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virus
small infectious particles that contain nucleic acid surrounded by a capsid of proteins
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bacteriophage
- bacterial viruses
- contian a sheath, base plates, and tail fibers
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viruses rely on host cells for replication of genetic material
- limited host range
- may or may not destroy host
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viral genome
- linear or circular
- relatively small
- RNA or DNA (not both)
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self-assembly (no assembly required)
- nucleic acid and capsid proteins spontanously bind to each other to form a mautre virus
- tobacco mosaic virus
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direct assembly (assembly required)
requires the involvement of non-capsid proteins to direct the proper assembly of the virus
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scaffolding proteins
catalyze the assembly process (direct assembly)
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protease-like proteins
- cleave viral capsid proteins into smaller units which allow for correct assemblages
- (protease= enzyme that cuts proteins)
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bacterial chromosomes
- highly compacted
- occurs within the nucleoid
- can be multi-copied
- circular molecule (majority but not all)
- millions of nucleotides long
- few thousand different genes interspersed throughout the chromosomes
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structural gene sequence
encodes proteins
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intergenic regions
nontranscribed regoins
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origin of replication
unique DNA sequence at which replication is initiated
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repetitive sequences
(<10 bp) found in multiple copies interspersed within the intergenic regions
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to fit within bacterial cells, chromosomal DNA must ____
compact to 1,000 fold
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loop domains
- 10 fold formation
- number vaires with species and size of chromosome
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_____ and ______ can induce supercoiling
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underwind
- left-handed
- negative supercoiling
- fewer turns
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overwinding
- right-handed
- positive supercoiling
- more turns
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topoisomers
strands that only differ in the direction they have been coiled
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effect of supercoiling
- reduction of size
- negatively supercoiled strands may separate in attempt to relieve tension
- promotes replication and transcription
- get an unwound area of DNA
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supercoil enzymes
- DNA gyrase (topoisomerase II)
- topoisomerase I
- competing action of both enzymes govern overall supercoiling of bacteria
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DNA gyrase (topoisomerase II)
- induces negative supercoils
- critical to the survival of bacteria
- relax positive supercoils
- antagonistic (negative vs. positive supercoils)
- cuts 2 strands of DNA
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topoisomerase I
- relax neaive supercoil
- cuts 1 strand of DNA
- induces positive supercoils
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Eukaryotic genomes
genome size is not equal to complexity
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origins of replication
- mulitple
- essential to replication
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centromeres
essential to proper segregation of chromosomes during mitosis and meiosis
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telomeres
- prevents "sticky ends"
- protect chromosomes from digestion
- prevents shortening with each round of DNA replication
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between centromere and telomere
- 100's to 1000's of different genes
- typical eukaryotic gene ranges 1kb to 100kb
- genes from less complicated chromosomes are small and mostly structural genes
- more complex organisms have longer genes with introns
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sequence complexity
the number of times a particular base sequence appears throughout the genome
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unique or nonrepetitive sequences
- sequences only found once or a few times within genome
- vast majority of proteins encoded for by gene present in one or a few copies
- only ~40% of human genome
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moderately repetitive sequenes
- those found a few hundred to several thousand times in the genome
- multiple copies of the same gene
- transposable elements
- something every cell is going to need
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highly repetitive sequences
- those found tens of thousands or even millions of times
- short (few to several hundred bp)
- tandem repeats
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tandem repeats
- very short sequences repeated many times in a row
- 5'-AATATAATATAATAT-3'
- commonly found in centromeric or telomeric regions
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rate of renaturation
- double stranded DNA is "melted" (denatured) into single-strands by heat and then cooled
- fewer the copies of base sequences, the harder and longer it takes for complementary strands to find each other (renature)
- the more repetitive the sequene, the faster it will renature
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how do you know if DNA is renatured?
if you only get one band you know its renatured, if you get two bands you kow some of it is renatured and some is not
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compaction of chromosomes
- accomplished through interaction between DNA and several different proteins
- protein compositoin changes during the cell cycle affecting the degree of compaction
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what is effected from the chromsome being tightly or loosly compacted
if a particular gene is being transcribed or not
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first level of compaction
- DNA makes 1.65 negative superhelical turn around the octamer
- requires 146 bp of DNA per octamer
- single nucleosome is about 11 nm in diameter
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nucleosome
- made up of 8 histone proteins and 146 nucleotide base pairs
- 11 nm in diameter
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octamer
two copies of each of the 4 different subunits
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linker regions
connect nucleosomes and var in length from 2-100 bp
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core histones
H2A, H2B, and H4
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linker histones
- H1
- binds to one side of nuclosome and linker region
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hostones contain a large number of _____ charged lysine and
positively
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_____ form electrostatic and hyrodgen-bonding interactions with phosphate DNA backbone
arginines
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compaction level 2
- nucleosomes (6-8) associate with each other to form a more compacted structure that is 30 nm in diameter
- looks like a string of pearls
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radial loop domains (3rd level of compaction)
- 30 nm fibers interact with filamentous network of proteins in nucleus called the nuclear matrix to form loops
- network of irregular 10 nm fibers and other proteins
- some line the inner nuclear membrane
- some fill the nuclear interior
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matrix-attachment regions (MARs) or scaffolding-attachment regions (SARs)
- bind to specific proteins in the nuclear matrix causing loops to form
- loops can conatin up to 200kb
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importance of radial loops
- regulation of gene expression
- maintain territories (discrete, non-overlapping regions)
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euchromatic
less condensed regions capable of gne transcription
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heterchromatin
tightly compacted regions of chromosome (highly repetitive DNA sequences) generally transcriptionally inactive
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two types of heterochromatin
- constitutive heterochromatin
- facultative heterochromatin
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constitutive heterochromatin
- always heterochromatic and permanently inactive with regards to transcription
- highly repetitive DNA
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facultative heterochromatin
- ability to convert between heterochromatin and euchromatin
- ex. Barr body
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histone code hypothesis
histones can be reversibly modified at specific sites in their N-terminal tails protruding from the nucleosome core
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why is histone code important
important role in altering DNAaccessibility and chromatin structure
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particular amino acids in the amino terminal tail can be _____, _____, and _____.
- acetylated
- methylated
- phosphorylated
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acetlyation
best characterization histone modification
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acetylation associated with ______
- transcriptionally active genes
- enzyme: histone acetyltransferases (HATs)
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deacetylation associated with ____
- transcriptional repression and heterochromatin formation
- enzyme: histone deacetylases (HDACs)
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cancer genes either have an _______ or an _______ on either HDAC or HAT
- overexpression
- underexpression
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compaction in interphase
- most chromosomal DNA is in a 300 nm configuration
- some regions are heterchromatically compacted to a diameter of ~700 nm
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by the end of ______ sister chromatids are entirely heterochromatic and have larger diameter (1,400 nm) but shorter in diameter
prophase
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what ceases all transcriptional activity?
- highly condensed metaphase chromosomes
- still remain anchored to scaffolding
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structural maintenence of chromosome proteins (SMC proteins)
- proteins that use ATP to catalyze changes in chromosome structure
- dimers connected at the hinge region
- fold tether and manipulate DNA
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two types of SMC proteins
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condensin
promotes greater comopaction of the radial loops; regulated differently
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type II of condensin
- located in cell nucleus during interphase
- involved in early chromosome condensation of prophase
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type I of condensin
- located in cytoplasm during interphase
- gains access to chromosomes only after nuclear envelope breaks down
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cohesin
promotes the binding between sister chromatids along their entire length from S phase until middle of prophase
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separase
- hydrolyzed subunit called securin
- protease
- rapidly degrades cohesin at centromeric region until anaphasse
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