Do Eukaryotes have peptidoglycan?

Is the nucleoid membrane-bound?

What two characteristics do clinicians base bacterial classification upon?

Shape and Staining characteristics (Gram or acid-fast reactions)

What are Pallisades and what is an example?

rods lined up side by side like fence (corynebacterium diptheriae)

Which bacterium takes on a pleomorphic shape and why?

Mycoplasmas have no peptidoglycan

What bacteria does acid-fast staining identify?

Mycobacteria

How does the acid fast stain work?

Mycolic acid in mycobacteria cell wall binds to basic fuchsin and cannot be washed out by treatment with acid alcohol.

What do mycobacterium cause?

What is the primary stain in Gram staining? 

What fixes the gram positive and what is the secondary stain?

Quiz question - What protein do gram positives uniquely contain?

LTA, lipoteichoic acid. LTA links the inner membrane to the peptidoglycan

What is the major type of bond in peptidoglycan?

B-1,4-glycosidic

Which two sugars does peptidogylcan link?

N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)

Quiz question - How do B-lactams affect cell wall crosslinking?

They bind carboxypeptidases and inactivate them. The carboxypeptidases normally cleave the terminal D-alanine in order to allow crosslinking between the secondary alanine and DAP

How are gram positive bacteria linked?

They are linked by a series of glycines that attach to lysine. Gram+ have much more crosslinking.

How does lysozyme work?

It cleaves the b-1,4 linkages between NAG and NAM

What is the function of LPS (endotoxin)?

Lipopolysaccharides compose the outer membrane of gram negative cells (along with phospholipid) and forms a tight hydrophobic barrier. It is released upon death and acts as an endotoxin, activating inflammatory mediators. It is heat-stable.

What is the function of murein lipoprotein?

Stabilization of outer membrane to periplasm

What is the importance of Lipid A and where is it found?

In LPS (or endotoxin). It is a glucosamine disaccharide whose hydroxyl groups are esterified with FA. It is essential for cell viability. It is the source of toxicity which is mediated through induction of TNF-a

What does the periplasm contain and where is it located?

In between the inner membrane and the cell wall. It has solute binding proteins, hydrolytic enzymes, and detoxifying agents.

What do S layers do?

S layers are a patterned array of glycoprotein on the surface of bacteria. Helps glycocalx with protection, shape, and adhesion

What do capsules do?

Fibrous material that is generally polysaccharide. Helps glycocalyx in adhesion and protection against phagocytosis

What are Fimbriae?

Proteinaceous structures composed of pilins, found more often on gram negatives. Functions in adherence using an adhesin.

Where are flagella found in spirochetes?

Internally - called axial fibrils/filaments

Which bacteria form spores?

Spores are formed by Bacillus and Clostridium (gram positive rods) in response to nutrient depravation. 

What types of bacterial vaccines are there?

Capsular polysaccharide for the most part although a few are made up of live or killed bacteria.

Which enzymes are involved in supercoiling?

Gyrase (topo II) - relaxes DNA to introduce supercoils

topoisomerase I - relaxes supercoils

What inhibits DNA gyrase and topoisomerase and therefore DNA synthesis?

Fluoroquinilones (Ciprofloxacin)

What drug inhibits RNA polymerase?

Rifampin, which is bacteriacidal, (prevents DNA->RNA, ie rna synthesis)

What is Imipenem?

its a beta lactam, interferes with peptidoglycan synth

What is the action of Tetracycline

What is a conjugative plasmid?

A plasmid that encodes the information for their own transfer to other organisms. It is also known as a mobile plasmid and can mobilize nonmobile plasmids.

Which life cycle of the bacteriophage is considered panic or attack mode?

Lytic, which involves phage DNA replication, phage assembly, and cell lysis. Lysogenic simply involves DNA intergration and bacterial replication.

What is the difference between insertion sequences and transposons?

Insertion sequences are much smaller (1 kb) and only contain information for transposition. Transposons are much larger (5-20kb), carry additional genes, and are organized in two classes - one has insertion sequences on either side and the other doesn’t.

What are the two types of transposition?

Cute and paste and replicative transposition.

What is the difference between transformation and transduction?

Transformation involves the uptake of naked, extracellular DNA and transduction is the transfer of DNA via phage infection.

Which three bacteria are naturally competent?

S. pneumoniae, H. influenzae, and N. gonorrhoeae are capable for natural transformation. (SpHiNg)

What does Competence Factor do?

Competence factor is secreted and induces the expression of mostly cell surface proteins. This enables DNA to bind to the surface of the cell, and one 7-10kb strand enters and recombines.

Where in the body is conjugation most common and why?

Conjugation is most significantly used in the intestines where gram negative facultative rods (E. coli) and other Enterobacteriaceae transfer antibiotic resistance gene among themselves.

What is a Random Transducing Phage Particle?

Virus particle with non-viral DNA - 1/1000 chance of being produced. It cannot replicate but introduces the foreign DNA. Transduction only occurs when this DNA is accepted and recombined into the chromosome.

What is MIC?

Minimum inhibitory concentration - the smallest amount of antimicrobial that inhibits growth

What is MLC?

Minimum lethal concentration - the smallest amount that kills 99.9% of a portion of bacterial sample in a given amount of time

What is therapeutic index? 

The ratio of the dose which is toxic to the hose to the dose which is effective against infection.

How does cephalosporin work?

It inhibits bacterial cell wall synthesis. Similar to penicillin, the beta-lactam ring mimics the peptide bond formed during the transpeptidation (cross-linking) step of bacterial cell wall synthesis and binds the enzyme responsible. This induces autolysis of the cell.

What kind of bacteria is vancomycin effective against and how does Vancomycin work?

Vancomysin is only effective against gram positive bacteria. Vancomycin is bactericidal and recognizes L-D-D configuration, which occurs only in NAM. It blocks crosslinking and the bactoprenol attachment, inhibiting the catalytic addition of the disaccharide to the growing peptigoglycan chain. Inhibits cell wall synthesis.

What are aminoglycosides most effective against and how do they work?

Aminoglycosides are bacteriacidal (streptomycin, gentamycin, neomycin) and target the 30S subunit. They are useful against many gram-negative rods. They both block the formation of the initiation complex and cause the ribosome to misread the genetic code. No protein synthesis. Ototoxic

How do Tetracyclines work?

Tetracyclines inhibit a broad spectrum of bacteria (mycoplasmas, chlamydiae, rickettsiae). They bind to the 30S ribosome and make the binding of aminoacyl-tRNA unstable, interrupting elongation. No protein synthesis. Limitation in that they can also bind eurkaryotic ribosomes. 

Where does Chloramphenicol target?

Chlorampenicol targets the 50S subunit and blocks peptidyl transferase activity by blocking tRNA binding to the A site. It is bacteriacidal against SpHiNm.  No protein synthesis.

How does Clindamycin work?

Clindamycin is a lincosamide and interacts with both the A and P sites, causing the ribsoome to disassemble. It is bacteriostatic.  No protein synthesis.

What the mechanism of action for Rifampin?

It binds to the beta subunit of RNA polymerase and blocks the initiation of transcription. No RNA synthesis. It is bacteriacidal.

How do Fluroquinolones work (ciprofloxacin)?

They work by binding the A subunit of DNA gyrase, interfering with supercoiling required for DNA replication.

What is the action of sulfonamides (sulfamethoxazole)(?

They block folic acid synthesis by competitively inhibiting PABA. It is bacteriostatic. Without folic acid, bacteria cannot grow

What is Trimethoprim-sulfamethoxazole?

A combination of a sulfonamide and trimethoprim. Trimethoprim is a dihydrofolate reductase inhibitor. This prevents the conversation of DHF to THF and folic acid/de novo AA synthesis

Which drug inhibits an alanine racemase?

Cycloserine, used to treat TB

How does Bacitracin work?

Prevents linkage of NAM to NAG by binding bactoprenol, the lipid carrier, and preventing its dephosphorylation. Only used on gram positive infections due to toxicity.

What does Erythromycin do?

It binds to the 50S subunit and creates malformed peptides

What are the two types of resistance to antimicrobials?

Intrinsic (vancomycin cant penetrate gram neg outer membrane)

Acquired (mutation allows resistance or new DNA with resistance proteins)

What is the driving force in efflux pumps?

Multi-drug resistant pumps have evolved. Most are antiporters driven by proton motive force. There are also ABC transporters powered by ATP.

How do proton-driven antiporters work in antimicrobial resistance?

They have internal drug binding pockets (with glutamate) which are exposed in binding. This one transporter can bind  a range of cationic drugs (bind to a glutamate).

How does tetracycline resistance happen?

An efflux pump may only be active when an antibiotic binds its repressor. Also, conjugation increases a thousand fold when the drug is present. Plasmid mobility genes are turned on.

In other drugs, binding can change secondary structure, allowing for transcription of normal proteins.

How does normal flora help fight disease?

First step in infection is attachment - it can competitively inhibit this. Flora can also help with antibacterial factors, metabolism, stim of immune system, cross reactive antibodies.

Loss of NF allows abnormal bacteria to proliferate

What is the normal flora of the Nose?

Corynebacterium spp

S epidermidis

S. aureus

Streptococci

What is normal Oral mucosa look like?

- alpha hemolytic streptococci

(most dominant - tightly bound to squamous cells)

-gram neg anaerobic bacilli (lots), facultative cocci, etc

What does the flora of the Pharnyx look like? 

-Alpha streptococci

-Gram neg anerobic bacilli (lots) and cocci

-haemophilus spp (lots)

What happens with Low acid in the stomach? 

more yeast in stomach, high density, many organisms. This replaces the streptococci and lactobacillus (gram pos bacillus)

Small Bowel flora?

Enterococci

facultative Gram negative bacilli

anaerobic bacteria

Colon flora?

- anaerobic gram negative bacilli - most abundant

-Anaerobe:facultative = 100:1

-E coli = high turnover

Vaginal flora?

-lactobacilli maintain pH and are very important

-group B streptococcus = transient NF during reproductive time

What is Bronchogenic aspiration?

Normally lung has no anaerobes but can cause issue if large number of bacteria from pharynx enter

What can go wrong with normal flora?

Dental trauma can lead to alph strep

Bacteremia can lead to endocarditis, where extremely sticky alph strep stick to mucosa.

What are the major issues with antibiotics and normal flora?

-pathogens can now attach, will find facultative gram neg bacilli

-treating a small number of pathogens can cause a larger problem in GI

-vagina can lose protective pH

-greater susceptibility to enteric pathogens

-C difficile constitutively produces toxin when antibiotics are produced, normally in low numbers

What are the 3 types of structural proteins in a virus?

Nucleocapsid proteins which bind to the genome

Capsid proteins which surround the genome

Envelope which is made up of host lipids and surrounds the virus and work in attachment

What are the functions of viral proteins?

Protect the genome, attach and enter permissive cells, and to initiate virus gene transcription and genome replication.

The Tobacco Mosaic Virus is an example of what type of capsid?

Naked Helical Capsid.

What is the capsid structure of Adenovirus (dsDNA linear)?

Naked Icosahedral 

What is the capsid structure of Influenza virus (-ssRNA)and Ebola virus (-ssRNA)?

Enveloped Helical 

What is the structure of Herpesvirus (dsDNA linear)?

Enveloped Icosahedral Capsid - the amount of glycosylated protein makes it look like a fried egg

What is the only example of an enveloped complex capsid (dsDNA with covalently joined ends?

Poxvirus

What receptors do viruses use to get into the cell?

Virus uses receptors to get into the cell, namely cell membrane proteins, ECM proteins, and receptor mediated endocytosis.

How do dsDNA viruses go about viral protein synthesis?

Uses host RNA polymerase to make a +strand which can be used to make proteins

How do dsDNA viruses replicate their genome? What is the exception and what does it do instead?

Normal dsDNA viruses use either host or viral DNA polymerase to copy. Hepadnavirus, however, makes RNA out of its DNA using host RNA polymerase, and then uses its own viral reverse transcriptase to generate a copy.

How do ssDNA viruses generate proteins and replicate their genome?

ssDNA uses host RNA polymerase to make protein and host DNA polymerase to copy - only package one strand.

How do ss+RNA synthesize protein and genome?

Protein synth - just read off of +RNA

Genome rep - copy to neg strand and then make copies off of that using its own RNA pol

How do ss-RNA synthesize protein and genome?

Protein synth - need to make complement using their own RNA-dependent RNA polymerase

Genome rep - copy to pos strand and then make copies off of that using its own RNA pol.

How do dsRNA synthesize protein and genome?

Protein synth - use their own RNA polymerase to make message (off of neg strand)

Genome rep - use message to make copies, using its own RNA pol

How do retroviruses synthesize protein and genome?

Genome rep and Protein synth - use its own reverse transcriptase (RNA dependent DNA polymerase) to create DNA, integrates this into host genome, and then uses the hosts DNA-dependent RNA pol II to make mRNA or a genome copy. This can be translated to protein.

In replication of Pircornavirus (polio), a ss+RNA virus with naked icosahedral:

one long polyprotein gets chopped up into peptides. Later, ATP dependent processes open up pores.

ss-RNA enveloped vius (Rhabdovirus which causes rabies) replicates how?

Doesn’t make one long message but several short messages.

Have additional steps of transcription to + strand and glycoprotein envelope maturation.

dsDNA virus, naked icosahedral (adenovirus) replication:

Things go in different phases - Nucleus (in and out), early intermediate and late transcription/translation

dsDNA virus, enveloped icosahedral (herpesvirus, which causes HSV-1) - replication?

Same as naked icosahedral except need to Pick up gel layer 

In HSV latent infection

the latency associated transcript (LAT) produces only one pre-mRNA, which makes a lariat -> no virus replication and daughter cells will be latently infected.

What is the most common type of infection?

Subclinical infections, no apparent disease

What is the disease path in acute generalized infections?

Enter at portal, spread to local lymph notes, replicate at local lymph, spread to bloodstream = primary viremia, which hits the central focus. Secondary viremia takes the virus to the target organ, the infection of which makes the disease apparent.

How is papiloma (dsDNA circular, icosahedral naked)  an acute persistent infection

It persists in the epithelium of cervix but is acute localized

What are the 3 types of persistent infections?

Chronic, latent (waves of activation and replication but undetectable when gone), and slow (low levels, takes years, mostly asymptomatic).

What is a hallmark of chronic infections?

Infectious virus is always detectable and is often shed. Latent infections can always be checked.

What are some chronic viruses

In addition to adenovirus and HIV, we have:

Rubella = togavirus (ss+RNA, icosahedral env)

HBV = hepadnavirus (dsDNA circular, icosahedral env)

Hep C = flavivirus (ss+RNA, icosahedral env)

human T cell = retrovirus

PS Measles SSPE (paramyxo) is slow

What are viable targets for therapy of fungal infection?

organelles, sterol in cell membrane, chitin in cell wall, spores, thermal dimorphism, requirement for organic carbon.

What is the only fungi that has aseptate hyphae?

Zygomycota.

Basidiomycota, ascomycota, and deuteromycetes all have septate hyphae.

Which fungi have sexual (meiotic) spores?

Zygomycota, Basidiomycota, Ascomycota.

Deuteromycetes is also known as mitosporic fungi.

What is Chromista?

Separate kingdom from Fungi and forms oomycota

What are the two unique proteins in fungal cell walls?

Glucan and chitin (inner layer).

The cell wall is 90% carbohydrate and gives shape and plasticity. Glycoproteins mediate outer layer recognition of fungi.

What makes fungi successfully virulent?

-Adaptation to in vivo environment

-escape from host recognition

-persistence and dissemination

What is the importance of dimorphism in fungi?

Primary pathogenic fungi and switch shape from hyphae to rounded yeast-like cell and the other way around, contributing to virulence. Multifactorial processes and biofilm formation are the other two main forms of virulence.

What is the least harmful infection by fungi?

Colonization, which only leads to a superficial infection.  Fungi can get deep-seated infection with the use of immunomodulators and disseminated infection with antioxidants.

What type of immunity is required against fungal pathogens?

Need Th1 adaptive immunity (IFN-y) against fungus

What are the 4 clinical classifications of mycosis?

Cutaneous, subcutaneous, systemic, and opportunistic (nonpathogenic until introduced to a specific environment)

What do Polyenes target? 

disrupt membrane function

(Amphotericin B - binds to ergosterol - water insoluble). This is fungicidal.

What do Azoles do?

Azoles - block ergosterol synthesis (water soluble) - fungostatic - fungus fight back using efflux pumps

Allylamines work similarly

Lanosterol C-14 demethylase is a crucial intermediate enzyme in fungal sterol biosynthesis pathway.  It is targeted by azole class of antifungals.

How do echinocandins work?

Echinocandins - target cell wall synthesis (water insoluble) - inhibit B-1,3-D-glucan synthase and disrupt cell wall - fungus fights back by changing the targeted gene conformation

Which drug inhibits DNA/RNA synthesis of fungi?

(Flucytosine 5FC - inhibits DNA/RNA synthesis)

What is subcutaneous mycoses?

Dematiceous fungi can also come from implantation from soil and vegetation, which is the primary disease. Inhalation may affect debilitated patients.

What are the three opportunistic pathogenic fungi?

Cadidiasis, Aspergillosis, Cryptococcosis

What is invasive candidiasis?

One of the most common nosocomial infections and predisposition develops in antibiotic therapy (kill surrounding bacteria), catheters, immunosupression, burns, drug use, surgery