Genetics Exam 1 (Organization of DNA and Packing)

Lectures

DNA in Prokaryotes (5)

• dsDNA

• Circular

• Chromosomes, may contain plasmids

• Found in nucleoid (no nucleus)

• Horizontal Gene Transfer

Horizontal Gene Transfer

Bacteria can acquire genetic material from the environment (versus a parent cell)

ex) antibiotic resistance gene

What allows for all DNA material to fit inside cell?

Supercoiling

Twist

One strand crosses over the other

Writhe

Both strands cross over itself

What causes writhe?

As dsDNA is twisted or untwisted, bond angles and length constraints cause it to writhe

Positive supercoiling

• More twist added

• “overwound’

• Found ahead of transcription or replication bubbles and in thermophilic organisms

Negative supercoiling

• Less twist added

• “unwound”

• Most DNA in cells is negatively supercoiled

What controls superpoiling

Highly conserved family of proteins called topoisomerase

How do topoisomerases work (3 steps)

Cuts DNA

introduced + or - twist in DNA

then reseals DNA

Type I Topoisomerase

Nicks 1 strand

Type II Topoisomerase

Nicks 2 strands

DNA in Eukaryotes (4)

• Linear chromosomes found in nucleus

• Circular chromosomes found in mitochondria and chloroplasts

• Wound around histones

• C-value

C-value

The amount of haploid DNA in base pairs in an organism

C-value paradox

Increased C-value does not mean increased complexity

Chromatin

DNA and associated protein in the nucleus

Each chromosome exists as _____

Chromatin

• each chromosome is precisely positioned into its territory within the nucleus

• How DNA is arranged and positioned plays a large role in gene expression regulation

Histones

Make up chromatin

• help pack DNA pack into chromatin

• HIGHLY conserved

Nonhistone proteins

• Various function (replication, repair, transcription, recombination)

• may or may not be highly conserved

_____ is supercoiled around histone

dsDNA

Octomer

Two of each subunit: H2A, H2B, H3, H4

Higher order chromatin structure in eukaryotes (6)

DNA - 2 nm

Nucleosome (beads under string) - 11 m

Chromatine - 30 nm

Chromatine Loops - 300 nm

Condensed chromatine loops - 700 nm

Chromosome: 1400 nm

DNA size

2 nm

Nucleosome (Beads under string) size

11 nm

Chromatine size

30 nm

Chromatine Loop Size

300 nm

Condensed Chromatine Loop size

700 nm

Chromosome size

1400 nm

Packing along chromosomes is less uniform during _____

interphase, but still highly organized

10 nm fiber (tight or loose)

loose

30 nm fiber (tight or loose)

tight

Lower levels of transcription (tight or loose)

tight

Higher level of transcription (tight or loose)

loose

Euchromatin

open and accessible to transcription machinery, expressed

Heterochromatin

Packed tight; closed and silenced

Two types of heterochromatin

1.) Constitutive heterochromatin

2.) Facultative heterochromatin

Constitutive heterochromatin

• present in ALL cells at the SAME position on the chromosome

• typically repetitive DNA

• ex) centromeres and telomeres

Facultative heterochromatin

• can VARY between cell type, developmental stage, homologous chromosome

• Euchromatin becomes heterochromatin under certain conditions

• ex) one of the two X chromosomes in XX mammals (wild-type genetic female) is deactivated to form a Barr body

Distribution of sequences in a genome (2)

1.) Unique-sequence DNA

2.) Repetitive DNA Sequence

Unique-sequence DNA

• One or only a few copies of the sequence in the genome

• could be heterochromatin OR euchromatin

• Makes up 60% of eukaryotic genome

  ex) genes that encode protein

Repetitive DNA sequences

• Repeated SEVERAL to MILLIONS of times in the genome

• Could be dispersed (ex. transposons, rRNA genes)

• Could be tandemly repeated (in a row)

• Often heterochromatin

  ex) satellite DNA of telomeres and centromeres

satDNA

satellite DNA

• centromere

• separate differently from rest of genome during centrifugation

• huge stretch of repeats

Centromere

Constriction points of a chromosome where 2 sister chromatids

Catenated

Interlinked strands

Decatenation

What type of topoisomerase was used

Type II

Draw a beads-on-a-string model of chromatin

do it..

beads-on-a-string size and/or can also be called

10 nm fiber

a _____ shows the complete set of chromosomes during mitosis

karyotype

Satellite DNA

Is NOT found outside the nucleus

Is NOT used to describe very small

Is NOT less subject to breakage than other chromosome regions

Is NOT only found in telomeres

Why is satellite DNA called “satellite”

separates separately from main band after centrifugation

What is centromeres made of

heterochromatin, it’s satellite DNA, it does NOT contain genes

What are telomeres made of, where are they located

• Heterochromatin

• Located at the ends of linear chromosomes —> protects the ends

• Repeated DNA sequences

The # of repeats for telomeres depends on

Organism’s age

Exonucleases