to be packed in the energetically most favourable 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.

Question 11

What causes the twisting of the DNA helix and how frequently does it turn?

Answer 11

To maximise the efficiency of base-pair packing, the two sugar-phosphate backbones wind around each other to form a right-handed double helix, with one complete turn every ten base pairs

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- the sequences of nucleotides are thus complimentary

Question 12

The discovery of the structure of DNA immediately suggested answers to the two most fundamental questions about heredity. First, how could the information to specify an organism be carried in a chemical form? And second, how could this information be duplicated and copied from generation to generation?

How were these two questions answered?

Answer 12

The answer to the first question came from the realisation that DNA is a linear polymer of four different kinds of monomer, strung out in a defined sequence like the letters of a document written in an alphabetic script.

The answer to the second question came from the double-stranded nature of the structure: because each strand of DNA contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand, each strand can act as a template, or mould, for the synthesis of a new complementary strand. 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.

Question 13

What was left to figure out? Aka what was the issue ofthe genetic code?

Answer 13

The properties of a protein, which are responsible for its biological function, are determined by its three-dimensional structure. This structure is determined in turn by the linear sequence of the amino acids of which it is composed.

The linear sequence of nucleotides in a gene must therefore somehow spell out the linear sequence of amino acids in a protein. The exact correspondence between the four-letter nucleotide alphabet of DNA and the twenty-letter amino acid alphabet of proteins—the genetic code—is not at all obvious from the DNA structure, and it took over a decade after the discovery of the double helix before it was worked out.

Question 14

What is meant by the term genome?

Answer 14

The complete store of information in an organism’s DNA is called its genome, and it specifies all the RNA molecules and proteins that the organism will ever synthesise.

Question 15

Where is nearly all the DNA in eukaryotic cells sequestered?

Answer 15

Nearly all the DNA in a eukaryotic cell is sequestered in a nucleus, which in many cells occupies about 10% of the total cell volume.

Question 16

How is the nucleus separated from the rest of the cell?

Answer 16

This compartment is delimited by a nuclear envelope formed by two concentric lipid bilayer membranes. These membranes are punctured at intervals by large nuclear pores, through which molecules move between the nucleus and the cytosol.

Question 17

What is the nuclear envelope connected to and what supports it?

Answer 17

The nuclear envelope is directly connected to the extensive system of intracellular membranes called the endoplasmic reticulum, which extend out from it into the cytoplasm. And it is mechanically supported by a network of intermediate filaments called the nuclear lamina—a thin feltlike mesh just beneath the inner nuclear membrane

Question 18

What function does the nuclear envelope serve?

Answer 18

The nuclear envelope allows the many proteins that act on DNA to be concentrated where they are needed in the cell, and, as we see in subsequent chapters, it also keeps nuclear and cytosolic enzymes separate, a feature that is crucial for the proper functioning of eukaryotic cells.

Question 19

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. This is geometrically equivalent to packing 40 km (24 miles) of extremely fine thread into a tennis ball.

How is this achieved?

Answer 19

The complex task of packaging DNA is accomplished by specialised proteins that bind to the DNA and fold it, generating a series of organised coils and loops that provide increasingly higher levels of organisation, and prevent the DNA from becoming an unmanageable tangle.

Amazingly, although the DNA is very tightly compacted, it nevertheless remains accessible to the many enzymes in the cell that replicate it, repair it, and use its genes to produce RNA molecules and proteins.

Question 20

What does each chromosome in a eukaryotic cell consist of?

Answer 20

Each chromosome in a eukaryotic cell 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.

Question 21

In addition to the proteins involved in packaging, chromosomes are also associated with many other proteins. What are these required for?

Answer 21

These are required for the processes of gene expression, DNA replication, and DNA repair.

Question 22

What is meant by the term chromatin?

Answer 22

The complex of DNA and tightly bound protein is called chromatin

Question 23

How does DNA storage differ in bacteria compared to eukaryotes?

Answer 23

Bacteria lack a special nuclear compartment, and they generally carry their genes on a single DNA molecule, which is often circular

Question 24

Do bacteria have proteins associated with their DNA?

Answer 24

Yes, this DNA is also associated with proteins that package and condense it, but they are different from the proteins that perform these functions in eukaryotes. Although the bacterial DNA with its attendant proteins is often called the bacterial “chromosome,” it does not have the same structure as eukaryotic chromosomes, and less is known about how the bacterial DNA is packaged.

Question 25

What is common among all cells of the body bar a few exceptions (sperm, RBCs)

Answer 25

With the exception of the gametes (eggs and sperm) and a few highly special- ized cell types that cannot multiply and either lack DNA altogether (for example, red blood cells) or have replicated their DNA without completing cell division (for example, megakaryocytes), each human cell nucleus contains two copies of each chromosome, one inherited from the mother and one from the father.

Question 26

What is meant by the term homologs?

Answer 26

The maternal and paternal chromosomes of a pair are called homologous chromosomes (homologs)

Question 27

What are the only non-homologous pair of chromosomes?

Answer 27

The only nonhomologous chromosome pairs are the sex chromosomes in males, where a Y chromosome is inherited from the father and an X chromosome from the mother.

Question 28

Thus, how many chromosomes are present in each human cell?

Answer 28

Thus, each human cell contains a total of 46 chromosomes—22 pairs common to both males and females, plus two so-called sex chromosomes (X and Y in males, two Xs in females).

Question 29

What do the ‘bands’ often visualised on a chromosome correspond to?

Answer 29

traditional way to distinguish one chromosome from another
is to stain them with dyes (giemsa stain) that reveal a striking and reproducible pattern of bands along each mitotic chromosome. These banding patterns presumably reflect variations in chromatin structure, but their basis is not well understood. Nevertheless, the pattern of bands on each type of chromosome is unique, and it provided the initial means to identify and number each human chromosome reliably.

Question 30

What is meant by a karyotype?

Answer 30

The display of the 46 human chromosomes at mitosis is called the human karyotype. If parts of chromosomes are lost or are switched between chromosomes, these changes can be detected either by changes in the banding patterns or—with greater sensitivity—by changes in the pattern of chromosome painting (exposing the chromosomes to a large collection of DNA molecules whose sequence matches known DNA sequences, coupled to a different combination of fluorescent dyes, from the human genome)

Question 31

How is a gene often defined?

Answer 31

A gene is often defined as a segment of DNA that contains the instructions for making a particular protein (or a set of closely related proteins), but this definition is too narrow.

Question 32

Why is this definition too narrow?

Answer 32

Genes that code for protein are indeed the majority, and most of the genes with clear-cut mutant phenotypes fall under this heading. In addition, however, there are many “RNA genes”—segments of DNA that generate a functionally significant RNA molecule, instead of a protein, as their final product. We shall say more about the RNA genes and their products later.

Question 33

To what extent does the number of genes correspond to the complexity of an organism?

Answer 33

As might be expected, some correlation exists between the complexity of an organism and the number of genes in its genome. For example, some simple bacteria have only 500 genes, compared to about 30,000 for humans. Bacteria, archaea, and some single-celled eukaryotes, such as yeast, have concise genomes, consisting of little more than strings of closely packed genes.

However, the genomes of multicellular plants and animals, as well as many other eukaryotes, contain, in addition to genes, a large quantity of interspersed DNA whose function is poorly understood. Differences in the amount of DNA interspersed between genes, far more than differences in numbers of genes, account for the astonishing variations in genome size that we see when we compare one species with another.

Question 34

Why may there be so much of this non-coding DNA in multicellular organisms?

Answer 34

Some of this additional DNA is crucial for the proper control of gene expression, and this may in part explain why there is so much of it in multicellular organisms, whose genes have to be switched on and off according to complicated rules during development

Question 35

How conserved is the manner in which the genome is divided into chromosomes?

Answer 35

How the genome is divided into chromosomes also differs from one eukaryotic species to the next. For example, while the cells of humans have 46 chromosomes, those of some small deer have only 6, while those of the common carp contain over 100. Even closely related species with similar genome sizes can have very
different numbers and sizes of chromosomes

Question 36

How can species complexity be measured from genetics then?

Answer 36

There is no simple relationship between chromosome number, complexity of the organism, and total genome size. Rather, the genomes and chromosomes of modern-day species have each been shaped by a unique history of seemingly random genetic events, acted on by poorly understood selection pressures over long evolutionary times.

Question 37

Only a few percent of the human genome codes for proteins. What striking feature makes up around half of chromosomal DNA?

Answer 37

Transposable elements: Nearly half of the chromosomal DNA is made up of mobile pieces of DNA that have gradually inserted themselves in the chromosomes over evolutionary time, multiplying like parasites in the genome

Question 38

What is the average size of a gene and how much of this is usually used to code for a protein?

Answer 38

The average gene size is quite large—about 27,000 nucleotide pairs. A typical gene carries in its linear sequence of nucleotides the information for the linear sequence of the amino acids of a protein. Only about 1300 nucleotide pairs (exons) are required to encode a protein of average size (about 430 amino acids in humans). Most of the remaining sequence in a gene (introns) consists of long stretches of noncoding DNA that interrupt the relatively short segments of DNA that code for protein.

Question 39

In addition to introns and exons, what is each gene associated with?

Answer 39

In addition to introns and exons, each gene is associated with regulatory DNA sequences, which are responsible for ensuring that the gene is turned on or off at the proper time, expressed at the appropriate level, and only in the proper type of cell.