Chromosome structure
3.4
3.5
eukaryotic chromosome structure
centromeres and telomeres
3.6 @ slide 94
Eukaryotic Chromosomes
•a single DNA molecule
•can be visualized by pulsefield gel electrophoresis
see fig 3.13A
Eukaryotic Chromosomes
•different sizes
•different geometries
Fig. 3.13B. Histogram of sizes of the 16 yeast chromosomes.
© 2006 Jones & Bartlett
Eukaryotic Chromosomes
•not just DNA
•chromatin DNA + proteins
•euchromatin
less condensed
(not visible with light microscope)
•heterochromatin more condensed
•chromosomes
seen during cell
division
heterochromatin
euchromatin
nucleolus
light micrograph
ec
hc
nu
electron micrograph
© 2006 Jones & Bartlett
Eukaryotic Chromosomes
•chromatin
DNA and histone proteins
nucleosomes
beads on a string
http://chemistry.umeche.maine.edu/CHY431/Nucleic3.html
Eukaryotic Chromosomes
•chromatin
DNA and histone proteins
nucleosomes
http://edoc.hu-berlin.de/dissertationen/seitz-stefanie-2004-10-20/HTML/chapter1.html
five major histone proteins
H1, 2xH2A, 2xH2B, 2xH3, 2xH4
20-30% lysine and arginine (+)
DNA
(-)
Fig. 3.15A. Organization of nucleosomes, A.
© 2006 Jones & Bartlett
Eukaryotic Chromosomes
•histones - highly conserved
97%-identity cow/pea
http://edoc.hu-berlin.de/dissertationen/seitz-stefanie-2004-10-20/HTML/chapter1.html
Fig. 3.15B. Organization of nucleosomes, B.
© 2006 Jones & Bartlett
Eukaryotic Chromosomes
•chromatin
string coils and
bead stack up
30 nm fiber
http://edoc.hu-berlin.de/dissertationen/seitz-stefanie-2004-10-20/HTML/chapter1.html
Fig. 3.17B, C. Model of nucleosomes packed into a 30-nm
chromatin fiber. [After B. Dorigo et al. 2004. Science 306: 1571.]
© 2006 Jones & Bartlett
Fig. 3.19. Chromosome
condensation.
© 2006 Jones & Bartlett
Fig. 3.19. Chromosome
condensation.
© 2006 Jones & Bartlett
if the DNA were a spaghetti noodle…
1 mm in diameter
25 miles long
during metaphase
16 feet long
2 feet wide
during metaphase
during interphase…
chromosome unwinds … some
30 nm fibers = euchromatin
gene-rich
30 nm fibers are organized into
“chromosome territories”
fig 3.18
http://embryology.med.unsw.edu.au/Notes/week1_12.htm
during interphase…
chromosome unwinds … some
30 nm fibers = euchromatin
gene-rich
not as much = heterochromatin
gene poor
(darker staining areas of chromosomes)
heterochromatin
few genes
tandem repeats
satellite DNA
often found:
around centromeres
at telomeres
Fig. 3.21B. Drawing of metaphase chromosome.
© 2006 Jones & Bartlett
Chromosome structure
3.4
3.5
eukaryotic chromosome structure
centromeres and telomeres
Essential parts of chromosomes:
centromeres
specialized for moving chromosomes
during cell division
telomeres
caps for ends of chromosomes
Essential parts of chromosomes:
centromeres
place of attachment of kinetochore
protein complex
attachment of spindle fibers
shortening of spindle fibers
http://www.utexas.edu/courses/utgeneticstamu/kinetchr.htm
Essential parts of chromosomes:
centromeres
in yeast
simple
200-250 bp
binding of spindle fiber
Fig. 3.22. A yeast centromere.
[After K. S. Bloom, M. Fitzgerald-Hayes, and J.
Carbon. 1982. Cold Spring Harbor Symp. Quant. Biol. 47: 1175.]
© 2006 Jones & Bartlett
Essential parts of chromosomes:
centromeres
in yeast
simple
200-250 bp
binding of spindle fiber
higher eukaryotes
more complicated
170 bp sequence
repeated 1001000 times
Fig. 3.23. Human chromosome centromere.
[After Xinwei She et al. 2004. Nature 430: 857.]
© 2006 Jones & Bartlett
Essential parts of chromosomes:
telomeres
DNA / protein structure at
end of chromosome
Essential parts of chromosomes:
telomeres
repetitive sequences at end of
chromosome-TTGGGGTetrahymena
-TTAGGGvertebrates
with each cell division some of the
repeats are lost
5’ RNA primer
extension
3’
original strand 5’
3’
5’
3’
3’ overhang is degraded
Fig. 6.23A,B. Joining of adjacent precursor fragments
© 2006 Jones
© 2006and
Jones
Bartlett
& Bartlett
Publishers
Fig. 3.25A,B. The function of telomerase
© 2006 Jones & Bartlett
if chromosome gets shorter
with each cell division…
eventually the cell stop dividing
(cultured cells)
telomerase
enzyme can extend 3’ end of telomere
then DNA polymerase makes complement
can rebuild the telomere
Fig. 3.26. Telomere formation in Tetrahymena.
© 2006 Jones & Bartlett
telomerase
what cells have telomerase
protozoa cells
unicellular eukaryotes
germ line cells
(divide indefinitely)
many cancer cells
end of 3.5
Chromosome structure
3.1
3.2
3.3
chromosomes
mitosis
meiosis
Each species has a “set” of chromosomes
chromosomes
first seen ~ 1880’s
the nucleus of somatic cell
contains a fixed number of
chromosomes in a given
species
karyotype
Fig. 3.1. Chromosome complement of a human male.
[Courtesy of David
C. Ward and Michael R. Speicher]
© 2006 Jones & Bartlett
chromosomes
the number of chromosomes
varies greatly between species
Table 3.1. Somatic chromosome numbers of some
plant and animal species
© 2006 Jones & Bartlett
chromosomes
chromosomes in somatic cells
are paired (one from each parent)
(homologous pairs)
cells are called diploid
chromosomes
germ cells have only one
chromosome from each pair
cells are called haploid
(gametes)
Chromosome structure
3.1
3.2
3.3
chromosomes
mitosis
quiz time
meiosis
interphase cell
1. dipliod/haploid?
2. what is N?
3. what would this cell look like at metaphase
interphase cell
1. dipliod/haploid? diploid
N = 2 (2N=4)
2. what is N?
3. what would this cell look like at metaphase
metaphase cell
Mitosis
nuclear division that results in two
cells each having a complete
diploid complement of
chromosomes from the original cell
usually accompanied by cytokinesis
(splitting of the cytoplasm)
Mitosis
cytokinesis
part of the cell cycle
Interphase
G1
S synthesis (DNA replication)
G2
Mitosis
checkpoints at transitions
Mitosis
cell cycle
18-24 hrs in eukaryotes
mitosis is the shortest
chromatids
Fig. 3.2. The cell cycle of a typical mammalian cell
© 2006 Jones & Bartlett
Mitosis
divided into four phases
prophase
metaphase
anaphase
telophase
condense
alignment
movement
cytokinesis
Mitosis
during interphase…
prophase (before)
chromatin (replicated already)
condenses as visible
chromatids held together at
the centromere
nuclear membrane and
nucleoli disappear
Mitosis
metaphase (after)
formation of mitotic spindle
microtubules spanning from
“poles” to kinetochore
chromosomes line up at the
metaphase plate (equator)
Mitosis
anaphase (up)
centromeres divide
chromatids separate and
move to opposite poles of cell
Mitosis
telophase (end)
new nuclear envelope forms
around each set of chromosomes
spindle disappears
chromosomes decondense
cytoplasm divides-cytokinesis
Fig. 3.3. Mitosis
© 2006 Jones & Bartlett
interphase cell G1
What’s wrong with this picture?
interphase cell G
S2
prophase cell
asters
metaphase cell
anaphase cell
2N
cytokinesis
2N
telophase cell
Chromosome structure
3.1
3.2
3.3
chromosomes
mitosis
meiosis
meiosis
produces gametes
with genetic differences
reduced # of chromosomes
homologs are separated
involves two rounds of division
meiosis I and meiosis II
interphase cell
prophase I cell
alignment as
homologous pairs
metaphase I cell
separation of
homologous pairs
anaphase I cell
telophase I cell
interphase cells no DNA replication
prophase II cell
alignment at
the equator
metaphase II cell
separation of
chromatids
anaphase II cell
telophase II cell
gametes
gametes
Fig. 3.4A, B Overview of the behavior of a single pair of homologous
chromosomes in meiosis
© 2006 Jones & Bartlett
Fig. 3.4C-E Overview of the behavior of a single pair of homologous
chromosomes in meiosis
© 2006 Jones & Bartlett
Fig. 3.4 Overview of the behavior of a single pair of homologous
chromosomes in meiosis
© 2006 Jones & Bartlett
Fig. 3.05. The life cycle of a typical animal.
© 2006 Jones & Bartlett
alternation
of
generations
Fig. 3.06. The life cycle of corn, Zea mays.
© 2006 Jones & Bartlett
prophase I
5 substages
synapsis
tetrads, X-over
chiasmata
separation
leptotene
zygotene
pachytene
diplotene
diakinesis
thin threads
paired threads
thick threads
double threads
moving apart
crossing over
tetrads
synapsis
bivalent
Fig. 3.07. Meiosis
© 2006 Jones & Bartlett
chiasma
separation
Fig. 3.07. Meiosis
© 2006 Jones & Bartlett
Fig. 3.09B. Drawing of a bivalent consisting of a pair of homologous chromosomes. [(A)
Courtesy of James Kezer]
© 2006 Jones & Bartlett
Fig. 3.07. Meiosis
© 2006 Jones & Bartlett
Mendel to chapter 2 now
© 2006 Jones & Bartlett
Back to Chapter 3
3.6 Genes are located on chromosomes
3.7 More probability and statistics
© 2006 Jones & Bartlett
Best early evidence
study of the sex chromosomes
some insects:
male have an unpaired chromosome
the “X”
found in all somatic cells
found in 1/2 of sperm cells
other animals (including us)
females had two X’s
male had one X and a non-match Y
male gets X from mom
male gives X to
daughters
Fig. 3.27. Chromosomal sex determination in humans.
© 2006 Jones & Bartlett
X and Y are called the sex chromosomes
all other chromosomes are called
autosomal chromosomes or autosomes
Humans:
pairs 1-22 (by size)
genes on the X chromosome are said to
be X-linked (sex-linked)
white eyes in Drosophila
Thomas Hunt Morgan (1917)
male with white eyes
female with red eyes (wt)
all F1 had red eyes
fig 3.28
W
w
ww
w-
=
=
=
=
red eyes
white eyes
female
male
white eyes in Drosophila
Thomas Hunt Morgan (1917)
male with white eyes
female with red eyes (wt)
all F1 had red eyes
F1 cross
fig 3.28
2459 red-eyed females
1011 red-eyed males
782 white-eyed males
white eyes in Drosophila
Thomas Hunt Morgan (1917)
did reciprocal cross
white eyes in Drosophila
Thomas Hunt Morgan (1917)
male with red eyes
male with white eyes
female with red eyes (wt) female with white eyes
all females had red eyes all females had red eyes
all males had red eyes all males had white eyes
white eyes in Drosophila
Thomas Hunt Morgan (1917)
male with white eyes
female with red eyes (wt)
WW
x
Ww,
wW-
all F1 had red eyes
white eyes in Drosophila
Thomas Hunt Morgan (1917)
F1
Ww
x W-
F2
WW
W-
Ww
w-
white eyes in Drosophila
Thomas Hunt Morgan (1917)
male with red eyes
male with white eyes
female with red eyes (wt) female with white eyes
WW x
Ww,
wW-
all F1 had red eyes
ww
x
Ww,
W-
W-
all females had red eyes
all males had white eyes
white eyes in Drosophila
Thomas Hunt Morgan (1917)
F1
Ww
x W-
F2
F1
Ww x w-
F2
WW
W-
Ww
W-
Ww
w-
ww
w-
Fig. 3.29. Crosses of Drosophila.
© 2006 Jones & Bartlett
X-linked human conditions
hemophilia A
Duchennes Muscular Dystrophy
some color blindness
all recessive
pedigrees
(see fig. 2.17)
mating
female
male
normal
phenotype of interest
deceased
Fig. 3.30. Genetic transmission of hemophilia A among the
descendants of Queen Victoria.
© 2006 Jones & Bartlett
X-linked human conditions
most affected individuals are male
affected males have normal sons
women whose father is affected
will have 1:1 ratio of normal to
affected sons
birds, moths and butterflies
sex chromosomes are reversed
males
(XX)
ZZ
females
(XY)
WZ
Fig. 3.31. Sex determination in birds.
© 2006 Jones & Bartlett
Another Mendelian “glitch”
disjunction
separation of homologous
chromosomes during meiosis
(law of segregation)
About 1 of 2000 flies:
white-eyed female
or red-eyed male
?
© 2006 Jones & Bartlett
white-eyed female
or red-eyed male
Fig. 3.32. Nondisjunction
© 2006 Jones & Bartlett
Dosage
number of copies of a gene in a cell
Dosage compensation
mechanism to even out gene activity
of genes on the X chromosome
Dosage compensation
for XX-XY organisms
female has
male has
two X’s
one X
increase activity of X in males
reduce activity of X’s in females
Dosage compensation
in mammals:
one X chromosome in embryonic
female cells is randomly inactivated
Once inactivated,
it stays inactivated
in all descended cells
Dosage compensation
in mammals:
female cells have Barr body
http://www.britannica.com/ebc/art/print?
id=1690&articleTypeId=0
Dosage compensation
consequences of inactivating an X
# of active X genes are about
the same in males and females
female is a mosaic of cells with
different genotypes
Dosage compensation
female is a mosaic of cells with
different genotypes
XAXB heterozygote
cells will express only
XA or XB but not both
Dosage compensation
female is a mosaic of cells with
different genotypes
heterozygous for X-linked recessive gene that
results in the absence of sweat glands
some patches of skin have sweat glands
… other areas don’t have sweat glands
Dosage compensation
female is a mosaic of cells with
different genotypes
marsupials inactivation is not random
the male X is the one inactivated
Dosage compensation
female is a mosaic of cells with
different genotypes
calico cats:
alleles
black
X
orange
X
other white
http://www.nature.com/nature/journal/
v434/n7031/images/434279a-f1.2.jpg
3.7
more
probability and statistics
randomness
alignment of homologs
recombination of gametes
XX x
X
Y
X
XX
XY
X
XX
XY
XY
probability
0
1
never
always
probability of either of two
independent events happening
probability of one event
plus
probability of second event
(addition rule)
3.7
more
probability and statistics
probability of having a
daughter or having a son
1/2 + 1/2
= 1
X
Y
X
XX
XY
X
XX
XY
probability
0
1
never
always
probability of two independent
events both happening
probability of one event
times
probability of second event
(multiplication rule)
probability of having a daughter
and having a second daughter
prob. of having daughter
1/2
X
prob. of 2nd daughter
1/2 x 1/2 = 1/4
X
X
Y
XX
XY
XX
XY
to test the “goodness” of your data
Chi-square analysis
randomness
genetic events are like tossing a coin
sample size
as the sample size gets bigger the
deviation should become less
to test the “goodness” of your data
Chi-square analysis
null hypothesis
assume there is no (null) difference
between what you observe and what
you expected to observe
to test the “goodness” of your data
Chi-square analysis
statistical test to see if the null hypothesis
should be:
1) rejected
2) fail to be rejected
if we reject the null hypothesis, then it is
more than chance causing the difference
between observed and expected
(our genetic explanation is not too good)
to test the “goodness” of your data
Chi-square analysis
statistical test to see if the null hypothesis
should be:
1) rejected
2) fail to be rejected
if we fail to reject the null hypothesis, then it
is it likely that random chance caused the
difference between observed and expected
(our genetic explanation is supported)
Chi-square analysis
X2
sum (observed-expected)2
=
expected
of all
X 2 < 1 is usually a good sign
degrees of freedom:
n-1
n = number of different possible results
Chi-square analysis
X2
sum (observed-expected)2
=
expected
of all
flip coins
4 tosses;
record results
probability of getting worse results
great fit
good fit
not so good fit
really bad fit
Fig. 3.34. Chi-square test.
© 2006 Jones & Bartlett
Chi-square analysis
X2
sum (observed-expected)2
=
expected
of all
flip coins
10 tosses;
record results
probability of getting worse results
Fig. 3.34. Chi-square test.
© 2006 Jones & Bartlett
Chi-square analysis
analysis of Mendels F1 cross
ob
ex
ob-ex (o-e)2
315 312.75 2.25 5.06
round, yellow
108 104.25 3.75 14.06
round, green
wrinkled, yellow 101 104.25 -3.25 10.56
wrinkled, green 32 34.75 -2.75 7.56
556
X2 =
/ ex
0.016
0.135
0.101
0.218
0.470
probability of getting worse results
Fig. 3.34. Chi-square test.
© 2006 Jones & Bartlett
Done with chapter three for now
© 2006 Jones & Bartlett