Class notes 11.23 - 12.4
Class notes 11.23 - 12.4 BIO 1500
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This 7 page Class Notes was uploaded by Diane Notetaker on Monday December 7, 2015. The Class Notes belongs to BIO 1500 at Wayne State University taught by Daniel M. Kashian in Summer 2015. Since its upload, it has received 28 views. For similar materials see Basic Life Diversity in Biology at Wayne State University.
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November 23, 2015 Think about evolutionary history and the development of complexity when studying for the exam Mammalian Kidney - If you take a slice out of kidney you see they have a series of nephrons and vessels that drain into collecting ducts that follow into the ureter, then down to the bladder and out - In each kidney are many loops of henle which go into the distal convoluted tubule in the cortex, which then drains into a collecting duct, which drains into the renal pelvis - The major function of the kidney is the elimination of toxins; this also includes maintenance of osmotic balance and ion concentrations - How does the kidney work? Though filtration within the glomerulus; larger things remain in blood, small stuff passes through; then some important solutes are removed from the renal tube and reabsorbed into blood; the waste is moved into urine. - From the glomerulus, fluid moves into the tubule and then into a series of segments (proximal tubule, loop of henle, distal tubule, and collecting ducts) - Different parts of the tubule have different functions; NaCl is removed in two places (through active transport in the proximal tubule; and through active extrusion from the loop of Henle, which is impermeable to water) - Water only leaves the descending portion of the Henle loop (see diagram); this creates an osmotic gradient from the outer to inner part of kidney providing efficient extraction of desired solutes and water - Again, the countercurrent system occurs – fluid is flowing in opposite directions in different parts of the loop; this is what allows the kidney to create very concentrated urine. Osmoregulation under hormonal control - Remember, these systems don’t act alone; they always act in conjunction with another - Ex. Antidiuretic hormone (ADH) is produced by the hypothalamus; this is released with reduced osmolarity of blood leading to a sensation of thirst and a reabsorption of water by the kidney (negative feedback loops to regulate ion concentrations) Where do we go from here? - Let’s think about how individuals within a population differ and how these differences lead to the existence of different species. - These questions need to be considered in the context of ancestry and descent; how are traits transmitted from one generation to the next? Gregor Mendel – Understanding transmission of genetic information - Mid 1800’s conducted experiments on pea plants to determine how traits are inherited; identified “factors” (now known as genes) that were responsible for predictable transmission of traits - Before Mendel, how did people thing inheritance worked? “Spermists” – traits were inherited from the father, the mother just carried the baby “Blenders” – traits in offspring are blended between parents, like paint Mendel – information is inherited as discrete particles; each parents gives one unit of information (exactly the same amounts each) - Mendel chose pea plants because they are easy to grow, reproduction would be controlled (have both male & female flowers), and demonstrated a wide range of characteristics (height, color, pod shapes, etc.) - What is true breeding? Offspring always the same as parents; there is no variation - Cross 1: crossed plants with smooth seeds and wrinkled seeds; spermists would think seeds would look like male parents, blenders would think seeds to be intermediate, Mendelians would think seeds should look like both parents The first generation yielded all smooth seeds. How does this fit our expectations? It didn’t matter whether the father was wrinkly or smooth, the seeds were not an intermediate form, and one trait didn’t show up. - Cross 2: took first generation and crossed with themselves Second generation yielded both round and wrinkled seeds - How do we explain these results? Each individual has two units of information for a specific traits; each parent passes on one of these units to their offspring - How does this fit with meiosis? Mendel didn’t know about this, but each trait is on one of the two chromosomes; they are sorted, split, and two of the four haploid gametes have each trait; traits are passed on equally to gametes (50/50 proportion) allele = different forms of a gene (S vs s) genotype = specific combinations of alleles in an individual (SS, Ss, ss) phenotype = observed trait of an individual (smooth vs. wrinkled appearance) phenotype = genotype + environment homozygous = two of the same kinds of alleles; “true breeding” heterozygous = genotype that has two different alleles Dominant and recessive are terms to describe whether a given allele is expressed or masked in the phenotype Incomplete dominance = a cross between organisms with two different phenotypes produces an offspring with a third phenotype that is a blending of the parental traits (ex. white and red snapdragon flower parents creating a pink baby) Codominance = a cross between organisms with two different phenotypes producing an offspring with a third phenotype in which both parental traits appear together (ex. white & red flow parents create a red-white striped baby) Punnett squares! Aa x Aa! - takes the gametes from two parents and combines them randomly in a probability matrix Gametes A a from: A AA Aa a Aa aa - Probability of getting an A or a is 50%; and are independent of each other - What’s the probability of the offspring getting A from mom? 50% - What’s the probability of the offspring getting A from mom AND dad? 25% = 0.5 x 0.5 - What’s the probability of the offspring getting Aa? 50% - Mendel’s first law (Law of Segregation) = when any individual produces gametes, the alleles separate, so that each gamete receives only one member of the pair of alleles Transmission of alleles to progeny is like tossing a fair coin; it’s completely independent of the other gametes within the individual or of either parent. - Now, looking back to the pea plants – the original parents were both homozygous, thus all offspring had to be heterozygous (Ss), meaning all had to be smooth (the dominant trait). - But the second generation was breeding heterozygous, so expected phenotypic ratios were 75% smooth (SS or Ss) and 25% wrinkled (ss), and they were! How can we tell what alleles an individual carries? - A recessive phenotype will always be homozygous, but that’s not true for a dominant phenotype. - How can tell a homozygous dominant apart from a heterozygous dominant trait? You can find out by corssing dominant type individuals with a recessive. - Test cross: If male is heterozygous (Ss) and female is homozygous (ss) we expect half the offspring to be smooth and half to be wrinkled. - Mendel tested a bunch of different traits for inheritance and dominance. - Most all traits followed the 3:1 ratio for recessive-dominant genes - Do Mendel’s law apply to humans? Yes they do! This is important for tracking genetic diseases. November 30, 2015 - Sex as a phenotypes: XX & XY chromosomes sorting in a Mendelian manner; 50/50 probability to be male or female Thinking about multiple characters Example 1 - Mendel crossed plants that were yellow-smooth & green-wrinkled; characters were seed color & seed shape - In the F1 generation, all offspring were yellow-smooth; meaning yellow & smooth traits were both dominant; these offspring are heterozygous (could be composed of SY, Sy, sY, sy) - The F2 generation produces smooth-yellow, smooth-green, wrinkled-yellow, wrinkled-green - What’s the probability of the gametes producing SY? 25% Because p(smooth) x p(yellow) = .25 - There are 16 gamete possibilities for the F2 offspring Example 2 - Now let’s cross 2 peas from the F1 generation. That’s a dihybrid cross = SsYy x SsYy; the F1 gametes can produce 4 different gamete types SY, Sy, sY sy - The F2 generation produces individuals that may have the same phenotype, but not the same genotype because of dominant-recessive traits - We’re witnessing independent assortment here – random assortment of genes at one locus independent of those on another locus. - *Refer to the table in lecture slides: smooth-wrinkled = 3:1 ratio, yellow-green = 3:1 ratio Why does this happen? - The S s Y y genes are on different chromosomes during meiosis; they do not line up with each other. How they sort is totally by chance. It’s just how the cookie crumbles. - Remember, non-homologous chromosomes line up independently in Meiosis 1 - This is the Law of Independent Assortment, brought to you by Mendel. - What is the probability of having double heterozygous offspring when crossing SsYy x SsYy? - Answer: The product of probabilities from the independent characters. 4:16 - You can also do back crossing! - Law of Segregation = individuals have two hereditary alleles for any given trait; these homologous alleles separate from each other during gamete formation (it’s a physical process – they are sorting independently) - These laws only apply for multiple genes on non-homologous chromosomes In conclusion Monohybrid cross (Aa x Aa) - There is one dominant trait - Genotypic ratio = 1Aa : 2Aa : 1 aa - Phenotypic ratio = 3 dominant : 1 recessive Dihybrid cross (AaBb x AaBb) - There are two dominant traits - Genotypic ratio = 1AABB : 1Aabb : 2AABb : 2AaBB : 4AaBb : 2Aabb : 2aaBb : 1aaBB : 1 aabb (9 in total) - Phenotypic ratio = 9 dom-dom : 3 dom A – recs b : 3 recs a- dom B : 1 resc-resc (4 in total) - Dominance is hiding some of the genotypes. They’re still around, and could pop up later. - Incomplete dominance (i.e. crossing RR red flowers and rr white flowers to produce pink flowers) - Produces 3 phenotypes, but the genotypic ratio is still also 3 because dominance doesn’t play a role. Do these things apply to humans? Blood! - An enzyme (transferase) mediates production of specific modified glycoproteins that are placed on the surface of blood cells; there are two different alleles at the enzyme locus – allele A yields protein A, allele B yields protein B - Glycoproteins acts as antigens and the body will react if a blood type enters that is not its own; anti-A will react with blood type A; anti-B will react with blood type B; AB is a co-dominant trait; O doesn’t have glycoprotein - If you’re blood type A, your body produces anti-B and vice-versa - There are three alleles in this system: A, B and O - What is the gene locus we’re talking about? The transferase - How many genotypes are there? AA, AO, AB, BB, BO, OO (6 in total) - How many phenotypes are there? A, B, AB, O (4 in total) There is both dominance and co-dominance. (A dom over O, B dom over O, A & B co-dominant together) How are genotypes translated into phenotypes? - DNA is replicated, then transcribed into RNA which is then translated into protein (amino acids). Within these processes is where problems can arise – mutations and independent assortment yield variation. - replication = process by with DNA is copied - transcription = process by which information in DNA is transferred into messenger RNA (mRNA) - translation = process by which information in mRNA is utilized to create protein - Proteins interact to form functional structures which themselves interact to make up organisms - Mutation = an inherited change along a very narrow portion of nucleic acid sequence - In DNA, A pairs with T, C pairs with G. The order of nucleotides matter because each sequence of 3 codes for a specific protein. There are 20 amino acids, but 64 triplets. There is redundancy in the code. How do mutations happen? - They can be spontaneous or be induced by environmental factors. - Micromutations can be synonymous (no change in the protein that’s coded), missense (coded protein is changed), nonsense (codes for a STOP and the rest of the translation doesn’t take place), frameshift (inserts a base, and shifts the whole sequence over one) - Which has the greatest impact on the phenotype? Nonsense or Frameshift - Macromutation = deletion or duplication of whole chunks of chromosomes; inversions flip flop sequences; or reciprocal translation where different genes are being encoded - Transcription: mRNA that is generated in the nucleus, must be transported to cytoplasm where ribosomes await - Proteins must then be processed so they can be folded into appropriate functional structures (sliced, sugar added, phosphate added) - There are many different stages where things could go wrong! These all can have impacts on the phenotype - Hemoglobin is a tetramer w/4 subunits (2 copies of A monomer, 2 copies of B monomer) - Is it possible for an organism to have genetically identical hemoglobin, but be phenotypically different? Yes. December 2, 2015 What is sickle cell anemia? It’ a disease of the red blood cells, usually found in people of African descent - sickle-shaped cells interrupt blood flow by blocking smaller capillaries; tissues without blood are damaged and cause pain - sickle cells have different shapes because of a difference in a single amino acid in the hemoglobin B gene (AA is normal, AS is normal & sickled, SS is sickled); sickle cell is co-dominant at level of hemoglobin - People with AS genotypes have enough functional red blood cells that they do not suffer many ill-efects (unless when in low-oxygen environments because of the increased need for normal cells); A allele seems to be dominant (i.e. normal phenotype) - Remember, hemoglobin holds 4 oxygen molecules to transport throughout body, but a change in one amino acid can interrupt red blood cell shape. - Normal cells vs. Sickle cells: Normal cells perform better; they are soft, easily flow through blood, and live longer. Sickle cells are hard, get stuck easily, and die early. - In central Africa, sickle cell anemia is more common, but so also is malaria; malaria is a parasite that rides along on red blood cells - People w/ sickle cell anemia (SS) often die before adulthood, but are malaria resistant; people that have normal RBC (AA) are susceptible to malaria; heterozygote carriers (AS) are also resistant to malaria - The fitness of AA, AS, and SS allele types change depending on environment! They are phenotypically different in regards to this aspect of life. pleiotropy = a single gene has many phenotypic effects; the phenotypic effect (dominance) of a gene depends on which level we’re observing Are all negative genetic diseases recessive? - No, negative mutations don’t have to be recessive - Ex. Huntington’s disease is a lethal genetic disease that is dominant; it is retained in populations because it does not appear until later in life, after reproductive age – carriers are able to pass on genetic info before they die. Do all mutations have negative effects? - No, synonymous mutations are neutral. They cause no change in the phenotype. - The impact of a mutation will depend on the context; depends where it’s being expressed - Some mutations can be positive if it provides for better fitness in the given environment monogenic trait = simple trait; determined by a single gene locus - an individual can carry at most two different alleles (one on each member of a homologous pair of chromosomes) - Most of Mendel’s experiments dealt with monogenic traits polygenic trait = complex trait; determined by multiple gene loci - an individual’s phenotype is determine by numerous alleles on several different chromosomes discrete traits = either/or traits (i.e. you have sickle cell anemia or you don’t) continuous traits = traits that do not fall into distinct categories but instead are continuously distributed (i.e. height of a person); continuous distribution is an indication of polygenic inheritance - Ex. For skin color, there are three genes at work; some add melanin, some do not (melanin provides color); a combination of the 3 genes can yield 7 possible phenotypes with an 8 x 8 Punnett square (each gene occurs at a 1/8 probability) What else contributes to phenotype? Environmental factors! - Laying out in the sun can change your color; oak leaves growing in the shade can be less lobed - Cichilids with different diets will have different morphologies; soft food yields a papilliform pharyngeal, hard food yields a molariform pharyngeal plate) - Looking at something like height, you want to think about both the average as well as the spread; the spread tells us about how much variation there is within a population; variation is key for evolution! - Phenotypic variance = genetic variance + environmental variance - PKU (phenylkeptonuria) is a childhood disease – pp toxin builds up in the body causing brain damage, small head size, light skin, and poor thyroid function - Within the utero the baby is protected by the mother’s processing of pp; newborns are checked for PKU and can then avoid high-toxin diets. - By modifying the environment, we can alleviate the impacts of certain genetic diseases Hardy-Weinberg & Genetics & Populations - Alleles at a locus segregate randomly relative to each other (segregation) - Alleles for different traits on non-homologous chromosomes segregate randomly relative to each other (independent assortment) - On the individual level gametes are produced at a certain frequency; on the population level gene frequencies can change as well. - Mendel’s Law of Segregation = for each pair of alleles, there is a 50% change of a specific allele ending up in a gamete - If mating is random, the frequency with which individuals mate (and thus gametes combine to form offspring) is also a matter of probability The proportion of Red (RR) & White (WW) alleles in a population: p(red alleles) = [2(#RR) + #RW] / 2(total # individuals in population) p(white alleles) = [2(#WW) = #RW] / 2(total # individuals in population) - You multiple #RR and #WW by 2 because the homozygote is contributing 2 genes to the gene pool. - p(any allele) = total # of alleles / total # of individuals - pink is not an allele, it is a genotype (R allele + W allele = RW pink genotype) *Follow the calculations in the lecture slides - segregation of the alleles (R and W) and random mating means that the probability of different genotypes in the next generation is solely determined by allele frequencies - Hardy-Weinburg Equilibrium p^2 + 2pq + q^2 = 1 - parental genotypes dump all their genes into a big gene pool, the probability of getting a certain genotype in an offspring population is determined by the allele frequencies of the parents - If there are no disturbances in the population, allele and genotype frequencies will remain constant through time. - But disturbances HAPPEN. They include finite population size, mutations, selection, non-random mating. So, this must mean that in real life, allele and genotype frequencies will NOT remain constant through time. - Evolution = the change in allele frequency over time - The Hardy-Weinberg Equilibrium is a null model; populations following this model do NOT evolve; any occurrence that causes the model to be untrue is evidence that evolution is occurring. It is a “constant” in which to test the theory of evolution. December 4, 2015 Populations & Allele Frequencies - Remember, populations have their own frequencies of alleles & genotypes. * Follow frequency calculations in lecture slides. - What’s the probability that a male in this population is going to transport a red allele? Answer = the frequency of red alleles. - How can you tell if one allele is dominant over the other? Look at the heterozygote – what homozygous phenotype is similar to the heterozygote? (i.e. AS can look like AA or SS; if it looks like A, then A is dominant) - Why is the change of allele frequencies of a population important? Because evolution occurs through the accumulation of genetic differences over time, and biodiversity is generated through the process of evolution - Natural selection is operating on phenotypes; this is because the phenotype is what is visible and exposed to the environment. Environment drives selection. - Remember however, that the genotype is what transmits and contains the information for the phenotype. This creates a very interesting dynamic. - Natural selection is a deterministic process; we can exactly predict its outcome – it is NOT random - Allele frequencies follow direction from the frequency of the previous generation and from fitness (measure of survivorship) – genotypes with greater fitness leave more offspring and contribute more to the next gene pool Basic types of Selection a. Directional – one of the homozygotes (and perhaps the heterozygote) has the highest survivorship b. Balancing – heterozygote has the highest survivorship c. Disruptive – heterozygote has the lowest survivorship Ex. Proportional survival of genotypes: AA=1, Aa = 1, aa = 0.5 - A is the dominant over a (because Aa survives like AA does) - What is the impact of allele frequency? Population will trend towards a higher frequency of A over time because a does not have as good of survivorship, it will eventually be weeded out.