Genetics+and+Evolution+Chapter!

** Mendelian Genetics: **  **A Common Misconception about Mendelian Genetics**: All traits are equal in dominance
 * Genetics and Evolution **

While studying pea plants, Mendel discovered that there are two alleles for each trait. Some alleles are dominant and some alleles are recessive. ** Dominant ** alleles are those that mask the effects of the other allele; these other alleles are called ** recessive ** alleles. When a dominant allele is paired with a recessive allele, the recessive allele is “masked” and the dominant allele will be expressed. Recessive alleles are only expressed when two recessive alleles are paired together. Through his work and discoveries Mendel came up with two laws. Mendel’s first law is the ** Law of Segregation. ** This law states that the copies of a gene separate and each gamete only receives one copy. Each parent provides a gene for every trait for each gamete that is formed. Mendel also noticed that all the different traits of the pea plants seemed to be independent of each other. He came up with his second law, the Law of ** Independent Assortment. ** This means that the alleles of different genes sort independently of each other during gamete formation. There are also some alleles that are neither dominant nor recessive. This is called ** Incomplete dominance ** and means both alleles have equal expression. An example of this is a while and red flower mating and producing pink flowers. Neither the red allele nor the white allele is dominant so both are equally expressed. The ** genotype ** is the genetic make-up of the organism. The ** phenotype ** is the physical expression of the genotype.
 * DNA ( **deoxyribonucleic acid) is found in the nucleus of cells and is refered to as the "blueprint" of life. DNA is copied every time a new cell is formed in the body of an organism. The DNA wraps around protein to make chromatin and then the chromatin folds up to make chromosomes. ** Genes ** are regions of DNA on a chromosome that code for a specific trait. Every gene is made up of one maternal allele and one paternal allele. The location of the gene on the chromosome is called a ** locus **. Different forms of a gene are called ** alleles ** of that gene and two alleles make up a gene.

A way of showing the possible genetic outcomes when two organisms mate is called a ** Punnett Square **. It is used to determine the probability of an offspring having a certain genotype. A punnett square illustrates every possible combination of one maternal allele and one paternal allele. When heterozygous maternal alleles and heterozygous paternal alleles are crossed the result is a ** 3:1 ratio ** of dominant to recessive. As in the example punnett square three of the possible combinations will be expressed as dominant and one of the possible combinations will be expressed as recessive


 * Mitosis & Meiosis: **

**A Common Misconception About Mitosis & Meiosis:** Mitosis and Meiosis are commonly believed to essentially be the same process of copying and dividing cells. **The Truth:** Mitosis and Meiosis describe the process by which the body prepares cells to participate in either asexual or sexual reproduction to make an entire organism. Mitosis is a process of cell division which results in the production of two daughter cells from a single parent cell. The daughter cells are identical to one another and to the original parent cell. Meiosis is a process of reductional division in which the number of chromosomes per cell is cut in half.

In mi **T** osis, each daughter cell ends up with TWO complete sets of chromosomes. In mei **O** sis, each daughter cell ends up with ONE complete set of chromosomes.

Mitosis = Mi- TWO -sis! Meiosis = Mei- ONE -sis!

**Mitosis** : One cell becomes two cells -The new "daughter" cell has exactly the same number of chromosomes and information as the "parent" cell. 1 cell divides and becomes 2 cells.

**Meiosis** : One cell becomes 4 cells - there are 4 new "daughter" cells. Each new gamete cell contains only one-half of the number of chromosomes of the parent cell. Each sex cell goes through the division process twice in order to have the correct number of cells, and the correct chromosomal information.

The **Red Queen’s Hypothesis** is an evolutionary hypothesis taken from the Red Queen’s face in Lewis Carroll’s “Through the Looking-Glass.” The Red Queen said, “It takes all the running you can do, to keep in the same place.” The Red Queen Principle states, “For an evolutionary system, continuing development is needed just in order to maintain its fitness relative to the systems it is co-evolving with.” This hypothesis is used to explain the advantage of sexual reproduction (meiosis) over asexual reproduction (mitosis). Every individual is an experiment because every person is a mix of their mother’s and father’s genes. Sexual reproduction may allow a species to evolve quickly just to hold onto the ecological niche that it already occupies in the ecosystem.

Let’s look at mitosis and meiosis in more detail…

**MITOSIS:** Mitosis is the reproduction of skin, heart, stomach, cheek, hair, etc. cells. These cells are known as somatic cells (or body cells). This is also a form of **asexual reproduction**, where one organism or cell reproduces itself.

Asexual : “A” = “without” ; “sex” = “to cross”

We need to make new cells before the old ones die. We keep the blueprint going so we can keep on building. Mitosis produces EXACT copies of the cell. Somatic cells divide themselves frequently in order to replace or refresh the cell.

First, DNA **replication** must take place so that a cell can give it’s DNA to a copied cell. The DNA “unzips” and copies which results in 2 identical DNA molecules called **sister chromatids**. The duplicated DNA (as sister chromatids) line up in the middle of the cell where the spindle fibers pull the sister chromatids apart. New cells pinch apart… so now we have 2 identical cells with the exact same DNA.

So, mitosis makes exact copies of cells through asexual reproduction for new cell growth in somatic cells. The daughter cells it produces are **diploid (2n)**, meaning that the cell contains two sets of chromosomes (one from each parent). Mitosis differs from meiosis because meiosis makes gametes through sexual reproduction. **Gametes** are sex cells that contain the haploid set of chromosomes. Meiosis occurs in special cells in the ovary and testes. The daughter cells ( gametes ) are haploid, meaning that these cells contain only one set of chromosomes. We have to have egg and sperm come together in order for **fertilization** to form a **zygote**. How do we make egg and sperm? Meiosis!

**MEIOSIS:**

Meiosis allows us genetic recombination, whereas mitosis is essentially cloning. An advantage of genetic variation ensures adaptation because environments are constantly changing. That is why meiosis functions through **sexual reproduction** because sex allows many opportunities for genetic variation. Sex randomly divides half of your alleles through meiosis and randomly combines sperm and egg through sex.

Meiosis occurs in specialized cells (called germ cells) in our ovaries and testes. The first thing is to duplicate the chromosomes, leading to sister chromatids which are held together by a **centromere**. Each duplicated chromosome pairs with a homologue. Homologues may swap segments which is called crossing over. When crossing over is happening, each chromosome becomes zippered to its homologue. All four chromatids are closely aligned. Nonsister chromosomes exchange segments. When crossing over is complete, each chromosome contains both maternal and paternal segments (which creates new allele combination's in their offspring).

Now, the chromosomes are getting ready to separate. They are pushed and pulled into the middle of the cell. It is important to note that maternal and paternal chromosomes do not have a designated “side.” This happens through Independent Assortment and ensures genetic diversity. The chromosomes separate. **Homologous chromosomes** segregate and the sister chromatids remain attached at the centromere.

http://www.biology.iupui.edu/biocourses/N100/images/8mitosiscropped.jpg

The cells are now 2 diploid daughter cells. 2nd division now begins; this is called Meiosis II. Duplicated chromosomes line up at the equator. Sister chromatids separate to become independent chromosomes. The chromosomes arrive at opposite ends of the cell. A nuclear envelope forms around each set of chromosomes, resulting in FOUR haploid cells.

http://www.biology.iupui.edu/biocourses/N100/images/8mitosiscropped.jpg

A human egg is haploid (because it has 23 chromosomes) and a sperm is haploid (also has 23 chromosomes.) Upon fertilization, the new baby now has the "correct" human number of 46 chromosomes in each of its somatic cells. Fertilization of the egg by the sperm restores the diploid number of 36 chromosomes.

Drawing by: Angie

Drawing by: Angie

Our deoxyribonucleic acid or **DNA** is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms as well as some viruses. The main role that DNA has is the long is long-term storage of information. DNA strands are wrapped around to make **chromatin**. Chromatin folds up to make chromosomes. The nitrogenous bases that compose DNA are **adenine (A), thymine (T), cytosine (C), and guanine (G).** Adnine and guanine are called **purines**, whereas thymine and cytosine are called **pyrimidines**. A always binds to T and C always binds to G. With this, the amount of adenine always matches the amount of thymine, and the amount of guanine always equals the amount of cytosine. The DNA is made has a sugar-phosphate backbone.
 * Molecular Genetics: **



DNA is found in the nucleolus of our cells but must remain there. You may ask, “Why can’t DNA leave the nucleus of the cell? “. The answer is that our DNA is too precious to be lost or damaged. Instead our bodies make copies of our DNA into something called messenger ribonucleic acid or more commonly, **mRNA**. There is another nucleic acid helper in this process of reading DNA and that is Transfer RNA or **tRN.** tRNA is a smaller RNA molecule whose job is to transfer a specific active ** amino acid ** to a growing polypeptide chain at the ribosomal site of protein synthesis. Ribosomal RNA or **rRNA** is the central component of the ribosome, the protein manufacturing machinery of all the living cells. The function of the rRNA is to provide a mechanism for decoding the mRNA into amino acids and to interact with the tRNA’s during translation by providing something called peptidyl transferase acitivity. From there the tRNA then brings the necessary amino acids corresponding to the appropriate mRNA codon. In RNA there is no **thymine (T)**, instead there is **uracil (U)**. To understand how both tRNA and mRNA are involved you would need to understand the process of protein synthesis.

**Protein synthesis** is a process where DNA encodes for the production of particular amino acids and proteins. The process is broken into two parts, the first is called ** transcription ** and the second is called translation. ** Transcription ** is when in the beginning of synthesis of the proteins, the corresponding RNA molecule is produced by RNA transcription. One strand of the DNA double helix is used as a basis by the RNA polymerase to synthesize a mRNA. This particular mRNA migrates from the nucleus to the cytoplasm of the cell. In this step, mRNA goes through different types of maturation including one called splicing, when the non-coding sequences are eliminated. The coding mRNA can be described as a unit of three nucleotides called a **codon**. This is the way our genes are read, along a DNA strand or an mRNA molecule that designates a specific amino acid to be added. The order that the codons fall into along the DNA or mRNA determines the sequence of the amino acids in the polypeptide. **Translation** is when the ribosome binds to the mRNA at the start codon (e.g. AUG) that is only recognized by the initiator tRNA. The ribosome proceeds to the elongation phase of protein synthesis. In this stage, complexes, made of an amino acid linked to tRNA, in sequence bind to the appropriate codon in mRNA by forming the complimentary base pairs with the tRNA anticodon. The** anticodon ** is the three-base sequence in tRNA complementary to a codon on mRNA. The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one, translated into polypeptidic sequences that are determined by DNA and represented by mRNA. At the end of this, a release factor binds the stop codon,, terminating translation and releasing the complete polypeptide from the ribosome. One specific amino acid can correspond to more than one codon.



**Truth:** There are several ways a mutation (the sequence of a gene) can be altered. Gene mutations depend on a variation of effects on the health of the person that are dependent upon where the mutation occurs and if they make alterations the function of proteins that are essential.
 * A Common Misconception About Mutations: **There is only one kind of mutation

**Mutations** can be classified from the structure of genes into small-scale mutations or large-scale mutations. **Point mutations** are a small-scale mutation, which is often cased by chemicals or a malfunction of an exchange of a single nucleotide for another in DNA replication. The changes found in this mutation are categorized as transitions of transversions. **Transitions** are the most commonly found, which transitions that the replacement of a purine base with another purine or replacement of a pyrimidine with another pyrimidine. ** Transversions ** are the replacement of a purine with a pyrimdine and vice versa. The point mutations that occur within the protein-coding region of a gene can be put into three categories dependent upon what the inaccurate condon codes for. The first is a //silent mutation,// which codes for the same amino acid. The second is a //missense mutation//, which code for a different amino acid. The third is //nonsense mutations//, which code for a stop and can shorten the protein.

Another small-scale mutation is a **frameshift mutation** caused by the insertion or deletion of a few nucleotides that during the DNA sequence was not evenly devised by three. Genes have a triplet nature that is expressed in codons, the **insertion or deletion** can disrupt the reading frame, or the group of codons, then leading in a translation that is completely different from the intended original. The earlier in the sequence the deletion or insertion occurs, the more altered the protein produced is. ** Insertion disturbs one or a few basses by adding genetic message. Deletion occurs when there is a removal of one or a few bases from a nucleotide chain. It has been seen that even just one removal of a base can throw the genetic message out of frame beyond the point of deletion. **

This frameshift causes the reading of all the codons after the mutation to code for different amino acids. The stop codon, which is UAA, UGA, or UAG, will not be read or a stop codon could be created at another site. The protein being created could be abnormally short, abnormally long and/or contain the wrong amino acids. It would most likely be non-functional.



Point mutation and frameshift mutation are both naturally occurring due to errors in DNA replication, repair, and recombination. There is however, something called a **mutagen** being a physical or chemical agent that changes the genetic material, usually DNA, of an organism. This basically increases the frequency of mutations above the natural background level. Many mutations can cause cancer, mutagens are generally also **carcinogens**.


 * Microevolution: **

**A Common Misconception About Evolution:** Individual living things can choose to adapt. **Evolution** is change in the genetic material of a population of organisms from one generation to the next. Much of this change is random, and caused by processes like mutation. Although the changes produced in a single generation are normally small, the accumulation of these differences over time can cause substantial changes in a population, a process that can result in the emergence of a new species.



**Microevolution** is evolution that occurs at or //below// the level of species, such as a change in the gene frequency of organisms or in the creation of new species, also called speciation. These kinds of smaller evolutionary changes could be caused by several processes: mutation, gene flow, genetic drift, and natural selection. In contrast, Macroevolution involves changes at or //above// the level of species, which, as a result of time and scale, can cause something like the formation of feathers to transform a reptile (like the dinosaur) into a bird.



**Mutation** is the permanent alteration of an organism's DNA. This process increases variation in the **gene pool** (the complete set of unique alleles in a species or population), however it can have drastic effects, whether big or small, positive or negative, and it is always indifferent. There are many genetic diseases, like Down Syndrome, that are a result of mutation. There are two mutations that can be caused during DNA replication: Base-Pair Substitutions and Frameshift Mutations. Base-Pair Substitutions occur when an incorrect amino acid is placed in the corresponding position of the encoded protein. This can result in altered protein function. Frameshift mutations come in two forms: Insertion and Deletion. Insertion is when an extra base is added into the gene region. Deletion is the removal of a base from the gene region. Both shift the reading frame of the DNA. **Gene Flow** is the movement of alleles from one **population** (all the organisms that constitute a specific group or occur in a specified habitat) of species to another by interbreeding, migration, dispersal of seeds, cross-pollination, etc. This process allows new alleles to be added, or existing ones to be maintained, in the gene pool. Below is an example of gene flow. The gene for beetles with brown coloration is moving into a population of green coloration.

The **Founder Effect** is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It is thought to lead to the speciation and subsequent evolution of new species. A population **bottleneck**, an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing, can also cause a founder effect.

**Genetic Drift** is a chance in the relative frequency in which an allele occurs in a population due to random sampling and chance. It is an important evolutionary process which leads to changes in allele frequencies (the fraction of the gene copies that share a particular form) over time. It may cause alleles to completely disappear, which in turn reduces gene variability. Allele frequencies can change in a number of ways, including sexual reproduction – Meiosis, crossing over, Law of Segregation, and Law of Assortment, as well as the random combination of sperm and egg – mutations, and gene flow. In contrast to natural selection, genetic drift is not driven by environmental or adaptive pressures, and may be beneficial, neutral, or detrimental to reproductive success. **Natural Selection** is the process of “weeding out” unfavorable alleles because of environmental pressures, and keeping the good ones. If certain alleles are selected, and that organism survives long enough to reproduce, then it is fit for survival, which is why natural selection is also known as “Survival of the Fittest.” **Fitness** is the capability of an individual of a certain genotype to reproduce, and usually is equal to the proportion of the individual's genes in all the genes of the next generation. For example, there is a species of moth, called the Peppered Moth, that has been used in many studies concerning natural selection. Usually, these moths are white in color with black speckles spread across their wings, and they are well camouflaged on the speckled lichens on tree trunks. However, there is a genetic mutation that causes some of the moths to be all black, and since they are on the light lichened trees, they become easy prey because they stick out so much more than the white moths.

There is also **Sexual Selection**, which was defined by Darwin as the effects of the struggle between the individuals of one sex, generally the males, for the possession of the other sex. Peacocks are a great example because they use their beautiful tails to attract mates. A male with bigger and brighter tails will be able to pass on his genes because a female is more likely to mate with him.



Macroevolution: ** **Macroevolution** is evolution on a large scale. Macroevolutionary studies focus on change that occurs at or above the level of species, in contrast with microevolution, smaller evolutionary changes in allele frequencies within a population. **Speciation**  is the evolutionary process by which new biological species arise. One of the best definitions is that of the evolutionary biologist Ernst Mayr: //"A species is an actually or potentially interbreeding population that does not interbreed with other such populations when there is opportunity to do so."// There are four geographic modes of speciation in nature, based on the extent to which speciating populations are geographically isolated from one another:
 * **Allopatric speciation**  is also known as geographic speciation, which is a phenomenon where biological populations are physically isolated by and extrinsic barrier and evolve intrinsic or genetic reproductive isolation. If that barrier ever vanishes, the individuals of the populations can no longer interbreed.


 * **Peripatic speciation** is where new species are formed in isolated, small peripheral populations that are prevented from exchanging genes with the main population. It is related to the concept of founder effect, since small populations undergo bottleneck.


 * **Parapatric speciation**  happens when the zones of two diverging populations are separate but do overlap. There is only partial separation afforded by geography, so individuals of each species may come in contact or cross the barrier from time to time, but reduced fitness of the heterozygote leads to selection fro behaviors or mechanisms that prevent breeding between the two species.


 * **Sympatric speciation** , species diverge while inhabiting the same place. Examples of this are found in insects that become dependent on different host plants in the same area. Sympatric speciation refers to the formation of two or more descendent species from a single ancestral species all occupying the same geographic location.



**Fossil Records** are ways of keeping track of these evolutionary changes. A fossil record is the collective accumulation of artifacts that have been fossilized all around the world. It can provide interesting information about the evolution of life on Earth. Scientists can look at them as a whole to see evolution on a very large scale, or they can look at specific time periods in an attempt to learn more about the history of the Earth and the organisms that now inhabit it.

An **isolation mechanism**  is an obstacle to interbreeding, either ** extrinsic **, such as a geographical barrier, or <span style="color: #800080; font-family: Arial,Helvetica,sans-serif;"> **intrinsic** <span style="font-family: Arial,Helvetica,sans-serif;">, such as a structural or behavioral incompatibility. Good examples of extrinsic isolating mechanisms are mountains and rivers.

** Intrinsic isolating mechanisms ** The evolution of internal characteristics that keep organisms from interbreeding. Evolved differences in anatomy, physiology, or behavior that prevents interbreeding between individuals of the same species or of closely related species. A ** temporal isolation ** refers to breeding at different times during the day or year. It is genetic isolation achieved due to temporal differences in breeding. There are many examples of animals and plants that could breed only if they were reproductively active at the same time. A reproductive constraint is any factor that will not allow the production of a fertile offspring. These factors can be classified as ** prezygotic **(constraint that makes mating difficult) and <span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">**postzygotic** <span style="font-family: Arial,Helvetica,sans-serif;"> (constraint that prevents a zygote from developing). Temporal isolation is a prezygotic constraint. (Krough 2004).

In g**ametic isolation**, two organisms may have mated, but the male’s sperm is incompatible with the egg or the female’s reproductive system. This does not mean the male or the female is infertile, it just means that when those particular two organisms mate they cannot create offspring. **Behavioral Isolation**, also called Ethological Isolation, is the prevention of one species mating with another. These isolation mechanisms include differences in courtship behavior, differences in chemical signals or vocalizations, and differences in color or morphology that allow individuals to recognize their own species. It is a very common mechanism on keeping closely-related sympatric animals from interbreeding. For example, there are two different species of cricket that would be indistinguishable unless you heard their mating song: they are of a noticeably different pitch. A behaviorally isolated creature will only be able to conduct successful courtship with an animal with similar mating behavior.
 * Ecological isolation ** is when two species do not intact but live in common area. Example is lions and tigers. They both live in the same areas of the world, but the lions live and breed in the grasslands and the tigers live and breed in the forests. So, even though the two species live by each other, they do not interbreed and therefore do not create offspring, making lions and tigers two separate species.



**Geographical barriers** are pretty simple to understand, just think of why it is called “geographic barriers.” If two populations of the same species can't reach each other to have sex, they can't mix their genes. Imagine two ponds of the same kind of fish. The land between the ponds is a geographical barrier preventing them from mingling. If a population should become divided into two by a geographic barrier, evolution of each new population continues independently due to the forces of natural selection, genetic drift, migration, nonrandom mating, and mutation.



**Mechanical isolation** is a form of reproductive isolation that occurs because of an incompatibility in structure of the male and female sex organs. These barriers maintain the integrity of a species over time, reducing or directly impeding gene flow between individuals of different species, allowing the conservation of each species characteristics. The songs of birds, insects and many other animals are part of a ritual to attract potential partners of their own species. These songs present specific patterns recognizable only by members of the same species, they therefore represent a mechanism of reproductive isolation. Clearly, a bird cannot mate with an insect.



**Hybrid Inviability** - also known as Infertility - happens when two organisms who are seemingly the same species mate and are unable to produce a viable offspring. Their offspring is either unhealthy or unable to reproduce themselves. An example of this is the Mule. A mule is created when a Horse and a Donkey mate, but Mules are unable to reproduce and create other Mules. This can happen for a number of reasons.



**Bibliography:** <span style="font-family: 'Times New Roman',Times,serif;">

Chiras, Daniel (1993). "Biology: The Web of Life." West Publishing Company: St. Paul, MN.

<span style="font-family: Arial,Helvetica,sans-serif;">Krogh, David. Biology: A Guide to the Natural World. Second Edition. Upper Saddle River, NJ: Prentice Hall, 2002. Print. McClean, Phillip (2000). "Mendelian Genetics <span style="color: #000000; font-family: 'Times New Roman',Times,serif; font-size: 12pt;">. "http://www.ndsu.edu/pubweb/~mcclean/plsc431/mendel/mendel1.htm"

<span style="font-family: Arial,Helvetica,sans-serif;">Purves, William. <span style="font-family: arial,helvetica,sans-serif;">//<span style="font-family: Arial,Helvetica,sans-serif;">Life: The Science of Biology // <span style="font-family: Arial,Helvetica,sans-serif;">. 6th ed. Sunderland, Massachusetts: Sinauer Associates, Inc., 2001. Print.