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DNA
The Nuclear genome consists of DNA in the
nucleus of eukaryotic cells – this is what we
typically think of as our Genome:
A Genome is the unique set of chromosomes
(or DNA) in one cell of an organism.
• Humans have 2 sets of chromosomes
(one from each parent: we are
diploid.)
• Our genome consists of 3 x109 base
pairs
• ~25,000 genes (no one knows
exactly yet).
Plant Cell
Animal Cell
Nucleus
Chloroplast
Mitochondrion
Chloroplasts (photosynthesis machinery in plants,
algae) have their own DNA (called the
Plastid genome)
• 7.5-25 x 103 base pairs
• 100-1000 copies depending on whether the cell
is actively dividing (more when dividing).
• ~100 genes
Mitochondria have their own DNA (called the
Mitochondrial genome)
• ~1.7 x 104 base pairs
• several copies
• ~40 genes
Nucleic Acids
•DNA
•RNA
DNA
•Deoxyribonucleic acid
•double helix
•“intelligent molecule”
•made of nucleotides
One human cell
Has ~1 meter of DNA
DNA is partitioned into
46 separate linear
molecules
(chromosomes, 23 from
each parent)
Nucleus
CELL
All of it is crammed into
the cell's nucleus
(a few micrometers)
Robert H. Austin, James P. Brody,
Edward C. Cox, Thomas Duke
and Wayne Volkmuth
FEBRUARY 1997 PHYSICS TODAY
image from the National Human Genome Research Institute
(NHGRI) Genetic Illustrations.
DNA
2 nm
11 nm
30 nm
Chromatin
300 nm
700 nm
Chromosome
1400 nm
Richarddawkins.net
Nucleotide
•Sugar (deoxyribose)
•Phosphate
•Nitrogenous Base
•adenine (A)
•thymine (T)
•cytosine (C)
•guanine (G)
•DNA is double-stranded
•adenine is always across from thymine
•cytosine is always across from guanine
•bases are held across from each other by
weak hydrogen bonds
A
T
C
G
The Sugar in the
“backbone” is
RNA: ribose
DNA: deoxyribose
This OH group is replaced by
H (hydrogen atom) in
Deoxy-ribose
5’
3’
DNA is anti-parallel:
One strand is 5’to 3’
The strand across from it
is 3’ to 5’
3’
5’
How do We Know the Structure of DNA?
Watson & Crick 1953
Diffraction Patterns
Reciprocal Space
http://www.matter.org.uk/diffraction/geometry/3D_reciprocal_lattices.htm
Click here for a groovy interactive experience
(Grab and drag one of the white dots)
X-ray crystallography revisited
DNA X-ray diffraction pattern
X-ray crystallography revisited
34 Angstroms
X-ray crystallography revisited
3.4 Angstroms
X-ray crystallography revisited
X-ray crystallography revisited
X-ray crystallography revisited
X-ray crystallography revisited
X-ray Diffraction pattern → Molecular Structure
1953 Discovery → Nobel Prize
Wavelength of diffracted light should match size of object
for optimal resolution
Why x-rays?
A DNA molecule
• not a rigid, static structure
(as x-ray diffraction pictures might
suggest)
• under constant thermal fluctuations
local twisting, stretching, bending, and
unwinding of the double-strands.
X-ray crystallography revisited
http://www.uic.edu/classes/phys/phys461/phys450/ANJUM04/
The most common
DNA structure in
solution is B-DNA.
B
Z
DNA has several
helical conformations
A-DNA, Z-DNA, SDNA
A
Under conditions of
• applied force
• low hydration
...
B-DNA
Long and thin
Most common in solution
Right-handed helix
27.3 A diameter
3.4 A rise/base pair
~ 10 bases/turn
A-DNA
Short and broad
Low hydration
Right handed helix
25.5A diameter
2.3A rise/base pair
~11 bases/ turn
Z-DNA
Longer and thinner
Left-handed helix
18.4 A diameter
3.8 A rise/base pair
~12 bases/ turn
DNA Replication
•2 strands of DNA “unzip” - separate
•primers are placed on each strand
•DNA polymerase (an enzyme) builds
new strands of DNA, using the
original strands as templates
RNA
•Ribonucleic acid
•single stranded
•also made of nucleotides
RNA nucleotides
•Sugar (ribose)
•Phosphate
•nitrogenous base
•adenine
•cytosine
•guanine
•uracil
Types of RNA
•mRNA: messenger RNA, carries the
DNA code out of the nucleus to the
ribosome
•tRNA: transfer RNA, carries amino
acids to the ribosome
•rRNA: ribosomal RNA, part of the
ribosome
Transcription (making RNA)
•DNA unzips
•one strand of DNA acts as a template
•RNA polymerase reads the DNA bases
•RNA nucleotides are placed across from
the complimentary DNA bases
•RNA separates from DNA
•DNA zips back up
•The “code” of DNA is the order of the
bases
•The code is universal among organisms
•DNA from one organism can be read in
the cells of another organism