Chromosome Structure and Transposons (Lec 13) Flashcards
Postive supercoiling occurs when DNA is ___ rotated, while negative supercoiling occurs when DNA is ___rotated
over; under
What is supercoiling?
the over-winding or under-winding of DNA causing it to twist on itself
supercoiling occurs when the strain of over rotation or under rotation cannot be compensated for by what?
turning of the free ends of the DNA molecule
In eukaryotes, the linear DNA molecules are often folded into ___ which are themselves stabilized by proteins resulting in supercoiling
loops
What are topoisomerases? What do they do?
enzymes that add or remove rotations from DNA;
can temporarily break nucleotide strands, rotate ends around each other, rejoin broken ends
True or false?
Topoisomerase’s can induce and relieve supercoiling
true
What advantage does negative supercoils DNA have over nonsupercoiled DNA?
makes separation of the two strands easier during replication and transcription; allows DNA to be packed into smaller space compared to relaxed DNA
True or false?
most DNA is positively supercoiled
false; negatively supercoiled
A combination of DNA and proteins is called what?
chromatin
True or false?
Euchromatin undergoes the normal process of condensation and decondensation in the cell cycle
true
Heterochromatin remains in what type of state throughout the cell cycle?
highly condensed
What is a nucleosome and what are its components?
core particle; consists of DNA + 8 histone proteins
Which histones form the nucleosome?
H2A, H2B, H3, H4 (2 each)
What is the function of the histone, H1?
attaches DNA to nucleosome
Nucleosome + H1 = ?
chromatosome
note: consists of 167 bp of DNA
What are chromatosomes separated by?
linker DNA (about 30-40 bp)
What is the name of the enzyme that cleaves the linker DNA (string) from the core particles (beads)?
nuclease
In regards to chromatin structure, how is a polytene chromosome created?
by repeated rounds of DNA replication with no cell division
DNase I sensitivity correlates with what?
gene activity
In regards to chromatin structure, what do epigenetic changes consist of?
methylation
Does chromatin structure change during transcription?
yes
True or false?
epigenetic change causes inherited phenotypic change without affecting the DNA sequence
true
What are centromeric sequences?
binding sites for the kinetochore, where spindle fibers attach
Centromeres are mostly heterochromatic, and probably defined by ___ changes rater than ____ ____
epigenetic; DNA sequnces
What role does CenH3 play in the organization of a centromere?
replaces H3 in most eukaryote centromeres
Centromeres signal what?
the beginning of anaphase
What is the function of telomeres?
stabilize ends of chromosomes
Describe telomeric sequences. How are they oriented?
usually consist of a repeated sequence of A or T nucleotides followed by several G nucleotides
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
True or false?
Organisms differ in amount of DNA per cell
true
Define gene family
similar but not identical copies of unique DNA sequences that arose through duplication of an existing gene
Describe moderately repetitive DNA
150-350 bp long and thousands to 100s of thousands of repeated units; tandem repeat sequences; interspersed repeat sequences
Describe highly repetitive DNA
less than 10 bp long and repeated 100s of thousands to millions of times
In regards to DNA sequences, what does C value refer to?
the amount of DNA per cell in a given organism
What does unique-sequence DNA consist of?
DNA sequences that are present once or only a few times in the genome
In regards to unique-sequence DNA, genes present in a single copy represent what percentage of protein-encoding genes in most multicellular organism?
25%-50%
Repetitive DNA makes up about how much of the human genome?
half
___ ____ sequences are arranged in tandem and clustered at particular locations on the chromosomes
tandem repeat
Interspersed repeat sequences are scattered through the genome and most are ____ elements
transposable
Long interspersed sequences comprise about how much of the human genome?
17%
Highly repetitive DNA is often called what?
satellite DNA
Transposons make up at least how much of human DNA?
45%
Most transposons are able to insert at many different locations and rely on mechanisms distinct from what?
homologous recombination
True or false?
Transposons often cause mutations
true
Short flanking repeats from 3 to 12 bp long are present on both sides of the transposable elements. Do these repeats travel with the transposable element? Where are they regenerated?
Do not travel with transposable element; regenerated at the point of insertion
Does replication of single stranded or double stranded DNA create the flanking direct repeats?
single stranded
Terminal, inverted repeats are found at ends of many transposable elements. How long are these repeats?
9 to 40 bp
The terminal inverted repeats found at the ends of many transposable elements are recognized by what?
enzymes that catalyze transposition
Are the terminal inverted repeats found at the ends of many transposable elements required for transposition to take place?
yes
What are the two ways transposons cause mutations?
Inserting into another gene; promoting DNA rearrangements
Describe the mechanism of transposition
staggered breaks are made in the target DNA; transposable element is joined to single-stranded ends of the target DNA; DNA is replicated at the single-strand gaps
Why is replicative transposition process referred to as “copy and paste” transposition?
A new copy of the transposable element is introduced at the new site while the old copy remains at the original site; results in increase in the number of copies of the transposable element; can be either between two different DNA molecules or between two parts of the same DNA molecule
The following are needed for what event to occur:
Single copy of the transposable ; two DNA molecules are joined; transposable element is replicated; production of cointegrate structure; crossing over = resolution of the cointegrate
cointegrateformation
What two enzymes are involved in replicative transposition?
transposase; resolvase
This enzyme involved in replicative transposition may be encoded by cellular gene or often by transposable element and makes single-strand breaks at each end of the transposable element and on either side of the target sequence where insertion occurs
transposase
This enzyme involved in replicative transposition may be encoded by either cellular genes or by transposable element and is responsible for resolution
resolvase
Why is non-replicative transposition referred to as “cut and paste” transposition?
transposable element is excised from old site and inserted into a new site; does not increase number of copies
Describe how non-replicative transposition works
cleavage requires a transposes enzyme produced by the transposable element; joining of the transposable element is carried out by normal replication and repair enzymes; original site is typically repaired using homologous template on sister chromatid
Elements that transpose through an RNA intermediate are called what?
retrotransposons
How is RNA copied back to another DNA site by a retrotransposons?
reverse transcriptase
True or false?
Retrotransposons only use non-replicative transposition
fase; replicative
True or false?
Only DNA transposons are found in bacteria
true
What are the two transposons found in bacteria?
insertion sequences; composite transposons
This type of DNA transposon found in bacteria, also infects plasmids and viruses, carries the only information required for movement, and typically includes one or two genes that encode transposase
insertion sequence
This type of DNA transposon found in bacteria, is more complex DNA segments flanked by two copies of an insertion sequence, contains DNA sequences not directly related to transposition, and designated by Tn followed by a number
composite transposons
What are the two groups of eukaryotic transposons?
structurally similar to transposable elements found in bacteria; retrotransposons
How much of the human genome do SINEs constitute?
11%
How much of the human genome do LINEs constitute?
21% approx 900,000 copies
True or false?
One of every mutations that cause significant disease results from the transposition of a SINE or LINE
true
Do transposable elements provide benefit to the cell?
no
What are some of the reasons that transposable elements exist?
may generate genetic diversity; may exist because of their relationship to telomeres
In regards to chromosomal rearrangements, pairing by looping and crossing over between two transposable elements oriented in the same direction leads to what?
deletion
In regards to chromosomal rearrangements, pairing by bending and crossing over between two transposable elements oriented in opposite directions leads to what?
inversion
In regards to chromosomal rearrangements, misalignment and unequal exchange between transposable elements located on sister chromatids leads to what?
one chromosome with a deletion and one chromosome with a duplication
Describe the structure of a class I transposable element
long terminal direct repeats, short flanking direct repeats at target site
Describe the structure of class II transposable elements
short terminal inverted repeats; short flanking direct repeats at target site
What genes do class I transposable elements encode for?
reverse transcriptase
What genes do class II transposable elements encode for?
transposase
Class I transposable elements execute transposition by RNA or DNA?
RNA intermediate
Class II transposable elements execute transposition by RNA or DNA?
DNA
