1. Nucleic Acids and Protein Synthesis
Created By
Prof. Gary F. Porter, Ph.D.
Copyright © 2014 by John Wiley & Sons, Inc. All rights reserved.

2. Table of Contents (hyperlinked)
Introduction
Nucleotides and Nucleosides
3. Laboratory Synthesis of Nucleosides and Nucleotides
4. Deoxyribonucleic Acid: DNA
5. RNA and Protein Synthesis
6. Determining the Base Sequence of DNA: The Chain-Terminating (Dideoxynucleotide) Method
7. Laboratory Synthesis of Oligonucleotides
8. The Polymerase Chain Reaction
9. Sequencing of the Human Genome: An Instruction Book for the Molecules of Life
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Introduction
Nucleic acids carry genetic information in cells
DNA – deoxyribonucleic acids (2 deoxyribose)
RNA – Ribonucleic acids (ribose)
DNA has
two strands,
twisted ladder (α helix),
is antiparallel
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Introduction
23 pairs of chromosomes
30,000 to 35,000 genes
One gene – one protein
Chromosome 19 (to the right)
Four Nitrogenous Bases
Adenine
Cytosine
Thymine (Uracil in RNA)
Guanine
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2. Nucleotides and Nucleosides
Nucleotide hydrolysis yields
one of four heterocycles,
one of two pentoses, and
phosphate.
Nucleoside hydrolysis yields
heterocyclic base, and
pentose.
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2. Nucleotides and Nucleosides
Practice Problem 25.1
Write the structures of other tautomeric forms of adenine, guanine, cytosine, thymine, and uracil
Other uses of nucleotides and nucleosides
They are found in NADH, coenzyme A (enzymic cofactors).
Cyclic AMP is a hormone.
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3. Laboratory Synthesis of Nucleosides
and Nucleotides
A basic sugar and base moiety are coupled together.
Note Bz protective group
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3. Laboratory Synthesis of Nucleosides
and Nucleotides
A heterocyclic molecule is added to a protected ribosylamine.
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3. Laboratory Synthesis of Nucleosides
and Nucleotides
A chlorinated heterocyclic nucleoside can be modified.
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3. Laboratory Synthesis of Nucleosides
and Nucleotides
A nucleoside is converted to a nucleotide.
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3. Laboratory Synthesis of Nucleosides
and Nucleotides
3A. Medical Applications
6-Mercaptopurine is used to treat acute leukemia.
Allopurinol is used to treat gout.
Acyclovir is used to treat herpes virus.
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4. Deoxyribonucleic Acid: DNA
4A. Primary Structure
Links occur on the 3’ OH and 5’ OH of the pentose
Phosphate between the pentoses.
Termini for the strands are
3’ OH and
5’ OH.
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4. Deoxyribonucleic Acid: DNA
4B. Secondary Structure
Chargaff’s Rules
(%G + %A)
(%C + %T)
%A/%T
% G/%C
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4. Deoxyribonucleic Acid: DNA
4B. Secondary Structure
X-Ray Crystallography confirmed presence of the repeating units.
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4. Deoxyribonucleic Acid: DNA
4C Replication of DNA
Involves three key ingredients:
DNA template
DNA product
DNA polymerase
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5. RNA and Protein Synthesis
5A. Messenger RNA Synthesis – Transcription
Involves three key ingredients:
DNA – Template,
mRNA – product, and
RNA Polymerase.
DNA  RNA  protein
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5. RNA and Protein Synthesis
5B. Ribosomes – rRNA
Protein synthesis is catalyzed by ribosomes.
Ribosomal parts include a
30S subunit – binding mediation site, and
50S subunit – catalytic site.
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5. RNA and Protein Synthesis
5C. Transfer RNA
20 tRNA exist
One for each amino acid
Make up of tRNA
70 to 90 monomeric units,
and has four folds.
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5. RNA and Protein Synthesis
The Genetic Code
One AA per Codon
Codon is a triplet
Duplicates exist
Primer AA is N-formylmethionine
Chapter 25, P 1125
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5. RNA and Protein Synthesis
5D. The Genetic Code
DNA is transcribed to an antisense DNA.
Antisense DNA is transcribed to mRNA.
DNA code = mRNA code
mRNA is translated to Amino Acids / Protein.
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5. RNA and Protein Synthesis
Translation
Involves three key ingredients
mRNA Template,
tRNA, and
Amino Acids/Protein product.
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5. RNA and Protein Synthesis
Practice Problem 25.10
Practice Problem 25.11
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6. Determining the Base Sequence of DNA: The
Chain-Terminating (Dideoxynucleotide) Method
Restriction Endonucleases
Cleave double stranded DNA, and
Are space sequence specific.
AluI – cleaves AG/CT
No sticky end
EcoR1 – cleaves G/AATTC
Has a sticky end
Forms a palindrome segment. – AATT--- / /
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6. Determining the Base Sequence of DNA: The
Chain-Terminating (Dideoxynucleotide) Method
6A. DNA Sequencing by the Chain-Terminating (Dideoxynucleotide) Method
Unnatural Nucleotides with Markers
Are used as unnatural terminators
The dye is attached to the heterocyclic ring.
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6. Determining the Base Sequence of DNA: The
Chain-Terminating (Dideoxynucleotide) Method
6A. DNA Sequencing by the Chain-Terminating (Dideoxynucleotide) Method
Gel Electrophoresis is
earlier method,
size & charge separation, and
slower.
Capillary Electrophoresis is
current method,
size separation, and
faster.
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7. Laboratory Synthesis of Oligonucleotides
Antisense Oligonucleotides
bind to crucial sequences in viral DNA or RNA.
Prevents viral replication
are used as primers in synthetic DNA synthesis
Automated synthesizers are used. These are similar in design to those used for protein synthesis.
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8. The Polymerase Chain Reaction
Amplification of DNA Molecule
Uses DNA polymerase and Thermal Cycler Device.
Small amount of starting material (picogram) is used.
One key use is to diagnose genetic-related diseases by amplifying and characterizing DNA sequences.
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8. The Polymerase Chain Reaction
Thermophilic bacteria are used to speed up the reaction. The entire process can be done at elevated temperatures.
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9. Sequencing of the Human Genome:
An Instruction Book for the Molecules of Life
Human Genome Project
All human genes (35,000) have been mapped out.
Only a small % of the genes is understood.
This research is useful for
testing DNA for potential genetic disorders,
engineering proteins based upon knowledge of identified protein, and
synthesizing drugs from database enzymes.
© 2014 by John Wiley & Sons, Inc. All rights reserved.