Prokaryotic Genetics: Chromosomes, Plasmids & DNA Replication

What is the usual shape of a prokaryotic chromosome?

Usually one circular double-stranded DNA chromosome.

What is the usual shape of a eukaryotic chromosome?

Linear double-stranded DNA chromosomes.

Where is the bacterial chromosome located?

In the nucleoid region of the cell.

How do prokaryotes mainly compact their chromosomes?

By supercoiling the DNA into compact supercoiled domains.

How do eukaryotes mainly compact their chromosomes?

DNA wraps around histone proteins to form chromatin and nucleosomes.

What are histones?

Positively charged proteins that DNA wraps around to help compact eukaryotic chromosomes.

What is a nucleosome?

DNA wrapped around a histone octamer; it is a basic unit of eukaryotic chromatin.

Prokaryotic vs. eukaryotic chromosome compaction

Prokaryotes mainly use supercoiling; eukaryotes mainly use histones and nucleosomes.

What does DNA gyrase (Topoisomerase II) do?

It introduces negative supercoils and helps manage DNA twisting.

What does Topoisomerase I do?

It makes a single-strand nick to relax DNA supercoils.

Why does DNA need to be compacted?

DNA is much longer than the cell, so compaction lets it fit and be properly distributed.

What is an operon?

A group of related bacterial genes controlled together and transcribed into one mRNA.

What does polycistronic mean?

One mRNA contains information for multiple proteins.

Are bacterial genes commonly polycistronic or monocistronic?

Polycistronic, especially when genes are organized in operons.

Are eukaryotic genes usually polycistronic or monocistronic?

Usually monocistronic: one mRNA generally codes for one protein.

What is an intron?

A non-protein-coding DNA sequence removed from RNA during processing.

Are introns common in prokaryotes?

No. Prokaryotes rarely contain introns.

Why are prokaryotic genomes considered compact?

A large proportion of their DNA directly encodes proteins, with little unused DNA.

What is one major difference in gene organization between prokaryotes and eukaryotes?

Prokaryotes often use operons; eukaryotic genes are usually individually organized.

What types of genetic material can viruses have?

DNA or RNA, which may be single- or double-stranded.

What type of genome do bacteria and archaea generally have?

Double-stranded DNA, usually arranged as a circular chromosome.

What type of chromosome do eukaryotes have?

Double-stranded DNA arranged into linear chromosomes.

Why are microbial genomes useful to molecular biologists?

They are small, easier to sequence, and easier to genetically manipulate.

Why is circular microbial DNA useful in research?

It makes cloning and DNA manipulation easier.

What is a plasmid?

A small extrachromosomal DNA molecule that replicates independently of the chromosome.

Are plasmids usually essential for survival?

No. They usually carry nonessential but often beneficial genes.

What useful traits can plasmids provide?

Fertility, drug resistance, toxins, virulence, or new metabolic abilities.

What is an R plasmid?

A plasmid carrying resistance genes, often including antibiotic resistance.

What is the F plasmid?

A fertility plasmid containing genes used for DNA transfer between bacterial cells.

What is special about the F plasmid?

It can integrate into the chromosome, making it an episome.

Chromosome vs. plasmid

The chromosome carries essential genes; plasmids usually carry extra beneficial traits.

What does semiconservative DNA replication mean?

Each new DNA molecule contains one parental strand and one newly synthesized strand.

Where does bacterial chromosome replication begin?

At the origin of replication called oriC.

Is bacterial DNA replication unidirectional or bidirectional?

Bidirectional; two replication forks move away from oriC.

What is DnaA?

The origin-binding protein that recognizes oriC and helps open the DNA to begin replication.

What does DnaC do?

It helps load the DnaB helicase onto DNA at the origin.

What does DnaB helicase do?

It uses ATP to unwind and separate the two DNA strands.

What does SSB do during replication?

Single-strand binding protein keeps separated DNA strands from reannealing.

What does primase do?

It makes a short RNA primer that provides the 3′-OH needed for DNA synthesis.

Why is an RNA primer necessary?

DNA polymerase cannot begin a new strand by itself; it needs an existing 3′-OH.

What does DNA polymerase III do?

It is the main enzyme that adds DNA nucleotides to the growing strand.

In what direction does DNA polymerase synthesize DNA?

5′ → 3′.

What is the leading strand?

The strand made continuously in the same general direction as the replication fork.

What is the lagging strand?

The strand made discontinuously as short Okazaki fragments.

What are Okazaki fragments?

Short pieces of DNA produced during lagging-strand replication.

What does DNA polymerase I do?

It removes RNA primers and replaces them with DNA.

What does DNA ligase do?

It seals remaining nicks between DNA fragments.

What does gyrase do during DNA replication?

It relieves overwinding and positive supercoiling ahead of the replication fork.

What happens if gyrase cannot work during replication?

Positive supercoils build up and DNA replication can stop.

What is the simple order of major replication events?

Open DNA → stabilize → prime → build DNA → remove primers → seal gaps.

Replication protein memory sequence

Helicase → SSB → Primase → Pol III → Pol I → Ligase.

If DnaA stops functioning, what would you predict?

Replication initiation would fail because oriC would not be properly opened.

If DnaB helicase stops functioning, what would you predict?

The DNA double helix would not properly unwind, so replication would stop.

If primase stops functioning, what would you predict?

RNA primers would not form, so DNA polymerase could not begin new DNA synthesis.

If DNA polymerase III stops functioning, what would you predict?

New DNA strands could not be properly elongated.

If DNA polymerase I stops functioning, what would you predict?

RNA primers would not be properly removed and replaced with DNA.

If DNA ligase stops functioning, what would you predict?

Nicks between DNA fragments would remain unsealed.

How should you solve a replication-mutant question?

Identify the protein's normal job, then predict what fails when that job is lost.

What is the main structural advantage of a bacterial operon?

Several related genes can be controlled together using one regulatory system.

Why are operons efficient for bacteria?

Genes needed for the same pathway can be turned on or off together.

What does one bacterial operon often produce?

One polycistronic mRNA containing multiple related genes.

What are the main subunits of bacterial core RNA polymerase?

α2ββ′ω.

What does the α subunit of RNA polymerase do?

It helps assemble the core RNA polymerase.

What does the β′ subunit do?

It binds DNA.

What does the β subunit do?

It binds ribonucleotide substrates used to make RNA.

What does the ω subunit do?

It helps stabilize the β′ subunit.

What is the RNA polymerase holoenzyme?

Core RNA polymerase plus a sigma factor.

Can core RNA polymerase recognize promoters well by itself?

No. It can make RNA but lacks strong promoter specificity.

What does the sigma factor do?

It helps RNA polymerase recognize and bind the correct promoter.

Easy way to remember sigma factor

Sigma = finds the Start site/promoter.

What happens to sigma after transcription begins?

It is released after the first few nucleotides are added.

How can different sigma factors affect gene expression?

Different sigma factors direct RNA polymerase to different groups of promoters.

What are the 3 stages of bacterial transcription?

Initiation, elongation, and termination.

What happens during transcription initiation?

RNA polymerase holoenzyme recognizes the promoter and begins making RNA.

What happens during transcription elongation?

RNA polymerase moves along the DNA template and lengthens the RNA molecule.

What happens during transcription termination?

RNA synthesis stops and the RNA and polymerase are released.

What are the two major bacterial termination mechanisms?

Rho-dependent and Rho-independent (intrinsic) termination.

What happens in Rho-independent termination?

The RNA forms a hairpin that stalls RNA polymerase and helps the RNA detach.

What does Rho do in Rho-dependent termination?

Rho helps cause RNA polymerase to dissociate and stop transcription.

Initiation vs. elongation vs. termination

Start transcription → build RNA → stop transcription.