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Biol251 > Eukaryotic Chromosomes > Flashcards

Eukaryotic Chromosomes Flashcards

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
Q

Core particles

A

unconnected DNA-nucleosome beads

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26
Q

Significance of core particles as a result of endonuclease digestion

A

The DNA lost in digestion links the nucleosomes together.

This linker DNA is associated with the histone H1

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27
Q

H1 histone

A

Associated with linker DNA connecting core particles

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28
Q

Nucleosomes

A

Large proteins made of H2A*H2B and H3*H4 histones
Repeating structural unit in the chromatin
DNA wraps around these nucleosomes

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29
Q

First level of DNA packing

A

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.

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30
Q

Second level of DNA packing

A

H1 histones pack adjacent nucleosomes into 30-nm fiber

6x increase in compaction

Characteristic of an uncoiled chromatin fiber during interphase

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31
Q

Third level of DNA packing

A

The 30-nm fibers are folded into 300-nm looped domains

32
Q

Fourth level of DNA packing

A

300-nm looped domains compact into chromosomal arms / chromatids

33
Q

30-nm fiber

A

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
Q

300-nm looped domains

A

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
Q

mtDNA replication depends on what?

A

Enzymes created from nuclear DNA

36
Q

Chromatin remodeling

A

the induction of chromatin to change its conformation and structure

37
Q

Why do we need chromatin remodeling?

A

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
Q

Histone tails

A

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
Q

Acetylation

A

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
Q

HAT enzyme

A

attaches acetyl group to lysine on histone tails

41
Q
A
42
Q

Methylation of histone tail

A

Methyl group added to histone tail

Increase or decrease transcription, depending on which amino acids are methylated

43
Q

Methylation of DNA

A

Cytosine in the DNA is methylated, creating 5-methyl cytosine
Negatively impacts gene expression
Occurs most often when C is next to G

44
Q

5-methyl cytosine

A

A cytosine that has been methylated to reduce gene expression

45
Q

CpG island

A

an area in the genome with a higher frequency of CG dinucleotides compared to the rest of the genome

46
Q

Heterochromatin

A

Remains condensed during interphase
Genetically inactive; lack genes, or contain repressed genes
Replicates later than euchromatin

47
Q

Euchromatin

A

Remains uncondensed during interphase
Contains most genes

48
Q

Is the chromosome structurally uniform? Why?

A

The chromosome is not structurally uniform. Some parts of the chromosome remain condensed during interphase, while most are uncondensed.

49
Q

Position effect & example

A

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.

50
Q

Examples of heterochromatin

A

Telomere & centromere

51
Q

Chromosome banding

A

Differential staining used to differentiate chromosomes of similar appearance

52
Q

G-banding

A

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

53
Q

C-banding

A

uses heat denatured chromosomes.
Stains only the heterochromatin centromeres

54
Q

Composition of eukaryotic genome

A

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

55
Q

Pseudogenes

A

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

56
Q

Single-copy sequences

A

Make up a large amount of non-repetitive non-gene DNA in eukaryotes
don’t seem to code for anything; many are pseudogenes

57
Q

Why/how are pseudogenes vestigial and mutated?

A

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

58
Q

Types of repetitive DNA

A

Highly repetitive
Moderately repetitive

59
Q

Types of highly repetitive DNA

A

Satellite DNA

60
Q

Types of moderately repetitive DNA

A

Tandem repeats
Interspersed repeat sequences

61
Q

Types of tandem repeats

A

VNTR
STRs
Multi-copy genes

62
Q

Types of interspersed repeat sequences

A

Retrotransposons (SINEs and LINEs)

63
Q

How can you tell if a sequence is repetitive?

A

Repeat sequences have an easier time finding a complementary sequence, so repetitive DNA reanneals quicker

64
Q

What do repetitive sequences encode?

A

NOT PROTEINS. sometimes RNA but not often.

65
Q

Satellite DNA

A

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

66
Q

Why is satellite DNA a different density

A

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.

67
Q

Tandem repeat sequences

A

The repeating DNA sequences repeat one after another
Clustered at a few locations on the chromosome

68
Q

VNTR

A

“minisatellite”

Variable number tandem repeats

Found within and between genes

Dispersed throughout genome; # of repeats varies in individuals

repeat unit size = hundreds of bps

69
Q

Multi-copy genes

A

Multiple copies of a single gene
None code for proteins
Many are rRNA genes

70
Q

STRs

A

‘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

71
Q

Interspersed repeat sequences

A

The repeating DNA sequences, short or long, are scattered throughout the genome

Mostly retrotransposons

72
Q

Retrotransposons

A

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

73
Q

SINEs

A

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

74
Q

LINEs

A

long interspersed elements
more than 6000 bps long
less present than SINEs

75
Q
A

Biol251 (8 decks)

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