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Biol251 > Eukaryotic Chromosomes > Flashcards

Eukaryotic Chromosomes Flashcards

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1
Q

Bacterial and viral DNA characteristics (compared to eukaryotes)

A

Usually a single molecule

Much less genetic information

DNA is not as extensively bound to proteins

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2
Q

Virus chromosomes

A

can be either DNA or RNA.
can be either single-stranded or double-stranded.
can be linear or circular

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3
Q

How do you tell apart ss and ds viral DNA?

A

If a virus has an ssDNA genome, its ratios of complementary base pairs will not be 1:1.

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4
Q

What proteins are bacterial chromosomes associated with? Why?

A

HU and H-NS proteins
They help fold and bend DNA

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5
Q

How are mtDNA and cpDNA inherited?

A

maternally through the cytoplasm

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6
Q

mtDNA

A

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

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7
Q

mtDNA H and L strand

A

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.

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8
Q

cpDNA

A

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

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9
Q

Polytene chromosomes

A

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

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10
Q

Chromomeres

A

condensations of chromatin

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11
Q

Polytene chromosome puffs

A

The bands undergo localized uncoiling for the sake of genetic activity. This creates a “puff”.

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12
Q

Lampbrush chromosome

A

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

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13
Q

Lampbrush chromosome loop

A

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

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14
Q

The storage problem

A

All DNA has to fit in the nucleus, but the nucleus is very small, and eukaryotes have a lot of DNA

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15
Q

Solution to the storage problem

A

eukaryotic DNA is associated with proteins that assist in coiling and condensing it. This creates chromatin

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16
Q

Chromatin

A

the DNA/protein material making up a chromosome

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17
Q

How is eukaryotic DNA organization more complex than that of viruses and bacteria, and why?

A

Bacteria and viruses do not have protein association to the degree of eukaryotes

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18
Q

Characteristics of eukaryotic DNA

A

larger chromosomes; greater amount of genes and DNA per chromosome

more chromosomes

DNA associated with proteins to assist in coiling and condensing

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19
Q

Chromatin structure

A

DNA-associated proteins are mostly histones, which are positively charged.

Histones are the “main” DNA protein, and are important for chromosomal structure.

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20
Q

Histone types and structure

A

H1
H2A
H2B
H3
H4

primarily composed of lysine and arginine

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21
Q

Significance of the charge of lysine and arginine

A

lysine and arginine are positively charged
This positive charge allows for binding with the negatively charged phosphate groups in DNA

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22
Q

What observations led to the development of the model of chromatin structure?

A

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

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23
Q

Histone tetramers

A

H2A*H2B
H3*H4

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24
Q

Significance of chromatin nuclease digestion leaving small DNA fragments

A

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

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25
Core particles
unconnected DNA-nucleosome beads
26
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
27
H1 histone
Associated with linker DNA connecting core particles
28
Nucleosomes
Large proteins made of H2A\*H2B and H3*H4 histones Repeating structural unit in the chromatin DNA wraps around these nucleosomes
29
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.
30
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
31
Third level of DNA packing
The 30-nm fibers are folded into 300-nm looped domains
32
Fourth level of DNA packing
300-nm looped domains compact into chromosomal arms / chromatids
33
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
34
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
35
mtDNA replication depends on what?
Enzymes created from nuclear DNA
36
Chromatin remodeling
the induction of chromatin to change its conformation and structure
37
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
38
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
39
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
40
HAT enzyme
attaches acetyl group to lysine on histone tails
41
Methylation of histone tail
Methyl group added to histone tail Increase or decrease transcription, depending on which amino acids are methylated
42
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
43
5-methyl cytosine
A cytosine that has been methylated to reduce gene expression
44
CpG island
an area in the genome with a higher frequency of CG dinucleotides compared to the rest of the genome
45
Heterochromatin
Remains condensed during interphase Genetically inactive; lack genes, or contain repressed genes Replicates later than euchromatin
46
Euchromatin
Remains uncondensed during interphase Contains most genes
47
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.
48
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.
49
Examples of heterochromatin
Telomere & centromere
50
Chromosome banding
Differential staining used to differentiate chromosomes of similar appearance
51
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
52
C-banding
uses heat denatured chromosomes. Stains only the heterochromatin centromeres
53
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
54
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
55
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
56
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
57
Types of repetitive DNA
Highly repetitive Moderately repetitive
58
Types of highly repetitive DNA
Satellite DNA
59
Types of moderately repetitive DNA
Tandem repeats Interspersed repeat sequences
60
Types of tandem repeats
VNTR STRs Multi-copy genes
61
Types of interspersed repeat sequences
Retrotransposons (SINEs and LINEs)
62
How can you tell if a sequence is repetitive?
Repeat sequences have an easier time finding a complementary sequence, so repetitive DNA reanneals quicker
63
What do repetitive sequences encode?
NOT PROTEINS. sometimes RNA but not often.
64
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
65
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.
66
Tandem repeat sequences
The repeating DNA sequences repeat one after another Clustered at a few locations on the chromosome
67
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
68
Multi-copy genes
Multiple copies of a single gene None code for proteins Many are rRNA genes
69
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
70
Interspersed repeat sequences
The repeating DNA sequences, short or long, are scattered throughout the genome Mostly retrotransposons
71
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
72
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
73
LINEs
long interspersed elements more than 6000 bps long less present than SINEs

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