Final Exam Flashcards.txt

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Final Exam Flashcards.txt
2010-12-16 00:36:45
Bio Final Exam Review

Bio115 Final Exam Review
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  1. Prokaryote
    lack nuclear membrane and possess no membrane-bound organelles
  2. Eukaryotes
    Have a nuclear membrane and membrane-bound organeles
  3. What is the fundamental unit of heredity?
    the gene
  4. Principle of segregation
    Diploid's alleles separate in equal proportions
  5. What is a testcross?
    Crossing an individual of unknown genotype with a homozygous recessive individual to reveal the unknown.
  6. When a het has a phenotype intermediate between the phenotypes of two homo, the trait is said to be _______
    incomplete dominance
  7. When two alleles separate, their separation is independent of the separation of alleles at other loci. What principle is this?
    Independent assortment
  8. What kind of crosses reveal the principle of independent assortment?
  9. How do you determine the chi-square value for inheritance of crosses?
    chi-square = sum((obs_i - exp_i)/exp_i), with degrees of freedom one less than the expected number of phenotypes
  10. What type of sex determination has males with only one X?
    XX-XO sex determination
  11. What type of sex determination has males with two of the same chromosome?
    ZZ-ZW sex determination
  12. What determines phenotype in Drosophila?
    X:A ratio, A is number of autosomes
  13. In humans, what does the combination of XO chromosomes lead to?
    Turner's syndrome
  14. In humans, what does the combination of XXY chromosomes lead to?
    Klinefelter syndrome
  15. In humans, what does the combination of XXX chromosomes lead to?
    Poly-X females
  16. What is a reciprocal cross?
    It is a breeding experiment designed to test the role of parental sex on a given inheritance pattern. In one cross, a male expressing the trait of interest will be crossed with a female not expressing the trait. In the other, a female expressing the trait of interest will be crossed with a male not expressing the trait.
  17. If only one copy of a chromosomal region is present, such as X-linked genes in humans, this is called ______
  18. __________ equalizes the amount of protein produced by X-linked genes in the two sexes.
    Dosage compensation
  19. What is the Lyon hypothesis?
    Darkly staining bodies in the nuclei of female cats (known as Barr bodies) were inactive X chromosomes
  20. _______ is when the phenotype of the het is intermediate between the two homozygotes.
    Incomplete dominance
  21. The MN blood group is an example of _________.
  22. __________ is the percentage of individuals with a particular genotype that express the expected phenotype.
  23. _______ describes the degree to which a genotype is phenotypically expressed.
  24. A ____________ causes death at an early stage of development, often before birth
    lethal allele. Note that this affects the phenotypic ratio outcome
  25. An allele is said to be ______ when it has more than one phenotype.
  26. _______ occurs when genes at multiple loci affect a single phenotype.
    Gene interaction
  27. The mallard example with duck feather pattern highlighted _________
    multiple alleles at a single locus.
  28. ______ is a phenomenon in which a one gene masks (hides) the effect of another gene at a different locus
  29. The gene that does the masking is called the _______
    epistatic gene
  30. The gene that is masked is called the ______ gene.
  31. The presence of either of two recessive alleles at two different loci resulting in a recessive phenotype is called ______
    duplicate recessive epistasis
  32. When a single copy of an allele is sufficient to mask the phenotype of alleles at a second locus, this is ______
    dominant epistasis
  33. Interpreting dihybrid cross ratios is often easier if the amount is ...
    multiplied by 16 and then divided by the total
  34. ______ traits are present in males and females, but are inherited only from the mother and can result in phenotypic variation.
    Cytoplasmically inherited
  35. __________ is a phenomenon in which the phenotype of the offspring is determined by the genotype of the mother.
    Genetic maternal effect. Note that the offspring's phenotype is determined by mother's genotype, not her phenotype.
  36. _________ is the differential expression of genetic material depending on whether it is inherited from the male of female parent.
    Genomic imprinting
  37. At the ______________, the mutant protein functions normally.
    permissive temperature
  38. At the ____________, mutant protein is inactivated and endocytosis is halted, resulting in paralysis.
    non-permissive temperature
  39. Characteristics that have a few easily distinguished characteristics, such as seed color or shape, are called _____.
    discontinuous characteristics
  40. _________ are characteristics, such as height, for which a continuous distribution of phenotypes is observed. Also called _________.
    Continuous characteristics, quantitative characteristics
  41. Continuous characteristics frequently arise because genes at many loci interact to produce the phenotype: ________.
    polygenic characteristics
  42. What is the number of genotypes encoded by n loci with two alleles?
  43. Name useful characteristics of genetic model organisms.
    • short generation time
    • large number of progeny
    • adaptable to lab environment
    • housed and propagated relatively inexpensively
    • genomes sequenced
  44. What model organism has a homolog whose mutant in a human eye disease?
    Drosophila melanogaster
  45. What model organism taught us about differences in skin color?
    Zebrafish (Danio rerio)
  46. What is the most widely studied prokaryote?
    Escherichia coli, regulation of expression of genes
  47. What is the simplest eukaryotic genetic model organism?
    Baker's yeast (Saccharomyces cerevisiae), DNA damage/repair
  48. What is the most basic multicellular animal that is a genetic model organism?
    roundworm (Caenorhabditis elegans), neurotransmitters
  49. What is the mammalian genetic model organism?
    House mouse (Mus musculus), white blood cells
  50. What is the primary plant model organism?
    Thale cress plant (Arabidopsis thaliana); genome structure, plant evolution
  51. _______, the person from whom the pedigree is initiated.
  52. Characteristics of autosomal recessive traits in pedigrees
    • Normal parents have affected children
    • Equal number of males and females
    • 1/4 of offspring of two carriers are affected
    • Normal children with affected siblings have a 2/3 chance of being a carrier
    • Consanguineous marriages are sometimes involved
    • Example: tay-sachs
  53. Characteristics of autosomal dominant traits in pedigrees
    • Does not skip generations (unless incompletely penetrant/express)
    • Approx equal number males and females
    • Most affected individuals are heterozygous
    • 1/2 offspring of an affected individual are affected
    • These alleles tend to be very rare, even more so for homozygous
    • Example: elevated blood cholesterol
  54. Characteristics of X-linked recessive traits in pedigrees
    • Males usually affected
    • Usual transmission from carrier woman to son
    • Daughters of carrier mothers have 1/2 chance of being carriers
    • Not passed from father to son
    • Affected woman must have an affected father and either an affected mother or carrier mother
    • Example: Hemophilia A
  55. Characteristics of X-linked dominant traits in pedigrees
    • Affected males only have affected daughters.
    • Affected mothers have 1/2 affected kids, and 1/2 normal
    • Trait does not skip generations
    • Rare: assume heterozygous
    • Example: Hypophosphatemia - vitamin D resistant rickets
  56. Characteristics of Y-linked traits in pedigrees
    • Very rare
    • Father to son transmissions
    • All male offspring are affected
  57. ______ genes do not assort indepently.
  58. ______ is the soring of alleles into new combinations
  59. Genes on the same chromosome belong to the same ________
    linkage group
  60. If the genes of interest are linked, only _______ progeny are produced.
  61. Genes that exhibit crossing over are ________.
    incompletely linked
  62. A single crossover produces what ratio of recombinant to nonrecombinant gametes?
  63. _____ is the percentage of progeny produced in a cross.
    Recombination frequency
  64. Wild-type alleles in a _____ configuration are on the same chromosome.
  65. Wild-type alleles in a _____ configuration are on different chromosomes.
  66. What are the two types of recombination?
    Interchromosomal and intrachromosomal.
  67. Which type of recombination arises from independent assortment?
  68. Who discovered that Intrachromosomal Recombination Results from Physical Exchange Between Chromosomes?
    Harriet Creighton and Barbara McClintock
  69. ______ are chromosome maps calculated by using the genetic phenomenon of recombination.
    Genetic maps, 1 m.u. = 1% recombination
  70. ______ are chromosome maps calculated by using physical distances along the chromosome.
    Physical maps, distance in base pairs
  71. Why are genetic maps based on short distances more accurate than those based on long distances?
    Double crossovers are not detected
  72. In a 3-point cross, classes with the fewest progeny are ____.
  73. In a 3-point cross, classes with the most progeny are ____.
  74. In a 3-point cross, the recombination frequency is calculated by adding all the crossovers (single and double) between two genes and dividing by the total number of progeny.
    See example Lecture 10, Slide 7
  75. The degree to which one crossover interferes with additional crossovers in the same region is termed ________.
  76. The ratio of observed double crossovers to expected double crossovers is called the _______.
    coefficient of coincidence
  77. The number of expected double crossovers can be calculated by multiplying the total number of progeny by _____.
    the product of the probability of recombination for the single crossovers.
  78. Interference =
    1- coefficient of coincidence
  79. Disease causing genes are mapped by _______ analysis which examines the probability of having linkage at a particular RF compared to the probability of independent assortment.
    logarithm of odds
  80. A LOD score of 3 indicates linkage with the specified recombination is _____ times as likely to produce what was observed as independent assortment.
  81. Variable genes with easily observable phenotypes are called ____.
    genetic markers
  82. Variations in in DNA sequence detected by cutting the DNA with restriction enzymes are called _____.
    Restriction Fragment Length Polymorphisms (RFLPs)
  83. Variable numbers of short DNA sequences repeated in tandem are called ____.
  84. Individual variations in the DNA nucleotides are called ____.
    Single Nucleotide Polymorphisms (SNPs)
  85. Describe deletion mapping.
    • Individual homozygous for a recessive mutation in the gene of interest is crossed with an individual heterozygous for a deletion.
    • If the gene of interest is in the deletion region, half of the progeny will dislay the mutant phenotype.
    • If it's not, all the progeny will be wild type.
  86. Describe somatic-cell hybridization
    See first 3 slides of Lecture 11. It's used for gene mapping
  87. _____ is a method for determining the chromosomal location of a particular gene through molecular analysis.
    in situ hybridization
  88. Wild-type bacteria are called ____.
  89. _____ contains all the nutrients required by prototrophic bacteria.
    Minimal media
  90. Mutant strains called _____ lack enzymes necessary for metabolizing nutrients or synthesizing essential molecules.
  91. _____ contains all substances required by bacteria for growth and reproduction.
    Complete media
  92. Most bacteria have __#__ _____ (shape) chromosome(s) several million base pairs long.
    1, circular
  93. Many bacteria also contain small (several thousand base pairs), circular DNA molecules called ____.
  94. _____ are plasmids capable of freely replicating and able to integrate into the bacterial chromosome.
  95. The ______ in E. coli controls mating and gene exchange between E. coli cells.
    F (fertility) factor
  96. Plasmids Replicate _____ of the Bacterial Chromosome.
  97. What are three types of gene transfer in bacteria?
    Conjugation, transformation, and transduction
  98. In ______, a cytoplasmic bridge forms allowing transfer of part of DNA from one bacteria to another.
  99. In _____, naked DNA is tken up by the recipient cell/bacteria.
  100. In ______, a virus attaches to a bacteria cell to inject DNA.
  101. _____ is usually the only DNA transferred during conjugation.
    F factor
  102. Conjugation between an F+ cell with an F- cell results in an ____ cell.
  103. ____ cells contain an F factor integrated into the bacterial genome.
    Hfr (high frequency)
  104. Bacterial genes can be transferred from an ___ cell to an F- cell in conjugation.
  105. An Hfr cell can be converted into an F' cell during ______.
  106. Sexduction produces _______, cells with two copies of some genes.
    merozygotes (partial diploids)
  107. The transfer times of genes between bacteria indicate the order and relative distances which can be used to construct a ______.
    genetic map
  108. _______ are small circular plasmids that carry genes that encode antibiotic resistance and can be transferred by conjugation.
    R plasmids
  109. Cells that take up DNA through their outer membranes are called _____ cells.
  110. Competence is influenced by _____.
    Growth stage, concentration of available DNA, and composition of medium; heat shock, chemical treatment
  111. The cell that receives DNA in a transformation is called the _______.
  112. When genes are transformed together, they are ______.
  113. The rate of cotransformation is _______ proportional to the distances between the genes which is useful for gene mapping.
  114. Sometimes bacteria acquire DNA from eukaryotes in a process called ___________.
    horizontal gene transfer
  115. The process of passing passing genetic information through reproduction is called ____________.
    vertical gene transfer
  116. A simple replicating structure made up of nucleic acid surrounded by a protein coat is called a _____.
  117. __________ are viruses that infect bacteria, and have been used extensively for genetic studies.
    Bacteriophages (phages)
  118. Virulent phages reproduce only through the _____ cycle and always kill their host.
  119. _________ phages can undergo either the lytic or the lysogenic cycle.
  120. Phage DNA integrates into the bacterial chromosome and becomes a ________.
  121. When a bacteria lyses, the adjacent bacteria are infected which also lyse resulting in a clear patch called a _____.
  122. If a phage containing bacterial DNA transfers genes to another bacterium, recombination may take place and produce a _______.
  123. The rate of transduction is ___.
  124. The rate of cotransduction is _____ proportional ot the distances between genes.
  125. _____ transduction can only occur near an att site.
  126. In specialized transduction, a phage called ________ can be produced resulting in either an unstable transductant or a stable transductant with a gal+ allele.
    lambda gal defective
  127. _______ used the awesome power of phage genetics to make inferences about gene structure.
    Seymour Benzer
  128. The sites of different mutations in the same gene can be mapped, referred to as _______.
    intragenic mapping
  129. A _______ test indicates whether two mutations occur in the same or different genes.
  130. A _______ is a functional gene defined by a complementation test.
  131. _______ occurs when there is at least one wild-type copy of each gene, i.e. the mutations are in different genes.
  132. What are the four basic types of chromosomes?
    metacentric, submetacentric, acrocentric, telocentric
  133. A complete set of chromosomes possessed by an organism presented as an ordered image is called a _____.
  134. What are three types of chromosome mutations?
    rearrangements, aneuploids, and polyploids
  135. What are four types of chromosomes rearrangements?
    duplications, deletions, inversions, and translocations
  136. When a single copy of a gene is not sufficient to produce a wild-type phenotype, it is said to be a ______ gene.
  137. ______ inversions do not include the centromere, while ______ do.
    Paracentric, pericentric
  138. ______ genes are nonviable in both peri and paracentric inversions.
  139. A _______ involves the movement of genetic material between nonhomologous chromosomes.
  140. In a _______ translocation, there is a two-way exchange of segments between two chromosomes.
  141. In a _______ translocation, two long arms of chromosomes are combined creating a large metacentric chromosome.
  142. In homologous pairing in translocation heterozygotes, the best option is ______ segregation.
  143. ________ is an increase of a decrease in the number of individual chromosomes.
  144. Aneuploidy in meiosis ___ (I or II) results in 2 trisomic and two monosomic zygotes.
  145. Aneuploidy in meiosis ___ (I or II) results in 1 trisomic, 1 monosomic, and 2 normal (diploid) zygotes.
  146. In humans, ______ results in 44 chromosomes.
  147. In humans, monosomy results in how many chromosomes?
  148. In humans, trisomy results in how many chromosomes?
  149. In humans, ______ results in 48 chromosomes.
  150. What mechanism for controlling gene dosage could account for viability of XXX females?
  151. What creates a carrier in familial Down syndrome?
    Robertsonian translocation
  152. ____ is the presence of more than two sets of chromosomes.
  153. ____ are 5n in chromosome number.
  154. _____ is a type of polyploidy where chromosome sets are from a single species.
  155. _____ is a type of polyploidy where chromosome sets are from different species.
  156. The primary structure of DNA is the _____.
    nucleotide sequence
  157. Secondary structure of DNA is the _____.
    double-stranded helix.
  158. One type of tertiary structure in DNA is ______, which takes place when the DNA helix is subjected to strain by being overwound or underwound.
  159. Supercoiling is controlled by _______, enzymes that add or remove rotations from the DNA helix.
  160. Two types of eukaryotic chromatin are the more common one, ____, and ____, which is present near centromeres and telomeres and along X-inactivated chromosomes.
    Euchromatin, Heterochromatin
  161. Most abundant proteins in chromatin are ____ - small, positively charge proteins of 5 major types.
  162. ____ consist of DNA wrapped about 4 pairs of histones.
  163. A _____ consists of a nucleosome plus the ____ histone acting as a clamp.
    chromatosome, H1
  164. _____ chromosomes arise when repeated rounds of DNA replication take place without cell divisions in certain tissues in Drosophila.
  165. Acetylation occurs when enzymes called _____ attach acetyl groups to lysine amino acids on the histone tails.
  166. Centromeric sequences Serve as binding sites for _____ proteins that provide anchor sites for spindle fibers.
  167. ____ was awarded the nobel prize for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase.
    Elizabeth Blackburn
  168. _____ are stabilizing sequences at the ends of chromosomes.
  169. ______ proteins bind to the G-rich single-stranded sequence of telomeres.
    POT (Protection Of Telomere)
  170. A structure called the _____ also functions in protecting the telomere from degradation.
  171. Artificial chromosomes such as the YAC or BAC contain what there essential elements?
    Centromere, pair of telomeres, origin of replication
  172. Sequences present at one or a few times in the genome are called ___.
    Unique-sequence DNA
  173. Groups of related genes arising from duplication of unique-sequence DNA are called ___.
    gene families
  174. The two types of repititive DNA are called ___ and ___ DNA.
    moderately repetitive and highly repetitive
  175. Two types of moderately repetitive DNA are called ____ and ___ .
    tandem repeat sequences and interspersed sequences
  176. _____ DNA sequences are sometimes called lite DNA and are often found at ___ and ___.
    Highly repetitive, centromeres, telomeres
  177. ____ are mobile DNA sequences.
    Transposable elements
  178. ______ result from staggered cuts made in the target DNA when a transposable element is inserted.
    Flanking direct repeats
  179. ____ are present in many TEs are recognized by enzymes that catalyze the transposition.
    Terminal inverted repeats
  180. Terminal inverted repeats are ____ and ____ .
    inverted and complementary
  181. What are two classes/mechanisms of transposition?
    Class I/DNA transposons, and Class II/Retrotransposons
  182. What are two kinds of Class I/DNA transposons?
    non-replicative and replicative
  183. Class II/retrotransposons are always ____.
  184. DNA transposons require an enzyme called ____ which is usually encoded by the TE.
  185. In replicative transposition, two DNA molecules are joined and the TE is replicated, producing a ____.
  186. Retrotransposons use an ____ intermediate used to reverse transcribe back into DNA.
  187. An enzyme called ____ is usually encoded by retrotransposons.
    reverse transcriptase
  188. Transposable elements were discovered in eukaryotes by _____.
    Barbara McClintock
  189. Ds in maize was able to transpose nonautonomously using transposase from Ac elements. What is a possible reason Sleeping Beauty wasn't able to do this?
    The inverted repeats were also mutated. Transposase REQUIRES inverted repeats.
  190. What are three types of TEs in bacteria?
    Insertion sequences, composite transposons, and noncomposite transposons
  191. The simplest types of transposons in bacteria are the ___ and have 1-2 genes which encode ___.
    insertion sequences, transposes(s)
  192. A segment of DNA flanked by insertion sequences can transpose and is called a ____.
    composite transposon
  193. ____ transposons do not have insertion sequences.
  194. ___ found in fruit flies have both a transposase and a repressor of transposition.
    P elements
  195. What were three models of proposed DNA replication?
    conservative, dispersive, and semiconservative
  196. ____ performed an experiment to determine which of three models of DNA replication applied to E. col.
    Meselson and Stahl
  197. ____ replication of DNA takes place in circular DNA in bacteria.
  198. _____ replication of DNA takes place in some viruses and in the F factor of E. coli.
  199. Eukaryotic genomes require multiple ____.
    origins of replication
  200. The process of DNA replicaiton includes many componets including (3):
    a template, substrates (dNTPs), and enzymes
  201. DNA synthesis always goes in the ____ direction.
  202. Short fragments of DNA produced by discontinuous synthesis on the _____ strand are called ____.
    lagging, Okazaki
  203. Which mode/l of DNA replication does not have a lagging strand?
    Rolling-circle model
  204. Four steps of DNA Replication
    • Initiation
    • Unwinding
    • Elongation
    • Termination
  205. DNA Helicase binds to...
    The lagging-strand in the 5' to 3' direction and breaks hydrogen bonds while moving along the replication fork
  206. DNA Gyrase ...
    relieves torsional strain that builds up ahead of the replication fork due to unwinding
  207. Primase ...
    sysnthesizes short strands of RNA including a 3'OH group for replication to begin
  208. How many primers are required on the leading strand?
    Just one
  209. DNA polymerase III ...
    • 5' to 3': polymerase activity: adds nucleotides (primary)
    • 3' to 5': exonuclease activity for error correction
  210. DNA polymerase I ...
    • 5' to 3': polymerase activity: adds nucleotides
    • 3' to 5': exonuclease activity
    • 5' to 3': exonuclease activity - remove RNA primers
    • Not as efficient as DNA polymerase III
  211. DNA ligase ...
    links together DNA at nicks/Okazaki fragments by forming a phosphodiester bond between adjacent nucleotides
  212. Initiator protein
    Binds to origin and separates strands of DNA to initiate replication
  213. Single-strand-binding proteins
    Attach to single-stranded DNA and prevent secondary structures from forming (stabilizes)
  214. Termination can occur when...
    • Replication forks meet
    • A termination protein (Tus in E. coli) binds to specific sequences to block helicase
  215. What is an Autonomously Replicating Sequence?
    Origin of replication found in yeast
  216. Why do origins of replication typically have numerous A-T base pairs?
    Easier to break - only 2 H-bonds compared to 3 for C-G base pairs
  217. What is an Origin-Replication Complex?
    In eukaryotes, an ORC binds to origins and unwinds the DNA in this region
  218. What is licensing?
    In eukaryotes, it is the regulation of precise replication once per cell cycle from a large number of origins
  219. What is telomerase?
    Telomerase is a ribonucleoprotein which maintains telomeres by extending the DNA and filling in the gap due to removal of the RNA primer after replication
  220. When does homologous recombination/crossing over take place?
    Prophase I, after DNA replication
  221. What are the two models of recombination?
    • Holliday
    • Double-strand break(*)
  222. What are three DNA binding motifs?
    • Helix-turn-helix
    • zinc fingers
    • leucine zipper
  223. lac operon is ...
    negative inducible
  224. trp operon is ...
    negative repressible
  225. trp operon is also regulated by attenuation - when tryptophan level is high:
    region 3 and 4 pair resulting in termination of transcription
  226. Antisense RNA regulates transcription by ...
    binding to mRNA to create double-stranded RNA blocking the ribosome-binding site
  227. Riboswitches with a regulatory protein...
    blocks the ribosome binding site by conformation change
  228. Ribozymes with a regulatory molecule ...
    induce cleavage
  229. Histone modification includes:
    Methylation, acetylation, and phosphylation
  230. Acetyl groups are added by:
    acetyl transferase
  231. Chromatin remodeling complexes...
    bind to sites in DNA and reposition nucleosomes allowing transcription factors to bind to promoters and initiate transcription
  232. Heavily methylated DNA ...
    is associated with the repression of transcription in vertebrates and plants
  233. Transcriptional activator proteins...
    bind to sites on DNA and stimulate transcription specific to a gene or subset of genes
  234. In eukaryotes, repressors ...
    do not directly block RNA polymerase, but instead compete with activators or interfere with the basal transcription apparatus
  235. Enhancers ...
    can operate at distant promoters by way of DNA looping out
  236. Insulators ...
    block the action of enhancers
  237. An example of coordinated gene regulation is:
    Several eukaryotic genes respond via consensus sequences to extreme heat producing heat-shock proteins
  238. Alternative splicing allows pre-mRNA to...
    be spliced in multiple ways generating different proteins in different tissue or at different times in development
  239. A female fruit fly has a ratio of:
  240. A male fruit fly has a ratio of:
  241. A ratio of 1.0 in fruitfly embryos activates the Sxl gene to produce a protein that causes ...
    tra pre-mRNA to be spliced at a downstream 3' site resulting in tra protein which leads to female fruit flies
  242. RNA is degraded by ...
  243. P bodies are:
    specialized complexes in which RNA molecules are degraded or sequestered for later release
  244. RNAi inhibits gene expression through:
    • Cleavage of mRNA leading to degradation using Dicer, siRNAs and RISC
    • Inhibition of translation using Dicer, miRNAs and RISC
    • Transcriptional silencing using RITS, siRNA and methylation
    • Degradation of mRNA (not via cleavage) using Dicer and RISC
  245. Posttranslational modifications of proteins includes
    • Selective cleavage and trimming of amino acids from the ends
    • Acetylation
    • Addition of phosphate groups
    • Addition of carboxyl groups
    • Addition of methyl groups
    • Addition of carbohydrates
  246. When the tinman gene has a mutation, ...
    the transcription factor is not produced and the heart doesn't develop
  247. What are the three major types of gene mutations?
    • Base substitution
    • Base insertion
    • Base deletion
  248. Purine to purine mutations are
    transition mutations
  249. The phenotypic effects of base mutations are:
    • Missense
    • Nonsense
    • Silent mutations
  250. A neutral mutation is:
    a missense mutation that alters the amino acid, but does not change its function
  251. Examples of spontaneous mutations are
    • Wobble
    • Unequal crossing over
    • Deamination
    • Depurination
  252. A base analog is
    a chemical with a structure similar to any of the four standard bases
  253. Chemical mutagens include
    • EMS: alkylation
    • Nitrous acid: deamination
    • Hydroxylamine: hydroxylation
  254. intercalating agents
    molecules which insert into DNA in place of nitrogenous bases causing insertions and deletions, e.g. proflavin and acridine orange
  255. Hermann Muller
    1927: showed mutations in fruit flies inducible by radiation
  256. x-rays, gamma rays, cosmic rays
    alter base structure, break phosphodiester bonds, and even cause double-strand breaks
  257. UV light
    less energy, but still mutagenic
  258. pyrimidine dimers
    can be caused by UV light; create covalent bonds between bases which block replication
  259. SOS system
    eukaryotic system of eta polymerase that can bypass pyrimidine dimers
  260. Four mechanisms of DNA repair are:
    • Mismatch repair
    • Direct repair
    • Base excision
    • Nucleotide excision
  261. Mismatch repair
    Replication errors, including mispaired bases and strand slippage
  262. Direct repair
    Pyrimidine dimers; other specific types of alterations
  263. Base excision
    Abnormal bases, modified bases, and pyrimidine dimers
  264. Nucleotide excision
    DNA damage that distors the double helix, including abnormal bases, modified bases, and pyrimidine dimers
  265. Mismatch repair Mechanism
    • Detects 3D distortion
    • cuts out distored part with exonuclease
    • fill in using original strand as template with DNA polymerase
    • repairs nicks with DNA ligase
    • Methylation at GATC sequence on old strand for differentiation
  266. exonuclease
    removes nucleotides usually at end of DNA strand
  267. DNA polymerase
    replaces nucleotides
  268. DNA ligase
    seals nick in sugar-phosphate backbone
  269. Direct Repair Mechanism
    • Converts modified nucleotides to original form
    • e.g. O6-Methyltransferase removes methyl group restoring base to guanine
    • e.g. photolyase uses light to break covalent bonds that link pyrimidine dimers
  270. photolyase
    an enzyme that uses light energy to break covalent bonds in pyrimidine dimers
  271. Base-excision repair mechanism
    • Excises modified bases and then replaces entire nucleotide
    • DNA glycosylase recognizes and removes damaged base
    • AP endonuclease cleaves phosphodiester bond on 5' site and removes sugar
    • DNA polymerase adds new nucleotide to 3'
    • DNA ligase fixes nick in sugar-phosphate backbone
  272. AP endonuclease
    removes nucleotide usually in middle of DNA strand
  273. Nucleotide-excision repair mechanism
    • Enzyme complex recognizes 3D distortion
    • DNA strand is separated and stabilized with binding proteins
    • An enzyme cleaves the strand on both sides of the damage
    • Part of damage strand is removed
    • Gap filled by DNA polymerase
    • Sealed by DNA ligase
  274. Homologous recombination
    A type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks.
  275. Interstrand cross-link
    Two DNA strands are connected thru covalent bonds. Not much know about this.
  276. Common Mechanisms for Nucleotide removal
    • Detection
    • Excision
    • Polymerization
    • Ligation
  277. Detection
    Damaged section of DNA is recognized
  278. Excision
    DNA repair endonucleases nick phosphodiester backbone on one or both sides of the DNA damage and one or more nucleotides are removed
  279. Polymerization
    DNA polymerase addes nucleotides to the newly exposed 3'-OH group by using the other strand as a template and replacing the damaged nucleotides
  280. Ligation
    DNA ligase seals the nices in the sugar-phoshate backbone
  281. Differences in Mechanisms for Nucleotide removal
    How detection and excision are accomplished
  282. xeroderma pigmentosum
    autosomal recessive condition caused by nonfunctional repair mechanism for pyrimidine dimers
  283. 1973, Cohen and Boyer at UCSF
    Created first recombinant DNA molecule
  284. Recombinant DNA technology
    Set of molecular techniques for locating, isolating, altering, and studying DNA segments
  285. Stemps requiring Recombinant DNA techniques
    • Find gene
    • Separate gene
    • Make copies of gene
    • Insert gene into plasmid without degredation
    • Induce bacteria to take up plasmid
    • Select bacteria that take up plasmid
  286. Restriction enzymes/endonucleses
    • Enzymes that recognize and make double-strand cuts in DNA at specific nucleotide sequences
    • Produced naturally by bacteria to defend against viruses
  287. Type I and III Restriction enzymes
    Cut outside recognition sequence
  288. Type II restriction enzyme
    • Cuts within recognition sequence
    • Used in molecular genetic work
    • Names indicate original bacteria
    • More than 800 isolated
  289. Characteristics of restriction enzymes
    • Palindromic recognition sequence
    • Fragment end either cohesive or blunt
  290. Cohesive end restriction enzyme
    Staggered cut -> sticky ends
  291. Restriction Digest
    Reaction of mixture of DNA, buffer, restriction enzyme, water heated at about 37 C
  292. Electrophoresis
    Standard technique for separating molecules on basis of size/electrical charge
  293. agarose
    polysaccharide isolated from seaweed
  294. Viewing DNA fragments using electrophoresis
    DNA fragments move to positive pole with smaller fragments moving faster
  295. probe
    fluorescent or radioactive DNA or RNA fragment complementary to sequence of interest
  296. Southern blotting
    Transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by radioactive probe
  297. Northern blotting
    • A technique used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample.
    • Size of mRNA molecule
    • Relative abundance of mRNA
    • Tissue in which MRNA is transcribed
  298. Western Blotting
    • Transfer of proteins from gel to a membrane
    • Probe is usually an antibody
    • Determine size of protein
    • Pattern of protein's expression
  299. Gene cloning
    create identical copies of a piece of DNA
  300. Cloning vector
    DNA molecule into which a foreign DNA fragment can be inserted for introduction into and replication in a cell
  301. Characteristics of an effective cloning vector
    • Origin of replication
    • selectable marker
    • one or more unique restriction sites where DNA can be inserted
  302. Types of cloning vectors
    • Plasmid, e.g. pUC19
    • Bacteriophage
    • Cosmid
    • BAC
    • YAC
    • Retroviral vectors
    • Transposons
    • Expression
  303. Transformation
    The capacity of bacterial cells to take up DNA from the environment
  304. Cosmid
    Plasmids that are packaged into empty viral protein coats and transferred to bacteria by viral infection
  305. BAC
    Originally contructed from F plasmids
  306. YAC
    DNA molecule that has a yeast ORI, pair of telomeres, and a centromere
  307. Ti plasmid
    Plasmid that can be used to introduce DNA into plants
  308. Expression vector
    Vector that allows the production of protein (i.e. transcription and translation)
  309. PCR Steps
    • 1) Heat to 90-100 C for denaturation
    • 2) Cool to 30-65 C for primers to anneal
    • 3) Heat to 60-70 C for DNA synthesis
    • Repeat
  310. PCR Limitations
    • Requires knowledge of at least part of sequence for primers
    • Taq polymerase is poor at proofreading
    • Fragments larger than 50Kb cannot be isolated
  311. PCR as a diagnostic tool
    Detects presence of a particular sequence, e.g. HIV
  312. Shotgun cloning
    Clone all sequences in an organism into vectors
  313. DNA library
    Collection of clones containing all the DNA fragments from one source
  314. Genomic library
    Set of bacterial colonies or phages containing fragments in a DNA library
  315. cDNA library: isolating mRNA
    isolation of mRNA using oligo(dT) chains
  316. cDNA library: making cDNA from mRNA
    • oligo(dT) act as primers
    • reverse transcriptase for DNA strand
    • Rnase digests most of RNA strand
    • Remaining RNA act as primers for second DNA strand
  317. In situ hybridization
    A type of hybridization that uses a labeled complementary DNA or RNA strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue
  318. Restriction Fragment Length Polymorphisms (RFLPs)
    Variations in the patterns of fragments produced when DNA is cut with a restriction enzyme typically caused by mutation
  319. Dideoxyribonucleoside triphosphate(ddNTP)
    No OH groups
  320. Sanger Method of DNA sequencing
    Uses ddNTP to terminate synthesis of strands of different length which can be read by electophoresis to sequence
  321. Pyrosequencing
    allows sequencing of entire genomes in a couple months
  322. DNA fingerprinting
    • PCR used to amplify STR loci each with large numbers of alleles which assort independently
    • Difference in number of tandem repeats have no phenotypic consequence
    • Probability of two randomly selected people having the same DNA profile is less than 1 in 10 billion
  323. DNA fingerprinting procedure
    • DNA extracted from tissue samples
    • PCR primers for specific STR loci used to amplify fragments
    • DNA from sample is compared with reference DNA
    • Usually use genomic DNA, but mitochondrial DNA can be used as well
  324. Forward Genetic Approach
    • Function -> gene
    • Frequently used in less complex organisms to discover new genes
  325. Forward Genetic Procedure
    • 1. Isolate mutants that have phenotypic mutation.
    • 2. Map the mutations.
    • 3. Sequence the gene to find the mutation.
    • 4. Clone the gene using molecular techniques.
    • 5. Further genetic, molecular genetic, and biochemical experiments can further define a gene's function in that process.
  326. Reverse Genetic Approach
    • gene -> function
    • Frequently used in mice to see if genes discovered in simpler organisms
    • have a similar phenotype in mammals
  327. Reverse Genetic Procedure
    • 1. Begin with a gene with known sequence.
    • 2. Induce a mutation in that gene.
    • 3. Look to see what effect these mutations have on the phenotype of the organism
  328. Transgenic animal
    An organism with an added transgene
  329. Transgene
    non-innate DNA added to an organism
  330. Knockout mice
    Mouse in which known gene has been disabled via homologous recombination
  331. Knockin mouse
    wildtype gene is replaced with known mutant gene
  332. Knockout mouse procedure
    • Target "normal" gene disabled by inserting neo+ gene in the middle and a tk+ gene is added at the end
    • Disabled gene is transferred to embryonic mouse stem cells to undergo recombination with normal cells resulting in some neo+ tk- cells
    • Cells grown in antibiotic, and only recombinated ones survive
    • Surviving cells injected into early mouse embryo resulting in variegated mouse
    • Variegated progeny interbred resulting in some homozygous mice for the knocked-out gene
  333. Site-Directed Mutagenesis: Method 1
    • Short sequence of nucleotides removed and replaced by synthetic sequence containing mutated bases
    • Requires flanking restriction sites that are nowhere else in DNA
  334. Site-Directed Mutagenesis: Method 2
    • Oligonucleotide created that differs from target sequence by single nucleotide
    • Two sequences pair
    • Oligonucleotide used as primer which yields molecule with single mismatched pair
    • DNA transferred back to bacteria where about half are repaired
    • Bacteria then screened for altered sequence
  335. Oligonucleotide-directed mutagenesis (2)
    • Often used for making small changes in DNA sequences already cloned into plasmids
    • Can't be used in multicellular organism: long, noncircular DNA, multiple ori, etc.
  336. Silencing with RNAi: RNA Knockdown
    Can be delivered to cell by injecting or soaking to turn down expression without inducing mutation
  337. Short hairpin RNA (shRNA)
    Can be cloned into vectors and used to make transgenic animals
  338. RNAi for the treatment of disease
    • siRNAs could be used against RNA viruses, such as HIV
    • siRNAs could be used to treat genetic diseases, high cholesterol and cancer
  339. Stable nucleic-acid-lipid-particles (SNALPs)
    Used in delivery of siRNA to lower cholesterol thru silencing in monkeys
  340. Gene therapy targets what kinds of cells?
  341. What is genomics?
    It is the field of genetics that attempts to understand the content, organization, function, and evolution of genetic information contained in whole genomes
  342. The first living organism to be sequenced was ?
    Haemophilus influenza
  343. For the Human Genome Project, what kind of method was used for sequencing?
    A map-based method
  344. Craig Venter and Celera Genomics used what method to sequence the human genome?
    A whole-genome shotgun technique using computers
  345. What is a single nucleotide polymorphism (SNP)?
    A site in the genome at which individual members of a species differ in a single base pair
  346. Why are SNPs more commonly found in non-coding regions?
    Because there is no selective pressure to weed out the mutations.
  347. What is a haplotype?
    It is the set of SNPs and other genetic variants found on a particular part of a chromosome.
  348. Of Africans, Japanese, Chinese, and Europeans, which group has the greatest diversity of SNPs and why?
    Africans, as this is consistent with many other studies that suggest humans first evolved in Africa.
  349. What is a contig?
    A continuous stretch of DNA
  350. What is bioinformatics?
    A field that fuses molecular genetics and computer science
  351. What are two methods to identify genes?
    • ab initio approach: scans the sequences looking for characteristics such as an open reading frame
    • comparative approach: Looks for similarities between a new sequence and sequences of all known genes
  352. What is an open reading frame?
    A frame which includes a start and stop codon in the same reading frame
  353. What is BLAST?
    Basic Local Alignment Search Tool, is a program to determine whether a similar gene sequence has already been found in the same or another species
  354. What are two types of homologs?
    • Orthologs are homologous genes found in different species that evolved from the same gene in a common ancestor.
    • Paralogs are homologous genes in the same organism that arise by duplication of a single gene
  355. What is a protein domain?
    A region in a protein that has a specific function or shape
  356. What is a microarray?
    An array of numerous microscopic DNA fragments/probes used to find complementary sequences corresponding to known genes
  357. What is a reporter gene?
    A gene that researchers attach to a regulatory sequence of another gene of interest that allows for visual identification (e.g. Green Fluorescent Protein, GFP)
  358. Genomic screening for newborns
    • Screening for large number of genetic diseases
    • Better/earlier preventative treatement
  359. Genomic screening for personalized medicine
    • Able to predict responses to different treatments and fine-tune drug therapy for individual
    • Genetic testing of both patients and pathogens will allow faster and more precise diagnosis of many diseases
  360. What is population genetics?
    The study of the genetic makeup of groups of individuals and how a group�s genetic composition changes with time
  361. What is a gene pool?
    A common set of genes in a population
  362. Population geneticists study:
    • The variation in alleles within and between groups
    • The evolutionary forces that shape patterns of genetic variation
  363. What causes phenotypic varation within a population?
    Genotypic variation
  364. Genotypic frequency: f(AA)
    f(AA) = (number of AA individuals)/N, where N is the number of individuals in the sample
  365. Calculating the frequency of an allele
    freq of an allele = (# of copies of allele)/(# of copies of alleles at the locus)
  366. Allele frequency: p = f(A)
    f(A) = (2nAA + nAa)/(2N)
  367. Calculate allelic frequencies from individual frequencies
    p = f(A) = f(AA) + (1/2)f(Aa)
  368. Calculate allelic frequencies at loci with three alleles
    p = f(A1) = (2nA1A1 + nA1A2 + nA1A3)/2N
  369. Calculate allelic frequencies from individual frequencies with three alleles
    p = f(A1A1) + (1/2)f(A1A2) + (1/2)f(A1A3)
  370. Calculate allelic frequencies at X-linked loci
    p = f(XA) = (2nXAXA + nXAXa + nXAY)/(2nfemales + nmales)
  371. Calculate allelic freq's at X-linked loci from individual frequencies
    p = f(XA) = f(XAXA) + (1/2)f(XAXa) + f(XAY)
  372. Study example on slide 15
    human MN blood-type antigens
  373. What assumptions does the Hardy-Weinberg law make?
    The population is large, randomly mating, and not affected by mutation, migration, or natural selection
  374. The Hardy-Weinberg Law predictions:
    • Prediction 1: The allelic frequencies of a population do not change
    • Prediction 2: The genotypic frequencies stabilize (do not change) after one generation in the following proportions:
    • p^2, 2pq, q^2
    • The allelic frequencies determine the frequencies of genotypes
  375. If a population meets the Hardy-Weinberg assumptions, can it evolve?
    Yes, but it requires external pressure.
  376. When a population is in Hardy-Weinberg equilibrium, the genotypic frequencies are determined by ...
    the allelic frequencies
  377. Hardy-Weinberg Law: Comparing Genotypic exp with freq
    • 1. Calculate the allelic frequencies
    • 2. Find the expected genotypic frequencies
    • 3. Compare the observed and expected genotypic frequencies using a chi-square test
  378. How do you calculate the degrees of freedom for the Chi-Square test in Hardy-Weinberg proportions?
    In general, the degrees of freedom for a chi-square test of Hardy-Weinberg equilibrium equal the number of expected
  379. genotypic classes minus the number of associated alleles
  380. Positive assortative mating
    Tendency for individuals sharing a particular trait to mate
  381. Negative assortative mating
    Tendency for individuals that do not share a particular trait to mate
  382. Inbreeding
    Preferential mating between related individuals
  383. Outcrossing
    Avoidance of mating between related individuals
  384. How does inbreeding affect homozygosity and allele frequencies?
    Inbreeding leads to an increase in homozygosity at all loci, but no change in allele frequencies
  385. Inbreeding depression
    The increased appearance of lethal and deleterious traits with inbreeding
  386. Processes that bring about change in allelic frequency
    • Mutation
    • Migration
    • Genetic Drift
    • Natural selection
  387. Genetic Drift
    Sampling error/random effects due to small population size
  388. What are the overall affects of migration?
    • Gene pools of populations become more similar
    • Increases genetic variation within the recipient population
  389. Genetic drift results in...
    the divergence of populations and often results in one allele becoming fixed
  390. What are two causes of genetic drift?
    • Founder Effect
    • Genetic bottleneck
  391. Three related effects of genetic drift are:
    • 1. Change in allelic frequency
    • 2. Reduced genetic variation
    • 3. Different populations diverge genetically with time
  392. Natural Selection
    The differential reproduction of genotypes when individuals with adaptive traits produce a greater number of offspring than that produced by others in the population
  393. Fitness
    The reproductive success of one genotype compared with the reproductive successes of other genotypes in the population
  394. Calculating fitness (W)
    Divide the mean number of offspring produced by a genotype by the mean number produced by the most proli?c genotype
  395. Selection coefficient (s)
    The relative intensity of selection against a genotype
  396. Calculating the selection coefficient
    s = 1 - W
  397. General Selection Model
    know table 25.4
  398. Three Different types of selection
    • Selection against a dominant allele is very efficient
    • Selection against an autosomal recessive allele is inefficient
    • Balancing selection where the heterozygous genotype is most fit
  399. Do problem on slide 21
    calculate relative fitness and next generation frequency of an allele
  400. Mutation's long-term effect on allelic frequency
    Equilibrium reached between forward and reverse mutations
  401. Migration's long-term effect on allelic frequency
    Equilibrium reached when allelic frequencies of source and recipient population are equal
  402. Genetic drift's long-term effect on allelic frequency
    Fixation of one allele
  403. Natural Selection's long-term effect on allelic frequency
    • Directional selection: fixation of one allele
    • Overdominant selection: equilibrium reached
  404. What's the first step in discovering a gene and determining its function?
    Select an appropriate model organism
  405. What are the steps in conducting a mutagenesis screen? (assume we're studying "touch")
    • Mutagenize many animals
    • Isolate F_2 animals that fail to sense touch
    • Map mutation to a small region of genome
    • Sequence genes in region
    • Look for loss-of-function mutation
  406. Genes are frequently named for their ____.
    mutant phenotype
  407. What kind of search is performed to see if their are homologs that have been studied?
    A BLAST or SMART search
  408. What are the steps in subcloning a gene?
    • Use a database to find a cosmid that contains the gene of interest
    • Determine what restriction sites can be used to cut out the gene of interest
    • Digest the plasmid with the same enzyme
    • Use gel electrophoresis to separate the fragments from the cosmid
    • Ligate the gene fragment from the cosmid to the plasmid vector
    • Transform E. coli with the new recombinant plasmid
  409. How do you determine where and when the gene is expressed
    • In situ
    • Northern
    • Western
    • Reporter gene like GFP
  410. How do we determine what genes it interacts with?
    Determine the subcellular localization of the protein
  411. How do we determine the subcellular localization
    • antibody staining
    • fuse GFP to the mec-1 coding sequence and inject into animal
  412. What else could we do now to determine if MEC-1 protein can bind collagen and the extracellular domain of the sensory channel?
    Biochemical binding assays
  413. What should we do to test whether the mec-1 homolog is necessary for touch sensation in mammals?
    Make knockout mice and see if they have defects in sensing touch
  414. If we find that loss-of-function mutations in the mec-1 homolog plays a role in human disease, how could we cure these diseases?
    Use gene therapy to reintroduce a wild-type copy of the gene