PCB 3063 - Lecture notes All of them PDF

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This is from Karen McGinnis' class. She does not post power points, so these are all the notes from her power points. These are pretty detailed notes and have some good drawn diagrams. ...

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1/9 Ch. 1 Tuesday, January 9, 2018

12:31 PM

• Genes affect our susceptibility to many diseases and disorders. • Green revolution in the 1960s was due to using genetics to select for more successful plant crops to increase crop yield. ○ Norman Borlaug won the Nobel peace prize for being the "Father of the Green Revolution". • Genes are important in biotechnology and medicine. ○ Ex. Insulin being able to be made through bacterial growth instead of organic synthesis. • Genes are important in development.

• A genome is a complete set of genetic instructions for any organism. ○ Either RNA or DNA • Coding system for genomic information is very similar among organisms. ○ Implications of this? • Transmission genetics ○ How traits are passed from one generation to the next. Looks at ratios of characteristics between individuals in families • Molecular genetics ○ Focuses on properties of the gene and how the gene is utilized. Focuses on the biochemistry of the gene (transcription/translation) • Population genetics ○ The distribution of alleles in a population. ▪ Won't be covered in this class. • Model genetic organisms are organisms with characteristics that make them useful for genetic analysis. ○ Short generation time ○ Production of numerous progeny ○ The ability to be reared in a laboratory environment. • Six have been the most intensively studied genetically. ○ Drosphila melanogaster (fruit fly) ○ E coli (bacterium) ○ C elegans (nematode) ○ Arabidopsis thaliana (thale-cress plant) ○ Mus musculus (house mouse) ○ Saccharomyces cerevisiae (baker's yeast) • The zebrafish model organism is good for studying different pigmentation in skin in humans because they are related to how this variation occurs in humans. • Humans have been using genetics for thousands of years: 1. 10k-12k years ago: domestication of plants and animals 2. Ancient Jewish Writing: understanding of genetics of hemophilia 3. Ancient Greeks: theories of inheritance. • Table 1.1 in textbook displays early concepts of heredity. • Important Theories: ○ Germ-plasm Theory: All cells contain a complete set of genetic information (Weismann). ○ Cell Theory: All life is composed of and cells arise only form other cells (Schleiden and Schwann) ○ Mendelian Inheritance: Traits are inherited according to specific principles proposed by Mendel. ○ Chromosome organization: chromosome -> DNA wrapped around protein histones -> DNA ○ Fundamental Concepts in Genetics: ▪ Eukaryotic vs prokaryotic ▪ Genes are the fundamental unit of heredity ▪ Genes come in multiple forms called alleles ▪ Genes confer phenotypes ▪ Genetic information is carried in DNA and RNA ▪ Genes are located on chromosomes. ▪ Chromosomes separate through mitosis

▪ DNA to RNA to Protein

1/11 Ch. 2 Thursday, January 11, 2018

12:20 PM

• Prokaryote ○ Eubacterium ○ Archaean • Prokaryotes have a cell wall, plasma membrane, ribosomes, and DNA. • Eukaryotes ○ Plant Cell ○ Animal cell • Eukaryotes have membrane organelles and nucleus unlike prokaryotes. The plant cell also has a chloroplast, vacuole, and ce wall. • Mitochondria and Chloroplasts have their own DNA. ○ Evidence for endosymbiosis theory • Figure 2.1 part 3 goes over prokaryotic and eukaryotic differentiating factors.

• Prokaryotes ○ Unicellular, no membrane bound organelles. ○ Prokaryotic DNA does not exist in the highly ordered and packaged arrangement. ○ Include eubacteria and archaea. • Eukaryotes ○ Both unicellular and multicellular with membrane-bound organelles. ○ Genetic material is surrounded in a nuclear envelope to form a nucleus. ○ DNA is closely associated with histones to form tightly packaged chromosomes. • Chromatin consists of the DNA and the organizational proteins together. • For most of the cell cycle, chromosomes are not condensed, and are considered chromatin. • Viruses ○ Neither prokaryotic nor eukaryotic ○ Outer protein coat surrounding nucleic acid ○ They are acellular because they are only an outer protein coat around a nucleic acid (either DNA or RNA) • Prokaryotic Cell Reproduction ○ Origin of Replication ○ High rate of replication ▪ Will divide as fast as they can dependent on the available resources for the cells.

• Eukaryotes - mitosis in diploid organisms ○ Will also talk about mitosis in haploid organisms ○ In humans, we have 22 somatic chromosomes and 1 sex chromosome (X/Y) ▪ In diploid, there will be two of each chromosome. In haploid there will only be one of each chromosome. ○ Diploid vs haploid is something exclusive to eukaryotes. • Eukaryotic Cell Reproduction ○ Eukaryotic chromosomes: ▪ Homologous pairs ▪ Chromosome structure ▪ The cell cycle ▪ Genetic consequences of the cell cycle ○ Eukaryotes do not divide as rapidly as possible by prokaryotes, cell division is directed by the cell-cycle. • A karyotype is an image of all of the chromosomes from an individual. They are in mitotic chromosome form. • A diploid organisms has two sets up chromosomes organized as homologous pairs. ○ Leads to alleles ○ These two versions of a gene encode a trait such as hair color.

• Chromosomes are typically have one or two chromatids in eukaryotes. • Loci or Locus: the location on chromosome where gene or other feature resides.

• When a gene is on the smaller side of the chromosome divided by the centromere, it is called 'p'. And genes on the larger part are called 'q'. ○ Ex. BRCA1 resides on 17q21.31 ▪ The breast cancer gene ▪ Some alleles of this gene has missing genetic information, which leads to the fact that there could be a change to an organism. • Sister chromatids are replicates of an another - will have same allele composition. • Centromere placement:

submetacentric

acrocentric telocentric metacentric

• During interphase Figure 2.8 of the cell cycle ○ The DNA is in chromatin. ○ When the cell is doing its normal function (metabolism) and growing. ○ To many highly differentiated/specialized cells like nerve cells, will for the most part stay in G0 until they go through apoptosis. ○ Grows then goes through G1/S checkpoint and if passes, goes to S phase to replicate DNA. ○ After replication, goes through G2 to grow some more until the G2/M checkpoint which decides if it can go into mitosis. • M phase: nuclear and cell division • Interphase: metabolism and cell growth. • M phase: ○ Mitosis: separation of sister chromatids ▪ Prophase - chromatin condense into chromatids ▪ Prometaphase - nuclear membrane breaks down, spindle microtubules attach to chromatids. ▪ Metaphase - chromosomes are lined up at the metaphase plate ▪ Anaphase - sister chromatids separate and moved towards opposite poles. ▪ Telophase - chromosomes arrive at spindle poles. Nuclear membrane reforms. ○ Cytokinesis: separation of cytoplasm

• Genetic Consequences of the Mitotic Cell Cycle

○ Producing two cells that are genetically identical to each other and with the cell that gave rise to them. ○ Newly formed cells contain full complement of chromosomes. ○ Each newly formed cell contains approximately half the cytoplasm and organelle content of the original parental cell. • Table 2.1 lays out features of the cell cycle. • Figure 2.10 is a good figure for studying. Exercise: 4

4

4

4

4

4

4

4

4->8

8

8

8

8->4

4

1/16 Ch. 2 Tuesday, January 16, 2018

12:31 PM

• Meiosis: the production of haploid gametes or spores. ○ In fungi, meiosis makes spores, and another cell division (mitosis) creates gametes. ○ A haploid cell cannot go through meiosis. ○ The difference between spores and gametes is spores undergoes more differentiation to become gametes, and gamete fuse to fertilize. • Fertilization: the fusion of haploid gametes. • Genetic Variation: consequences of meiosis. • Meiosis: ○ Interphase: DNA synthesis and chromosome replication phase. ○ Meiosis I: separation of homologous chromosome pairs, and reduction of the chromosome number by half. Known as reductional division. ▪ Goes from diploid to haploid. ○ Meiosis II: separation of sister chromatids, also known as equational division. • Interkinesis: the pause between meiosis I and meiosis II. ○ Is not interphase because no synthesis occurs. ○ May return to chromatin at this point. • • • •

Sources of genetic variation in Meiosis. Four cells are produced from each original cell. Chromosome number in each new cell is reduced by half. The new cells are haploid. Newly formed cells from meiosis are genetically different from one another and from the parental cell. ○ Possible gamete combinations (not considering crossing over) is indicated by 2n • Separation of Sister Chromatids and Homologous Chromosomes ○ Cohesion: a protein that holds sister chromatids together and is key to the behavior of chromosomes in mitosis and meiosis. • Gametogenesis Male (spermatogenesis)

Female (oogenesis)

Spermatogium (2n)

Oogonium (2n)

Primary spermatocyte (2n)

Primary oocyte (2n)

• Secondary spermatocytes (n) Secondary oocyte (n) or first polar body Spermatids (n) Ovum (n) or second polar body both created from secondary oocyte (n) maturation

Ovulation

fertilization

Fertilization

• Oogenesis stays at primary oocyte until the egg is ready to ovulate and under meiosis II. The oogonium and primary oocyte formation occurs pre-birth. • The polar bodies are not given enough nutrients and die off. • Meiosis in the Life Cycle of Animals and Plants: ○ Meiosis in animals: ▪ Spermatogenesis: male gamete production ▪ Oogenesis: female gamete production ○ Meiosis in plants ▪ Through meiosis, the diploid (2n) sporophyte produces haploid (1n) spores, which become the gametophyte. ▪ Through mitosis, the gametophytes produce haploid gametes Study figure 2.19 • In spores, most of its lifecycle is haploid.

• Sexual reproduction: two haploid cells fusing together to make the next generation. • What one thing do all sexually reproducing organisms have in common? ○ They all undergo meiosis. • Why is meiosis important? ○ It reduces the ploidy. G1

S

G2

Prophase I & Prometaphase Metaphase I Anaphase Telophase I & I I cytokinesis

Drawing

• Chromosomes per cell

6

6

3

DNA molecules / cell

6

12

6

DNA picograms / cell 10

20

10

Haploid or diploid

2n

N

2n

Prophase II & prometaphase II

1/18 Ch.2 Thursday, January 18, 2018

12:30 PM

In bees, a queen will lay either unfertilized or fertilized eggs. ○ The fertilized egg (diploid) will make a female offspring which will become a worker bee or queen. ○ The unfertilized egg (haploid) will create a male offspring which will become a drone. • PRACTICE PROBLEM: ○ A certain species has 3 pairs of chromosomes: one acrocentric, one telocentric, and one metacentric. Ploidy & chromosome some? ○ Draw a cell of this species at metaphase I and metaphase II. •

Gene

Inherited factor (region of DNA) that helps determine a characteristic

Allele

One of two or more alternative forms of a gene

Locus

Specific place on a chromosome occupied by an allele

Genotype

Set of alleles possessed by an individual organism

Heterozygote

An individual organism possessing two different alleles at a locus

Homozygote

An individual organism possessing two of the same alleles at a locus

Phenotype or trait

The appearance of manifestation of a characteristic

Characteristic or character An attribute or feature possessed by an organism •

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Gregor Mendel and his success in genetics ○ Proper experimental model ○ Used an experimental approach and analyzed results mathematically ○ Studied easily differentiated characteristics. Characteristics: seed color, seed shape, seed coat color, etc. Traits or phenotypes: yellow seeds, green seeds, round seeds, wrinkled seeds, constricted pods, etc. Mendel's work was successful because the plant he was testing had two discrete options in genotype->phenotype traits. Monohybrid cross: cross between two parents that differ in a single characteristic. ○ What are the conditions of the cross? ▪ You need two parents that differ in a single characteristic. ○ What are the expected outcomes? ▪ In a monohybrid cross with two pure parents, the F1 generation always shows the dominant trait. ○ What are the limitations? ▪ Discrete phenotypes, and/or multigenic traits can't be analyzed with this approach. ○ Why would a geneticist use this cross? ▪ To determine the dominant trait. ▪ To determine if there is more than one gene affecting this phenotype. To get true breeding individuals, you keep one self-pollinating it with itself. In the pea plants, the traits of the parent plants do not blend. Although F1 plants display the phenotype of one parent, both traits are passed to F2 progeny in a 3:1 ratio. Monohybrid cross conclusions: ○ Conclusion 1: one character is encoded by two genetic factors. ○ Conclusion 2: two genetic factors (alleles) separate when gametes are formed. ○ Conclusion 3: the concept of dominant and recessive traits. ○ Conclusion 4: two alleles separate with equal probability into the gametes. Principle of Segregation (Mendel's first law): each individual diploid organism possesses two alleles for any particular characteristic. These two alleles segregate when gametes are formed, and one allele goes into each gamete. Test Cross: used to determine the genotype of an individual. ○ Testcross individual x homozygous recessive individual

• Dihybrid Crosses ○ Examine two traits at a time. ○ The principle of independent assortment ▪ Figure 3.8 ○ The conditions of this cross is that you are looking at two different traits with two discrete alleles that are genetically unrelated.

1/23 Ch. 3 Tuesday, January 23, 2018

12:19 PM

Probability • Probability: the likelihood of the occurrence of a particular event. • Used in genetics to predict the outcome of a genetic cross. • Multiplication rule ○ If you want to roll a 4 on a dice twice in a row, you multiply the independent events because you need both. ○ So you're rolling a 4 and a 4 but overall 2 rolls. ○ 2 independent events happening at the same time. • Addition rule ○ The probability that you roll a three or a four, which means you have 2 different outcomes. You either roll a three or four first. Which means you add the independent probabilities. ○ So you're rolling a 3 or a 4 but overall one 1 ○ 2 different ways to get the same outcome. • Dihybrid Cross: ○ Parental: AABB x aabb ○ F1: AaBb everyone --> cross AaBb x AaBb ○ F2: 9:3:3:1 ratio ▪ 9 - both dom, 3- one dom, one rec, 3- one rec, one dom, and 1- both rec • Table 3.2 phenotypic ratio, table 3.3 genotypic ratio • Applying probability and the branch diagram to dihybrid crosses.

• Chi-Square Goodness of Fit ○ Indicates the probability that the difference between the observed and expected values is due to chance. ○ Ho: Any observed difference is due to chance (there is no "real" difference between observed and expected.) • If you reject the null, there is a low probability that chance explains the difference. • If you fail to reject the null, there is a high probability that the chance explains the difference. • Pedigree: pictorial representation of a family history, a family tree that outlines the inheritance of one or more characteristics. • Proband: the person from whom the pedigree is initiated. • Figure 3.13 pedigree legend ○ Adoption has dashed line between adopted parents and solid line between biological. Also has a bracket around them. ○ Cosanguity: mating between two related people.

PCB 3063 P

10

1/25 Ch 3 & 4 Thursday, January 25, 2018

12:31 PM

• Autosomal recessive traits usually appear with equal frequency in males and females, and they often skip generations. ○ Autosomal recessive traits are more likely to appear among progeny of related parents. • In the datura plant, purple flower color is controlled by a dominant allele P. White flowers are found in plants homozygous for the recessive allele p. A purple-flowered datura plant is self-fertilized, and its offspring are 27 purple-flowered plants and 9 white flowered plants. If the 27 purple flowered plants are self-fertilized, how many of the 27 would you expect to segregate both purpled-flowered and white-flowered plants in the offspring? ○ Answer: 18 ▪ Because PpxPp is self-fertilized. And of the 27 purple flowered ones, which would be PP or Pp, 1:2 would segregate to make both white and purple alleles.

• Albinism is caused by an autosomal allele that interferes with skin pigmentation in animals. Two normally pigmented parents have an albino child. What is the probability their next child will have albinism. ○ Answer: 1/4 ▪ What is the probability that their next child will be a boy with albinism? □ Answer: 1/8  Because 1/2 x 1/4 = 0.125 ▪ What is the probability that their first male child will have albinism? □ Answer: 1/4 □ It is the same as a child being born with albinism, just specifying that the child is male, it is not a condition.

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Sexual reproduction: alternates between haploid and diploid states. Most organisms have two sexual phenotypes, male and female. There are several different mechanisms of sex determination. The X and Y chromosome pair during meiosis, even though they are not homologous (the genes located on each are different). On the ends of sex chromosomes, there are called primary pseudoautosomal region (on top) and secondary pseudoautosomal region (on bottom). This allows them to be similar enough on the ends to line up during meiosis. XX-XO ○ XX - female ○ XO - male ▪ O means there is no second chromosome. ▪ Grasshoppers XX-XY ○ XX - female ---> homogametic ○ XY - male ---> heterogametic ▪ Mammals ZZ-ZW system: ○ ZZ - male ○ ZW - female ▪ Birds, snakes, butterflies, some amphibians There is also organisms with no sex chromosomes, only the sex-determining genes on autosomes. ○ Found in some plants, fungi, protozoans, and fish. Environmental factors: ○ Limpet's position in the stack ○ Temperature in turtles Not all organisms with XY chromosomes have the same sex determination system.

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○ Fruit flies use a genic balance system. ○ X: A ratio (X, number of X chromosomes; A, number of haploid sets of autosomes). ○ X:A ration determination table on table 4.1 ○ XO in flies is male because of ratio SRY gene on Y chromosome determines maleness. Turner Syndrome: XO; 1/3000 female births Klinefelter Syndrome: XXY, or XXXY, or XXXXY, or XXYY; 1/1000 male births Poly-X females: 1/1000 female births

• Females will have a barr body, and males will not. ○ The barr body is a condensed x chromosome. • Lyon hypothesis: why x inactivation occurs. ○ In some cells the activated x is paternal, and in others the activated x is maternal. The mitotic division of each cell then furthers and creates the mosaic pattern. ○ This determination is through epigenetic silencing, through methyl groups effecting chromatin organization. • Y-Linked Characteristics: ○ Only present in males ○ All male offspring will exhibit the trait ○ Y chromosome lost DNA over time ○ Important for sex determination in SRY. • Genes at the same locus - two versions of the same gene; each version of the same gene is defined as allele. • Types of Dominance: ○ Complete dominance ○ Incomplete dominance ○ Codominance

1/30 Ch. 4 Tuesday, February 6, 20...