Embed Size (px)
Citation preview
Basic Atomic StructureBasic Atomic Structure
A Whole New RealityA Whole New Reality
The Atomic ScaleThe Atomic ScaleA Whole New RealityA Whole New Reality
The Atomic ScaleThe Atomic Scale
In a word we’re talking small!In a word we’re talking small!
If an atom were the size of a BB, If an atom were the size of a BB, you’d be 23,000 miles tall!you’d be 23,000 miles tall!
Atoms are 99.9999999999999% Atoms are 99.9999999999999% empty space! empty space!
Can we “see” them?Can we “see” them?
Platinum and Oxygen AtomsPlatinum and Oxygen Atoms
The Umbrellas ProjectThe Umbrellas Project
CurtainAcross Rifle Gap
SurroundedIslands
Wrapped Reichstag
Scanning Tunneling Microscope (STM) Scanning Tunneling Microscope (STM)
The local geometric The local geometric topography of a sample topography of a sample surface is “probed”surface is “probed”
Overlap of electron wave Overlap of electron wave functions for the tip and functions for the tip and sample creates a sample creates a “tunneling current” “tunneling current”
Changes in the tip-sample Changes in the tip-sample distance are indicted by distance are indicted by changes in the “tunneling changes in the “tunneling current”current”
Scanning Tunneling Microscope (STM) Scanning Tunneling Microscope (STM)
Scanning Tunneling Microscope (STM) Scanning Tunneling Microscope (STM)
The Physical Object is Here
The “Scan” reflects the density of the electron cloud.
Do You Really “See” the Atoms?
STM Image of DNASTM Image of DNAThe Image The Model
Nucleic AcidsNucleic AcidsNucleic AcidsNucleic Acids The Stuff Upon Which Everything in The Stuff Upon Which Everything in
Biology Ultimately Depends Biology Ultimately Depends Elemental Composition Elemental Composition
Carbon, Hydrogen, Oxygen, Phosphorous, Carbon, Hydrogen, Oxygen, Phosphorous, and Nitrogenand Nitrogen
Subunits:Subunits: Ribose/Deoxyribose SugarsRibose/Deoxyribose Sugars PhosphatesPhosphates Nitrogenous BasesNitrogenous Bases
Purines: Guanine, AdeninePurines: Guanine, Adenine Pyrimidines: Cytosine, Thymine, UracilPyrimidines: Cytosine, Thymine, Uracil
RNA versus DNARNA versus DNA Deoxyribonucleic acid (DNA)Deoxyribonucleic acid (DNA)
(The shy and timid one)(The shy and timid one) Ribonucleic acid (RNA)Ribonucleic acid (RNA)
(The bold and shameless one)(The bold and shameless one)
Why does everything that is Why does everything that is biologically significant revolve biologically significant revolve around nucleic acids?around nucleic acids?
Because…….Because……. All organisms are fundamentally All organisms are fundamentally
packages for the expression and packages for the expression and replication of nucleic acids.replication of nucleic acids.
At its core, everything that an organism At its core, everything that an organism does is a reflection of the expression of does is a reflection of the expression of its nucleic acids.its nucleic acids.
Our understanding of every area of Our understanding of every area of modern biology has been touched by modern biology has been touched by and has benefited from recombinant and has benefited from recombinant DNA technology.DNA technology.
DNA is Everywhere
DNA is Everywhere
Japanimation/MangaJapanimation/Manga ResearchResearch ForensicsForensics Business and MarketingBusiness and Marketing MedicineMedicine
Nitrogenous Base StructureNitrogenous Base StructureNitrogenous Base StructureNitrogenous Base Structure
PurinesPurines Double Ring Double Ring
BasesBases(A and G)(A and G)
PyrimidinesPyrimidines Single Ring Single Ring
BasesBases(T and C)(T and C)
DNA Building BlocksDNA Building Blocks Nitrogenous Base Pentose Sugar Triphosphate
5’ Phosphate 3’ Hydroxyl
DNADNASugar-phosphate Sugar-phosphate backbone serves as backbone serves as a “backbone”. a “backbone”.
The “backbone” The “backbone” has directionality has directionality (PO(PO44 / OH). / OH).
Bases encode the Bases encode the genetic information.genetic information.
The First Clues to DNA StructureThe First Clues to DNA Structure
G A T C22.1% 28.1% 30.1% 19.7%15.4% 33.6% 37.1% 13.940.4% 9.0% 11.7% 38.9%8.9% 42.6% 39.9% 8.6%
DNADNABasepairingBasepairing
A pairs with TA pairs with T (2 bonds) (2 bonds)
G pairs with CG pairs with C (3 bonds)(3 bonds)
Almost no Almost no exceptionsexceptions
An
ti-p
aral
lel
Bo
nd
ing
5’ PO4
PO4 5’ 3’ OH
3’ OH
Alfred Hershey and Martha Chase (1952) Alfred Hershey and Martha Chase (1952) DNA is genetic material.DNA is genetic material.Watson and Crick (1953) DNA is a double Watson and Crick (1953) DNA is a double helix.helix.
The Big Bang
The Big Bang
3.4Å between
bases
20Å Diameter
34Å Turn
From A to Z DNAFrom A to Z DNARight Handed 10.7-11 bp/turn 23A DiameterdsRNA and RNA-DNA Hybrids
Right Handed 10-10.6 bp/turn 19A Diameter“Normal DNA”
Left Handed 12 bp/turn 18A Diameterdinucleotide repeats Pu-Py (GCGCGCGC)
Denaturation / Renaturation Denaturation / Renaturation
The bonds The bonds that hold that hold DNA DNA strands strands together together are easily are easily broken broken and and reformed.reformed. P
OH
5'
3'
TAC
G
CC
T
G
TT
TC
T
A
AA
P
OH
5'
3'
ATG
C
GG
A
C
AA
AG
A
T
TT
......
......
......
......
......
......
......
......
......
......
.........
.........
.........
.........
.........
.........
P
OH
5'
3'
TAC
G
CC
T
G
TT
TC
T
A
AA
P
OH
5'
3'
ATG
C
GG
A
C
AA
AG
A
T
TT
DNA Structure
DNA Structure
DNA exists as a DNA exists as a double helix. double helix.
DNA strands DNA strands are anti-parallelare anti-parallel
If you know one If you know one strand, you can strand, you can predict the predict the other strand. other strand.
A pairs with T A pairs with T G pairs with CG pairs with C
Eve n Mo re Simplif ie d Mo de l
P
OH
5 '
3 '
A
T
G
C
G
G
A
C
A
A
A
G
A
T
T
T
P
OH
5 '
3 '
T
A
C
G
C
C
T
G
T
T
T
C
T
A
A
A
P
OH
5 '
3 '
A
T
G
C
G
G
A
C
A
A
A
G
A
T
T
T
......
......
......
......
......
......
......
......
......
......
.........
.........
.........
.........
.........
.........
DNA Replication
DNA Replication
Basepairing rules Basepairing rules determine which determine which nucleotide is added nucleotide is added next.next.
DNA replication DNA replication requires a template requires a template strand from which strand from which to copy.to copy.
Either stand can be Either stand can be used a template.used a template.
More building blocks for DNA?More building blocks for DNA?
Nucleotide Nucleotide AnalogsAnalogs
DideoxyinosineDideoxyinosine
Didehydro-Didehydro-dideoxythymidinedideoxythymidine
DideoxycytidineDideoxycytidine
Azido-Azido-dideoxythymidinedideoxythymidine
CopyingDNA
CopyingDNA
Semiconservative Semiconservative ReplicationReplication
Parent strands Parent strands split to serve split to serve as templates as templates for synthesis for synthesis of daughter of daughter strands.strands.
DNA Replication
DNA Replication
The Lagging StrandThe Lagging Strand
Primase synthesizes a Primase synthesizes a start point on the start point on the lagging strand.lagging strand.
DNA Polymerase DNA Polymerase extends the DNA from extends the DNA from the start point.the start point.
This process is This process is repeated over and over. repeated over and over.
At the end all the small At the end all the small gaps in the new DNA gaps in the new DNA strand are sealed up.strand are sealed up.
DNA Replication
DNA Replication
It’s not just smoke It’s not just smoke and mirrors!and mirrors!
DnaB - Helicase unwinds DNA.DnaB - Helicase unwinds DNA.
Pol III Catalytic Core:Pol III Catalytic Core:
(polymerase)(polymerase)
(dimerization component)(dimerization component)
(dimeric clamp)(dimeric clamp)
(clamp loader)(clamp loader)
DnaG - Primase DnaG - Primase
SSB - Single stranded binding protein SSB - Single stranded binding protein (straightens out the DNA)(straightens out the DNA)
Can you say MechanicalCan you say Mechanical
Form follows function. The clamp part of Form follows function. The clamp part of DNA Polymerase keeps the replication DNA Polymerase keeps the replication machine on the DNA. Now that’s just cool!machine on the DNA. Now that’s just cool!
DNA Replication and Mitosis http://www.stolaf.edu/people/giannini/flashanimat/celldivision/crome3.swf
DNA Replication and Mitosis http://www.stolaf.edu/people/giannini/flashanimat/celldivision/crome3.swf
Normal Body Cell (2n Chromosomes)
Replicate all the DNA (4n Chromosomes)
Split all the DNA Divide into two Daughter Cells
(2n Chromosomes in each cell)
Repeat
DNA Replication and Mitosis http://www.stolaf.edu/people/giannini/flashanimat/celldivision/crome3.swf
DNA Replication and Mitosis http://www.stolaf.edu/people/giannini/flashanimat/celldivision/crome3.swf
(Splitting the 4n Chromosomes)(2n Chromosomes
in each Daughter Cell)
DNA Replication and MeiosisDNA Replication and Meiosis
Normal Body Cell (2n Chromosomes)
Replicate the DNA (4n Chromosomes)
Split the DNA into two Daughter Cells (2n Chromosomes in each cell)
Looks like Mitosis so far.
Immediately split the cells (and the DNA) again into
two sets of Daughter Cells (1n Chromosomes in each cell)
The Importance of Meiosis The Importance of Meiosis
