Concepts of Genetics
PCB 3063
Kim Hughes, Yingxue Ren, Denise Everhart
Chapter 12
DNA Organization in Chromosomes
12.1 Viral and Bacterial Chromosomes Are
Relatively Simple DNA Molecules
Bacterial and viral chromosomes are
usually:
• a single nucleic acid molecule
• largely devoid of associated proteins
• much smaller than eukaryotic chromosomes
Section 12.1
Chromosomes of viruses consist of single- or
double-stranded DNA or RNA.
Can be linear or circular.
Phage l
Double-stranded DNA
DNA is linear before infection, circular after
DNA molecule = 7 mm. Phage head <0.1mm
DNA is inert when packaged in the phage head
Section 12.1
Chromosomes of viruses consist of single- or
double-stranded DNA or RNA.
Can be linear or circular, depending on the virus.
Phage T2
Double-stranded DNA
Linear molecule = 52 mm
Phage head = 0.1mm
Section 12.1
Bacterial chromosomes are double-stranded DNA and
are compacted into a nucleoid
DNA binding proteins
HU and H1 (positively charged)
E. coli
Circular DNA molecule = 1200 mm.
Bacteria = 2 mm
Unlike viruses, DNA is active even
though it is highly compacted
within the cell
12.2 Supercoiling Facilitates Compaction of
the DNA of Viral and Bacterial
Chromosomes
• Supercoiling compacts DNA.
• Most closed circular DNA molecules in
bacteria are slightly underwound and
supercoiled.
Figure 12.4
Eukaryotic Chromosomes
• Larger
• More complex (chromatin)
• More compacted
• Some specialized eukaryotic
chromosomes were invaluable for
early insights into structure:
Polytene and Lampbrush
Chromsomes
Unusual eukaryotic chromosomes
• Polytene chromosomes and lampbrush
chromosomes are very large and can be
visualized by light microscopy.
• Polytene: Salivary glands and guts of
some flies, protozoans, and plants
(somatic cells)
• Lampbrush: vertebrate oocytes (germ
cells--meiotic)
Section 12.3
• Polytene chromosomes:
• have distinctive banding patterns
• represent paired homologs
• are composed of many DNA strands
Figure 12.5
Section 12.3
The DNA of the paired homologs of polytene
chromosomes undergoes many rounds of
replication without strand separation or
cytoplasmic division.
Section 12.3
Polytene chromosomes have puff regions
where the DNA has uncoiled and are
visible manifestations of a high level of
gene activity.
Puffs where active RNA
transcription is occurring
Figure 12.6
Section 12.3
• Lampbrush chromosomes are large and
have extensive DNA looping.
• They are found in oocytes in the diplotene
stage of meiosis.
• Thought to be extended, uncoiled versions
of normal meiotic chromosomes
Loops where active RNA
transcription is occurring
Figure 12.7a
Coiled and uncoiled DNA
• “Uncoiling” seems to be associated with
gene activity
• But DNA in cells is usually highly coiled
and compact.
12.4 Eukaryotes: DNA Is Organized into
Chromatin
• Nucleosomes are condensed several times to
form the intact chromatids
• The DNA in a human cell would be ~2 meters long
if it were “unwound”.
• The nucleus is 5-10 mm (5 x 10-6 m) in diameter
• Eukaryotic chromosomes are complexed into a
nucleoprotein structure called chromatin.
• Chromatin is bound up in nucleosomes with
histones H2A, H2B, H3, and H4
Metaphase
Mitosis/Meiosis
Interphase
Figure 12.9
The nucleosome core particle
derived from X-ray crystal analysis
at 2.8 Å resolution. The doublehelical DNA surrounds four pairs of
histones.
Histone tail
Table 12.2
Section 12.4
Chromatin remodeling must occur to allow the DNA to be
accessed by DNA binding proteins.
Histone tails are important for histone modifications such as
acetylation, methylation, and phosphorylation.
Histone Methylation usually turns a gene
off.
Histone Acetylation usually turns a gene
on.
Histone Phosphorylation -- we're not sure
what that does.
Inactive chromosomal regions
Inactivated X in
eutherian mammals
The H4 histones are
under-acetylated
Unique to eukaryotic DNA
Euchromatin is uncoiled and
active
Heterochromatin remains
condensed and is inactive.
Heterochromatic Regions
Centromeres
Telomeres
Mammalian Y chromosome
Inactive Mammalian X (Barr
Body)
C-banding
Chromosome Banding
• Mitotic chromosomes have a characteristic
banding pattern.
• In C-banding, only the centromeres are
stained.
• G-banding is due to differential staining
along the length of each chromosome.
Section 12.5
Differential staining in G banding reflects the
heterogeneity & complexity of the chromosome.
Used to identify inversions and
translocations
Eukaryotic Chromosomes have nonrepetitive and repetitive DNA
• Repetitive DNA sequences are repeated many
times within eukaryotic chromosomes.
• There are a number of categories of repetitive
DNA
There are several different kinds of
repetitive DNA
Repetitive DNA sequences are repeated
many times within eukaryotic chromosomes.
Multi-copy genes:
Some coding genes occur in multiple copies (e.g.,
genes encoding ribosomal DNA).
However, most repetitive DNA is non-coding
Repetitive DNA
Satellite DNA: highly repetitive, consists of
short repeated sequences.
Centromeres
• are the primary constrictions along eukaryotic
chromosomes
• mediate chromosomal migration during
mitosis and meiosis
• D. melanogaster centromeres characterized
by AATAACATAG, repeated many times
Section 12.6
Satellite DNA: highly repetitive, consists of
short repeated sequences.
Telomeres
• DNA sequences consist of short tandem
repeats that contribute to the stability and
integrity of the chromosome.
• In vertebrates 5’-TTAGGGG-3’ is repeated
many times
• Up to 1000 telomeric repeats in some
organisms
Section 12.6
Moderately repetitive DNA includes:
• Minisatellites (variable number tandem
repeats or VNTRs): DNA sequences 15-100
bp, repeated hundreds of times.
• Microsatellites: Sequences 2-4 bp, repeated 5
to 100 times.
VNTRs and microsatellites are used in DNA
fingerprinting and other forms of genetic identity
and kinship analysis because number of repeats
highly variable among individuals
Section 12.6
Short interspersed elements (SINES) and long
interspersed elements (LINES) are dispersed
throughout the genome rather than tandemly
repeated, and constitute over 1/3 of the human
genome.
SINEs are ~ 500 bp, and may occur >500,000 times in
the human genome
LINEs are ~6000 bp, and may occur up to 850,000
times in the human genome.
LINEs are retrotransposons because they encode
RNAs that are reverse-transcribed back to DNA,
which integrates back into genome in a new place.
SELFISH GENES
Section 12.7
The Vast Majority of a Eukaryotic Genome
Does Not Encode Protein-coding Genes
• Only a small portion of the eukaryotic genome (2%–
10%) constitute protein-coding genes.
• In addition to repetitive DNA, there are also a large
number of single-copy noncoding regions, some of which
are pseudogenes.
• Pseudogenes are evolutionary vestiges of functional
genes that are no longer functional.
• Pseudogenes are previously functional genes that have
acquired “stop codons” and other mutations that make
them non-functional.