9.3: Genes along chromosomes - Biology

9.3: Genes along chromosomes - Biology

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Genomes are typically divided into chromosomes, which are distinct DNA molecules together with all of the other molecules that associate with them in the cell. That said, their effects will be influenced by the rest of your genome, so for most traits there is no simple link between genotype and phenotype.

In humans, only ~5% of the total genomic DNA is involved in encoding polypeptides. The amount of DNA used to regulate gene expression is more difficult to estimate, but it is clear that lots of the genome (including the 50% that includes dead transposons) is not directly functional. That said, gene organization can be quite complex. We can see an example of this complexity by looking at organisms with more “streamlined” genomes. While humans have an estimated ~25,000 genes in ~3.2 x 109 base pairs of DNA (about 1 gene per 128,000 base pairs of DNA), the single circular chromosome of the bacterium E. coli (K-12 strain) contains 4,377 genes in 4,639,221 base pairs of DNA, of which 4,290 encode polypeptides and the rest RNAs261. That is about one gene per 1000 base pairs of DNA.

In prokaryotes and eukaryotes, genes can be located on either strand of the DNA molecule, typically referred (arbitrarily) as the “+” and the “–“ strands of the molecule. Given that the strands are anti-parallel, a gene on the “+” strand runs in the opposite direction from a gene on the “–“ strand. We can illustrate this situation using the euryarchaea Picrophilus torridus. This archaea organism can grow under extreme conditions, around pH 0 and up to ~65°C. Its genome is 1,545,900 base pairs of DNA in length and it encodes 1,535 polypeptides (open reading frames), distributed fairly equally on the + and – strands262.

While most prokaryotic genes are located within a single major circular chromosome, the situation is complicated by the presence of separate, smaller circular DNA moleculesknown as plasmids. In contrast to the organism’s chromosome, plasmids can (generally) be gained or lost. That said, because plasmids contain genes it is possible for an organism to become dependent upon or addicted to a plasmid. For example, a plasmid can carry a gene that makes its host resistant to certain antibiotics. Given that most antibiotics have their origins as molecules made by one organism to kill or inhibit the growth of others, if an organism is living in the presence of an antibiotic, losing a plasmid that contains the appropriate antibiotic resistance gene will be lethal. Alternatively, plasmids can act selfishly. For example, suppose a plasmid carries the genes encoding an “addiction module” (which we discussed previously.) When the plasmid is present both toxin and anti-toxin are made. If, however, the plasmid is lost, the synthesis of the unstable anti-toxin ceases, while the stable toxin persists, becomes active (uninhibited), and kills the host. As you can begin to suspect, the ecological complexities of plasmids and their hosts are not simple.

Like the host chromosome plasmids have their own “origin of replication” sequence required for the initiation of DNA synthesis; this enables them to replicate independently of the main chromosome. Plasmids can be transferred from cell to cell either when the cell divides (vertical transmission) or between “unrelated” cells through what is known as horizontal transmission. If you think back to Griffith’s experiments on pneumonia, the ability of the DNA from dead S-type bacteria to transform R-type bacteria (and make them pathogenic) is an example of horizontal transmission.

Chromosomes. These ensure that each cell receives the proper amount of DNA during cell division. And usually people have 46 of them, 23 from each parent.

Each species has a characteristic number of chromosomes. Chromosomes are coiled structures made of DNA and proteins called histones (Figure below). Chromosomes are the form of the genetic material of a cell during cell division. See the "Chromosomes" concept for additional information.

The human genome has 23 pairs of chromosomes located in the nucleus of somatic cells. Each chromosome is composed of genes and other DNA wound around histones (proteins) into a tightly coiled molecule.

The human species is characterized by 23 pairs of chromosomes, as shown in the Figure below.

Human Chromosomes. Humans have 23 pairs of chromosomes. Pairs 1-22 are autosomes. Females have two X chromosomes, and males have an X and a Y chromosome.


Of the 23 pairs of human chromosomes, 22 pairs are autosomes (numbers 1&ndash22 in the Figure above). Autosomes are chromosomes that contain genes for characteristics that are unrelated to sex. These chromosomes are the same in males and females. The great majority of human genes are located on autosomes.

Sex Chromosomes

The remaining pair of human chromosomes consists of the sex chromosomes, X and Y. Females have two X chromosomes, and males have one X and one Y chromosome. In females, one of the X chromosomes in each cell is inactivated and known as a Barr body. This ensures that females, like males, have only one functioning copy of the X chromosome in each cell.

As you can see from the Figures above, the X chromosome is much larger than the Y chromosome. The X chromosome has about 2,000 genes, whereas the Y chromosome has fewer than 100, none of which are essential to survival. (For comparison, the smallest autosome, chromosome 22, has over 500 genes.) Virtually all of the X chromosome genes are unrelated to sex. Only the Y chromosome contains genes that determine sex. A single Y chromosome gene, called SRY (which stands for sex-determining region Y gene), triggers an embryo to develop into a male. Without a Y chromosome, an individual develops into a female, so you can think of female as the default sex of the human species. Can you think of a reason why the Y chromosome is so much smaller than the X chromosome?

Human Genes

Humans have an estimated 20,000 to 22,000 genes. This may sound like a lot, but it really isn&rsquot. Far simpler species have almost as many genes as humans. However, human cells use splicing and other processes to make multiple proteins from the instructions encoded in a single gene. Of the 3 billion base pairs in the human genome, only about 25 percent make up genes and their regulatory elements. The functions of many of the other base pairs are still unclear.

The majority of human genes have two or more possible alleles, which are alternative forms of a gene. Differences in alleles account for the considerable genetic variation among people. In fact, most human genetic variation is the result of differences in individual DNA bases within alleles.


The genome of the red flour beetle, Tribolium castaneum, has recently been sequenced and is currently being annotated. Tribolium has enjoyed a long history as a model for population genetics, and the recent development of genetic and genomic tools has contributed to its current status as a powerful genetic model organism for studies in pest biology as well as comparative studies in developmental biology [1]. In addition, as the first coleopteran genome to be sequenced, it will provide insight into the genomics of the largest metazoan order known.

Scaffolds containing approximately 90% of the genome sequence have been anchored to the ten chromosomes (Tribolium Genome Sequencing Consortium) in the molecular recombination map [2]. Understanding the structure and organization of this genome is the next major task. Automated analyses have been used to identify coding regions and to predict more than 16,000 gene models. In contrast, the much larger, non-coding part of the genome is more difficult to analyze, a situation that is exacerbated by the presence of considerable amounts of repetitive DNA. Although the role of repetitive DNA is not always clear, it has been implicated in gene regulation [3], disease-associated gene mutation [4] and genome evolution [5, 6]. Understanding the abundance and distribution of repetitive DNA in Tribolium is required to understand the structure and function of the genome. In addition, once identified, different types of repetitive DNA can be masked to improve the quality of other homology-based searches.

Estimates of the repetitive DNA content in insect genomes vary widely. For example, reassociation kinetics indicate only 8-10% of the honey bee (Apis mellifera) genome and up to 24% of the Drosophila melanogaster genome are composed of repetitive DNA [7, 8], while the repetitive DNA content in the Tribolium genome appears to be over 42% [9, 10], nearly the level observed in the human genome [11]. In light of this estimate, we might expect to find repetitive DNA elements that are highly dispersed throughout the Tribolium genome, such as transposable elements, as well as those clustered in tandem arrays, such as microsatellites (repeat units of 1-6 bp), minisatellites (7-100 bp) and satellites (>100 bp).

Whether highly dispersed or tandemly repeated, repetitive DNA is not randomly distributed throughout a genome. Heterochromatic regions near centromeres and telomeres are often rich in repetitive sequences, including transposable elements and satellites. Heterochromatin is distinguished from euchromatin by its molecular and genetic properties, such as DNA sequence composition, high levels of condensation throughout the cell cycle [12], low rates of meiotic recombination [13] and the ability to silence gene expression [14]. Most eukaryotic genomes include a significant fraction of heterochromatin. In insects, large blocks of pericentric heterochromatin have been identified by C-banding. In tenebrionid beetles, including Tribolium, large blocks of pericentric heterochromatin often constitute 25-58% of the genome [15]. C-banding in Tribolium species has revealed large blocks of pericentric heterochromatin. For example, 40-45% of the Tribolium confusum genome consists of pericentric heterochromatin [16] and pericentric heterochromatin has been characterized by HpaII-banding in T. castaneum [17]. The highly repetitive nature of heterochromatic DNA makes it refractory to cloning, sequencing and subsequent assembly, resulting in its under-representation in genome sequencing projects. Indeed, special efforts had to be directed towards analysis of heterochromatin in Drosophila [18].

We used three complementary approaches to identify repetitive DNA in the newly assembled T. castaneum genome. Specifically, we used Tandem Repeat Finder (TRF) [19] to find tandem arrays of repetitive DNA, TEpipe [20] to identify transposable elements based on structural features and sequence conservation, and RepeatScout [21] for de novo identification of repeat families in large, newly sequenced genomes such as that of Tribolium, for which hand-curated repeat databases are not available. We then used RepeatMasker (version open-3.1.0, RepBase Update 10.05) [22] with these newly compiled repeat sequence libraries to find homologous copies and determine the abundance and distribution of repetitive DNA in the Tribolium genome. Not surprisingly, over 50% of the unmapped DNA sequence consists of repetitive DNA. However, we were surprised to find that within the scaffolds included in the chromosomes, repetitive DNA accumulates in patterns resembling the large blocks of pericentric heterochromatin previously identified in Tribolium [17]. Analyses of gene content, intron size, and recombination rates across the genome provide additional evidence for the identification of putative heterochromatic versus euchromatic regions, and suggest that the T. castaneum genome sequence assembly and scaffold mapping efforts successfully captured not only the euchromatin, but a significant fraction of the heterochromatic DNA as well.

DNA is transcribed into RNA, which is translated to form proteins

Francis Crick coined the phase “the Central Dogma” to describe the flow of information from nucleic acid to protein. Information encoded in DNA is transcribed to a similar alphabet called RNA (still four letters only, but not quite the same four letters as DNA). RNA is translated to a linear sequence of amino acids in protein. This video gives a concise overview of the central dogma of molecular biology:

We will go into more detail about gene expression later in the course.

Your chromosomes provide the instructions for how your body will develop before you’re born, and how it will function as you grow. Typically, humans are born with 23 pairs of chromosomes (46 chromosomes in total). Human chromosomes 1 through 22 are called autosomes, and the final or 23rd chromosome is a pair of sex chromosomes, so-called because they determine the biological sex of the human.

Recall that half of your chromosomes come from your mother and half come from your father. Through a process called meiosis each of your parents creates a sex cell (either a sperm or an egg) that contains half of their chromosomes. When the sperm cell and the egg cell combine, they create a zygote that contains 46 chromosomes.

Linkage of Chromosomes | Genetics

The seven pairs of characters in garden peas with which Mendel worked were located in separate chromosomes. But when genes for different characters stay together in the same chromosome a very confusing phenomenon occurs.

Genes in the same chromosome do not abide by the principles of independent assortment. Independent assortment does not hold good in cases where genes are located in the same chromosome. Thus, Mendel’s law of independent assortment is not uni­versal but is limited to genes situated in different chromosomes.

The exception to this law was first noticed by Bateson and Punnet in England in 1906.

They bred a dihybrid strain of sweet peas in which one pair of characters was Purple (P) and Red (p) in the colour of the flowers and the other pair of characters Long (L) and Round (1) in the shape of pollen grains. The F1 dihybrids were all purple long when a cross was made bet­ween purple long and red round peas be­cause purple and long and dominant cha­racters.

But when these dihybrids having PL, PI, pL and pi were crossed together to form the F2 generation the four expected phenotypic kinds in the ratio of 9:3-3: 1 never turned up. What actually turned up was purple long. 4831 purple long, 390 purple round, 393 red long and 1338 red round were obtained out of a total of 6952.

To account for this deviation from the expected assortment, Bateson and Punnet put forward the view that when two domi­nant characters go in together from the same parent to form the dihybrid offsprings there is a tendency for the same pair of characters to enter the same gamete and to be transmitted together.

This pheno­menon, they called coupling occurs when a dominant and a recessive factor enters the F1 dihybrid from each parent instead of two dominant factors from one parent and two recessive factors from the other. There occurs always a tendency for two dominant factors entering separately and likewise for two recessive factors to avoid or repel each other. This tendency of unlike pairs (one dominant and one recessive) to stay to­gether avoiding union with their own domi­nant or recessive sort is termed repulsion.

Similar situation encountered by Mor­gan in Drosophila in the year 1910 result­ed in his putting forward a satisfactory ex­planation of coupling and repulsion. Mor­gan advocated that coupling and repulsion are but two aspects of a single phenomenon called linkage. He supposed that this ten­dency of linked genes to remain in their original combination was due to their resi­dence in the same chromosome.

Thus certain genes located on the same chromosome tend to remain linked together while passing from one generation to another. This tendency of certain genes to stick together in the way in which they entered the cross has been termed linkage and such genes are called linked genes.

2. Operation of Linkage from Morgan’s Data:

A wild type Drosophila having gray body (G) and long wings (L) is- crossed with a fly having two recessive mutations of black body (g) and vestigial wing (1). The members of F1 generation were all like wild types, that is, gray bodied and long winged as gray body colour and long wings are dominant over black body and vestigial wings (Fig. 2.12).

Now a male fly from this, dihybrid is back-crossed to a double recessive black vestigial female. Had there been indepen­dent assortments, the kinds of flies would have been formed in the following way as shown in Table Genetics—6.

But from actual experiments only two classes of offsprings namely, gray long and black vestigial like two grandparents were obtained (Fig. 2.12). This shows that gray body and long wings entering the dihybrid cross from one parent stay linked together.

3. Linkage—its Characteristics:

(a) Linkage is an exception to Mendel’s principle of independent assortment.

(b) Linked genes are housed in the same pair of chromosomes.

(c) Lesser the distance between the link­ed genes stronger is the linkage bond. Genes lying farther apart show less linkage.

(d) Linked genes tend to be transmitted together from one generation to the other.

(e) Separation of linked genes occurs very seldom.

If a certain gene X is linked to two other genes Y and Z, then it is true that Y and Z are linked. In plants or animals where several genes exist, crosses are arranged to ascertain the existence of linkage of pairs or of groups of several pairs of genes. The genes known to exist in a species is thus divided into linkage groups.

Constancy of percentages of crossing over and fixed location of genes on chromo­somes offer an opportunity to measure the comparative linear distance between any two genes in question. The units for mea­suring such a distance between two genes is called a ‘Morgan’.

One unit or Morgan is actually the percentage of crossing over. If two genes show 10 per cent of crossing over it is assumed that the genes for these two characters are 10 Morgans apart along the length of the chromosome on which they are housed.

From linkage and cross­ing over studies it has become possible to determine the specific location of genes on chromosomes with reference to one an­other. This plotting of specific location of genes on the chromosomes is known as linkage map, genetic map or chromosome map. This has been done thoroughly for hundreds of genes in Drosophila and many other organisms.

Method for construction:

Let US assume that three genes K, L and M are located in a chromosome along its length and we want to know the order of the genes on the chromosome and the relative distance bet­ween them. If the genes K and L upon breeding back to the recessive show 10 per cent of crossing over with k and 1, we can say that they are 10 Morgans apart.

If the genes L and M upon breeding back to the recessive show 30 per cent of crossing over with 1 and m, then it is clear that L and M are 30 Morgans apart.

Thus it becomes obvious that the relative distance between K and M will be 40 units (10+30) in case K, L and M are serially arranged. In case K, L, M are not serially arranged along the length of the chromosome the relative distance between K and M will be (30—10) or 20 units and the order of the genes will be M, K and L.

The work of gene localization is an amazing work. It ranks equal to the ac­complishment of the mathematicians and astronomers who have been able to mea­sure the vast distances that separate the stars. The wise application of genetic map stands in a good way to discover a good many facts about the orderly mechanism of heredity (Fig. 2.22).

Crossing Over is Random

Many factors affect crossing over, so the position on the chromosome where crossing over will occur is unpredictable. Crossing over is a random event based on chance. The location of the break points on the DNA sequence of the chromosomes are somewhat random, but the recombination frequency is relatively constant between homologous chromosomes. (For a given chromosome, N number of breaks will occur, but where they will occur is random.)

The probability of crossing over between genes on a chromosome is dependent on the distances between the genes. This shouldn't surprise you because the greater the distance between two genes, the greater the chance a break will occur.

Genes that are located on the same chromosome and that tend to be inherited together are termed linked genes because the DNA sequence containing the genes is passed along as a unit during meiosis. The closer that genes reside on a particular chromosome, the higher the probability that they will be inherited as a unit, since crossing over between two linked genes is not as common.

Linked genes do not follow the expected inheritance patterns predicted by Mendel's Theory of Independent Assortment when observed across several generations of crosses. Usually, crossing over between nonsister chromatids will occur between genes when they are relatively far apart on the homologous chromosomes when pairing occurs. This results in the production of an equal number of nonrecombinant and recombinant chromosomes. Thus, the ratio of offspring produced from test crosses will be 1:1:1:1 (fully paternal, paternal-maternal recombinant, maternal-paternal recombinant, and fully maternal). When half of all offspring have recombinant chromosomes, a 50% frequency of recombination is observed. Recall that in a test cross, a 1:1:1:1 ratio indicates that the genes are unlinked. Therefore, unlinked genes may either reside on different chromosomes or reside far apart on the same chromosome.

When two genes are very close together on each homologue, break points for crossing over between the two genes will be rare and fewer recombinant chromosomes will be produced. Under this circumstance, a ratio that deviates from the usual 1:1:1:1 will be observed, indicating that the genes are linked. Thus, crossing over between two particular genes on the same chromosome can be used as an indirect indicator of the distance between the two genes.

Evidence for Linked Genes in Drosophila

This figure demonstrates a test cross between flies differing in two characters: body color (b) and wing size (vg). The females are heterozygous for both genes and their phenotypes are wild type, so they display gray bodies and normal wings (b+ b and vg+ vg). The males are homozygous recessive and express the mutant phenotypes for both characteristics, so they display black bodies and vestigial wings (b b and vg vg). When T.H. Morgan scored this particular experiment and classified the offspring according to phenotype, he found that the parental phenotypes were disproportionately represented among offspring. If the two characters were on different chromosomes and assorted independently, Morgan would have expected to see a ratio of recombinant phenotypes to parental phenotypes of 1:1:1:1. Yet Morgan's observation of disproportionate offspring led him to conclude that the genes for body color and wing size in Drosophila were usually transmitted together from parents to offspring because they were located on the same chromosome. Therefore, the black body color gene and the vestigial wing gene are linked. This means that the genetic location for these genes are found close to one another and on the same chromosome.

Figure. Crossing over accounts for recombinant phenotypes. (Click image to enlarge)

Problem 10: Exceptions to the 9:3:3:1 ratio of offspring? - Go over this question from The Biology Project Website. You may recall having seen this problem previously when you learned about dihybrid crosses, but it is particularly applicable to the subject of this tutorial.


Humans have about 20,000 to 23,000 genes.

Genes consist of deoxyribonucleic acid (DNA). DNA contains the code, or blueprint, used to synthesize a protein. Genes vary in size, depending on the sizes of the proteins for which they code. Each DNA molecule is a long double helix that resembles a spiral staircase containing millions of steps. The steps of the staircase consist of pairs of four types of molecules called bases (nucleotides). In each step, the base adenine (A) is paired with the base thymine (T), or the base guanine (G) is paired with the base cytosine (C). Each extremely long DNA molecule is coiled up inside one of the chromosomes.

Structure of DNA

DNA (deoxyribonucleic acid) is the cell’s genetic material, contained in chromosomes within the cell nucleus and mitochondria.

Except for certain cells (for example, sperm and egg cells and red blood cells), the cell nucleus contains 23 pairs of chromosomes. A chromosome contains many genes. A gene is a segment of DNA that provides the code to construct proteins.

The DNA molecule is a long, coiled double helix that resembles a spiral staircase. In it, two strands, composed of sugar (deoxyribose) and phosphate molecules, are connected by pairs of four molecules called bases, which form the steps of the staircase. In the steps, adenine is paired with thymine, and guanine with cytosine. Each pair of bases is held together by a hydrogen bond. A gene consists of a sequence of bases. Sequences of three bases code for an amino acid (amino acids are the building blocks of proteins) or other information.

Synthesizing proteins

Proteins are composed of a long chain of amino acids linked together one after another. There are 20 different amino acids that can be used in protein synthesis—some must come from the diet (essential amino acids), and some are made by enzymes in the body. As a chain of amino acids is put together, it folds upon itself to create a complex three-dimensional structure. It is the shape of the folded structure that determines its function in the body. Because the folding is determined by the precise sequence of amino acids, each different sequence results in a different protein. Some proteins (such as hemoglobin) contain several different folded chains. Instructions for synthesizing proteins are coded within the DNA.


Information is coded within DNA by the sequence in which the bases (A, T, G, and C) are arranged. The code is written in triplets. That is, the bases are arranged in groups of three. Particular sequences of three bases in DNA code for specific instructions, such as the addition of one amino acid to a chain. For example, GCT (guanine, cytosine, thymine) codes for the addition of the amino acid alanine, and GTT (guanine, thymine, thymine) codes for the addition of the amino acid valine. Thus, the sequence of amino acids in a protein is determined by the order of triplet base pairs in the gene for that protein on the DNA molecule. The process of turning coded genetic information into a protein involves transcription and translation.

Transcription and translation

Transcription is the process in which information coded in DNA is transferred (transcribed) to ribonucleic acid (RNA). RNA is a long chain of bases just like a strand of DNA, except that the base uracil (U) replaces the base thymine (T). Thus, RNA contains triplet-coded information just like DNA.

When transcription is initiated, part of the DNA double helix opens and unwinds. One of the unwound strands of DNA acts as a template against which a complementary strand of RNA forms. The complementary strand of RNA is called messenger RNA (mRNA). The mRNA separates from the DNA, leaves the nucleus, and travels into the cell cytoplasm (the part of the cell outside the nucleus—see Figure: Inside a Cell). There, the mRNA attaches to a ribosome, which is a tiny structure in the cell where protein synthesis occurs.

With translation, the mRNA code (from the DNA) tells the ribosome the order and type of amino acids to link together. The amino acids are brought to the ribosome by a much smaller type of RNA called transfer RNA (tRNA). Each molecule of tRNA brings one amino acid to be incorporated into the growing chain of protein, which is folded into a complex three-dimensional structure under the influence of nearby molecules called chaperone molecules.

Control of gene expression

There are many types of cells in a person’s body, such as heart cells, liver cells, and muscle cells. These cells look and act differently and produce very different chemical substances. However, every cell is the descendant of a single fertilized egg cell and as such contains essentially the same DNA. Cells acquire their very different appearances and functions because different genes are expressed in different cells (and at different times in the same cell). The information about when a gene should be expressed is also coded in the DNA. Gene expression depends on the type of tissue, the age of the person, the presence of specific chemical signals, and numerous other factors and mechanisms. Knowledge of these other factors and mechanisms that control gene expression is growing rapidly, but many of these factors and mechanisms are still poorly understood.

The mechanisms by which genes control each other are very complicated. Genes have chemical markers to indicate where transcription should begin and end. Various chemical substances (such as histones) in and around the DNA block or permit transcription. Also, a strand of RNA called antisense RNA can pair with a complementary strand of mRNA and block translation.


Cells reproduce by dividing in two. Because each new cell requires a complete set of DNA molecules, the DNA molecules in the original cell must reproduce (replicate) themselves during cell division. Replication happens in a manner similar to transcription, except that the entire double-strand DNA molecule unwinds and splits in two. After splitting, bases on each strand bind to complementary bases (A with T, and G with C) floating nearby. When this process is complete, two identical double-strand DNA molecules exist.


To prevent mistakes during replication, cells have a “proofreading” function to help ensure that bases are paired properly. There are also chemical mechanisms to repair DNA that was not copied properly. However, because of the billions of base pairs involved in, and the complexity of, the protein synthesis process, mistakes may happen. Such mistakes may occur for numerous reasons (including exposure to radiation, drugs, or viruses) or for no apparent reason. Minor variations in DNA are very common and occur in most people. Most variations do not affect subsequent copies of the gene. Mistakes that are duplicated in subsequent copies are called mutations.

Inherited mutations are those that may be passed on to offspring. Mutations can be inherited only when they affect the reproductive cells (sperm or egg). Mutations that do not affect reproductive cells affect the descendants of the mutated cell (for example, becoming a cancer) but are not passed on to offspring.

Mutations may be unique to an individual or family, and most harmful mutations are rare. Mutations that become so common that they affect more than 1% of a population are called polymorphisms (for example, the human blood types A, B, AB, and O). Most polymorphisms have little or no effect on the phenotype (the actual structure and function of a person’s body).

Mutations may involve small or large segments of DNA. Depending on its size and location, the mutation may have no apparent effect or it may alter the amino acid sequence in a protein or decrease the amount of protein produced. If the protein has a different amino acid sequence, it may function differently or not at all. An absent or nonfunctioning protein is often harmful or fatal. For example, in phenylketonuria, a mutation results in the deficiency or absence of the enzyme phenylalanine hydroxylase. This deficiency allows the amino acid phenylalanine (absorbed from the diet) to accumulate in the body, ultimately causing severe intellectual disability. In rare cases, a mutation introduces a change that is advantageous. For example, in the case of the sickle cell gene, when a person inherits two copies of the abnormal gene, the person will develop sickle cell disease. However, when a person inherits only one copy of the sickle cell gene (called a carrier), the person develops some protection against malaria (a blood infection). Although the protection against malaria can help a carrier survive, sickle cell disease (in a person who has two copies of the gene) causes symptoms and complications that may shorten life span.

Natural selection refers to the concept that mutations that impair survival in a given environment are less likely to be passed on to offspring (and thus become less common in the population), whereas mutations that improve survival progressively become more common. Thus, beneficial mutations, although initially rare, eventually become common. The slow changes that occur over time caused by mutations and natural selection in an interbreeding population collectively are called evolution.

Mendel’s laws and meiosis

Mendel’s laws of segregation and independent assortment are both explained by the physical behavior of chromosomes during meiosis.

Segregation occurs because each gamete inherits only one copy of each chromosome. Each chromosome has only one copy, or allele, of each gene therefore each gamete only gets one allele. Segregation occurs when the homologous chromosomes separate during meiotic anaphase I . This principle is illustrated here:

Source: Adapted from Wikimedia Commons (

Independent assortment occurs because homologous chromosomes are randomly segregated into different gametes ie, one gamete does not only get all maternal chromosomes while the other gets all paternal chromosomes. Independent assortment occurs when homologous chromosomes align randomly at the metaphase plate during meiotic metaphase I . This principle is illustrated here, where the patterns on the left and right show two independent ways that the little r allele from the round gene can be matched with an allele (y or Y) from the yellow gene:

chromosomes. Source: Adapted from Wikimedia Commons ( and OpenStax Biology (

Random, independent assortment during metaphase I can be demonstrated by considering a cell with a set of two chromosomes (n = 2). In this case, there are two possible arrangements at the equatorial plane in metaphase I. The total possible number of different gametes is 2 to the power of n, where n equals the number of chromosomes in a set. In this example, there are four possible genetic combinations for the gametes. With n = 23 in human cells, there are over 8 million possible combinations of paternal and maternal genotypes in a potential offspring.

Here’s a quick summary of many of these ideas from Ted Ed:

and here is Khan Academy’s take:

Crossing Over of Genes: Mechanism, Theories and Types

The linkage is caused due to linked genes borne on the same chromosome. Morgan pointed out that the phenomenon of complete linkage occurs rarely because sometimes the linked genes show the tendency to separate during meiosis and new combinations are formed.

This is due to interchange of parts between two homologous chromosomes for which the term “crossing over” is used.

Thus, crossing over may be defined as a “mechanism of the recombination of the genes due to interchange of chromosomal segments at the time of pairing.”

In the linkage experiment with maize, it is seen that the genes for seed colour C and full seed S remain associated in the parental combination in about 96 per cent but break apart in about 4 per cent (see Fig. 5.8). This recombination of linked genes to interchange parts between homologous chromosomes is termed as crossing over.

Crossing over takes place in the segment of the chromosome between the loci of the genes C and S in some cells but not in others, so that about 96 per cent of the gametes contain the parental gene combination and 4 per cent contain recombination’s.

Mechanism of Crossing Over:

During the zygotene stage of the first prophase of meiosis, the homologous maternal and paternal chromosomes start pairing and lie closely side by side. This phenomenon is called synapsis. This pairing of homologous chromosomes is brought about by the mutual attraction between the allelic genes. The paired chromosomes are known as bivalent. A recent study reveals that synapsis and chiasma formation is facilitated by a highly organised structure of filaments called synaptonemal complex. Synapsis is followed by the duplication of chromosomes which change the bivalent nature of chromosome pair into tetravalent.

During this each of the homologous chromosomes in a bivalent split longitudinally into two sister chromatids attached to the undivided centromere. Thus, four chromatids are formed which remain side by side as two pairs. Later, in pachytene stage crossing over takes place during which the non-sister chromatids of homologous pair twist over each other, the point of contact of cross over chromatids being called as chiasma (Fig. 5.9).

In crossing over two or three chromatids are involved and accordingly two or more chiasmata are formed. At each chiasma the chromatid breaks and the broken segment rejoin a new chromatid (Fig. 5.10A & B). Thus exchange of parts of chromatids brings about alteration of original sequence of genes in the chromosome.

After crossing over is completed, the non-sister chromatids repel each other due to lack of attraction between them. The repulsion or separation of chromatids starts from the centromere towards the end just like a zipper and this separation process is named as terminalization. The process of terminalization continues through diplotene, diakinesis and ends in metaphase I.

At the end of terminalization the twisting chromatids separate so that the homologous chromosomes are separated completely and move to opposite poles in Anaphase I. The crossing over thus brings about alteration of the linear sequence of gene in chromosomes that produce gametes and thus add new combination of character in progeny.

Theories of Crossing Over:

(i) Contact First Theory (by Serebrovsky):

According to this theory the inner two chromatids of the homologous chromosomes undergoing crossing over first touch each other and then cross over. At the point of contact breakage occurs. The broken segments again unite to form new combinations (Fig. 5.11).

(ii) The Breakage-First Theory (By Muller):

According to this theory the chromatids under-going crossing over first of all break into two without any crossing over and after that the broken segments reunite to form the new combinations (Fig. 5.11).

(iii) Strain Theory (by Darlington):

According to this theory the breakage in chromosomes or chromatids is due to strain caused by pairing and later the breakage parts again reunite.

Types of Crossing Over:

(i) Single Crossing Over:

In this type of crossing over only one chiasma is formed all along the length of a chromosome pair. Gametes formed by this type of crossing over are called single cross over gametes (Fig. 5.10A and B).

(ii) Double Crossing Over:

In this type two chiasmata are formed along the entire length of the chromosome leading to breakage and rejoin of chromatids at two points. The gametes produced are called double cross over gametes (Fig. 5.14B).

(iii) Multiple Crossing Over:

In this type more than two chiasmata are formed and thus crossing over occurs at more than two points on the same chromosome pair. It is a rare phenomenon.

Factors Influencing Crossing Over:

In Drosophila, crossing over is completely suppressed in male but very high in female. Also there is a tendency of reduction of crossing over in male mammals.

Gowen first discovered that mutation reduces crossing over in all the chromosomes of Drosophila.

Inversion is an intersegmental change in the chromosome. In a given segment of chromosome crossing over is suppressed due to inversions.

Plough has experimentally shown that when Drosophila is subjected to high and low temperature variations, the percentage of crossing over in certain parts of the chromosome is increased.

Muller demonstrated that X-ray irradiations increase crossing over near centromere. Similarly Hanson has shown that radium increases crossing over.

Bridges has demonstrated that the age also influences the rate of crossing over in Drosophila. When the female becomes older the rate of crossing over increases.

High calcium diet in young Drosophila decreases crossing over rate where as diet deficient of metallic ions increases crossing over.

8. The frequency of crossing over is less at the ends of the chromosome and also near the centromere in comparison to other parts.

Significance of Crossing Over:

1. Crossing over provides direct proof for the linear arrangement of genes.

2. Through crossing over segments of homologous chromosomes are interchanged and hence provide origin of new characters and genetic variations.

3. Crossing over has led to the construction of linkage map or genetic maps of chromosomes.

4. Linkage group and linear order of the genes help to reveal the mechanism and nature of the genes.

5. Crossing over plays a very important role in the field of breeding to improve the varieties of plants and animals.

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