Download A DNA

DNA Chapter 2 – read principal points
Timeline for genetics
Deoxyribonucleic acid
 Functional Properties
1. 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
Neutral, harmful, adaptive?
http://3quarksdaily.blogs.com/3quarksdaily/images/wolfe_seal_1.jpg
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
isolate live IIIS
from mouse
S pneumococcus kills mouse in 24 hours. But 100
million IIR strain bacterial cells is harmless
S
R
Appearance when grown on an agar plate
(Research photographs of Dr. Harriet Ephrussi-Taylor, courtesy of The Rockefeller University.)
http://biology.kenyon.edu/courses/biol114/KH_lecture_images/How_DNA_works/how_
DNA-works.html
 Rough strain IIR is avirulent
-> isolate live IIR
IIR lacks capsule
The experiment:
 Heat kill IIIS strain  mouse ?
Heat killed IIIS strain + live strain IIR
 mouse ?
Which strain is isolated?
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
3. Divide into 3 and treat with:
protease
RNase
DNase
 next, add live R cells to each
1952 Hershey and Chase
Used T2 bacteriophage + E. coli
A phage is a virus that infects bacteria
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
S  infect E. coli
 strip phage off cell surface
1. Label phage protein with
35
 New phage are not radioactive
2. Label phage DNA with 32 P -> infect E.coli ->
blend ->
 New phage contain 32 P
http://osulibrary.orst.edu/specialcollections/coll/pauling/dna/pictures/hersheych
ase-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
How big IS a nucleotide?
UTAH cell scale
Purines attached to 1 carbon of sugar at 9 nitrogen, covalent bond, pyrimidines attached to 1 carbon at 1 nitrogen
Pyrimidines
Thymine T
Cytosine C
RNA contains uracil
U
2. Deoxyribose sugar
RNA (ribose) 2’ OH makes RNA less stable than DNA
Sugar + base = nucleoside
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 another
9 N (purine) or 6N (pyrimidine) covalently bonded to 1C of sugar
DNA is a polymer of nucleotides
polarity 5’carbon to 3’hydroxyl
DNA (double helix)
Watson and Crick 1953
cavorite-lis
n
-fGET
tg/stores/d
communit
rate-item
cust-rec
just-say-no
true
m/justsay
X-ray diffraction data Rosalind
Franklin, Maurice Wilkins
 DNA properties include:
Complementary base pairing
1. Hydrogen bonds between
complementary bases
How many bonds in a G-C pair?
A-T?
Which is stronger?
Complementary base pairs
Which are the G-C
pairs?
2. antiparallel stands
5’  3’ and 3’  5’
3. Sugar phosphate backbones
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+T
Chargaff
(1950)
5. DNA can denature and renature
 Melt hydrogen bonds (chemical or heat)
And
5. Right handed helix
6. Complete turn of the helix is 0.34 nm,
10 bases per turn
7. Major and minor grooves
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 DNA
10.4 bp/turn
Replication of DNA by
Complementary Base Pairing
HHMI interactive DNA replication advanced
Organization of DNA in
chromosomes
 Genome

Full amount of genetic material in a
single cell
Viral chromosome
Single or double stranded DNA or RNA
Circular or linear
Parvovirus ssDNA
Influenza ssRNA
Bacteriophage
ds DNA
HIV ssRNA
Herpes ds DNA
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
 Some bacteria contain extra-chromosomal
DNA called a plasmid
Eukaryotic Chromosomes
C value - Amount of DNA varies among species
The structure of chromatin
 DNA + proteins
 Highly conserved
Histones and non-histones
Histone proteins
basic
net + charge interacts with – charged DNA
Package DNA
Highly conserved
Non-histone proteins
vary among species
http://faculty.jsd.claremont.edu/jarmstrong/images/chromatin.gif
What do histones do?
1. pack DNA into chromatin
Condense DNA 10,000X (2 meters  nanometers)
1. Modifications to histone proteins affect gene
expression
5 histone proteins
Histone type
H1
H2A
H2B
H3
H4
#amino acids
200-265
129-155
121-155
135
102
content_________________
27%lysine, 2%arginine
11% lysine, 9% arginine
6% lysine, 6% arginine
10%lysine, 15% arginine
11% lysine, 4% arginine
Note: all are lysine/arginine rich, they contain other amino acids, but at small percentages.
Basic, + charge
Gel electrophoresis
epigenetics
 Modification of histone proteins changes
gene expression.
 Chemical tags can be inherited and are
stable in cell division
Pbs: A Tale of Two Mice
Epigenetics with deGrassi
http://www.pbs.org/wgbh/nova/scienceno
w/3411/02.html
Agouti Mice
Epigenetics and gene silencing
Mouse and twin studies
Diet and the epigenome
Methyl group tags
Chromosome packaging
1. Nucleosomes
“beads on a string” The 10 um chromatin fiber
2(H2A).2(H2B) 2(H3).2(H4) octomer
1 nucleosome
Dual role of nucleosomes
 stable to shelter DNA and compact it
 labile to allow DNA information to be used
2. The 30 nm chromatin fiber
Histone H1 attaches linker DNA to
nucleosomes
The 30 nm chromatin fiber
(11nm string-> 30 nm helical fiber)
See Science article
3. Further packaging into loops and
scaffolds……
Summary of DNA packaging
30nm chromatin fiber
Nucleosomes
DNA helix
Metaphase chromosome is
10,000 X condensed compared
to double helix
Condensed scaffold
The scaffold with loops
Euchromatin and Heterochromatin
1. Heterochromatin



Condensed
Transcriptionally inactive
Ex. centromeres
Heterochromatin stains darkly
Heterchromatin example
Barr body (facultative, extent of inactivity varies)

Inactivated X chromosome in females
2. Euchromatin
 Lighter staining regions of DNA that contain
genes
 Transcriptionally active
Unique Sequences and Repetitive DNA
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
Example: Beta globin (encode subunits of hemoglobin)
e encodes embryonic beta globin
g encode fetal beta globin
y is a pseudogene (not functional)
d encodes normal beta globin
b encodes normal adult beta globin
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
SINES
100 – 400 bp
Ex. Alu repeats repeated 1 million times = 10% of genome
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'
Ex. rRNA genes