Test 2 Study Guide Part 1

What are the General Features of Chromosomes?

* This study guide is arranged in order of how the material was covered in class.* Chapter 3: Chromosome Transmission during Cell Division and Sexual Reproduction 

1. General Features of Chromosomes 

a. Prokaryotes

i. Nucleoid region

ii. Circular double stranded DNA

iii. Rigid Cell wall

b. Eukaryotes

i. Mostly diploid

ii. Linear DNA in membrane bound nucleus

iii. 40% DNA and 60% proteins make up chromosomes (chromatin)

iv. Organelles (some contain their own DNA)

v. 2 Types of Animal cells

1. Somatic: 2n

2. Germ Cells (Gametes): n

vi. 2 sets of chromosomes

1. Form homologous pairs containing 2 homologues that are

1. Are nearly identical in size  

2. Have the same banding pattern

3. Have the same centromere location

i. Metacentric: middle

What is Cytogenetics?

ii. Sub Metacentric: close to middle

iii. Acrocentric: close to end

iv. Telocentric: end

4. Have the same genes (not necessarily the same alleles)

2. Humans

1. 46 total chromosomes (23 per set)

c. Cytogenetics

i. Microscopic examination of chromosomes (from dividing cells).

ii. Cytogeneticists examine the chromosomal composition of a particular cell  or organism

1. Detect individuals with abnormal # or structure

2. Distinguish between 2 closely related species

iii. Karyotype: Complete complement of homologues in order of size

1. Know how karyotype is built

2. Cell Division 

a. Purposes: Asexual reproduction and multicellularity

b. Binary Fission: Reproduction in Bacteria

i. Increase nutrients and volume

ii. Signal produced by cell to induce division

iii. DNA replicated and cell elongates (FTsZ present)

What is Cell Division?

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iv. FTsZ proteins form septum Z (ring structure that separates DNA  

v. Constriction by FTsZ

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vi. Other proteins come in to allow cell to create a septum in the middle and  split.

3. Mitosis

a. G0: Postponed division or never will divide again

i. Ex: Nerve cells  

b. Interphase

i. Chromosomes decondensed (cannot be condensed in interphase)

1. G1: First Gap

2. Increases density and volume

3. Restriction point: committed on pathway to divide

ii. S: Synthesis

1. DNA, Histones, Centromeres replicate

2. 2 copies of replicated DNA are chromatids and they join at the  

centromere to form a pair of sister chromatids (dyad)

iii. G2: Second Gap

1. Cell accumulates materials necessary for division  

1. Organelles replicate We also discuss several other topics like · What is the difference between satellites and radar?

2. Kinetochore deposition (protein deposited around  

centromere)

c. Prophase We also discuss several other topics like soc gen 5 ucla

i. Chromosome compaction

1. Euchromatin (300nm) to heterochromatin (700nm)

2. No nucleolus

ii. Nuclear membrane converted to vesicles

iii. Physical assembly of spindle apparatus

1. Aster Microtubules: hold spindle apparatus together

2. Polar Microtubules: Help push poles away from one another

3. Kinetochore Microtubules: attach to sister chromatids

4. All microtubules made of α and β tubulin

d. Prometaphase  

i. Spindle fibers polymerize and interact with sister chromatid pairs and  connect each pair to both poles

ii. If kinetochore microtubules make contact with a sister chromatid pair,  they connect. If not, they depolymerize.

e. Metaphase

i. Sister chromatid pairs align along the metaphase plate

f. Anaphase

i. Connection holding sister chromatids breaks

ii. Kinetochore microtubules depolymerize and pull each sister chromatid to  opposite poles. We also discuss several other topics like organic chemistry exam 3

iii. Polar microtubules polymerize, pushing poles farther apart

iv. Proper sorting of sister chromatids

v. # of chromosomes maintained in this step

g. Telophase

i. Chromosomes reach their respective pole and decondense.  

ii. Nuclear membrane reforms to form 2 separate nuclei

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h. Cytokinesis

i. In animals: formation of cleavage furrow

1. Actin fibers overlap and depress to create cleavage furrow

ii. In plants: formation of cell plate

iii. Ultimately produces 2 identical diploid daughter cells

4. Meiosis

a. Sexual Reproduction: The most common way for eukaryotic organisms to  produce offspring

b. Haploid cells are produced from diploid cells

c. Some species are isogamous (produce gametes that are morphologically similar)  but most are heterogamous (gametes are morphologically different)

d. Meiosis begins after Interphase (G1, S, G2)

e. Contains 2 divisions

f. Meiosis I:

i. Prophase:  

1. Leptotene: Replicated chromosomes condense and homologues  

seek one another out

2. Zygotene: Bivalents and Synaptonemal complex forms

3. Pachytene: Crossing over has occurred; recombination nodule:  

enzymes recognize areas of homology, make breaks and create  Don't forget about the age old question of 600000/30000

exchanges

4. Diplotene: Synaptonemal complex dissociates

5. Diakinesis: Nuclear envelope fragmenting

1. Homologues always move together.  

ii. Prometaphase:  

1. Spindle apparatus is complete  

2. Chromatids attached to poles via kinetochore microtubules

iii. Metaphase

1. Bivalents line along metaphase plate

2. Sister chromatids now aligned in a double row.

3. Arrangement is random with regards to the homologues

4. Each pair of sister chromatids is connected to one pole

iv. Anaphase

1. The step where reduction division occurs

2. Homologues separate from one another

3. Connection holding sister chromatids does not break!

v. Telophase and Cytokinesis

1. Sister chromatids reach respective poles and decompact

2. Reappearance of nuclear membrane to form 2 separate nuclei

3. Cytokinesis (division)

g. Interphase 2

i. G1

ii. G2

iii. No S because DNA is already replicated Don't forget about the age old question of kutztown university nursing

h. Meiosis II

i. Similar to mitosis

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ii. Prophase: Similar to Mitosis except there are less chromosomes

iii. Metaphase: Connected to both poles

iv. Anaphase: Sister chromatids separated into single chromosomes

v. Telophase and Cytokinesis: Nucleolus reappears, chromosomes  decompact, complexes reappear.

vi. Results in 4 genetically different haploid gametes

5. Spontaneous Aneuploidy

a. Isodisomy: Non disjunction in Meiosis II

i. Two normal gametes, one empty gamete, one gamete with 2 sets of  chromosomes

b. Heterodisomy: Non disjunction in Meiosis I  

i. 2 gametes end up with nothing, the other two have two sets of  

chromosomes

c. The correction for Heterodisomy is to reject the paternal chromosome to end up  with the right number of chromosomes

6. Spermatogenesis

a. Production of sperm

b. In male animals, it occurs in the testes

c. A diploid spermatogonium cell divides mitotically to produce two cells d. Primary spermatocyte progresses through meiosis I and II  

e. 4 resulting spermatids undergo differentiation to mature into haploid sperm cells i. Gain a head and a long flagellum

ii. Head contains the nucleus and is capped by the acrosome which lets the  sperm cell penetrate the egg cell

7. Oogenesis

a. Production of egg cells

b. In female animals, it occurs in the ovaries

c. Early in development, diploid oogonia produce diploid primary oocytes. These  undergo mitosis and become a secondary oocyte and a polar body

(Asymmetrical cytokinesis). The secondary oocyte undergoes meiosis II to  become the egg.  

8. Gamete Formation in Plants

a. Life cycles of plant species alternate between haploid and diploid organisms. i. Gametophyte: haploid: have specialized cells that produce gametes ii. Sporophyte: diploid:  

1. Sori: specialized cells that undergo meiosis to form spores which  

undergo mitosis to form the gametophyte

b. Angiosperms: Plants with seeds

i. Go through 3 rounds of mitosis to produce 7 total cells (asymmetrical  cytokinesis)

ii. Embryo sac composition

1. Egg

2. Synergids

3. Antipodals

4. Central cell (2 polar nuclei)

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iii. Once tube cell and generative cell are formed, they differentiate to  

produce a pollen grain.

iv. Pollen grain comes in contact with stigma and tube cell becomes a tube  that extends into the ovule. Generative cell undergoes mitosis and the  

resulting 2 cells become sperm

v. 1st sperm fertilizes the egg. 2nd sperm fertilizes the central cell (double  fertilization). Central cell is then the endosperm that provides storage  material for the developing embryo.

vi. Ovule becomes the seed and the rest becomes the fruit

9. Sex determination

a. In some insects,  

i. Males are XO females are XX

b. In other insects (Ex: fruit fly)

i. Males are XY females are XX

c. Humans have X and Y: Y determines maleness

d. Haplo-diploid system: Ex: Bees

i. Males are known as the drones: haploid

ii. Females are the workers and queen: diploid

e. Alligators

i. @ 33°C you get male, below that you get female

f. Reciprocal crosses

i. Crosses between different strains in which the sexes are reversed

ii. Reveals whether a trait is carried on an autosome or a sex chromosome

Chapter 10: Chromosome Organization and Molecular Structure 

1. Introduction

a. Genome is comprised of all the chromosomes that an organism possesses. b. Extrachromosomal DNA comes from either the mitochondria or the chloroplasts c. At the molecular level, the main function of the chromosomal sequences are i. Synthesis of RNA and cellular proteins

ii. Proper segregation of chromosomes

iii. Replication of chromosomes

iv. Compaction of chromosomes

2. Viruses

a. Now considered living

b. Small infectious particles containing nucleic acid surrounded by a capsule of  proteins.

c. For replication, rely on host cells

d. Target a specific # of cells

e. Limited host range

f. Bacteriophages may also contain a sheath, base plate and tail

g. Head

i. Icosahedron: 20 equilateral triangles binded together  

ii. Most symmetrical

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iii. Contains genetic material

h. Retrovirus: AIDS

i. Lytic cycle: virulent viruses

i. Enter cell, synthesize, multiply, lysis

ii. All viruses go through lytic phase

iii. Mobilomes: mobile genetic elements between species

j. Lysogenic Cycle: Dormant phase

i. Integrate nucleic acid into genome of infected cell (prophage)

k. Viral genomes

i. Most complex viral genome = evenphages

ii. Genetic material of the virus

iii. Can be DNA or RNA, Single stranded or double stranded, circular or  linear

iv. Shape of genome determines shape of virus

v. Vary in size from a few thousand to more than a hundred thousand  nucleotides

vi. During infection process mature viral particles are assembled

1. Simple structured viruses may self-assemble

2. Complex viruses: directed assembly

1. Proteins of host assemble viral proteins, proteases break  

down proteins to correct length, assembly then occurs

i. Ex: T2  

3. Non capsid proteins have 2 main functions

1. Carry out assembly process

2. As proteases that cleave viral capsid proteins

3. Bacterial Chromosomes

a. Found in nucleoid (not membrane bound)

b. May have 1-4 identical copies of the same chromosome

c. Million bp in length

d. 1 origin of replication

e. Chromosomal DNA compacted about 1000 fold.

i. This involves formation of loop domains (50-100 loops w/ 40,000 – 80,000 bp) = 10 fold

ii. Supercoiling/ twisting = 1000 fold

f. Chromosome Function – Influenced by DNA supercoiling

i. Chromosomal DNA in bacteria is negatively supercoiled

1. 2 effects

1. Helps in the compaction of the chromosome

2. Creates tension that may be released by DNA strand  

separation

2. DNA topoisomerase II

1. DNA gyrase induces (-) supercoil and relaxes (+)  

supercoils

2. DNA topoisomerase I relaxes (-) supercoils

3. Look at slide to see how this works

4. Eukaryotic Chromosomes

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a. Eukaryotes have one or more sets of chromosomes composed of several different  linear chromosomes

b. DNA - protein complex = chromatin

c. Variation not related to complexity of species

d. Genome size based on number of introns (repetitive sequences)

5. Organization in Eukaryotic Chromosomes

a. 3 types of DNA sequences are required for chromosomal replication and  segregation

i. Origins of replication: humans have several

ii. Centromeres: point, regional (125 bp) (CENP – A)

iii. Telomeres: maintain length and prevent digestion of chromosome.  Prevent translocation (when a piece of chromosome breaks off).

b. Centromere, Telomere = heterochromatin

c. Point centromere = lower organism

d. Regional centromere = tandem repeats (small 10-60 bp repeated) up to million  bp long, no H3 histone in centromere region (CENP – A) instead)

6. Repetitive Sequences:  

a. Sequence complexity: # of times a particular base sequence appears in the  genome

b. Unique or non-repetitive: Found once or a few times in a genome i. Includes structural genes as well as some intergenic areas

c. Moderately repetitive: Found a few hundred to a few thousand times i. Ex: Genes for rRNA and histones, origins of replication, transposable  elements (retroelements), regulation of gene transcription and translation d. Highly repetitive: Found tens of thousands to millions of times

i. Each copy is relatively short

ii. Some sequences are interspersed throughout the genome

iii. Ex: Alu family in humans. 300 bp long and is found every 5000-6000 bp iv. Other sequences are clustered together in tandem arrays

1. Ex: AATAT, AATATAT sequences in drosophila

2. Commonly found in centromeric regions

7. Eukaryotic Chromatin Compaction

a. Compaction of linear DNA in eukaryotes involves interactions between DNA and  various proteins

b. Nucleosomes

i. Repeating structural unit within eukaryotic chromatin

ii. Composed of double-stranded DNA wrapped around an octamer of  histones

1. Octomer = 2 copies each of H2A, H2B, H3, H4

2. 146 bp of DNA make 1.65 negative superhelical turns around the  

octamer

c. On an average human…  

i. 100 nm cell with 2-4 nm nucleus and 3 billion bp in DNA

ii. To fit DNA in nucleus, 2nm wide strands wrap around an octamer of  histones to make an 11nm wide nucleosome. H1 compacts further into a  random “zig zag” pattern that makes it 30nm wide.

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1. Positive tails of histones interact with negative phosphates on  

DNA

iii. The part of DNA wrapped around octamer has 146-147 bp. Nucleosome  and DNA coming off has a total of 200 bp w/ linker proteins in 1 histone d. Rate of renaturation

i. Experiment

1. Break H bonds and make them single stranded DNA (denatured)

2. Let settle and remove denaturing agents; DNA will renature

ii. Highly repetitive sequences will renature fastest (can find their partners  easy because there are so many copies)

iii. Unique sequences take longest

e. Nucleosome structure

i. Know experiment carried out by Markus Noll with DNase I and DNA  ii. Bead on a string model

f. Further compaction

i. At bead on a string level, DNA has been compacted 49 fold

ii. Third level of compaction involves interaction between the 30nm fiber and  the nuclear matrix to form radial loops.

iii. SARS and MARS: sequences of DNA that attach DNA to nuclear matrix  to form radial loops.

iv. During replication, every part of chromosomes unwind but SARS and  MARS never detach

v. Euchromatin:

1. Sparsely stained

2. Lightly compacted (30nm)

3. 300nm radius

4. Transcriptionally active

5. Most of the chromosome is Euchromatin

vi. Heterochromatin:

1. Thick staining

2. Densely compacted

3. 700nm radius

4. Don’t know level of compaction

5. Transcriptionally inactive  

6. Localized to centromeres and telomeres usually

vii. Constituted Heterochromatin

1. Always compacted, never unwind during gene expression.

1. Ex: centromeres and telomeres

viii. Facultative Heterochromatin

1. Doesn’t stay compacted during gene expression

1. Ex: Barr Bodies

8. Metaphase Chromosomes  

a. As cells enter M phase, the level of compaction changes dramatically i. By the end of prophase, sister chromatids are entirely heterochromatic ii. 2 parallel chromatids have an overall diameter of 1,400

b. Undergo little transcription

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c. 2 multiprotein complexes help to form and organize metaphase chromosomes i. Condensin

1. Critical role in chromosome condensation (tie together) which  

plays a role in compaction

ii. Cohesin

1. Plays a role in sister chromatid alignment

iii. Both are classified as SMC proteins

1. Structural maintenance chromosomes

iv. Separase: enzyme that breaks down cohesin  

Chapter 8: Variation in Chromosome Structure and Number 

1. Introduction

a. Genetic variation: genetic differences between members of the same species of  those of different species

b. A change in chromosome number is called a genome mutation

i. The result of changes in the number of sets of chromosomes of numbers of  individual chromosomes in a set

2. Cytogenetics

a. Microscopic examination of chromosomes

b. Cytogeneticist examines the chromosomal composition of a particular cell or  organism

c. Cytogeneticists use three main features to identify and classify chromosomes i. Size  

ii. Location of the centromere: metacentric, telocentric, acrocentric, sub  

metacentric

iii. Banding patterns

iv. These features are seen in a Karyotype

d. For detailed identification, chromosomes are treated with stains to produce  characteristic banding patterns

i. Ex: G-banding

1. Chromosomes exposed to Giemsa dye

2. Some regions bind the dye heavily to produce dark bands

3. Some regions do not bind the stain well and make light bands

e. In humans

i. 300 G bands are seen in metaphase

ii. 2000 G bands in prophase

3. Mutations Can Alter Chromosome Structure

a. There are two primary ways in which the structure of chromosomes can be altered i. The total amount of genetic information in the chromosome can change 1. Deficiencies/Deletions: Ex. Cri du chat, Angelman, Prader Willi

a. Terminal deletion: Terminal segment of chromosome is  

lost

b. Interstitial Deficiency

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i. Any piece not connected to the chromosome will be  

digested

ii. Very dangerous!  

c. Most common deletions occur in misaligned crossover (can  

also result in duplication or both at the same time)

2. Duplications

3. Intensity in which gene disease will show depends on length of  

chromosome and how many genes have been deleted or duplicated

4. Moderately repetitive sequences present in multiple locations and  

still function may affect intensity

ii. The genetic material remains the same, but is rearranged

1. Inversions  

2. Translocations

3. Person with inversion or translocation usually has a normal life but  may be sterile because the homologues can’t align

b. FISH

i. Fluorescent Insitu Hybridization

ii. Used to detect deletions and duplications

iii. Cytogenetic method: looking at bands after staining

iv. Molecular method: (Review methods)

1. Locus Specific probes: look at small segments of DNA that have  

been deleted or duplicated

2. Small Probes: Identify centromeres and telomeres using FISH

3. Paint Probes: Not popular. Use segments of DNA for entire  

chromosome. Very expensive

4. Duplications and Gene Families

a. Most small duplications have no phenotypic effect

b. Can have benefits

i. Alternative splicing

ii. Paralogues

iii. Turn to new genes by obtaining slightly different characteristics

c. Provide raw material for additional genes leading to the formation of gene  families (two or more genes that are similar to each other)

d. Globin gene family

i. Composed of 14 homologous genes on three different chromosomes ii. Myoglobin: better at binding and storing oxygen in muscle cells

iii. Hemoglobin: better at binding and transporting oxygen via red blood cells 5. Inversions

a. Pericentric: centromere lies within inverted region

b. Paracentric: centromere lies outside inverted region

c. Rarely, a person with inversions can have deleterious effects

d. A great number of inversions have no phenotypic effects

e. Rarely, there are phenotypic effects

i. Break point effect: breaks leading to inversion occur in a vital gene ii. Position effect: gene is repositioned in a way that alters its gene  

expression

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f. 2% of the population has inversions seeable under light microscope i. Most are phenotypically normal

ii. Can produce offspring w/ genetic abnormalities

6. Inversion Heterozygotes

a. Individuals with one copy of a normal chromosome and one copy of an inverted  chromosome

b. May be phenotypically normal

c. May have high probability of producing abnormal gametes

d. During Meiosis I, homologous chromosomes synapse with each other i. Inversion loop must form to compensate for inverted sequence

1. If crossover happens in an inversion loop, highly abnormal  

chromosomes are produced

7. Translocations

a. When a segment of one chromosome becomes attached to another

b. Reciprocal translocations: Two non-homologous chromosomes exchange  genetic material

i. Reciprocal translocations have 2 different mechanisms

1. Chromosomal breakage and DNA repair

2. Abnormal crossovers

c. Simple translocations: the transfer of genetic material occurs in only one  direction

d. Unbalanced translocations  

i. Can result from non-homologous chromosomes with similar banding  patterns

ii. Phenotypic abnormalities or even lethality

e. Robertsonian translocation: whole arm/centric fusion

i. common in acrocentric chromosomes

ii. Down Syndrom

1. Majority of chromosome 21 is attached to chromosome 14

2. Has 3 copies of genes found on a large segment of chromosome 21 f. When crossing over occurs between a normal and one with balanced  translocation, unbalanced offspring can be a result

8. Balanced translocations and Gamete Production

a. Individuals with balanced translocations have a greater risk of producing gametes  with unbalanced combinations of chromosomes

i. Depends on segregation patterns in meiosis I

b. In Meiosis I, homologous chromosomes synapse together

i. Translocation cross must form for the translocated chromosome to  synapse properly

c. 3 types of meiotic segregation

i. Alternate segregation: chromosomes on opposite sides of translocation  cross segregate into same cell

1. Leads to unbalanced gametes

ii. Adjacent 1 segregation: adjacent, non-homologous chromosomes  

segregate into the same cell

1. Unbalanced gametes

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iii. Adjacent 2 segregation: Adjacent homologous chromosomes segregate  into the same cell

1. Unbalanced gametes

9. Variations in Chromosome Number

a. Polyploidy: Variation in the number of complete sets of chromosomes (abnormal phenotype)

i. Humans and higher level eukaryotes cannot be polyploid

b. Aneuploidy: Variation in the number of particular chromosomes within a set (abnormal phenotype)

c. Euploidy: Exact multiple of a set of chromosomes (normal phenotype) i. Occur occasionally in animals and frequently in plants

d. Extra 21 chromosome = 2n + 1 = trisomy

e. 1 chromosome missing = 2n – 1 = monosomy

10. Aneuploidy

a. Commonly causes an abnormal phenotype

i. Leads to an imbalance in the amount of gene products

ii. Any aneuploid condition with autosomes is deleterious

1. Trisomy 21 & 22; normal life span

2. Trisomy 18 &13; early death

b. Possibility of incidence rises with age of either parent, especially mothers i. Ex: possibility of down syndrome increases with parent’s age

11. Euploidy

a. Most animals are diploid

b. Some euploidy variations are naturally occurring

i. Female bees diploid

ii. Male bees (drones) monoploid

iii. Polyploid rat

iv. In humans, liver and muscle cells are commonly polyploid because they  need more gene products to carry out their function. (endopolyploidy) 1. Megakaryocytes

v. Trophoblasts: eukaryotic version of endosperm

c. Polytene chromosomes of insects provide an unusual example of natural  variation in ploidy

d. Reasons for polyploidy

i. Endoreplication: Replication in S phase

1. Endocycling: G1 – S – G2 – G1, no mitosis

2. Endomitosis: G1 – S – G2 – M (either goes all the way to telophase  or stops at anaphase)

12. Polytene Chromosomes

a. Occur mainly in the salivary glands of Drosophila and a few other insects b. Chromosome undergoes repeated rounds of chromosome replication, skipping  division

c. Produces a bundle of chromosomes that lie together in a parallel fashion  (polytene chromosome)

d. Because of size are easier to see under a microscope

e. Exhibit a characteristic banding pattern

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i. DNA in dark band is more compact than that in the interband region 1. Each dark band is a chromomere

13. Euploidy: Plants

a. Plants commonly display polyploidy

b. Heterosis: genes from unrelated species combined for a certain result i. Allosomes

c. Polyploids with an odd number of chromosome sets are usually sterile 14. Ways to Produce Variation in Number

a. 3 natural mechanisms

i. Meiotic nondisjunction

1. Failure of chromosomes to segregate properly during anaphase

a. Can produce haploid cells that have too many or too few  

chromosomes

2. Complete nondisjunction: all chromosomes can undergo  

nondisjunction and migrate to one daughter cell

a. Cell left w/o chromosomes is nonviable but can participate  

in fertilization with a normal gamete  

b. Results in a triploid gamete (non-fertile)

ii. Mitotic abnormalities

1. Often occur after fertilization

a. After mitosis not meiosis

b. Retinoblastoma

2. Mitotic disjunction

a. Sister chromatids separate improperly

b. Leads to trisomic and monosomic daughter cells

3. Chromosome loss

a. One of the sister chromatids does not migrate to a pole

i. This leads to a normal and monosomic daughter  

cell.

ii. Ex: gynandromorph: half female and half male: lost  

one X during 1st mitotic division

iii. Interspecies crosses