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Deoxyribonucleic acid
Functional Properties1. Replication – DNA is
copied prior to cell division why?
2. Storage of information DNA inherited
from parent to offspring from cell to cell
Gene expression – Genes encode proteins
3. Mutation – DNA changes to allow variation and adaptation, the basis of evolution
A six-legged green frog. (Reproduced by permission of JLM Visuals http://www.isogenic.info/assets/images/autogen/a_image16.jpg
http://3quarksdaily.blogs.com/3quarksdaily/images/wolfe_seal_1.jpg
Neutral, harmful, adaptive?
DNA History
1869 Meischer extracted nuclein from pus
1900s – chromosomes discovered
The genetic material must have the 3 functional properties
microscopy.bio.cmich.edu
Griffith finds “transforming factor”1928 London
Streptococcus pneumoniae bacterium
pneumonia in mice, deadly to humans
sputum with bacteria
Smooth strain (IIIS) virulent polysaccharide capsule capsule allows bacteria to evade immune
system
Fluorescent stain of capsule
S pneumococcus kills mouse in 24 hours. But 100 million IIR strain bacterial cells is harmless
S R
(Research photographs of Dr. Harriet Ephrussi-Taylor, courtesy of The Rockefeller University.)
Appearance when grown on an agar plate
Griffith’s experiment and conclusion
A “transforming factor” in killed S strain transformed live R strain into S
DNA or protein?
1944 Avery, McCarty, Macleod
1. Heat kill IIIS
2. Remove lipids and sugars – how?
FYI iGenetics: DNA as Genetic Material: Avery’s Transformation Experiment
How phage work
1. phage adsorbs onto bacterial surface
2. Genetic material injected
3. Cell makes progeny phage
IS the genetic material DNA, or protein?
Experiment
1. Label phage protein with 35 S infect E. coli strip phage off cell surface
New phage are not radioactive
http://osulibrary.orst.edu/specialcollections/coll/pauling/dna/pictures/hersheychase-experiment.html
Hershey and Chase conclusion
DNA is responsible for function and reproduction of phage virus = the genetic material
Structure of DNA = nucleotide polymers
NUCLEOTIDES
1. Nitrogenous base
Purines = guanine and adenine
G A
Purines attached to 1 carbon of sugar at 9 nitrogen, covalent bond, pyrimidines attached to 1 carbon at 1 nitrogen
How big IS a nucleotide? UTAH cell scale
3. Phosphate (PO4)
Nucleotide = base + sugar + phosphate
Phosphate covalently (phosphodietster bond) attached to 5’C of sugar Phosphodiester bond - Covalent bond between phosphate of one nucleotide and 3’ sugar carbon of another9 N (purine) or 6N (pyrimidine) covalently bonded to 1C of sugar
DNA (double helix)Watson and Crick 1953
X-ray diffraction data RosalindFranklin, Maurice Wilkins
GETncm/justsaycust-recrate-itemcommunittg/stores/dtg/stores/d-favorite-listruejust-say-no
Complementary base pairing
1. Hydrogen bonds between complementary bases
How many bonds in a G-C pair?
A-T?
Which is stronger?
4. Base composition
DNA 50% purine 50% pyrimidine
A = T G = C
A/T = 1 C/G = 1
A +T does not equal C+G
A + G = C + TChargaff
(1950)
And
5. Right handed helix6. Complete turn of the helix is 0.34 nm,
10 bases per turn7. Major and minor grooves
Forms of DNA
B DNA right helix
10 bp/ turn
A DNA right helix
10.9 bp/ turn
Z DNA left helix
12 bp/turn (role?)
Cellular DNA closest to B DNA10.4 bp/turn
Influenza ssRNA HIV ssRNA
Bacteriophage
ds DNA
Viral chromosomeSingle or double stranded DNA or RNACircular or linear
Herpes ds DNA
Parvovirus ssDNA
Genetic material in prokaryotes
1 (usually) chromosome Circular (most) chromosome Supercoiled DNA located in nucleoid region
Neisseria gonorrhoeae
E. coli = 4.6 million bp, circular chromosome
1500 um genome stuffed into a 1 um cell via supercoiling
E. Coli cells E. coli DNA map of chromosome
Histones and non-histones
Histone proteins basic
net + charge interacts with – charged DNA
Package DNA
Highly conserved
Non-histone proteinsvary among species
http://faculty.jsd.claremont.edu/jarmstrong/images/chromatin.gif
What do histones do?
1. pack DNA into chromatinCondense DNA 10,000X (2 meters nanometers)
1. Modifications to histone proteins affect gene expression
5 histone proteins
Histone type #amino acidscontent_________________
H1 200-265 27%lysine, 2%arginine
H2A 129-155 11% lysine, 9% arginine H2B 121-155 6% lysine, 6% arginine
H3 135 10%lysine, 15% arginine H4 102 11% lysine, 4% arginine
Note: all are lysine/arginine rich, they contain other amino acids, but at small percentages.Basic, + charge
epigenetics Modification of histone proteins changes
gene expression. Chemical tags can be inherited and are
stable in cell division
Pbs: A Tale of Two MiceEpigenetics with deGrassi http://www.pbs.org/wgbh/nova/sciencenow/3411/02.html
Agouti Mice
Epigenetics and gene silencing
Mouse and twin studies
Diet and the epigenome
Methyl group tags
Chromosome packaging
1. Nucleosomes 1 nucleosome
“beads on a string” The 10 um chromatin fiber 2(H2A).2(H2B) 2(H3).2(H4) octomer
Dual role of nucleosomes
stable to shelter DNA and compact it labile to allow DNA information to be used
Metaphase chromosome is 10,000 X condensed compared to double helix
Condensed scaffold
The scaffold with loops
Heterchromatin example
Barr body (facultative, extent of inactivity varies)
Inactivated X chromosome in females
What genes are on a chromosome?
http://www.dnalc.org/ddnalc/resources/chr11.html
Chromosome 11 flyover
Terms:
Transposon
Pseudogene
Olfactory
Polymorphism
1. Unique Sequence DNA
(1 to a few copies)
a.Genes Encode proteins
~60% of DNA
Only 2% of DNA is coding (H. sapiens)
Estimated 20,000 genes in humans
b. Gene families
encodes embryonic beta globin encode fetal beta globin is a pseudogene (not functional) encodes normal beta globin encodes normal adult beta globin
Example: Beta globin (encode subunits of hemoglobin)
2. Repetitive DNA
Repeated 10 – 1000sX in the genome
a. Dispersed repeated DNA
LINES = long interspersed elements
1000 – 7000 bp
Ex. humans have 500,000 copies of L1 = 15 % of genome.
some are transposons= copy and move
b. Tandem repeats
1 – 10 bp long
tandemly repeated
Centromeres, telomeres, rRNA genes
Ex. telomere sequence repeated 2000X
5'...TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG..3' 3'...AATCCC AATCCC AATCCC AATCCC AATCCC AATCCC..5'