Genetics study guide exam I

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Genetics study guide exam I
2014-10-08 17:05:27
genetics concepts

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  1. What is a gene?
    a gene is a segment of DNA that produces a functional product
  2. How can you specifically label protein vs. DNA using radioactive atoms?
    Add the radioactive label of a virus. Have the virus infect the cells.
  3. What is the structure of DNA, and how does it differ from RNA?
    1. Nucleotides form the repeating structural unit of nucleicacids.2. Nucleotides are linked together in a linear manner to forma strand of DNA or RNA.3. Two strands of DNA (and sometimes RNA) interact witheach other to form a double helix.4. The three-dimensional structure of DNA results from thefolding and bending of the double helix. 

    RNA is usually single stranded but a make bulge loops, internal loop, multibranch junctio, and stem loops. Contains Uracil instead of Thymine.
  4. You also need to know the structure of a gene – where are
    all of the necessary elements (promoter region etc..).
  5. What is a model organism? Why do we use more than one kind?
    • organisms studied by many different researchers sothey can compare their results and determine scientific principlesthat apply more broadly to other species.
    • Escherichia coli (a bacterium), Saccharomycescerevisiae (a yeast), Drosophila melanogaster (fruit fly),Caenorhabditis elegans (a nematode worm), Danio rerio (zebrafish),Mus musculus (mouse), and Arabidopsis thaliana (a floweringplant). Model organisms offer experimental advantages overother species. For example, E. coli is a very simple organism thatcan be easily grown in the laboratory. By limiting their work to afew such model organisms, researchers can more easily unravelthe genetic mechanisms that govern the traits of a given species Furthermore, the genes found in model organisms often functionin a similar way to those found in humans.
  6. What is the difference between genotype and phenotype.
    genotype refers to the genetic compositionof an individual. TT and tt are the genotypes of the Pgeneration in this experiment. The term phenotype refers to anobservable characteristic of an organism. In the P generation, theplants exhibit a phenotype that is either tall or dwarf
  7. Be prepared to discuss the molecular mechanism of DNA
    replication, know the function of major protein and what would happen if they
    weren’t there. bacteria
    • DNaA -binding boxes recognition sites.
    • DNaC - helicase loader  form complex w/ DNaB
    • Helicase - breaks hydrogen
    • primase - making RNA primers - bp
    • polymerase II: repairs
    • pol I: removes RNA primers + fill gap
    • pol III: Main replicating enzyme
    • ligase: covalent bonds on backbone
    • Topoisomerase II: Reduce supercoiling
    • other induce supercoiling.
    • SSD- single stranded binding protien, prevents H-bonds from forming protects DNA.
    • Primosome- helicase together with primase
    • repisome: promosome  + pol III working in leading and lagging strand.
    • Alpha: catalyses covelent bonds between base pairs.
    • Epsilon- proofreading 3' to 5'
    • theta:stimulates proofreading
    • beta clamp - holds pol III on DNA
  8. euk proteins for DNA rep
    • alpha polymerase: begins the process works with primase.
    • epsilon poly: adds the leading strand, DNA synthesis. 
    • ε poly: lagging strand sythesis.
    • gamma poly - works with mitochondria genome other repairs.
    • FEN - flap endonucleases - cuts primers off
  9. Understand telomerase, telomeric ends and how this ultimately protects the ends of chromosomes.  Make sure you understand that while telomerase works at the 3’end, what
    proteins are responsible for adding to the 5’ end?
    • The term telomere refers to the complex of telomeric sequenceswithin the DNA and the special proteins that are bound to thesesequences. Telomeric sequences consist of a moderately repetitivetandem array and a 3ʹ overhang region that is 12 to 16 nucleotidesin length.
    • telomerase that prevents chromosomeshortening. It recognizes the sequences at the ends of eukaryoticchromosomes and synthesizes additional repeats of telomericsequences.
    • It is catalyzed bytwo identical protein subunits called telomerase reverse transcriptase(TERT) . TERT’s name indicates that it uses an RNAtemplate to synthesize DNA. Following polymerization, thetelo merase can then move—a process called translocation—tothe new end of this DNA strand and attach another six nucleotidesto the end. This binding-polymerization-translocation cycleoccurs many times in a row, thereby greatly lengthening the 3ʹend of the DNA strand in the telomeric region.
  10. What is karyotype analysis, how is it used? What can it show you regarding disease? How are chromosomes arranged?
    • •In a cytogenetics laboratory, the
    • microscopes are equipped with a camera
    • •Microscopic images of chromosomes can now be visualized using a computer
    • •There, chromosomes can be organized in a standard way, usually from largest to smallest
    • •A karyotype is an organized representation of the chromosomes within a cell
  11. What is the chromosome theory of inheritance?  How does it relate to the mendelian
    inheritance of traits?
    • •The chromosome theory of inheritance describes how the transmission of chromosomes account for Mendelian patterns of inheritance
    • –.  Analysis of the transmission of traits from
    • parent to offspring
    • •Mendel’s plant hybridization studies
    • •The chromosome theory of
    • inheritance is based on a few
    • fundamental principles
    • –1.  Chromosomes contain the genetic material
    • –2.  Chromosomes are replicated and passed from parent to offspring
    • –3.  The nuclei of most eukaryotic cells contain
    • chromosomes that are found in homologous pairs, they are diploid
    • •During meiosis, each homolog segregates into one of the two daughter nuclei
    • –4.  During the formation of gametes, different types of (nonhomologous) chromosomes segregate independently
    • –5.  Each parent contributes one set of
    • chromosomes to its offspring
    • •The sets are functionally equivalent
    • –Each carries a full complement of genes
    • •The chromosome theory of
    • inheritance allows us to see the
    • relationship between Mendel’s laws and chromosome transmission
    • –Mendel’s law of segregation can be explained by the homologous pairing and segregation
    • of chromosomes during meiosis
    • •Refer to Figure 3.16
    • –Mendel’s law of independent assortment can be explained by the relative behavior of
    • different (nonhomologous) chromosomes during meiosis
  12. How do sex chromosomes play into the theory of inheritance?
    • •In many animal species, chromosomes play a role in sex determination
    • •Humans have 46 chromosomes
    • –44 autosomes
    • –2 sex chromosomes
    • •Males contain one X and one Y chromosome
    • –They are termed heterogametic
    • •Females have two X chromosomes
    • –They are termed homogametic
    • •The Y chromosome determines maleness
  13. What is the difference between meiosis and mitosis?  Be prepared to be able to tell differences in
    terms of chromatids, sister chomatids, homologous chromosomes and number of
    each (these are just a few idea of how to differentiate between the two, there
    are others i.e. outcome of ploidy etc)
    • •Mitosis vs Meiosis
    • –Mitosis produces two diploid daughter cells
    • –Meiosis produces four haploid daughter cells
    • –Mitosis
    • produces daughter cells that are genetically identical
    • –Meiosis produces daughter cells that are not 
    • genetically identical
    • •The daughter cells contain only one homologous chromosome from each pair
    • •The daughter cells contain many different combinations of the single homologs
  14. Understand what is happening at the various stages of mitosis and meiosis (in general).
    • •Mitosis is subdivided into five phases
    • Interphase 
    • •Chromosomes are decondensed •By the end of interphase, the chromosomeshave already replicated–But the six pairs ofsister chromatids are not seen untilprophase•The centrosome, the attachmentpoint of the mitotic spindle, divides
    • –Prophase
    • •Nuclear envelope dissociates into small vesicles
    • •Chromatids condense into more compact structures
    • •Centrosomes begin to separate
    • •The mitotic spindle apparatus is formed
    • Composed of mircotubules (MTs
    • –Prometaphase 
    • •Centrosomes move to opposite ends of the cell, forming the spindle poles
    • •Spindle fibers interact with the sister chromatids
    • •Kinetochore microtubules grow from the two poles
    • –If they make contact with a kinetochore, the sister chromatid is “captured”
    • –If not, the microtubule depolymerizes and retracts to the centrosome
    • The two kinetochores on a pair of sister chromatids are attached to kinetochore MTs on opposite pole
    • –Metaphase
    • •Pairs of sister chromatids align themselves
    • along a plane called the metaphase plate
    • •Each pair of chromatids is attached to both
    • poles by kinetochore microtubules
    • –Anaphase
    • •The connection holding the sister chromatids together is broken
    • •Each chromatid, now an individual
    • chromosome, is linked to only one pole
    • •As anaphase proceeds
    • –Kinetochore MTs shorten
    • •Chromosomes move to opposite poles
    • –Polar MTs lengthen Poles themselves move
    • further away from each other
    • –Telophase
    •  •Chromosomes reach
    • their respective poles and decondense
    • •Nuclear membrane reforms to form two separate nuclei
    • •In most cases, mitosis is quickly followed by cytokinesis
    • –In animals
    • •Formation of a cleavage furrow
    • –In plants
    • •Formation of a cell plate
  15. Be able to document Meoisis, when do chromosomes cross over?  What are key components involved in crossing over, how do they function? What happens if they are not there?
    • •Unlike mitosis, meiosis involves two successive divisions
    • –These are termed Meiosis I and Meiosis II
    • –Each meiotic division is subdivided into
    • •Prophase
    • •Prometaphase
    • •Metaphase
    • •Anaphase
    • •Telophase
    • •Prophase I is further subdivided into five stages known as
    • –Leptotene
    • –Zygotene
    • –Pachytene
    • –Diplotene
    • –Diakinesis
    • Crossing over occurs in prophase, pachytene
    • The Synaptonemal Complex
    • Lateral element - Bound to chromosomal DNA of homologous chromatids.
    • central element -provides link between lateral elements
    • Transverse filament - connects lateral to central.
  16. And how does crossing over affect gene segregation?
    • •During meiosis, each homolog segregates into one of the two daughter nuclei
    • –4.  During the formation of gametes, different types of (nonhomologous) chromosomes segregate independently
  17. What is Mendel’s law of Independent assortment?
    During gamete formation, the segregation of any pair of hereditary determinants is independent of the segregation of other pairs
  18. When would you perform a testcross? Know how to determine whether you need to do a testcross AND generate a conclusion from the testcross
    Independent assortment is also revealed by a dihybridtest cross. In this type of experiment, dihybrid individuals aremated to individuals that are doubly homozygous recessive forthe two characters. For example, individuals with a TtYy genotypecould be crossed to ttyy plants. As shown below, independentassortment would predict a 1:1:1:1 ratio among the resultingoffspring:
  19. What is the difference between a monohybrid and a dihybrid cross? Know how to do a punnett square for monohybrid and dihybrid
    • •His first experiments
    • involved crossing two variants of the same characteristic
    • –This is termed a monohybrid cross
    • –A single characteristic is being observed
    • •dihybrid crosses
    • –Crossing individual
    • plants that differ in two characters
  20. Be able to diagram:
  21. Alleles are types of genes—so how do mutations relate to alleles?
    Mutation would create a new version of the allele and introduce it to a population.
  22. What is a loss of function allele? Knowing that, what would a gain of function allele be?
    • •The defective copies of genes are
    • termed loss-of-function alleles
    • •Unknowingly, Mendel had used seven
    • loss-of-function alleles in his studies on pea plants
    • •Loss-of-function alleles are commonly
    • inherited in a recessive manner
  23. What is the product rule? How is it applied? Be able to apply it to a problem like those given in the homework.
    • •The probability that two or more independent events will occur is equal to the product of their respective probabilities
    • •Note
    • –Independent events are those in which the occurrence of one does not affect the probability of another
  24. What is the sum rule? How is it applied? Be able to apply it to a problem like those given in the homework.
    •The probability that one of two or moremutually exclusive events will occur is the sum of their respective probabilities
  25. How do you analyze a pedigree, what do each of the symbols mean?
    • -female
    • -male
    • - sex unknown or not specified
    • -miscarriage
    • -deceased individual
    • -unaffected individual
    • -affected individual
    • - presumed heterozygotes (dot means sex linked)
    • -Consanguineous mating (between related individuals)
    • -Fraternal
    • -Identical
  26. In a pedigree, how can you see X-linked vs. Autosomal mutations?

    In a pedigree, how can you see Dominant vs. recessive mutations?

    Know how to distinguish these by looking at an unlabeled pedigree.
    • Autosomal Dominant (rare)
    • -affected males and females in each generation
    • -transmit condition to sons/daughters
    • -proportional affected males and females

    • Autosomal recessive
    • -appearance of phenotype of disorder in male/female progeny but parents are unaffected people.
    • Sexlinked (x) Dominant
    • - affected males pass condition to all daughters (none of sons)
    • - female carriers pass 1/2 to sons and 1/2 to daughters.
    • Sex linked recessive 
    • - more males then females will show the rare phenotype.
    • - Affected males = 0 progeny will should phenotype, but daughters are all carriers.
  27. What is the molecular basis for dominance or
    recessiveness of mutant alleles?
    • –.  50% of the normal protein is enough to
    • accomplish the protein’s cellular function
    • –2. The heterozygote may actually produce more than 50% of the functional protein
    • •The normal gene is “up-regulated” to compensate for the lack of function of the
    • defective allele.
    • –Three explanations for most dominants
    • •Gain-of-function
    • –Protein encoded by the mutant gene is changed so it gains a new or abnormal function
    • •Dominant-negative
    • –Protein encoded by the mutant gene acts antagonistically to the normal protein
    • •Haploinsufficiency
    • –mutant is loss-of-function
    • –heterozygote does not
    • make enough product to give the wild type phenotype
  28. Incomplete Dominance
    • •In incomplete dominance the heterozygote exhibits a phenotype that is intermediate between the corresponding homozygotes
    • ex 4' clock flower phenotypic ratio: 1:2:1
  29. X-linked Genes
    • •Many species have males and females that differ in their sex chromosome composition
    • –Certain traits are governed by genes on the sex chromosomes
    • –A pedigree for an X-linked disease shows that it is mostly males that are affected with their
    • mothers as carriers
  30. Lethal Alleles
    • •A lethal allele is one that has the potential to cause the death of an organism
    • –These alleles are typically the result of mutations in essential genes
    • They are usually inherited in a recessive manner.
    • mice, phenotypic ratio: 2:1
  31. Pleiotropic Effects
    • •Most genes actually have multiple effects
    • •Multiple effects of a single gene on the phenotype of an organism is called pleiotropy
    • •Can be caused because
    • –The gene product can affect cell function in more than one way
    • –The gene may be expressed in different cell types
    • The gene may be
    • expressed at different stages of development
  32. Epistasis
    • •Epistasis is when the alleles
    • of one gene mask the phenotypic effects of the alleles of another
    • –Epistasis is considered
    • relative to a particular phenotype
    • –The case of walnut comb is recessive epistasis because the homozygote  or r or p is required to mask the walnut phenotype.
  33. Dominant Epistatic
    • (squash colors)
    • There is a dominant series:
    • Wwhite>wcolor>GYellow>g,green
    • phenotypic ratio: 9:3:3:1
  34. Recessive suppression epistasis
    • 1 gene suppressesthe expression of mutant gene.
    • Su-suppressor susu supressee
    • flies, phenotypic ration 13:3
  35. complementary gene action
    • A phenomenon in which two different parents that express the same or similar recessive phenotypes produce offspring with a wild-type phenotype. 
    • flower color in sweet peas 
    • phentotypic ratio: 9:7
  36. Recessive epistasis
    • Labrador retrievers
    • phenotypic ratio 9:3:4
    • ex ee means to pigment even if other allele is dominant.
  37. How can you distinguish whether or not two genes are linked?
    My making a prediction using mendel's law of independent assortment and and testing the theory if the results are much different than that of mendel's laws, then it could be genetic linkage.
  38. How does recombination frequency distinguish tightly linked, loosely linked, or unlinked genes?
    • •Genetic maps allow us to estimate the relative distances between linked genes, based on the likelihood that a crossover will occur between them
    • •Experimentally, the percentage of recombinant offspring is correlated with the distance between the two genes
    • –If the genes are far apart à many recombinant offspring
    • –If the genes are close à very few recombinant offspring
  39. What is crossing over? How does it occur?
    • •Genes that are far apart on the same chromosome may independently assort from each other.
    • –This is due to crossing over
    • A dihybrid cross studies linkage
    • between two gene
    • •In diploid eukaryotic species, linkage can be altered during meiosis as a result of crossing over
    • •Crossing over
    • –Occurs during prophase I of meiosis
    • •replicated sister chromatid homologues associate as bivalents
    • –Non-sister chromatids of homologous chromosomes exchange DNA segments
  40. How do you use the Chi square test to check linkage results?