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Describe the Viral Genome.
- Viruses are small infectious particles that contain nucleic acid surrounded by capsid of proteins.
- Linear or Circular
- Relatively Small
- RNA or DNA (not both)
What are the components of a Bacteriophage?
- Base Plate
- Tail Fibers
What are the two types of Assembly found in viruses?
- No assembly required: Nucleic acid and capsiid proteins spontaneously bind to each other to form a mature virus.
- Assembly required: requires the involvement of non- capsid proteins to direct the proper assembly of the virus.
What are the proteins associated with directed assembly of viruses?
- Scaffolding proteins: catalyze assembly process.
- Protease-like proteins: cleave viral capsid proteins into smaller units which allows for correct assemblages.
Describe the bacterial chromosome.
- Highly compacted.
- Occurs in the nucleoid.
- Can be multi copied.
- Millions of base pairs long.
- Contains a few thousand genes.
What types of genes can be found in the bacterial chromosome?
- Structural gene sequences: encode proteins.
- Intergenic regions: nontranscribed regions.
- Origin of replication: unique DNA sequence at which replication is initiated.
- Repetitive sequences: (<10bp) found in multiple copies interspersed within the intergenic regions.
What are the two types of supercoiling?
- Underwinding (left handed) = negative supercoiling (fewer turns)
- Overwinding (right handed) = positive supercoiling (more turns)
What are topoisomers?
Strands that only differ with regards to supercoiling.
What are the effects of supercoiling?
- Reduction of size.
- Promotes replication and transcription of these small regions.
What are the enzymes associated with supercoiling?
- DNA gyrase (toposimoerase II) : induces negative supercoiling.
- Topoisomerase I : Relax negative supercoils.
What are functionally important sequences in Eukaryotic organisms?
- Origin of replication: Multiple, which are essential to replication.
- Centromeres : Essential to proper segregation of chromosomes during mitosis & meiosis.
- Telomeres : Prevents sticky ends, protect chromosomes from digestion, prevents shortening in DNA replication.
What is the typical gene length in eukaryotic organisms?
Describe Unique or non repetitive sequences.
- Sequences only found one or a few times within a genome.
- This includes the vast majority of proteins encoded for by genes present in one or a few copies.
- 40% of the human genome (some genes are only used in portions of our body because tissues only use certain genes their entire lifespan.)
Describe moderately repetitive sequences.
- Those found a few hundred to several thousand times in the genome.
- Multiple copies of the same gene.
- Transposable elements.
Describe highly repetitive sequences.
- Those found 10k to 1mil times in the genome.
- Relatively short. (few to several 100 bp)
- Repeats can also occur as tandem repeats (often found in centromeric or telomeric regions)
Describe the relationship of complexity of DNA to the rate of renaturation.
- The faster DNA renatures the less complex (more highly repetitive) it must be.
- The slower DNA renatures the more complex (more unique) it has to be.
What is an Octamer?
- Two copies of each of the four different histone subunits.
- DNA makes 1.65 negative superhelical turns around the octamer.
- Requires 146bp of DNA per octamer.
What is a nucleosome?
146 nucleotide base pairs wrapped around an octamer.
What is a linker region?
- It connects nucleosomes.
- Varies in length from 20-100bp.
What are the Core Histones?
What is a linker histone?
- binds to one side of the nucleosome and to the linker region.
What causes DNA to adhere to the histones?
Histones contain large numbers of positively charge lysine and arginine amino acids. The electrostatic & hydrogen bonding between the histones and phosphate backbone keep them bound.
What is level one of compation?
Formation of a nucleosome.
What is level two of compaction?
- 30 nm fiber.
- Nucleosome (6-8) associate with each other to form a more compacted structure.
- DNA enzymes can not transcribe in this state.
What is the third level of compaction?
Formation of Radial loop domains.
How are radial loop domains formed?
30nm fibers interact with a filamentous network of proteins in the nucleus to form 10nm loops lining the inner membrane and nucleus.
What are MARs and SARs?
- Matrix attached regions
- Scaffold- arrached regions
- Sequences which bind specific proteins in the nuclear matrix causing loops to form.
- Up to 200kbp
What is the importance of radial loops?
- Regulation of gene expression.
- Maintain chromosome territories ( discrete, non-overlapping regions)
What is the difference between Euchromatin and Heterochromatin?
- Euchromatin is less condensed regions capable of gene transcription.
- Heterochromatin is tightly compacted regions of chromosome (highly repetitive DNA sequences) generally transcriptionally inactive.
What are the two types of Heterochromatin?
- Constitutive : always heterochromatic and permanently inactive with regards to transcription. Highly repetitive DNA.
- Facultative : ability to convert between heterochromatin and euchromatin. (barr body)
Describe the Histone code hypothesis.
Histones can be reversibly modified at specific sites in their N-terminal tails protruding from the nucleosome core. Important in the role of altering DNA accessibility and chromatin structure. Amino acids on the tail can be acetylated, methylater, and phosphorylated.
Describe the process of histone acetylation/deacetylation in regards to transcription.
- The enzyme HAT ( Histone acetyltransferase ) acetylates histones so that transcription can more readily occur.
- The enzyme HDAC ( Histone Deacetylase ) deacetylates histones to repress transcription.
Describe the compaction of chromosomes in Interphase.
Most chromosomal DNA is in a 300nm configuration (corresponds to euchromatin). Except for the centromeres which are heterochromaticaly compacted to a diameter of 700nm.
Describe the compaction of chromosomes by the end of prophase.
Sister chromatids are entirely heterochromatic and have a diameter of 1.4k nm, but are short in length.
What are SMC proteins?
- Proteins (along with topisomerases) that use ATP to catalyze changes in chromosome structure.
- Dimers connected at the hinge region.
- Fold, Tether, and manipulate DNA.
What are the two types of SMC protiens?
What is the function of Condensin?
- Promotes greater compaction of the raidial loops.
- Regulated differently.
What are the two types of condensin?
- Type 1: Located in cytoplasm during interphase. Gains access to chromosomes only after nuclear envelope breaks down.
- Type 2: Located in cell nucleus during interphase. Involved early chromosome condensation of prophase.
What is the function of Cohesin?
- Promotes the binding between sister chromatids along their entire lengths from S phase untile middle of prophase.
- Remains at centromeric regions until anaphase at which time is rapidly degraded by a protease called Separase (hydrolyzed subunit called "Securin").