5B

Prokaryote genome features

No nuclear membrane; genome located in cytoplasm (nucleoid); small genome; circular chromosome; no histones; no introns; RNA not processed; transcription and translation occur together because there is no nucleus

Eukaryote genome features

Nuclear membrane present (double lipid bilayer); large genome; linear chromosomes; histones and chromatin present; introns in most genes; RNA processed; transcription occurs in nucleus and translation in cytoplasm

Location of prokaryote genome

Nucleoid region within cytoplasm

Location of eukaryote genome

Stored in chromosomes inside nucleus

Prokaryote chromosome

Circular DNA chromosome

DNA storage in prokaryotes

E.coli chromosome is folded and supercoiled so genome fits into small cell and remains usable

Why prokaryote DNA folds

Allows circular chromosome to fit into small cell and remain functional

Human somatic cell chromosomes

46 chromosomes total

Human chromosome composition

22 pairs autosomes + 1 pair sex chromosomes

Female karyotype

46, XX

Male karyotype

46, XY

Diploid

Cells with two copies of each chromosome; 2n = 46 in humans

Haploid

Cells with one copy of each chromosome; n = 23 in humans

Human gametes

Egg and sperm cells; haploid

Human haploid genome

3.2 × 10⁹ nucleotides packaged into 23 chromosomes

The "packaged into 23 chromosomes" part tells you those 3.2 billion nucleotides aren't one continuous string; they're divided up among 23 separate chromosomes.

Important chromosome fact

One chromosome = ONE molecule of double-stranded DNA

DNA length problem

Haploid genome DNA length ≈ 1.02 m; diploid cell ≈ 2.04 m but nucleus only ~10 μm so DNA requires packaging

Unwound chromosome

Single chromosome not duplicated or condensed

Chromosome duplication

After DNA replication one chromosome contains two sister chromatids

Homologous chromosomes

Pair of chromosomes inherited from different parents with same genes in same locations

Chromosome telomeres

Protective ends of chromosome

Centromere

Region joining sister chromatids and containing centromeric proteins

Chromosome p arm

Short arm (“petit”)

Chromosome q arm

Long arm (“q” = next letter after p)

Metaphase chromosome

Fully condensed duplicated chromosome seen during metaphase

Stages of eukaryotic DNA packaging

Double helix → nucleosome/chromatin → 30 nm fibre → looped domains → metaphase chromosome

1st level DNA packaging

Double-stranded DNA helix (2 nm)

2nd level DNA packaging

Nucleosomes / chromatin (11 nm)

The second level of DNA packaging is the nucleosome — the "beads on a string" arrangement that gives chromatin its 11 nm width

3rd level DNA packaging

30 nm fibre

the 11 nm beads-on-a-string fiber coils up on itself into a thicker, more compact thread about 30 nanometres across.

it folds and coils so that neighbouring nucleosomes pack tightly against each other, roughly tripling the width from 11 nm to 30 nm.

4th level DNA packaging

Looped domains (~300 nm)

The 30 nm fiber doesn't just keep coiling uniformly; instead it gets organized into a series of big loops,

The bases of these loops attach to a central protein framework called the nuclear scaffold (or chromosome scaffold).

5th level DNA packaging

Further coiling to form metaphase chromosome (~700 nm per chromatid)

The looped domains from level four (the 300 nm fiber) coil and fold even more tightly on themselves, packing the looped fiber into the dense, compact rod-shaped structure of a chromosome.

only occurs in meiosis/mitosis

Chromatin

DNA + histone proteins

DNA charge

DNA carries net negative charge due to phosphate groups

Reason DNA is negatively charged

Phosphate groups ionise at cellular pH giving negative charge

Histone charge

Histones are positively charged due to many basic amino acids

Histone amino acids

Arginine and lysine contribute positive charge

DNA-histone interaction

Negative phosphate groups of DNA interact ionically with positively charged histones

Nature of DNA-histone interaction

Electrostatic, reversible, forms without damaging DNA or histones

Nucleosome

DNA wrapped around histone octamer

Histone octamer composition

2 × H2A + 2 × H2B + 2 × H3 + 2 × H4

Histones in nucleosome

H2A, H2B, H3, H4 (2 copies each)

Histone conservation

Histones are highly conserved proteins with little variation between species

Core nucleosome DNA

145 bp wrapped around histone core

Linker DNA

DNA segment between nucleosomes

Linker DNA length

8–114 bp

Chromatin appearance

“Beads on a string” = nucleosomes joined by linker DNA

10 nm fibre

Nucleosome chain / beads-on-string chromatin

Histone H1 function

Binds nucleosome and adjoining linker DNA

Role of histone H1

Links nucleosomes into 30 nm fibre

The four core histones (H2A, H2B, H3, H4) form the octamer that DNA wraps around to make the nucleosome bead itself — that's level 2. H1 is not part of that octamer.

the core histones build the nucleosome; H1 is the separate linker histone that stabilizes the nucleosome and drives the packing of the 11 nm fiber into the 30 nm fiber.

30 nm fibre

More compact chromatin formed by nucleosome packing with H1

Looped domains

30 nm fibres looped and linked by DNA-binding proteins

300 nm fibres

Further compaction level formed by looped domains

700 nm chromatid

Highly condensed metaphase chromatid

Proteins linking loops

DNA-binding proteins connect looped domains

The proteins that link the loops together are the non-histone scaffold proteins — condensin and topoisomerase II,

Interphase chromosomes

More extended and less condensed than metaphase chromosomes

Replication and transcription effects

Usually only slightly disrupt beads-on-string chromatin

Fully condensed chromosomes

Only metaphase chromosomes are fully condensed

Chromatin composition

DNA + histones

Other nuclear components

Nonhistone proteins + RNA + nonchromatin nuclear constituents

Examples of nonchromatin nuclear proteins

Transcription factors, telomere-binding proteins, methyl-CpG binding proteins, centromere proteins, repressors, promoters, DNA replication enzymes, transcription enzymes, DNA repair proteins

Human genome protein coding

Only ~1.5% of genome codes for proteins

Regulatory DNA

~20% of genome

Repetitive DNA

~50% of genome

Importance of repeats

They drive genome evolution in three ways:

• Rearrange the genome — recombination between similar repeats causes deletions, duplications, and translocations

• Create new genes — duplicated copies can mutate and evolve novel functions

• Modify existing genes — repeating gene inserts into or near another gene can disrupt, alter, or regulate it

Human non-protein coding DNA

Humans have highest proportion; important for regulation

Humans have one of the highest proportions of non-coding DNA, and this correlates with biological complexity.

• Regulating gene expression — promoters, enhancers, silencers, and regulatory non-coding RNAs (miRNA, lncRNA)

• Maintaining chromosome structure — telomeres and centromeres

Human genome project

Started 1990; draft genome announced 2000; published 2001; completed 2003

Genome size facts

Human genome ≈ 3164.7 million bases

Average gene size

~3000 bases

Largest known gene

Dystrophin ≈ 2.4 million bases

Human genetic similarity

99.9% of nucleotide bases identical between people

SNPs

~1.4 million estimated single-base variation sites

Unknown gene function

~50% of discovered genes still have unknown functions

Packaging DNA exam focus

Differences between prokaryote/eukaryote genomes; chromatin structure; nucleosomes; histones; DNA-histone interaction; packaging hierarchy; chromatin fibres; loops; nuclear proteins

euchromatin and heterochromatin

• Euchromatin is loosely packed DNA. It is highly accessible, contains actively expressed genes, and is involved in transcription.

• Heterochromatin is densely condensed DNA. It is tightly packed, making it generally inaccessible to the proteins that drive gene expression, leaving it genetically and transcriptionally inactive

How does DNA interact with histone proteins to form chromatin?

DNA wraps around histone proteins to form the basic units of chromatin. The negatively charged phosphate backbone of DNA is attracted to the positively charged (basic) amino acids — lysine and arginine — of the histones. About 147 base pairs of DNA wrap roughly 1.65 turns around a core of eight histones (the octamer: two each of H2A, H2B, H3, and H4), forming a nucleosome. Repeated nucleosomes connected by linker DNA give chromatin its "beads on a string" appearance.

nuceleosome

A nucleosome is the basic structural unit of chromatin: a segment of DNA (~147 bp) wrapped about 1.65 turns around a core of eight histone proteins (a histone octamer of two each of H2A, H2B, H3, H4). Histone H1, the linker histone, binds outside the core where DNA enters and exits, stabilizing the structure. Nucleosomes joined by linker DNA produce the 11 nm "beads on a string" fiber.

How is human genomic DNA further compacted into a chromosome?

Through successive levels of coiling and folding:

• The 11 nm nucleosome fiber coils (helped by histone H1) into a thicker 30 nm fiber

• The 30 nm fiber folds into looped domains (~300 nm) anchored to a non-histone protein scaffold (condensin, topoisomerase II)

• These loops coil and condense further into the fully compacted metaphase chromosome (~1400 nm)