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UT / Biology / BIOL 240 / What is the intermediate phenotype?

What is the intermediate phenotype?

What is the intermediate phenotype?


School: University of Tennessee - Knoxville
Department: Biology
Course: General Genetics (Bio 240)
Professor: Hughes
Term: Summer 2015
Cost: 50
Name: Exam 1 Bio 240 Study guide chapters 2-5
Description: Hey guys! So in preparation for the first exam, I've bundled an extensive set of notes with chapters 2-5 five that include the information from the textbook as well as Dr. Hughes' lecture! They are detailed and vocab specific, so be sure to check it out!
Uploaded: 09/18/2015
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Biology 240 Exam 1 Chapter 2-5 Study guide!  

What is the intermediate phenotype?

Chapter 2

DNA is organized into chromosomes and virtually all cells within the individual  contains the same nuclear genetic material. Gene regulation determines gene  expression.  

In eubacteria such as E coli, genetic material is present as a long circular DNA  molecule compacted in an unenclosed nucleoid. Extends to a large part of the cell  and does not undergo extensive coiling, nor is it associated extensively with  proteins. They do contain genes specifying rRNA.  

The remainder of a eukaryote within the plasma is the cytoplasm, containing  colloidal material called the cytosol, encompassing cellular organelles. Contain  tubules and filaments, composing of cytoskeleton to provide support structures  consisting of microtubules, which are composed of protein tubulin and  microfilaments, derived from the protein actin. It maintains the shape and facilitates mobility for the cell, anchoring organelles. The endoplasmic reticulum  compartmentalizes the cytoplasm, increasing surface area. The ER is smooth where  fatty acids and phospholipids are synthesized; in others rough because of  ribosomes.  

What is heterogeneous trait?

Ribosomes are sites where genetic information in mRNA is translated into proteins.  Mitochondria are found in most eukaryotes and are sites of oxidative phases of cell  respiration. It generates ATP. Chloroplasts (mostly found in plants) are associated  with photosynthesis. Both contain DNA in a form distinct from the nucleus; it is also  capable of duplicating, transcribing and translating its own genetic information.  They closely resemble prokarya. These organelles were once primitive free-living  organisms that established a relationship with primitive eukaryaꟷendosymbiont  hypothesis.  

Centrioles, located in centrosomes, are associated with spindle fibers that function  during cell division. The organization of spindle fibers by centrioles occurs early in  mitosis/meiosis and plays a role in movement of chromosomes as they separate  during cell division. They are composed of microtubules consisting of tubulin.  

What is the conditional mutation?

Don't forget about the age old question of What is a corporation?

Each chromosome contains a constricted region of the centromere which  establishes the appearance of each chromosome.  Don't forget about the age old question of What is an orientalism?

Somatic cells derived from the same species contain the same number of  chromosomes, representing a diploid number (2n). With the exception of sex  chromosomes, these exist in pairs; members of each pair being homologous  chromosomes. There are exceptions like bacteria, viruses, certain plants, yeast,  mold (for they live haploid for most of their life). Humans have 2n number of 46

chromosomes. Each of the 46 is a double structure consisting of 2 sister chromatids  connected by a centromere.  Don't forget about the age old question of What are the characteristics of emerging economies?

Haploid number (n) is equal to half of the diploid. The genetic information contained in the haploid set of chromosomes constitutes the genome, which includes a copy of all genes including noncoding ones.  

Homologous chromosomes have identical gene sites, called loci (singular: locus).  These are identical in traits and genetic potential. In sexual organisms, one member of each pair is derived from ovum and sperm. Each diploid organism contains two  copies of each gene as bi-parental consequence/inheritance, which come from both  parents. Members of each pair of genes can influence each pair of genes that are  not identical. Alleles are different versions of the same gene.  

During meiosis, the diploid number of chromosomes becomes haploid. Gametes or  spores contain 1 member of each homolog pair-1 complete haploid set. Fusion re establishes the diploid set and becomes a zygote. Constancy of genetic material is  thus maintained. In many species, one pair of homologs, sex-determining  chromosomes are often not homologous in size, centromere placement, etc. (Ex: X  and Y chromosomes).  We also discuss several other topics like What is the purpose of the trial?

Multicellular diploid organisms begin life as single-celled fertilized eggs (zygotes).  The mitotic activity of the zygote is the foundation for development and growth of  the organism. In adults, mitotic activity is the basis for wound healing and cell  replacement. Karyokinesis is the partition of genetic material into daughter cells  during nuclear division. Nuclear division is very exact; results in the production of  daughter nuclei with exact same chromosome composition. This is followed by  cytokinesis where it parts and splits the plasma membrane. As the cytoplasm is  reconstituted, organelles replicate themselves and arise from existing membrane  structures or synthesized de novo in each cell.  

The cell cycle is the continuous alternation between non-division and division. The  events in between constitute the cell cycle: If you want to learn more check out What is hussein-mcmahon?

Interphase: the initial stage of the cell cycle, the interval between divisions and  includes the replication of DNA in each chromosome.

S Phase: DNA synthesis before mitosis. G1∧G2 are gap phases in which no DNA is

synthesized. It includes the metabolic activity, cell growth and cell differentiation.  By the end of G2 , the cell has doubled in size and DNA has been replicated.  If you want to learn more check out What is the purpose of 4th ammendment?

Mitosis begins. During G1 cells either enter the G0 stage or proceed through  G1 . Those in G0 do not proliferate.

Prophase: characterized by migration of centrioles to the ends of the cell outside  the nuclear envelope. Centrosomes organize microtubules into spindle fibers,  creating an axis on which the chromosome separation occurs. Fungi, plants, and  some algae lack this. The nuclear envelope begins to break down and the nucleolus  to disintegrate. Chromatin fibers begin to condense. Two parts of each chromosome  are called sister chromatids because DNA in each is genetically identical. These are  held together by cohesin. The molecular complex formed between and during the S  Phase is when DNA is replicated.  

The next stages are leg by migration of the chromosomes; which in turn are led by  centromere regions to the equatorial plane/metaphase plateꟷperpendicular to the  axis established by spindle fibers. Prometaphase is the period of chromosome  movement and metaphase is applied to the chromosome configuration following  immigration.  

Migration is possible by the binding of the spindle fibers to the kinetochore, an  assembly of multilayered proteins associated with centromeres. This forms on  opposite sides of each paired centromere in association with sister chromatids.  Once attached the cohesin is disintegrated by separase and sisters disjoin except at the centromere. The protein family of shugoshin protects cohesion from being  degraded at the centromere.

Mutations of the kinetochore proteins can potentially lead to errors during  chromosome migration along the diploid content of daughter cells. Kinetochore  microtubules from spindle fibers lengthen and shorten as a result of addition or  reduction of polarized tubulin subunits. They each have one end near the  centrosome region and another at the kinetochore.  

Anaphase is the event critical to chromosome distribution and the shortest stage of  mitosis. Sister chromatids of each chromosome disjoin in disjunctionꟷpulled to  opposite ends of the cell:

1. Shugoshin must degrade

2. Cohesin must be cleaved by separase

3. Chromatids must go to opposite end of the cell.  

Each migrating chromatid is now a daughter chromosome. Movement is dependent  on the kinetochore-spindle fiber attachment. Results from motor proteins. Molecular motors use energy generated by hydrolysis of ATP, and its effect shortens spindle  fibers, drawing chromosomes to opposite ends.  

Steps in anaphase are critical. In human cells, there would be 46 chromosomes at  each pole of the cell, one from each sister pair.  

Telophase: the final stage in mitosis. At the beginning, 2 complete sets of  chromosomes are at each pole. The most significant event is cytokinesis,  partitioning of the cytoplasm. In plant cells, the cell plate is synthesized and laid

down across the region of the metaphase plate. Animal cells undergo constriction of the cytoplasm, the cell plate in plants is laid down and becomes the middle lamella.  Primary and secondary layers of the cell as are deposited between the membrane  and m. lamella in each daughter cell. In animal cells, constriction produces a cell  furrow. Chromosomes begin to uncoil, the nuclear envelope reforms, spindle fibers  disperse, etc. The cell enters Interphase.  

Cell division cycle (cdc) mutations: Normal products of many mutated genes are  kinases that can add phosphates to other proteins. Some act as a “master control”  molecules functioning with the protein cyclin. Cyclin binds to kinase activating at  times during the cycle. Then it phosphorylates to other target proteins that regulate the process of the cell cycle. Cdc mutations help establish 3 checkpoints in the  cycle:

G1/S checkpoint: monitors cell size and condition of DNA. If DNA is damaged or  

growth is inadequate, progress is arrested. If adequate, the cell moves into  Synthesis.  

G2/ M checkpoint: DNA is monitored prior to mitosis. If replication is incomplete  or if DNA is damaged, the process is arrested.

M checkpoint: Occurs during mitosis, successful spindle fiber formation and spindle  fibers to kinetochores necessary.  


Crossing over results in genetic exchange between members of each homologous  pair of chromosomes. Sexual reproduction reshuffles genetic material; major source  of recombination within species.  

Early in meiosis, homologous chromosomes form pairs, synapsis. Each synapsed  structure, bivalent, gives rise to tetrad, composed of 4 chromatids, demonstrating  both homologs duplicated. First division in meiosis I is reduction division.  Components of each tetrad separate into dyads, which are composed of 2 sister  chromatids joinder at the centromere. Second division in meiosis II is equatorial  division. Each dyad splits into 2 monads of once chromosome each. Both divisions  produce 4 haploid cells.  

Prophase I: same as mitosis except each homologous pair of chromosomes pair  through synapsis, crossing over occurs. 5 substages: leptonemia, zygonema,  pachynema, diplonema, diakinesis.  

Leptonema: interphase; chromatin material condenses, chromosomes visible. Along  each chromosome are chromomeres, localized condensations resembling string.

Homology search precedes and is initial pairing of homologs, begins during  leptonema.  

Zygonema: chromosomes continue to shorten and thicken. Rough pairing complete  at end of zygonema. During meiosis, lateral elements along chromosomes increases and synaptonemal complex begins to form between homologs. It is the vehicle  responsible for proper alignment during pairing of homologs. In diploids, synapsis  acts in zipper-like fashion, beginning at ends. Upon completion, homologs are  referred to as bivalents. The number of bivalents equals the haploid number.  

Pachynema: chromosomes continue to coil and shorten, and the development of the synaptonemal complex continues between 2 members of each bivalent. This leads  to synapsis, and referred to as a tetrad.  

Diplonema: apparent tetrad has 2 pairs of sister chromatids. Each pair begins to  separate, but some areas remain intertwined (chiasma) at a point of crossing over.  

Diakinesis: chromosomes pull apart, but non-sister chromatids remain loosely  associated at the chiasmata. The chiasmata move to end of the tetrad in  separation.  

Terminalization begins at later diplonema and completed in diakinesis, in the  nucleolus and nucleus breakdown; two centromeres of each tetrad form spindles. By the end of prophase I, the centromeres are present on the metaphase plate.  

Metaphase I: terminal chiasmata hold non-sister chromatids together, tetrad  interacts with spindles, alignment of each tetrad is random. Half of the tetrad will be pulled to one end of the pole.  

Anaphase I: cohesin is degraded between sister chromatids, except at centromere. . The dyad is then pulled to each pole, disjunction occurs. When separation is not  achieved, nondisjunction occurs.  

Telophase I: reveals nuclear membraned forming around the dyads. In this case, the nucleus enters a short interphase. If it occurs, the chromosomes do not replicate  because they already have two chromatids. In others, they enter meiosis II. Much  shorter than mitotic telophase.

Meiosis II: essential if each gamete/spore relieves one chromatid from each original  tetrad.

Prophase II: each dyad has 1 pair of sister chromatids attached to the centromere. Metaphase II: centromeres positioned on metaphase plate.  

Anaphase II: occurs when shugoshin is degraded and sister chromatids pull apart.  Telophase II: results in 4 haploid gametes, each chromosome being a monad.

Spermatogenisis: takes place in testes, enlargement of an undifferentiated diploid  germ cell-spermatogonium. Grow into a primary spermatocyte, which undergoes the first meiotic division. Products: secondary spermatocytes, which contain a haploid  number of dyads. They undergo meiosis II for spermatids and spermiogenesis to  become sperm. To become sperm, there must be equal amounts of cytoplasm when  dividing.  

Oogenesis: same process as spermatogenesis, but there are not equal amounts of  cytoplasm in each cell. Most occurs in the primary oocyte that is derived from the  oogonium which is concentration in 1 of the daughter cells. Necessary for  nourishment of the embryo. In the first polar body of telophase I, most of the  cytoplasm is in the secondary oocyte, which then divides to become an ootid and  second polar body. These divisions may not be continuous like sperm. The second  meiotic division of the secondary oocyte produces a mature ovum.  

Chapter 3  

Transmission genetics: study of how genes are transmitted from parents to  offspring. Derived directly from Mendel’s experimentation. 1856-Mendel performed  first set of hybridization experiments with garden pea. Continued until 1868.  

Traits: contrasting forms of an organism-characteristics are visible features. Mendel  used these to compare garden peas in experimental fertilization.

Monohybrid cross: cross involving only one pair of contrasting traits. Done by  mating true-breeding individuals from two parent strands, each exhibiting one out  of two contrasting forms of character in study. First generation examined, ton of  offspring selfing: self-fertilization.  

Parental generation ( P1¿: original parents. First filial generation ( F1 ): offspring  of Parental Generation. Second filial generation ( F2 ): offspring of selfing. Ex:  breed between tail and dwarf plants.

Genetic data usually expressed/analyzed in ratios.  

Reciprocal crosses: when patterns of inheritanceꟷfrom one trait (sperm) and the  other (egg) are the same no matter who fertilized. Ex: results of Mendel’s peas are  not sex-dependent.  

To explain, unit factors for each trait are applied and serve as basic units of heredity unchanged from generation to generation.  

Mendel’s Postulates:

1. Unit factors are in pairs: genetic characters are controlled by unit factors  existing in pairs of individual organisms. In a monohybrid cross, the specific  unit factor for each trait. Each diploid receives one from each parent. Ex: 2 for tall, 2 for dwarf, one of each.

2. Dominance/recessiveness: when two unlike unit factors responsible for a  single character are present in an individual, one unit is dominant to the  other. Traits that are not usually expressed are recessive. Ex: tall-D, dwarf-R.  

3. Segregation: During formation of gametes, paired units separate/segregate  randomly so one of each gamete receives with equal likelihood. Ex:  probability for tall and dwarf traits.  

Phenotype: physical expression of a trait.

Gene: units of inheritance (unit factors). For any given character (such as height),  the phenotype is determined by the alternative forms of a single gene; alleles/

Genotype: alleles written in pairs to represent unit factors. Designates genetic  makeup of an individual. By reading the genotype, we know the phenotype  (dominant/recessive traits). When both alleles are the same, they are homozygous.  When the alleles are different, they are heterozygous.  

Test cross: method used to distinguish the genotype. Organism with a dominant  phenotype but unknown genotype is crossed with a homozygous recessive  individual.

Dihybrid cross: two factor cross that analyzes 2 characters simultaneously. Best  thought of as 2 separate monohybrid crosses. Ex: Yellow and green seeds  independent of round and wrinkled.

Product law of probabilities: when two independent events occur simultaneously,  probability of two outcomes occurring in combination is equal to the product of their individual probabilities of occurrence. Ex: (3/4)(3/4)=9/16--- ¾ should be yellow, ¾  should be round.  

Independent Assortment: during gamete formation. Segregating pairs of unit factors assort independently of each other. Stipulates segregation of any pair of units occur  independent of others. As a result, each gamete receives 1 member of every pair of  units. For 1 pair, factor does not influence segregation of others. All combinations  

should be in equal frequency.  

Mendel’s 9:3:3:1 ratio/dihybrid ratio: ideal ratio based on probability that events  involve segregation, independent assortment and random fertilization. Actual  results are unlikely to match the ideal.  

Trihybrid cross: segregation and independent assortment applies to this 3-factor  cross as well. In this, all individuals produced are heterozygous.  

Another method developed--fork-line method/branch diagram. Each gene pair is  assumed to behave independently during gamete formation can be used for any  number of gene pairs, provided all gene pairs sort independently from one another.

For two or more gene pairs:  

1. Determine the number of different heterozygous gene pairs (n) involved in  the cross. Ex: AaBb x AaBb (n=2), AaBBCcDd x AaBBCcDd (n=3)---because B is not heterozygous.  

2. Once n is determined, 2n is the number of different gametes that can be  formed, 3n is the number of different genotypes of fertilization; 2n is the  phenotype from genotypes. Applied only if independently assorted.  

Continuous variation: held by students of evolutionary theory; describes offspring as a blend of their parent’s phenotypes. Ex: Darwin.  

Discontinuous variation: held by Mendel due to the dominant-recessive relationship  of genes.  

Chromosomal theory of inheritance: deduced by Sutton and Boveri, the idea that  genetic material in living organisms is contained in chromosomes.

-Following independent segregation of each pair of homologs, each gamete receives one member from each pair. All possible combinations are formed with equal  probability. Independent behavior of unit factors is due to separate pairs of  homologous chromosomes. Chromosomes are composed of a large number of  linearly ordered information containing genes. The location of any particular gene  on a chromosome is called a locus. Different alleles of a given gene contain slightly  different genetice information that determines the same character. Most genes have more than 2 allelic forms.

Probabilities range from 0.0---certain not to occur---to 1.0----certain to occur.

Product law: probability of 2 or more events occurring simultaneously is equal to the product of their individual probabilities.

Sum law: calculation of probability when possible outcomes of 2 events are  independent of one another can be accomplished in more than one way. The  probability of obtaining any single outcome, where that outcome can be achieved  by 2 or more events, is equal to the sum of the individual possibilities of the event.  

Binomial theorem: analyzes cases where there are alternative ways to achieve a  combination of events, a+b ¿n=1

¿, a and b being probabilities of alternative  

outcomes and n number of trials.


(s!)(t !)asbt where n equals the number of trials, s the number one variable, t Ex:  

the same, and a and b is the probability of the outcomes of s and t.  

Mendel’s independent assortment and random fertilization is influenced by chance  deviation, like observing the ratio of heads/tails coin. As the number of tosses is  reduced, the impact of chance deviation increases--independent assortment and  random fertilization is subject to random fluctuations from the predicted outcome  due to chance deviation. As sample size increases, the chance deviation decreases.  

Null hypothesis: in observing deviation it assumes no difference between measured  and predicted values. Any difference is chance. If rejected, the deviation observed is not due to chance. If not rejected, deviations are due to chance.  

Chi square analysis: test that assesses goodness of fit of null-hypothesis. Takes into  account the observed deviation in each component of a ratio (expected) as well as

sample size and reduces to single number value x2 then estimates frequency of  deviation: x2=εd2 

e where e is the expected value, ε the sum of each ratio

Interpreting x2 is evaluated by degrees of freedom (df)= n-1 where n is the  number of different categories data is divided into.  

**The greater the number of categories, the more deviation by chance that is  expected.  

Probability of value (p): form of interpretation of x2 after df is determined. The  

percentage indicates the percentage expected for the experiment to exhibit the  chance deviaton as great or greater than in initial, or less. Less=more chance  More=less chance. The p-value should be less than .05

Pedigree: family tree that observes presence/absence of traits for each member. By  analyzing the pedigree, allowed to predict how a trait is inherited.

Consanguineous: related.  

-Siblings are in order of birth from left to right. Generations are in Roman numerals.  Identical twins are monozygotic. Fraternal twins are dizygotic. An individual whose  phenotype is brought attention to the family is proband. In albinism the synthesis of pigment of melanin is obstructed. Autosomal dominant diseases like Huntington’s is  rare. If so, the parent always exhibits the trait, usually offspring too.  

Chapter 4

Gene Interaction: situation in which a single phenotype is affected by more than one set of genes.  

-Neo-Mendelian genetics investigates observations of genetic data that did not  conform precisely to expected Mendelian alleles.  

Allele: alternative form of a gene. Allele that occurs most frequently (or is normal) is referred as the wild type allele(represented by a +, ex: abc+). It is often but not  always dominant.  

**The process of mutation is the source of new alleles. For a new allele to be  recognized by observation of an organism, the allele must cause a change in  phenotype. A new phenotype is formed from a change in functional activity of  cellular products specified by that gene.

Loss of function mutation: causes a gene to create an enzyme that loses/reduces  the affinity for substrate. A null allele results if loss is complete.  

Gain of function mutation: enhances the function of the wild-type product and  increases the quantity of gene product. Results in dominant alleles. Ex:Proto oncogens changed to oncogens, which override regulation of gene product. Function is always turned on. Neutral mutations cause no phenotypic change or evolutionary  fitness change.  

-Traits are influenced by many gene products. Mutations can have a common effect  in metabolic pathways―with a failure to produce an end product.  

Incomplete/Partial Dominance: no one gene dominates the phenotype. Creates an  intermediate phenotype. There can be alleles that are neither dominant nor  recessive.  

Haplo-insufficiency: when a single allele is not sufficient to produce the wild type  phenotype and mask the other allele. (The dominant allele does not produce  enough gene product/dose). Ex: red and white snapdragons―  

 RR-red (anthocyamin-receives two doses)-1/2  rr-white (receives no doses of pigment)-1/4

 Rr-pink (receives one dose of anthocyamin-not  enough to make red)-1/4

 1:2:1 ratio

-Examination of gene product and activity often reveals intermediate gene  expression (not in the phenotype). Tay-Sachs disease is related to lipid-storage  deficiency. Those that are homozygous are affected, but heterozygotes are only  partially affected. Threshold effect: normal phenotypic expression occurs any time a certain level of gene product is attained. In Tay Sachs, it is less than 50% of the  time.  

Codominance: occurs when joint expression of both alleles occurs. 2 alleles of a  single gene are responsible. Ex: MN blood group  

 Both alleles expressed.  

-Codominant inheritance is characterized by distinct expression of gene products of  both alleles. Different from incomplete dominance, where products of both alleles.  Different from incomplete dominance, where heterozygotes express intermediate  blended phenotype.

-When mutation modifies information on a gene, each change produces a different  allele.  

Multiple Alleles: when present in a population, inheritance may be unique. Multiple  alleles can only be studied in populations―one organism may have at most 2  homologous gen loci coupled by different alleles of the same gene. Among  members of a species, numerous alternate forms of the same gene can exist. Ex:  ABO Blood Groups―characterized by the presence of antigens on the surface of red  blood cells―different from MN antigens. Once combination exhibits co-dominant  forms of inheritance. IAIB for AB blood type are codominant to each other but  

dominant to i, (for O blood type). All individuals possess H substance, to which half  of sugars are added (carbohydrates are terminal sugars that determine A or B blood type). Type O, unlike A, cannot add the H substance.  

-However, there are mutants of FUT1 gene that cannot express the sugar for the H  substance even though they are type A or B functionally―Bombay Phenotype

-Mutations resulting in nonfunctional genes can be tolerated in heterozygotes,  where the wild type might be enough to produce the essential product.  

Recessive Lethal Allele: mutations resulting in a nonfunctional gene; lethal to  homozygotes. May respond as phenotype in heterozygotes. Ex: yellow pigment in  mice. Dominant in coat to wild-type, so heterozygotes are yellow. Homozygotes die  before birth.  

 AYAY−homozygousrecessive (death)   A A−homozygous dominant (agouti )   AYA−heterozygote( ¿) 

2:1 ratio signals lethal gene

Dominant lethal allele: the presence of just one copy of the allele results in death.  Ex: Huntington’s disease: Delayed until adulthood in heterozygotes, that results in  motor and neurological degradation. (Dominant lethal alleles are rarely observed).  

-For dihybrid corsses such as albinism risk and blood type, the 9:3:3:1 ratio converts to 2:6:3:1:2:1, establishing the probability of each phenotype. Phenotype in many  cases is affected by more than one gene. Genetic influence on phenotype is more  complex than Mendel’s encounters. Gene Interaction expresses the idea that  several genes influence a particular characteristic. DOES NOT MEAN THAT TWO OR  MORE GENES INTERACT DIRECTLY TO INFLUENCE. DOES MEAN THAT CELLULAR

FUNCTION OF NUMEROUS GENE PRODUCTS CONTRIBUTES TO GENE DEVELOPMENT  OF A COMMON PHENOTYPE. Epigenesis: a point in which each step of development  increases the complexity of an organ or feature and is under the control/influence of many genes. Ex: formation of inner ear in mammals. Forms as a result of a cascade  

of intricate developmental events influenced by many genes. Mutations that  interrupt these events leads to hereditary deafness. In a sense, many genes  “interact” to produce a common phenotype. Mutant phenotype then becomes the  heterogeneous trait.  

Epistasis: the expression of one gene pair masks/modifies the effect of another.  Sometimes the genes involved influence the same general phenotypic characteristic in an antagonistic manner, which leads to masking. But other times, the genes  involved exert influence on one another in a complementary fashion. Ex: recessive  homogeneous allele (epistatic) may override the expression of other alleles  (hypostatic) at another locus. 2 gene pairs may also complement one another such  that at least one dominant allele in each pair is required to express a particular  phenotype. (9:7 ratio or 9:3:4).  

**When a single character is being studied, a ratio of 16 parts (ex: 3:6:3:4) suggests that two gene pairs are “interacting” in the expression of the phenotype under  consideration (epistasis has an effect of combining one or more of 4 phenotypic  categories in various ways).  


1. In each case, a distinct phenotype classes produced, disassemble from  others. Illustrate discontinuous variation―phenotypic traits are discrete and  different from each other.  

2. Genes considered in each cross are on different chromosomes and assort  independently during gamete formation . Ex: A,a,B,b.  

3. When we assume complete dominance (AA,Aa,BB,Bb) is equivalent to genetic effects of A- or B- (- means other alleles present)

4. P1 crosses are with homozygous individuals (AABB, aabb,AAbb, aaBB).  Each F1 has heterozygote (AaBb)

5. F2 is the main focus. When 2 genes are involved, genotypes fall into 9/16  

A-B-, 3/16 A-bb and 1/16 aabb. All genotypes are equivalent on the effect for  the phenotype. Ex: mice A- agouti aa-black bb-albino.  

 bb masks A or a alleles  (recessive epistasis)


-Novel Phenotypes may be expressed in the F2 generation in addition to the  modified dihybrids Ex: squash shape. F1 = AaBb x AaBb (both disc). A-bb and  aaB- yield sphere shape (new phenotype). (gene interaction) 

**When 16th in ratios of dihybrid crosses where inheritance pattern is unknown think 2 gene pairs involved.  

Heterogeneous trait: go back to hereditary deafness.  

Complementation analysis: allows to determine whether 2 independently isolated  mutations are in the same gene (alleles) or represent mutations in separate genes.  May reveal if only a single gene is involved in a mutation or multiple genes. Ex:  Drosophila bugs F1 generation.  

Case 1: All offspring have wings―2 recessive mutations (that make bugs wingless)  in separate genes and not alleles―being heterozygotes, both genes have a normal  copy of each gene and complement.  

Case 2: No wings―2 mutations affect the same gene and are alleles of one another.  No complementation, homozygous for 2 mutant alleles. No normal product  produced.  

Complementation group: is for all mutations present in a single gene. Complement  mutations are in all other groups. Helps predict the number of genes involved in the determination of a trait.  

Pleiotropy: when a single gene has multiple phenotypic effects. Ex: Marfan  Syndrome: results from autosomal dominant mutations in the gene encoding  fibrillin. Also, Poryphyria variegate: does not allow for the metabolization of  hemoglobin when the respiratory pigment is broken down. Leads to toxic buildup.  

-A major portion of the Y chromosome is inert genetically. There is only a small  portion that is homologous to the X chromosome in order to separate during  meiosis. X-linkage―genes present on the X chromosome exhibit patterns of  inheritance different from those with autosomal genes. One of the first examples  was the white eye of the Drosophila female, which was an X-linked mutation that  was expressed in male offspring only.

-Since the Y chromosome lacks homology with almost all genes on the X alleles  present on the X will be directly expressed in the phenotype. Males cannot be  homozygous or heterozygote for X-linked possession of only one copy of a gene in  diploid is heterozygosity. One result of X-linkage is in a crisscross pattern, where  recessive X-linked genes passed from homozygous mom to all males. Occurs  because females express recessive mutant allele on both chromosomes. Ex:  colorblindness.  

-If X-linked disorder debilitates/lethal to individuals prior to reproduction, disorder  exclusively in males―only source of lethal allele in heterozygote female “carriers”.  Pass on to ½ of males. Ex: Duchenne muscular dystrophy.  

-In sex-linked inheritance and sex-influenced inheritance: autosomal genes  responsible for contrasting phenotypes but expression dependent on hormone  constitution of the individual. So, heterozygotes may exhibit a phenotype in males  and contrast in females. Ex: domestic fowl plumage distinctly different in males and  females, demonstrating sex limited inheritance―controlled by a single pair of  autosomal alleles modified by hormones.  

Sex influenced patterns of inheritance include pattern baldness in humans, horn  formation in sheep and coat patterns in cattle. Autosomal genes are responsible,  while trait may show in both sexes, expression dependent on hormone constitution.  

-Most gene products function within a cell, cells interact with one another in various  ways. Organisms exist under diverse environmental influences. **Gene expression  and resultant phenotype modified through interaction between individuals’  genotype and external environment. Degree of expression can be shown by  determining penetrance and expressivity.  

Penetrance: Percentage of individuals that show at least some degree of expression  of a mutant genotype. Ex: If 15% of flies have a mutant genotype with wild-type  appearance, penetrance of mutant gene is 85%

Expressivity: range of expression of mutant genotype. Ex: eyeless gene in flies can  range from normal to partial to none―experiments show genetics and  environmental factors influence expression.  

Position effect: effect of genetic background; where physical location of a gene in  relation to other genetic material may influence expression. Ex: if a region of  chromosome is relocated, normal expression of genes in that region may be  modified more. True if gene is relocated to areas condensed and genetically inert  (heterochromatin) Ex: white eye of X-linked Drosophila―if a region of X  chromosome with w+ allele is relocated, caused red and white phenotype.  

-Temperature affects/influences phenotypes through chemical activity―dependent  on kinetic energy. Ex: a primrose is red at 23 degrees Celsius and white at 18

degrees. Siamese cat and Himalayan rabbit-fur black in cold areas and white in  warmer ones. (temperature sensitive mutations). These are rexamples of  conditional mutations. Permissive conditions allow an organism to grow, restrictive  conditions require and organism to use essential genes and arrests. Nutritional  mutations are crucial in bacteria―mutations that prevent synthesis of nutrient  molecules may kill microorganisms. They can also prevent organisms from  metabolizing a substance Ex: lactose intolerance.  

-Some genes are expressed at different phases of life: prenatal, childhood, pre-adult and adult. Genetic Anticipation: a form of heritable disorders that exhibit  progressively earlier ages of onset and increased severity of the disorder in each  successive generation. Es: Myotonic dystrophy.  

-Genomic/Parental Imprinting: process of selective gene silencing that occurs during early development, impacting subsequent phenotypic expression. Impact depends  on parental origin of genes/regions involved. Leads to direct phenotypic expression  of allele(s) on homologs that are not silenced.  

Chapter 5

-Goals for Bio: DNA is organized into chromosomes which are units of heredity;  chromosomes are segregated (you should be able to describe linkage and what it  does to segregation ratios)

Most chromosomes contain a large number of genes. Those that are part of the  same chromosome are linked and demonstrate linkage in genetic crosses. Because  chromosomes and not genes are the units of transmission in meiosis, linked genes  are not free to undergo independent assortment. Instead, alleles at all loci are  transmitted as a unit. In many cases, this does not occur.  

Crossing over or reshuffling/recombination shuffles alleles between genes and  always occurs during the tetrad stage (prophase-the exact moment is still  unknown). This is currently viewed as a physical breaking and rejoining process. The frequency of crossing over is proportional to the distance between genes.  Chromosome maps indicate the relative locations of genes on chromosomes.  

Chiasma shows consequences of crossing over―exchange of material of 2  homologous chromatid segments.  

Genes on the same chromosome may be inherited together.  

Complete linkage produces only parental/noncrossover gametes. Two parental  gametes are formed in equal proportions when genes are linked on the same  chromosome and only two genetically different kinds of gametes are formed.  Crossover between linked genes involves non-sister chromatids―this generates 2

new allele combinations―recombinant/crossover gametes. As distance between 2  genes increases, the proportion of recombinant gametes increases and parental  gametes decreases.

Recombination can occur between any 2 of 4 chromatids of a homologous pair.  Genetically occurs between sister chromatids. The only way to tell if recombination  has occurred in homologous chromosomes is if the alleles are different.  

If complete linkage exists between 2 genes because of close proximity and  organisms that are heterozygous at both loci are mated, a unique F2 phenotypic  ratio results―a linkage ratio.  

Ex: Drosophila; hv-heavy wing vein (mutant recessive) hv+-thin wing vein (wild  type)  

 bw-brown eye(mutant recessive) bw+-red eye (wild type)  1:2:1- one heavy wing, 2 wild type, 1 brown eyed

When large numbers of mutant genes in a species are investigated, genes on the  same chromosome are linked―linkage groups can then be identified (one for each  chromosome). Genes on a single chromosome comprise a linkage group (there are  24 linkage groups in the human genome (22 autosomes, 2 sex chromosomes)). The  number should correspond to the haploid number of chromosomes.  

Alternate possibilities of genetic recombination―independent assortment.   unlinked


 partially linked (like unlinked) Crossing over  indicated by ×

-Morgan( who discovered X linkage) postulated that linked genes are arranged in a  linear sequence along the chromosome and that variable frequency of exchange  occurs between any 2 genes during gamete formation. 2 genes relatively close to  each other alonge a chromosome are less likely to have a chaisma form between  them than if the 2 genes are farther apart on the chromosome. The closer the genes are, the less likely that an exhacne will occur between them.  

The frequency of crossing over(recombination) between 2 genes is proportional to  the distance between the genes.  

Ex: Drosophila; rate of occurrence for phenotype 1. Yellow, white .5% →  sum of 1 and 2=3

**Recombination frequencies between linked 2. white, minute 34.5% genes are additive 3. yellow, minute 35.4%

The distance between yellow and white is .5 (mu-map units) and the distance  between yellow and minute is 35.4 mu. The distance between white and minute is  35.4-.5=34.9 mu

X-linkage and crossing over are not restricted to the X chromosome, but can apply  to autosomes. In Drosophila, there is more crossing over in females than males.  

-During meiosis, a limited number of crossover events occur in each tetrad. These  recombinant events occur randomly along the length of the tetrad. The closer that  two loci reside along the axis of the chromosome, the less likely that any single  crossover event will occurs between them → occurs between 2 nonsister  

chromatids, but not the two loci that are being studied. Where two loci are far apart, crossover does occur. When crossover occurs, the other two chromatids of the  tetrad are not involved. These are used to determine the distance between two  linked genes.

The percentage of tetrads involved in an exchange between 2 genes is 2x as great  as the percentage of recombinant gametes produced. Theoretical limitation of  observed recombination due to crossing over is 50%.  

Double exchanges of genetic material result from double crossovers (DCOs). 3  genes pairs must be investigated to do this. 2 independent and separate  events/exchanges must occur (refer to the product law). Ex: single crossover  between A and B is 20% (p=.20); B and C is 30% (.30). The chance of a double  crossover is (.20)(.30)=.06 or 6%. Double exchanges of genetic material are used to determine the distance between 3 linked genes. Genes must be heterozygous for  both alleles.

A test cross is used to test whether an organism is a heterozygote or homozygote  for certain traits.  

Ex: Aa × aa (all linkage studies use this to study recombination in a  heterozygote) 1:1 ratio

Class Question: If no crossing over occurs between these two, what phenotypes  result?  

 pr-purple eyes pr+-wild type vg- vestigial wing vg+-wild type

 Answer: Wild type pr and vg recessive  Class Question: If crossing over does occur, what phenotypes?

Answer: wild type, purple vestigial (recessive), vestigial (wild type) and purple eye **If a trait is not specifically stated, assume wild type  

Class Question: If the genes are unlinked?

Answer: wild type, purple vestigial (recessive), vestigial and purple eye For a successful mapping cross:

1. The genotype of the organism producing the crossover must be a  heterozygote at all loci under consideration.

2. The cross must be constructed so genotypes of all gametes can be accurately determined by observing phenotypes of the resulting offspring.

3. A sufficient number of offspring must be produced.

To diagram a 3 point cross successfully, ** we must assume some theoretical  sequence, even though we do not yet know if it is correct.  

Ex: Drosophila; white eye, yellow body, echinis eye shape.  

P1 -males hemizygous for all 3 wild type; females homozygous-recessive

F1 -females are heterozygous, males hemizygous recessive

F2 - females and males will express genotype from F1 

-To create a chromosome map, we must determine which F2 phenotypes  correspond to noncrossover and crossover categories. For noncrossover in F2 

phenotypes, we must identify individuals derived from parental gametes from the F1 female. Each such gamete contains an X chromosome unaffected by crossing  

over. Genotypes of parental gametes and F2 phenotypes complement one  

another. Ex: if one is wild type, the other is a mutant for all 3 genes. In other  situations, if one chromosome shows a mutant allele, the second shows the other  two mutant alleles―these are the reciprocal classes of gametes and phenotypes.  

-2 noncrossover phenotypes are most easily recognized because ** they occur in  the greatest proportion of offspring.  

-The 2nd category is easily represented by double-crossover phenotypes, ** present  in the least numbers.  

-The remaining categories for the 4 phenotypic classes result from single  crossovers. Double crossovers represent 2 simultaneous single crossovers.  

To determine gene sequence (Method I):

1. Assume any of the 3 orders (w-y-ec, y-ec-w, y-w-ec), then determine the  arrangement of alleles along each homolog of the heterozygous parent giving rise to noncrossover and crossover gametes.  

2. Determine whether a double-crossover even occurring within the  arrangement will produce the observed double-crossover phenotypes (which  occur least frequently).

3. If this order does not produce the correct phenotypes, try each of the other 2  orders.  

Method II: assumes that following a double crossover event, the allele in the middle  position will fall between the outside/flanking alleles that were present on the  opposite parental homolog.  

Interference (I): the inhibition of further crossover events by a crossover event in a  nearby region of the chromosome causes the reduction. To quantify discrepancies  that result from interference, we calculate the coefficient of coincidence (C):

C=observed DCO

expected DCO . To quantify interference: I=1-C. If interference is complete and

no double crossovers occur, I=1 . If fewer DCOs than expected occur, I is positive  and positive interference has taken place. If more DCOs than expected occur,  negative interference has occurred. Positive interference is most commonly  observed in eukaryotes.

Lod score method: helps to demonstrate linkage of 2 genes when they are  separated to the degree that recombinant gametes are formed. Assesses the  probability that a particular pedigree involving 2 traits reflects genetic linkage  between them. A value of of 3 or above indicates linkage―-2 or below does not. If  the result is between -2 and 3 → inconclusive.  

DNA markers: short segments of DNA whose sequence and location are known,  making them useful for mapping purposes. Ex: Cystic Fibrosis ― a gene located  using markers.  

Sister chromatid exchanges: occur during mitosis, do not produce new allelic  combinations. Frequency of SCEs significant but unknown why.  

Cis and Trans configuration: The way alleles of a gene are organized on  chromosomes

Cis configuration: Trans configuration: 


Crossover depends on whether  

mother is cis or trans!  

Cis crossover: Trans crossover:  


P1 AABB x aabb

F1 AaBb If A and B genes are linked, the offspring has Cis  configuration

 If the genotype of the offspring is recombinant:    

 If A and B are trans, the parental crossover of the  offspring looks like this: Ab

**In linkage studies, you are really looking at meiosis of the mother    



Noncrossover gametes: y+ ec+ y ec  

 y ec

Crossover gametes: y+ ec ** Difference between  unlinked genes and linkage  

 y ec+ with crossing over:  crossing over is much rarer

 than noncrossing over

To determine the distance of genes: divide the sum of crossovers by the total  number of offspring to get the percentage. Ex: there are 10,000 flies for offspring.  To find the percentage of noncrossover gametes: [275+273]/10000= .05 or 5%  (created numbers).  

Percent crossover is equivalent to the crossover map units.

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