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Chapter 5: Introduction to the N l i A idNucleic Acids
DNA, RNA, and the Flow of G i I f iGenetic Information
• DNA and RNA are long polymersg p y– Carry information that is passed on to the next
generationG ti i f ti i t d i th f• Genetic information is stored in the sequence of bases along a nucleic acid chain
• Base pairing occurs• Base pairing occurs• Base pairs provide the mechanism for copying
the genetic information in an existing nucleic g gacid chain to form a new chain.
Central Dogma of Information FlowCentral Dogma of Information Flow
DNA
DNA RNA P t i F ti
DNAWhat is this?
• DNA RNA Protein Function
What is this? What is this? What is this?What is this?
Th G ti C d i C i l!The Genetic Code is Crucial!
General Schematic of a NucleicGeneral Schematic of a Nucleic Acid polymer.
Sugar DifferencesDifferences
Nitrogen Bases in the Nucleic Acids
Making a NucleosideMaking a Nucleoside
N-glycosidicN-glycosidic bond
Nucleosides• Combining Nitrogen bases with sugars
• RNA– AdenosineAdenosine– Guanosine– CytidineCytidine– Uridine
• DNADNA– Deoxy- prefix– ThymidineThymidine
Making a NucleotideMaking a Nucleotide
Adding a phosphate to the nucleoside structureAdding a phosphate to the nucleoside structure.
Nucleotide NomenclatureNucleotide Nomenclature
• 5’- nucleoside phosphate5 nucleoside phosphate• 5’- nucleotide
Adenosine 5’-triphosphate
A.K.A
3’- deoxyguanosine monophosphatemonophosphate
Tedious Method to show the polymerpolymer…
Short-Hand Method to show the polymerpolymer
The Very Short-Hand Method to
• P-5’ACG 3-OHshow the polymer
P 5 ACG 3 OH• By convention: nucleic acid polymers are
always written with the 5’ end to the leftalways written with the 5 end to the left and the 3’end to the right.P l it t th l l 5’ 3’• Polarity to these molecules 5’ 3’
• ACG is DIFFERENT than GCA
Anatomy of the DNA helixAnatomy of the DNA helix
Launch animation
htt // j h k k /DNA t ht lhttp://www.johnkyrk.com/DNAanatomy.html
Visit this link as a study guide!!!
Billions of nucleotides join to form G
• ProkaryotesGenomes.
– Contain genes (coding regions)– Control areas (regulatory regions)
• Eukaryotes– Contain genes (coding regions)g ( g g )– Control areas (regulatory regions)– “Useless” stretches of DNA (noncoding Use ess st etc es o ( o cod g
regions)• Introns – intervening sequences in DNA• Exons - are the coding regions in Eukaryotes.
An E. coli’s genomegenome exposed!
Structure of DNA
• A 1950’s Race
Structure of DNA
A 1950 s Race• Maurice Wilkins and Rosalind Franklin
J W t d F i C i k• James Watson and Francis Crick– Building a structural model from scientific data
d h th !and hypotheses!
– Read their Paper!!! (link is on the class website)
X-ray DiffractionDiffraction of DNA…R li dRosalind Franklin’s
Data
Watson-Crick Model from the data
• 1 two helical polynucleotides coiled
Watson Crick Model from the data
1. two helical polynucleotides coiled around a common axis
• 2 The sugar phosphate backbones are• 2. The sugar-phosphate backbones are on the outside and the bases lie on the insideinside
• 3. bases are perpendicular to the axis of th h li 34 A t t 10the helix. 34 Angstrom repeat 10 bases/turn (bases separated by 3.4 Ang.)
• 4. diameter is 20 Angstroms.
Chargaff’s Results on NucleotideChargaff s Results on Nucleotide Ratios
Paper scissorsPaper, scissors, and Hydrogen
B dBonds…
The secret of the Base Pairs!Base Pairs!
Nitrogen “Base Stacking”Stacking”
helps stabilize the helixthe helix.
W kWeak forces…
Genetic Molecule• Copies are made of the DNA before
Genetic Moleculep
each MITOSIS event.• The enzyme that copies the DNA for theThe enzyme that copies the DNA for the
daughter cells is called DNA polymerasepolymerase– For humans, 3 billion bases have to be
copied to form the new strands of DNAp– Very rapid, very accurate…– Only 1 mistake in every 1 million baseOnly 1 mistake in every 1 million base
pairs.
What was the mechanism of DNA R li i ?Replication?
• PossibilitiesPossibilities– Conservative
Semiconservative– Semiconservative• How can you find out?
S i C tiSemi-Conservative Replication Model…Replication Model…
Meselson and Stahl E i tExperiment
Animation link: http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html#
Density Gradient equilibrium Sedimentation
Heavy N-15 isotopelight N-14 isotope
Hybrid…1/2 Heavy…½ light.
Semi-Conservative R li tiReplication
Uses the following amazing enzymes:Uses the following amazing enzymes:
1. Helicases/topoisomersase – help to open up the double helixdouble helix
2. RNA primase – lays down a short RNA primer to provide replication enzymes with a 3’-OH.
3. DNA polymerase – builds off of the RNA primers p y pto 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 bet een the neighboringphosphodiester linkage between the neighboring DNA fragments making all of the separate fragments one continuouse nucleic acid strand.
S i C tiSemi-Conservative Replication inReplication in
Action!Animation of DNA Replication
http://www.johnkyrk.com/DNAreplication.html
Another animation of DNA replication
Another animation of DNA replication
REALLY COOL ANIMATION OF DNA PACKAGING AND REPLICATION!DNA PACKAGING AND REPLICATION!
HypochroismHypochroism of DNA
Helicases “melt” the helix in the cell!
Here is melting outside the cell using heatg g
Circular DNA…l
DNA can Supercoil….enzymes called TopoisomerasesDeal with the supercoiling inside the cellDeal with the supercoiling inside the cell.l
Stem Loop and Hairpin structures ithi i l t d d l i idcan occur within single stranded nucleic acids
Single StrandedSingle Stranded RNA can take on a variety of complex
structures!structures!(and Functions)( )
Magnesium Ions often help stabilizeMagnesium Ions often help stabilizeThe structures….
Same Molecule in “3-D”Same Molecule in 3 D
DNA is Replicated by P l EPolymerase Enzymes
What are the requirements?
Phosphodiester BridgePhosphodiester Bridge
RNA Genomes…a carry-over f i t d ?from ancient days?
Retrovirus Mechanismhttp://www.whfreeman.com/kuby/content/anm/kb03an01.htm
Gene Expression…and RNAGene Expression…and RNA
Transcription Start Signals in prokaryotes
Transcription Start Signals in eukaryotes
Terminator sequenceTerminator sequenceIn prokaryotes…
The end of the geneC t i h i iContains a hair pinStructure that tells the RNA polymerase to Stop transcription.p p
Rho factor may alsoBe involved
Methyl Guanosine cap added to 5’ end
PolyA tail added to 3’ endPolyA tail added to 3 end
Molecular ushers…theMolecular ushers…the Transfer RNAs
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”3. The Code has no punctuation4. The Genetic Code is degenerate.
First amino acids inThe prokaryotes
Translation Start Signals in prokaryotes
Translation Start Signals in eukaryotes
Animation of Translation:
http://www johnkyrk com/DNAtranslation htmlhttp://www.johnkyrk.com/DNAtranslation.html