Prokaryotes: Features of the prokaryotic cell

Did prokaryotes come first or second?

First

Prokaryotic cell size

1-3μM

What does a prokaryote lack

A cell envelope and nucleus

Prokaryote general structure

A capsule or cell wall containing stuff, sometimes have folds on the external outer membrane which have specialised reactions happening on them

Cell envelope

Everything around the cell and can include the capsule, cell wall, and cell membrane

Features of gram negative bacteria

Big inner membrane, a chunk of peptidoglycan, and a and an extra outer membrane

Features of gram positive bacteria

Have an inner membrane and a big thick peptidoglycan layer which is almost exposed to the outside

Peptidoglycan layer

Very thick and rigid. Make the bacteria resistant to their environment and not prone to drying out

Gram positive stain test

Gram stain can get in and cannot get washed out again, so the gram stain tends to stain the outer peptidoglycan layer.

Gram negative stain test

The stain doesn't tend to cross the outer membrane

Site of energy production in almost all bacteria

Prokaryotic membrane

Transport proteins in prokaryotic membrane

Designed to pump out antibiotics and unwanted chemicals and to pump in chemicals it does want such as nutrients

Nucleoid

The nucleoid is the name for when the genetic material happens to be. It will have ribosomes and plasmids.

Plasmids

Accessory pieces of DNA that are used to exchange genetic information - horizontal gene transfer from bacteria to bacteria. Contain quite a lot of DNA structural proteins.

Prokaryotic ribosomes

Smaller than eukaryotic, no separate compartments, transcription and translation are coupled. This is sometimes called the mRNA: RNAP: Ribosome complex.

Polysome

Multiple ribosomes get loaded onto a single mRNA

Transcription and translation are coupled

Prokaryotes translate their protein at the same time that they transcribe their mRNA. You tend to get polysome complexes. The translation of mRNA into protein by ribosomes happens simultaneously.

Quorum sensing

A behaviour where the bacteria realises there are other bacteria present so they transition from individual behaviour to group behaviour.

Extracellular Polymeric substances (EPS)

Sticky or slimy material on the surface of a bacteria or archaea that consist of polysaccharides, proteins, glycoproteins, or glycolipids.

Capsule

Tight and around a single bacteria

Slime layer

A slime layer is the transition between lots of bacteria with their capsules and their EPS and the environment. They are loosely attached and easily deformed.

How are Capsules and slime layers important?

Important for the survival of the bacteria and infecting a host.

Flagella

Used for locomotion. Hollow tube-like appendages composed entirely of flagellin that are 20-30 nm in diameter.

How flagella move

Motor proteins convert hydrogen ions into energy and cause the rotation of the miniscule molecular motor which causes the flagella to spin quickly and therefore allowing the bacteria to move.

How controlling gene expression helps to preserve resources in bacteria

Transcribing and translating all genes all the time would be very resource intensive and may also lead to toxicity

How controlling gene expression helps to regulate bacterial behaviour (examples)

infection behaviour, biofilm formation, sporulation, responding to environments, Quorum sensing

How sigma factors work

The sigma subunit/ sigma unit contacts the mRNA. It needs to land in promoter regions. Binding to the promoter sequence occurs via the sigma factor. If the sigma factor is not present, binding does not occur. Once transcription has started, the sigma factor can be removed from the complex, and then the sigma factor floats about and can accumulate around other promoter regions.

Ways that a cell can transcribe only some genes from DNA into mRNA at once

1. By activating only some genes at once

2. By inhibiting genes until they are needed

How can a cell transcribe only some genes from DNA into mRNA at once: activating only some genes at once

We can activate only some genes at once by using selective sigma factors. For example, Sigma factor 1 is selective for promoter region 1, and sigma factor 2 is specific for promoter region 2. Sigma factor 1 prefers the sequence in promoter region 1 and sigma factor 2 prefers the sequence in promoter region 2. This leads to selectivity. This method requires a way to tell between the genes and requires different proteins to be present for the same gene.

Certain families of genes have certain upstream recognition sequences

Upstream recognition sequences

Different sequences that different sigma factors are binding to

How can a cell transcribe only some genes from DNA into mRNA at once: Inhibiting genes until you need them

More common and energy efficient than only activating some genes at once. Involves turning most genes off most of the time by using repressors so the sigma factor can't bind to the promotor region anymore. There are 3 ways to do this: by repressors, anti-sigma factors, and by degrading the sigma factors.

Anti-sigma factors

Anti-sigma factors bind to the sigma factor and stop it from binding.

Protein turnover degrading sigma factors

You can degrade the sigma factor and make sure it never builds up to a critical level to activate genes.

Regulator proteins

Like transcription factors but for prokaryotes

-35 and -10 sequences

Specific landing pads for sigma factors to bind to and recruit RNA polymerase in order to transcribe RNA

Termination sequence

So that when the polymerase gets to the end it will fall off.

Operon

A cluster of genes in the same functioning unit.

What does an operon do?

Leads to multiple genes in the same area so leads to a transcribed region which translates into multiple genes. Multiple proteins can be produced from a single mRNA.

Operator region

Analogous to an enhancer. Acts as a binding site for regulator proteins.

How to regulate operons and operator regions

A repressor could bind to the operator region and due to its physical arrangement this forms a steric block to the progression of RNA polymerase, causing the RNA polymerase to fall off

Negative control

Involves the control of repressor proteins. It is either recruiting a repressor protein and deactivating it, or switching on an inactive repressor (leading to repression)

Repressing a repressor...

Induces gene expression

Positive control

Either involves an activator which you switch on, or an activator that you switch off

for example of positive and negative control see notes

:)

Anti-sigma factors

Anti-sigma factors bind to the sigma factor and stop it from binding.

Protein turnover degrading sigma factors

You can degrade the sigma factor and make sure it never builds up to a critical level to activate genes.

Regulator proteins

Like transcription factors but for prokaryotes

-35 and -10 sequences

Specific landing pads for sigma factors to bind to and recruit RNA polymerase in order to transcribe RNA

Termination sequence

So that when the polymerase gets to the end it will fall off.

Operon

A cluster of genes in the same functioning unit.

What does an operon do?

Leads to multiple genes in the same area so leads to a transcribed region which translates into multiple genes

Operator region

Analogous to a

Anti-sigma factors

Anti-sigma factors bind to the sigma factor and stop it from binding.

Protein turnover degrading sigma factors

Upstream recognition sequences

Different sequences that different sigma factors are binding to

How can a cell transcribe only some genes from DNA into mRNA at once: Inhibiting genes until you need them

Upstream recognition sequences

Different sequences that different sigma factors are binding to