Genome Structure I

  1. Within the cell, DNA is associated with proteins, and each DNA molecule and its associated protein is called a ________. Name three applicable situations

    prokaryotic, eukaryotic, and viruses
  2. DNA is not a pure, naked molecule, it always works in conjunction with ________. Some are ________ (state 2 examples) and some are ________(1 example). _______ increase stability and make _______ possible.
    • proteins
    • active (polymerases, topoisomerase)
    • structure (histones)
    • Proteins
    • compacting
  3. ________ make up 50% of the total chromosome
  4. Two types of different chromosomes
    Linear & circular covalently closed DNA (cccDNA)
  5. Cells maintain a constant number of _________
  6. Name the chromosome number for:
    E. coli
    influenza virus
    M. musculus (house mouse) 
    S. cerevisae
    S. pombe
    D. melanogaster (fruit fly)
    A. thaliana (plant)
    • E. coli-1
    • influenza virus-8
    • Homosapiens-22+X/Y
    • M. musculus(house mouse)-19+X/Y
    • S. cerevisae-16
    • S. pombe-3
    • D. melanogaster(fruit fly)-4
    • A. thaliana(plant)-5
  7. State the type of cell, number of chromosomes, number of copies, chromosome type, and presence of plasmids of E. coli & Homosapians
    • E. coli: prokaryote, one, one, circular and several plasmids
    • H. sapiens: eukaryote, 22 chromosome, 2 copies and linear
  8. Not all of the genome ______ for proteins. The genome is comprised of _______ sequences (___% in human genome). Those sequences are found between _____ and have _______ functions.
    • codes 
    • intergenic sequences
    • 60%
    • genes
    • regualtory
  9. _______ are coding for proteins but are not necessarily genes.
  10. Genes are bigger in _______ organisms however, _______ are the same size.
    • complex
    • proteins
  11. Packaging of the DNA into chromosomes serves several functions, name 4:
    • chromosome is compact form of DNA, so it readily fits into the cell
    • protects the DNA from damage
    • transmitted efficiently to both daughter cells when cell divides
    • confers an overall organization to the molecule of DNA
  12. Half of the molecular mass of a eukaryotic chromosome is _______. In eukaryotic cells, a given region of DNA with its associated proteins is called _______, and the majority of the associated proteins are small, basic proteins called _______.
    • protein 
    • chromatin
    • histones
  13. Although not nearly as abundant, other proteins that are not small or basic are called ________ proteins and they are associated with _______ chromosomes. Name four types of such proteins
    • nonhistone proteins
    • eukaryotic chromosomes 
    • proteins that regulate: replication, repair, recombination, and transcription of cellular DNA
  14. Most compaction in human and all other ________ cells is the result the regular association of DNA with histones to form _______.
    • eukaryotic cell
    • nucleosomes
  15. What is the cost of compacting DNA through association with histones and other packaging proteins?
    Limits accessibility of the DNA which can interfere with proteins that direct replication, repair, recombination and (perhaps) most significantly transcription of the DNA
  16. Eukaryotic cells exploit the _________ properties of chromatin to regulate gene expression and many other events involving DNA. Alterations to individual _________allow specific regions of the chromosomal DNA to interact with other proteins. What mediates these alterations?
    • inhibitory 
    • nucleosomes 
    • enzymes that modify and move nucleosomes
  17. Although prokaryotic cells typically have _______ genomes than eukaryotic cells and still must have their DNA ________, however, the process is less understood.
    • smaller
    • compacted
  18. Bacteria have no ______ or _______ but they do have other small basic proteins that may serve similar functions.
    histones or nucleosomes
  19. The traditional view is that prokaryotic cells have a ______ _______ chromosome and eukaryotic cells have ______ ______ chromosomes. Although the most familiar prokaryotes like ______ obey this rule, many have been discovered that have _______ ______  or _______ _______ or both.
    • single circular chromosome
    • multiple linear chromosomes
    • E. coli or Bacillus subtilis (either is fine)
    • multiple chromosomes
    • linear chromosomes or both
  20. Eukaryotes always have multiple linear chromosomes but can depending on the organism, the number of chromosomes vary from about ____ to _____. In rare instances, they can number in the thousands like the _______ known as Tetrahymena
    • 2 to <50
    • protozoa
  21. Circular chromosomes require enzymes called _________ to separate daughter molecules after they are _______. Without these enzymes the two daughter molecules would remain interlocked or ________, with each other after replication.
    • topoisomerases
    • replicated 
    • catenated
  22. The ends of linear eukaryotic chromosomes have to be protected from ______ that normally degrade DNA ends and present a different set of difficulties during DNA _______.
    • enzymes
    • replication
  23. Prokaryotic cells typically have ____ complete copy of their chromosome(s) that is packaged into a structure called the _______. However, when they are dividing rapidly, portions of the chromosome (while replicating) are present in _____ and sometimes even ____ copies.
    • nucleoid 
    • two 
    • four
  24. Prokaryotes frequently carry one or more independent circular DNAs called ______. Unlike the larger chromosomal DNA, ______ typically are not essential for bacterial growth but carry ______ that confer desirable traits to the bacteria such as _______ resistance. Also unlike chromosomal DNA, ______ are often present in _____ complete copies per cell.
    • plasmids
    • plasmids
    • genes
    • antibiotic 
    • plasmids 
    • many
  25. The majority of eukaryotic cells are _____; that is, they contain two copies of each chromosome. The two copies of a given chromosome are called _______, one being derived from each ______.
    • diploid
    • homologs
    • parent
  26. A subset of eukaryotic cells are either ______ or ______. ______ have more than two copies of each chromosome while _______ cells contain a single copy of each chromosome and are involved in _______ _______.
    • haploid or polyploid 
    • Polyploid 
    • haploid 
    • sexual reproduction
  27. If the polyploid cells were the majority in adulthood, it would be a type of global genome amplification that allows a cell to generate larger amounts of ______ and in turn ______. Eukaryotic chromosomes are always contained within a membrane bound organelee called the ______.
    • RNA 
    • proteins
    • nucleus
  28. Genome size
    the length of DNA associated with one haploid complement of chromoses
  29. More _____ are required to direct the formation of more complex organisms for example bacteria vs single cell eukaryotes vs multicellular eukaryotes (least to most complex). As a result, genome size is roughly correlated with an organism's _______.
    • genes 
    • complexity
  30. Prokaryotic cells typically have genomes of _____, single cell eukaryotes are typically ______, although some complex protozoans can have genomes _____. Multicellular organisms have even larger genomes that can reach sizes ________.
    • <10Mb
    • <50Mb
    • >200Mb
    • >100,000Mb
  31. T or F: Some organisms have similar complexities and yet different genome size.
  32. Most of the single chromosome of the bacteria E. coli encodes _____ or ______ ____. The majority of the non-coding sequences are dedicated to regulating ______ _______. Just one site where _______ occurs controls the expression of several genes. The ______ keeps these regulatory regions to a minimum
    • proteins or structural RNAs
    • gene transcription
    • transcription
    • genome
  33. The E. coli _______, or origin of replication is dedicated to directing the assembly of the _______ machinery, not necessarily the genes or sequences that regulate gene expression. Despite its role, this region is still very _____.
    • genome 
    • replication 
    • small (just a cpl hundred base pairs)
  34. The differences in genome size between organism of similar complexity is largely related to _____ _______. How do we measure this?
    • gene density 
    • average number of genes per megabase (Mb) of genomic DNA
  35. When the gene densities of different organisms are compared, it becomes clear that different organisms use the ____-______ potential of DNA with varying efficiencies.
  36. There is a roughly _______ correlation between organism complexity and gene density. Meaning? Gene density in _______ organisms is consistently lower and more variable than in their _______ counterparts
    • inverse 
    • the less complex the organism, the higher the gene density.
    • eukaryotic 
    • prokaryotic
  37. Among eukaryotes there is a general trend for gene density to _____ with increasing organism complexity.
  38. Two factors that contribute to the decreased gene density observed in eukaryotic cells:
    increases in gene size and increases in the DNA between genes (called intergenic sequences).
  39. The major reason that gene size is larger in more complex organisms is that protein-encoding genes in eukaryotes frequently have _________ protein-coding regions. The interspersed non-protein-coding regions, called ______ are removed from the RNA after _______ in a process called ____ ______
    • discontinuous 
    • introns
    • transcription
    • RNA splicing
  40. The presence of _____ can dramatically increase the length of DNA required to encode a gene. For instance, the average transcribed region of a human gene is ~27kb, whereas the avg protein-coding region of a human gene is 1.3kb. Only 5% of avg human protein-encoding gene encodes proteins, the rest is made up of ______.
    • introns
    • introns
  41. Simpler eukaryotes with higher _____ _____ have far fewer introns. In more complex organism, an increase in the amount of ______ _____ is responsible for the remaining decreases in gene density
    • gene density
    • intergenic sequences.
  42. Intergenic DNA is the portion of a genome that does not encode ______ or ______ RNA. More than _____ percent of human DNA is composed of intergenic sequences, and much of this DNA has no known function.
    • proteins or structural RNA
    • 60 percent
  43. Two types of intergenic DNA
    unique and repeated
  44. How much unique DNA is present and how would you increase this number
    • 1/4
    • by increasing the number of regulatory sequences (DNA regions required to direct and regulate transcription)
  45. The more complex the organism, the more (larger/ more complex) ______ sequences required to coordinate gene expression
    regulatory sequences
  46. Unique intergenic DNA many nonfunctional relics such as: (3)
    • mutant genes
    • gene fragments
    • pseudogenes
  47. Mutant genes and gene fragments, arise from simple random _______ or mistakes in DNA ______. While Pseudogenes arise from the action of an enzyme called _______ ______
    • mutagenesis
    • recombination
    • reverse transcriptase
  48. Reverse transcriptase copies RNA into _______-_______ _____ (known as ____ ____ or ______). The enzyme is only expressed by certain types of _______ that require the enzyme to reproduce
    • double-stranded DNA 
    • copy DNA or cDNA
    • viruses
  49. What happens when someone is infected by a virus with reverse transcriptase (3-story)
    • cellular mRNAs can be  copied into DNA 
    • resulting DNA fragments reintegrate into the genome at a low rate
    •  these copies are not expressed because they lack the correct regulatory sequences to direct their expression
    • **such sequences are generally not part of a gene's RNA product
  50. microRNAs
    miRNAs (coding but not genes) are small structural RNAs that regulate the expression of other genes by altering either the stability of the product mRNA or its ability to be translated
  51. The majority of Human Intergenic sequences are composed of ______ DNA, they are almost half of the human genome. What are the two general classes
    • repetitive DNA
    • microsatellite DNA & genome-wide repeats
  52. Microsatellite DNA is composed of very _____ (<13bp), tandemly repeated sequences. The most common are _______ repeats (e.g. CACACACACA). They are caused by difficulties in accurately _______ the DNA and represent nearly 3% of human genome
    • short
    • dinucleotide 
    • duplicating
  53. Genome wide repeats are much ______ than microsatellite repeats. Each genome wide unit is >100bp in length and many are 1kb. These sequences can be found either as _____ copies dispersed throughout the genome or as _____ _____ clusters.
    • larger
    • single
    • closley spaced
  54. The common feature between all genome-wide repeat is that they are all forms of ________ ________. Define
    transposable elements: sequences that ccan move from one place in the genome to another
  55. During ________, as the element moves to a new position in the genome, often leaving the orginal _____ behind. The sequences can multiply and ______ throughout the genome
    • transposition
    • copy 
    • accumulate
  56. Transposition is ______ in human cells but over long periods of evolution they have been so successful at propagating copies of themselves that they now comprise ~____% of the human genome
    • rare
    • 45%
  57. Plants with very large genomes indicate a larger presence of ______ _____ in their genomes. Even compact genomes like E. coli have _____ _____ and ______ repeats but they have proven less successful at occupying these genomes, why?
    • transposable elements
    • transposable elements & microsatellite
    • a combination of inefficient duplication and more efficient elimination either by repair events or natural selection
  58. Repeated DNA should not be called "junk DNA," because their stable mainenance over thousands of generations confers a positive value or _____ advantage to the host organism
  59. Origins of replication are the sites at which the DNA replication machinery ______ and _____ is initiated. They are found in both prokaryotes and eukaryotes in both they are likely found in ____-_____ regions but in prokaryotes, the chromosomes typically have ____ site(s) of replication initiation
    • assembles  
    • replication 
    • non-coding regions
    • one
  60. Centromeres are required for the correct _______ of the chromosomes after DNA replication. The two copies of each replicated chromosome are called ______ chromosomes and during cell division they must be separated with one copy going to each of the two ______ cells
    • segregation 
    • sister 
    • daughter
  61. Like origins of replication, centromeres direct the formation of an elaborate protein complex called a ______. It assembles at each ______ DNA, and before chromosome segregation, it binds to protein filaments called ________ that eventually pull the sister chromosomes away from each other and into the two ______ cells.
    • kinetochore
    • centromere DNA 
    • microtubules 
    • daughter cells
  62. In contrast to eukaryotes, it is critical that each chromosome include only one _______. In the absence of one, the replicated chromosomes segregate ______, resulting in daughter cells that? (2)
    • centromere
    • randomly
    • either lost a chromosome or have two copies of a chromosome
  63. What happens if there is more than one centromere on each chromosome?
    If the associated kinetochores are attached to filaments pulling in opposite directions, this can lead to chromosome breakage
  64. Centromere vary greatly in ______ and largely of _______ ____ sequences
    size repetitive DNA sequences
  65. _______ are located at the two ends of a linear chromosome. Like origins of replication and centromeres, _______ are bound by a number of proteins.
    • Telomeres
    • telomeres
  66. Two function of telomeric proteins
    • distinguish thee natural ends of the chromosome from sites of chromosome breakage/other DNA breakage in the cell
    • act as specialized origins of rep. that allow the cell to replicate the ends of the chromosome
  67. Ordinarily, DNA ends are sites of frequent _______ and DNA ______. The proteins that assemble at telomeres form a structure that is resistant to both of these events. Additionally, because the standard DNA rep. machinery cannot completely replicate the ends of a linear chromosome, telomeres facilitate end rep. through the recruitment of a DNA polymerase called _______
    • recombination & degradation 
    • telomerase
  68. In contrast to most of the chromosome, a portion of the telomere is maintained in a ____-____ form. Telomeres also are notorious for simple repeats of ______ and _____
    • single-stranded
    • thymine & guanine (TTAGGG)
  69. During cell division, the chromosomes must be ______ & ______ into the daughter cells. In bacterial cells, these events occur _________. Meaning during DNA rep. the resulting two copies are separated into ______ sides of the cell. This process is less understood for ______
    • duplicated and segregated 
    • simultaneously
    • opposite
    • bacteria
  70. The events required for a single round of cell division are collectively known as the ____ _____. Most eukaryotic cell divisions maintain the number of _______ i the daughter cells that were present int he parental cell. This type of division is called _____ ______ division
    • cell cycle 
    • chromosomes 
    • mitotic cell division
  71. Four phases of mitotic cell division:
    G1, S, G2 and M
  72. Chromosome replication occurs during the ______ or __ phase of the cell cycle, resulting in the _______ of each chromosome
    • synthesis or S phase
    • duplication
  73. Each chromosome of the duplicated pair is called a _______, and both (of a given pair) are called _____ ______.
    • chromatids
    • sister chromatids
  74. Sister chromatids are held together after duplication through a process called _____-_____ _______, and this tethered state is maintained until the chromosomes segregate from one another. The process is mediated by a structural maintenance of chromosome protein or (SMC) called _____.
    • sister-chromatid cohesion
    • cohesin
  75. Chromosome segregation occurs during _____ or __ phase of the cell cycle. First, each pair of sister chromatids is bound to a structure called the ______ ______. This structure is composed of long protein fibers called _______ that are attached to one of the two microtubule-organizing centers (aka _________ in animal cells or _____ ___ bodies in yeast and other fungi).
    • mitosis or M phase
    • mitotic spindle
    • microtubules
    • centrosomes
    • spindle pole bodies
  76. In mitosis, the microtubule-organizing centers are located on ______ sides of the celll, forming poles toward the microtubules that pull the _______. Attachment of the ______ to the micriotubules is mediated by the _______ at each centromere.
    • opposite 
    • chromatids
    • chromatid
    • kinetochore
  77. In the second step of mitosis, the cohesion between the chromatids is dissolved by ______ of ______. AFTER cohesion is dissolved, the third major event in mitosis ______-_______ _______ occurs. The chromatids are rapidly pulled toward opposite poles of the _______ _______. This process must be carefully coordinated
    • proteolysis of cohesin
    • sister-chromatid separation 
    • mitotic spindle
  78. There are two main states for chromosomes:
    during chromosome condensation & interphase
  79. Chromosomes are in their most compact form as cells _______ their chromosomes and the process is called _______ ______. In this condensed state chromosomes are disentangled from each other which facilitates the ______ process.
    • segregate
    • chromosome condensation
    • segregation
  80. During the cell cycle when segregation is not occurring, aka the ________, the chromosomes are significantly less ______. The chromosome can be highly _______ resembling a bowl of spaghetti.
    • interphase 
    • compact
    • intertwined
  81. Sister chromatid cohesion is established right after _______, linking the newly replicated chromatids to each other.
  82. The chromosome condensation that accompanies chromosome segregation also requires a structural maintenance of chromosome protein or (SMC) containing complex called ________. It shares many features of the cohesin complex which suggest that it too is a ____-____ complex. If so, it may use its ____-like nature to induce chromosome _______. State an example
    • condensin
    • ring-shaped complex
    • ring-like
    • chromosome condensation
    • By linking different regions of the same chromosome together, condensin could reduce the overall linear length of the chromosome.
  83. The overall process of Mitosis maintains the _____ _____ number. During prophase, the action of ______ and _____ __ _______ (untangle chromosome) drives chromosomes to ______ into the highly compact form required for segregation at the end of prophase, in most cells the ______ envelope breas down adn the cell enters ______.
    • parental chromosome number
    • condensin & type II topoisomerase 
    • condense 
    • nuclear
    • metaphase
  84. During metaphase, the _____ ____ forms and the _______ of sister chromatids attach to the microtubules. It is a proper/bivalent attachment when sister chromatids attach to microtubules are ______ each other.
    • mitotic spindle 
    • kinetochores
    • opposite
  85. Monovalent attachment can lead to both copies of a chromosome moving into one ______ _____
    daughter cell
Card Set
Genome Structure I
Chapter 8