DNA in Prokaryotes and Eukaryotes (HSC SSCE Biology): Revision Notes

DNA in Prokaryotes and Eukaryotes

Introduction to DNA across cell types

All living organisms share fundamental principles of molecular biology and genetics. The genetic code is universal, meaning the same nucleotide base-pairing code instructs protein synthesis in all living things, from simple bacteria to complex humans. This universal code provides strong evidence that all present-day cells evolved from a common ancestor.

Both prokaryotic and eukaryotic cells use similar mechanisms to translate information from DNA into polypeptides and proteins. However, whilst the basic principles are the same, important differences exist in how DNA is structured, packaged, and expressed in these two cell types.

Model organisms in molecular biology

Scientists have developed a common model system for studying molecular biology. Simple cells like the bacterium E. coli serve as excellent research models because they:

• Grow easily in laboratory conditions
• Divide rapidly (every $20$ minutes at $37°\text{C}$)
• Model the same type of translation as eukaryotic cells
• Have precisely regulated metabolism

The main differences between bacterial and eukaryotic genetics occur at the level of gene expression (how DNA instructions are converted into products such as proteins).

Prokaryotic DNA

The term 'prokaryote' comes from Greek, meaning 'before nucleus'. These primitive cells have a much simpler structure than eukaryotic cells.

Location and structure of prokaryotic DNA

Prokaryotic cells contain a single chromosome in the form of a circular strand of DNA. This chromosome lacks a surrounding membrane and floats freely in the cytoplasm, in a dense region called the nucleoid. The DNA codes for proteins that will be synthesized on ribosomes in the surrounding cytoplasm.

Non-chromosomal DNA: plasmids

In addition to their main chromosome, prokaryotic cells may contain one or more small rings of DNA called plasmids. These plasmids:

• Float separately in the cytoplasm
• Carry genes for non-essential features
• Often provide selective advantages (such as antibiotic resistance)
• Replicate independently of the main chromosome

Packaging of prokaryotic DNA

Prokaryotic DNA must fit into an extremely small space. For example, the circular chromosomal DNA of E. coli is approximately $1300~\mu\text{m}$ in length but must fit into a cell only about $3~\mu\text{m}$ long.

To achieve this compact packaging, the circular DNA becomes supercoiled and forms loops around a central protein scaffold to form the nucleoid. This dense protein differs from the histone proteins found in eukaryotic cells. The supercoiling and looping allow the large DNA molecule to fit efficiently into the small prokaryotic cell.

Gene regulation in prokaryotes

Through millions of years of evolution, prokaryotes have been exposed to varied selective pressures. Scientists believe this has led to the evolution of a highly refined mechanism for regulating gene expression called the operon system. This system allows prokaryotes to respond rapidly to environmental changes by switching genes on or off as needed.

Eukaryotic DNA

The term 'eukaryote' means 'true nucleus' in Greek, reflecting the presence of a membrane-bound nucleus containing the DNA.

Location and structure of eukaryotic DNA

Eukaryotic DNA is located in a membrane-bound nucleus within the cell. Individual DNA molecules are arranged into multiple separate chromosomes, and each chromosome is larger and more complex than the single prokaryotic chromosome.

Chromosome numbers in eukaryotes

Interestingly, the number of chromosomes does not correlate with organism complexity. The table below shows the diploid chromosome number ($2n$) for various eukaryotic organisms:

Organism	Number of chromosomes ($2n$)
Fruit fly (Drosophila melanogaster)	$8$
Eastern grey kangaroo	$16$
Earthworm	$36$
Cat	$38$
Peanut	$40$
Human	$46$
Orangutan	$48$
Platypus	$52$
Sheep	$54$
Chinese giant salamander	$60$
Horse	$64$
Black mulberry	$308$

Coding and non-coding DNA

A significant proportion of eukaryotic DNA is non-coding DNA—DNA sequences that are not directly used to make proteins or RNA. These non-coding sequences are called introns.

In humans, only approximately 3% of DNA is coding DNA. The coding sequences in DNA are called exons. The remaining 97% consists of introns and other non-coding sequences.

The exact function of non-coding DNA is still being researched, but scientists believe it plays important roles in:

• Spatial organisation of genes
• Control of gene expression

Packaging of eukaryotic DNA

Eukaryotic DNA is linear (not circular) and winds tightly around proteins called histones. Unlike prokaryotic DNA, it does not supercoil. Instead, it coils in a way that forms nucleosomes—bead-like structures made up of long DNA sequences wrapped around eight histone protein cores.

Key features of histone packaging:

• There are five main types of histones in eukaryotic cells
• All histones play a role in packaging DNA
• Histones contain many positively charged amino acids
• These positive charges allow binding to the negatively charged phosphate groups of DNA
• The nature of chromatin changes as cells progress through the cell cycle
• These changes are linked to histone binding

This packaging system is much more complex than the simple scaffold protein system in prokaryotes.

Non-nuclear DNA in eukaryotes

Mitochondrial DNA (mtDNA)

Mitochondria and chloroplasts are organelles in eukaryotic cells that contain their own DNA. This DNA, referred to as non-nuclear DNA, is inherited independently of nuclear (chromosomal) DNA.

Mitochondrial DNA (mtDNA) is found in the respiratory organelles (mitochondria) of all eukaryotic cells. The discovery of mtDNA has proved extremely useful in studies of evolutionary relatedness.

Maternal inheritance of mtDNA

During sexual reproduction, the egg and sperm each contribute half the zygote's nuclear DNA. However, sperm cells have very little cytoplasm, whilst the larger egg cell contributes all the cytoplasm and the organelles within it, including mitochondria.

Structure and characteristics of mtDNA

Mitochondrial DNA has distinctive features:

Size and structure:

• Very small circular molecule ($70~\text{nm}$ in diameter)
• Only 37 genes (compared to approximately $20,000$ in human nuclear DNA)
• $16,500$ base pairs in humans (compared to approximately $3$ billion base pairs in human nuclear DNA)

Gene content:

• $13$ genes make proteins for the electron transport chain during cellular respiration
• $22$ genes make transfer RNA (tRNA)
• $2$ genes make ribosomal RNA (rRNA)

Abundance:

• Each mitochondrion contains approximately 5-10 circular DNA molecules
• Each cell has between 100 and 1000 mitochondria
• Therefore, small tissue samples yield large amounts of mtDNA

Advantages of mtDNA for research

The rate of mutation of mtDNA is approximately ten times that of nuclear DNA. This higher mutation rate, combined with other features, makes mtDNA particularly useful for:

Evolutionary studies:

• Tracing evolutionary relatedness
• Constructing evolutionary trees
• Determining human ancestral lines

Forensic science:

• Human identification
• Identity testing when nuclear DNA is degraded

Medical genetics:

• Family relatedness testing
• Investigating mitochondrial diseases

Why mtDNA is advantageous for research

Mitochondria offer several advantages for genetic studies:

Mitochondrial mutations and disease

You might wonder how mitochondria can function if mtDNA undergoes so many mutations. Most changes in mtDNA occur in sequences that do not code for proteins, so these mutations are usually not harmful.

Comparing prokaryotic and eukaryotic genomes

The table below compares different genomes used as models for studying molecular genetic mechanisms:

Feature	mtDNA (Human)	Prokaryote (E. coli)	Yeast (S. cerevisiae)	Eukaryote (Human)
Genome size (base pairs)	$\pm 16,500$	$4.6$ million	$12$ million	$\pm 3$ billion
Number of genes	$37$	$\pm 4,300$	$\pm 6,000$	$\pm 20,000$
Types of proteins encoded	$13$ (and $24$ RNAs)	$4,000$	$5,000$	$100,000$
Number of chromosomes	$1$	$1$	$16$	$46$
Significance for study	Maternal inheritance allows study of direct lineages. High mutation rate makes it easier to distinguish between individuals	Small size makes analysis easy	Three times larger than E. coli, but much simpler than humans	Complex and large amounts of non-coding DNA make it more difficult to study

Summary of key differences

Chromosomal structure

• Prokaryotes: Single, circular, double-stranded DNA molecule
• Eukaryotes: Multiple, linear, double-stranded DNA molecules (chromosomes)

Location

• Prokaryotes: DNA floats freely in cytoplasm in the nucleoid region (no membrane)
• Eukaryotes: DNA enclosed within a membrane-bound nucleus

Packaging

• Prokaryotes: Supercoiled DNA forms loops around a central protein scaffold
• Eukaryotes: Linear DNA winds around histone proteins to form nucleosomes, which further condense into chromatin

Additional DNA

• Prokaryotes: May contain plasmids (small circular DNA) in cytoplasm
• Eukaryotes: Contain mtDNA in mitochondria (and chloroplast DNA in plants)

Coding DNA

• Prokaryotes: Most DNA codes for proteins; introns are rare
• Eukaryotes: Only approximately 3% codes for proteins; contain many introns (non-coding sequences)

Gene regulation

• Prokaryotes: Use operon system for efficient gene regulation
• Eukaryotes: More complex gene regulation mechanisms

Remember!