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"Principles of Biology Unit 2: Mendelian Genetics

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"Principles of Biology Unit 2: Mendelian Genetics BIOL 2107K

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These notes cover Cell Division (specifically Meiosis), Mendelian Genetics, ABO blood types, the Rhesus factor, Sex-Linked traits, Genetic Variation within a Population, certain Chemistry fundament...
Principles of Biology I
Biology, Chemistry, Math
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Date Created: 03/27/16
Lecture 10-12 Lec. 10: Review Cell Division - Mendelian Genetics I, How Mendel fits into the Equation(s)......with some rearranging  Meiosis results in some genetic constancy from generation to generation, but also provides genetic variability. o Consists of two nuclear divisions that reduce # of chromosomes in the diploid form to the haploid number. Major roles of Meiosis: reduce the chromosome number from diploid to haploid & ensure each daughter cell (in diploids this would be a gamete) gets a complete set of each chromosome; also promotes a quite incredible degree of genetic diversity among the progeny w/o introducing mutations or errors in the distribution of the chromosomes in to any of the gametes.  1 meiotic division reduces chromosomal # o Meiosis I led by an interphase (DNA is replicated) o Meiosis I begins with a long prophase, prophase I.  In the testis cells of human males, prophase I takes about a week.  In the egg cells of human females, prophase I begins before birth in some eggs and can continue for ~50 years depending on their release in the monthly ovarian cycle. o During prophase I, synapsis occurs: Two homologs appear to be joined together by a synaptonemal complex of proteins.  Forms a tetrad, or bivalent- Consists of two homologous chromosomes with two sister chromatids. o Early Mid-Prophase 1: At a later point, chromosomes repel each other except at the centromere and at points of attachments (chiasmata) - gives appearance of multiple associated chromosomes.  How and when the male and female gametes develop is both species and sex dependent. Nondisjunction- The most commonly occurring error; either homologous chromosomes fail to separate during anaphase I, or sister chromatids fail to separate during anaphase II Aneuploidy- Presence of an abnormal number of chromosomes in a cell, for example when having 45 or 47 chromosomes when 46 is expected in a human cell; can give rise to a number of genetic abnormalities, many of which do not survive past formation of the egg. *Meiosis demonstrates one of the apparent “truisms" of living world, "all things biological come in pairs" (Francis Crick) =copies of genetic information are transferred to the gametes by division of the germ-line cells into four "gametes" (two by two) *Sutton and Boveri (1902) Gregor Mendel - An Augustinian friar who already finished and published his work almost forty years earlier (in 1865/1866) but no one had taken any notice.  True-breeding plants experiment- observe" and "record" phenotypic traits of each generation in sufficient quantities to explain (through mathematical analysis) relative proportions of different "phenotypes" of the various progeny.  Chose garden peas as his subjects (they were easily grown and their pollination was easily controlled)  Controlled pollination by manually moving pollen between plants. Self=PollnationThe transfer of pollen from the anther to the stigma of the same flower, another flower on the same plant, or the flower of a plant of the same clone  Define "trait" as being particular form or a character, e.g. white flowers and looked for characters with well-defined, alternative traits and true-breeding (when it was the only trait that occurred after many generations of breeding individuals that exhibited that particular trait-phenotype)  A true-breeding white-flowered plant has only white-flowered progeny when crossed with others in its strain. Parental generation, designated P- True-breeding plants, when used for crossing with other plants with an alternative trait; the first set of parents crossed "Filial generation", designated "F1"- The progeny from such a cross consists of all the offspring from the parents - their children. Designated F2- When F1 individuals are themselves crossed to each other or "self- fertilized" Monohybrid cross- Mating between two individuals with different alleles at one genetic locus of interest; A monohybrid cross involves one (mono) character and different (hybrid) traits; Pollen from true-breeding pea plants with wrinkled seeds (one trait) was placed on stigmas of true- breeding plants with spherical seeds (another trait) *The F1 seeds were ALL spherical (somehow the wrinkled trait failed to appear at all), spherical trait appeared to completely mask wrinkled trait; when 2 "true-breeding" parental plants are crossed, the spherical trait was called dominant, and the wrinkled trait was called recessive. *The F1 plants were then allowed to "self-pollinate" *The units responsible for inheritance were discrete particles, and that they existed within an organism in pairs; that they separated during gamete formation, and that they retained their integrity. *Recognized that each pea had two units of inheritance that kept on showing through for each character. Gregor Mendel's hypotheses: 1. Hereditary determinants are of a particulate nature. Each genetic trait is governed by unit factors, which "hang around" in pairs (or gene pairs) within individual organisms. 2. When two different unit factors governing the same phenotypical trait occur in the same organism, one of the factors is dominant over the other one, which is called the recessive trait. 3. During the formation of gametes the "paired" unit factors separate or segregate randomly so that each gamete receives either one or the other of the two traits, but only one. 4. The union of one gamete from each parent to form a resultant zygote is random with respect to that particular characteristic. 5. During production of gametes, only one of the "pair members" for a given character passes to the gamete. 6. When fertilization occurs, the zygote gets one from each parent, thus restoring the pair. *Mendel’s units of inheritance are now equivalent to the genetic units or genes. *Different forms of which are called alleles; each allele is given a symbol. In the case of wrinkled seeds, "S" might represent smooth and "s" wrinkled. *Uppercase always represents dominant trait; lowercase represents the recessive *If Mendel's appreciation of hereditary holds true, then "true-breeding" individuals would each have two copies of the same allele Homozygous- two copies of same allele (Wrinkled would be ss) Homozygous- two copies of same allele (Smooth true-breeding would be SS) Heterozygous- As a consequence of a cross between true-breeding round and true-breeding wrinkled seed plants, the smooth-seeded plant offspring would be Ss, and would not themselves be true-breeding parents for their own offspring *Actual composition of any organism's alleles for a gene is its genotype: Ss would be a genotype. *When an individual produces gametes, its alleles separate, so that each gamete receives one member of the pair of alleles. Mendel's first law, the law of segregation- Two members of a gene pair segregate from each other into the gametes, whereby one half of the gametes carries one of the traits, the other half carries the other. *Cambridge Professor (William Punnett) devised the Punnett square- A simple box-like device that helps us consider all genetic combinations; can provide clarity by showing the expected frequencies of genotypes; shows that the genotypes and associated ratios for a monohybrid cross are: 1 SS: 2 Ss: 1 ss, even though the "phenotype" of the progeny exhibits a phenotypic ratio of 3 smooth to 1 wrinkled. Locus (plural being loci) - A gene is a portion of the chromosome that resides at a particular site Test cross- Can determine the genotype (heterozygous or homozygous) of an individual that may exhibit a dominant phenotype of a given trait; involves crossing "unknown" individual to true-breeding recessive or homozygous recessive. *If unknown is homozygous dominant for particular trait and unknown is heterozygous for a given trait, approx. half progeny will have the dominant trait and half the recessive trait. Mendel's second law, the law of random assortment- During gamete formation the segregation of one gene pair is independent of all other gene pairs; describes outcome of dihybrid (two character) cross, or hybrid cross involving additional characters/traits. Dihybrid- an individual that is a double heterozygote (e.g., with the genotype SsYy). *Second law states that the Ss alleles assort into gametes completely independent of the Yy alleles; dihybrid, Ss Yy, produces gametes that have one allele of each gene. In this cross, four different gametes are possible and will be produced in equal proportions: SY, Sy, sY, and sy. Random fertilization of gametes yields the outcome visible in the more complex Punnett square. Note that it is now 4 x 4 table construction to accommodate 16 possible genotypes. Filling in the table and adding the like cells reveals a 9:3:3:1 ratio of the four possible phenotypes (smooth yellow, smooth green, wrinkled yellow, and wrinkled green). You can go on from here... Trihybrid crosses (Punnett square would be an 8 x 8 construction), Tetrahybrid crosses (Punnett square would be a 16 x 16 construction) etc..... but ALWAYS the same principles are used - Mendel's 2nd Law. In point of fact, this particular law is NOT always true So, given all that we have just talked about, Mendel's laws are potentially appropriate for genes on different chromosomes, but what about genes that are located on the same chromosome? According to a cellular appreciation of meiosis, wouldn't that suggest that genes, which are considered to be linked on the same chromosome would assort in a non-random manner? At this juncture you have to revisit Meiosis, carefully observe the process........and look more carefully at the formation of those chiasmata! It turns out that the probability of these chiasmata (exchange of genetic information from one paired chromosome to another) are critical ingredients for the Mendelian school of thought. They appear to happen randomly for each chromosome, at least once per meiotic event. Now, if that were true, then genes located at loci that are far enough apart on a chromosome would be highly likely to experience a chiasmatic event somewhere in between their respective locations, which would potentially have a somewhat dramatic effect upon their degree of "random assortment"? Alleles are variations of a gene at a specific locus on a given chromosome. New alleles arise by mutation or change in the DNA sequence. An allele, therefore, can arise due to mutation at a given locus, and -if it has become present in sufficient quantity it will have been incorporated into the gene pool. Alleles can be randomly mutagenized to become different alleles as a result of changes in their DNA sequence. The genetic consequences of a shuffling of these alleles within a gene pool would be a relatively random phenomenon, unless their presence in the pool was subject to selective pressure "Wild Type" is a term used for the most common allele in the population. (Note: being the "most common" in a population does not always mean that the wild-type alleles will be the dominant alleles). Indeed, in the early twentieth century, G. H. Shull crossed two varieties of corn, and the yield went from 20 to 80 bushels per acre. Thus defining a now common agricultural practice to increase production in plants. This is called either hybrid vigor or heterosis and it is a result of the fact that continued "in- breeding" leads to deleterious traits becoming "fixed in the gene pool. The use of such hybridization techniques, therefore, has been a common agricultural practice ever since -to increase production in crops and cattle etc..... remember gene flow?? A hypothesis called overdominance proposes that the heterozygous condition -in certain important genes- is often considered to be selectively "superior" to either homozygote. How can this be? If all of Mendel's ideas were to hold true for, the particulate mechanism of genetics would suggest that one gene in any given gene pair is simply dominant over the other. Again, Mendel wasn't perfect. Some Heterozygotes may show a different phenotype to the expected DOMINANT and recessive traits that Mendel observed. Some Heterozygotes may show an intermediate phenotype, that is a distinct variation of the two "true breeding" parental phenotypes. For example, red-flowered snapdragons when crossed with their white counterparts will generate pink-flowered plants. While this phenotype (on the surface) might tend to support the blending theory that Mendel was so avidly trying to overcome, the F2 progeny, of a "selfing" of the pink flowers admirably demonstrates, Mendelian "particulate" genetics. The reason for the change in color results from a phenomenon called "incomplete dominance". Another example, where Mendelian Genetics apparently falls down, can be seen in some blood types. Yet again, however, even in this instance, Mendel’s laws are not compromised. These blood types are said to exhibit codominance, where both alleles are expressed. Note that in codominance the phenotype of the heterozygote is completely different (not just a "blend" of the two homozygotic phenotypes). It turns out that Mendel made a series of artful choices in choosing traits in peas that "just happened" to be examples of complete dominance. Consequently, Mendel analyzed his "units" in terms of dominant and recessive traits. Even so, there are many examples, where variations at a single locus, can give rise to multiple phenotypic effects. So, let's look a little closer at the behavior of these genes and their alleles. Alleles and their Interactions Remember, differences in alleles of genes are often slight differences in the DNA sequence at the same locus, which result in slightly different products, and can give rise to different phenotypes. Many genes can have more than one variation -"multiple alleles". In rabbits, coat color is determined by one gene with four different alleles. Five different colors result from the combinations of these alleles. Please note, even if more than two alleles exist in a population, any given individual can have no more than two of them: one from the mother and one from the father. Again, as can be observed, Dominance need not be complete Another example The AB of the human ABO blood group system is an example. The alleles for blood type are IA, IB and IO. They all occupy one locus. These alleles determine which antigens (proteins) are present on the surface of red blood cells. A population might have more than two alleles for a given gene. The ABO blood types are an example of multiple alleles. The alleles for blood type are IA, IB and IO. They all occupy one locus. These alleles determine which antigens (proteins) are present on the surface of red blood cells. These "antigens" react with proteins called antibodies in the serum of certain individuals. The result of mixing blood from each of the different ABOtypes can result in red blood cell agglutination, or clumping, which may prove to be fatal. Multiple Alleles: The "ABO" blood-type system or "ABH-antigens" are not primary gene products but instead the enzymatic reaction products catalyzed by the enzymes called glycosyltransferases. The ABO system is now known to be polymorphism of complex carbohydrate structures of glycoproteins and glycolipids expressed at the surface of red blood cells. N.B. An individual who lacks a particular antigen(s) will automatically possess the opposing antibody (e.g. if you have the A antigen you will not have the B antibody....unless the individual is AB) ABO Enzymes RBC Antigens Blood Type Genotypes Serum Antibodies Present Present "A" AA, Ai "H", "A" A, H anti-B "B" BB, Bi "H", "B" B, H anti-A "AB" AB "H", "A", "B" A, B, H none "O" ii "H" H anti-A, anti-B Note that blood-types A and B can also be considered to be "codominant", as the presence of both alleles AB gives rise to a completely different phenotype, when compared to their homozygous AA and BB equivalents. As a clarification on blood-types....we also use the additional classification of Rhesus factors...these are a whole new set of antigens, discovered when blood from rhesus monkeys was injected into guinea pigs (circa 1940's). There are over 50 different types of Rh factors, but the most commonly known one is the D antigen (Rho[D]), which -if it is present indicates that that individual is Rh-positive; conversely if the D antigen is absent, that person is Rh-negative. In contrast to the ABO system, however, antibodies to Rh antigens aren't necessarily inherent to the person's blood, but can develop as an immune response after a transfusion or (perhaps) during pregnancy. >Gene Interactions Some genes give rise to gene products that alter the effects (phenotypes) of other genes. Epistasis occurs when the alleles of one gene cover up or alter the expression of alleles of another gene. While blood groups would be a more than adequate example of this phenomenon, a more overt example of this would be life and death! In this instance the same gene that effects coat color in the mouse also has some influence upon development of the embryo. Thus, one gene, does not always mean one function. If, as in this case the gene in question in seen to have more than one function, it is therefore considered to be pleiotropic. Another example is coat color in mice. In the example shown in the picture: The B allele determines a banded pattern, called agouti. The recessive b allele results in "unbanded" hairs. The genotypes BB or Bb are agouti. The genotype bb is solid colored (black). Another gene, at an entirely different locus, determines if any coloration occurs at all. The genotypes AA and Aa have color, whereas the double recessive aa are albino, which do not allow any color to show through, as the aa genotype blocks all pigment production. Mice that are heterozygous for both genes are agouti. An F2 phenotypic ratio of an initial parental cross between a BB, AA and a bb, aa -followed by a "selfing" of the F1 generation- would be: 9 agouti: 3 black: 4 white. The corresponding genotypes are 9 agouti (1 BBAA + 2 BbAA + 4 BbAa):3 black (1 bbAA + 2 bbAa):4 albino (1 BBaa + 2 Bbaa + 1 bbaa). Other examples of gene/allelic expression which differ from expected patterns of Medelian inheritance are: Duplicate genes, occur when two distinct genes affect the same phenotype in the same way. One of the best examples of this would be the shape of the shepherd's purse pollen sac. Multiple Genes or Polygenes mediate quantitative inheritance. Individual heritable characters are often found to be controlled by groups of several genes, called polygenes. Each allele of each gene at a different intensifies or diminishes the phenotype. Variation is continuous or quantitative (“summation" or "adding up” of all the traits). Examples of continuous characters are height, skin color, and (possibly) intelligence. Nature vs. Nurture? When thinking about the importance of either genotypes or phenotypes, one must always consider the immense importance of.....the environment, and how it can affect the action(s) of any given gene. Variables such as light, temperature, and nutrition can dramatically affect the translation of a genotype into a phenotype. For example, the darkness of the fur on the extremities of a Siamese cat is markedly affected by the temperature of that region. Darkened extremities normally have a lower temperature than the rest of the body. Same goes for some rabbits. Such coloration can be manipulated experimentally. The proportion of individuals in a group with a given genotype that express the corresponding phenotype can sometimes be measured, and that measurement is called penetrance. The expressivity of the genotype is the degree to which it is expressed in an individual. Gene linkage and the role of the sex chromosome: Mendel did all his analyses with plants, which -like corn- exhibit both male and female reproductive structures in the same adult plant (termed monoecious, or "one house"). What about animals and plants, which have individuals that are either one or the other sex (termed dioecious, or having “two houses”). In most dioecious organisms, sex is determined by differences in the presence (or absence) of specific chromosomes. Remember, that equate Mendel with meiosis we had to understand the role of chiasmata occurring between two gene loci on adjacent chromatids in paired chromosomes during prophase I of meiosis. I glibly stated that, if the probability of a chiasma forming between two genes is "one" (i.e. a certainty), then the assortment of alleles would, in essence, be the same as if they were on separate chromosomes (i.e. random). But what happens if there is no chiasmata formation? Lecture 12-13 Ch. 16 and 17 What about Rhesus factors...these are a whole new set of antigens, discovered when blood from rhesus monkeys was injected into guinea pigs (circa 1940's). There are over 50 different types of Rh factors, but the most commonly known one is the D antigen (Rho[D]), which -if it is present- indicates that that person is Rh-positive; if the D antigen is absent, that person is Rh-negative.  In contrast to the ABO system, however, antibodies to Rh antigens aren't necessarily inherent to the person's blood, and can develop as an immune response after a blood transfusion, or during pregnancy.  At a mother's first antenatal screening, blood tests are taken in order to determine her blood type (A, B, AB or O) as well as her rhesus status (Rh-positive or Rh-negative).  If the mother has the Rhesus factor (which is a protein on the surface of her red blood cells) then she is said to be Rh-positive. If not, then she is Rh-negative.  80 - 85% of people are Rh-positive.  The Rhesus state only really begins to play a role during pregnancy if the mother is Rh-negative, the father is Rh-positive and the baby is also Rh-positive.  Rh (D) positive cells contain the D antigen, which can stimulate Rh (d) negative blood to produce harmful antibodies that can destroy red cells. The harmful antibody is called ‘anti-D’ antibody, and can be produced by a mother who is Rh-negative carrying a baby who is Rh-positive.  Rhesus incompatibility doesn’t cause any problems with a first pregnancy because (unlike the AB antibodies) the rhesus antibodies aren’t present in the mother’s blood, but can be induced by pregnancy with an Rh- positive baby.  In subsequent pregnancies, if the babies are Rh-positive, there may be a problem. The mother’s antibodies (which have now been induced) can / will cross over the placenta into the baby’s blood -causing a reaction.  This causes problems with the baby’s hemoglobin levels (the iron-carrying element in the red blood cells) which could then fall, causing anemia. Blood transfusion would then be necessary (see chart below) at birth and the babies could also be severely jaundiced. In most dioecious organisms, the sex of the organism is determined by differences in the presence/absence of a set of chromosomes, or the presence/absence of discrete chromosomes. In honeybees, for example, eggs are either fertilized -and become diploid females, or they are not fertilized -and become haploid males, drones. Humans have different sex chromosomes, X and Y. Males have X and Y; females have X and X. Again, the sex of the offspring is also determined by the sperm. If a sperm with an X chromosome reaches the egg, the resulting offspring will be female (XX). If a sperm with a Y chromosome reaches the egg, the resulting offspring will be male (XY). In the Fruit fly (or Drosophila melanogaster) chromosomes also have distinct X and Y chromosomes, wherein the male is XY and the female is XX. As a consequence, like humans, the male fruit flies are said to have a set of paired "autosomal" chromosomes and then one X and one Y chromosomal. They are, therefore said to be hemizygous. The X and Y chromosomes have different functions The gene that determines maleness in mammals was identified by studying people with chromosomal ploidy aberrations... as unlike most autosomal ploidy variations animals can handle some variation in the numbers of X and Y chromosomes. XY females often have a piece of the Y chromosome missing, whereas the XX males have a piece of a Y attached to the X. The fragment missing from the Y chromosome in XY females or that needs to be present on the X chromosome in XX males contains the maleness-determining gene. The gene was named SRY (for Sex-determining Region on the Y chromosome). The SRY gene codes for a functional protein involved in primary sex determination. A gene on the X chromosome called DAX1 produces an "anti-testes" factor. The SRY gene product in a male inhibits the gene DAX1, and consequently no "male-specific" inhibitor is made. Secondary sexual traits like breast development, body hair, and voice are also influenced by hormonal levels of key sex hormones -such as testosterone and estrogen. The presence of Sex chromosomes allows for a special type of genetic inheritance to be analyzed..... Sex-linked inheritance. In essence, while a female can be heterozygous for a particular gene that is present on the X chromosome, her male offspring will be hemizygous for that particular trait. If the allele on the X chromosome is recessive, while it may be "masked" in a heterozygous female it will always show through in her male offspring. Consequently it is relatively easy to trace an X-linked trait that has an overt phenotype. One such trait, which has become somewhat infamous among geneticists (especially in England because there are lots of data available with respect to lineage and heritable traits) is the passage of Hemophilia within the English royal family. On a less morbid note about another type of X-linked trait Red, Green Color blindness.... _true story_ While the X and Y chromosomes normally behave according to the laws of meiotic cell division (and thus according to Mendelian genetics) the ability to "visualize" the presence of each of the alleles that is located on either of the X- chromosomes of a mother (by observing the different phenotypes) challenge the ubiquity of Mendel's 2nd law, or in other words Mendel's 2nd Law DOES NOT ALWAYS APPLY Remember, that equate Mendel with meiosis we had to invoke the role of chiasmata occurring between two gene loci on adjacent chromatids in paired chromosomes during prophase I of meiosis. This CANNOT occur for X and Y chromosomes, but what about ALL the genes on the other autosomal chromosomes. Again, I glibly stated that, if the probability of a chiasma forming between two genes is "one" (i.e. a certainty), then the assortment of alleles would, in essence, be the same as if they were on separate chromosomes (i.e. random). But, what happens if there are no chiasmata formations? Then the genes on the same chromosome cannot assort randomly, which would be in marked contrast to Mendelian expectations. However, this phenomenon can and does happen. Such aberrations were first hypothesized to exist by Bateson and Punnett, who observed some curious "associations" of heritable traits. However, it was really verified by an American geneticist, Morgan (1909) who was working on chromosomally-linked genes that resided on the X chromosome of the fruit fly Drosophila melanogaster. Ch. 16 Vocab Transmission Genetics- The manner in which genetic differences among individuals are passed from generation to generation Trait- A characteristic of an individual Blending Inheritance- The now-discredited model in which heredity factors transmitted by the parents become intermingled in the offspring instead of retaining their individual genetic identities Hybridization- Interbreeding between two different varieties or species of an organism True Breeding- Describes a trait whose physical appearance in each successive generation is identical to that in the previous one F1generation- The first filial, or offspring, generation F generation- The second filial generation; the offspring of the F generation 2 1 P1generation- The parental generation in a series of crosses Reciprocal Cross- A cross in which the female and male parents are interchanged Dominant- The trait that appears in the heterozygous offspring of a cross between homozygous genotypes Recessive- The trait that fails to appear in heterozygous genotypes from a cross between the corresponding homozygous genotypes Alleles- The different forms of a gene, corresponding to different DNA sequences in each different form Genotype- The genetic makeup of a cell or organism; the particular combination of alleles present in an individual Phenotype- The expression of a physical, behavioral, or biochemical trait; an individual’s observable phenotypes include height, weight, eye color, and so forth Homozygous- Describes an individual who inherits an allele of the same type from each parent, or a genotype in which both alleles for a given gene are the same Gamete- A reproductive haploid cell resulting from meiotic cell division (in some species gametes are called spores). In many species, there are two types of gametes: eggs in females, sperm in males Segregate- Separate; applies to chromosomes or members of a gene pair moving into different gametes Principle of Segregation- The principle by which half the gametes receive one allele of a gene and half receive the other allele Zygote- The diploid fertilized egg cell formed by the fusion of two haploid gametes Heterozygous- Describes an individual who inherits different types of alleles from the parents, or genotypes in which the two alleles for a given gene are different Punnett Square- A worksheet in the form of a checkerboard used to predict the consequences of a random union of gametes Testcross- Any cross of an unknown genotype with a homozygous recessive genotype Incomplete Dominance- Describes inheritance in which the phenotype of the heterozygous genotype is intermediate between those of homozygous genotypes Probability- Among a very large number of observations, the expected proportion of observations that are of a specified type  Sometimes it becomes necessary to combine the probabilities of two or more possible outcomes of a cross, and in such cases either of two rules may be helpful. Addition Rule- The principle that the probability of either of two mutually exclusive outcomes occurring is given by the sum of their individual probabilities Multiplication Rule- The principle that the probability of two independent events occurring together is the product of their respective probabilities Principle of Independent Assortment- The principle that segregation of one set of alleles of a gene pair is independent of the segregation of another set of alleles of a different gene pair Linked- Describes genes that are sufficiently close together in the same chromosome that they do not assort independently Epistasis- Interaction between genes that modifies the phenotypic expression of genotypes Pedigree- A diagram of family history that summarizes the record of the ancestral relationships among individuals Multiple Alleles- Two or more different alleles of the same gene, occurring in a population of organisms Incomplete Penetrance- The phenomenon in which some individuals with a genotype corresponding to a trait do not show the phenotype, either because of environmental effects or because of interactions with other genes Variable Expressivity- The phenomenon in which a particular phenotype is expressed with a different degree of severity in different individuals Genetic Test- A method of identifying the genotype of an individual Ch. 17 Vocab. Sex Chromosome: One of the chromosomes associated with sex, in most animals denoted the X and Y chromosomes X chromosome- (in humans and other mammals) a sex chromosome, two of which are normally present in female cells (designated XX) and only one in male cells (designated XY) Y chromosome- (in humans and other mammals) a sex chromosome that is normally present only in male cells, which are designated XY Autosome- Any chromosome other than the sex chromosomes Wild Type- The most common allele, genotype, or phenotype present in a population; non-mutant Crisscross Inheritance: A pattern in which an X chromosome present in a male in one generation is transmitted to a female in the next generation, and in the generation after that can be transmitted back to a male Hemophilia- A trait characterized by excessive bleeding that results from a recessive mutation in a gene encoding a protein necessary for blood clotting Recombinant- An offspring with a different combination of alleles from that of either parent, resulting from one or more crossovers in prophase I of meiosis Non-Recombinants- Progeny in which the alleles are present in the same combination as that present in a parent Crossover- The physical breakage, exchange of parts, and reunion between non-sister chromatids Frequency of Recombination- The proportion of recombinant chromosomes among the total number of chromosomes observed Genetic Map- A diagram showing the relative positions of genes along a chromosome Map Unit- A unit of distance in a genetic map equal to the distance between genes resulting in 1% recombination Haplotype- A haploid genotype, as the particular combination of alleles present in any particular region of a chromosome Types of inheritance of cytoplasmic organelles  Maternal Inheritance- Organelles in the offspring cells derive from those in the mother.  Paternal Inheritance- Organelles in the offspring cells derive from those in the father.  Bi-parental Inheritance- Organelles in the offspring cells derive from those in both parents. Lectures 13 (cont.)-16 Again, I glibbly stated that, if the probability of a chiasma forming between two genes is "one" (i.e. a certainty), then the assortment of alleles would, in essence, be the same as if they were on separate chromosomes (i.e. random -as predicted by Mendel). Such aberrations were first hypothesized to exist by Bateson and Punnett, who observed some curious "associations" of heritable traits. However, it was really verified by an American geneticist, Morgan (1909) who was working on chromosomally-linked genes that resided on the X chromosome of the fruit fly Drosophila melanogaster. To me it is a curious irony that the vindication of Mendel/Sutton-Boveri's ideas that merged Mendelian genetics with cytological analysis of chromosomes, came about through research on sex-linked genes (that don't obey Mendel’s 2nd law) because Mendel's early experiments, were carefully chosen to be sex independent, i.e. he only worked with autosomal genetic traits. Thus, Morgan (1909) who was working on chromosomally-linked genes that resided on the X chromosome of the fruit fly Drosophila melanogaster also able to confirm that crossing over didn't ALWAYS occur in X chromosomal traits.... if the gene pairs were SO close together that crossing over COULD NOT HAPPEN. Morgan went one stage further and suggested that the frequency of such cross-over events (occurring between two genes that were physically very close together) was actually a function of the genetic distance between the two loci. He thus defined the unit of genetic distance as being: One crossover event/100 products of meiosis = one map unit or 1 centiMorgan (cM). Subsequently he and his student demonstrated that such linkage could be used to map the relative position of genes that are linked on the chromosome, as they determined that the probability of crossing over between two loci appeared to be additive. So, now we have analyzed two "variations" from the "predictable" Mendelian-type of inheritance, (a) Variations that arise as a consequence of "extensions to Medelian genetics, where the function of the genes in question interact to give different 2 phenotypes. (b) Variations that arise because of "chromosomal linkage" (thus defying Mendel's second law). There is a third form of non-Mendelian genetics..... (c) Cytoplasmic / Maternal Inheritance Mendelian genetics is the genetics of the nucleus, yet other cytoplasmic organelles can also carry genetic material. Mitochondria, chloroplasts, and other plastids possess a small amount of DNA. Humans have about 60,000 genes in the nucleus, and 37 genes in their mitochondria. Plastid genomes in plants are five times larger than those of mitochondria. Thus, any true definition of an organism's genome must include the total configuration of genetic material. Note: Mitochondria and plastids are passed on by the mother only, as the egg contains abundant cytoplasm and organelles. The mitochondria in sperm do not take part in gamete union. The hunt for the Mitochondrial Eve?? Is there a male equivalent to this purely female based inheritance? Well yes, but it's not cytoplasmic......... it is sex-linked... on the Y chromosome Playing with different types of crosses... Mendel not always right. Are the two types of location compatible? Yes.... Having now fully understood (?) all the major types of variations from the "normal" Medelian type genetic patterns of inheritance how might our newly found insight into Mendelian genetics have an impact upon our appreciation of evolution? Remember, while "....populations evolve and individuals do not", the gene pool of a population is the summation of all the individual genomes within that population. To rephrase the question, therefore, how might an understanding of Mendelian genetics (which addresses phenotypic expression of an individual's genes) allow us to understand phenotypic/genetic changes within a population? Genetic Variation within Populations To recap (in the light of recent lectures): For a population to evolve, its members must possess variation, which is the raw material on which agents of evolution act (genetic variation within a gene pool). We observe phenotypes in nature: i.e. the physical expressions of genes. A heritable trait is a characteristic of an organism that is at least partially influenced by the organism's genes (we cannot forget, however, the influence of environment on this expression). The genetic component that governs a given trait is called its genotype. A population evolves when individuals with different genotypes survive or reproduce at different rates. Genes have different forms called alleles. A single individual has only some of the alleles found in a population. The sum of all the alleles in a population is its gene pool, which contains the variation (different alleles) that produces the differing phenotypes, upon which agents of evolution act. Most populations are genetically variable. Natural populations possess genetic variation (a phenomenon which cannot always be expected for unnatural or artificially selected populations that have been manipulated by Man for reasons of his/her own). The reproductive contribution of a genotype or phenotype to subsequent generations relative to the contribution of other genotypes or phenotypes in the same population is called fitness. This "fitness" of any particular genotype is determined by the average rates of survival and reproduction of individuals within that population with that particular genotype; I.e. the relative reproductuctive contribution of a given genotype. For example, Man's highly selective preferences for certain edible crops have placed a selective pressure on the crops that are produced, giving rise to seemingly quite different and important crop plants. Artificial selection in laboratories that have analyzed genetic variation in Drosophila melanogaster also reveals genetic variation in these fruit flies. In Ecological terms a locally interbreeding group within a geographic population is called a Mendelian population. The relative proportions, or frequencies, of all alleles in this population are a measure of its population's genetic variation. Population Geneticists can estimate such allele frequencies for any given locus by measuring the numbers of alleles in a sample of individuals from within a population. Such measurements can be seen in terms of probability, which can range from 0 to 1, wherein the sum of all allele frequencies at any given locus = 1. The allelic frequency (p) for any given trait can be calculated by dividing the number of copies of that particular allele in a population by the sum of alleles in the population. According to Mendelian genetics; If only two alleles (A and a) are present for a given locus, and are found among the members of a diploid population, they may combine to form three different genotypes: AA, Aa, and aa. Thus: The Allelic frequencies can be calculated using simple mathematics with the following variables.  n AA = the number of individuals that are homozygous for the A allele (AA).  n Aa = the number of individuals that are heterozygous (Aa).  n aa = the number of individuals that are homozygous for the a allele (aa). Note that n AA + n Aa + n aa must always = N, the total number of individuals within the population. Now let's look at it from the perspective of each allele at a given locus, For the sake of discussion, let p = the frequency of allele A. q = the frequency of allele a. It is possible that the numbers of homozygous dominant and heterozygotes and homozygous recessives can change without changing the probability of finding individual alleles (p's and q's). What about an example of how such equations can be used to calculate the frequencies of allele "A" and "a" within a population. In essence, a population that is not changing genetically is said to be at Hardy–Weinberg equilibrium; in that the allelic and genotypic frequencies within a population that has reached this state do not change from generation to generation. To appreciate the importance of the HW equilibrium, five essential assumptions about the population must be made.  Mating is random.  Population size is very large.  There is no migration between populations.  Mutation can be ignored.  Natural selection does not affect the alleles under consideration. If the above conditions of the Hardy–Weinberg equilibrium are met, two consequences must follow. (a) The frequencies of alleles at a given locus will remain constant from generation to generation. (b) After one generation of random mating, the genotypic frequencies will not change. Restating the second result in the form of an equation that takes into account the allelic frequencies, produces the Hardy equation: 2 2 p + 2pq + q = 1. An example of the Hardy–Weinberg equation in use, and how it is derived from Mendelian first principles. Note that this example also shows that there are two ways to produce a heterozygote, hence the overall probability for obtaining a heterozygote is "2pq", not just "pq". So, why is the Hardy–Weinberg equilibrium important? Because it suggests that allelic frequencies remain the same from generation to generation unless some agent acts to change them. Thus, dominant alleles would not necessarily "dominate" the presence of the recessive allele unless either one had an effect upon any of the five criteria necessary to appreciate the HW equilibrium. It also illustrates the distribution of genotypes to expect for a given population at genetic equilibrium for any value p or q (which can be determined empirically). But the conditions for any maintenance of the equilibrium are far too stringent for any given natural population, so is it relevant to the real world? Yes. It is the equivalent of a "null hypothesis" to the scientific method. As such, it allows scientists to determine (a) whether evolutionary agents are operating and (b) the identity of the agents that might be operating to change the pattern away from the equilibrium.... Erin Brokovitch story Microevolution: Changes in the Genetic Structure of Populations "Evolutionary agents" cause changes in the allelic and genotypic frequencies within a population. Since the changes in the gene pool of a population constitute small-scale evolutionary changes, they are referred to as microevolution. We have discussed -to varying degrees- that some of the known evolutionary agents are mutation, gene flow, random genetic drift, non-random mating, and natural selection. As I'm sure you are already aware, mutations are changes in the genetic material, which can either be deleterious or beneficial to a population. While most of these mutations appear to be random (e.g. copying errors, as the DNA is synthesized), and are normally either harmful or neutral (i.e. they do not affect their bearers ability to survive, and or procreate), some mutations are actually beneficial. Whatever the direct consequence they provide for a heterogeneous population. Indeed, the origin of all genetic variation is heterogeneity in the germ-line cells (why do we not care about somatic cell variations?) Even though mutations are sufficient to create considerable genetic variation mutation rates, are relatively low; approximately one mutation per million loci is a typical frequency. Even though the very presence of mutations within a population means that one of the principle conditions that are necessary for the Hardy–Weinberg equilibrium to exist can never be met, the rate at which mutations arise at any particular locus is so low that the consequences of any neutral mutations would result in only very small deviations from Hardy–Weinberg expectations. If large deviations are found within a population, then either the mutation is selective, or it would be appropriate to dismiss mutation as the cause and look for evidence of other evolutionary agents. Such analyses have added important insights into how we can view evolutionary changes that have occurred over the ages, and appreciate that evolutionary rates can vary in two ways: slowly through "neutral" mutational changes to a gene pool and/or quite dramatically by some other changes in the assumptions that would normally hold a gene pool in some form of equilibrium. Hopefully helping to understand some of the different variables that have helped create evolutionary changes over evolutionary time and how the rates of change can differ for different types of living organisms. For example, it can detect potential "bottlenecks" in population development, as the frequency of alleles, under this circumstance would be severely reduced. The important highlights of Chemistry -from a Biologist's perspective Bonds between atoms / ions vary in strength; the strongest bonds are covalent bonds, which involve sharing electrons. Electrons shells and orbitals allow for bonds to be formed between and among different elements. Covalent bonds consist of shared pairs of electrons a covalent bond is the sharing of a pair of electrons between two atoms. In hydrogen molecules, H , 2 pair of electrons share a common orbital and spend equal amounts of time around each of the two nuclei. The balanced distance between the two nuclei in H is ~2.1 nm. Each covalent bond has a predictable length, angle, and direction. These features make it possible to predict the 3D structures of molecules. Sometimes more than one covalent bond is required to provide the appropriate "duet" or "octet" of electrons the gas ethylene, C 2 ,4has a double-bonded pair of carbon atoms. Nitrogen gas, N 2 the form of nitrogen found in the atmosphere, has a triple covalent bond (N: N). Moreover, electrons are not always shared equally between covalently bonded atoms. N 2 H 2 O 2 and other bonds between atoms of the same element share electrons equally because their nuclei are identical to each other. When a molecule has nuclei with different attractive forces, an electron spends most of its time around the nucleus with the greater attractive force for that electron. The attractive force that an atom exerts on electrons is called electronegativity (more specifically attraction force of an atom to bonding pairs of electrons). The degree of electronegativity is determined by the number of protons in an atom and the distance of its electrons from its nucleus. Oxygen has six electrons in its outermost shell and requires two more to fill it. When oxygen forms covalent bonds with atoms that have weaker electro negativities, such as carbon or hydrogen, the electrons are often shared unequally. With bonds involving hydrogen such unequal sharing of electrons causes a partial negative charge (symbolized d , – “delta negative”) around the more electronegative atom, and a partial positive charge (symbolized d , “delta+ positive”) around the less electronegative atom, resulting in a polar covalent bond. Molecules that exhibit these polar, covalent bonds are called polar molecules. Some molecules are so large that they are said to have polar regions and nonpolar regions. In biological molecules this polarity is best exhibited by hydrogen bonds: e.g. the d portion of a water molecule (the + area around the oxygen) has a weak attraction to the d portion of another water molecule, the area around the hydrogen. Each of these attractions is called a hydrogen bond. Hydrogen bonds differ from covalent bonds in one important way: Hydrogen bonds do not actually share electrons, but they can provide considerable strength, in an ordered form they provide the "glue" of life; holding DNA together. In a disorganized way they can change the very properties of molecules...e.g. keeping water as a liquid (at standard temperatures and pressure). Unlike the sharing—or even the unequal sharing—that characterizes covalent bonds, ionic bonds involve a complete transfer of one or more electrons. Ions are formed when an atom completely loses or gains electrons. Ions are always symbolized by + or – superscripts, designating which ion has lost or gained an electron. Positively charged ions are called cations: Na is an example. Negatively charged ions are called anions: Cl is an example. 2+ Calcium ion Ca is an example of an ion that has two more protons than electrons. The Ca 2+ion is a cation and is said to be divalent. The aluminum ion is Al . 3+ 2+ 3+ 2+ 3+ Iron can be either Fe (ferrous ion) or Fe (ferric ion). In solution Fe sometimes changes to Fe and vice versa. Cuprous ion is Cu , and cupric ion is Cu . 2+ Complex ions commonly occur in biological +ystems. These are groups2–f covalently bonded ato3– that together carry an electrical charge. Examples are NH 4 (ammonium ion), SO 4 (sulfate ion), and PO 4 (phosphate ion). Ionic bonds are formed by the attractions of opposite charges. The most obvious form of a mixture of ions is Table salt, which has chloride and sodium ions, which are held together by opposite charge attractions. These attractions are strong, but when introduced into water, the partial charges of the water molecules can easily interfere with the ionic bonds. For example, the figure below shows how water molecules cluster around cations and anions to "dissolve" table salt. As we suggested previously, water has a rather unique structure and special properties. It is the most common molecule (45 to 90%) in all organisms, and also participates in -or is the medium for- most of an organism’s chemical reactions. A water molecule is composed of one oxygen and two hydrogen atoms (H O). 2 It is an excellent solvent; it takes a lot of heat to change its temperature relative to its weight; it has high cohesion. Each molecule forms hydrogen bonds with four other molecules. These four hydrogen bonds actually increase the space water molecules take up in their solid state, so water expands when it freezes, and ice is less dense than liquid water. Ice is held in a crystalline structure by the orientation of water molecules’ hydrogen bonds. Because ice floats, it forms an insulating layer on lakes and helps keep them from freezing solid.....might be important if you are a fish, as this insulation protects such organisms in the cool, lower liquid layers from sub-freezing temperatures. As most biological substances dissolve in water, most biologists discuss "solutions" in which water is the "solvent".  Qualitative analysis is the study of substances dissolved in a solvent and their reactions.  Quantitative analysis measures the amounts of substances and solvents. Chemists are finicky about quantification.  Molecular formula: a compound depicted by its chemical symbols.  Molecular weight (or mass): the sum of all the atomic weights in a molecule. The molecular weight of H is 22 Mole: the amount of a substance in grams whose weight is equal to its molecular weight. One mole of H we2ghs 2 g. One mole of any given compound contains approximately 6.02 x 10 23 molecules of that compound (Avogadro's number). A 1 molar (1 M) solution is one mole of a compound dissolved (normally in water) to make one liter. One mole of sodium chloride (table salt) is the atomic weight of sodium (23.0) plus the atomic weight of chlorine (35.5), or 58.5(in grams). When 58.5 grams of sodium chloride are dissolved in some amount of water, and then additional water is added to create a final volume of a liter, the solution is said to be a 1 molar solution. Acids, Bases, and the pH Scale  Acids donate H ; bases accept H . + If a compound increases the H ion concentration when added to water, then the compound is acidic. + – If the reaction is complete, such as HCl --> H + Cl , it is a strong acid. Not all acids "dissolve" fully into their ionic forms in water. Acetic acid, for instance, does not completely react and is therefore called a weak acid. – If a compound increases the OH ion concentration when added to water, then the compound is basic. Just as with acids, there are strong and weak bases. Water is actually a very "weak" acid, and has a slight tendency to ionize (break apart) into H and OH . – This ionization is very important for living creatures and the chemical reactions they must perform. A strong base completely reacts: NaOH ---> Na + OH . – + A weak base, such as bicarbonate, does not completely react, and accepts H ions in several ways, one being the formation of weak carbonic acid. Reversible chemical reactions -in principle- can proceed in either direction, but the extent of reversibility may vary. + + —NH + 2 <---> —NH 3 A carboxyl group (—COOH) is common in a number of biological compounds. As we will discuss further, carboxyl groups also function as both an acid and as a base, because —COOH <--> — – + COO +H . pH is the measure of hydrogen ion concentration, and was first introduced in 1909, Soren Sorensen, a Danish biochemist, who proposed what is now known as the pH scale. Sorensen developed a simple equation to express the hydronium ion concentrations logarithmically. The pH of a solution is -1 times the logarithm (of the base 10) of the hydronium ion concentration (expressed in moles per liter). The equation for the pH of a solution is: pH = - log [H O ] 3 + The pH scale indicates the strength of a solution of an acid or base. The scale is arrayed as a set of values 1 through 14. These values may be measured by electronic instruments. The pH value is defined as the negative logarithm of the hydrogen ion concentration in moles per liter (molar concentration). A pH 7 means that the concentrat+on of hydrogen ions (or more specifically –7e concentration of hydro (xo) nium ions (which are simply H attached to a water molecule) is [1 x 10 ]. Even strongly acidic solutions have mostly water molecules and not ions. A solution with pH 1 has one H for every 556 water molecules A solution at pH 1 can have a powerfully corrosive effect on a variety of materials including metals, polysaccharides, proteins, nucleic acids, and bone. Buffers minimize pH change A Buffer is a mixture of a weak acid and its corresponding base. Because buffers can react with both added bases and acids, they make the overall solution more resistant to changes in. Different buffers transition to and from ionic forms at their particular characteristic pH ranges. Buffers are common in biology and extremely important in the regulation of the internal environments of organisms. Many important biological buffers transition around pH 7, which keeps the pH near neutral. Buffers illustrate the law of mass action: The addition of components to one side of a reaction drives the reaction in the direction that uses that component. As an acid or a base is added to a solution, the buffer will change form, transitioning between ionic and non-ionic bonds The Properties of Molecules Molecules range in size and molecular weight from the very smallest, H ,2to the relatively massive, such as the DNA molecule that makes up the length of a chromosome and contains millions of atoms. Carbon-containing molecules are called "organic molecules", most of which contain hydrogen and oxygen, and many contain nitrogen and phosphorus. Nitrogen, oxygen, and carbon are also all found in the air.... and can even be found on Mars Hydrogen and oxygen are found in water. All molecules have three-dimensional shapes. CH is 4etrahedral. Properties of Water (H O) ... somewhat unique... 2 Larger molecules have potentially more complex shapes that are the result of a combination of the atoms present and the ways they are linked together. Some molecules are long and ropelike; some are ball-shaped; any which way, shape influences the behavior and function of molecules. Indeed, Chemists use the characteristics of composition, structure, reactivity, and solubility to help classify molecules. Macromolecules: Giant Polymers There are four major types of biological macromolecules: proteins, carbohydrates, lipids (?), and nucleic acids. These macromolecules are made the same way in all living things, and they are present in all organisms in roughly the same proportions. Macromolecules are essentially giant polymers, which are formed by covalent linkages of smaller units called monomers. Molecules with molecular weights greater than 1,000 Daltons (atomic mass units) are usually classified as "macromolecules". Some of the many roles of macromolecules include:  Energy source  Energy storage  Structural support  Catalysis  Transport  Protection and defense  Regulation of metabolic activities  Maintenance of homeostasis  Means for movement, growth, and development  Heredity The diverse functions of macromolecules are invariably related to their shape and the chemical properties of their monomers. Carbohydrates (sugars) link to form cellulose (the wood fiber of trees), or starches for storing energy. Some types of macromolecules contain many different kinds of monomers, such as proteins, which are formed from long, chains of amino acids that can contract and cause movement Some contain the same simple units, repeated many times. Condensation Reactions Macromolecules are made from smaller monomers by the removal of water. This is called a condensation (loss of water) reaction. Energy must be added to make or break a polymer. The reverse reaction, breaking polymers back into monomers, is a hydrolysis, which involves the addition of water; reacting with the bond that links the units together. Most hydrolytic reactions in biological systems require some form of enzymatic input, although a strong acid or base solution can hydrolyze many types of polymers. For example; stomach acid hydrolyzes some of the linkages found in the polymers we eat. Proteins: Polymers of Amino Acids Proteins are molecules with diverse structure and function. Proteins have important roles including: Structural support Protection Catalysis Transport Defense Regulation Movement Enzymes increase the rates of chemical reactions in cells. This function is known as catalysis. These enzymes are highly specific; in general, each enzyme catalyzes only one chemical reaction. Proteins range in size from a few amino acids to one or more thousand. Some proteins are composed of a single chain of amino acids, called a polypeptide. Other proteins, as we have seen, have more than one polypeptide chain Folding is crucial to the function of most protein, a factor that is largely influenced by the sequence of its component amino acids. Each different type of protein has a characteristic amino acid composition and order. Some proteins have additional, non-amino acid chemical structures called prosthetic groups, which can include carbohydrates, lipids, phosphate groups, ion-containing haeme groups, metal ions, and others. Even with or without these additions, proteins are composed of amino acids. + The amino group is the nitrogen-co-taining part (NH )3 the acid is a carboxyl group (COO ) Differences in amino acids come from the side chains, or the R groups, found attached to the same carbon as the amino group. The 20 common amino acids vary widely in properties. All but one have four different groups that are attached to the a-carbon. Hydrogen atom, an amino group, and a carboxyl group are bonded to the alpha-carbon of all the different amino acids. Amino acids can be classified based on the characteristics of their R groups. Five of the 20 amino acids form ions in solution depending on pH. Four of the 20 have polar side chains. Eight have nonpolar R groups. Three amino acids, cysteine, glycine, and proline, have some special properties. Cysteine has a terminal disulfide (—S—S—). Proteins are synthesized by condensation reactions between the amino group of one amino acid and the carboxyl group of another. This forms a peptide linkage. The first amino acid of a peptide is called the N-terminus amino acid because the amino group is free, or unbound. The last is called the C-terminus amino acid and has a free carboxyl group. The C–N peptide linkage forms a partial double bond, which is a single covalent and polar attraction. This bond limits folding and restricts the ability of the adjacent atoms to rotate. Within the central axis of the protein, there is an asymmetry of charge favoring a tendency toward hydrogen bonding. (Oxygen is partially negative and nitrogen is slightly positive.) The primary structure of the protein is its amino acid sequence. As discussed previously, there are four levels of protein structure: primary, secondary, tertiary, and quaternary. The precise sequence of amino acids is called its primary structure. The peptide backbone is repeating units of atoms: In the three-letter system, methionine is Met; in the one-letter system, it is M, but while Ala is A, Asp is D. You just eventually need to learn them. Given the 20 potential building blocks there are potentially an enormous number of different proteins, although not all variations are biologically functional. Secondary structure is the shape regions of the peptide take on as a folded polymer. This shape is influenced primarily by the amino acid sequence (the primary structure). There are two common secondary structures: one is the alpha-helix, which is a right-handed coil. Note that in this structure, the peptide backbone takes on the helical shape due to hydrogen bonds with its "R groups" pointing away from the peptide backbone. Insoluble fibrous structural proteins tend to have a-helical secondary structures. There are other structures....but not for this course. Tertiary structure is the three-dimensional shape of the completed polypeptide. The quaternary structure of a protein consists of subunits some proteins are composed of subunits, which are separate peptide chains that associate together to create the functional protein. Quaternary structure resul


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