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Genetics (Monohybrid Crosses image (Test crosses (genotype can be…

- - - - original parents, or parents of offspring called parental generation :check:
      - first generation from parental generation called F1 or forst filial generation, if these interbreed, they produce F2 generation :star:
      - each parent is diploid and has two copies of gene involved in monohybrid cross
      - a plant with genetic symbols RR or rr are said to be homozygous as they have identical alleles for the particular gene :<3:
        
        Rr means that the plant is heterozygous and have two different alleles for the particular gene
        
        if genotype if Rr, plant produces only half of normal amount of enzyme produced
        
        neither trait is expressed and the pair of alleles shows incomplete dominance :star:
        
        when a heterozygote matures and flowers, each spore mother cell produces two types of spores no just one like homozygote
        
        if gene has no effect, on spore metabolism, half R survive and half the time r cells live
        
        heterozygous phenotypes differ from both homozygous phenotypes
  - - - does not represent the outcome of any one process but gives a 1/4 chance for outcome.
    - - plant can also be selfed by being cross with a plant with the exact same genotype as its own.
      - can develop into a 50-50 expression of alleles having RR and rr genotypes. this crossing produces the 1:2:1 ratio :!!:
        
        ratio was discovered by Gregor Mendel, an Austrian monk who studied pea plants
        
        ratio works well for gametes that have one diploid and one copy that is haploid
  - - - when tested, if dominate trait prevails then genotype is TT if some show recessive trait then it is Tt
    - - these are important for plants studies in determining the genotype of other plants
  - - - Xs and a number are used to label these alleles instead of the uppercase and lowercase letters :check:
      - concept of complete dominance is more complex in these types of alleles
      - can still produce mutations but reactions are carried out more slowly
      - all alleles can produce varying functional proteins and all can be varied even from same plant producing many different phenotypes
- - - - insertion mutation can make protein be coded too long to where it cannot fold properly
      - promoter region mutations can completely inactivate gene or cause it to be active at wrong time or place
      - however a mutation to exon can cause gene to code for a protein whose active site is disrupted and protein cannot function :red_flag:
      - point mutation could have profound effect in deleting or stopping codons.
      - larger the mutation the higher the probability that critical part of DNA is affected :star:
    - - majority are deleterious, minority beneficial
      - natural selection eliminates deleterious mutations and preserves beneficial ones : :check:
      - any mutation that changes the structure of proteins, rRNA, or tRNA is more likely to produce a less useful that a more useful form
  - - - no 2 nuclei are the same in adult as DNA would be useless with no repair mechanism
      - would be impossible to produce sperm and eggs that were not extensively mutated and under circumstances complicated organism would not exist
    - - modern mutagen present society can contaminate environment with mutagens that we have no repair mechanism for :skull:
    - - identical cells would make sexual reproduction useless thus no difference in natural selection and no selective advantages :warning:
      - mutations must occur at low rate that does not endanger individual and help adapt to environment
      - if repairs were perfect, all cells would be identical
  - - - one method is due to short regions of a self-complementary sequence :black_flag:
      - strand could form a loop as DNA unwinds, DNA polymerase may pass by loop without reading base and create short DNA molecule
    - - transposable elements are most interesting and useful causes of insertion and deletion :check:
        
        come in two forms, sequences and transposons
        
        insertion sequences are only few thousand base pairs ling and conrian genes for cutting and splicing insertion into other part of DNA
        
        Transposon is like sequences but much longer and carries genes that code for proteins not associated with transposition
        
        mutations caused by the two can vary in severity
        
        if on gene, can disrupt promotor or structural region
        
        suspect that transposable elements are viruses
        
        If element is inserted in spacer DNA, effect is not very important
        
        plants have mechanism to fight them and most contain transposable elements in nuclei :star:
        
        mutations caused by transposable elements may be most important tool for genetic analysis and engineering :red_flag:
        
        are able to study metabolic pathways by exposing plants to mutagens
        
        transposons are now being sequenced and engineered to contain markers to locate mutation points of interest
        
        are pieces of DNA that readily change their position from one chromosome to another
      - if small piece of foreign DNA is present after cutting, may accidentally be reincorporated into chromosomal DNA by DNA ligase :star:
  - - - important if affects part of plant that gives rise to vegetative shoot
      - as shoot grows and reproduces vegetatively, mutated cells could become auxillary buds, then become a sexual mutation :check:
- - - - this will not result in the 9:3:3:1 ratio but something very different
    - - the last two gametes in lower portions are called recombinant chromosomes :black_flag:
        
        they are product of crossing over of homologous chromosomes and recombination alleles
      - parental type chromosomes are the other two gametes in larger portion :black_flag:
        
        this means the most common outcomes are more like the parents while the least common outcomes are unlike the parents
      - if occurs, plant will produce 4 types of gametes but not in equal numbers
      - rate of crossing over is directly proportional to the physical spacing between the genes on the chromosomes :<3:
        
        the space between genes in recombination percentages is called one map unit, or one centimorgan :star:
        
        one map unit averages one million base pairs and from this we can construct a genetic map of the plant
        
        if enough genes are mapped then we can find how each gene is linked no matter distance or assortment :world_map:
    - - as genes are linked, several types of heterozygotes are possible
      - a set of cells known to be linked is known as a linkage group
      - when all genes are mapped, thee will be exactly as many linkage groups as there are chromosomes :star:
    - - gametes from the homozygous recessive parent will all be sy
      - 2 types of F1 will be produced, occur in 1:1 ratio and the 2 phenotypes will be like those of the parent :red_flag:
      - if we exclude crossing over, gametes of the first type of heterozygote will be SY and sy
  - - - after separation in meiosis 2, the chromosomes separate from each other producing 4 equal number haploid cells
      - these 4 types are produced by a single plant as the mother produces one set and some produce the other set :black_flag:
    - - all types of zygotes can occur if multiple fertilizations occur, but must analyze hundreds of progeny to be accurate :star:
        
        however easy to come by due to pollen and ovules producing large amounts due to the large fertilization numbers
      - after pollination plants can produce dozens to thousands of seeds, enough pogeny that all 16 zygotes occur
        
        different in mammals or other large animals as they are only able to produce 1-2 offspring a year
      - any one fertilization of one sperm cell and one egg cell can produce one of 16 zygotes :red_flag:
    - - characteristic phenotype ratio occurs
      - a 9:3:3:1 ratio occurs with 9/16 of plant having dominant phenotype for both traits :check:
        
        3/16 with dominate trait of first gene and recessive trait of the second
        
        3/16 with dominant 2 gene and recessive of the 1st gene
        
        and 1/16 having recessive for both traits
        
        ratio only occurs if all 4 types of gametes are produced in equal numbers and have equal opportunity :star:
        
        if only one trait is considered it behaves as a monohybrid cross
      - each gene showing complete dominance
- - - - each has their own enzyme
      - mutation in one may not be severe and alternative pathway may increase activity and produce sufficient amounts of intermediate
        
        mutation can be supressed if this happens even in homozygous conditions
        
        DNA associated with lots of pogeny may have to performed to determine what fraction of a particular phenotype is correlated with particular gene
        
        known as quantitative trait loci :check:
- - - - the only seeds that complete development are heterozygous or dominate homozygous and results in usual genotype/phenotype ratios :star:
      - can affect the basic metabolic functions of the plant
    - - no homologous chromosomes occur and recessive and lethal alleles are not masked by dominant homologous allele :star:
      - in animals, haploid phase restricted to sperm and egg which are simple and have many inactive genes
      - in gametophytes each gene only present as a single allele
      - in plants, haploid phase consists of pollen grain with 3 cells and a megagametophyte with seven cells
        
        phase is quite simple and most genes are inactive
        
        in gametophytes many types of central metabolisms are occuring and highly deleterious allele can cause poor or no development :forbidden:
        
        if gametophytes dies without producing sperm or egg, the allele is eleminated :skull_and_crossbones:
    - - lethal genes are usually recessive and only fatal in homozygous conditions
  - - - polyploid is all plants that have more than two sets of chromosomes :star:
    - - in secondary division of meiosis, 2 chromatids may remain together and a daughter cell will recieve both copies :red_flag:
        
        cell with extra chromosome can survive adn may produce a triploid zygote for that chromosome during fertilization
        
        this is tolerated in plants but can cause downs syndrome in humans with the extra chromosome :warning:
        
        the other daughter cell receives nothing
    - - this would be lethal to animals
      - do not affect plants but triplod zygotes that are produced are sterile due to inability to undergo homologous chromosome pairing
    - - nonessential genes, complete absence may not be harmful
      - creates a surplus of DNA in tetreploid plants :check:
        
        deleterious mutations have little effect on phenotype :+1:
        
        causes mutations to be slowly eliminated by natural selection :timer_clock:
        
        incapacitation of 1/4 alleles will not be deleterious as 2-4 alleles
        
        genes that are so similar that they can be recognized as having originated as duplicates of it are called paralogs :star:
        
        extra alleles can mutate and create different forms of the same protein :check:
        
        e.g. 5 histone proteins that make up nucleosomes are needed in such abundance that each nucleus may have up to 600 paralogs of genes
        
        the multiple copies constitute a gene family :star:
        
        Extra DNA can be extremely valuable and it can be raw material for new gene evolutions :<3:
        
        the new evolution can help plant adapt to changing environment and help thrive in various other environments
        
        other cases, mutations can create new genes that produce new enzymes
        
        function can be unrelated to original genes
        
        example are ferns and flowering plants that created new metabolic pathways for flowers/leaves as green algae had no genes for that :<3:
      - polyploids have more copies than needed for every gene :heavy_plus_sign:
      - very complex genetics
  - - - called uniparental inheritance, more specifically maternal inheritance :!!:
        
        mitochondria genetics difficult to study due to amount, shape and content of DNA received from the maternal parent :question:
        
        DNA mutations are also hard to spot in mitochondria :mag: can have a severe effect but cannot be spotted in examination
        
        plastid genetics are easier if alleles affecting chlorophyll synthesis are affected :warning:
        
        DNA mutated to where plastid cannot produce chlorophyll will turn the plant red or orange and even white
        
        these plants can survive but need to be grafted for nutrients, and those plants can be used for studies :recycle:
        
        when achlorophyllous plant is crossed with green chlorophyll plant, outcome depends on which plant is pollen parent and ovule parent
        
        if plant is ovule parent all progeny also have mutant plastids and are achlorophyllous
        
        conifers are the exception as their sperm cells do not destroy their plastids so plastids are inherited paternally :evergreen_tree:
        
        pollen parent will result in 100% green plant as they recieved plastids the normal way through eggs :check:
        
        Plastid inheritance also responsible for variegation in plants, presence of spots or sectors that are multiple colors on a primarily green tree :check:
        
        cell usually has mixture of plastids
        
        leaf can occasionally receive only mutant plastids and have a different color, can survive off nutrients of other plants
        
        because plant has many plastids, rarely do all plastids of an egg have same allele unless parent has one type like cacti :cactus:
        
        can grow a large path in leaf that contains no chlorophyll in new leaf, a old leaf will have a small spot
        
        when variegation affects stems, auxillary bud may contain achlorophyllous patch :red_flag:
        
        is maternally inherited, DNA is a double helix with on end attached to the other and no histones present
        
        plastid DNA may contain up to 21% of total DNA in a cell :star:
        
        entire bud/branch grown from this will be achlorophyllous
        
        genomes of plastids contain genes for numerous enzymes as well as a complete set of plastid ribosomal RNAs and 30 of transfer RNA :<3:
        
        estimated that 80 to 100 enzymes and membrane proteins are coded by plastid DNA, many being essential :!:
        
        cytochromes
        
        proteins that bind to chlorophyll a
        
        components of proton channel/ATP synthesis complex
        
        Mitochondrial DNA contains genes for
        
        4 more items...
        
        large subunit of RuBP carboxylase
    - - all genes in nucleus undergo this
- - - - ligated is where DNA pieces are attached to each other with covalent bonds :star:
      - the large amount of initiation sites allows numerous DNA polymerases to work simultaneously, if not S phase would be months long :timer_clock:
      - as replication forks advance, DNA partially dissociates from the histone octamers,
        
        2 new DNA double helixes are completed
        
        helixes are immediately reassociate with histones into complete nucleosomes
        
        enzymes migrate forward
        
        some old histone octamers go to one double helix and some to the other, and new histone octamers are added to both :checkered_flag:
  - - - strand of double helix is cut and two parts separate, in short region "bubble" called a replicon :star:
        
        nucleotides diffuse into regions of single stranded DNA and pair with the bases along both strands :handshake:
        
        act as a substrate for DNA polymerase which is a DNA-synthesizing enzyme :star:
        
        polymerase adds deoxyribonucleotides only to 3' end of growing nucleic acid causing copying on opposite ends of the separate strands :star:
        
        DNA continues to unwind and new pieces of primer RNA form new pieces and new pieces of DNA fragments make Okazaki fragments :check:
        
        original primer RNAs and depolymerized and new Okazaki fragments are joined to the first ones
        
        enters and adds deoxyribonucleotides onto the end of the primer RNA using open DNA as guide :red_flag: Is called semiconservative replication
        
        primer RNA is the ribonulcleotides that are polymerized into short pieces 10 nucleotides long