Lecture 13 Chromosome Structure and Transposons Ch. 11, 18 Flashcards
Why does tight DNA present a problem for cellular function?
Packing renders the DNA inaccessible for reading or copying
What is supercoiling?
Supercoiling is over-winding or under-winding of DNA, causing it to twist on itself
What is positive supercoiling?
Molecules are over rotated
What causes negative supercoiling?
Molecules are under rotated
What role do topisomerases play in supercoiling?
Enzymes that add or remove rotations from DNA: Can both induce and relieve supercoiling
Temporarily break nucleotide strands
Rotate ends around each other
Rejoin broken ends
What is the advantage of DNA being negatively supercoiled?
Makes separation of two strands easier during replication and transcription
Allows DNA to be packed into smaller sspace compared to relaxed DNA
Define chromatin
Combination of DNA and proteins
Euchromatin
Undergoes the normal process of condensation and decondensation in cell cycle
Heterchromatin
Remains in a highly condensed state through the cell cycle
What are the components of a nucleosome?
Core particle consisting of DNA + 8 histone proteins
What are the histones forming the nucleosome?
H2A, H2B, H3, H4 x 2
What histone attaches DNA to nucleosome?
H1
Nucleosome + H1 = ?
Chromatosome which consists of 167 bp
Chromatosomes are separated by what?
Linker DNA ~ 30-40 bp
What is polytene chromosome created by?
Repeated rounds of DNA replication with no cell division
What does epigenetic change cause?
Causes inherited phenotypic change without affecting the DNA sequence
What causes epigenetic changes?
Methylation; capable of being reversed and often due to environmental factors
What are centromeric sequences?
They are the binding sites for the kinetochore, where spindle fibers attach
Centromeres are mostly what?
Heterochromatic
What are centromeres probably defined by?
Epigenetic (nonsequence) changes rather than DNA sequences
What role does CenH3 play in the organization of a centromere?
Replaces H3 in most eukaryote centromeresl. Modified H3 histone
What do centromeres singal?
The begining of anaphase
What function is suggested by the fact that chromosomes that have telomeres are not degraded?
Telomeres stabilize ends of chromosomes
What do telomeric sequences consist of?
Repeated sequence of A or T nucleotides followed by several G nucleotides
How are the telomeric sequences oriented?
String of G and C sequence is always oriented away from the centromere
What is the relationship of shelterin to telomeres?
Protects ends of mammalian chromosomes from being repaired as double-stranded breaks
How are Het-A and Tart related to Drosophila telomeres?
Inserted transposable elements arranged in tandem repeats
Balance loss of telomeric sequences during replication
On the 5’-3’ strand in the telomeric sequence area, what is unique?
There is a overhanging of the telomeric sequence
Organisms differ in what?
Amount of DNA per cell (C value)
Melting temperature can cause what?
Denaturation- uncoil DNA and separate
After the DNA is denatured, the more repetative the DNA is the…
Faster it comes back together in renaturation
Describe unique sequence DNA
Gene family: similar but not identical copies of unique DNA sequences that arose through duplication of an existing gene (i.e. hemoglobin)
Moderately repetitive DNA is how long?
150~300 bp long and thousands to 100s of thousands of repeated units
What type of moderately repetitive DNA is in eukaryotes?
Tandem repeat sequences and interspersed repeat sequences
What are the types of interspersed repeat sequences?
Short interspersed elements: SINEs: Alu element
Long interspersed elements: LINEs
What are highly repetitive DNA?
less than 10bp long and repeated 100s of thousands to millions of times
What types of highly repetitive DNA is in eukaryotes?
Microsatellite DNA
What does C value refer to?
Refers to the amount of DNA per cell in a given organism
What are transposable elements?
Are mobile DNA sequences found in the genomes of all organisms
Tranposons make up how much of the human DNA?
45%
Most transposons are able to insert where?
Many different locations. Rely on mechanisms distinct from homologous recombination
What do transposons often cause?
mutations
What are on both sides of the transposable elements
Short flanking repeats from 3 to 12 bp long that are present on both sides of the transposable elements
What happens to the short flanking repeats on the ends of transposons
Do not travel with the transposable element
Regenerated at the point of insertion
How are flanking direct repeats created after transposable element moves?
Staggered cuts are made in the target DNA, leaving short, single-stranded pieces of DNA on either side of the transposable element.
Replication of single-stranded DNA creates the flanking direct repeats
What are found at the ends of many transposable elements?
Terminal, inverted repeats (9-40 bp)
- sequences are inverted and complementary on same strand
- recongized by enzymes that catylze transposition
- required for transposition to take place
Transposons cause mutations by what?
Inserting into another gene
promoting DNA rearrangements
What are examples of transposon induced mutations?
Approximately half of spontaneous mutations in Drosophila
Human genetic diseases
The color of grapes
Why is the process of replicative transposition referred to as “copy and paste” transposition?
A new copy of the transposable element is introduced at a new site while the old copy remains at the original site
What does replicative transposition result in?
An increase in the number of copies of transposable element
Where can replicative transpositon happen?
Can be either between two different DNA molecules or between two parts of the same DNA molecule
What are retrotransposons?
Elements that transpose through an RNA intermediate
Transposon-What is RNA transcribed from?
From a DNA tranposable element
Retrotransposons only use what type of process?
Replicative transposition, RNA is copied back to another DNA site using reverse transcriptase
What is more common? DNA transposon or retrotransposon in eukaryotes?
Retro
What general characteristics are found in many transposable elements?
Most transposable elements have terminal inverted repeats and are flanked by short direct repeats that are generated at insertion sites during the transposition process. Many also contain a gene encoded one of the enzymes necessary for transposition (transposase or reverse transcriptase)
How does a retrotransposon move?
Relocates through an RNA intermediate. First, it is transcribed in RNA. A reverse transcriptase encoded by the retrotransposon then reverse transcribes the RNA template into a DNA copy of the transposon, which then integrates into a new location in the host genome
What are some differences between Class I and Class II transposable elements?
Class I transposable elements utilize replicative transposition and transpose through an RNA intermedicate.
Class II transposable elements utilize either replicative or conservative transposition and transpose through a DNA intermediate
Why are transposable elements often called genomic parasites?
Because they may not have an apparent benefit to a cell or organism and may be harmful to it. They exist because they are efficient at replicating and spreading.
**they may serve an important role in genome plasticity and evolution
Describe the function and molecular structure of a telomere
Telomeres are the ends of the linear chromosomes in eukaryotes. They cap and stabilize the ends of the chromosomes to prevent degradation by exonucleases or joining of the ends. Telomeres also enable replication of the ends of the chromosome by an enzyme called telomerase.
repeat sequence 5’C(A/T)
