Chapter 12 - DNA Packing
Eukaryotes
- 10nm fiber - 147 base pairs of DNA - Octamer histones (H2A, H2B, H3, H4) - Whole thing holding it together is the nucleosome - Histones in the middle and DNA wrapped around it.
Prokaryotes
- Circular and smaller chromosomes - Have histone like proteins but not histones - Contain supercoiling (how they are arranged in the cell). - Need to be under supercoiled when replication occurs. Tension released.
- The gene expression level would go down (transform into heterochromatin) - Would be deacetylated - Methylation would probably increase
A gene normally found in euchromatin is transposed into the centromere. In what ways do you expect its expression level to change?
II
A type _____ topoisomerase cuts both strands of DNA
Chemical modifications
Affect the reading of the genetic information.
Chromatin Remodeling
Allow replication and gene expression, chromatin must relax its compact structure and expose regions of DNA to these proteins, and there must also be a mechanism for reversing the process during inactivity.
Chromatin
Allows DNA to fit in a tiny nucleus of only 10 micrometers in diameter.
positively, negative
Bacterial chromosomes have a high percentage of ________ charged amino acids that can ionically bond to the ________ charges in the phosphate groups of DNA.
Supercoiling
Both negative and positive forms of ______ are relieved by topoisomerase
Histone Methylation
Can be added to both arginine and lysine. Residues in histone, and this change up correlates with gene activity.
Nucleosomes
Chromatin fibers are composed of linear arrays of spherical particles. The particles occur regularly along the axis of a chromatin strand and resemble beads on a string. Initially referred to as v-bodies but now called this. - DNA wrapped around the histone
Repetitive DNA
Common in telomeres and centromeres
Non-Acetylated Histone Tails
Compact
Negative refers to how the supercoils are left-handed and the double helix is right handed. Positive would mean the supercoils are right handed.
Compare positive and negative supercoiling.
Centromeres
Constitutive heterochromatin. Tandemly repeated sequence. Satellite DNA. Spindle fibers attach during cell division. Important for segregation of chromosome during mitosis and meiosis.
Supercoiling
Contorting in a certain way in order to retain normal base pairing. Shape cause tighter packing and thus the increase in density.
Methylation of histones is often positively correlated with gene activity. 5 methyl cytosine is usually negatively correlated with gene activity.
Describe how 5-methyl cytosine modifications to DNA differ from methylation of histones within the nucleosome with respect to gene activity.
Number (or letter) of chromosome
Determined by size (or sex)
Looks like the thicker structure solenoid consisting of numerous nucleosomes could and stacked on top of each other. Characteristics of an uncoiled chromatin fiber in interphase.
How do chromosomes look during most of the cell cycle?
The DNA is packed within the phage head of the bacteria. Once packed within the head, the virus's genetic material is functionally inert until released in the host cell.
How is DNA typically organized in prokaryotes?
- Organization of DNA during the transitions is much more intricate and complex Ghan viruses or bacteria, which never exhibit a complex process like mitosis. - Greater amount of DNA per chromosome in eukaryotes - Larger number of proteins associated with eukaryotic DNA
Identify three ways in which prokaryotic and eukaryotic chromosomes are different.
Histone Phosphorylation
Increased chemical modification relates to chromatin unfolding and condensation.
Topoisomerase Type II
Introduces negative supercoils into DNA. Cleaves both strands in the helix.
Acetylated Histone Tails
Less compact
Interspersed Retrotrasposons
Move by first being transcribed into RNA followed by reverse transcription leading to DNA copy that recombines with genomic DNA.
Tandem Repeats
Occur in DNA when pattern of one or more nucleotides is repeated and repetitions are directly adjacent to each other.
Topoisomerase
One group of enzymes that cut one or both of the strands and wind or unwind the helix before resealing the ends.
- Linear Chromosomes - Generally large - Have multiple replication forks
Organization of DNA in eukaryotes
Heterochromatin
Parts of chromosomes that are condensed. Highly compact
Euchromatin
Parts of chromosomes that are uncoiled. Open for DNA expression.
Histones
Play the most essential structural role. Histones contain large amounts of the positively charged amino acids lysine and arginine, making it possible for them to bond electrostatically to the negatively charged phosphate groups of nucleotides. Play an important role in chromatin structure.
Karyotype
Process in which photographs of chromosomes are taken in order to determine the chromosome complement of an individual, including number of chromosomes or any abnormalities.
Unique Sequence DNA
Rare. Protein coding genes
Histone Acetylation
Remodels the chromatin fibers which increases in regions of active genes and decree in inactive regions.
Histone acetylation - Acetyl groups erase the positive charges Histone methylation - Positively charged. Histone phosphorylation - Negative charge, will increase the repulsion
Select all modifications to the chromatin that would result in increased gene expression.
Topoisomerase Type I
Serves to reduce the number of negative supercoils in a closed circular DNA molecule. Cleaves one strand in the helix.
Satellite DNA
Short sequences repeating a large number of times. - Form of repetitive DNA - Can sometimes cause diseases -- Huntington's Disease - Disrupts DNA expression - Pieces of DNA that repeat themselves. - Highly represented in the heterochromatin.
Chromosome Nomenclature
Shows where the chromosome banding occurs
Telomeres
Tandemly repeated DNA at the ends of linear chromosomes. Number of repeats depends upon the organism and age (as we age, telomeres get shorter and shorter). Important for stability of chromosomes.
Linker DNA
The DNA between each of the histone cores is referred to as a(n) __________.
C-Value
The amount in picograms, of DNA contained within a haploid nucleus or one half the amount in a diploid somatic cell of a eukaryotic organism.
Bacterial chromosomes have associated proteins HU and H-NS (histone-like and nucleic structuring) proteins. These proteins are homologous to eukaryotic histones. What does the conservation suggest about the function?
The proteins can fold and bend the DNA to have the effect of compacting the DNA constituting the nucleoid.
Epigenetics
The study of the mechanisms of which genes are turned on or off without changes in the underlying genetic sequence.
Chromatin fiber
Thickest strand that comes together to make a chromatid.
Lysine and arginine
What amino acids are found in high percentages in histones?
They are positively charged allowing them to bond electrostatic ally to the negatively charged phosphate groups of nucleotides.
What are the properties of lysine and arginine?
Digestion of the mitotic chromosomes with the proteolytic enzyme trypsin, folk head by Giemsa staining.
What causes the banding on karyotype?
Second
What is the level of packing during interphase?
Histone Tails
When they undergo acetylation, the structure of the nucleosome changes. Contain most of the positively charged amino acids, but they can be modified.
On the telomere and centromere. Position effect is the position of a gene or group of genes relative to all other genetic material possibly affecting their expression.
Where is heterochromatin found? What is the position effect and how does it affect gene expression?
The chromatid arms value undoubtedly vary among different organisms.
Why are varied levels of packing preferable to 700-nm diameter packing?
An underwound molecule will form supercoils in the direction opposite to that of underfunding.
Why would supercoiled DNA be desirable?
Arm of Chromosome
p (as in the French word petit, smaller side of centromere), q (long side)