Genetics Ch 10: Chromosome Organization and Molecular Structure

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What is the definition of a genome?

All of the genetic material inside of a cell

Prokaryotes: circular DNA

Eukaryotes: Nuclear chromosomes (that are linear)

Why are DNA sequences necessary (4 reasons)

1. Synthesis of RNA & Proteins

2. Replication of chromosomes

3. Proper segregation of chromosomes

4. Compaction of chromosomes

Features of a circular chromosome

• Structural genes: code for proteins

• Intergenic regions: non-transcribed DNA between genes

• Most species have a circular chromosome but some don’t

• Most species have a singular type of a circular chromosome and may have more than one copy

  • Most prokaryotes are considered haploid (one copy)

• Origin of replication required to initiate DNA replication

Where is the chromosome found in the prokaryote?

Nucleoid region (not bound by a membrane)

Chromosomal Compaction

First, chromosomes get condensed through loop domains

• Condensed 10-fold

Next, chromosomes are condensed through supercoiling

• Have to maintain 10 base pairs per turn or else DNA will become unstable

DNA Supercoiling

• If DNA has been underwound and has fewer turns: compensate by introducing negative supercoil (right)

• If DNA has been overwound and has more turns: compensate by introducing positive supercoil (left)

Topoisomers

Same DNA but different configuration

Ex: DNA w/ no supercoiling (10 bp/turn), DNA w/ one negative super coil (10 bp/turn), DNA w/ one positive super coil (10 bp/turn)

Why is negative supercoiling useful and which bacteria is negatively supercoiled?

E. coli is negatively supercoiled every 40 turns

Negative supercoiling is useful because

• Chromosomal compaction

• Introduce tension that will make it easier to separate DNA strands and will make it easier to do replication and transcription

DNA Topoisomerase 1 & DNA Topoisomerase 2 (DNA gyrase)

• DNA Topoisomerase 1: relax negative supercoiling by cutting the DNA & turning it the opposite way

• DNA Topoisomerase 2/DNA gyrase: Introduce negative supercoils using ATP and can remove positive supercoils; made up of 4 subunits (2 A subunits and 2 B subunits)

  • Crucial to bacterial survival

What are the names of the drugs that inhibit gyrase & topoisomerase 1

Quinolones & Coumarins

• Inhibits only prokaryotic gyrase & topoisomerase 1

Features of a linear chromosome

• Eukaryotic chromosomes are usually linear

• Eukaryotic chromosomes carry much more DNA than prokaryotic chromosome(s)

• Have many repetitive sequences, especially near the centromere & telomere

• Multiple origins of replication

Explain gene length in lower and higher eukaryotes

Lower eukaryotes (yeast): smaller genes; primarily have sequences that encode amino acids; short introns

Higher eukaryotes (mammals): longer genes; have many introns (non coding regions); 59% of genome is repetitive DNA

Three different types of Eukaryote Sequence Complexity

Unique or non-repetitive: found only a few times in the genome

• structural genes & intergenic regions

• 41% of genome in humans

  • 2% of exons (code for proteins), 24% are introns, 15% unique sequences not inside of genes

Moderately repetitive: found a few hundred or thousand times

• origin of replication, genes for rRNA & histones, regulation sequences

Highly repetitive: tens of thousands to millions of times

• Each copy is short

• Alu family in humans (1,000,000 copies)

How long is human DNA & what is a cell’s nucleus diameter?

Human DNA: 1 meter

Cell Nucleus Diameter: 2-4 micrometer

What is chromatin

DNA-protein complex

What is a nucleosome?

• Repeating structural unit within chromatin

• DNA wrapped around 8 histone proteins (octamer)

  • “Beads on a string”

  • Two copies of four distinct types of histone proteins

Histone Proteins and the five different types

• Histones are basic because they have positively charged amino acids

• Bind to DNA phosphates on the DNA backbone

• H1: linker histone; binds DNA to the linker region, less tightly bound to DNA

• H2A, H2B H3, H4: core histones

  • A copy of each makes the octamer

H1

• In moderate salt conditions: H1 is removed so no further compacting happens (beads on a string)

• In low salt conditions: H1 stays and further compacts DNA

30 nm fiber models

• Nucleosomes compact another 7-fold

• Form model that is 30 nm wide in one of two configurations

  • Solenoid: regular formation; nucleosomes are very close together with 6 nucleosomes per turn

  • Zigzag: irregular formation; nucleosomes not touching

3rd level of compaction

• Between the nuclear matrix and 30 nm fibers

Nuclear matrix

• Internal space inside the nucleus that helps organize and anchor chromatin

  • Nuclear lamina: Fibers that line the inner nuclear membrane

  • Inner nuclear matrix proteins: Proteins connected to the nuclear lamina

How do radial loops form and why are they important?

• 30 nm fiber is attached between two MARs which causes a loop

• Further compact chromosomes (available for transcription)

• Chromosome territory: organizes chromosomes into own non-overlapping place

MAR: Matrix Attachment Region

• A DNA sequence that anchors to the nuclear matrix

• Attaches to 30nm model and anchors it to the nuclear matrix

• Radial loop becomes euchromatin (some parts may be heterochromatin)

Heterochromatin vs Euchromatin

Heterochromatin: Highly condensed repetitive sequences found in telomeres and centromeres; generally doesn’t get transcribed; parts of radial loops are compacted further

Euchromatin: Less condensed; gets transcribed; parts of radial loops that aren’t compacted further

Two different types of heterochromatin

• Constitutive heterochromatin: always heterochromatin; permanently inactive to transcription; has many repetitive sequences

• Facultative heterochromatin: can convert between euchromatin and heterochromatin. Ex: Barr body

Explain how sister chromatids are at the end of prophase 1

They are heterochromatic

• Radial loops become fully heterochromatic and can’t do transcription anymore

At which phase is DNA most compacted?

Metaphase

SMC: Structural Maintenance of Chromosomes

• Both complexes have proteins that use ATP to change chromosomal structure (SMC)

• Condensin: chromosome condensation

• Cohesin: sister chromatid alignment

• Both are used to compact interphase chromosomes into metaphase chromosomes

What role does condensin play?

When nuclear envelope opens during prophase, condensin binds to chromosomes and compacts radial loops into heterochromatin

What role does cohesin play?

During G2 phase sister chromatids are stuck together by cohesin; middle of prophase cohesin is broken and only stays in centromere; at anaphase sister chromatids separate