Eukaryotic Chromosomes Flashcards
Bacterial and viral DNA characteristics (compared to eukaryotes)
Usually a single molecule
Much less genetic information
DNA is not as extensively bound to proteins
Virus chromosomes
can be either DNA or RNA.
can be either single-stranded or double-stranded.
can be linear or circular
How do you tell apart ss and ds viral DNA?
If a virus has an ssDNA genome, its ratios of complementary base pairs will not be 1:1.
What proteins are bacterial chromosomes associated with? Why?
HU and H-NS proteins
They help fold and bend DNA
How are mtDNA and cpDNA inherited?
maternally through the cytoplasm
mtDNA
dsDNA circle.
Different eukaryotes have different sizes
It has no chromosomal proteins.
It has no introns.
There are few gene repetitions and little spacer DNA.
H strand and L strand
mtDNA H and L strand
The two strands vary in density. There is a heavy (H) strand, and a light (L) strand.
The H strand encodes most of the genes.
cpDNA
dsDNA circle.
Uniform in size across most organisms
Much larger than mtDNA
It has no chromosomal proteins.
It has more genes than mtDNA
It has introns, duplications, and lots of noncoding sequences
Polytene chromosomes
display a banded pattern due to chromomeres
more DNA in a band than needed for one gene
Visible in interphase nuclei
Polytene chromosomes are paired homologs, IN SOMATIC CELLS
The DNA strands that compose them undergo replication without strand separation or cytoplasmic division
Chromomeres
condensations of chromatin
Polytene chromosome puffs
The bands undergo localized uncoiling for the sake of genetic activity. This creates a “puff”.
Lampbrush chromosome
Meiotic chromosomes
In a synpased pair, instead of condensing, the chromosomes extend in length, and later revert to normal
extended, uncoiled versions of the normal meiotic chromosomes
contain a large number of chromomeres. From each chromomere is a pair of loops, creating the brush appearance
Lampbrush chromosome loop
Loops extend off of chromomeres
Loops are DNA that has reeled out from the central chromomere axis during transcription, for the sake of genetic activity
Loops contain more DNA than needed to encode a gene
Composed of one DNA double helix
The storage problem
All DNA has to fit in the nucleus, but the nucleus is very small, and eukaryotes have a lot of DNA
Solution to the storage problem
eukaryotic DNA is associated with proteins that assist in coiling and condensing it. This creates chromatin
Chromatin
the DNA/protein material making up a chromosome
How is eukaryotic DNA organization more complex than that of viruses and bacteria, and why?
Bacteria and viruses do not have protein association to the degree of eukaryotes
Characteristics of eukaryotic DNA
larger chromosomes; greater amount of genes and DNA per chromosome
more chromosomes
DNA associated with proteins to assist in coiling and condensing
Chromatin structure
DNA-associated proteins are mostly histones, which are positively charged.
Histones are the “main” DNA protein, and are important for chromosomal structure.
Histone types and structure
H1
H2A
H2B
H3
H4
primarily composed of lysine and arginine
Significance of the charge of lysine and arginine
lysine and arginine are positively charged
This positive charge allows for binding with the negatively charged phosphate groups in DNA
What observations led to the development of the model of chromatin structure?
Digestion of chromatin by endonuclease yields DNA fragments of 200 bps
Chromatin contains large spherical particles (nucleosomes)
Histones occur as two types of tetramers which make up a nucleosome
DNA wraps around the nucleosome as 200 bps
Prolonged endonuclease digestion leaves a series of unconnected core particles
Histone tetramers
H2A*H2B
H3*H4
Significance of chromatin nuclease digestion leaving small DNA fragments
shows that repeating units of DNA/protein are in the chromatin
this unit structure protects the DNA/protein from cleavage except where it joins another unit
Core particles
unconnected DNA-nucleosome beads
Significance of core particles as a result of endonuclease digestion
The DNA lost in digestion links the nucleosomes together.
This linker DNA is associated with the histone H1
H1 histone
Associated with linker DNA connecting core particles
Nucleosomes
Large proteins made of H2A*H2B and H3*H4 histones
Repeating structural unit in the chromatin
DNA wraps around these nucleosomes
First level of DNA packing
H2B*H2A and H3*H4 histones join to form a nucleosome.
DNA wraps around nucleosomes; each wrappage takes 200 bps.
The core particles are connected by linker DNA, which is associated with an H1 histone.
Second level of DNA packing
H1 histones pack adjacent nucleosomes into 30-nm fiber
6x increase in compaction
Characteristic of an uncoiled chromatin fiber during interphase
Third level of DNA packing
The 30-nm fibers are folded into 300-nm looped domains
Fourth level of DNA packing
300-nm looped domains compact into chromosomal arms / chromatids
30-nm fiber
created from adjacent nucleosomes by H1 histones in the second level of DNA packing
Fold to create 300-nm looped domains in the third level of DNA packing
300-nm looped domains
Created in the third level of DNA packing from 30-nm fibers
Compact in the fourth level of DNA packing into chromosomal arms / chromatids
mtDNA replication depends on what?
Enzymes created from nuclear DNA
Chromatin remodeling
the induction of chromatin to change its conformation and structure
Why do we need chromatin remodeling?
The coiling and condensing of the chromatin fiber prevents access to the DNA.
This prevents enzymatic and regulatory proteins from interacting with it.
To allow protein-DNA interaction, chromatin must change its structure
Histone tails
packed into the folded domains within the nucleosome’s core
protrude through the minor groove channels of the DNA helix
may connect with adjacent nucleosomes
provide targets for reversible chemical modifications that impact gene function
Acetylation
HAT enzyme attaches acetyl group to lysine on histone tail
This neutralizes the charge of the histone
The addition of the acetyl group “opens up” the chromatin fiber at that spot, increasing gene expression
HAT enzyme
attaches acetyl group to lysine on histone tails
Methylation of histone tail
Methyl group added to histone tail
Increase or decrease transcription, depending on which amino acids are methylated
Methylation of DNA
Cytosine in the DNA is methylated, creating 5-methyl cytosine
Negatively impacts gene expression
Occurs most often when C is next to G
5-methyl cytosine
A cytosine that has been methylated to reduce gene expression
CpG island
an area in the genome with a higher frequency of CG dinucleotides compared to the rest of the genome
Heterochromatin
Remains condensed during interphase
Genetically inactive; lack genes, or contain repressed genes
Replicates later than euchromatin
Euchromatin
Remains uncondensed during interphase
Contains most genes
Is the chromosome structurally uniform? Why?
The chromosome is not structurally uniform. Some parts of the chromosome remain condensed during interphase, while most are uncondensed.
Position effect & example
the position of a gene or group of genes may affect their expression
When heterochromatic sections are translocated to a new site on another chromosome, adjacent genetically active areas become inactive.
Examples of heterochromatin
Telomere & centromere
Chromosome banding
Differential staining used to differentiate chromosomes of similar appearance
G-banding
involves the digestion of metaphase chromosomes with an enzyme
Stains DNA regions rich in A-T base pairs
Each chromosome has a unique pattern of bands
C-banding
uses heat denatured chromosomes.
Stains only the heterochromatin centromeres
Composition of eukaryotic genome
Most of the eukaryotic genome doesn’t represent a gene.
Only 2-10% of a eukaryotic genome codes for proteins.
Most of it is repetitive DNA which doesn’t have protein products.
A non-repetitive non-protein sequences are single-copy sequences
Pseudogenes
Represent a large number of eukaryotic single-copy sequences
DNA sequences representing evolutionary vestiges
Copy of a gene; this copy has since undergone significant mutation. Contain many insertions and deletions
Show some homology to parent gene; not transcribed
Single-copy sequences
Make up a large amount of non-repetitive non-gene DNA in eukaryotes
don’t seem to code for anything; many are pseudogenes
Why/how are pseudogenes vestigial and mutated?
free to mutate because there’s another copy there; mutation will not be lethal if the copy is of an essential gene
most mutations of these copies are loss-of-function, however; thus the copy is vestigial
Types of repetitive DNA
Highly repetitive
Moderately repetitive
Types of highly repetitive DNA
Satellite DNA
Types of moderately repetitive DNA
Tandem repeats
Interspersed repeat sequences
Types of tandem repeats
VNTR
STRs
Multi-copy genes
Types of interspersed repeat sequences
Retrotransposons (SINEs and LINEs)
How can you tell if a sequence is repetitive?
Repeat sequences have an easier time finding a complementary sequence, so repetitive DNA reanneals quicker
What do repetitive sequences encode?
NOT PROTEINS. sometimes RNA but not often.
Satellite DNA
highly repetitive
Short sequences repeated large number of times
Present as tandem repeats in very specific chromosomal areas known to be heterochromatic
Differs from main-band DNA in its molecular composition
Why is satellite DNA a different density
in a centrifuge density gradient, it will be apart from the rest of the DNA. “Main-band” DNA is present as a single band of uniform density
This is because it’s AT-rich. The combination of G-C is heavier than A-T, so satellite DNA separates out.
Tandem repeat sequences
The repeating DNA sequences repeat one after another
Clustered at a few locations on the chromosome
VNTR
“minisatellite”
Variable number tandem repeats
Found within and between genes
Dispersed throughout genome; # of repeats varies in individuals
repeat unit size = hundreds of bps
Multi-copy genes
Multiple copies of a single gene
None code for proteins
Many are rRNA genes
STRs
‘microsatellite’
Short tandem repeats
Repeated sequences consist of di, tri, tetra, and pentanucleotides
Dispersed throughout genome; # of repeats varies in individuals
repeat unit size = 2-6 bps
Interspersed repeat sequences
The repeating DNA sequences, short or long, are scattered throughout the genome
Mostly retrotransposons
Retrotransposons
transpose through RNA intermediates via reverse transcription
DNA sequence first transcribed into an RNA molecule
RNA serves as template for DNA complement using reverse transcriptase
transposable element contains reverse transcriptase
New DNA copy integrates into chromosome at new site
SINEs
short interspersed elements
less than 500 bps
may be present 500,000 times or more in the genome
i.e, Alu sequences; 200-300 bps long, present more than a million times
LINEs
long interspersed elements
more than 6000 bps long
less present than SINEs
