SURVEY OF BIOCHEMISTRY Nucleic Acids

Week #1 CHEM 3511 - Summer 2008 1

SURVEY OF BIOCHEMISTRY

Nucleic Acids


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


PRS Question

• Which is not found in DNA?

1. Thymine2. 2’-OH on pentose3. 3’-OH on pentose4. Phosphodiester bond


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


Nucleic Acids

• Basics of Nucleic Acid Structure

• Supercoiling & Topoisomerases

• RNA Structure

• Recombinant DNA Technology


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?


Rotational Degrees of Freedom

Glycosidic Bond

Only 2 permissible conformations of base:

syn or anti


Glycosidic Bond Conformations

“Anti” conformation is most stablein B-DNA and A-DNA


Sugar Pucker

B-DNA has a C2’-endo conformation…


Sugar Pucker

A-DNA has a C3’-endo conformation…


DNA Supercoiling

Increasing supercoiling


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


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


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


Where do we observe supercoiling of DNA?


Topoisomerases

• Topoisomerases are enzymes that cleave DNA, thereby relieving supercoiling tension.

– Type 1A: ss breaks

– Type 1B: ss breaks

– Type 2: ds breaks


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


Transfer RNA Structures

Carnegie Mellon U. NIH


Ribosomal RNA Structures

Frog5S rRNASubunit


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


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


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

http://www.ipn.uni-kiel.de/aktuell/ipnblatt/ip400/ip400b02.gif


How does PCR work?

One PCR Cycle:

SURVEY OF BIOCHEMISTRY Nucleic Acids

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