errata 23862

modules/m62828/index.cnxml

@@ -73,7 +73,7 @@
 </exercise>
 
 </note><para id="fs-id1385221">The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5' to 3' direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5' to 3' direction and the other is oriented in the 3' to 5' direction. One strand, which is complementary to the 3' to 5' parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the <term id="term-00006">leading strand</term>. The other strand, complementary to the 5' to 3' parental DNA, is extended away from the replication fork, in small fragments known as <term id="term-00007">Okazaki fragments</term>, each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the <term id="term-00008">lagging strand</term>.</para>
-<para id="fs-id2962574">The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. A protein called the <term id="term-00009">sliding clamp</term> holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. <term id="term-00010">Topoisomerase</term> prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the exonuclease activity of DNA pol I, and the gaps are filled in by deoxyribonucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA <term id="term-00011">ligase</term> that catalyzes the formation of phosphodiester linkage between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment.</para>
+<para id="fs-id2962574">The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. A protein called the <term id="term-00009">sliding clamp</term> holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. <term id="term-00010">Topoisomerase</term> prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the <term id="term-00012">exonuclease</term> activity of DNA pol I, and the gaps are filled in by deoxyribonucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA <term id="term-00011">ligase</term> that catalyzes the formation of phosphodiester linkage between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment.</para>
 <para id="fs-id1752302">Once the chromosome has been completely replicated, the two DNA copies move into two different cells during cell division. The process of DNA replication can be summarized as follows:</para>
     <list id="fs-id2017788" list-type="enumerated">
 <item>DNA unwinds at the origin of replication.</item>
@@ -214,6 +214,7 @@ The enzyme likely to be mutated is DNA ligase, which seals the gaps between the
 </section>
  </content>
 <glossary>
+    <definition id="def-00001"><term>exonuclease</term><meaning>enzymes that cleave nucleotides one at a time from the end of a polynucleotide chain</meaning></definition>
 <definition id="fs-id1635058"><term>helicase</term> <meaning id="fs-id1407439">during replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds</meaning></definition>
 <definition id="fs-id1479286"><term>lagging strand</term> <meaning id="fs-id1715240">during replication, the strand that is replicated in short fragments and away from the replication fork</meaning></definition>
 <definition id="fs-id1442893"><term>leading strand</term> <meaning id="fs-id1506798">strand that is synthesized continuously in the 5'-3' direction which is synthesized in the direction of the replication fork</meaning></definition>

modules/m66390/index.cnxml

@@ -25,7 +25,7 @@
 Credit: Rao, A., Ryan, K. Fletcher, S. and Tag, A. Department of Biology, Texas A&amp;M University.</caption></figure></para>
 <para id="fs-id1368727">Question: You isolate a cell strain in which the joining of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?</para>
 </note><para id="fs-id1385221">The replication fork moves at the rate of 1000 nucleotides per second. Topoisomerase prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. Because DNA polymerase can only extend in the 5' to 3' direction, and because the DNA double helix is <emphasis effect="italics">antiparallel</emphasis>, there is a slight problem at the replication fork. <emphasis effect="italics">The two template DNA strands have opposing orientations:</emphasis> one strand is in the 5' to 3' direction and the other is oriented in the 3' to 5' direction. Only one new DNA strand, the one that is complementary to the 3' to 5' parental DNA strand, can be synthesized continuously towards the replication fork. This continuously synthesized strand is known as the <term id="term-00004">leading strand</term>. The other strand, complementary to the 5' to 3' parental DNA, is extended away from the replication fork, in small fragments known as <term id="term-00005">Okazaki fragments</term>, each requiring a primer to start the synthesis. New primer segments are laid down in the direction of the replication fork, but each pointing away from it. (Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the <term id="term-00006">lagging strand</term>.)</para>
-<para id="fs-id2962574">The leading strand can be extended from a single primer, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. A protein called the <term id="term-00007">sliding clamp</term> holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the exonuclease activity of DNA pol I, which uses DNA behind the RNA as its own primer and fills in the gaps left by removal of the RNA nucleotides by the addition of DNA nucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA <term id="term-00008">ligase</term>, which catalyzes the formation of phosphodiester linkages between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment.</para>
+<para id="fs-id2962574">The leading strand can be extended from a single primer, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. A protein called the <term id="term-00007">sliding clamp</term> holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the <term id="term-00009">exonuclease</term> activity of DNA pol I, which uses DNA behind the RNA as its own primer and fills in the gaps left by removal of the RNA nucleotides by the addition of DNA nucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA <term id="term-00008">ligase</term>, which catalyzes the formation of phosphodiester linkages between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment.</para>
 <para id="fs-id1752302">Once the chromosome has been completely replicated, the two DNA copies move into two different cells during cell division.</para>
 <para id="fs-id1753302">The process of DNA replication can be summarized as follows:</para>
     <list id="fs-id2017788" list-type="enumerated">
@@ -185,6 +185,7 @@ Credit: Rao, A., Ryan, K. Fletcher, S. and Tag, A. Department of Biology, Texas
 </section>
  </content>
 <glossary>
+  <definition id="def-00001"><term>exonuclease</term><meaning>enzymes that cleave nucleotides one at a time from the end of a polynucleotide chain</meaning></definition>
 <definition id="fs-id1635058"><term>helicase</term> <meaning id="fs-id1407439">during replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds</meaning></definition>
 <definition id="fs-id1479286"><term>lagging strand</term> <meaning id="fs-id1715240">during replication, the strand that is replicated in short fragments and away from the replication fork</meaning></definition>
 <definition id="fs-id1442893"><term>leading strand</term> <meaning id="fs-id1506798">strand that is synthesized continuously in the 5'-3' direction, which is synthesized in the direction of the replication fork</meaning></definition>

modules/m66391/index.cnxml

@@ -35,7 +35,7 @@
 </tbody>
 </tgroup>
 </table>
-<para id="fs-id2018337">A helicase using the energy from ATP hydrolysis opens up the DNA helix. Replication forks are formed at each replication origin as the DNA unwinds. The opening of the double helix causes over-winding, or supercoiling, in the DNA ahead of the replication fork. These are resolved with the action of topoisomerases. Primers are formed by the enzyme primase, and using the primer, DNA pol can start synthesis. Three major DNA polymerases are then involved: α, δ and ε. DNA pol α adds a short (20 to 30 nucleotides) DNA fragment to the RNA primer on both strands, and then hands off to a second polymerase. While the leading strand is continuously synthesized by the enzyme pol <emphasis effect="italics">ε</emphasis>, the lagging strand is synthesized by pol <emphasis effect="italics">δ</emphasis>. A sliding clamp protein known as PCNA (proliferating cell nuclear antigen) holds the DNA pol in place so that it does not slide off the DNA. As pol δ runs into the primer RNA on the lagging strand, it displaces it from the DNA template. The displaced primer RNA is then removed by RNase H (AKA flap endonuclease) and replaced with DNA nucleotides. The Okazaki fragments in the lagging strand are joined after the replacement of the RNA primers with DNA. The gaps that remain are sealed by DNA ligase, which forms the phosphodiester bond.</para>
+<para id="fs-id2018337">A helicase using the energy from ATP hydrolysis opens up the DNA helix. Replication forks are formed at each replication origin as the DNA unwinds. The opening of the double helix causes over-winding, or supercoiling, in the DNA ahead of the replication fork. These are resolved with the action of topoisomerases. Primers are formed by the enzyme primase, and using the primer, DNA pol can start synthesis. Three major DNA polymerases are then involved: α, δ and ε. DNA pol α adds a short (20 to 30 nucleotides) DNA fragment to the RNA primer on both strands, and then hands off to a second polymerase. While the leading strand is continuously synthesized by the enzyme pol <emphasis effect="italics">ε</emphasis>, the lagging strand is synthesized by pol <emphasis effect="italics">δ</emphasis>. A sliding clamp protein known as PCNA (proliferating cell nuclear antigen) holds the DNA pol in place so that it does not slide off the DNA. As pol δ runs into the primer RNA on the lagging strand, it displaces it from the DNA template. The displaced primer RNA is then removed by RNase H (AKA flap <term id="term-00002">endonuclease</term>) and replaced with DNA nucleotides. The Okazaki fragments in the lagging strand are joined after the replacement of the RNA primers with DNA. The gaps that remain are sealed by DNA ligase, which forms the phosphodiester bond.</para>
 <section id="fs-id1272063">
 <title>Telomere replication</title>
 <para id="fs-id2030086">Unlike prokaryotic chromosomes, eukaryotic chromosomes are linear. As you’ve learned, the enzyme DNA pol can add nucleotides only in the 5' to 3' direction. In the leading strand, synthesis continues until the end of the chromosome is reached. On the lagging strand, DNA is synthesized in short stretches, each of which is initiated by a separate primer. When the replication fork reaches the end of the linear chromosome, there is no way to replace the primer on the 5’ end of the lagging strand. The DNA at the ends of the chromosome thus remains unpaired, and over time these ends, called <emphasis effect="bold">telomeres,</emphasis> may get progressively shorter as cells continue to divide.</para>
@@ -102,6 +102,7 @@
 </section>
  </content>
 <glossary>
+<definition id="def-00001"><term>endonuclease</term><meaning>enzymes that cleave the phosphodiester bond within a polynucleotide chain</meaning></definition>
 <definition id="fs-id1808238"><term>telomerase</term> <meaning id="fs-id1780142">enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends</meaning></definition>
 <definition id="fs-id2642866"><term>telomere</term> <meaning id="fs-id1406190">DNA at the end of linear chromosomes</meaning></definition>
 </glossary>