L7 Flashcards
What are the two main intracellular structures in prokaryotic cells?
Nucleoid, cytoplasm.
What is a major distinction of prokaryotes?
No true nucleus
How do prokaryotes compact their DNA?
Within the cytoplasm structure called the nucleoid. This allows prokaryotes to couple transcription and translation
How is DNA organised in prokaryotes?
In chromosomes, which are circular. Most of bacteria have a single chromosome. DNA needs to be compacted 1000 fold to fit into the cell. The DNA double helix in the circular bacterial chromosome is folded by DNA-binding proteins into supercoil loops. Supercoil loops protrude from a denser core.
What can supercoils be?
Negatively and positively supercoiled
What is a negative supercoil?
When DNA is twisted in the opposite direction to the double helix. Most common for bacterial genomes during normal growth.
What is a positive supercoil?
DNA is twisted in the same direction as the double helix
What is the process of DNA replication in prokaryotes?
DNA replication starts at the origin of replication (oriC) where a specific protein (DnaA) binds and separates the two DNA strands. Specific proteins are recruited at each of the two replication forks and DNA replication is carried out from oriC in each direction. DNA replication stops when the DNA replication machinery enters the terminus region (terC).
What are the three major challenges faced in DNA replication in prokaryotes?
Unwinding the DNA helix, replicating each DNA strand simultaneously, separating the two daughter chromosomes.
In DNA replication in prokaryotes how is the double helix unwound?
After binding of DnaA has separated the two DNA strands : DNA helicase is responsible for separating the two parental DNA strands. The strands are kept apart by single-stranded DNA binding proteins (SSB). Separating and relaxing the two strands of DNA in a circular DNA molecule tightens the double helix in the unopen region and induces the formation of positive supercoils. These supercoils can block DNA replication. DNA gyrase eases the tension formed by rapid unwinding of the helix carried out by the DnaB helicase.
In DNA replication in prokaryotes how is each DNA strand replicated simultaneously?
DNA primase synthesises the RNA primer. The leading strand is synthesised continuously, the lagging strand is synthesised discontinuously and produces Okazaki fragments, Okazaki fragments are ligated, and primers removed. Each molecule contains one template strand from the original molecule and one new DNA molecule.
In DNA replication in prokaryotes how are the two daughter chromosomes separated?
Right after DNA replication the two chromosomes are interlocked. DNA gyrase decatenates the two daughter chromosomes.
What are the roles of DNA gyrase in DNA replication?
Releases supercoiling by cutting the double helix at the supercoil crossover, passes the unbroken one through this break and reseals the cut. Decatenates the two sister chromosomes by cutting the double helix of one of the chromosomes. The unbroken chromosome passes through the gap. The cut chromosome is resealed.
Where does transcription happen in prokaryotes?
Prokaryotes have only one RNA polymerase, transcription in prokaryotes happens in the nucleoid-cytoplasm interface. Ribosomes have immediate access to the nascent transcripts even before being fully transcribed.
Prokaryotic transcription - what happens in coupled transcription/translation?
As soon as a prokaryote gene begins to be transited into a mRNA molecule the ribosome latches onto the transcript and translates the information into protein. Many ribosomes can translate the same mRNA transcript. Proteins are made faster in prokaryotes than in eukaryotes.
Prokaryotic transcription - what initiates transcription?
RNA polymerase (RNAP) has to be associated with a protein subunit called sigma factor. The sigma factor subunit of RNA polymerase allows it to be recognised and bind to a specific promoter sequence. There are different sigma factors, each recognises the consensus sequences that characterises the various promoters. Binding of the RNAP and the sigma factor to the promotor opens the transcription bubble
Prokaryotic transcription - how does elongation occur in transcription?
Once the RNAP clears the promoter region, the sigma factor is released. NusA proteins associates with the RNAP to assist with hairpins in the growing RNA strand. Hairpins can interrupt transcription.
Prokaryotic transcription - how is transcription terminated?
Termination can be a) rho-independent or b) rho-dependent
Prokaryotic transcription - rho-independent termination
Occurs when RNAP reaches a termination signal a GC-rich region followed by a string of A residues this forms a hairpin that stall the RNAP.
Prokaryotic transcription - rho-dependent termination
Rho factor binds specific sequences within the newly formed mRNA moving towards the mRNA 3’ end. Rho catches up with RNAP helping to release the mRNA from the DNA template and RNAP.
How is gene expression regulated in prokaryotes?
Genomic DNA contains both structural genes, which encode products that serve as cellular structures or enzymes. And regulatory genes which encode products that regulate gene expression. In prokaryotes gene expression primarily ensures that a cell’s resources are not wasted making proteins that the cell does not need all the time. In bacteria and archaea, structural proteins with related functions are usually encoded together within the genome in a block called an operon.
What is an operon?
Single transcriptional unit that corresponds to multiple genes whose expression is also controlled by a single promoter and a single terminator. Most prokaryotic mRNA transcripts are polycistronic this means they will encode several peptides. Each operon has DNA sequences that influence its own transcription, located in the regulatory region. Regulatory region includes the promoter and the region surrounding the promoter to which a regulatory gene will bind.
What is a regulatory gene?
A gene that encodes for a protein that controls transcription by binding to a particular site of the DNA. Regulatory genes are termed transcription factors. Transcription factors influence the binding of RNA polymerase to the promoter and allow its progression to transcribe structural genes.
What are transcription factors an example of?
Trans-acting factors. They modify or regulate the expression of distant genes by acting on cis-regulatory elements. Cis-acting factors - mechanism that affect gene expression in the vicinity of the gene.
What occurs in the negative regulation of transcription in bacteria?
The operator is the binding site for a regulatory protein, if a transcription factor is a repressor when it binds the operator RNA polymerase does not initiate transcription.
What occurs in the positive regulation of transcription in bacteria?
A transcription factor (activator) is required to bind at the promoter to enable RNAP to initiate transcription
What processes can antibiotics target different in a cell?
DNA replication, transcription, translation
How can antibiotics block DNA replication?
Many broad spectrum antibiotics target the DNA gyrase which blocks DNA replication by : preventing gyrase-DNA binding, impair DNA re-ligation, inhibit ATPase activity.
Why do antibiotics target transcription?
Broad-spectrum antibiotics such as rifampin target transcription as : prokaryotes only have one DNA polymerase, transcription is essential for cell viability, Bacterial RNAPs are highly conserved. Prokaryotic RNAP is different to eukaryotic RNAP
Why do antibiotics target translation?
Broad spectrum antibiotics such as tetracycline and chloramphenicol. Inhibit formation of a functional 70s ribosome. Impair aminoacyl-tRNA translocation to the A site or peptide bond formation. Inhibits ribosome recycling.
Cytoplasmic structures in prokaryotes - what are plasmids?
Found in the cytoplasm of many prokaryotes, are extra chromosomal double-stranded DNA molecules. Can replicate independently, encode important genetic info.
Cytoplasmic structures in prokaryotes - inclusion bodies or storage granules?
Bacteria do not live in environments that contain large amounts of nutrients at all times. Some bacteria use inclusion bodies to store nutrients. Poly-beta-hydroxybutyrste is produced by microorganisms response to stress from limited nutrients. PHB is a carbon polymer that can be used to make biodegradable plastics.
Cytoplasmic structures in prokaryotes - gas vesicles?
Aquatic prokaryotes, harvest light for photosynthesis or to obtain energy need to be close to the water surface. To keep buoyancy these microbes have gas vesicle in their cytoplasm. By regulating the gas content in the vesicle aquatic microbes can perform vertical migration. Gas vesicles allow microorganisms to maintain optimal salinity and migrate to areas richer in oxygen. These vesicles are surrounded by a protein shell which is impermeable to gases and impermeable to water. Gas vesicles usually have the shape of a cylindrical tube.
Cytoplasmic structures in prokaryotes - thylakoids?
Membrane-bound compartments inside chloroplasts and Cyanobacteria. Stacks of membranous sacs, interconnected to form a common internal space of lumen. These stacks are underneath the plasma membrane and are organised as concentric shells. They have perforations that allow the cytoplasm to flow through them. Thylakoids contain all the pigments, proteins and cofactors need to capture light energy and convert it into chemical energy. Thylakoids are a way to increase the surface available for photosynthesis in Cyanobacteria.
Cytoplasmic structures in prokaryotes - carboxysomes?
Intracellular structures found in many autotrophic bacteria. Consists of polyhedral protein shell filled with enzymes, contains rubisco for CO2 fixation. Found in phototrophs and chenolithotrophs
Cytoplasmic structures in prokaryotes - magnetosomes?
Present in motile aquatic bacteria, are intracellular structures surrounded by a membrane contain iron crystals which function as a magnet. Iron crystal are chained and act as the needle of a compass.
