Download - SURVEY OF BIOCHEMISTRY Nucleic Acids
![Page 1: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/1.jpg)
Week #1 CHEM 3511 - Summer 2008 1
SURVEY OF BIOCHEMISTRY
Nucleic Acids
![Page 2: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/2.jpg)
Week #1 CHEM 3511 - Summer 2008 2
PRS Question
• Which statement is INCORRECT?
1. B-DNA is double helical2. In DNA, two H-bonds form between
adenine and thymine3. In DNA, molar amounts of A+T = molar
amounts of G+C 4. DNA strands run antiparallel to each
other
![Page 3: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/3.jpg)
Week #1 CHEM 3511 - Summer 2008 3
PRS Question
• Which is not found in DNA?
1. Thymine2. 2’-OH on pentose3. 3’-OH on pentose4. Phosphodiester bond
![Page 4: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/4.jpg)
Week #1 CHEM 3511 - Summer 2008 4
PRS Question
• The link between the adenine base and the ribose sugar occurs:
1. From N1 of A to the C1’ of ribose2. From N3 of A to the C1’ of ribose3. From N7 of A to the C1’ of ribose4. From N9 of A to the C1’ of ribose
![Page 5: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/5.jpg)
Week #1 CHEM 3511 - Summer 2008 5
Nucleic Acids
• Basics of Nucleic Acid Structure
• Supercoiling & Topoisomerases
• RNA Structure
• Recombinant DNA Technology
![Page 6: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/6.jpg)
Week #1 CHEM 3511 - Summer 2008 6
Limitations to DNA Flexibility
• Glycosidic Bond
• Sugar Pucker
• Sugar-Phosphate Backbone
What is a torsion angle and how does it play a role in biomolecular
structure?
![Page 7: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/7.jpg)
Week #1 CHEM 3511 - Summer 2008 7
Rotational Degrees of Freedom
Glycosidic Bond
Only 2 permissible conformations of base:
syn or anti
![Page 8: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/8.jpg)
Week #1 CHEM 3511 - Summer 2008 8
Glycosidic Bond Conformations
“Anti” conformation is most stablein B-DNA and A-DNA
![Page 9: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/9.jpg)
Week #1 CHEM 3511 - Summer 2008 9
Sugar Pucker
B-DNA has a C2’-endo conformation…
![Page 10: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/10.jpg)
Week #1 CHEM 3511 - Summer 2008 10
Sugar Pucker
A-DNA has a C3’-endo conformation…
![Page 11: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/11.jpg)
Week #1 CHEM 3511 - Summer 2008 11
DNA Supercoiling
Increasing supercoiling
![Page 12: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/12.jpg)
Week #1 CHEM 3511 - Summer 2008 12
DNA Supercoiling
L = T + W
Linking Number (L)
Number of times one strand crosses another strand
Here the red strand of DNA crossesthe blue strand of DNA 10 times
L = 10
![Page 13: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/13.jpg)
Week #1 CHEM 3511 - Summer 2008 13
DNA Supercoiling
L = T + W
Twist (T)
Number of times one strand makes a complete revolution about the helical axis.
Here the red strand of DNA makes 10 revolutions about the helical axis
T = 10
![Page 14: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/14.jpg)
Week #1 CHEM 3511 - Summer 2008 14
DNA Supercoiling
L = T + W
Writhe (W)
Number of times a duplex makes a complete revolution about itself.
Counterclockwise turns are negativeClockwise turns are positive
W = 0
![Page 15: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/15.jpg)
Week #1 CHEM 3511 - Summer 2008 15
Where do we observe supercoiling of DNA?
![Page 16: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/16.jpg)
Week #1 CHEM 3511 - Summer 2008 16
Topoisomerases
• Topoisomerases are enzymes that cleave DNA, thereby relieving supercoiling tension.
– Type 1A: ss breaks
– Type 1B: ss breaks
– Type 2: ds breaks
![Page 17: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/17.jpg)
Week #1 CHEM 3511 - Summer 2008 17
Types of RNA
Messenger RNA - carries genetic information for protein synthesis
Transfer RNA - covalently binds amino acids corresponding to its anticodon sequence
Ribosomal RNA - RNA molecules that play a role in protein synthesis in conjugate with ribosomal proteins
![Page 18: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/18.jpg)
Week #1 CHEM 3511 - Summer 2008 18
Transfer RNA Structures
Carnegie Mellon U. NIH
![Page 19: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/19.jpg)
Week #1 CHEM 3511 - Summer 2008 19
Ribosomal RNA Structures
Frog5S rRNASubunit
![Page 20: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/20.jpg)
Week #1 CHEM 3511 - Summer 2008 20
Recombinant DNA Technology
• Goal: Introduce foreign gene into a host organism
– Reproduction of the gene or gene product
– Function of the new gene product on the host
– Players: Gene insert, host, vector used to carry gene into host
![Page 21: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/21.jpg)
Week #1 CHEM 3511 - Summer 2008 21
Gene Insert
• Genomic DNA– All of the DNA carrying genetic information
for normal functioning of an organism
• cDNA– DNA copied from mRNA
• PCR – DNA that has been copied from a template
in a polymerase chain reaction
![Page 22: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/22.jpg)
Week #1 CHEM 3511 - Summer 2008 22
What is Polymerase Chain Reaction (PCR)?
• In vitro DNA synthesis
– Components include: • Heat-stable DNA polymerase (Taq polymerase)• Two Primers (DNA oligonucleotides)• Deoxynucleotides –dATP, dTTP, dCTP, dGTP• DNA template • Mg++, buffer components, and water
![Page 23: SURVEY OF BIOCHEMISTRY Nucleic Acids](https://reader035.vdocuments.us/reader035/viewer/2022062221/56814764550346895db4a1df/html5/thumbnails/23.jpg)
Week #1 CHEM 3511 - Summer 2008 23
How does PCR work?
One PCR Cycle: