Chapter 16: The Molecular Basis of Inheritance

The idea that there is a specific pairing of __in DNA was the flash of inspiration that led __ and __to the correct __.
At the same time, they saw the functional significance of the base-pairing rules.

The two strands of DNA are __; each stores the information necessary to reconstruct the other.
When a cell copies a DNA molecule, each strand serves as a __for ordering __into a new, complementary strand.

__line up along the __strand according to the __and are linked to form the new strands.
Where there was one double-stranded DNA molecule at the beginning of the process, there are soon two, each an exact replica of the “parent” molecule.
This model of DNA replication remained untested for several years following publication of the DNA structure.

__ predicts that when a __ replicates, each of the two daughter molecules will have one old strand.
· This __ can be distinguished from a __, in which the two parent strands somehow come back together after the process (that is, the parent molecule is conserved.)

In the __, all four strands of DNA following replication have a mixture of old and new DNA. Although mechanisms for conservative or dispersive DNA replication are not easy to devise, these models remained possibilities until they could be ruled out.

__d evised a clever experiment that distinguished between the three models. Their experiment supported the __ of DNA replication.

Each of your cells has __ DNA molecules in its nucleus, one long double-helical molecule per chromosome.
More than a dozen enzymes and other proteins participate in DNA replication.

The replication of a DNA molecule begins at special sites called __, short stretches of DNA having a specific sequence of nucleotides.
· Proteins that initiate __ recognize this sequence and attach to the DNA, separating the two strands and opening up a replication “__.” Replication of DNA then proceeds in both directions until the entire molecule is copied.

In contrast to a bacterial chromosome, a eukaryotic chromosome may have hundreds or even a few thousand replication origins. Multiple replication __ form and eventually fuse, thus speeding up the copying of the very long DNA molecules.
-As in bacteria, eukaryotic DNA replication proceeds in both directions from each __.

At each end of a replication bubble is a __, a Y-shaped region where the parental strands of DNA are being unwound.

Several kinds of proteins participate in the unwinding.
o __are enzymes that untwist the double helix at the __, separating the two parental strands and making them available as template strands.

After the parental strand separation, __bind to the unpaired DNA strands, stabilizing them. The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork.
o __helps relieve this strain by breaking, swiveling, and rejoining DNA strands.

The unwound sections of the parental DNA strands are now available to serve as __for the synthesis of new complementary DNA strands. However, the enzymes that synthesize DNA cannot initiate the synthesis of a __; they can only add __ to the end of an already existing chain that is base-paired with the __strand.
o This RNA chain is called a __and is synthesized by the enzyme __.

__starts an RNA chain from a single __ , adding __, one at a time, using the parental DNA strand as a template. The completed __, generally 5 to 10 nucleotides long, is thus base-paired to the template strand. The new DNA strand will start from the 3’ end of the __.

Enzymes called __catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain.
· In E. coli, there are several different __, but two appear to play the major roles in DNA replication: __ and __

Most __ require a __and a DNA template strand, along which complementary DNA nucleotides line up.

In E. coli, __adds a DNA nucleotide to the __and then continues adding DNA nucleotides, complementary to the parental DNA template strand, to the growing end of the new DNA strand. The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells.

Each nucleotide added to a growing DNA strand comes from a __, which is a __ with __
· Similar to ATP.
-----------Difference between the ATP of energy metabolism and __, the __that supplies an __to DNA, is the sugar component which is __in the building block of DNA, but __in ATP.
· Like ATP, the __ used for DNA synthesis are chemically reactive, partly because their triphosphate tails have an unstable cluster of negative charge.

As each monomer joins the growing end of a DNA strand, two __ are lost as a molecule of __. Subsequent hydrolysis of the __to two molecules of __is a coupled exergonic reaction that helps drive the __reaction.

The two strands of DNA in a double helix are __, meaning that they are oriented in opposite directions to each other.
· Clearly, the two new strands formed during DNA replication must also be __to their template strands.

How does the antiparallel arrangement of the double helix affect replication? (don't answer)
· Because of their structure, __ can add nucleotides only to the free 3’ end of a __or growing DNA strand, never to the 5’ end.
· Thus, a new DNA strand can elongate only in the __direction.

Reexamining the __:
o Along one template strand, __ can synthesize a complementary strand continuously by elongating the new DNA in the mandatory __ direction. __ simply nestles in the __on that template strand and continuously adds nucleotides to the new complementary strand as the fork progresses.
o The DNA strand made by this mechanism is called the __. Only one __is required for __to synthesize the __.

To elongate the other new strand of DNA in the mandatory __direction, __ must work along the other template strand in the direction away from the __. The DNA strand elongating in this direction is called the __.

In contrast to the __, which elongates continuously, the __is synthesized discontinuously, as a series of segments.
§ These segments of the lagging strand are called __.
· The fragments are about 1000-2000 nucleotides long in E. coli and about 100-200 long in eukaryotes.

Whereas only one __is required on the __, each __on the __must be primed separately. Another DNA polymerase, __, replaces the RNA nucleotides of the __with DNA versions, adding them one by one onto the 3’ end of the adjacent __.
§ __ can’t join the final nucleotide of this replacement DNA segment to the first DNA nucleotide of the __ whose primer was just replaced.
§ Another enzyme, __, accomplishes this task, joining the sugar-phosphate backbones of all the __into a continuous DNA strand.

Representing DNA polymerase as locomotives moving along a DNA railroad track is inaccurate in two ways. What are they?
-->Many protein-protein interactions facilitate the efficiency of this complex.
-->In eukaryotic cells, multiple copies of the complex, perhaps grouped in to “factories” may be anchored to the nuclear matrix, a framework of fibers extending through the interior of the nucleus.

Recent studies support a model in which two __molecules, one on each template strand, “reel in” the parental DNA and extrude newly made daughter DNA molecules. Additional evidence suggests that the __is looped back through the complex, so that when a __ completes synthesis of an __ and dissociates, it doesn’t have far to travel to reach the __for the next fragment, near the __.
· This looping of the __ enables more __to be synthesized in less time.

Initial pairing errors between incoming nucleotides and those in the template strand are 100,000 x more common- an error rate of one in 100,000 nucleotides.
· During DNA replication, __ proofread each nucleotide against its template as soon as it is added to the growing strand.
· Upon finding an incorrectly paired nucleotide, the __removes the nucleotide and then resumes synthesis.

Mismatched nucleotides sometimes evade proofreading by a __.

In __, enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors.
Incorrectly paired or altered nucleotides can also arise after replication.
In fact, __of the genetic information encoded in DNA requires frequent repair of various kinds of damage to existing DNA.

DNA molecules are constantly subjected to potentially harmful chemical and physical agents.
· Reactive chemicals, radioactive emissions, X-rays, UV light, and certain molecules in cigarette smoke can change nucleotides in ways that affect encoded __.
· In addition, __often undergo spontaneous chemical changes under normal cellular conditions. However, these changes in DNA are unusually corrected before they become __perpetuated through successive replications. Each cell continuously monitors and repairs its genetic material.

True or False:
Because repair of damaged DNA is so important to the survival of an organism, it is no surprise that many different DNA repair enzymes have evolved.
True False

True or False:
Most cellular systems for repairing incorrectly paired nucleotides, whether they are due to DNA damage or to replication errors, use a mechanism that takes advantage of the base-paired structure of DNA.
True False

Often, a segment of the strand containing the damage is cut out (__) by a DNA-cutting enzyme- a __- and the resulting gap is then filled in with nucleotides, using the undamaged strand as a template. The enzymes involved in filling the gap are a DNA __ and __. One such DNA repair system is called __.

An important function of the __ in our skin cells is to repair genetic damage caused by the UV rays of sunlight.
· One type of damage is the covalent linking of thymine bases that are adjacent on a DNA strand.
o Such __cause the DNA to buckle and interfere with DNA replication.

importance of repairing this kind of damage (thymine dimers) is underscored by the disorder xeroderma pigmentosum, which in most cases is caused by an inherited defect in a __
§ Individuals with this disorder are hypersensitive to sunlight; mutations in their skin cells cause skin cancer.

There is a small portion of the cell’s DNA that __can neither replicate nor repair.
For linear DNA, the fact that a __ can add nucleotides only to the 3; end of a preexisting polynucleotide leads to an apparent problem.

A Problem:
The usual replication machinery provides no way to complete the 5’ ends of daughter DNA strands. Even if an __can be started with an __ bound to the very end of the template strand, once that primer is removed, it cannot be replaced with DNA because there is no 3’ end available for nucleotide addition.
· As a result, repeated rounds of replication produce shorter and shorter DNA molecules with uneven ends.

True or False:
The shortening of DNA doesn’t occur in most prokaryotes because their DNA is circular and has no ends.
True False

What protects the genes of eukaryotes from being eroded away during successive rounds of DNA replication?
· It turns out that eukaryotic chromosomal DNA molecules have special nucleotide sequences called __ at their ends.
o __do not contain genes; instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence. __protects the organism’s genes.

In addition, the specific proteins associated with __ prevent the staggered ends of the daughter molecule from activating the cell’s systems for monitoring DNA damage. (Staggered ends of a DNA molecule, which often result from double-strand breaks, can trigger STP leading to cell cycle arrest or cell death.)

__ do not prevent the shortening of DNA molecules due to successive rounds of replication; they just postpone the __ of genes near the ends of DNA molecules.
· __ become shorter during every round of replication. __ does tend to be shorter in dividing __ of older individuals and in cultured cells that have divided many times.
o It has been proposed that shortening of __ is somehow connected to the aging process.

What about the cells whose genomes must persist unchanged form an organism to its offspring over many generations?
· If the chromosomes of germ cells (which give rise to gametes) became shorter in every __, essential genes would eventually be missing from the gametes they produce.
· This does not occur: an enzyme called __ catalyzes the lengthening of __ in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication.
o Not active in most human somatic cells, but its activity in germ cells results in __ of maximum length in the zygote.

Normal shortening of __ may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo.
· Cells from large tumors often have unusually short __.
· Further shortening would presumably lead to self- destruction of the tumor cells.

Researchers have found __ activity in cancerous somatic cells, suggesting that its ability to stabilize __ length may allow these cancer cells to persist.
Many cancer cells do seem capable of unlimited cell division, as do immortal strains of cultured cells.
If __ is indeed an important factor in many cancers, it may provide a useful target for both cancer diagnosis and chemotherapy.