1: Chemistry to Chromosomes - Biology

1: Chemistry to Chromosomes

13.1 Chromosomal Theory and Genetic Linkages

In this section, you will explore the following question:

Connection for AP ® Courses

Proposed independently by Sutton and Boveri in the early 1900s, the Chromosomal Theory of Inheritance states that chromosomes are vehicles of genetic heredity. As we have discovered, patterns of inheritance are more complex than Mendel could have imagined. Mendel was investigating the behavior of genes. He was fortunate in choosing traits coded by genes that happened to be on different chromosomes or far apart on the same chromosome. When genes are linked or near each other on the same chromosome, patterns of segregation and independent assortment change. In 1913, Sturtevant devised a method to assess recombination frequency and infer the relative positions and distances of linked genes on a chromosome based on the average number of crossovers between them during meiosis.

The content presented in this section supports the Learning Objectives outlined in Big Idea 3 of the AP ® Biology Curriculum Framework. The AP ® Learning Objectives merge essential knowledge content with one or more of the seven Science Practices. These objectives provide a transparent foundation for the AP ® Biology course, along with inquiry-based laboratory experiences, instructional activities, and AP ® exam questions.

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.A Heritable information provides for continuity of life.
Essential Knowledge 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization.
Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales.
Learning Objective 3.10 The student is able to represent the connection between meiosis and increased genetic diversity necessary for evolution.
Essential Knowledge 3.A.3 The chromosomal basis of inheritance provides an understanding of the pattern of passage (transmission) of genes from parent to offspring.
Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain.
Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas.
Learning Objective 3.12 The student is able to construct a representation that connects the process of meiosis to the passage of traits from parent to offspring.

Teacher Support

Introduce genetic linkage using visuals such as this video.

Students can read about corn genetics in this review article.

Students can read about linked genes and Mendel’s work in this article.

Have students work through inheritance scenarios where genes are linked and where they are on different chromosomes using the following activity sheet.

Teacher preparation notes for this activity are available here.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 3.2][APLO 3.11][APLO 3.14][APLO 3.15][APLO 3.28][APLO 3.26][APLO 3.17][APLO 4.22]

Long before chromosomes were visualized under a microscope, the father of modern genetics, Gregor Mendel, began studying heredity in 1843. With the improvement of microscopic techniques during the late 1800s, cell biologists could stain and visualize subcellular structures with dyes and observe their actions during cell division and meiosis. With each mitotic division, chromosomes replicated, condensed from an amorphous (no constant shape) nuclear mass into distinct X-shaped bodies (pairs of identical sister chromatids), and migrated to separate cellular poles.

Chromosomal Theory of Inheritance

The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and re-evaluate his model in terms of the behavior of chromosomes during mitosis and meiosis. In 1902, Theodor Boveri observed that proper embryonic development of sea urchins does not occur unless chromosomes are present. That same year, Walter Sutton observed the separation of chromosomes into daughter cells during meiosis (Figure 13.2). Together, these observations led to the development of the Chromosomal Theory of Inheritance , which identified chromosomes as the genetic material responsible for Mendelian inheritance.

The Chromosomal Theory of Inheritance was consistent with Mendel’s laws and was supported by the following observations:

  • During meiosis, homologous chromosome pairs migrate as discrete structures that are independent of other chromosome pairs.
  • The sorting of chromosomes from each homologous pair into pre-gametes appears to be random.
  • Each parent synthesizes gametes that contain only half of their chromosomal complement.
  • Even though male and female gametes (sperm and egg) differ in size and morphology, they have the same number of chromosomes, suggesting equal genetic contributions from each parent.
  • The gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents.

Despite compelling correlations between the behavior of chromosomes during meiosis and Mendel’s abstract laws, the Chromosomal Theory of Inheritance was proposed long before there was any direct evidence that traits were carried on chromosomes. Critics pointed out that individuals had far more independently segregating traits than they had chromosomes. It was only after several years of carrying out crosses with the fruit fly, Drosophila melanogaster, that Thomas Hunt Morgan provided experimental evidence to support the Chromosomal Theory of Inheritance.

Genetic Linkage and Distances

Mendel’s work suggested that traits are inherited independently of each other. Morgan identified a 1:1 correspondence between a segregating trait and the X chromosome, suggesting that the random segregation of chromosomes was the physical basis of Mendel’s model. This also demonstrated that linked genes disrupt Mendel’s predicted outcomes. The fact that each chromosome can carry many linked genes explains how individuals can have many more traits than they have chromosomes. However, observations by researchers in Morgan’s laboratory suggested that alleles positioned on the same chromosome were not always inherited together. During meiosis, linked genes somehow became unlinked.

Homologous Recombination

In 1909, Frans Janssen observed chiasmata—the point at which chromatids are in contact with each other and may exchange segments—prior to the first division of meiosis. He suggested that alleles become unlinked and chromosomes physically exchange segments. As chromosomes condensed and paired with their homologs, they appeared to interact at distinct points. Janssen suggested that these points corresponded to regions in which chromosome segments were exchanged. It is now known that the pairing and interaction between homologous chromosomes, known as synapsis, does more than simply organize the homologs for migration to separate daughter cells. When synapsed, homologous chromosomes undergo reciprocal physical exchanges at their arms in a process called homologous recombination , or more simply, “crossing over.”

To better understand the type of experimental results that researchers were obtaining at this time, consider a heterozygous individual that inherited dominant maternal alleles for two genes on the same chromosome (such as AB) and two recessive paternal alleles for those same genes (such as ab). If the genes are linked, one would expect this individual to produce gametes that are either AB or ab with a 1:1 ratio. If the genes are unlinked, the individual should produce AB, Ab, aB, and ab gametes with equal frequencies, according to the Mendelian concept of independent assortment. Because they correspond to new allele combinations, the genotypes Ab and aB are nonparental types that result from homologous recombination during meiosis. Parental types are progeny that exhibit the same allelic combination as their parents. Morgan and his colleagues, however, found that when such heterozygous individuals were test crossed to a homozygous recessive parent (AaBb × aabb), both parental and nonparental cases occurred. For example, 950 offspring might be recovered that were either AaBb or aabb, but 50 offspring would also be obtained that were either Aabb or aaBb. These results suggested that linkage occurred most often, but a significant minority of offspring were the products of recombination.

Visual Connection

  1. Yes, the predicted offspring frequencies range from 0\% to 100\%
  2. No, the predicted offspring frequencies cannot be higher than 30\% .
  3. Yes, the predicted offspring frequencies range from 0\% to 60\% .
  4. No, the predicted offspring frequencies range from 0\% to 50\% .

Science Practice Connection for AP® Courses

Think About It

A test cross involving F1 dihybrid flies produces more parental-type offspring than recombinant-type offspring. How can you explain these observed results?

Teacher Support

The question is an application of Learning Objective 3.12 and Science Practices 1.1 and 7.2, and Learning Objective 3.10 and Science Practice 7.1 because students are explaining how meiosis can result in gametes with genetic variation in turn, these gametes can introduce variation in offspring.


More parental type offspring are produced because the genes that are being examined in the dihybrid cross are linked. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during meiosis as a result of chromosomal crossover. Therefore, there will be more offspring with the parental phenotype than the recombinant phenotype.

More information about linked genes can be found at the following resources:

Everyday Connection for AP® Courses

Genetic Markers for Cancers

Scientists have used genetic linkage to discover the location in the human genome of many genes that cause disease. They locate disease genes by tracking inheritance of traits through generations of families and creating linkage maps that measure recombination among groups of genetic “markers.” The two BRCA genes, mutations which can lead to breast and ovarian cancers, were some of the first genes discovered by genetic mapping. Women who have family histories of these cancers can now be screened to determine if one or both of these genes carry a mutation. If so, they can opt to have their breasts and ovaries surgically removed. This decreases their chances of getting cancer later in life. The actress Angelia Jolie brought this to the public’s attention when she opted for surgery in 2014 and again in 2015 after doctors found she carried a mutated BRCA1 gene.

  1. Genes responsible for temperament are on the same chromosome as genes responsible for certain facial features.
  2. A single gene codes for both temperament and certain facial features, such as jaw size.
  3. Genes responsible for mild temperament are only expressed when genes encoding a cute face are also present.
  4. The products of genes encoding temperament interact with the products of genes encoding facial features.

Genetic Maps

Janssen did not have the technology to demonstrate crossing over so it remained an abstract idea that was not widely accepted. Scientists thought chiasmata were a variation on synapsis and could not understand how chromosomes could break and rejoin. Yet, the data were clear that linkage did not always occur. Ultimately, it took a young undergraduate student and an “all-nighter” to mathematically elucidate the problem of linkage and recombination.

In 1913, Alfred Sturtevant, a student in Morgan’s laboratory, gathered results from researchers in the laboratory, and took them home one night to mull them over. By the next morning, he had created the first “chromosome map,” a linear representation of gene order and relative distance on a chromosome (Figure 13.4).

Visual Connection

Which of the following statements is true?
  1. Recombination of the red/brown eye and long/short aristae alleles will occur more frequently than recombination of the alleles for wing length and body color.
  2. Recombination of the body color and red/cinnabar eye alleles will occur more frequently than recombination of the alleles for wing length and aristae length.
  3. Recombination of the body color and aristae length alleles will occur more frequently than recombination of red/brown eye alleles and the aristae length alleles.
  4. Recombination of the gray/black body color and long/short aristae alleles will not occur.

As shown in Figure 13.4, by using recombination frequency to predict genetic distance, the relative order of genes on chromosome 2 could be inferred. The values shown represent map distances in centimorgans (cM), which correspond to recombination frequencies (in percent). Therefore, the genes for body color and wing size were 65.5 − 48.5 = 17 cM apart, indicating that the maternal and paternal alleles for these genes recombine in 17 percent of offspring, on average.

To construct a chromosome map, Sturtevant assumed that genes were ordered serially on threadlike chromosomes. He also assumed that the incidence of recombination between two homologous chromosomes could occur with equal likelihood anywhere along the length of the chromosome. Operating under these assumptions, Sturtevant postulated that alleles that were far apart on a chromosome were more likely to dissociate during meiosis simply because there was a larger region over which recombination could occur. Conversely, alleles that were close to each other on the chromosome were likely to be inherited together. The average number of crossovers between two alleles—that is, their recombination frequency —correlated with their genetic distance from each other, relative to the locations of other genes on that chromosome. Considering the example cross between AaBb and aabb above, the frequency of recombination could be calculated as 50/1000 = 0.05. That is, the likelihood of a crossover between genes A/a and B/b was 0.05, or 5 percent. Such a result would indicate that the genes were definitively linked, but that they were far enough apart for crossovers to occasionally occur. Sturtevant divided his genetic map into map units, or centimorgans (cM) , in which a recombination frequency of 0.01 corresponds to 1 cM.

By representing alleles in a linear map, Sturtevant suggested that genes can range from being perfectly linked (recombination frequency = 0) to being perfectly unlinked (recombination frequency = 0.5) when genes are on different chromosomes or genes are separated very far apart on the same chromosome. Perfectly unlinked genes correspond to the frequencies predicted by Mendel to assort independently in a dihybrid cross. A recombination frequency of 0.5 indicates that 50 percent of offspring are recombinants and the other 50 percent are parental types. That is, every type of allele combination is represented with equal frequency. This representation allowed Sturtevant to additively calculate distances between several genes on the same chromosome. However, as the genetic distances approached 0.50, his predictions became less accurate because it was not clear whether the genes were very far apart on the same chromosome or on different chromosomes.

In 1931, Barbara McClintock and Harriet Creighton demonstrated the crossover of homologous chromosomes in corn plants. Weeks later, homologous recombination in Drosophila was demonstrated microscopically by Curt Stern. Stern observed several X-linked phenotypes that were associated with a structurally unusual and dissimilar X chromosome pair in which one X was missing a small terminal segment, and the other X was fused to a piece of the Y chromosome. By crossing flies, observing their offspring, and then visualizing the offspring’s chromosomes, Stern demonstrated that every time the offspring allele combination deviated from either of the parental combinations, there was a corresponding exchange of an X chromosome segment. Using mutant flies with structurally distinct X chromosomes was the key to observing the products of recombination because DNA sequencing and other molecular tools were not yet available. It is now known that homologous chromosomes regularly exchange segments in meiosis by reciprocally breaking and rejoining their DNA at precise locations.

Link to Learning

Review Sturtevant’s process to create a genetic map on the basis of recombination frequencies here.

  1. Chromosomal crossover is a specific, non-random process during which chromosomes are linked together and exchange DNA, which contributes to the genetic diversity.
  2. Chromosomal crossover occurs during meiosis when chromosome pairs are linked and exchange DNA. Thus, crossover increases the variance of genetic combinations in the haploid gamete cell.
  3. Chromosomal crossover results in the inheritance of enhanced genetic material by offspring, and the subsequent recombination event is not variable in frequency or location.
  4. Chromosomal crossover occurs during the mitotic process when chromosomes are linked together and recombination takes place, increasing the variance of genetic combinations in the haploid mitotic cells formed from mitosis.

Mendel’s Mapped Traits

Homologous recombination is a common genetic process, yet Mendel never observed it. Had he investigated both linked and unlinked genes, it would have been much more difficult for him to create a unified model of his data on the basis of probabilistic calculations. Researchers who have since mapped the seven traits investigated by Mendel onto the seven chromosomes of the pea plant genome have confirmed that all of the genes he examined are either on separate chromosomes or are sufficiently far apart as to be statistically unlinked. Some have suggested that Mendel was enormously lucky to select only unlinked genes, whereas others question whether Mendel discarded any data suggesting linkage. In any case, Mendel consistently observed independent assortment because he examined genes that were effectively unlinked.

As an Amazon Associate we earn from qualifying purchases.

Want to cite, share, or modify this book? This book is Creative Commons Attribution License 4.0 and you must attribute OpenStax.

    If you are redistributing all or part of this book in a print format, then you must include on every physical page the following attribution:

  • Use the information below to generate a citation. We recommend using a citation tool such as this one.
    • Authors: Julianne Zedalis, John Eggebrecht
    • Publisher/website: OpenStax
    • Book title: Biology for AP® Courses
    • Publication date: Mar 8, 2018
    • Location: Houston, Texas
    • Book URL:
    • Section URL:

    © Jan 12, 2021 OpenStax. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution License 4.0 license. The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, and OpenStax CNX logo are not subject to the Creative Commons license and may not be reproduced without the prior and express written consent of Rice University.

    Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

    We describe design, rapid assembly, and characterization of synthetic yeast Sc2.0 chromosome VI (synVI). A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encoding an essential proteasome subunit Sc2.0 coding changes reduced Pre4 protein accumulation by half. Completing Sc2.0 specifies consolidation of 16 synthetic chromosomes into a single strain. We investigated phenotypic, transcriptional, and proteomewide consequences of Sc2.0 chromosome consolidation in poly-synthetic strains. Another "bug" was discovered through proteomic analysis, associated with alteration of the HIS2 transcription start due to transfer RNA deletion and loxPsym site insertion. Despite extensive genetic alterations across 6% of the genome, no major global changes were detected in the poly-synthetic strain "omics" analyses. This work sets the stage for completion of a designer, synthetic eukaryotic genome.

    1: Chemistry to Chromosomes - Biology

    Theme reflection 1: The biological theme of science as a process was particularly present in this unit. Each lab that was completed in this unit was based off of this process where an experiment was designed to test a variable. A hypothesis was also needed for each lab to be tested. Each lab had an independent and a dependent variable and a control needed in each lab to compare the results to. This can tell you if the change was due to the variable you controlled or due to an unknown outside factor. The TOOTHPICK-ASE lab was designed to test how outside factors effect enzyme activity and to show how it worked first hand with YOU (your fingers) as the enzyme. In a process with the factors like temperature being putting your fingers in ice to see how it effects your toothpick breaking speed. Your hands being put in ice would slow down your breaking speed just like it would to an actual enzyme.An inhibitor was showed with colored toothpicks that you can not break slowing down the reaction. This shows how science is really put into organization for learning and for discovery.

    YouTube Video

    Theme reflection 2: Another biological theme that stood out to me in this unit was relationship of structure and function. Nothing shows this more than the enzyme catalysis lab. The testing of the enzyme catalase with hydrogen peroxide truly showed the aspects in front of me. The boiling of the enzyme made it not react, meaning that when the temperature changed, so did the structure, changing the properties. Enzymes have a key hole reaction spot where only certain enzymes have the "key" to react with other substances. This is so there is no chaos of all substances reacting with every other substance. Every molecule that is different from each other is different for a purpose. Waters structure gives it its characteristics that are so important to life. Without this structure, water would not have its hydrogen bonds that make it cohesive and other things that are so important for life. Here is the conclusion from my lab report, showing what i learned and how it relates to structure and function.

    Conclusion out of my enzyme lab - The hypothesis, if the enzyme catalase is added to H2O2, then it will swiftly react at first, forming bubbles but will slow down, still eventually decomposing the solution into water faster than if it was never added, is correct. It is correct because the graph of table 3 shows the reaction speeding up and eventually slowing down, evening out because the enzyme is reacting all of the H2O2. Another reason it is accepted is because in part A, when the catalase is reacted with H2O2, it forms bubbles, just like it says in the hypothesis. The bubbles also slow down just like the line in the graph shows it would.

    In part A we see how a enzyme reaction is supposed to look in order to do it right in the later parts of the lab when testing. We also see how the reaction can be effected by things such as temperature when the heated catalase has no affect on the H2O2. Another thing in part A is the testing of catalase in living tissue (the liver) and we see that it is very much present when there is a reaction. In part B we find the baseline of 5.4 mL of H2O2 present in the solution in order to compare it to other test. The part C shows the natural rate of decomposition of H2O2 without the enzyme to compare and see how much faster the reaction time is with the catalase added. It decomposes at a rate of 7 ml for every 24 hours exposed.

    Finally on part D we see the different amounts of H2O2 reacted with different amounts of time exposed to the catalase. There is -.3 mL decomposed at 10 seconds to 5.2 mL decomposed at 180 seconds. The reaction obviously speeds up and gets the job done. This negative decomposed number is obviously impossible. The amount of error in this lab is immense. The human error in this lab could be measuring the amounts of liquid, calculating the equation, and the overdosing of the titration liquid when finding the amount of substance. This throws off the whole lab because with an inaccurate amount of substance measured as a baseline ruins the amount of substance catalyzed equation. No matter how accurate you are with all the next measurements, the final results will be wrong.

    One thing I learned from this lab that I can apply to real life is that enzymes are needed for life and react with certain things. I know that I could not live without these enzymes that speed up reactions to make life necessary. I also know that certain enzymes react with certain things. If I have a bottle of H2O2 in the wild and need water, I know to simply add an animal liver to react it into H2O.

    Theme reflection 3: The last biological theme apparent in unit one was regulation. In the enzyme lab, we tested how enzymes worked and how they only effected certain other substances. The only protein that could speed up the decomposition of hydrogen peroxide is called catalase. Without the enzyme helping the reaction, the natural rate of hydrogen peroxide decomposition is not fast enough to be relevant. But WITH the enzyme, it makes the reaction helpful enough for life. This protein is crucial for life and is a perfect example of regulation. The molecules worked together to support and sustain life. Another example of regulation was shown in the cricket virtual lab when temperature is a factor that changes the rate at which crickets chirp. Only the certain temperature would make the crickets chirp at different rates. This shows two factors working together to complete a part of life that could not exist without it. This is how regulation was so apperent in this unit and why I learned so much from it.

    I had a large amount of previous knowledge coming into this unit from my chemistry and biology class. The water characteristics, basic molecular structures, and science as a process was all covered, but not to the extent of this class. I feel that my expertise of the topics covered in this unit has drastically increased. The main ideas like water structure and characteristics were covered to a much larger extent. The characteristics given to water through hydrogen bonds was particularly interesting. Without this seemingly simple bond, water could not support its most unique and most important trait (to me at least) life. Another topic from this unit that stood out to me was simple molecular structure. This included things such as carbohydrates, lipids, protiens, and nucleic acids. All of these structures are essential for life. The enzyme (a protein) is needed to speed up reactions that would otherwise be to slow to matter at all. Carbohydrates provide energy and structure. Nucleic acids form such molecules as DNA and RNA that are the gene carriers that create such factors as natural selection and mutation. In chapter three we discussed the basics of chemistry such as the four main elements of carbon, hydrogen, oxygen, and nitrogen. The rest of the elements are know as trace elements. This was mainly a review: nevertheless, a needed review.

    Some new things that i have learned that are interesting are that everything in life is interdependent, with the absence of just one building block the whole universe would not be what it is today. The enzyme unit was interesting because without the certain conditions a specific enzyme needs, it cannot preform its reaction with the specific molecule it reacts with. This showed me how specific life is and its needs. This spectacular unit has shown me what to expect from this class, gave me a taste of a true college level interesting class, and gave me incite on biology. From water molecules to basic molecular structure to the themes of biology, I will never forget this unit. Most of the information from this unit was a review for me. Most was learned in biology and chemistry before this class. Now i feel that I have mastered this material and can use it in real life applications.

    Homologous Chromosomes vs Sister Chromatids

    Homologous chromosomes are often confused with the similar term, sister chromatids. Sister chromatids are formed when DNA is copied. DNA is made of two complimentary strands, which wrap around each other in a helix formation. As proteins replicate the DNA they split the strands apart, and match new nucleotides to each side. The new strands grow, until two newly formed strands of DNA are completed. These sister chromatids will be fully separated during mitosis.

    In contrast, new homologous chromosomes are created during meiosis when duplicated chromosomes are created and separated into individual gametes. When two gametes fuse together, these homologous chromosomes will contribute the maternal and paternal alleles for each gene. When this organism matures and undergoes meiosis to create gametes, these homologous chromosomes will be rearranged, recombined, and repackaged into unique genetic combinations.

    Watch the video: Simple Explanation of Structure of Chromosome. ICSE Class 10 Biology. Cell Cycle and Cell Division (January 2022).