Lecture 24: Bacterial Organelles and Substructures

organelles are a _____ structure inside a cell

specially restricted

organelles are typically surrounded by either a _____ or _____ barrier to keep it separate from other cell contents and it performs a _____ function at a specific sub cellular _____

proteinaceous; membranous; specialized; location

sometimes factors must be partitioned from the rest of the cell to _____ their function from _____ chemicals or enzymes (what is an example of this?)

protect; incompatible; carboxysome

organelles must be _____ or _____ during replication as well as properly _____ into daughter cells

synthesized; expanded; segregated

true or false: Every bacterial cell has some type of sub-cellular structure

TRUE! (ex. nucleoid)

the bacterial nucleotide is a highly _____ region in the center of the cell where the _____ resides

compacted; DNA

What is being stained in this cell?

DNA

What is being stained in this cell?

ribosomes

in bacterial cells, ribosomes are found where DNA _____

ISN’T

each cell has 2 _____ of SNA which helps keep replicated chromosomes _____

lobes; separated

True or False: the nucelois is surrounded by a membranous barrier to separate it form the rest of the cell

FALSE: it need to be accessible!

the compacted DNA IS accessible to _____ proteins, but is not permeable to _____ components like _____

medium/smaller; larger; ribosomes

the nucleoid serves an _____ function in all bacteria by organizing the DNA in a _____ YET _____ manner and _____ it into daughter cells before devision

ESSENTIAL; compact; accessible; segregating

most bacterial have a _____, _____ chromosome

single; circular

True or False: all bacterial chromosomes are aligned horizontally with the origin at one pole and the terminus at another

FALSE: some are vertical, like E. coli

how are E. coli chromosomes aligned in slow growth?

terminus and origin are at the center (vertically)

how are sporulating B. subtitles bacterial chromosomes aligned?

two copies, termini in center and origin at either poles (origin → terminus → terminus → origin)

bacteria are _____ meaning that have 1 instance of each gene, what is the abbreviation for this?

haploid; 1n

humans have 23 pairs of _____ chromosomes with 2 _____ instances of each gene, what is the abbreviation of this?

homologous; non-identical; 2n

before replication, we refer to the single bacterial chromosome as _____, AFTER replication there are 2 _____ copies, which is called _____

1c; identical; 2c

non-identical = _____ and identical = _____

n; c (remember: c like Copies, n in Non)

DNA replication STARTS at the _____ and ENDS at the _____

origin of replication; terminus

bacterial chromosome replication proceeds _____ from the origin

bi-directionally

in rich media, the cell will begin _____ at the origin _____ finishing the previous replication; what is this called?

replication; BEFORE; multifork replication

Why do cells do multifork replication?

DNA rep is slower than the cell’s growth, if they have an abundance of nutrients, you can speed up this process and give it a head start

DNA replication is _____ than cell growth

SLOWER

We can determine where specific genomic loci localize within a cell through a system called _____

FROS

what does FROS stand for?

fluorescent reporter operator system

FROS uses a ligand- _____ transcriptional regulator by fusing it with a _____

dependent; fluorescent protein

what is an example of a transcriptional regulator/operator system used in FROS?

LacI and LacO

what is LacI

reporter

What is LacO?

operator

FROS uses a _____ DNA binding protein fused to a _____ protein

site specific'; fluorescent

to visualize a specific loci, you can play an array of _____ near the locus you want to investigate and the fluorescence will _____ into a focus at that site

binding sites; coalesce

different DNA-binding protein/sites labeled with different colors can be used to probe _____

multiple sites!

What happens if you use the same operator AND reporter to visualize different loci?

both sites will be indistinguishable (same color)

in prokaryotes, transcription and translation are _____

COUPLED

Why doesn’t translation and transcription occur simultaneously in eukaryotes?

processes occur in different parts of cell → needs to be transported to be transl.

what is it called when the genes encoding a MEMBRANE protein are transcribed, translated, and the polypeptide is inserted into the membrane at the SAME time?

transertion

the circular chromosome is highly _____

supercoiled

the DNA is _____ for transcription by RNAP and the _____ mRNA is translated by ribosomes

available; nascent

Transcription causes the DNA to _____, potentially through formation of _____ or multiple _____ interacting with each other

CONDENSE; supercoils; RNAPs

Translation causes DNA to _____, likely because the ribosomes lie _____ the nucleoid and the DNA must travel to the membrane for _____

expand; outside; transertion

if a cell is inhibited for transcription, what would you expect to see?

expansion of DNA

if a cell is inhibited for translation, what would you expect to see?

contraction of DNA

what chemical is used to inhibit transcription?

rifampicin

what chemical is used to inhibit translation?

chloramphenicol

_____ are used to compact the bacterial chromosome

proteins

_____ proteins bind to DNA and help compact it

nucleoid-associated

some regions, like the _____ of replication are more highly _____ than others

origin; organized

what are the two main proteins used for organization of the DNA?

ParABS and SMC proteins

ParB is a _____ protein that binds to binding sites called _____ that are close to the _____

DNA-binding; ParS; origin

once bound, ParB proteins _____ along the DNA near the ParS site, _____ it and recruiting _____ proteins

spread out; condensing; SMC

what does SMC stand for?

structural maintenance of chromosomes

SMC is a _____ shaped protein complex that is thought to encircle the _____

ring; DNA double helix

_____ of SMC proteins are found in all domains of life!

analogs

what are the human analogs of SMC in humans?

cohesin and condensin

SMC rings are loaded at _____ sites and travel _____ the chromosome, this helps to _____ and _____ the newly replicated chromosomes

parS; down; compact; resolve

the SMC must traverse _____, _____, and _____ complexes, which _____ the SMC process

DNA loops; DNA binding protein; trascription/translation; slows down

protein ParA binds to _____ and _____ the replicated chromosomes apart

ParB; pulls/pushes

What are the two main proteins involved in segregating replicated chromosomes?

SMC and ParA

the double helix makes a _____ every 10 bp

full turn

to separate the 2 replicated stands, they need to be _____

unlinked

what is a chromosome concatenation?

interlinked chromosomes

what is a chromosome dimer?

2 chromosomes fused together (make one large circle)

_____ are enzymes that cut and twist DNA to relax it, they remove many of the _____ during replication

topoisomerase; links

Often topoisomerase doesn’t finish the job and the chromosomes end up _____

linked

_____ between the replicated chromosomes can turn them into a single chromosome dimer

homologous recombination

True or False: chromosomes dimers are extremely rare

FALSE: 15% of E. coli cells do this!

linked chromosomes are resolved during _____ at the closing _____

cell division; septum

resolving of linking happens at the _____ region of the chromosomes

terminus

what protein is primarily responsible for recruiting the necessary proteins to resolve linkages and dimers

FtsK

FtsK is a _____ machine that pumps the DNA _____ towards the _____

DNA-pumping; outwards; terminus

once FtsK reaches the _____, it activates _____ and _____ to fix the linkages and dimers

terminus; topoisomerase; recombinases

FtsK activates _____ to resolve concatenated DNA

topoisomerases

FtsK activates _____ to resolve DIMERS

recombinases

what are the two recombinases that FtsK activates

XerC and XerD

Where (in the cell) does the segregation of replicating chromosomes occur?

closing septum

what are two examples of topoisomerase that are used to prevent linkages?

gyrase and topoIV

XerCD only works at a specific region of the _____ called the _____ region

terminus; dif

other than the nuceloid, what are 4 main functions of other organelles?

nutrient storage, energy generation/metabolism, motility, protecting contents

organelles that store nutrients are often called _____

storage granules

what are 3 examples of nutrients stored in granules?

polyhydroxybutyrate, polyphosphate, sulfur

storing all the nutrients as one large molecule reduces _____

osmotic pressure

granules are _____ bound

membrane

polyhydroxybutyrate granules are used in __(species)__. They form during _____ starvation under _____ conditions and act as a _____ reservoir

Ralstonia; nitrogen; carbon-rich; carbon

the polyhydroxybutyrate granules can be used as a source of _____ under conditions of _____

carbon; carbon starvation

Polyphosphate storage granules are formed in _____ under _____ starvation and are used as a _____ reservoir

P. aeruginosa; nitrogen; phosphate

Polyphosphate storage granules are used as a phosphate reservoir for _____ synthesis and _____ synthesis. They can also accumulate _____ and other ions

ATP; phospholipid; Ca2+

what are iron storage granules called?

ferrosomes

ferrosomes are _____ bound _____ storage compartments

membrane; iron

ferrosomes store _____ and some other _____ and are very important for the _____!

Fe2+; cations; ETC

what genes are responsible for the assembly of ferrosomes?

fez genes

fez proteins were ID via the _____ of ferrosomes

mass spectrometry

expression of fex genes in E coli resulted in _____

ferrosome formation

are fez genes sufficient or necessary for ferrosome formation?

sufficient → expression in E. coli = ferrosome formation

ferrosome membranes contain an _____ called _____ that helps to accumualte Fe2+

iron pumping channel; FezB

Magnetosomes are _____ bound inclusions of _____ or _____ that form linear chains

membrane; magnetite; greigite

magnetosomes enable _____

magnetotaxis

magneto taxis is locomotions oriented along the _____

Earth’s magnetic field