Eukaryotic Chromosome Structure and Genome Organization

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Eukaryotic Chromosome Structure and Genome Organization
2013-07-22 01:01:05
Biology GRE

Biology GRE
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  1. Nucleosome
    • Chromosome packing
    • essentially spools of DNA wrap around histone protein
    • Each is linked to the next by small protein strand
    • Nucleosomes coil together to form chromosomes
  2. Euchromatin
    • Looser chromatin
    • Gets transcribed
  3. Heterochromatin
    Tightly packed chromatin that is not transcribed
  4. Deletion
    Chromosomes fragment from end or middle is lost as chromosome repeats
  5. Duplication
    • If fragment detaches from a chromosome during a deletion event reattached itself
    • If reattaches to the homologous chromosome, that chromosome will have two sets of identical genes in a particular region, and original chromosome where the deletion occurred will be too short
  6. Ploidy
    • Refers to the number of copies of a chormosome an organism has
    • Haploid- one copy
    • Diploid- two copies, humans
  7. ___ Linear chromosomes that are arranged in ___ homologous pairs
    46 Linear chromosomes that are arranged in 23 homologous pairs
  8. Homologous
    Two paired chromosome, are similar in length, but may not have the same alleles
  9. Inversion
    The deleted fragment could also attach back into the chromosome from which it came but in reverse direction
  10. Translocation
    • Common alteration in which the piece of DNA that breaks off attached to the end of another chromosome
    • Usualy not the homologous chromosome, but to a chromosome that is not its pair
  11. Reciprocal Translocation
    • The chromosome giving a piece of DNA also receives one back that is comparable in size from the receiving chromosome 
    • In many cases these mistake render large group of genes useless
  12. Transcription
    • Base sequence of DNA is transcribed to mRNA
    • DNA double helix unwinds and is transcribed in a 5'-->3' direction, using only one DNA strand as as a template
    • RNA transcription proceeds from only one DNA template called the anitsense strand
    • RNA transcription doesnt require an RNA primer
    • RNA poly both initiates the synthesis and catalyzes the addition of nucleotides
  13. 5' and 3'
    The two strands of DNA run in opposite directions to each other and are therefore anti-parallel, one backbone being 3′ (three prime) and the other 5′ (five prime). This refers to the direction the 3rd and 5th carbon on the sugar molecule is facing.
  14. RNA polymerase I and II
    • are main molecules responsible for trancribtion with DNA and RNA codons
    • Must bind to the promotor sequence before it can access the structural genes to be transcribed
    • Transcription occurs until RNA poly reaches termination sequence
  15. Codon
    Set of three nucleotides
  16. Exons
    • Coding sequences of DNA
    • 5% of eukaryotic DNA codes for proteins
    • Exons EXIT the nucleus and go to ribsome for translation
  17. Introns
    • Several noncoding sequences or Junk DNA
    • Makes up 95% of eukaryotic DNA
    • Introns remain IN the nucleus
  18. hnRNA
    • Heterogenous nuclear RNA
    • mRNA that is initially transcribed off a DNA template
    • a 'precursor' molecule
    • Contains both introns and exons
    • During hnRNA introns are removed and exons are spliced together
    • Therefore mRNA is only made up of exons
  19. 5' Capping
    • Methylated guanines (G) are added to the 5' end of the mRNA
    • Protects the 5'end against degradation and damage as mRNA travels through nuclear membrane and cell at start of protein synthesis and at ribosome for translation
  20. 3' Poly A tail
    • After being cleaved at a specific site the mRNA recursor receives a poly A tail made of 100-300 adenine nucleotides
    • Similar to 5'cap poly A tail aids in stabilization and protection of mRNA transcript and later at translation
  21. snRNPS (snurps)
    • Short Nucler RiboNuclearProteins
    • are similar to histone proteins in that RNA winds ands wraps around them
  22. Splicesome
    Large ribonucleoprotein that forms during the excision of introns and spicing together of exons
  23. Transpons
    • Pieces of DNA that can move form place to place within an organisms genome
    • Some transpons can replicated themselves before they move, so insert themselves in new place and maintain attached
  24. Bacterial Transpons
    Move from central chromosome to plasmids or vice versa
  25. Inverted Repeats
    • Transposons are always found between inverted repeats
    • Nucleotide sequences that are upside down mirror images of each other
  26. Insertion sequence
    • Simplest Transposon
    • Two inverted repeats and transposase gene
    • Tell DNA where to go after detached from location
  27. Complex transposons
    • Allow genes to move from chromosome to plasmid (in bacteria)
    • Usually they return after replicated and transferred to another bacteria via plasmid
    • *This is how bacteria can rapidly transfer antibiotic resistance to a colony
  28. Major Differences between Prokaryotic gener and Bacterial Genes
    Are introns/junk DNA and enchancers
  29. Enchancers
    • Non coding regions of DNA that influence activation of genes
    • RNA poly must bind to promotor 
    • Enhancers are far upsteam from target genes and bring transcription factors into contact with promotor region and act to enhance transcription
  30. Transcription Factors
    • Hundreds of thousands of proteins that exert transcriptional control over genome
    • Alll Help RNA poly find and bind to given promotor region
    • Have a high rate of conserved DNA binding domain
    • Allows it to attache to DNA nucleotides
    • Most are specific for enhancer or promoter sequence
  31. Enhancers pic
  32. TATA Box
    • Are A-T rich regions of DNA that are involved in positioning the start of transcription
    • Regions of AT rich separate more easily because they form a double bond while C-G form a triple bond
    • DNA unzips at these regions for RNA access
  33. Internal Promotors
    Other types of promotors that exist within introns of genes and usually occur in genes that encode rRNA and tRNA
  34. Methylation
    • The attachment of methyl (CH3-) Groups to nitrogenous bases 
    • When Methalized bases cannot be transcribed and are a way to inactivate certain genes at times
  35. C-G Islands
    • Promotor regions rich in CG upstream of genes
    • They remain unmethalyzes because they are the start to many genes
    • If they become methylzed they turn off many sequences and block RNA poly from attaching
    • CG islands are key to scientists that exons are nearby
  36. Genomic Imprinting
    • Regulated through selective methylation of DNA
    • Maternal Alleles are methylated with certain patterns and paternal with another
    • Allows differential expression of identical alleles depending upon which parent gives it
  37. Gene amplication
    • Rapidly copied and multiple copies accumulate in genome
    • Usually during embryonic development
  38. DNA Packing
    • DNA forms a complex with a core of eight histone proteins
    • Each sections of DNA and protein core comprise an individual nucleosome
    • Each nucleosome is connected to another via linker DNA
    • This thread forms a hollow helix called solonoid
    • The solonoid interacts with other proteins to forms chromatin
    • chromatin condenses to form chromosomes
  39. Chromatin
    • Solonoid interacts with other proteins and forms chromatin
    • Chromatin condenses to form chromosomes
  40. Solonoid
    Thread of histone proteins forms a hollow helix
  41. Nucleotides
    • Basic unit of DNA made up of:
    • A nitrogenous base
    • Sugar
    • Phosphate group
  42. Purines
    • Adenine and Guamine
    • Bases with two fused rings of N and C
  43. Pyrimidines
    • Thymine and Cyctosine
    • Bases with single rings of N and C
  44. Antiparallel Orientation
    • Two strands of DNA have antiparallel orientation
    • One Strand is positioned in the 5'-->3' the other in 3'--->5' direction
    • 5' Phosphate, and 3' hydroxyl groups are exposed at opposite ends
    • Carbons in the sugar ring are numbered 1'-->5'
    • A nucleotides phosphate group is attached to the 5' carbon of its own sugar and the 3' carbon of the next sugar
  45. Origin of replication
    • usually at TATA rich regions where DNA can separate more easily
    • Prokaryotes only have one region
  46. DNA Helicase
    Enzyme that catalyzes the separation of DNA Helix
  47. DNA replication
    • Each strand acts as a template for production of a new strand
    • DNA synthesis begins at more than one location on each strand
    • Synthesis will occur at these points with the enzyme primase
  48. Bidirectional Synthesis

                    ^Replication fork. ---> Movement
    • Synthesis that proceeds in two directions because DNA poly can only synthesize in 5'-->3' direction
    • On top strand DNA syntheis will begin at primer and proceed in the same direction as the movement of the fork (here: R)
    • As more parent DNA is unwound, synthesis is continuous
    • On the bottom strand DNA synthesis proceeds in the opposite direction of the fork (here:L)
    • To stay consistent with 5'-->3' rule primase and DNA poly must jump back as more parental DNA is unwound and then move forward, not continuous
  49. Primer
    • RNA nucleotide that provides a free hydroxyl (OH) group and allows dNTP's to join
    • At the end of replication RNA primers are cut out by DNA poly and replaced with DNA nucleotides
  50. Primase
    • RNA polymerase that makes an RNA primer that can be elongated
    • Initiates the replication of DNA
  51. Replication Forks
    • Primase initiates the replication of DNA and synthesis continues from the sites of origin at replication forks
    • The two prongs replicate in opposite directions
  52. Leaving Groups
    • Each arriving nucleotide comes as a dNTP (deoxyribosenucleotide triphosphate) as it binds to a strand it loses two terminal phosphates
    • This reaction releases energy and provides the E needed to attach nucleotides
  53. DNA polymerase
    • Enzyme the elongates DNA at replication forks
    • Catalyzes the addition of nucleotides to the primer to make the new DNA stand and align nitrogenous bases in position opposite to the parent strand 
    • Cannot add nucleotides to parent DNA needs RNA primer
    • **Will only add nucleotides in one direction 5'-->3', so only to the 3' end
  54. DNA synthesis always occurs in the _____ direction, and the parent strand is read ____
    DNA synthesis always occurs in the 5'-->3' direction, and the parent strand is read 3'--->5'
  55. Okazaki Fragments
    • Fragments of DNA that were replicated discontinously 
    • To stay consistent with 5'-->3' rule primase and DNA poly must jump back as more parental DNA is unwound and then move forward, not continuous
  56. Leading strand/Lagging strand
    Because synthesis of the discontinuous strand lags behind synthesis of the continuous strand, the discontinuous strand is also known as the lagging strand and the continuous strand as the leading strand
  57. DNA ligase
    Okazaki Fragments are connected to one another by DNA ligase
  58. DNA replication picture
  59. Semiconservative
    • Each daughter strand is synthesized according to a parent template
    • Once complete there are two resulting daughter strands, one each wound with a side of the parent template
    • The parent strand is therefore semi conserved in each daughter strand
  60. Antisense strand and sense strand
    • Antisense- the DNA strand the RNA uses as template
    • Sense- the DNA strand that is not transcribed
  61. Primary Trancript
    • mRNA that has just been trancribed
    • Contains a seq of exons and introns
    • Introns are excised from primary transcript once a cap and tail have been added
  62. Topoisomerases
    • Regulate the super coiling of DNA into Chromosomes
    • Aids in DNA unwinding for transcription and Replication

    Topoisomerase I causes single stand breaks and ligations which affect the nature of coiling

    Topoisomerase II causes double strand breaks
  63. DNA mismatch repair
    Fixes errors in replication when DNA poly adds wrong base, it usually cut out and replaced with correct base
  64. Exonulease
    When DNA poly corrects mistakes in a 3'-->5' direction
  65. Endonucleases
    Errors that are corrected within a strand or middle of a strand
  66. Thymine dimers
    • are adjacent thymine nucleotides that become covalently bonded due to UV E and UV damage
    • They prevent DNA poly from copying DNA beyond site
    • UV specific nucleases cleave the dimer and insert two new thymines, which are sealed together with ligase.
  67. RNA Polymerase
    • Pushes apart the double helix in a certain region and bind to a promoter sequence and beings to transcribe the structural genes
    • 5'-->3'
    • Must synthesize mRNA off 3'-->5'
    • No proofreading function
  68. Genetic Code
    Combination of all codons
  69. Translation
    • The process by which mRNA codons are translated into a sequence of amino acids
    • Occurs at ribosome (Free and bound to ER)
    • tRNA is used at ribosome to carry correct amino acids in place
    • In cytoplasm in prokaryotes
  70. ER bound ribosomes, and free ribososome secret proteins to ...
    • ER bound secrete proteins to ER lumen then golgi body
    • Free ribosomes secrete proteins right into cytoplasm
  71. Nuclear Localization Signal
    Allows proteins designated for the nucleus to pass through the nuclear membrane and remain in the nucleaus
  72. Signal Sequences
    Tell ribosomes to remain bound to ER until after protein synthesis
  73. Translation of Proteins: 3 Parts
    • Initation
    • Elongation
    • Termination
    • All require ATP and enzymes
  74. Aminoacyl tRNA Synthetase
    Enzyme that loads tRNA with amino acids
  75. Aminoacyl tRNA
    A tRNA with an amino acid
  76. tRNA
    • transfer RNA
    • Specific for 1/20 amino acids
    • Brings amino acid to sequence on mRNA (tRNA holds the complementary sequence, anticodon, of bases on one end and an amino acid on the other)
    • Polypeptide chain is attached to carboxyl end
  77. Amino Acids
    • Come from digestion of food or from the environment
    • 20 naturally occurring amino acids
    • Many different codons can code for the same amino acids
  78. Genetic Code Redundancy
    • Also called degenerate
    • Many different codons can code for the same amino acids
    • The idea is that the third base is not as important as the first two. 
    • tRNA binds more tightly to the first two bases and the third is more varriable
  79. Initiation
    • mRNA binds to the small ribosomal unit
    • tRNA imitator carries the amino acid methionine and binds with initiator start codon (AUG)
    • The anticodon of the initiator tRNA is UAC
    • The Large ribosomal unit binds to small unit around mRNA
    • Creates a complete ribosome with MET tRNA complex in the P site
  80. Ribosome: Units
    • Two units
    • Small Unit  (40S) goes under mRNA
    • Large unit (60S) is U-shaped and goes around tRNA and amino acid, and locks to the smaller unit (80S)
    • This locks mRNA in place
    • This complex slides along mRNA
  81. A site
    aminoactyl tRNA
  82. P site
    • Petidyl tRNA
    • First spot on small ribosome
  83. Methionine
    Start codon/initiator
  84. Elongation
    • H bonds for between mRNA codon in the A side
    • Enzyme peptidyl trasnferase forms a peptide bond between the amino acids tRNA (aminoactyl tRNA) in the A spot to MET in the P spot
    • Translocation-Ribosome moves three bases along mRNA in 5'-->3' direction
    • tRNA from a moves to P and tRNA in P is expelled
    • A is empty for new tRNA
  85. Enzyme peptidyl trasnferase
    Forms a peptide bond between the amino acids tRNA
  86. Translocation
    • Ribosome moves three bases along mRNA in 5'-->3' direction
    • Requires GTP
  87. Termination
    • Polypeptide synthesis stops when mRNA termination codon arrives in the A site
    • Protein called a release factor binds to termination codon and adds a water molecule to the end of the protein chain 
    • The poly chain releases from ribosome
  88. Termination codon's
    • UAA
    • UGA
    • UAG
  89. Polyribosome
    mRNA is read by multiple ribosomes at the same time
  90. Signal Peptides
    Sort signals as the end of the protein chains that direct protein to a certain location
  91. Signal Patches
    Sort signals from the middle of proteins 3D structure
  92. ER bound made proteins are secreted into
    the ER lumen then golgi body
  93. All proteins go where after synthesis
    • into the golgi body
    • They are then wrapped in a vesicle
    • This vesicle merge with membranes and the proteins are dumped out
  94. ER Retention Signal
    • Proteins that remin in ER have this signal added to their structure
    • Group of four amino acids added to carboxyl terminal that restricts protein to ER lumen
  95. Chaperons
    Proteins that aid in the folding of new ER proteins
  96. Glycosylation
    • The addition of sugars to protiens
    • Usually glycosylation signals that proteins are destined for export out of the cell or for membranes
    • Rarely do proteins in cytoplasm have sugars
    • Makes proteins more resistant to being digested and form a selectively permeable layer above the cell
  97. Cytosolic
  98. N Linked olgosaccharides
    • Most common sugar group added to a protein in ER
    • Sugar is added to NH2 group of asparagine amino acid
    • NH2 --> N linked
  99. GPI Anchor
    • A carboxyl terminal of a protein is changed to a GPI anchor  that allows proteins to eventually anchor in exterior of cell membrane
    • It enters Golgi body and is packaged and the vesicle merges with cell membrane on excretion and the protein is stuck
  100. O Linked Glycosylation
    Sugars are added to the carobxyl group (OH) off serine and thronine amino acids side chains
  101. Clathrin
    Proteins that coats vesicles carrying lysosomal proteins
  102. Mutations in DNA are caused by
    • Inheritance, only possible in mutations found in sperm and egg cell can be inherited
    • Mutagens
  103. Mutagens
    • external cancer causing agents
    • EX: UV light, radon, asbestos
  104. Point Mutations
    When a single base is substituted by another
  105. Silent Mutations
    • When mutations cause no change in function
    • Can occur when:
    • Mutations are in introns
    • Mutations codes for same amino acid
  106. Frame Shift Mutations
    • Involves change in the reading frame of mRNA
    • Occurs when a base is inserted or deleted, the codons of mRNA are shifted
    • Can render the whole structure non functional
  107. Nonsense mutations
    Produces a premature termination of a protein chain, base is changed into a stop codon
  108. Differences in Protein Synthesis in Prokaryotes
    • The first tRNA (initiator tRNA) carrier formyl methionine (fMert) instead of methionine
    • mRNA does not need to be process (capping, tailing, splicing) in prokaryotes before translation
    • Because no processing of mRNS is needed, and transcription occures in the same place (Cytoplasm) they can occur at the same time
  109. Translation Picture