Microbiology Exam 3 (Plasmids - fungi)

Fertility, Resistance, and Virulence

What are the the types of plasmids?

Fertility Plasmid

The ______ ______ (F-plasmid or F-factor) is a circular DNA molecule found in donor bacteria (F+) that enables reproduction-like genetic transfer, known as conjugation, to recipient cells (

F-). It encodes proteins that form the sex pilus (a conjugative bridge), allowing efficient, rapid spread of genetic material throughout bacterial populations.

Colonizing Peptide, Killing Peptide, and Signaling Peptide

What are the 3 peptides involved in Bacteriocin?

Colonizing Peptides

These peptides are involved in the ability of bacteria to adhere to and establish themselves on surfaces or within host tissues. (STAMPs)

Killing Peptides

Also known as antimicrobial peptides (AMPs) or membrane-disruptive peptides (MDPs), these are designed to destroy pathogens.

Signaling Peptide

These are crucial for intercellular communication, guiding protein location, and regulating cellular processes.

Resistance Plasmids

______ _____ (R-plasmids) are small, circular, extrachromosomal DNA molecules found in bacteria that carry genes conferring resistance to antibiotics and other toxic substances. They are key drivers of horizontal gene transfer (conjugation), allowing rapid, multi-drug resistance to spread between bacteria, even across different species, significantly impacting clinical and agricultural settings.

Virulence Plasmids

are large, low-copy-number, extra-chromosomal DNA molecules that turn bacteria into pathogens by encoding factors that promote host infection, such as toxins, adhesins, and secretion systems. Essential for virulence in many enteric pathogens (e.g., Shigella, Salmonella, Yersinia), they are often stably maintained and transferred via horizontal gene transfer.

Rolling Circle Replication

A type of replication common in E. coli and other microorganisms possessing circular DNA

Replication of Origin

Double stranded DNA unwinds at the ______

Replication Bubble

When double stranded DNA unwinds at the Replication of Origin, it produces single stranded templates for the synthesis of new DNA. A _________ forms, usually having a replication fork at each end

two circular DNA molecules are produced

When the replication bubble forms (because each end has a replication fork), the forks proceed around the circle, and eventually,

Self termination

transcription of GC-rich terminator region produces a hairpin loop, which creates tension, loosening the grip of the polymerase on the DNA.

Rho-dependent termination

Rho pushes between polymerase and DNA. This causes the release of polymerase, RNA transcript, and Rho.

Introns

Express RNA molecules that regulate gene expression; are removed using enzymes. Only found in Eukaryotes

Exon

are protein-coding DNA sequences that are expressed and retained in mature mRNA to guide protein synthesis

75%

What percentage of genes are expressed at all times

to conserve energy

Why are genes strict with the regulation of transcription and translation?

operons

What is involved in Transcriptional Regulation?

siRNA and Riboswitch

What is involved in Translational Regulation?

Operon nature

Functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter. Code for enzymes and structures. Some operons are controlled by a regulatory element called an operator

Inducible operons

is usually "off" (repressed) but can be turned "on" (induced) in the presence of a specific substrate. (lac operon, which is repressed by the lack of lactose)

Repressible Operons

is typically active (ON) but can be inactivated (turned OFF) when a repressor protein binds to the operator, often triggered by high concentrations of the pathway's end product (trp operon)

Yes

Can genetic expression can be regulated at level of translation?

Short Interference RNA (siRNA)

RNA molecule complementary to a portion of mRNA, tRNA, or a gene that binds and renders the target inactive

Riboswitch

mRNA molecule that blocks translation of the polypeptide it encodes

Dicer

Enzyme that separates pre-cursor RNA by breaking H bonds (Type of siRNA)

RISC

RNA inducing silencing complex (type of siRNA)

Riboswitch

cis-acting elements (part of the same mRNA they regulate) that directly bind small molecules to control gene expression, primarily in bacteria.

Genetic Transfer

Exchange of nucleotide sequences often mediated by homologous sequences

Recombinants

Cells with DNA molecules that contain new nucleotide sequences

Horizontal gene transfer

the movement of genetic material between organisms that are not in a parent-offspring relationship, distinct from vertical inheritance.

Vertical gene transfer

Organisms replicate their genomes and provide copies to descendants

Transformation, Transduction, Bacterial conjugation

Types of horizontal gene transfer

Transformation

One of the conclusive pieces of proof that DNA is genetic material. Competent bacterial cells take up DNA from their environment due to alterations in their cell wall and membrane.

Transduction

a mechanism of horizontal gene transfer in bacteria where DNA is transferred from a donor cell to a recipient cell via a bacteriophage (virus). This process is "accidental," occurring when viruses mistakenly package host bacterial DNA instead of viral DNA, enabling the spread of genetic traits like antibiotic resistance.

donor bacterial cell

In the first part of General Transduction, the phage infects the _______

broken down

In the second part of General Transduction, the phage DNA and proteins are made, and the bacterial chromosome is ______ into pieces

Donor Cell lysis and releases phage particles/bacterial DNA

What happens when, during phage assembly in General Transduction, pieces of bacterial DNA are packaged into a phage capsid?

Infect new cells

In General Transduction, when the donor cell lysis and phages escape, what do they do?

Recombination

The last step of General Transduction, what can occur?

Bacteriophage DNA

In Specialized Transduction, _______ ____ is incorporated into the bacterial genome.

reproduce/replicate

In Specialized Transduction, the cell can _____ and _____ the DNA.

viral capsid

In specialized Transduction, Bacteriophages begin to replicate and have both phage and bacterial DNA in ______ ______.

new cell

In specialized transduction, Bacteriophage transfers bacterial DNA to _____ ______.

molecularly

Bacteria react ________ to viral infection

Endonucleases

Enzymes that cleave the phosphodiester bond of nucleotide chains. Three types I, II, III

Type 2

Which type of Endonucleases recognize methylated adenines on bacterial genome, but only cleaves within non-methylated palindrome sequence

Type 1 and 3

Which type of endonucleases cleave some distance away from recognition site

unmethylated

Phage DNA is _____

methylated

Bacterial DNA is _______

palindrome sequence

Endonucleases (EcoRI) recognize ______ ________ in DNA.

EcoRI

Makes phosphodiester bond cuts between G & A, then cuts hydrogen bonds between strands.

CRISPR

Clustered regularly interspaced short palindromic repeats

Spacers

Are separate short-direct sequences. Are all uniform in length

Archaea

The most ecologically diverse domain

No

Does the archaea domain have pathogens?

True

Archaea are most abundant in moderate habitats, such as soil, ocean, and surface of plant roots

Archaea traits

Cell membrane lipids, Cell wall components, Certain metabolic pathways, Certain genome features

L, Ether (R-O-R)

Archaeal lipids use _____glyceral, _____ bonds,

branched, isoprenoid, unsaturations

Archaea have ______ chains of lipids made of _____units. There is no _____ in lipids

dead, nutrients

Fungi decompose _____ organisms and recycle their _____

water, minerals

Fungi help plants absorb _____ and _____

antibiotics

Fungi produces _______

30%

Fungi can be pathogenic and cause _____ of food spoilage

chitin, hyphae, and mycelia

All the Kingdom of Fungi have these three things

Chitin

Is in the cell wall of fungi

Hyphae

multinucleate cellular filaments in fungi

Mycelia

branched masses of extending hyphae in fungi

Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, and Chytridiomycota,

Fungi are divided into 5 taxonomic categories

Dueteromycota

Fungi imperfecti; fungi that do not fit the 5 taxonomic categories

Ascomycota

Sac Fungi, Defining character is the formation of a sac-like structure called an ascus, where sexual spores (ascospores) are produced.

ascus

sac-like structure where sexual spores (ascospores) are produced

Basidiomycota

Club Fungi; Defining character formation of specialized club-shaped end cells called basidia where basidiospores are produced. Have 16 classes. Include rusts, smuts, mushrooms, and jelly fungi.

basidia

specialized club-shaped end cells called _____ where basidiospores are produced.

Glomeromycota

Defining character is that it forms arbuscular mycorrhizas (AMs) with the thalli of bryophytes and the roots of vascular land plants.

Zygomycota

water molds; Defining characteristic is fast-growing fungi characterized by primitive coenocytic (mostly aseptate) hyphae

Chytridiomycota

Zoosporic; Defining character releases zoospores. Known colloquially as chytrids. Mainly saprophobic. Synchytrium plant pathogens

Yeasts, Ascomycota, Basidiomycota

Unicellular Fungi include

Ascomycota

Saccharomyces cerevisiae

Used as baker’s yeast and beer/wine yeast

Basidiomycota

Ustilago maydis

Corn smut

Disease of corn

Delicacy

saprobes

Most fungi (specifically Chytridiomycota (Chytrids) ) are _____

feed off of dead organisms

saprobes are organisms that ____

Haustoria/Hautorium

Structure in plant pathogens that absorbs nutrients.

Does not penetrate cell membrane.

True

Most fungi are aerobic

facultative anaerobes

Many yeasts are_______, such as Saccharomyces cerevisiae

Ophiocordyceps unilateralis

Ascomycota; “Zombie ants”

Pribnow Box

(TATAAT): The binding site for RNA polymerase.

Shine-Dalgarno Sequence

AGGAGG): The site for ribosome attachment that initiates translation.

Pseudopeptidoglycan

Found in methanogens, this structure uses beta(1,3) linkages instead of beta(1,4), making them resistant to lysozymes and penicillin. (cell wall composition)

S-layers

Some archaea lack a cell wall entirely, possessing only a protein-based ______

Methanogenesis

the reduction of CO2 to methane (CH4) is a metabolic pathway found only in Archaea.

Methanogens

live in soil, water, the deep sea floor, and the digestive tracts of ruminants.

Impact: Methane produced by these organisms is a significant driver of climate change.

reverse gyrase

Hyperthermophiles use ______ ______ to maintain positive DNA supercoils.

tetraethers

Archaea can form ______, which create a rigid monolayer instead of a bilayer, or include cyclopentane rings for added strength.

Monolayer

Tetraethers in archaea can form a rigid ______

Plasmogamy

This is the "cytoplasmic fusion" stage. It is when the cell membranes of two different mating types meet and fuse, but their nuclei remain separate. This creates a cell with two distinct sets of genetic information.

Karyogamy

This is the "nuclear fusion" stage. This occurs when the two separate nuclei finally fuse together to form a diploid (2n) zygote. This is the equivalent of fertilization in humans.

dikaryotic stage

In Plasmogamy, the hyphae fuse. In many fungi (like mushrooms), the nuclei don't fuse right away, resulting in a ______ ______ where each cell has two separate nuclei.

diploid (2n) zygote

Karyogamy (The "Second Fusion") The two separate nuclei within the cell finally fuse together.

This creates a ______ _______. This is the only point in the life cycle where the fungus has a full double set of chromosomes in a single nucleus, similar to a human cell.