Ch.

2-Terms 1/27/20 3:47 PM

Chromosome
 DNA is organized into chromosomes, which transmit genetic information
 Prokaryotes:
o Does not contain a nucleus
o Have 1 circular chromosome
o Double stranded DNA
 Eukaryotes:
o Contains a nucleus
o Genes (DNA) found on chromosomes in the nucleus
o Linear chromosomes (1 or 2 sets)
 One set of linear chromosomes in the nucleus = a single nuclear
genome
o Contains mitochondria and chloroplasts
 Both contain multiple circular chromosomes
o Humans have 46 chromosomes 23 pairs
 22 pairs of autosomes (44 chromosomes)
 1 pair of sex-linked (2 sex-linked chromosomes)
o **Multiple protein products are often produced from single eukaryotic genes
Chromatin
 The material of which the chromosomes of organisms other than bacteria (i.e.,
eukaryotes) are composed of
Centromere
  The specialized DNA sequence of a chromosome that links a pair of sister chromatids
 During cell division, spindle fibers attach to the centromere. 
 The location of the centromere establishes the general appearance of each
chromosome

Diploid
 2n= two nuclear genomes
 **Cells that have 2 of each type of chromosome
o They reproduce by mitosis, making daughter cells that are exact replicas
 Most eukaryotes are diploid
o Ex. Humans- diploid number (2n) of 46
 Chromosomes in diploid cells exist in pairs called homologous chromosomes
o **Homologous chromosomes are:
 Alike in size and gene content
 They carry alleles for the same genes in the same relative positions
 They contain identical loci (gene sites along the chromosome’s length)
 They physically pair at meiosis
 They regularly exchange DNA by crossing over at meiosis
Haploid
 n= one nuclear genome (= ½ 2n)
 **A haploid cell: has one complete set of chromosomes; one complete copy of the
nuclear genome
 o They are a result of meiosis (diploid cells divide which make haploid cells
haploid cells merge with another haploid cell at fertilization)
 **The number of chromosomes in the basic genomic set of an organism is known as
its haploid set
 (One member of each homologous pair of chromosomes)
 Ex. Sperm and egg cells
Genome
 The genetic information contained in a haploid set of chromosomes constitutes the
genome of the species
 **The relationship between genome size and gene number is NOT linear they do
NOT depend on each other and there is NO direct proportional relationship
 **In a single human somatic cell there are: 2 copies of the nuclear genome, and many
copies of the mitochondrial genome
Karyotype
 “Nuclear type;” the number and visual appearance of the chromosomes in the cell
nuclei of an organism or species
 Defined by:
o Chromosome number
o Physical landmarks on the chromosomes e.g.
 Size
 Centromere position
 Banding
 Variation in thickness


Cell cycle (G1, S, G2, M)
 The events that occur from one completion of one division until the completion of the
next division


  Interphase- the initial stage of cell cycle; interval between divisions
o S phase- replication of the DNA of each chromosome occurs here
 Each of the 46 chromosomes is duplicated by the cell
o G1 and G2 phase- occur before and after S phase; comprised of intense
metabolic activity, cell growth, and cell differentiation
o Cells spend most of their time in interphase, mitosis happens quickly
 Mitosis
 **G0 stage- cells in this stage have withdrawn from the cell cycle (from G1)
o (still doing normal metabolic activity but not replicating)
Mitosis
 A type of nuclear division (occurring at cell division) that produces two daughter
cells identical with the parent nucleus
o Each daughter cell gets a diploid set of chromosomes identical to the parent
cell (2n  2n)
 Stages:
o Prophase
 Chromosomes coil up and condense
 Sister chromatids, the two parts of each chromosome, are present
o Prometaphase

Period of chromosome movement
 Chromosomes are clearly double structures; centrioles reach
the opposite poles; spindle fibers form
o Metaphase

Chromosome configuration following movement
 Centromeres align on metaphase plate
o Anaphase
 
Sister chromatids of each chromosome disjoin, and now the daughter
chromosomes are pulled to opposite ends
o Telophase
 Cytokinesis- division of cytoplasm daughter cells

Meiocyte
 A cell in which meiosis takes place
o Meiocyte divides twice to yield tetrad of four haploid cells
o Meiocyte effectively 4n prior to division, yielding four 1n cells
Meiosis:
 Two successive nuclear divisions (with corresponding cell divisions) that produce
gametes (in animals) or sexual spores (in plants and fungi) that have one-half (one
haploid set) of the genetic material of the original cell (2n  n)
o Cells produced get only 1 chromosome from each chromosome pair, resulting
number of chromosomes is haploid
o During sexual reproduction/fertilization- gametes combine to get back the
diploid complement found in parent cells
 **Meiosis allows:
o The generation of genetic variation among offspring
o The generation of new combinations of alleles on the same chromosome
o The transmission of equivalent genetic information from generation to
generation
o The genetic contribution of two individual parents to each offspring
 Stages:
 o

o Meiosis I (4n 2n (x2))

 Prophase I (synapse)- 2 homologous chromosomes (also known as
bivalent) synapse/form pairs
 Tetrad- consists of 4 chromatids
 (2 divisions are needed to get haploid)
 Division I:
 Separation of homologous chromosomes
 Components of each tetrad separate, yielding 2 dyads
o Dyad- A pair of sister chromatids joined at the
centromere, as in the first division of meiosis.
 Chromosomes segregate to opposite poles
 Spindle attaches to only one side of the centromere
 2 diploid cells
o Meiosis II (2n (x2) n (x4))
 Division II:
 Sister chromatids of each dyad are pulled apart and segregate
to opposite poles
 Separation of sister chromatids
 4 haploid cells tetrad
Tetrad
 (1) Four homologous chromatids in a bundle in the first meiotic prophase and
metaphase.
 (2) The four haploid product cells from a single meiosis.
 
Sexual reproduction (meiosis) generates genetic variation:
 3 mechanisms:
o 1. Fertilization- brings pairs of loci from two parents into new combinations
o 2. Independent assortment of chromosome homologs during meiosis
Consequence of independent alignment of chromosomes at the
equatorial plate during Anaphase I of meiosis
o 3.** Crossing-over takes place between non-sister chromatids during meiosis
 It occurs in meiosis I, and results in genetic exchange between member
of each homologous pair of chromosomes
 **Crossovers are needed to maintain the intact tetrad until anaphase I
of meiosis. If crossing-over fails, first division non-disjunction occurs.
Mitosis vs. Meiosis
 They both have:
o Chromatid formation
o Cell division
o Separation of homologous centromeres to opposite poles
o Chromosome condensation
 Only meiosis:
o One cross over per homologous pair of chromosomes
o Pairing of homologs

DNA is packaged into genes which are packaged into genomes

DNA
 DNA is a double helix composed of two complementary intertwined nucleotide
chains
 A genome is made up of one or more DNA molecules
 o Each DNA molecule in a genome is organized into chromosomes
Genes
 A gene is a chromosomal region capable of making functional transcripts
 Gene topography varies from species to species
o Scale of genome
o Space between genes
 The genes of eukaryotes contain noncoding regions called introns and coding regions
called exons
o **Exons are expressed into proteins; coding regions
 Different organisms have characteristic numbers of exons per gene
o Introns are excised during mRNA processing; noncoding regions
 Gene size variation mostly result of differences in intron number and
length not length of mRNA transcript
 **They contain sequence-specific information
Genome
 A genome is made up of one or more DNA molecules
o The genetic information contained in a haploid set of chromosomes
constitutes the genome of the species
 The characteristics of a species are coded in its genome
 Genome size varies across organisms
o Genome size across all of life varies by 5 - 6 orders of magnitude
 **The relationship between genome size and gene number is NOT linear they do
NOT depend on each other and there is NO direct proportional relationship
 **In a single human somatic cell there are: 2 copies of the nuclear genome, and many
copies of the mitochondrial genome
Mendelian Genetics (Single-Gene Inheritance)
Gregor Mendel
 Father of Genetics
 Hypothesized alternative forms of genes
Mendel’s First Law
 Law of equal segregation- the production of equal numbers (50 percent) of each
allele in the meiotic products (for example, gametes) of a heterozygous meiocyte.
o In meiosis, the members of a gene pair separate equally into the cells that
become eggs and sperm, the gametes
 Allele pairs separate when gametes form
o All 1:1, 3:1 and 1:2:1 ratios are diagnostic of single-gene inheritance
 These ratios are based on the equal segregation of alleles at meiosis


o **The law has its physical basis in the: random arrangement of chromosomes
on the metaphase plate in meiosis I
Wild type traits
 The genotype or phenotype that is found in nature or in the standard laboratory stock
for a given organism; that which is found “in the wild,” or in nature
Mutants
 Individual organisms having some abnormal form of a property; the heritable variants
observed in an organism that differs from the wild type
Allele
 One of the different/alternative forms of a gene that can exist at a single locus (on
homologous chromosomes)
 The gene comes in two forms called alleles
 Different alleles can produce differences in phenotypes
Monohybrid cross
 A cross between two individuals identically heterozygous at one locus/one gene pair
o Ex. A/a x A/a and AaBB x AaBB
Pure lines
 **A population of individuals all bearing the identical fully homozygous genotype
P generation
 The parental generation
F1 generation
 The offspring in a cross of the P individuals
 The progeny individuals arising from a cross of two homozygous diploid lines
F2 generation
 The offspring in a cross of the F1 individuals
 The progeny of a cross between two individuals (or selfing) from the F1 generation
o Selfed (F1 with F1) monohybrid produces progeny ratios:
 Phenotype: 3:1 ratio
 (3/4 looked like F1 plants, ¼ exhibited contrasting trait)
 Genotype: 1:2:1 ratio
 (1 AA, 2 Aa, 1 aa)
 If an individual from F1 is crossed with a homozygous recessive:
o Genotype/phenotype: 1:1 ratio
Dominant allele
  The phenotype/trait expressed by a heterozygote
Recessive allele
 An allele whose phenotypic effect is not expressed in a heterozygote
Phenotype
 (1) The form taken by some character (or group of characters) in a specific individual.
(2) The detectable outward manifestations of a specific genotype.
 **In the phenotypes that Mendel studied:
o Every character is controlled by one gene
o Two contrasting phenotypes of a given character display a complete
dominance
o There are 2 alleles for each character
o The allele of one character has no impact on another character
o All genes controlled by the 7 character are NOT located on the same
chromosome
Genotype
 The set of alleles for a given trait; allelic combinations underlying phenotypes
 Y/Y, Y/y, and y/y are all genotypes
Homozygous/Homozygote
 A pair of identical alleles
o Homozygous dominant- refers to a genotype such as A/A.
o Homozygous recessive- refers to a genotype such as a/a.
Heterozygous/Heterozygote
 The alleles of the pair differ
o Aa
Testcross
 A cross of an individual with unknown genotype with an individual homozygous
recessive for the trait in question


o If you cross a heterozygous (Aa) with a homozygous recessive (aa), you’ll get
a 1:1 phenotype and genotype ratio
 (Which follows single-gene inheritance and based on equal
segregation in a heterozygote)

Pedigree analysis
 Family trees that show information about genetic traits; deducing single-gene
inheritance of human phenotypes by a study of the progeny of matings within a
family, often stretching back several generations.


Autosome
 Any chromosome that is not a sex chromosome
 **A rare dominant trait, when exhibited in men, is transmitted to half their sons and
to half their daughter  gene for this trait is an autosome
Autosomal recessive disorder
 The normal allele is dominant, and the defective allele is recessive
o (Need to be homozygous recessive (aa) for disorder)
 In the pedigree you see:
o 1. The parents of the affected person are unaffected
o 2. The offspring- both males and females are affected
 When we know that both male and female progeny are affected, we
can infer that we are most likely dealing with simple Mendelian
inheritance of a gene on an autosome, rather than a gene on a sex
chromosome


o Both parents must be heterozygotes—say, A/a; both must have an a allele
because each contributed an a allele to each affected child, and both must
have an A allele because they are phenotypically normal.
 Parents are carriers- people who only have 1 copy of the allele for a
recessive disorder and do not exhibit symptoms of the disorder
 Ex. Cystic fibrosis (CF), albinism
Autosomal dominant disorder
 The normal allele is recessive, and the defective allele is dominant
o (Need to be heterozygous (Aa) for disorder)
 (Homozygous dominant (AA) is said to be lethal)
 In the pedigree you see:
o 1. The phenotype tends to appear/affected in every generation of the pedigree
o 2. The affected fathers or mothers transmit the phenotype to both sons and
daughters.
 
o Most affected people are heterozygotes, and virtually all matings that produce
progeny with dominant disorders are A/a × a/a.
 Therefore, if the progeny of such matings are totaled, a 1:1 ratio is
expected of unaffected (a/a) to affected (A/a) persons.
 Ex. Pseudoachondroplasia (dwarfism), Huntington disease
Autosomal polymorphism
 Polymorphism- the coexistence of two or more reasonably common phenotypes of a
biological property; the occurrence in a population of multiple forms of a trait or
multiple alleles at a genetic locus.
o Dimorphism- a polymorphism with only two forms.
 Ex. Brown versus blue eyes, pigmented versus blond hair, ability to
smell Freesias (a fragrant type of flower) versus inability, widow’s
peak versus none, sticky versus dry earwax, and attached versus free
earlobes
 The morph determined by the dominant allele is written first


 Populations of plants and animals (including humans) are highly polymorphic.
Contrasting morphs are often inherited as alleles of a single gene
Sex chromosomes
  A chromosome whose presence or absence is correlated with the sex of the bearer; a
chromosome that plays a role in sex determination.
o All genes on the sex chromosomes are said to be sex-linked
 **Reciprocal crosses of sex-lined genes do NOT show identical phenotypic ratios in
progeny
 **Human X and Y chromosomes synapse during meiosis
 P.20
X chromosome
 One of a pair of sex chromosomes, distinguished from the Y chromosome.
 Female: XX
 Male: XY
Y chromosome
 One of a pair of sex chromosomes, distinguished from the X chromosome.
 Male: XY
Homogametic sex
 The sex with homologous sex chromosomes (for example, XX) (females)
Heterogametic sex
 **The sex that has two different sex chromosomes (for example, XY) (males)
o Produces two different kinds of gametes with respect to the sex chromosomes.
X-linked recessive disorders
 In the pedigree you see:
o 1. Many more males than females show the rare phenotype under study.
 The reason is that a female can inherit the genotype only if both her
mother and her father bear the allele (for example, XA Xa × Xa Y),
 Whereas a male can inherit the phenotype when only the mother
carries the allele (XA Xa × XA Y).
 If the recessive allele is very rare, almost all persons showing the
phenotype are male.
o 2. None of the offspring of an affected male show the phenotype, but all his
daughters are “carriers,” who bear the recessive allele masked in the
heterozygous condition.
 In the next generation, half the sons of these carrier daughters show
the phenotype
o 3. None of the sons of an affected male show the phenotype under study, nor
will they pass the condition to their descendants.
 
 Ex. Red-green color blindness, hemophilia
X-linked dominant disorders
 In the pedigree you see:
o 1. Affected males pass the condition to all their daughters but to none of their
sons.
o 2. Affected females are mostly heterozygotes
o 3. Affected heterozygous females married to unaffected males pass the
condition to half their sons and daughters.


 Ex. Hypophosphatemia
Y-linked inheritance
 Only males inherit genes in the differential region of the human Y chromosome, with
fathers transmitting the genes to their sons
o The gene that plays a primary role in maleness is the SRY gene
Calculating Risks in Pedigree Analysis
 When a disorder with well-documented single-gene inheritance is known to be
present in a family, knowledge of transmission patterns can be used to calculate the
probability of prospective parents’ having a child with the disorder
 Ex. Husband and wife find out that each had an uncle with Tay-Sachs disease, a
severe autosomal recessive disease. The probability of the couple’s first child having
Tay-Sachs can be calculated in the following way
o
o If both are heterozygotes, then they each stand a chance of passing the
recessive allele on to a child, who would then have Tay-Sachs disease. We
must calculate 1. the probability of their both being heterozygotes, and then, if
so, 2. the probability of passing the deleterious allele on to a child
 1. The husband’s grandparents must have both been heterozygotes
(T/t) because they produced a t/t child (the uncle). Therefore, they
effectively constituted a monohybrid cross.
 The husband’s father could be T/T or T/t, but within the 3/4 of
unaffected progeny we know that the relative probabilities of
these genotypes must be 1/4 and 1/2, respectively (the expected
progeny ratio in a monohybrid cross is T/T, T/t, t/t.
Therefore, there is a 2/3 probability that the father is a
heterozygote (two-thirds is the proportion of unaffected
progeny who are heterozygotes: that is the ratio of 2/4 to 3/4).
 2. The husband’s mother is assumed to be T/T, because she married
into the family and disease alleles are generally rare. Thus, if the father
is T/t, then the mating with the mother was a cross T/t × T/T and the
expected proportions in the progeny (which includes the husband) are
T/T, T/t.
 3. The overall probability of the husband’s being a heterozygote must
be calculated with the use of a statistical rule called the product rule,
which states that: the probability of two independent events both
occurring is the product of their individual probabilities.
 Because gene transmissions in different generations are
independent events, we can calculate that the probability of the
husband’s being a heterozygote is the probability of his father’s
being a heterozygote (2/3) times the probability of his father
having a heterozygous son (1/2), which is 2/3 × 1/2 = 1/3.
 4. Likewise, the probability of the wife’s being heterozygous is also
1/3
 5. If they are both heterozygous (T/t), their mating would be a standard
monohybrid cross and so the probability of their having a t/t child is
1/4.
 6. Overall, the probability of the couple’s having an affected child is
the probability of them both being heterozygous and then both
transmitting the recessive allele to a child. Again, these events are
independent, and so we can calculate the overall probability as 1/3 ×
1/3 × 1/4 = 1/36. In other words, there is a 1 in 36 chance of them
having a child with Tay-Sachs disease.
Ch.3 Terms 1/27/20 3:47 PM
Ch.3
Notation:
 A slash symbolically separates the two homologs: A/a
 If two genes are on different (unlinked) chromosomes , the gene pairs are separated
by a semicolon: A/a; B/b.
 If they are on the same (linked) chromosome, the alleles on one homolog are written
adjacently with no punctuation and are separated from those on the other homolog by
a slash: AB/ab or Ab/aB
 If it is not known (unknown linkage) whether the genes are on the same chromosome
or on different chromosomes, use a dot to separate the genes: A/a · B/b
 **Ex. Relationship between 2 genes in a starfish: leg length (L) and striping (S).
These 2 genes have not been investigated before. How would you represent the alleles
for these genes in your crosses of pure lines?
o L/L · S/S x l/l · s/s
 Use the dot because don’t know if they’re on the same chromosome or
not
Dihybrid
 A double heterozygote such as A/a · B/b
Dihybrid cross
 A cross between two individuals identically heterozygous at two loci
o Ex. AB/ab X AB/ab (AaBb x AaBb)


o **Dihybrid self cross (produced F2 progeny ratio (phenotype)): 9:3:3:1
 o Dihybrid testcross: 1:1:1:1
 (Cross of F1 (R/r ; Y/y) with homozygous recessive (r/r ; y/y)
Law of independent assortment (Mendel’s second law)
 **Unlinked or distantly linked segregating gene pairs assort independently at meiosis
o The alleles of a gene segregate independently of the alleles of other genes, so
the inheritance of an allele of one gene does not influence the inheritance of
another gene
o During gamete formation, segregating pairs of unit factors assort
independently of each other
 For genes on different (nonhomologous) pairs of chromosomes, recombinant
frequency is always 50%
Branching diagram

Product law (of probability)

 When 2 independent events occur simultaneously, the probability of the two
outcomes occurring in combination is equal to the product of their individual
probabilities of occurrence
 
Sum rule
 **The probability of either one or the other of two mutually exclusive events
occurring is the sum of their individual probabilities.
o Probability of rolling two 4’s: 1/6 x 1/6 = 1/36 (same for two 5s)
 Probability of rolling two 4s OR two 5s: 1/36 + 1/36 = 2/36 (1/18)
How many genotypes and phenotypes

 **
o # of heterozygous pairs: n; # different gametes: 2^n; # different genotypes:
3^n; # different phenotypes: 2^n
o AaBbCc x AaBbCc  n=3
o AaBBCcDd x AaBBCcDd  n=3 (because B is not heterozygous)
Chi-square test
 A statistical test used to determine the probability of obtaining observed proportions
by chance, under a specific hypothesis
 χ2 = Σ (O – E)2/E
o χ2 = how frequently the observed deviation can be expected to occur strictly as
a result of chance
o O= observed category
o E= expected
  Add up the observed values then multiply it by the expected ratio
(monohybrid: ¾ and ¼; dihybrid: 9/16, 3/16, 3/16, 1/16)


 Degrees of freedom (df)= n-1
o Monohybrid2-1= 1 df
o Take the df and use it to find probability value (p) on chart
 Compare χ2 value to p of 0.05 for the correct df on chart
o X^2>0.05
reject null hypothesis
 there IS a difference between observed and expected values
o X^2<0.05
 fail to reject null hypothesis 
 there is NO real difference between observed and expected
values

Chromosomal Basis of Independent Assortment

Heteromorphic
 Chromosomes that show only partial homology
Recombination
 (1) In general, any process in a diploid or partly diploid cell that generates new gene
or chromosomal combinations not previously found in that cell or in its progenitors.
 (2) At meiosis, the process that generates a haploid product of meiosis whose
genotype is different from either of the two haploid genotypes that constituted the
meiotic diploid.
Meiotic recombination
 Recombination from assortment or crossing over at meiosis.
 
o To know the input gametes, we use pure-breeding diploid parents because
they can produce only one gametic type.
o To detect recombinant output gametes, we testcross the diploid individual
(with homozygous recessive) and observe its progeny
Recombinant
 Refers to an individual organism or cell having a genotype produced by
recombination (not the same as the parents)
 Recombinants are produced by two different cellular processes:
o 1. The independent assortment of genes on different chromosomes (ch.3)
o 2. The crossing over between genes on the same chromosome (ch.4)
Recombinant frequency
 Its numerical value is a convenient test for whether two genes are on different
chromosomes.
 1:1:1:1 ratio
 Genes on separate chromosomes:
o Recombinants are produced by independent assortment
 The progeny of the testcross are classified as either recombinant or
resembling the P (parental) input types
 The proportion of recombinants is clearly 50%
   If we observe a recombinant frequency of 50% in a testcross,
we can infer that the two genes under study assort
independently
 **Genes on separate chromosomes (unlinked) always show a
recombinant frequency of 50%
 ** Genes on same chromosomes always show a recombinant
frequency of less than (<) 50%
 (If not 50% ratio, then the genes are on the same chromosome)

Inheritance of Organelle Genes: Inheritance Independent of the Nucleus

A distinct and specialized subset of the genome is found in the mitochondria, and, in plants, also
in the chloroplasts
Mitochondrial DNA (mtDNA)
 The subset of the genome found in the mitochondrion, specializing in providing some
of the organelle’s functions.
 Maternally inherited
 Ex. Neurospora - poky phenotype

o
Chloroplast DNA (cpDNA)
 The small genomic component found in the chloroplasts of plants, concerned with
photosynthesis and other functions taking place within that organelle.
 Maternally inherited
 Ex. Leaf variegation in the 4 o’clock plant
o Organelle populations that contain mixtures of two genetically distinct
chromosomes often show segregation of the two types into the daughter cells
at cell division. This process is called cytoplasmic segregation.
o **In a cross made with variegated Four O’Clock plants, pollen is provided
from flowers on a green sector, and ovules from a white sector.
 The progeny are expected to be all white (because white is from the
mother)

 **The leaf types of the progeny seeds of the apical (top) flower would
be: a mixture of white leaves, green leaves, and variegated leaves
Uniparental inheritance
 Inheritance pattern for organelles in which the progeny have the genotype and
phenotype of one parent only; progeny inherit organelle genes exclusively from one
parent but not the other
o Ex. Inheritance of mitochrondrial genomes.
 Most cases the parent is the mother
o Maternal inheritance- a type of uniparental inheritance in which all progeny
have the genotype and phenotype of the parent acting as the female
 mtDNA and cpDNA are maternally inherited
 This is because the egg contributes the bulk of the cytoplasm to
the zygote


  Variant phenotypes caused by mutations in cytoplasmic organelle DNA are generally
inherited maternally and independent of the Mendelian patterns shown by nuclear
genes.
Mitochondrial diseases
 Mutations in human mitochondrial genes can lead to disease when, by random drift
and cytoplasmic segregation, they rise in frequency to such an extent that cell
function is impaired.
 The condition is always passed to offspring by mothers and never fathers
 **Ex. A mother heteroplasmic for a mitochondrial disease phenotype has identical
(monozygotic) twins. Which of the following results would you expect? (Assume the
heteroplasmy is associated with a mitochondrial DNA disease phenotype and is solely
determined by a mutation in a single mitochondrial gene.)
o The disease phenotype may manifest in one twin yet not in the other

Ex. A human disease associated with dysfunction of mitochondria, which results from a mutation
in a single autosomal gene locus in nuclear DNA, is most likely to:
 A. Be inherited from the mother, because mitochondria are not inherited from the
father
 B. Show heteroplasmy in the progeny of affected individuals, depending on chance
events during meiosis
 C. Show a non-Mendelian inheritance pattern, because the number of mitochondria
varies from cell to cell
 D. Show a Mendelian inheritance pattern
o NOT A because in the question it says autosomal
 E. None of the above
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Chromosome map
 A representation of all chromosomes in the genome as lines, marked with the
positions of genes known from their mutant phenotypes, plus molecular markers.
Based on analysis of recombinant frequency.
o Shows gene positions, known as loci, and the distances between the loci based
on some kind of scale.
 Genetic maps are useful for strain building, for interpreting evolutionary mechanisms,
and for discovering a gene’s unknown function. Discovering a gene’s function is
facilitated by integrating information on recombination-based and physical maps.
 2 types:
o Recombination-based maps
o Physical maps
Diagnostics of linkages
Recombination map
 A chromosome map in which the positions of loci shown are based on recombinant
frequencies; map the loci of genes that have been identified by mutant phenotypes
showing single-gene inheritance
 Uses linkage analysis
Linked genes
 The situation in which two genes are on the same chromosome as deduced by
recombinant frequencies less than 50 percent (alleles on any one homolog are
physically joined (linked) by the DNA between them)
o (Different chromosomes = 50%)
 Test cross:

 The ratio of dihybrid is NOT 1:1:1:1

 Look at the recombinants (bottom two)- they are approximately equal
in frequency (151 ~ 154). Their total is 305, which is a frequency of
(305/2839) × 100, or 10.7 percent.
 10.7<50%  linked genes
 Indications of linkages (same chromomse)
o 1. Two equally frequent parental classes totaling in excess of 50% AND
 o 2. Two equally frequent recombinant classes totaling less than 50%
 When two genes are close together on the same chromosome pair (that is, they are
linked), they do not assort independently but produce a recombinant frequency of less
than 50 percent. Hence, conversely, a recombinant frequency of less than 50 percent
is a diagnostic for linkage.
Cis conformation
 In a heterozygote having two mutant sites within a gene or within a gene cluster, the
arrangement A1A2/a1a2.
o The two recessive (dominant?) alleles are present on the same homolog 
 AB/ab or + +/ab
Trans conformation
 In a heterozygote with two mutant sites within a gene or gene cluster, the
arrangement a1 +/+ a2.
o The two recessive (dominant?) alleles are present on different homologs
 **Ab/aB or + b/a +
Notation:
 1. Alleles on the same homolog (linked) have no punctuation between them.
 2. A slash symbolically separates the two homologs.
 3. Alleles are always written in the same order on each homolog.
 4. Genes known to be on different chromosomes (unlinked genes) are shown
separated by a semicolon—for example, A/a; C/c.
 Genes of unknown linkage are shown separated by a dot, A/a · D/d.
Crossing over:
 The exchange of corresponding chromosome parts between homologs by breakage
and reunion (during meiosis)


 Crossovers are between nonsister chromatids (NOT chromosomes)
o Forms new chromatids because exchange genetic material
 o Multiple crossovers can include more than 2 chromatids (3 or 4)
o Crossover at chisama
o Recombinants are produced
 Consequences of cross overs:
o Frequency of recombinant gametes is 0-50%, depending on frequency of
meiocytes with crossing-over
 The farther apart the genes are, the more likely that a crossover will
take place and the higher the proportion of recombinant products will
be.
 The farther apart genes are, the more closely their recombinant
frequencies approach 50 percent
o Results in deviation from 1:1:1:1 in testcrosses
 Parental combination is most frequent
 Recombinant combination is rarest
o Allows drawing of linkage maps based on recombination frequencies (RF)
Linkage map- a chromosome map; an abstract map of chromosomal
loci that is based on recombinant frequencies.
Recombination frequency (RF)
 A number that describes the proportion of recombinant offspring produced in a
genetic cross between two organisms
o Experimentally determined from frequency of recombinant phenotypes in
testcrosses
o Roughly proportional to physical length of DNA between loci
 The greater physical distance between two loci (/linked genes), the greater chance of
recombination by crossing-over
 Genetic map unit (m.u. or cM)- a distance on the chromosome map corresponding
to 1 percent recombinant frequency. (1mu=1cM)
o 1% recombinants = 1 map unit (m.u. or cM)
 Ex. RF of 10.7% = 10.7 mu (loci close together, small chance of
recombination/cross over)
 Ex. RF of 36% = 36 mu (loci farther apart, bigger chance of
recombination/cross over)
  **10 cM = 10% crossing-over


o 1. Recombinant frequencies can be used to make maps
o 2. When given an established map with genetic distance in map units, we can
predict the frequencies of progeny in different classes
 Ex. Genetic distance between the pr and vg loci is 11 m.u.
  11% recombinants in the progeny from a testcross of a
female dihybrid heterozygote in cis conformation
(pr vg/pr+ vg+)
 These recombinants will consist of two reciprocal
recombinants of equal frequency: thus, 5.5 percent will
be pr+ vg+ and 5.5 percent will be pr+vg.
o We also know that 100 – 11 = 89 percent will be
nonrecombinant in two equal classes, 44.5
percent pr+ vg+ and 44.5 percent pr vg. 

Trihybrid cross is in ch.3.4 of other textbook (p.49-51)

Trihybrid
 A cross between two individuals who are heterozygous for 3 genes
o Ex. AaBbCc x AaBbCc
 **If the genes are unlinked and assorting independently, the segregation ration would
be: 27:9:9:9:3:3:3:1
 **Genotype and phenotype:
 o

three-point testcross:
 A testcross in which one parent has three heterozygous gene pairs.
 Determines gene order as well as relative gene distances
 Works best with large numbers of offspring
 Analysis:
o Identify pairs of parental and recombinant offspring

Parental (noncrossover); most abundant

Single crossovers; intermediate abundance
 Identify on the basis of reciprocal combinations of alleles
 Double crossovers; least abundant
 **Double recombinants are the rarest class of genotypes
o Determine gene order by inspection (the parental gene order yields double
crossovers by switching middle genes)
 A simple rule of thumb for deducing the gene in the middle is that it is
the allele pair that has “flipped” position in the double-recombinant
classes.
o Calculate RF for single crossovers, adding double crossovers each time
o Draw map

o
 o **https://www.ndsu.edu/pubweb/~mcclean/plsc431/linkage/linkage3.htm
Double-reccombinants
 Rarest

interference:
 Crossing-over in one region of chromosome sometimes influences crossing-over in an
adjacent region
o A measure of the independence of crossovers from each other, calculated by
subtracting the coefficient of coincidence from 1.
 Interference (I) = 1 – (coefficient of coincidence)
o Coefficient of coincidence (c.o.c.)- the ratio of the observed number of
double recombinants to the expected number.
 I= 1- [(#observed double recombinants) / (#expected double recombinants)]
o **Expected= the product of the frequency of single recombinants
o Usually, I varies from 0 to 1, but sometimes it is negative, meaning double
crossing-over is enhanced
 If more double crossovers occur than expected  I is negative
 (Occurrence of 1 recombination enhances the chances of
another)

o I=1 no double crossovers
o