OVERVIEW:
This lab has four sections.
First, you will prepare and observe cell squashes of onion root tips along
with observing commercially prepared slides of fly salivary glands.
You will see actual chromosomes arrested in the stages of mitosis in the
onion root, and you will see heterochromatic and euchromatic bands on the
polytene chromosomes found in fly salivary glands. This portion of
the lab should reinforce your understanding of what chromosomes are and
how they move during mitosis.
Second, you will conduct a quick mathematical exercise. You will use your understanding of the meiotic process to prove your genetic individuality. Bring your calculator!
Third, we will begin to look at some Mendelian genetics. Using corn as an example, we will observe a simple monohybrid cross.
Last, you will do a cut-and-paste exercise to familiarize yourself with karyotyping; a tool used by clinical geneticists to screen for genetic abnormalities. Based on arm ratios and banding patterns, you will sort chromosomes into homologous pairs, determine if there are any inconsistencies, and provide a genetic diagnosis of the human subject.
Section I. Chromosomes and Mitosis
A. Polytene Chromosomes of the Drosophila melanogaster.
1. Introduction
The larval stage of flies is primarily concerned with food-gathering, and large salivary glands aid in efficient digestion. These glands attain their large size by an increase in cell size, not an increase in cell number (as in most other organs). Even after mitotic divisions have stopped, the chromosomes continue to replicate as the cells enlarge. This produces thick chromosomes consisting of thousands of sister chromatids in a parallel arrangement. (this extra DNA may aid the oversized cell in satisfying its relatively large metabolic demand for enzymes and other proteins). This thickened mass is much easier to see than a single chromosome. And, as all the strands in these large polytene chromosomes are identical, they have the same areas of activity and banding.
These cells are locked in interphase permanently, and as a result, the chromosomes are elongated and active. The multiplicative effect of replication allows us to see areas of activity that would be impossible to distinguish in a single strand. These areas are bands. Areas that stain darkly are areas of high DNA concentration; the DNA is wrapped up so tightly it is largely non-functional. Light regions are areas where the DNA is diffuse; it is unraveled and active. When these areas are transcribed, the DNA uncoils, 'puffing out'. This creates a chromosomal puff which indicates active transcription. These are areas of highly concentrated RNA (as you might suspect!).
Additional anomalies also occur. First, the attractive forces of these strands is apparently very great; so great that homologous chromosomes often fuse in parallel (like synapsis in Prophase I of meiosis), thickening the strands even more. This effectively reduces the number of chromosomal bodies by half, giving these cells a haploid chromosome number. In addition, the ends of the chromosomes fuse at chromocenters. At this point, there is only one contorted chromosome; the infamous GIANT CHROMOSOME! The study of giant chromosomes has been of tremendous importance in genetics. Patterns of heredity and gene activity have been associated with specific regions and bands along the chromosome. So, giant chromosomes have helped geneticists understand how chromosome structure relates to function and gene expression.
2. Procedure
Observe the slides on demonstration on the front table. Answer the questions pertaining to the polytene chromosomes at the end of this laboratory section.
B. Onion Root Tip Squash - Mitosis
1. Introduction
Root tips are meristematic regions; areas of rapid cell division. They are the perfect place to look for cells proceeding through mitosis. During root development the meristematic region is located just behind the root cap, a protective covering on the root. This can be seen as the bright white tip in the preserved onion root tips we will use today in lab.
2. Procedures
a. Obtain two
small cups, label one HCl, and place enough HCl in to cover the
bottom.
b. Label the
other cup 'Carnoy', and cover the bottom with Carnoy solution.
c. Transfer an
onion root tip from the specimen bottle to your HCl cup. Leave for four
minutes.
d. After four
minutes, transfer the root tip to the Carnoy solution, and leave it for
four
minutes.
e. After four
minutes, transfer the root tip to a slide. Cut off the distal 1-2
mm, and
discard all but this tip.
f. Cover the
root tip in toluidine blue stain for two minutes.
g. After two
minutes, blot away the stain; do not touch the root tip!
h. After blotting
away the stain, cover the tip in water, and place a coverslip on the
slide.
i. Press on the
coverslip with an eraser; try not to twist the coverslip.
j. Find your
cells under low power, then use greater magnification to search the
tissue for cells in the various stages of mitosis. Recognize that
the process is
continuous; the discrete stages we have discussed are connected by
intermediate steps. Draw pictures of the stages you see, labeling
them as
appropriate. During telophase, notice cell wall deposition.
Section II. Your Genetic Individuality
Consider this: a diploid organism with 4 chromosomes (2n=4) can produce four different gametes (22), since chromosome 'A' of the first homologous pair is not identical to 'a' and 'B' is not identical to 'b'.
1st Homologous Pair = A a
2nd Homologous Pair = B b
Gametes: AB, Ab, aB, ab
An organism with 2n=6 can produce 8 gametes (23).
Extrapolate to an organism with 2n=46, such as Homo sapiens.
How many different kinds of gametes can one person produce?
Now, how many different zygotes can two humans produce? This is actually a gross underestimation of your uniqueness, since we haven't even considered recombination (crossing over)! Even so, this number is far in excess of the number of people who have ever lived, and so it is quite likely that you are 'one-of-a-kind' (but you knew that already, didn't you).
Section III: The Monohybrid Cross
1. Introduction:
Gregor Mendel, a nineteenth-century Austrian monk, devised a model that predicted patterns of inheritance. a report of his meticulous records, first printed in 1866, was discovered in 1900. The elements of heredity that Mendel called "factors" are now known to be genes. Even though Mendel did not know of chromosomes or genes, his work opened the door to an understanding of heredity. Mendel conducted his experiments with garden peas in three phases. First he established a true-breeding population. In this population of plants the offspring (F1, the First Filial Generation) carried the same characteristics as the parents.(P1). Mendel then crossed varieties of peas expressing alternative traits. For example, he crossed peas that were tall with peas that were dwarf. The offspring (F1) of these crosses would only express one of the two alternative traits. That trait which was expressed in the F1 generation was termed "dominant" while the alternative trait was termed "recessive". Finally, Mendel allowed the F1 offspring to self-pollinate (cross among themselves), and he counted and carefully recorded the number of each characteristic in the progeny. For the first time, numerical data pertaining to inheritance could be analyzed. Mendel discovered that the F2 generation (second filial generation) expressed alternative traits in a ratio of three of one trait to one of the alternate trait (3:1). This 3:1 ratio is a phenotype ratio. The phenotype of an organism is the observable features of an individual organism that result from an interaction between the genotype and the environment in which development occurs. The genotype is the genetic constitution of an individual, usually referring to specific characters under consideration. Thus, the two alternative alleles for the tall and dwarf genes of the pea plants could be written D and d. A capital letter is used to designate dominance while a lower case letter is used to designate the recessive trait. Mendel noted that traits always exist in pairs, thus for a plant showing the tall phenotype there are two possible genotypes DD and Dd. For a plant showing the dwarf phenotype there is only one genotype dd.
2. Procedure:
Observe the ears of corn.
Note that each kernel of corn is a seed that can establish an individual
plant. Thus, by counting the individual corn kernels, you are really
counting individual plants. Note the different characteristics of
the kernels. These are alternative traits, purple and yellow kernels,
follow Mendel’s observations. These ears of corn where obtained by
first crossing P1 that were all purple kernel (YY) plants with all yellow
kernel (yy) plants. The resulting F1 generation was then used to
produce the corn you are observing. Use these ears of corn to answer
the questions at the end of this laboratory exercise.
Section IV. Human Karyotype Analysis
Cytogenetics, the study of chromosomes, has its origin more than a century ago. However, not until the last 3O years or so have the human chromosome studies become a major field in the biomedical sciences. Chromosome banding methods, for example, are today's vital tools in clinical genetics and evolutionary studies. Furthermore, human cytogenetics coupled with molecular techniques has revolutionized the field of molecular genetics, including gene mapping and recombinant DNA technology.
Prior to 1956, the number of human chromosomes was estimated to be between 37 and 48. The difficulty of determining the exact chromosome number was due to the lack of proper techniques for cell culture and for spreading the chromosomes for microscopic observations. In the 1950's two major breakthroughs led to the rapid advancement in human cytogenetics: (1) the use of phytohemaglutinin (PHA), a substance from plants, to stimulate cell division of lymphocytes (white blood cells), so that a large amount of cells in metaphase could be obtained, and (2) the use of hypotonic (low salt) solution to cause cells to absorb water and swell, resulting in spreading and separating the individual chromosomes, so that they were readily distinguishable. In 1956, researchers in Sweden systematically counted 46 chromosomes in human cells. Three years later, the discovery of an extra chromosome 21 in patients with Down syndrome marked the beginning of clinical application of chromosome studies, and soon the identification of other chromosome disorders followed.
Conventional dyes such as aceto-orcein used for direct chromosome staining could only distinguish chromosomes according to their sizes and centromere positions. On the basis of these two criteria, human chromosomes were classified into seven groups, A to G. Accurate chromosome identification started in the late 1960's when quinocrine mustard (QM) was used to stain human chromosomes. With this technique, chromosomes were differentiated into bright and dark regions, called Q-bands. Since then, numerous banding techniques have been developed. Of these, G-banding is the most widely used technique for chromosome analysis. The banding techniques are extremely useful for the detection of structural changes. Clinical applications include the association of chromosome disorders with numerous diseases, including cancers.
Today chromosome analysis of cultured amniotic fluid cells is routinely performed in medical genetics laboratories for prenatal diagnosis. For structural changes which are too small to be detected by direct microscope examinations, other approaches, such as the use of known DNA sequence (DNA probe) to hybridize the homologous DNA of the chromosome (in situ hybridization), are available. The integration of cytogenetics with molecular technology has thus opened up an exciting field in modem biology.
Chromosome Morphology
1. The Cell Cycle
Chromosomes are not visible under the light microscope in non-dividing (interphase) cells. As the cell begins to divide, the threads of chromatin (DNA-protein complex) in the nucleus start to condense into multiple levels of coiled structure recognizable as chromosomes. There are two types of cell division: mitosis and meiosis. Mitosis is responsible for the proliferation of body (somatic) cells, whereas meiosis is responsible for the production of gametes. Because mitotic cells are easy to obtain, morphological studies are generally based on mitotic metaphase chromosomes.
The
transition of interphase to cell division (mitosis) and back to interphase
is called the cell cycle. For a dividing cell the interphase can
be divided into three stages: G1, S, and G2. (G means gap.) During the
G1 stage, cytoplasmic components such as membranes, organelles, and ribosomes
begin to proliferate. G1 is followed by S stage during which DNA
synthesis occurs so that the amount of DNA per chromosome is doubled, resulting
in two sister-chromatids visible during prophase and metaphase. S
is followed by a second period of growth, the G2 stage. At the end
of the G2 stage, the cell starts to divide, thus entering the M (mitosis)
stage. When the cell is not cycling, the interphase is said to be
in Go. The cell cycle for human cells averages about 24 hours (8
h for G1, 10 h for S, 5 h for G2, and 1 h for M).
Mitosis can be divided into four phases: prophase, metaphase, anaphase, and telophase. During prophase, chromosomes, consisting of two chromatids each, condense and undergo progressive coiling. In the early prophase they appear as thin threads. At the middle of late prophase the chromosomes can be seen as discrete structures, each with two chromatids and a constricted area called the centromere where the two chromatids are joined. The transitional period from late prophase to metaphase is called prometaphase, during which the nuclear envelope breaks down and the chromosomes move toward the equatorial plane (metaphase plate) of the cell.
2. Chromosome structure
At metaphase, the chromosomes are at the most condensed state with spindle fibers attaching to the area of the centromere called kinetochore, forming pole-chromosome fibers. The fibers which by-pass the centromeres are called pole-pole fibers. Anaphase begins with the division of the centromere and the separation of chromatids. Once separate, each chromatid is now known as a chromosome. Telophase marks the final stage of mitosis, during, which the cell undergoes a reverse process of prophase, including chromosome uncoiling, spindle fiber disappearing, and nuclear envelope and nucleolus reappearing. At the same time, the cytoplasm is divided (cytokinesis) into two parts, forming two daughter cells.
The best mitotic stage for chromosome analysis is prometaphase or metaphase. A typical metaphase chromosome consists of two arms separated by a primary constriction or centromere. Each of the two sister-chromatids contains a highly coiled double helix of DNA. A chromosome may be characterized by its total length and the position of its centromere (Fig. 2). A chromosome with the centromere at or near the middle is called metacentric. A submetacentric chromosome is referred to as the one with a centromere somewhat off the middle point. If the centromere is obviously off center (e.g., halfway between the middle and the tip of the chromosome), the term acrocentric may be used. Telocentric chromosomes, which are absent in human cells, have the centromere at the very tip of one end. The short chromosome arm is designated p (petite) and the long arm q (one letter after p). Certain human chromosomes may also contain a secondary constriction, which appears as an unstained gap (also called a satellite stalk) near the tip. The chromosomal segment distal to this gap appears as a satellite. Chromosome numbers 13-15 (D group) and 21-22 (G group) have satellites.
3. Chromosome number
The diploid chromosome number is the number of chromosomes in the somatic cell and is designated by the symbol 2N. The gametes, which have one-half the diploid number, have haploid number N. In humans, the diploid number is 46, with 23 from each parent through the sperm or the egg. Same (homologous) chromosomes form a pair with one member from each parent. Thus, there are 23 pairs of chromosomes in human cells. Of these, 22 pairs are not directly involved in sex determination, known as autosomes. The remaining chromosome pair which is directly involved in sex determination is called the sex chromosome. In females the two sex chromosomes are identical (XX); whereas in males the two sex chromosomes are not identical (XY). The Y chromosome is smaller than the X chromosome. A gene which is responsible for switching the embryo to male characteristics was recently discovered in the Y chromosome.
4. G-banding
The purpose of banding techniques is to uniquely identify chromosomes or portions of chromosomes, both normal and abnormal. Most laboratories in this country use a form of Giemsa banding (G-banding) as a general purpose banding method. Giemsa reagent is a DNA stain which consists of a mixture of dyes including the basic aminophenothiazine dyes (azure A, azure B, azure C, thionin, and methylene blue) and the acidic dye (eosin). Prior to staining, some form of protease (an enzyme which digests proteins) treatment is needed. This technique produces patterns of light-staining (G-light) regions and dark-staining (G-dark) regions. The pattern is consistent to each chromosome, and, therefore, it serves as a landmark for chromosome identification.
The G-light bands are thought to be relatively GC-rich, and the G-dark bands relatively AT-rich. Furthermore, the light bands represent the regions which are relatively open and which contain most of the genes including housekeeping genes (genes active in every cell type). On the other hand, the G-dark bands represent regions which are relatively compact and contain few genes. The genes in the dark regions are mainly tissue specific.
It should be noted that the pattern of light and dark bands changes with the stage in mitosis, ranging from 300 or less in late metaphase to more than 1000 bands in early prophase. As mitosis progresses, bands coalesce, accounting for the reduction of bands. Most routine lab work is done at 350-400 band level. For critical analysis, special techniques must be employed to produce 550 or more bands, known as high resolution analysis.
5. Karyotype
The term karyotype refers to a display of the chromosomes of a cell by lining them up, beginning with the largest and with the short arm oriented toward the top of the karyotyping sheet. A diagram of karyotype based on chromosome measurements in many cells is called an ideogram.
6. Nomenclature
Human chromosome nomenclature systems were developed in six international conferences on chromosome nomenclature. Two systems, one short and the other detailed, are currently used by cytogenetists. For writing a karyotype description, work from left to right and leave no spaces. Separate each item with a comma unless otherwise specified. The karyotype formula begins with the total number of chromosomes in the cell which is followed by the sex chromosomes (first the X's and then the 'Ys). For example, the formula for a normal male is "46,XY" and for a normal female is "46,XX". An extra or a missing chromosome is designated with a "+" or "-" sign, respectively, before the number of chromosome. Thus, a male with trisomy (three chromosomes) for chromosome 18 is 47, XY, + 18, and a female with a monosomy (one chromosome) for 22 is 45, XX -22. Addition or deletion of a chromosome segment is denoted with a plus "+" or "-" sign after the symbol of the chromosome arm, respectively. For example, the formula for a female with the cri du chat syndrome (resemblance of the cry of an affected newborn to cat mewing) is 46, XX, 5p-(missing a piece of short arm of chromosome 5). The formula for a male with translocation (exchanging chromosome segments) between chromosome 14 and 21 is 46, XY, t(14-21).
The following is a partial list of symbols for chromosome nomenclature.
A-G The chromosome groupsObjectives:
1-22 The autosome numbers
X,Y The sex chromosomes
del Deletion
der Derivative of chromosome
dup Duplication
ins Insertion
inv Inversion
p Short arm of chromosome
q Long arm of chromosome
s Satellite
t Translocation
+ or - Placed before the chromosome number, they indicate addition (+)
or loss (-) of the whole chromosome; e.g. +21 denotes an extra
chromosome 21, as in Down syndrome. Placed after the
chromosome number, these symbols indicate increase or decrease
in the length of the chromosome part; e.g., 5p- indicates loss of part
of the short arm of chromosome 5, as in cri du chat syndrome.
1. To learn the human chromosome classification system
2. To use G-banding landmarks to identify individual chromosomes
3. To learn the karyotyping procedure
Procedure:
1. First, familiarize yourself
with such terms as metacentric, submetacentric, very
submetacentric, acrocentric; p arm, q arm; proximal and distal regions
of a
chromosome arm; and satellite. Then study the banding pattern of
each
chromosome as well as the grouping of chromosomes from A to G (based on
size,
X chromosomes belong to C group and Y chromosomes belong to G group).
Note
that groups D and G are the only two groups having acrocentric chromosomes
with
satellites.
2. Count the total number of chromosomes on your work sheet (Metaphase Spread).
3. Use scissors to cut out each chromosome from the Metaphase Spread.
4. Arrange all individual
chromosomes according to size, with the longest one first, on a
smooth surface such as the clean lab bench.
5. Group similar chromosomes as a pair if possible.
6. Read the description of
the Human Chromosomes (below) and arrange each pair of
chromosomes.
7. When some of the chromosomes
are identified, place them on the Karyotype Form.
Critically identify the location of the centromers for each chromosome
and be sure
that the p arm is up and the q arm is down; upside down chromosomes are
frequent sources of misidentification.
8. Check with your instructor
for accuracy. When all the chromosomes are correctly
identified, arrange on the karyotype form. Use a glue stick to glue each
chromosome picture firmly on the Karyotype Form.
9. Write on the top of the Worksheet the karyotype formula of your sample.
Human Chromosome Descriptions
Chromosome 1 (Group A)
The longest chromosome,
metacentric; p arm fading at distal end, with least 2 dark bands above
centromere; q arm with a dark area just below centromere, a light band
below, followed by 4 dark bands of which the middle 2 are often more intense.
Chromosome 2 (Group A)
Almost as long as chromosome
1, submetacentric; p arm without light distal end, with 4 dark bands; q
arm with more than 4 dark bands.
Chromosome 3 (Group A)
Metacentric; both p and
q arms with a large light band in the middle; dark area (consisting of
2 or 3 close dark bands) distal to the light band of q arm thicker than
its counterpart in p arm.
Chromosome 4 (Group B)
Very submetacentric, p arm
with a thick dark band which may sometimes be resolved as double; q arm
with a distinct, prominent dark band below centromere.
Chromosome 5 (Group B)
Very submetacentric; p arm
with a single dark band; q arm without a prominent dark band below centromere,
with 3 close dark bands in the middle.
Chromosome 6 (Group
C)
Submetacentric; p arm with
a distinct, large light band in the middle; q arm with several dark bands.
Chromosome 7 (Group C)
Submetacentric; p arm with
a prominent flat dark band at the top; q arm with 2 distinct dark bands
followed by a much less intense dark band.
Chromosome 8 (Group C)
Very submetacentric; p arm
with 2 dark bands (sometimes unclear); q arm
with 2 (sometimes 3) dark bands, the distal dark band characteristically
more intense.
Chromosome 9 (Group C)
Varying from slight submetacentric
to very submetacentric; p arm with a broad (often square in shape ) dark
band (which may be resolved as double); q arm with a variable, proximal
light area (from as long as the p arm to almost non-existent) followed
by two distinct, equally intense broad dark bands with a light band between
them, these.' ) bands (2 dark bands and one light band) equal in thickness.
Chromosome 10 (Group C)
Submetacentric; p arm with
a dark band; q arm with 3 distinct dark bands, the proximal dark band most
intense.
Chromosome 11 (Group C)
Submetacentric; p arm with
I or occasionally 2 dark bands; q arm with a very large light area followed
by a dark band which may be resolved into 2 dark bands.
Chromosome 12 (Group C)
Very submetacentric; p arm
with a dark band; q arm with a proximal light band (which is relatively
thinner than the counterpart of chromosome I 1) followed by a dark area
in the middle which may be resolved into 2, or more often 3, bands.
Chromosome 13 (Group D)
Acrocentric- p arm with
satellites (visible or invisible); q arm with several dark bands.
Chromosome 14 (Group D)
Acrocentric; p arm with
satellites (visible or invisible); q arm with a distal dark band which
is more intense than other dark bands.
Chromosome 15 (Group D)
Acrocentric; p arm with
satellites (visible or invisible); q arm with dark proximal half and light
distal half
Chromosome 16 (Group E)
Metacentric or occasionally
submetacentric; p arm light or slightly dark; q arm with a prominent dark
band just below centromere, followed by I or 2 lesser dark bands.
Chromosome 17 (Group E)
Submetacentric or very submetacentric;
p arm with a thin dark band (may be invisible); centromere dark followed
by a distinct, large light band occupying most part of q arm, q arm with
I or 2 distinct dark bands near the terminal end.
Chromosome 18 (Group E)
Submetacentric or very submetacentric;
p arm often uniformly dark; q arm with 2 distinct dark bands, one proximal
and one distal; the light band between these 2 dark bands slightly smaller
than the counterpart of chromosome 17.
Chromosome 19
(Group F)
Metacentric; p and q arms
both light; centromere dark.
Chromosome 20 (Group
F)
Metacentric; p arm dark;
q arm light, with 2 narrow, less intense dark bands.
Chromosome 21 (Group
G)
Acrocentric; p arm with
satellites (visible or invisible); q arm with intense dark area proximally,
fading out toward distal end.
Chromosome 22 (Group G)
Acrocentric; p arm with
satellites (visible or invisible); centromere dark; q arm with a narrow,
less intense dark band.
X Chromosome (sex chromosome)
Submetacentric; p arm with
distinct, strong dark at the middle; q arm with a proximal dark band about
the same distance from the centromere as the p arm dark band, with two
less intense dark bands near distal end.
Y Chromosome (sex chromosome)
Very submetacentric; p arm
very short or invisible; q arm dark throughout.
Section IV. Wrap-Up
Make sure your station is clear and equipment is away.
1. Draw a Giant Chromosome. Label
euchromatin, heterochromatin, and
chromocenter.
a. How do polytene
chromosomes form?
b. Describe the
functional activity of dark and light bands.
2. Draw the stages of mitosis as seen in
the onion root tip.
3. How many genetically different
gametes can one person produce? How many
different zygotes can two people make?
4. a. Using the symbols YY for the purple
kernels and yy for the yellow kernels, show the
genotype of the F1 generation.
b. What would
be the phenotype of the F1 generation?
5. a. What would
be the genotypes and their ratios from a cross between two F1
individuals?
b. What would be the phenotypes and their ratios from a cross between two
F1
individuals?
6. Count the kernels on one ear of corn.
Number of Purple Kernels ________________
Number of Yellow Kernels_________________
Does this data fit the expected
Mendelian phenotype ratio? Use a Chi-Square test to
support your answer.
7. What letter was on your Karyotype
sheet? What was the karyotype of your patient?
How did you reach this conclusion? What are the physical manifestations
of this
genetic disorder?
8. Write a formula for a :
a. male with Down syndrome
(due to the presence of an extra chromosome 21)
b. female with
Turner Syndrome (only one X chromosome)
c. female with cri du
chat syndrome (deletion of a portion of p arm of chromosome 5
d. male with Klinefelter
Syndrome (two X chromosomes and one Y chromosome)
e. female with
a Philadelphia chromosome (translocation between chromosomes 9
and 22). People suffering from a form of leukemia (chronic myeloid
leukemia)
frequently harboring cells containing the Philadelphia chromosome.
9. DISCUSSION QUESTION: Abnormalities
in chromosome number are detrimental and usually lethal. Speculate
as to why the impacts of abnormal number in chromosome 21 and in the X
chromosome are relatively mild. [HINT: USE YOUR TEXTBOOK AS
A REFERENCE - LOOK UP DOWN'S AND SEX CHROMOSOMES]