Chapter 08 Lecture Outline Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education.

8.1 Microscopic Examination of Eukaryotic Chromosomes The characteristics that are used to classify and identify chromosomes Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Allelic variations are variations in specific genes Genetic variation refers to differences in alleles and chromosomes, either between members of the same species or between different species Allelic variations are variations in specific genes Typically single or a few nucleotide changes Variations in chromosome structure and number Typically affect more than one gene Important in evolution Can cause disease Important for new strains of crops Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Variations in Chromosomes Can be Seen by Light Microscopy Structure and number of chromosomes typically studied by light microscopy Cytogeneticist – Scientist who studies chromosomes under the microscope Different species can be distinguished from each other based on the number and size of chromosomes Human Fruit fly Corn © Carlos R Carvalho/Universidade Federal de Viçosa. © Scott Camazine /Photo Researchers © Michael Abbey/Photo Researchers Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Different chromosomes of the same species can be also distinguished from each other Chromosomes can be classified by Size Position of centromere Banding pattern Staining reveals bands Example: Giemsa stain – G bands

Centromere position Metacentric – centromere near the middle Submetacentric – slightly off center Acrocentric – more off center Telocentric – centromere at the end Metacentric Submetacentric Acrocentric p q Short arm; For the French, petite Long arm Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Banding pattern during metaphase Banding pattern during prometaphase 6 5 5 2 4 3 p 3 4 3 2 7 2 1 6 1 6 2 5 5 4 6 5 2 2 1 4 3 2 5 4 5 1 3 1 4 1 2 4 2 1 3 3 3 1 3 2 2 2 1 4 2 2 2 1 1 1 1 1 3 1 1 1 2 2 1 1 1 1 5 2 4 2 3 4 1 1 1 2 2 2 3 5 5 3 2 3 4 1 3 2 1 1 3 1 1 2 3 1 2 1 1 4 4 2 1 1 3 1 3 1 q 1 1 1 2 2 4 2 1 2 3 2 2 1 2 2 2 3 2 2 3 5 1 3 1 1 1 1 2 1 1 1 3 4 3 1 4 1 4 4 2 5 2 1 2 5 2 1 1 1 1 1 2 5 1 3 6 6 2 1 2 1 2 1 1 2 1 3 1 2 4 7 3 8 1 3 3 3 4 3 2 1 1 4 5 2 3 3 5 1 1 2 2 1 2 1 4 6 2 2 3 2 2 1 1 2 4 3 3 1 3 2 2 4 2 1 5 7 3 3 3 3 5 4 2 2 2 4 2 3 2 3 6 8 4 4 6 5 3 3 2 3 7 5 3 5 4 4 9 5 7 6 4 4 6 5 4 1 2 3 4 5 6 7 8 9 10 11 12 2 2 1 3 3 1 1 2 1 3 1 2 1 p 1 2 1 3 1 1 1 1 2 3 2 1 1 2 1 2 2 1 1 1 3 1 2 1 2 3 1 2 1 1 2 3 3 3 4 3 4 1 1 1 1 2 1 2 1 2 3 3 1 5 2 2 1 2 1 2 1 1 1 2 q 2 1 2 2 2 1 1 2 3 2 1 1 1 1 3 1 3 3 1 1 2 1 2 1 1 1 1 2 4 2 4 2 4 2 5 3 3 3 2 2 1 3 3 1 5 2 3 4 2 3 1 3 2 6 4 2 6 4 5 3 2 7 8 13 14 15 16 17 18 19 20 21 22 Y X

A karyotype is a micrograph of metaphase chromosomes from a cell arranged in standard fashion Karyotypes can be used to Detect abnormal chromosome number or structure, but not small changes of a few to a few thousand nucleotides

8.2 Changes in Chromosome Structure: An Overview The four types of changes in chromosome structure Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Mutations Can Alter Chromosome Structure Primary ways chromosome structure can be altered: Deletion (also called Deficiency) Portion of the chromosome is missing Duplication Portion of the chromosome is repeated Inversion A change in the direction of part of the genetic material along a single chromosome Translocation Segment of one chromosome becomes attached to a non-homologous chromosome Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Mutations Can Alter Chromosome Structure Simple translocations One way transfer Reciprocal translocations Two way transfer Simple 1 2 3 4 translocation Reciprocal 1 2 3 4 translocation Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

q p 4 3 2 1 1 2 3 4 3 1 1 2 3 Deletion (a) 4 3 2 1 1 2 3 4 3 2 3 2 1 1 2 3 Duplication (b) 4 3 2 1 1 2 3 4 2 3 1 1 2 3 Inversion (c) (d) Simple Reciprocal 1 2 3 4 translocation (e)

8.3 Deletions and Duplications How deletions and duplications occur How deletions and duplications may affect the phenotype of an organism. Definition of copy number variation Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Deletions The phenotypic consequences of deletions depends on Size of the deletion Chromosomal material deleted Are the lost genes vital to the organism? (a) Terminal deletion (b) Interstitial deletion Single break Two breaks and reattachment of outer pieces (Lost and degraded) + 4 3 2 1

When deletions have a phenotypic effect, they are usually detrimental Example: cri-du-chat syndrome in humans Caused by a deletion in the short arm of chromosome Deleted region © Jeff Noneley Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Duplications Like deletions, the phenotypic consequences of duplications tend to be correlated with size Duplications are more likely to have phenotypic effects if they involve a large piece of the chromosome A chromosomal duplication is usually caused by abnormal events during recombination Called nonallelic homologous recombination Repetitive sequences can cause this Duplication Deletion A B C D Repetitive sequences Misaligned crossover

Duplications tend to have less harmful effects than deletions of comparable size In humans, relatively few well-defined syndromes are caused by small chromosomal duplications Example: Charcot-Marie-Tooth disease

Duplicated genes accumulate mutations which alter their function Duplications can provide additional genes, forming gene families - two or more genes that are similar to each other Duplicated genes accumulate mutations which alter their function After many generations, they have similar but distinct functions They are now members of a gene family Two or more genes derived from a common ancestor are homologous Homologous genes within a single species are paralogs Gene Abnormal genetic event that causes a gene duplication Gene Gene Over the course of many generations, the 2 genes may differ due to the gradual accumulation of DNA mutations. Paralogs (homologous genes) Mutation Gene Gene

Example: The globin genes Ancestral globin gene has been duplicated and altered 14 paralogs on three different chromosomes Different paralogs carry out similar but distinct functions All bind oxygen Myoglobin stores oxygen in muscle cells Different globins in the red blood cells at different developmental stages Characteristics correspond to the oxygen needs of the embryo, fetus and adult Better at binding and storing oxygen in muscle cells Better at binding and transporting oxygen via red blood cells

Copy Number Variation Copy number variation – a type of structural variation in which a DNA segment 1000bp or larger has copy number differences in members of the same species A gene normally in two copies in a diploid cell may be found in one, three, or even more copies Some chromosomes are missing the gene Some chromosomes have extra copies These carry a segmental duplication (a) Some members of a species (b) Other members of the same species A Segmental duplication

8.4 Inversions and Translocations Definition of pericentric and paracentric inversions How inversion heterozygotes produce abnormal chromosomes due to crossing over Two mechanisms that result in reciprocal translocations How reciprocal translocations align during meiosis and how they segregate. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Inversions A chromosomal inversion is a segment that has been flipped to the opposite orientation Total amount of genetic information stays the same Therefore, the great majority of inversions have no phenotypic consequences Pericentric inversion – the centromere is within the inverted region Paracentric inversion – the centromere is outside the inverted region Inverted region A (a) Normal chromosome B C D E F G H I (b) Pericentric inversion GF (c) Paracentric inversion Centromere lies within inverted region Centromere lies outside inverted region

In rare cases, inversions can alter the phenotype of an individual Breakpoints The breaks leading to the inversion occur in a vital gene Position effect A gene is repositioned in a way that alters its gene expression About 2% of the human population carry inversions that are detectable with a light microscope Most of these individuals are phenotypically normal However, a few can produce offspring with genetic abnormalities

Inversion Heterozygotes Individuals with one copy of a normal chromosome and one copy of an inverted chromosome Such individuals may be phenotypically normal But they have a high probability of producing abnormal gametes Due to crossing-over in the inverted segment Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

During meiosis I, homologous chromosomes synapse with each other For the normal and inversion chromosome to synapse properly, an inversion loop must form If a crossover occurs within the inversion loop, highly abnormal chromosomes are produced Replicated chromosomes A B C D E F G H I e d h i f g c b a With inversion: Homologous pairing during prophase Crossover site Products after crossing over Normal: Acentric fragment Duplicated/ deleted Dicentric chromosome Dicentric bridge (a) Pericentric inversion (b) Paracentric inversion

Translocations 22 Environmental agent causes 2 chromosomes to break. Reactive ends Nonhomologous Reciprocal translocation 1 7 2 DNA repair enzymes recognize broken ends and incorrectly connect them. (a) Chromosomal breakage and DNA repair (b) Nonhomologous crossover Crossover between nonhomologous A chromosomal translocation occurs when a segment of one chromosome becomes attached to another In reciprocal translocations two non-homologous chromosomes exchange genetic material Reciprocal translocations arise from two different mechanisms 1. Chromosomal breakage and DNA repair 2. Non-homologous crossovers

Reciprocal translocations lead to a rearrangement of the genetic material, not a change in the total amount Thus, they are also called balanced translocations Reciprocal translocations, like inversions, are usually without phenotypic consequences In a few cases, they can result in position effect In simple translocations the transfer of genetic material occurs in only one direction These are also called unbalanced translocations Unbalanced translocations are associated with phenotypic abnormalities or even lethality

Example: the Robertsonian translocation Most common type of chromosomal rearrangement in humans Approximately one in 900 births The majority of chromosome 21 is attached to chromosome 14 This translocation occurs such that Breaks occur at the extreme ends of two non-homologous chromosomes The small acentric fragments are lost Larger fragments fuse at centromeric regions to form a single chromosome Translocated chromosome containing long arms of chromosome 14 and 21 containing short arms of (usually lost) 14 Crossover Robertsonian translocation 21 +

8.5 Changes in Chromosome Number: An Overview Definition of euploid and aneuploid Polyploidy and aneuploidy Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Variation in Chromosome Number Chromosome numbers can vary in two main ways Aneuploidy Variation in the number of particular chromosomes within a set Regarded as abnormal Examples: trisomy (2n+1), monosomy (2n-1) Euploidy Variation in the number of complete sets of chromosomes Occur occasionally in animals and frequently in plants Examples: triploid (3n), tetraploid (4n) Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Individual is said to be trisomic Chromosome composition Normal female fruit fly: Individual is said to be trisomic Polyploid organisms have three or more sets of chromosomes 1(X) 2 3 4 Diploid; 2n (2 sets) (a) Polyploid fruit flies: Aneuploid fruit flies: Triploid; 3n (3 sets) Trisomy 2 (2n + 1) Tetraploid; 4n (4 sets) Monosomy 1 (2n – 1) (b) Variations in euploidy (c) Variations in aneuploidy Individual is said to be monosomic

8.6 Variation in the Number of Chromosomes Within a Set: Aneuploidy Why aneuploidy usually has a detrimental effect on phenotype Examples of aneuploidy in humans Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Aneuploidy 100% 1 Normal individual Trisomy 2 individual Monosomy 2 individual 2 3 150% 50% Aneuploidy – Variation in the number of particular chromosomes within a set Aneuploidy commonly causes an abnormal phenotype It leads to an imbalance in the amount of gene products Three copies can lead to 150% production of the hundreds or even thousands of gene products from a particular chromosome

Sex chromosome aneuploidies generally have less severe effects Alterations in chromosome number occur frequently during gamete formation About 5-10% of embryos have an abnormal chromosome number Indeed, ~ 50% of spontaneous abortions are due to such abnormalities In some cases, an abnormality in chromosome number produces an offspring that can survive But this is relatively rare Autosomal aneuploidies that are most compatible with survival are trisomies 13, 18 and 21 Sex chromosome aneuploidies generally have less severe effects Explained by X inactivation All but one X chromosome transcriptionally suppressed Phenotypes of X chromosome aneuploidies may be due to Expression of X-linked genes prior to X-inactivation Imbalance in the expression of pseudoautosomal genes

Infants with Down syndrome Some human aneuploidies are influenced by parental age Older parents more likely to produce abnormal offspring Example: Down syndrome (Trisomy 21) Incidence rises with the age of either parent, especially mothers Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 90 1/12 80 70 60 Infants with Down syndrome (per 1000 births) 50 40 1/32 30 20 1/110 10 1/1925 1/365 1/1205 1/885 20 25 30 35 40 45 50 Age of mother

Age of oocytes may play a role Down syndrome Failure of chromosome 21 to segregate properly due to chromosomal nondisjunction, usually in meiosis I in the oocyte Age of oocytes may play a role Primary oocytes are produced in the ovary of fetus prior to birth Oocytes arrested in prophase I until the time of ovulation Length of time that oocytes are arrested in prophase I may contribute to an increased frequency of nondisjunction Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

8.7 Variation in the Number of Sets of Chromosomes Examples in animals that involve variation in euploidy Definition of endopolyploidy The process of polytene chromosome formation The effects of polyploidy among plant species and its impact in agriculture Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Euploidy Euploidy – Variation in the number of complete sets of chromosomes Most species of animals are diploid In many cases, changes in euploidy are not tolerated Polyploidy in animals is generally a lethal condition Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Some euploidy variations are naturally occurring Example: Bees are haplodiploid Female bees are diploid Male bees (drones) are monoploid Contain a single set of chromosomes A few examples of vertebrate polyploid animals have been discovered Example: The frog Hyla

Polyploidy Common in plants 30-35% of ferns and flowering plants are polyploid Many fruits and grains are polyploids In many instances, polyploid strains of plants display outstanding agricultural characteristics They are often larger in size and more robust Diploid (b) A comparison of diploid and tetraploid petunias (a) Cultivated wheat, a hexaploid species Tetraploid © James Steinberg/Photo Researchers

one copy of some chromosomes and two copies of other chromosomes Polyploids having an odd number of chromosome sets are usually sterile These plants produce highly aneuploid gametes Example: In a triploid organism there is an unequal separation of homologous chromosomes (three each) during anaphase I Each cell receives one copy of some chromosomes and two copies of other chromosomes

Although sterility is generally a detrimental trait it can be agriculturally desirable Seedless fruit Watermelons and bananas Triploid varieties Propagated by cuttings Seedless flowers Marigold flowering plants Keep blooming Need to buy seeds

8.8 Mechanisms That Produce Variation in Chromosome Number How meiotic and mitotic nondisjunction occur and their possible phenotypic consequences Autopolyploidy, alloploidy, and allopolyploidy How colchicine is used to produce polyploid species Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Chromosome Number Variation There are three natural mechanisms by which the chromosome number of a species can vary Meiotic nondisjunction Mitotic nondisjunction Alloploidy (interspecies crosses) Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Meiotic Nondisjunction Nondisjunction – Failure of chromosomes to segregate properly during anaphase Meiotic nondisjunction can produce cells that have too many or too few chromosomes If such a gamete participates in fertilization, the zygote will have an abnormal number of chromosomes Nondisjunction can occur in meiosis I Nonduisjunction can occur in meiosis II Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

These gametes can produce a trisomic zygoyte These gametes can produce a monosmic zygote All four gametes are abnormal

50 % Abnormal gametes 50 % Normal gametes Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

This is termed complete nondisjunction In rare cases, all the chromosomes can undergo nondisjunction and migrate to one daughter cell This is termed complete nondisjunction It results in one diploid cell and one without chromosomes The chromosome-less cell is nonviable The diploid cell can participate in fertilization with a normal gamete, yielding a triploid individual Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Mitotic Nondisjunction This cell will be monosomic Occurs after fertilization Usually only a subset of cells affected - mosaicism Mitotic nondisjunction Sister chromatids separate improperly Leads to trisomic and monosomic daughter cells Chromosome loss One of the sister chromatids does not migrate to a pole and is degraded if not included in reformed nucleus Leads to normal and monosomic daughter cells This cell will be trisomic This cell will be monosomic This cell will be normal Will be degraded if left outside of the nucleus when nuclear envelope reforms

The size and location of the mosaic region depends on the timing and location of the original abnormality Most severe example is when abnormality occurs during the first mitotic division after fertilization Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Autopolyploidy Complete nondisjunction can produce an individual with one or more extra sets of chromosomes Diploid species Polyploid species (tetraploid) (a) Autopolyploidy (tetraploid)

Alloploidy Much more common mechanism for changes in the number of sets of chromosomes Result of interspecies crosses Most likely occurs between closely related species Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Species 1 Species 2 Alloploid (b) Alloploidy (allodiploid) Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Allopolyploidy An allopolyploid contains a combination of both autopolyploidy and alloploidy Species 1 Species 2 An allotetraploid: Two complete sets of chromosomes from two different species Allopolyploid (c) Allopolyploidy (allotetraploid)

Experimental Treatments Can Promote Polyploidy Polyploid and allopolyploid plants often exhibit desirable traits Can be induced by abrupt temperature changes or drugs The drug colchicine is commonly used to promote polyploidy Binds to tubulin (a protein found in the spindle apparatus), promoting nondisjunction Caused by complete nondisjunction