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BIOL 205
Chin Sang

Biology 205 - Week 1 Notes (Including Ch. 1 notes) Lecture 2: Scientific Method 1) Observation 2) Hypothesis 3) Experimentation to test hypothesis 4) Analyze results: Accept or Reject the Hypothesis  The scientific method helps to minimize the influence of bias or prejudice in the experimenter Pax-6 genes:  Wild-type has eyes, Mutant is eyeless  Pax-6 eyeless gene=eyes; no gene = no eyes  Pax-6 mutation in mouse and humans cause absence of eyes  Ectopic eye production from the eyeless gene (eyes found elsewhere on the body) is due to the injection of the pax-6 gene to another area Cells function like a Rube Goldberg Machine: "accomplishing by extremely complex, roundabout means what seemingly could be done simply The fertilized egg contains information that specifies the sequence of developmental instructions to make an organism (why humans give rise to humans; corn to corn) The passage of genetic information must have four properties (*all found in DNA): 1) Diversity of structure: There must be information for the differences in cellular structure 2) Ability to replicate (produce offspring): There must be some mechanism for replication so information can be passed from generation to generation 3) Mutability (evolution): Information must be able to change 4) Translation (must have "workers"): A blueprint is not enough. You need the machinery to read and translate the information to build the structure Genes: a term introduced by Wilhelm Johannes in 1909 Genome: The collection of all genes in an organism Genetics: 1) The study of genes; 2) The study of inheritance; the field of biology concerned with understanding the mechanisms that govern the diversity, replication, mutation and translation of the information in genes Definitions of Gene has evolved over time  Modern definition now: "A gene is a union of genomic sequences (DNA or RNA) encoding a coherent set of potentially overlapping functional products"  Basic unit of hereditary involved in producing proteins (found within DNA) Typical Eukaryotic Gene Structure and Products (Review)  Eukaryotic Cell contains Promoter at the 5' end, and a coding region with exons and introns  Introns are removed/spliced out during transcription to mRNA from DNA  Translation occurs creating mRNA into a protein Founder of Genetics: Mendel (more about him later....) Genetic analysis, using organisms with mutations is a powerful method for investigating biochemical, physiological and developmental pathways Today, the vast majority of genes are identified by sequencing and computer programs Large scale DNA sequencing allow evolutionary biologists to compare entire genome of species and determine what changes there are between a man and a mouse (surprisingly, very few!) DNA has the form of a double helix - has all 4 properties from before DNA is composed of two nucleotide chains held together by complementary pairing of A with T and of G with C DNA has the four properties that characterize genetic information: n  1) Diversity of structure: only 4 nucleotides can lead to many combinations: 4 , where n is the number of base pairs. A sequence with 4 base pairs would have 256 combinations. Human genome has 3.4 billion base pairs = great diversity  2) Ability to replicate (semi conservatively w/ base-pairing): DNA is replicated by unwinding of the two strands of the double helix and the building up of a new complementary strand on each of the separated strands of the original double helix  3) Mutability: In the course of replication an incorrect base may be put in or bases may be lose or duplicated. Since each strand serves as a template, the new mutation would be transferred to subsequent copies  4) Translation into form and function: The sequences of A,T,C, and G must be used by the cell to create protein molecules having a particular amino acid sequence (Transcription and Protein Translation. During transcription, one of the DNA strands of a gene acts as a template for the synthesis of a complementary RNA molecule (RNA turns into protein) The RNA transcript acts as a "working copy" of DNA. Why RNA?  Increases the number of copies  Allows transport to a new location  Stability and lifetime of RNA acts as a regulator of protein production Protein Translation: The production of a chain of amino acids based on a sequence o nucleotides in mRNA: 20 kinds of amino acids, but only 4 different nucleotides - 3 nucleotides = 1 codon; 64 combinations, so there is genetic redundancy The information in genes is used by the cell tin two steps of information transfer: DNA is transcribed into mRNA, which is then translated into the amino acid sequences of a polypeptide (Note that the polypeptide chain itself is not a protein - changes in the amino acid chain can alter how the protein folds). Lecture 3: Red-eyed and white-eyed Drosophila: White mutant helps to understand eye colour (eye formation is eyeless gene) Mutation in promoter has the greatest delirious effect on agene  No binding to this region - rest of gene not expressed  Unless told this causes n transcription, choose the stop codon option Mutation: Change to a stop codon = rest of gene not expressed, meaning not functional  Stop codon can affect a protein/amino acid chain at any point!  Mutation in splicing location/marker causes issues that may lead to a null allele being transcribed Some Genetic Terms you must know: 1) Wild-type: The "normal" or most common form - reference strain 2) Mutants: variants of the wild-type form 3) Genotypes: Genetic composition 4) Phenotype: A measurable character 5) Allele: One of the different forms of a gene that can exist at a single locus 6) Gene locus: The specific region on a chromosomes where the gene is located 7) Diploid: Having two chromosome sets (1 from mom, 1 from dad) 8) Haploid: having one chromosome set 9) Homozygous: carrying a pair do identical alleles at one locus (A/A or a/a) 10) Heterozygous: carrying a pair of different alleles at one locus (A/a) 11) Dominant: An allele that expresses its phenotypic effect even when heterozygous with a recessive allele; if A is dominant over a, then AA and Aa have the same phenotype (dominant phenotype) 12) Recessive: An allele whose phenotypic effect is not expressed in a heterozygote . If a is recessive, then you will only observe the phenotype when homozygous: a/a (recessive phenotype) Genetic Variation  Genetic variation is the genetic differences among individuals. Most people (except for identical twins, typically) do not share the same sequence of DNA  How does variation arise? o During Meiosis the random mixing of maternal and paternal chromosomes. The union of which egg and sperm is also random o Variation arises by mutation:  Spontaneous (i.e. mistakes in replication)  Genetic variation can be produced in the laboratory by using high-energy radiation or chemicals to produce mutations Gene regulation is important  The genome of in the nuclei of the 50 trillion cells is the roughly identical, but we have so many different cell types. How? o Not all genes are expressed (turned on) in every cell o Muscles cells turn on muscle specific genes o Neurons turn on neuronal specific genes o Eye cells must turn on the right genes to build eyes  Gene regulation is important for all aspects of development, not just making different type so cells (e.x. cell division, cell movements, pattern formation, organ and tissue formation)  Messing up genes (mutations) and/or how they are regulated can lead many if not all human diseases. Genes control development Albinism  Mutant gene causes lack of pigment in organisms  Two copies of the gene allow for tyrosinase enzyme to work properly. Even 1 copy will lead to pigmented skin, but to a lesser degree; no A = no tyrosinase enzyme which is needed to convert the amino acid to produce melanin = no pigment Genes do not work alone:  The products of multiple genes are active in pathways that determine biological properties such as eye color or skin color  Geneticists can use crosses to create individuals with mutations in different combinations of genes  By observing the effects, investigators can begin to construct the biological pathway determining the property  Ultimately characterize the DNA changes of the different alleles and provide a mechanism how the gene functions to cause ea certain phenotype Forward genetics of classical genetics: Starts with a variant phenotype and tries to identify the genetic difference  Historically most genes were identified by mutations (beings with 1 mutant and 1 normal/wild phenotypes)  If a fruit fly had white eyes (mutant) it meant you altered a gene involved in forming red eyes (wild-type)  2 Phenotypically different individuals are crossed, offspring are noted, then the gene is identified and DNA sequenced  Mutant phenotype leads to the gene affected Reverse genetics: starts with a gene of unknown function and looks at what happens to the organism/cells when you alter that gene The genomes of humans and chimpanzees differ by only a small percentage of nucleotides (1%)  Look different, but few genetic differences (usually due to gene regulation) Studying genes allows us to understand biological systems:  Isolation of mutations affecting a biological process (e.x. creating eyes)  Analysis of progeny of controlled matings ("crosses") between mutants and wild-type (e.x. Mendel's peas)  Genetic analysis of the cell's biochemical processes  Microscopic analysis (e.x. GFP reporters)  Direct analysis of DNA (Sequencing) Probes can be used to detect specific macromolecules  DNA, RNA and proteins can be run on an electrophoresis gel (smaller fragments run to base, larger near top)  Probes for target: use complimentary base pairs in fluorescent dye on blot  RNA (whole transcript) is larger than DNA (piece of gene), while protein is smaller  On a protein, a probe is an antibody that is labelled, where as a probe on mRNA or DNA is a complementary nucleic acid Genetic model organisms  Easy to grow and maintain  Fast life cycle  Can "cross"  Cheap and abundant  Some examples: bacteriophage, Neurospora crassa, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans Chapter 1 Notes:  A system of information passage (e.x. gametes from father and mother to produce a daughter organism) must have four main properties: o 1) Diversity of structure: cellular structure must carry information to differentiate and produce all cells that make up the organism o 2) Ability to replicate: must have a mechanism to copy information within an organism to produce new cells and new organisms o 3) Mutability: information-bearing structure must be capable of undergoing changes (mutations); these can sometimes make organisms evolutionarily fitter o 4) Translation: system must have the ability to transcribe DNA/info and use appropriate machinery to do so  Basic elements of inheritance are now called genes (1909, Wilhelm Johansson), with a collection of genes being called the genome  Genetics is a field of biology, concerned with the diversity, replication, mutation, and translation of the information in the genes. 1.1 - Genetics and the Questions of Biology  Genetics began with the work of Gregor Mendel, who was an Austrian monk who worked with variations of the garden pea o Inferred that "factors' carried information from parent to offspring in his crosses; this later developed the concept of genes (portions of chromosomes) o This discovery allowed humans to select favourable trains  Key aspect of genetic analysis was through development in mutations o X-rays and chemicals caused inherited mutations o Using mutations helped to determine pathways in biological development (e..x. fruit fly mutations)  Using this evidence, scientists determined that DNA is the hereditary material, double helix shape: DNA replication used to create new cells ("dead cells")  Evolution is a result of differing rates of reproduction with individuals that are genetically different; this effects the frequency of traits for future populations 1.2 The Molecular Basis of Genetic Information  Majority of the active part of an organism is composed of proteins; to create these proteins, DNA (deoxyribonucleic acid) is used o DNA is double helical;, with a sugar-phosphate backbone, with complimentary nucleotide chains (A-T (2), G-C (3))  Four key properties of DNA: o 1) Diversity of structure: different combinations of base pair sequences determine characteristics unique to that sequence o 2) Ability to replicate: DNA replicates by unwinding the two strands of the double helix and building a new strand on each side of the original strand o 3) Mutability: during replication, an incorrect base pairing may occur, which causes a heritable change in the DNA o 4) Translation into form and faction: DNE creates amino acids, which forms proteins; also signals when this should occur  Processes of DNA replication to protein: o 1) Transcription: DNA strands are transcribed into mRNA, similar to DNA, but has ribose sugar and Uracil instead of thymine: this produces identical daughter strands off of the original transcript DNA molecule  Processing including cutting out introns (leaving exons), adding a 5' hat, and 3' poly A tail, create ea mature RNA transcript. This mRNA then goes into the cytoplasm for protein production o 2) Translation: creates and amino acid chain based on the sequences of the mRNA chain; this is read in groups of 3 base pairs called codons. This means there are 64 combinations of codons for 20 amino acids, allowing for redundancy yin case of some mutations  tRNA with anticodon complement to mRNA sequence contains the amino acids; enters the ribosome to deliver the amino acid onto the growing chain  Process ends at a stop codon  Primary structure now created (amino acid chain). Functional protein is when the chain folds up into a protein structure, making it active  Genes regulation: built into the DNA structure is regulatory function o During transcription, the RNA polymerase acts to match ribonucleotides to one another o Molecules within the RNA polymerase control this process, and can block the movement (negative control); blocking factor can also be removed to allow transcription to proceed (positive control)  This will allow the DNA's genes to only be transcribed when necessary (e.x. lactose breakdown genes/enzyme) 1.3 - The Program of Genetic Investigation  Within a species, there are natural occurring differences between members, especially in sexually reproducing species; this is referred to as genetic polymorphism  Determination of the function of a gene works through gene dissection and mutation, looking at the effects of individual mutations  Differences in genetic identify are related to the evolution of organisms, and differences in species (e.x. human vs. fly)  1) Forward genetics (starting with variation) o Used to search for differences in phenotypes caused by genetics o Crosses are made between "wild type/normal" organisms and "mutant.rar" organisms; this helps to determine the gene causing the mutation o Some mutations work on a pathway (e.x. creation of melanin or pigments, using several enzymes) o E.x. Albinism: 2AA = creates melanin, Aa=less melanin, but still coloured, aa - no melanin produced = albino  Mutations create albino individuals  After determining the gene involved, geneticists determine the allele(s) involved, and how they affect the phenotype  2) Reverse genetics (starts with DNA) o Starts with known genetic changes/mutations and looks at resulting organism changes  DNA changes can block the production of a protein or damage its metabolic activity, which is seen in the development of the phenotypes  Uses insertions of mutated DNA (or comparison to DNA of other genomes) to analyze the DNA sequences faster  E.x. Humans and Chimpanzees 1.4 - Methodologies Used in genetics  Methods used to study genes include: o 1) Isolation of mutations affecting the biological process under study: each mutant gene reveals an effect to the biological pathways within a human o 2) Analysis of progeny of controlled "crosses" /matings between mutants and wild-type individuals: this analysis can identify the genes, their chromosomal locations and inheritance patterns o 3) Genetic analysis of the cell's biochemical processes: Used to find out how cellular-level chemistry and processes are disturbed by the new mutant allele o 4) Microscopic analysis: ability, with new technology, to label and microscopically view the locations of genes on a chromosomes o 5) Direct analysis of DNA: analysis of the DNA< using techniques like cloning (gene is isolated and multiplied, usually through bacterial insertion-aid)  Genomics is the study of structure, function, and evolution of genomes, through the before-mentioned techniques  Comparative genomics describes differences and similarities in the genomes of species that are somewhat related (e.x. primates and humans)  Misinformation: the study of computational analysis of the information content of genomes  Detecting specific DNA, RNA, and protein molecules: o Probing: uses specificity of intermolecular binding (e.x. mRNA to DNA which it was transcribed form); probe is labelled with radioactivity on fluorescence and attaches to only the sought after macromolecules o 1) South - Probing for DNA  Cloned gene can act as a probe to find a specific segment of DNA with the same sequence  Must be done with separated DNA strand to open up the binding sites, usually by restriction enzymes (cut DNA into specific target sequences); fragments are separated into groups of similar length using electrophoresis  Southern blotting technique used: fragments placed onto a gel, ran with electricity, then blotted onto a porous membrane, which is then placed into the probe solution o 2) North - Probing for RNA  Used to determine if an RNA has been transcribed form a gene  northern blot used: total mRNA is extracted from the body location, fractioned using electrophoresis, then blotted onto a membrane with probe added o 3) West - Probing for Protein  Performed with antibodies (lock-and-key fit)  Western blot: same as North, but then bathes into the antibody solution (antibodies formed by another animal that has had the protein injected into them) 1.5 - Model Organisms  Model organisms are organisms who genetic mechanisms are common either to all species or to a large group of related species; used in experiments  Mendel established basic laws of inheritance held by model organisms: organism's gametes assemble randomly through reductive efforts  Model organisms must be used to determine the generality of traits, as each organism has different reproduction and development patterns  Model organisms include: o 1) Viruses: simple non-living particles lack metabolic machinery; infects a host cell or bacteria and diverts synthesis to production/replication of more viruses  Used to study structure of DNA, and replication and mutation mechanics o 2) Prokaryotes: single-celled organisms, haploid, no nuclear membrane, and few inner compartments (e.x. E.coli) o 3) Eukaryotes: all other cellular life made of 1_ cells with a nuclear membrane and cellular compartments  a) Yeast: single-celled fungi reproduce through division of haploid cells, but sexual through fusion of two cells; produce spores  b) Filamentous fungi: separated irregularly, with fusion to produce diploid cells, which undergo meiosis to form haploid have long threads called hyphae  Use a) and b) to study basic metabolic pathways, and they require basic carbon and minerals to function  c) Multicellular organisms: contain complex cell differentiation, with simple culturing in controlled environments, with short life cycles to breed quickly (e.x. fly, plant, roundworm, mouse (used in antigen-antibody systems) 1.6 - Genes, the Environment, and the Organism  Genes alone cannot dictate the structure of an organism; the environment plays a vital role (e.x. environment provides the raw materials for processing by the genes)  Three main models: o Model I: Genetic determination: Almost all difference between species are determined by the differences in their genomes  Some genetic differences cannot be changed by the environment  Exon mutations (through experimental genetics) depends on the fact that allelic differences are insensitive to environmental conditions  Power of genes are often seen mutant vs. normal genes (e.x. sickle cell anemic and hemoglobin)  Genes act as a set of instructions to feed in environmental materials, and put together a specific phenotype for the individual o 2) Model II: Environmental determination  Genes give general signal for development, but the environment determines the actual course of development (e.x. twins reared in different countries will speak different languages) o 3) Model III: Genotype - environment interaction  To predict the development of an organism, e must understand its genotype (genetic constitution it inherits) and the environment in which it has been exposed to ; depends on the environment, but also the sequence of development  Use of phenotype and genotype o Typically, an organism resembles its parents more than unrelated species o Organisms of the same genotype have the same set of genes; phenotype the same = look alike  All organisms (apart from twins) have different genotypes, at least slightly o Genotype is generally fixed, while Phenotype changes with environmental over time  Developmental noise o Random events in development that lead to variation in phenotype ( fruit flies and eye cells - infrabar and ultrabar) o Developmental processes contain feedback systems that tend to hold deviations within certain bounds, so that the variability does not differ too greatly  Three levels of development: o 1) First: genes alone determine phenotypes; phenotype remains constant, and not based on environment  Genes can be isolated during this point in development, and precisely because processes seem to be general across a variety of organisms o 2) Second: variation in basic developmental themes, which differ between species, but are the same within a species  Two species may differ in a characteristics, as they live in different environments, but we cannot be sure if it is the environment that is causing these changes, until we bring the organisms into the same environment o 3) Third: Differences between species caused by genetic, environment, and developmental noise factors become intertwined Biology 205 - Week 2 Notes (Including Ch. 2 notes) Lecture 4:  Structural comparison of the genome components of eukaryotes: 99.9% of genome is from nucleus; 0.1% from mitochondria (just inherited from mother); plants also have chloroplast  Structural comparison of the genome components of prokaryotes: bacterial chromosome makes up the genome, and the Plasmid is used to provide antigens to disease  Structural comparison of the genome components of viruses: DNA or RNA head, with a protein tail  Nature vs. Nurture Debate (3 models) o Model I: A model of determination that emphasizes the role of genetics (e.x. dogs will birth dogs; environment does not come into effect) o Model II: A model of determination that emphasizes the role of the environment (e.x. identical twins, separate within different cultures will show different phenotypes as a result of the environment o Model III: A model of determination that emphasizes the interaction of genes and environment (mixing of genetic and environmental factors with developmental interactions (e..x. heat shock on Drosophila wing development: abnormal wings due to heat increase during specific time; no effect if done later in life)  Random events in development lead to variation in phenotype called development noise o Identical twins do not have the same fingerprint; differences are a result of developmental noise  Not all mutations are equal: Go from silent too weak to intermediate to strong o Allele: one of many variants of a genes (variant meaning mutation o Simplest mutation is a base pair change: ex. G-C o Others include single BP insertion, small deletion, large deletions, inversions....etc.  The nature of alleles and their produces (e.x. Phenylketonuria) o This recessive disease is caused by a defective allele of the gene that encodes a liver enzyme called phenylalanine hydroxylase o Without this enzyme, phenylpyruvic acid is creased, which interferes with the development of the nervous system 9brain) leading to mental retardation o 5 possible treatments:  1) (Best) Removed/reduce phenylalanine from diet  2) Gene therapy: give new gene, bring phenylalanine hydroxylase  3) Inject drug/enzyme that breaks down phenylpyruvic acid  4) Inhibit pathway to make phenylpyruvic acid  5) Full liver transplant o Babies born with phenylalanine hydroxylase (PAH) mutations are not prisoners of their DNA. Changing their diet (i.e. lower phenylalanine intakes leads to less phenylpyruvic acid by=- product and therefore normal brain development o Important to diagnose and treat early; window for brain development is 0-3 years o Since tyrosine is a result of phenylalanine normally, and tyrosine produces melanin, the pigment in their skin is likely of a lighter pigment  Gene sides sensitive to mutation o Mutations in exons are more deleterious than those in introns o Mutation in promoter is sensitive o Intron mutations involved splicing and enhancer mutations that affect protein development  Not all mutations are equal: o Allele may receive a silent, weak, intermediate, or strong/null mutation o Product will be wild-type, leaky or lower function, or none o Phenotype as a result is wild-type, weak or intermediate, then strong o Leaky allele: some function o Silent allele: doesn't affect protein, but has different codes  When thinking about Dominant and Recessive, think about 1) phenotype and 2) Two alleles (wild-type (100% function) and null (0% function) o Dominant Phenotype (+/+ or +/n): wild-type allele in either homozygous state or heterozygous state with a null allele o Recessive Phenotype (n/n): only seen in homozygous with a null allele o Some exceptions - seen later!  Haplosufficiency o When phenotype is observable, most null alleles lead to a recessive phenotype. Why? Because most genes are haplosufficient "half is good enough" o Dominant allele masks the recessive allele o Found in eyeless, white eyes, tyrosinase, pku gene o some rare null alleles lead to a dominant phenotype. Why? Because those genes are haploinsufficient "half is not good enough" o Examples of this include the T genes in mice: lethal in recessive state, but deformed tail in heterozygous state. How is this explained?  Let's say gene T encodes for protein called T-Box: the T-Box protein is needed at a certain level in order for the tail to grow to a full length. Let's say 16 arbitrary units. Each wild-type allele of T can make 10 units of the T-Box  So: +/+ will make 20 units of the T-BOX, therefore you get the full length tail  +/T will make 10 units of the T-BOX, therefore not enough for full length tail, and will make short tail. T is dominant  T/T will make 0 units of the T-Box, therefore not enough for full length tail, but also dies because T-box is needed for other functions in addition to tail length  There are other ways to get a dominant phenotype other than null mutations in haploinsufficient genes (e.x. dominant negative mutations... but we will come back to this)  Why did Mendel succeed while others failed? o He used the Scientific Method o He has a model organism pea plant (7 types - created pure lines of each) o Mendel had mutations given to him, he didn't have to find them o Unlike most modern day geneticists, Mendel was not interested in what the genes were that caused the phenotypes, just how they were inherited (remember, there was no concept of gene or chromosomes back then)  Single gene inheritance o The rules for single-gene inheritance were originally elucidated in the 1860s by the monk Gregor Mendel are still used today o Many human disorders, such as cystic fibrosis, Tay-Sachs disease, PKU, are inherited as a single mutant gene o One of the first things you want to do when you observe a new phenotype is determine whether that phenotype is caused by a mutation in a single gene, or in multiple genes o You also want to know what type of allele: weak, leaky, null? Lecture 5:  Single gene inheritance o Mendel established pure lines of 7 phenotypic traits (crosses created to ensure pure lines) o Would study the round vs. wrinkled trait as it is very quick to know  Cross pollination v. selfing: o Cross-pollination: Transfer of pollen from plant to the stigma of another (removal of anthers from that plant to eliminate contamination); 2 plants used o Selfing (self-pollination): Transfer pollen to stigma on same plant; 1 plant used  Mendel's law of dominance (example) o Pure Yellow pea x Pure Green pea = All yellow progeny, due to dominance o At the time, the thought of having a blend of colours was the correct thinking o F1 progeny crossed to produce a 3:1 (Yellow: Green) ration o Means that All F1 plants are Y/y, F2 end up 1/4 Y/Y, 1/2 Y/y, and 1/4 y/y o Testing this model, an F1 plant (Y/y) could be crossed with a y/y (green pure line) and it will produce a 1:1 ratio green: yellow  Mendel's First Law: Law of equal segregation: From a monohybrid cross, each parent has an equal chance of contributing one of the two factors o Monohybrid = heterozygous for one trait o A monohybrid cross is a cross between parents who are heterozygous  What happened next? Nothing for Mendel; he died and people thought he was weird and still wanted to believe in the blending theory o 34 years later, studied cells and found chromosomes o Translation of coloured bodies discovered the chromosome theory of inheritance o Chromosome Theory: Chromosomes which are seen in all dividing cells and pass from one generation to the next, are the basis for all genetic inheritance o Chromosomal DNA is wrapped around histones to form histone octomers; this helps to coil the DNA finely o Representative chromosomal landscapes: bacterium are very efficient, with almost no space between genes. Humans are less efficient (lots of gaps for introns/junk DNA - but is it junk?!?)  Stages of the asexual cell cycle: G1, S, G2 all interphase, then Mitosis splits original cell into two daughter cells  Meiosis reduces the chromosome number (see figure 2-14 for a great diagram) o Mendel's view of equal segregation was that the members of the gene pair segregated equally in gamete formation. He did not know about the subcelllular events that take place when cells divide in the course of gamete formation  Mitosis and Meiosis: o Mitosis  2n (diploid)  Homologous chromosomes aka homologs (not identical (one from mom, one from dad)  Centromere  Telomere  Sister Chromatids (identical copies of one parent's chromosomes o Meiosis  Dyad (sister chromatids)  Tetrad: mom and dad find each other  Synapis (synaptonemal complex) - crossing over happens here; exchange material  1st division: one Dyad to each daughter cell; mom and dad move together  2nd division: one chromatids to each daughter cell (1n haploid): division same as mitosis here  Non-disjunction: when tetrad does not split up @ 1st division; can also happen in 2nd division (causes things like Trisomy 21) o See figures 2-15, and Box 2-1,2-2 for examples  What is the evidence for the equal segregation of alleles in meiocytes o So far, it has been indirect, based on the observation that crosses show the appropriate ratios of progeny expected under equal segregation o Example to prove: Baker's yeast provides a good evidence, because the four products of a single meiosis are temporarily held together in a type of sac o Haploid yeast cells, one coloured red (r+ mutant) another normal, mix cells to make cross, which produces a diploid cell. Chromosomes replicate o First products of division are the +/+ and r/r chromosomes in separate cells; four products of meiosis are 2 r and 2 +, making this a 1:1 ratio from looking at the final inoculated cells Lecture 6:  Example on two muntjac: one in China and one in India: You can't make predictions from the number of chromosomes  A larger genome doesn't mean more gene; a more complex organism doesn't necessarily have more genes  Meiosis and Mitosis revisited with Figure 2-19 o No meiosis in haploid cells, as meiosis is the division to make haploid cells; if already haploid, don't need to reduce further  What is going on at the molecular level during the formation of sister chromatids> o Dad: homolog GC --> Replication to produce 2 chromatids of GC o Mom: homolog AT --> Replication to produce 2 chromatids of AT o Genes are associated with alleles and their respective base pairs o DNA molecules replicate to form identical chromatids o b/b will produce 2 b chromatids  Can we track single gene inheritance at the DNA level? Why? o Saves time o A morphological phenotype not necessarily needed o Can distinguish heterozygous from homozygous states  Restriction Enzymes can cut DNA in a sequence specific way o Enzymes cut at certain BP sequence (polandrophic: cut at both DNA strands) o Mutations can either destroy or create a restriction enzyme site: used to determine if a mutation exists o RFLP: Restriction Fragment Length Polymorphism done o Single-gene inheritance tracked at the DNA level; mutations contribute to cuts and the probe hybridizes to region to determine gel run results o On gel: A/A = 1 line; A/a = 3 lines; a/a = 2 lines  What is the evidence for the chromosomal theory of inheritance? o From Mendel, he thought chromosomes and genes were the same (we now know genes are found in chromosomes) How do we know this? o Thomas Hunt Morgan worked with the model organism fruit fly  Looked at red-eyed and white-eyed (mutant) fruit flies; white gene needed for red eye pigmentations (pigment )red_ not found in the eyes for white flies  An example f X-linked inheritance  Crossed a red female and white male to find all F1 had red eyes (red eyes dominant over white, so white is mutant)  Crossed red female and red male to find 3:1 ratio red: white, but all white eye flies are male...  Third cross (test cross) some between F1 female (heterozygous for the white eye gene) and white male: produces half males and half females white  This means that the white mutation was on the X chromosome  Test of the model: Reciprocal crosses (red female x white male; and white female x red male) produces different F1 results = must be X-linked o First observation of a gene trait (white eyes) that segregated with gender o Best evidence that genes reside on chromosomes o Morgan's experiments in 1910 with the white eye fly was the birth of modern day genetics  human sex chromosomes: sex determination o Pseudoautosomal regions: used to ensure proper linking during meiosis o Differential region of the X (X-linked genes) and differential region of the Y (Y-linked genes) o Males are XY, Females are XX o Remember: dad determines if male or female!  Human Pedigree Analysis o Breeding Experiments cannot be applied to humans o But careful analysis of family pedigrees can help determine the genetic basis of a particular condition o See table 2-28 for pedigree symbols (square = male, circle=female, filled=infected) Chapter 2 Notes: Biology 205 - Week 3 Notes (Including Ch. 3 notes) Lecture 7:  Human Pedigree Analysis (Cont'd) o What patterns in a pedigree would reveal autosomal recessive inheritance?  1) Generally the disorder appears in the progeny of unaffected parents; and  2) The affected progeny include both males and females  e.x. Cystic Fibrosis, PKU, Albinism  Inbreeding also increases the chances of passing on a disorder! o What patterns in a pedigree would reveal autosomal dominant inheritance?  1) The phenotype tends to appear in every generation of the pedigree. Parents of affected children show the phenotype  2) Half the offspring are affected  3) Affected fathers or mothers transmit the phenotype to both sons and daughters  e.x. pseudoachondroplasia  Pseudoachondroplasia genotype (D): +/+ is unaffected, D/+ = short people, D/D lethal  Behaves similar to the Mouse T (T-box) mutation o Autosomal Polymorphisms (2+phenotype)  In natural populations of organisms, a polymorphism is the coexistence of two or more common phenotypes of a character. The alternative phenotypes of a polymorphism (morphs) are often thought to be inherited as alleles of a single autosomal gene in the standard Mendelian manner  The interpretation of pedigrees for polymorphisms is somewhat different t from that or rare disorders because, by definition, the morphs are common  E.x. brown vs. blue eyes, attached v. free ear lobes  Can two parents with blue eyes have a brown child? Yes: two genes are involved o What patterns in a pedigree would reveal X-linked recessive inheritance?  1) More males than females affected  2) None of the offspring of an affected male show the phenotype, but all his daughters are "carriers"  3) None of the sons of an affected male show the phenotype under study, nor will they pass the condition to their descendants: skips generations  4) Carrier females (heterozygous) pass the trait to half their sons  5) All affected females pass trait to their sons  Examples: red-green colorblindness, hemophilia, Duchene Muscular Dystrophy, Androgen Insensitivity Syndrome  e.x. Androgen Insensitivity Syndrome (AID): does not have the receptor to develop as a male, so infertile; coming through carrier mother  Individuals are genetically male (XY) but have female genetilia o What patterns in a pedigree would reveal X-linked dominant inheritance?  1) Affected males pass the condition to all their daughters but to none of their sons  2) Affected heterozygous females pass the condition to half their sons and daughters  Examples: very rare, but hypophosphatermia (vitamin D-resistant rickets) o Y-linked? A few genes on Y chromosomes, but no known Y-linked in heritance patterns  Probability! o Product rule: multiply probability of each event separately (e.x. probability of getting two heads from a flip of two fair coins: 1/2 x 1/2 = 1/4) o Sum rule:: states that the probability of either two mutually exclusive events occurring is the sum of their individual probabilities (e.x. probability of getting one head and one tail from a flip of two fair coins: T,H happens in 2 combinations: 1/4 + 1/4 = 1/2) o Example: What is the probability that a woman whose parents are not affected, but has a brother with Duchene's disease will have an affected child: probability woman inherited the X' allele = 1/2, probability to pass to child is 1/2, probability the child is affected 1/2 = product rule 1/8 Lecture 8:  Question: If you get half your genes from your mother and half from your father, it explains why you look different from your parents, but why do you look different from your samplings? Answer: Different recombination of alleles through law of independent assortment and segregation. This is because of the independent assortment of homologous chromosomes during meiosis. And...crossing over during meiosis makes "new" homologs chromosomes that even your parents didn't have  The Green Revolution in agriculture (1960-2000) o Food produced doubles; population also doubled o What made the green revolution possible? Identifying mutations in plants that would increase yield or nutritional value  Examples: sd1: an allele for a recessive trait that results in short stature. Makes plants more resistant to toppling over in wind and rain, also increases seed yield. Why? Stronger; shorter = save energy to use resources in seed production  bph2: an allele for a recessive trait that confers resistance to brown plant hoppers (insect eats rice)  Can we make a double sd1; bph2 mutant? Yes, make both at the same time; usually yes, but can be difficult if on same chromosome  Mendel's Law of Independent Assortment o A/a; B/b: Gene A and gene B are on different chromosomes o AB/ab or Ab/aB: Gene A and gene B are on the same chromosome o A/a · B/b: Unknown position for gene A and gene B o Heterozygote for a single gene: a/a = monohybrid; double heterozygote such as A/a; B/b = dihybrid  Dihybrid crosses (e.x. RRyy x rrYY) o Gametes from each are ry x rY o Dihybrid cross: parents do not look like children (more of a blend of both) o In F1, all progeny are RrYy (round and yellow) o F2, progeny produce a 9:3:3:1 ration in progeny phenotypes o Looking at 1 trait at a time (seed shape and seed colour): round: wrinkled and yellow: green both produce the 3:1 ratio. This 3:1 is hidden in the larger 9:3:3:1 dihybrid cross ratio o Mendel did these crosses for all seven traits and got 9:3:3:1 always o To visualize the random combination of these two ratios, we can use a branch diagra
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