BIOL 2030: Module 10

Chromosome Variations

• permanent chromosomal changes

• can be passed on to offspring if they occur in cells that will become gametes

  • germline cells

• two general types of chromosomal variation:

  • chromsome rearrangement

  • variation in chromosome numbers

Chromosome Rearrangement

• changes in the structure of individual chromosomes

• 4 types:

  • deletions

  • duplications

  • inversions

  • translocation

Variation in Chromosome #

• changes in the # of chromosomes

• 1 or more individual chromosomes are added or deleted 

Deletions

• type of chromosomal rearrangement in which there is a loss of a segment, either internal or terminal, form a chromosome 

• arise by:

  • terminal ends breaking off (one break)

  • internal breaking and rejoining of incorrect ends (two breaks)

  • unequal crossing over

• major effect: loss of genetic information 

  • importance depends on what, and how much is lost 

Detection of Deletions

• deletion loops can be detected during meiosis 

• also by a variety of molecular methods that detect lower heterozygosity or gene dosage

Consequences of Deletion

• loss of DNA sequences

• deletions that span a centromere result in an acentric chromosome that will most likely be lost during cell division, which may be lethal

• deletion can allow for the expression of alleles that are normally recessive

  • pseudodominance 

• deletions can affect gene dosage 

  • when a gene is expressed, the functional protein is normally produced at the correct level or dosage 

  • some (not all) genes require two copies for normal protein production 

    • if one copy is deleted, a mutant phenotype can result

• phenotypic effects depend on the size and location of deleted sequences

• cri du chat

Acentric Chromosome

• chromosome which lacks a centromere

Psuedodominance

• genetic phenomenon where a recessive trait appears to be dominant, often because the masking dominant gene has been deleted

• deletions can allow expression of alleles that are normally recessive

Haploinsufficiency

• when one working copy (allele) of a gene isn't enough to produce the normal amount of protein needed for a healthy function, leading to a genetic disorder, even though the other gene copy is fine

• some, though not all, genes require two copies of normal protein production.

  • if one copy is deleted, a mutant phenotype can result

Duplications 

• repetition of a chromosome segment 

  • simplest form: tandem duplication

• a single gene, or cluster of genes can be duplicated. nothing has been lost, so duplications often have little or no effect on phenotype/viability

  • offspring with duplications are usually viable

  • however, in some cases, excess or unbalanced dosage of gene products resulting from duplications can cause problems

• very important in evolution, because extra copies of genes provide raw material for new genes and adaptations

• about 5% of all human genome consists of duplications

Tandem Duplications

• a type of chromosomal mutation where a DNA segment is copied and inserted immediately next to the original sequence, creating a "head-to-tail" arrangement

• ex. ABC becomes ABCBC

Origin of Duplications

• unequal crossing over of misaligned chromosomes during meiosis generates duplications, and deletions

Detection of Duplications

• duplicated chromosomes (specifically in the case of tandem duplication) forms a loop during prophase I of meiosis

• also by various molecular methods that detect higher gene dosage

Consequences of Duplication

• 3 possibilites:

  • redundancy

  • pseudogene

  • neofunctionalization

• gene dosage may affect phenotype

  • amount of protein synthesized is often proportional to the # of gene copies present, so extra genes can lead to excess proteins

  • ex. bar region in Drosophila represent that the more copies of a gene (X chromosome), the fewer eye facets

Redundancy

• both copies remain the same post duplication

• alters gene dosage

Pseudogene

• one copy becomes inactive after duplication

Neofunctionalization

• after duplication, one copy acquires a new function

• source of new genes, and multigene families

  • ex. globin gene family

Inversions

• two breaks on a chromosome followed by reinsertion in the opposite orientation causes inversion

  • pericentric inversions: around

  • paracentric inversion: beside or beyond

Pericentric Inversions

• “peri” = around

  • think perimeter

• chromosomal rearrangement where a segment of a chromosome that includes the centromere is broken, flipped, and reinserted in reverse order. This changes the order of genes on the chromosome, but not the total amount of genetic information

Paracentric Inversion

• “para” = beside or beyond

  • think paranormal

• a type of chromosomal rearrangement where a segment of a chromosome breaks, flips, and reinserts itself without including the centromere. This results in both breaks occurring on the same arm of the chromosome

Inversion Effect on Phenotype

• often, no effect

• however, sometimes there is an effect driven by the change in the position of the genes

Inversion Consequences

• position effects:

  • change in position can sometimes alter expression

  • genes in/near chromatin may not be expressed

• suppression of recombination:

  • if no crossing over occurs, gametes produced are usually viable because genetic information is not lost or gained

  • if crossing over occurs OUTSIDE of the inverted region, the gametes are viable.

  • if crossing over occurs INSIDE of the inverted region, some nonviable gametes and reduced recombination frequency

Crossing Over Within a Paracentric Inversion

• crossing over between inverted and non-inverted chromosomes

  • C and D

• formation of an inversion loop, and a crossing over occurs within the inversions

  • see crossing over between inverted and non-inverted chromosome between C and D

• formation of a dicentric bridge

• resulting in:

  • reduced recombination frequency

  • reduced fertility

Dicentric Bridge

• a physical linkage of two centromeres (one from the inverted chromosome, one from the normal) that forms during meiosis when crossing over occurs within the inversion loop

• 1this bridge gets stretched and broken as chromosomes separate, creating unbalanced gametes with deleted/duplicated segments and an acentric fragment

Crossing Over Within a Pericentric Inversion

• crossing over between inverted and non-inverted chromosomes

  • C and D

• results in reduced recombination frequency

• reduced fertility

• recombinant gametes are non viable because genes are missing or present in too many copies

Gamete Viability if No Crossing Over Occurs

• if no crossing over occurs, gametes produced are usually viable because genetic information is not lost or gained

Gamete Viability if Crossing Over Occurs (OUTSIDE Inverted Region)

• if crossing over occurs OUTSIDE of the inverted region, the gametes are viable.

Gamete Viability if Crossing Over Occurs (INSIDE Inverted Region)

• if crossing over occurs INSIDE of the inverted region, some nonviable gametes and reduced recombination frequency

Translocation

• exchange of segments between non-homologous chromosomes, or to a different region on the same chromosome

• translocations between chromosomes can be reciprocal (two way) or non-reciprocal (one way)

• if no genetic material is lost, considered a balanced translocation

  

Reciprocal Translocations Consequences

• as with inversions, translocations change the positions of genes

• this can alter expression of genes because of association with different proteins, or formation of new gene products

  • fusion proteins

• ex. philadelphia chromosomes

  • fused BCR-ABL genes

Inversions and Recombination

• inversions suppress recombination

• Lack of recombination within inversions means that genes within the inversions are free to diverge to produce different adaptations.

  • ex. Ruff bird

• genes within alternate orientations of inversions can diverge dramatically even though there is no divergence anywhere else in the genome

  • no recombination within inversion

  • inside inversion: large divergence

  • outside inversion: no divergence

Ruff Bird Inversion Example

• 3 types of males: independent, faeder, satellite.

• both faeder and satellite males have a genetic variation which arose nearly 4 million years ago

• the inversion is lethal in the homozygous condition

Chromosomal Rearrangements in Atlantic Cod

• cod have a large chromosomal inversion

  • genes inside the inversion influence whether cod are adapted to warmer or colder water

• because recombination inside the inversion is suppressed, the warm and cold versions of the gene do not get scrambled by recombination

Terminology of Chromosome Types

• Metacentric

  • centromere near the middle; arms are ~equal length.

• Submetacentric

  • centromere slightly off-center; one arm longer.

• Acrocentric

  • centromere very close to one end

• Telocentric

  • centromere at the very end; essentially one arm (common in some animals, not humans

How Does Each Type of Chromosomal Variation Occur

• Deletion: where a segment of a chromosome is lost

  • Chromosome breaks and the fragment is not reattached

  • Unequal crossing over during meiosis

  • DNA damage not properly repaired

• Duplication: A chromosome segment is repeated.

  • Unequal crossing over during meiosis when homologous chromosomes misalign

  • Replication errors

• Inversion: A chromosome segment breaks, flips, and reinserts.

  • Two breaks occur in one chromosome

  • Segment rotates 180° before rejoining

    • Paracentric – does not include the centromere

    • Pericentric – includes the centromere

• Translocation: A segment moves to a non-homologous chromosome.

  • Chromosomes break and reattach incorrectly

    • Reciprocal translocation – two chromosomes exchange segments

    • Robertsonian translocation – two acrocentric chromosomes fuse at the centromere

Consequences of Each Chromosomal Variation

• deletion: Loss of genes → often severe effects
  Example: Cri-du-chat syndrome (5p deletion)

• duplication: Extra gene copies → altered gene dosage
  Example: Bar eye mutation in Drosophila

• inversion: Usually no gene loss, but can disrupt meiosis and recombination

• translocation: Often balanced in carriers, but can cause abnormal gametes. Example: Some cases of Down syndrome

Aneuploidy

• a genetic condition where cells have an abnormal number of chromosomes, meaning they have extra or missing ones, deviating from the typical 46 in humans (23 pairs)

  • “somy” refers to the number of particular chromosomes

• plants tolerate it better than animals

  • usually viable, though phenotype may be altered and fertility reduced

Aneuploidy in Human Genes

• normal human diploid individual: 2n= 46

  • 47 = (2n + 1)

    • gain of a single chromosome

  • 48 = (2n + 2)

    • gain of a pair of homologous chromosomes

Trisomy

• gain of a single chromosome

• ex. 47 = (2n + 1)

Monosomy

• loss of a single chromosome

• ex. 45 = 2n - 1

Nullisomy

• loss of both members of a pair of homologous chromosomes

• ex. 44 = 2n - 2

Double Monosomic

• loss of two members of non-homologous chromosomes

  • less common than nullisomy

• ex. 44 = 2n - 2

Tetrasomy

• gain of two homologous chromosomes

• ex. 2n + 2 = 48

Double Trisomic

• gain of two non-homologous chromosomes

• ex. 2n + 2 = 48

Aneuploidy Origins

• nondisjunction in meiosis or mitosis

• deletion of a centromere leads to chromosome loss

Nondisjunction Origin of Aneuploidy

• failure of homologous chromosomes or sister chromatids to separate

• may result in:

  • trisomic (still viable)

    • autosomal trisomy is thought to be the most common cause of miscarriages

  • monosomic (not viable, unless for sex chromosomes)

  • normal (still viable)

Trisomy 13

• patau syndrome

• viable

Trisomy 18

• edwards syndrome

• viable

Trisomy 21

• down syndrome

• viable

Monosomy X0

• turner syndrome

• only applies to girls

Primary Down Syndrome

• trisomy 21

  • 3 copies of chromosome 21

  • 2n+1 = 47 chromsomes

• accounts for most cases of Down Syndrome

• most cases arise from random nondisjunction during meiotic division

  • mother contributes the extra chromosome in most cases

  • the incidence of trisomy 21 rises sharply with increasing maternal age

Familial Down Syndrome

• an extra copy of chromosome 21 is attached to another chromosome, therefore cause of Down Syndrome in this case is Robertsonian translocation, not trisomy 21

  • accounts for 3-4% of cases

• carrier parent: Has 45 chromosomes, not 46

  • One chromosome is a fusion of 15 + 21

  • Has normal phenotype (NOT Down syndrome)

• depending on how those chromosomes segregate during meiosis, fertilisation can produce:

  • a normal child (carrier)

  • a child with Down syndrome

  • a non-viable embryo.

Trisomy 9

• developmental delay and intellectual disability

  • physical abornmalities

  • musculoskeletal problems

  • gastrointestinal issues

• however, trisomy 9 individuals survive because it is present as a mosaic, so not all cells have it.

Polyploidy

• an increase in the number of sets of chromosomes

  • “ploidy” refers to the total number of chromosomes

• common (and important) in plants, less common in animals, and not known at all in mammals (presumed to be lethal)

• may be either:

  • autopolyploid

  • allopolypoid

Autopolyploid

• multiples of the same genome

• origin can occur during either mitosis or meiosis

  • nondisjunction of all chromosomes during mitosis in early embryo can produce autotetraploid

  • nondisjunction of all chromosomes during meiosis produces diploid games

Effects of Autopolyploidy

• usually sterile

• most gametes produces are genetically unbalanced

Autotriploid

• diploid gamete + normal gamete

• 3n

Autotetraploid

• diploid gamete + diploid gamete

• 4n

Allopolyploid

• multiples of closely related genomes

How to Solve Infertility

• to convert sterile hybrid into fertile new species, they need chromosome doubling

  • hybrid is sterile

  • unbalanced gametes are nonviable

• but if ehte entire genome is doubled by mitotic non-disjunction, the fertility problem is solved

Polyploids in Agriculture

• cell volume correlated with nucleus volume, correlated with genome size

• polyploids often have bigger leaves, fruits, and seeds

  • bread wheat is a polyploid derived from 3 species

Mutations

• mutations are both rare and common

  • rare: because DNA with replication occurs with high fidelity

  • common: because there is a lot of DNA being replicated

    • there is about 64 new mutations in each human generation

• classified based on transmission

  • somatic

  • germ-line

Somatic Mutations

• are not transmitted from one generation to another

Germ-line Mutation

• may be transmitted to 50% of offspring

Point Mutations Classification

• classified by their effect on amino acid sequence of proteins

• can be classidfied into 3 categories, based on effect:

  • silent (synonymous): no change in amino acid sequence

  • missense (nonsynonymous): causes 1 aa to be substituted for another

  • nonsense: aa codon is substituted for stop condo

Indels

• cause frameshifts that alter reading frames, creating either nonsense or missense effects on protein

  • except when indels occur as multiples of 3 nucleotides. in such cases, the amino acid sequences will change, but the reading frame is preserved

• indels outside of reading frames usually have no effect on phenotype

Loss-of-function Mutation

• protein function completely or partially lost

• recessive inheritance

Gain-of-function Mutation

• new gene product, or gene product in the wrong tissue

• dominant inheritance

Neutral Mutation

• missense mutation that results in non-significant change in protein function, because one chemically similar amino acid substituted for another, or occurs in a part of the protein that is not important for function

Transition Point Mutation

• a common DNA change where a purine (Adenine/A or Guanine/G) gets swapped for another purine, or a pyrimidine (Cytosine/C or Thymine/T) is swapped for another pyrimidine, maintaining the base's ring structure class (e.g., A→G, C→T)

Transversion Point Mutation

• a genetic change where a purine (Adenine or Guanine) is swapped for a pyrimidine (Cytosine or Thymine), or vice versa, altering the DNA's ring structure, unlike transitions

Forward Mutation

• alters the wild phenotype

Reverse Mutations

• changes mutant phenotype back to wild phenotype.

  • true reversions

  • suppressor mutations

Suppressor Mutation

• where the first mutation is suppressed by a second mutation

  • intragenic suppressor mutation

  • intergenic suppressor mutation

Intragenic Suppressor Mutation

• in the same gene

• intra = “within”

Intergenic Suppressor Mutation

• a second mutation that occurs in a different gene from the original mutation, and it counteracts the original mutation's effects to restore the normal phenotype

• inter = “between”

How do Mutations Occur?

• spontaenously

• induced by physical and chemical agent

Spontaneous Mutations

• caused by errors during DNA replication

  • tautomeric shift

  • DNA strand slippage

  • misalignment

Tautomeric Shifts (spontaneous mutations)

• base tautomers can incorrect base-pair during DNA replication, thus creating a transition mutation

DNA Strand Slippage (spontaneous mutations)

• insertion/deletion owing to slipped-strand mispairing during DNA replication

Misalignment (spontaneous mutations)

• misalingment of homologous chromosomes during crossing-over at meiosis I

Mutagen Agents that Cause Mutation

• radiation

• chemical:

  • base analogs

  • base modifying agents

  • intercalating agents

Radiation Mutagen Types

• ionizing

• ultraviolet

Ionizing Radiation

• creates free radicals

• cosmic, gamma, or xrays bombard an atom, which dislodges an electron, and results in a change in stable molecules into a free radical which can alter the structure of bases and break phosphodiester bonds in DNA

Ultraviolet Radiation

• electromagnetic radiation of lower energy than ionizing radiation

• can still generate free radicals under some circumstances, but less likely to do some than higher energy radiation

• most common source is the sun

  • though can be generated by various types of lamps

Nucleotide Excision Repair

• dna repair enzymes correct damaged DNA…

  • protein recognizes mismatches

  • unwinds DNA in area of mismatch

  • excises out nucleoides

  • fills in correct nucleotides

Xeroderma Pigmentosum

• an autosomal recessive genetic disorder of DNA repair

• the ability to repair mutations caused by UV light is deficient

Chemical Mutagens Type

• base analogs

• base modifying agents

• intercalating agents

Base Analogs

• chemicals that appear similar to the normal bases in DNA, but causes incorrect base-pairing and introduce point mutations during DNA replication

  • ex. 5-Bromouracil: a nucleotide analong which resembles both thymine and cytosine (when ionized, it pairs with guanine rather than adenine)

Base Modifying Agents

• chemicals that modify groups on the normal bases in DNA that result in incorrect base-pairing and introduce point mutations during DNA replication

Intercalating Agents

• intercalating agents insert between adjacent bases, distorting them by 0.68 nm, the size of a base

  • first round of DNA replication, the DNA polymerase randomly selects any nucleoside triphosphate opposite the intercalating agent

  • result: frame-shift due to insertion of a base

Ames Test

• assay for chemical mutagenicity via His^- Salmonella

  • His- Salmonella cannot grow on minimal medium lacking the essential amino acid, histidine

  • His+ Salmonella will grow on the minimal medium

• increased reversions of His- to His+ Salmonella indicates the chemical is a mutagen, and thus a potential carcinogen

How Does the Ames Test Work?