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Chapter 5: Introduction to the Nucleic Acids
DNA, RNA, and the Flow of Genetic Information
• DNA and RNA are long polymers– Carry information that is passed on to the next
generation
• Genetic information is stored in the sequence of bases along a nucleic acid chainbases along a nucleic acid chain
• Base pairing occurs• Base pairs provide the mechanism for copying
the genetic information in an existing nucleic acid chain to form a new chain.
Central Dogma of Information Flow
• DNA RNA Protein Function
DNAWhat is this?
What is this? What is this? What is this?
The Genetic Code is Crucial!
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General Schematic of a Nucleic Acid polymer.
Sugar gDifferences
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Nitrogen Bases in the Nucleic Acids
Making a Nucleoside
N-glycosidic bond
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Nucleosides• Combining Nitrogen bases with sugars
• RNA– Adenosine– GuanosineGuanosine– Cytidine– Uridine
• DNA– Deoxy- prefix– Thymidine
Making a Nucleotide
Adding a phosphate to the nucleoside structure.
Nucleotide Nomenclature
• 5’- nucleoside phosphate
• 5’- nucleotide
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Adenosine 5’-triphosphate
A.K.A
3’- deoxyguanosine monophosphate
Tedious Method to show the polymer…
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Short-Hand Method to show the polymer
• P-5’ACG 3-OH
• By convention: nucleic acid polymers are always written with the 5’ end to the left and the 3’end to the right
The Very Short-Hand Method to show the polymer
and the 3 end to the right.
• Polarity to these molecules 5’ 3’
• ACG is DIFFERENT than GCA
Anatomy of the DNA helix
Launch animation
http://www.johnkyrk.com/DNAanatomy.html
Visit this link as a study guide!!!
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• Prokaryotes– Contain genes (coding regions)
– Control areas (regulatory regions)
• Eukaryotes
Billions of nucleotides join to form Genomes.
y– Contain genes (coding regions)
– Control areas (regulatory regions)
– “Useless” stretches of DNA (noncoding regions)
• Introns – intervening sequences in DNA
• Exons - are the coding regions in Eukaryotes.
An E. coli’s genome
d!exposed!
• A 1950’s Race
• Maurice Wilkins and Rosalind Franklin
• James Watson and Francis Crick
Structure of DNA
– Building a structural model from scientific data and hypotheses!
– Read their Paper!!! (link is on the class website)
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X-ray Diffraction of DNA…Rosalind Franklin’s
Data
• 1. two helical polynucleotides coiled around a common axis
• 2. The sugar-phosphate backbones are on the outside and the bases lie on the
Watson-Crick Model from the data
on the outside and the bases lie on the inside
• 3. bases are perpendicular to the axis of the helix. 34 Angstrom repeat 10 bases/turn (bases separated by 3.4 Ang.)
• 4. diameter is 20 Angstroms.
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Chargaff’s Results on Nucleotide Ratios
Paper, scissors, and Hydrogen
Bonds…
The secret of the Base Pairs!
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Nitrogen “Base Stacking”
helps stabilizestabilize the helix.
Weak forces…
• Copies are made of the DNA before each MITOSIS event.
• The enzyme that copies the DNA for the daughter cells is called DNA
Genetic Molecule
daughter cells is called DNA polymerase– For humans, 3 billion bases have to be
copied to form the new strands of DNA
– Very rapid, very accurate…
– Only 1 mistake in every 1 million base pairs.
What was the mechanism of DNA Replication?
• Possibilities– Conservative
– Semiconservative
H fi d t?• How can you find out?
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Semi-Conservative Replication Model…
Meselson and Stahl Experiment
Animation link: http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html#
Density Gradient equilibrium Sedimentation
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Heavy N-15 isotopelight N-14 isotope
Hybrid…1/2 Heavy…½ light.
Semi-Conservative Replication
Uses the following amazing enzymes:
1. Helicases/topoisomersase – help to open up the double helix
2. RNA primase – lays down a short RNA primer to id li ti ith 3’ OHprovide replication enzymes with a 3’-OH.
3. DNA polymerase – builds off of the RNA primers to incorporate nucleotide triphosphates into the new daughter strands….both quickly and accurately!
4. Exonucleases – Removes the RNA primer from the daughter strands
5. Ligase – will fill in the gaps and establish a new phosphodiester linkage between the neighboring DNA fragments making all of the separate fragments one continuouse nucleic acid strand.
Semi-Conservative Replication in
Action!Animation of DNA Replicationp
http://www.johnkyrk.com/DNAreplication.html
Another animation of DNA replication
Another animation of DNA replication
REALLY COOL ANIMATION OF DNA PACKAGING AND REPLICATION!
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Hypochroism f DNAof DNA
Helicases “melt” the helix in the cell!
Here is melting outside the cell using heat
Circular DNA…l
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DNA can Supercoil….enzymes called TopoisomerasesDeal with the supercoiling inside the cell.l
Stem Loop and Hairpin structures can occur within single stranded nucleic acids
Single Stranded RNA can take on a variety of complexvariety of complex
structures!(and Functions)
Magnesium Ions often help stabilizeThe structures….
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Same Molecule in “3-D”
DNA is Replicated by Polymerase Enzymes
What are the requirements?
Phosphodiester Bridge
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RNA Genomes…a carry-over from ancient days?
Retrovirus Mechanismhttp://www.whfreeman.com/kuby/content/anm/kb03an01.htm
Gene Expression…and RNA
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Transcription Start Signals in prokaryotes
Transcription Start Signals in eukaryotes
Terminator sequenceIn prokaryotes…
The end of the geneContains a hair pinStructure that tells the RNA polymerase to Stop transcription.
Rho factor may alsoBe involved
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Methyl Guanosine cap added to 5’ end
PolyA tail added to 3’ end
Molecular ushers…the Transfer RNAs
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Hydrogen Bonding is the link between mRNA and protein sequences.
1. Three nucleotides encode an amino acid2. The Code I nonoverlapping3. The Code has no “punctuation”4. The Genetic Code is degenerate.
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First amino acids inThe prokaryotes
Translation Start Signals in prokaryotes
Translation Start Signals in eukaryotes
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Animation of Translation:
http://www.johnkyrk.com/DNAtranslation.html
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