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DNA Replication, Recombination, Repair I

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Published on Oct 20, 2010

This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to http://ecampus.oregonstate.edu/ for the rest of the courses see http://www.youtube.com/playlist?list=...

Also check out the free textbook "Biochemistry Free and Easy" at: http://biochem.science.oregonstate.edu

1. DNA consists of a double helix. Each strand of the helix is a polymer of nucleotides joined together in phosphodiester linkages that have alternating sugar-phosphate-sugar-phosphate links. On the inside of the double helix are the complementary base pairs held together by hydrogen bonds. The arrangement of the double helix is in an 'anti-parallel' fashion, meaning that one strand oriented in the 5' to 3' direction is directly paired to a complementary strand oriented in the 3' to 5' direction. Phosphodiester bonds involve linkage between the 5' phosphate group of the incoming nucleotide and the 3' hydroxyl of the previous nucleotide in the chain.

2. DNA contains four bases - A,T,C, and G arranged with A paired with T and G paired with C on the internal portion of the double helix. Hydrogen bonds stabilize these base pairs - two for the A-T pair and three for the G-C pair. Thus, G-C pairs are harder to break than A-T pairs.

3. DNA has a major and a minor groove arising from asymmetric glycosidic linkages between the deoxyribose sugar and each base in the double helix.

4. DNA has three major forms - A,B, and Z. The A and B forms are right-handed helices, whereas the Z form is a left-handed helix. The B form of DNA is the most prevalent one and contains about 10.5 bases per turn of the helix.

5. Z-DNA may have roles in marking the location of genes in eukaryotic chromosomes.

6. Another DNA form is the A form (actually discovered by Rosalind Franklin), which is more "compressed" and is also a right handed helix. The A form is the form assumed by double strand RNA or RNA-DNA duplexes as well. RNA cannot exist in the B form due to steric hindrance arising from the oxygen on carbon number 2 of ribose, which is not present in the deoxyribose of DNA.

7. DNA consists of a double helix. Each strand of the helix is a polymer of nucleotides joined together in phosphodiester linkages that have alternating sugar-phosphate-sugar-phosphate links. On the inside of the double helix are the complementary base pairs held together by hydrogen bonds. The arrangement of the double helix is in an 'anti-parallel' fashion, meaning that one strand oriented in the 5' to 3' direction is directly paired to a complementary strand oriented in the 3' to 5' direction. Phosphodiester bonds involve linkage between the 5' phosphate group of the incoming nucleotide and the 3' hydroxyl of the previous nucleotide in the chain.

8. DNA contains four bases - A,T,C, and G arranged with A paired with T and G paired with C on the internal portion of the double helix. Hydrogen bonds stabilize these base pairs - two for the A-T pair and three for the G-C pair. Thus, G-C pairs are harder to break than A-T pairs.

9. The linking number (L) of a DNA is the sum of the number of twists (T) of a DNA plus the number of writhes (W). Thus, L = T + W. The twists are the number of times two the two helices cross each other. The writhe is the number of superhelical turns found in a DNA. Writhes can be positive or negative and in either case, when the W is a non-zero value, the molecule is said to be superhelical = to have superhelicity.

10. Writhing of DNA occurs in an attempt by a DNA molecule to "relax." A DNA molecule is relaxed when its number of base pairs (bp) per twist (T) is that of B-DNA (10.4-10.5 bp per turn). Thus, if one takes a circular DNA, opens it and removes two twists from it and then closes it, the number of twists will decrease, but the number of base pairs remains the same. In this case, the numbers of bp per twist will INCREASE. This causes a tension that is relieved by the DNA TWISTING two turns. This will cause the writhe to compensate by forming two negative superhelical turns, giving W a value of negative two. Note that the linking number remains the same.

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