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135 Cards in this Set
- Front
- Back
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genome organization for prokaryotes
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circular
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genome organization for eukaryotes
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linear
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Bacterial DNA is ___ to increase accessibility to proteins involved in replication or transcription
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negatively coiled
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Bacterial chromosome is localies to the ___
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nucleoid
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DNA folded into loops anchored in nucleoid is held in place by ___ and ___
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RNA and proteins
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Positive supercoiling
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in the direction of the helix-- overwound
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Negative supercoiling
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against the direction fo the helix-- underwound
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small circular DNA
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plasmids
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3 types of plasmids
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1. F-factor
2. R-factor 3. COl factor |
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__ condenses into chromosomes
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Chromatin
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Bead + DNA =
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nucleosome "Beads on a string"
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Histone
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octamer
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2 types of chromatin
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1. Euchromatin
2. Heterochromatin |
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the nuclear envelope contains 2 membranse separated by a ___
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perinuclear space
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transcriptivly active
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Euchromatin
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Transport through the nuclear pore complex requires ___
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enegry (GTP hydrolysis)
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short repeating DNA one after the other
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Tandemly
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longer repeating DNA scattered
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interspersed
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Topoisomerase
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Type I - single stranded knicks
Type II- double stranded breaks |
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DNA is folded into loops and anchored in nucleoid. What releases the loops?
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RNase
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What relaxes the supercoiling but does not release the loops?
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Topoisomerase
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Proteins that are bound to supercoiled DNA in prokaryotes are analogous to ___ in eukaryotes
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histone proteins
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Chromatin fibers
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DNA bound to proteins
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what is revealed when the chromatin is opened up?
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beads on a string
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histones are connected by what?
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thing filament of DNA
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The inner membrane of the nuclear envelope rests on a ___ while the outer memebrane is continuous with ___
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nuclear lamina, ER
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The nuclear pore complex is made up of __ subunits (nucleoproins) that project into the cytoplasm and nucleoplasm
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8
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when proteins are imported into the nuclear pore complex __ binds to the importin releasing the protein
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Ran
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meshwork of fibers lining the inner nuclear membrane
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nuclear lamina
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special intermediate filaments
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lamins
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special intermediate filaments that may form attachments with inner membrane proteins and may also provide attachment sites for chromatin
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lamins
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two types of heterochromatin
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1. constituative
2. facultative |
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highly condensed at all times
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constituative herterochromatin
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cell type specific heterochromatin
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facultative
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most DNA bound as ___
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heterochromatin
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chromatin occupies territories near the ___ of the nucleus
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periphery
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site of ribosome synthesis
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nucleolus
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genes for rRNA are present on multiple chromosomes but are active only in the nucleolus
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Nucleolar organizing region
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DNA replication is ___
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semiconservative, N1trogen isotope experiment
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Ori
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site of replication initiation
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Bacteria have __ ori
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single
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site where DNA duplex is replicated
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replication fork
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replication is
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bidirectional
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there are ___ sites of DNA synthesis in eukaryotes
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multiple
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one unit of replication
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replicon
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what makes a replication origin?
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ORC (origin replication complex) and MCM (mini chromosome maintenance comples) bound together mediated by helixase loaders
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why A-T rich region?
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2 bonds for A-T vs 3 bonds for G-C
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Autonomously replicating sequences are present in ___
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yeast
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__ replication forks per origin that go bidirectionally and fuse
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2
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DNA synthesized at forks by what?
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DNA polymerase
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growth is in what direction?
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5' to 3'
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what end is the lagging strand?
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5' end
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how do you add to the lagging strand?
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okazaki fragments
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why is there no 3' to 5'?
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1. DNA polymerase proofreads
2. 5' proofreading would remove high energy triphosphate |
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the primer is ___ synthesized by ___
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RNA, primase
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What can initiate new strand synthesis?
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primase
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why is the primer RNA?
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because if it were DNA it could no longer proofread
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removal of high energy __ prevents 3' to 5' synthesis
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phosphate
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DNA polymerase requires what?
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a template
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What unwinds DNA at the replication fork?
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DNA helicases
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what keeps DNA unwound?
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single-stranded DNA binding protein
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creates knick to relax DNA
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topoisomerase
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DNA replication complex that moves in the direction of replicaiton fork; causes lagging strand template to loop
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replisome
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occur spontaneously or in respone to encironmental agents (mutagens)
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mutations
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what are the two types of mutations?
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somatic and germline
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what type of mutation is passed to offspring?
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germline
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this type of mutation can cause cancer?
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somatic
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what are the two types of spontaneous mutations?
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depurination and deamination
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loss of a purine by hydrolisis of glycosidic bond linking purine to deoxyribose
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depurination
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removal of the amino group from a base
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deamination
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in this type of mutation cytosine is converted into uracil which acts like thymine (it pairs with adenine)
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deamination
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3 chemical mutagens
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1. Base analogs
2. Base modifying agent 3. Intercalated agents |
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what can incorporate into DNA and base pair with different bases?
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Base analogs
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alter base structure
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base modifying agent
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insert themselves between adjacent bases; cause distortion in helix
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intercalating agents
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UV radiation is an environmental mutagen that induces
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Thymine dimers
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In a thymine dimer the thymens are bound by what type of bond?
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covalent
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___ synthesis of new DNA where the template is damaged
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translesion
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what prevents that passage of initial mutations to a newly forming DNA strand
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damage tolerance
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explain excision repair
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endonuclease cuts out damage; DNA pol fills in missing nucleotides; DNA ligase seals the knicks
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what type of repair corrects single damaged bases?
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Base excision
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deaminated bases are detected by what?
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DNA glycosylase
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what type of repair recognizes distortions in DNA?
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Nucleotide excision repair
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what are the two ways to repair a thymine dimer?
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translesion and nucleotide excision
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methylation
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proves which strand is the existing strand
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this type of repair targets erros made during replication that are not corrected by proofreading
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mismatch repair
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newly synthesized DNA is not yet ___
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methylated
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Thymine is important in DNA because it can be ___ whereas uracil cannot.
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methylated
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when two strands of brokne DNA are joined they are error prone and are known as...
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non-homologous end joining
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cells have 2 copies of each chromosome; when breaks in one copy can be repaired using the second copy as the template it is known as...
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homologous recombination
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short repeating sequences at endo of each chromosome
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telomere
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generated additional copies; RNA- containing protein; RNA sequence is complementary to telomere sequence.
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Telomerase
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rapidly dividing cells spend little time in what phase?
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G1/G2
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what phase does DNA synthesis occur?
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S
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what factors influence the start transition?
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nutrient availability, cell size and growth factors
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what factors influence the G2-M transition?
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cell cycle can be arrested in G2 if division is not necessary
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what factors influence the Metaphase-Anaphase transition?
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proper separation of sister chromatids
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what demonstrated the presense of cell cycle control molecules?
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heterokaryons
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cdks are only active when bound to what?
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cyclin
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__ cyclins are required for start?
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G1
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__ cyclins are required for replication?
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S
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cyclin concentration ___ during cell cycle
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oscillate
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what was evidence for cell cycle control by cyclin? also induces trasition
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Maturation promoting factor (MPF)
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___ is a cdk-cyclin complex
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MPF
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how is cdk activity regulated?
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cyclin and phosphorylation
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promotes the separation of sister chromatids and degrades mitotic cyclin
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Anaphase promoting complex
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halt cell cycle until suitable conditions prevail
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checkpoints
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inhibits Cdc20 and indirectly inhibits APC
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MAD/Bub complex
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ensures DNA replication had been completed prior to G2-M transition
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DNA replication checkpoint
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ensures damaged DNA is repaired before cell cycle continues
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DNA damage checkpoint
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activates puma which initiates apoptosis
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P53
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what are the four types of RNA?
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1. mRNA
2. rRNA 3. tRNA 4. small RNA |
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DNA and RNA are in what orientation?
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antiparallel
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2 alpha and 2 beta subunits with the sigama factor form what?
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holoenzyme
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ensures initiation at proper site on DNA
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holoensyme
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what binds to the promoter sequence in transcription?
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RNA polymerase
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the first base transcribes which is usually an adenine is known as what?
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start point; +1
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-10 sequence
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pribnow box
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4 steps of transcription
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1. binding
2. initiation 3. elongation 4. termination |
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binds sequence 50-90 bases near 3' end of RNA
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Rho factor
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What are the two ways termination can occur?
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Rho factor
GC rich complementary region |
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How many RNA polymerases do Enukaryotes use? prokaryotes?
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3, 1
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in eukaryotes what is analogous to the pribnow box of prokaryotes?
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tata box
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located in nucleolus and is involved in the synthesis of rRNA precursors
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RNA polI
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located in the nucleoplasm and is involves in the synthesis of pre-mRNA and nuclear RNA for post transcriptional processing
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RNA polII
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located in the nucleoplasm and is involved in the synthesis of tRNA
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RNA polIII
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increase the levels of RNA expression
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enhancers
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promotes histone disassembly
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nucleoplasmin
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termination signal
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AAUAAA
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RNA processin gis type specific. What are the types?
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rRNA> tRNA> mRNA
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a small subunit and a large subunit make up...
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ribosome
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multiple RNAs cleaved froma single transcription unit
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rRNA
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__ blocks methylation and prevents mature rRNA from forming
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cycloleucine
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sequences in promary transcript that are removed from funtional mRNA
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introns
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what demonstrate introns?
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r looping and restriction enzymes
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