Microbio Exam 3

Why might one argue that a virus is living

because they can replicate 

Why might one argue that a virus is non-living? 

they do not generate ATP or synthesize proteins and require a host  

What is the basic structure of viruses? 

Nucleocapsid surrounding genome 

Naked Viruses (non-enveloped)  

• Nucleocapsid ONLY 

• More resistant to disinfectant because they do not have a lipid bilayer (which is what is targeted by disinfectants) 

Enveloped Viruses 

Nucleocapsid enclosed in a lipid bilayer (layer underneath spikes)  and includes matrix

Matrix=

protein layer or cluster attaching envelope to nucleocapsid 

Icosahedral

Radial Symmetry (kind of like a 20-sided dice) 

Helical/ Filamentous Capsids (Spiral) 

Tube around genome , however envelop can mask this nucleocapsid (may not be able to tell that its a rod)  

Complex/ Amorphous 

No symmetry and has a flexible core wall made of capsid proteins 

Complex-Tailed (Bacteriophages) 

Contain icosahedral head with separate nucleocapsid, tail that injects genome into hose cell, and tail fibers as attachment points

Group 1 (I)

• Double Stranded DNA (dsDNA) 

• Creates mRNA  

Group 2 (II)

• Single stranded DNA (ssDNA) 

• Converts to Double stranded DNA -> mRNA 

Group 3 (III)

• Double Stranded RNA (dsRNA) 

• RNA Dependent and RNA Polymerase-> mRNA 

Group 4 (IV)

• Single Stranded RNA (gram +) (ssRNA+) 

• RNA Dependant and RNA Polymerase-> mRNA  

• Group 5 (V)

• Single Stranded RNA (gram –) (ssRNA-) 

• RNA Dependant and RNA Polymerase-> mRNA -> RNA Dependant and RNA Polymnerase -> ssRNA (-) for Viral genome

Group 6 (VI)

• Single Stranded RNA (Gram +)  (ssRNA+) 

• Reverse transcriptase-> Double stranded DNA-> mRNA 

Group 7 (vII)

• Double Stranded DNA 

• MRNA-> Reverse transcriptase-> dsDNA for viral genome

How do scientists study viruses?  

Examining them on agar plates

What is a plaque? 

Clearings on lawns of bacteria on agar plates that show phage infection occurred. Is used to measure the number of active phage in a culture.

Lytic growth=

Productive stage, goes through 5 steps of infection, lysis host cell, and host cell dies 

Lysogenic (Latent) growth=

non-productive stage where viral genome integrates or replicates as cellular DNA and host cell grows and divides. Also where prophage is made

What is a filamentous phage? 

bacteriophage that does not directly burst or kill the host but uses host secretion or pili structure to exit. Some are always productive some can also go latent 

Step 1 of animal virus infection

Host cell recognition and attachment- Includes interactions between viral surface proteins and binding to host receptor  

Step 2 of animal virus infection

Genome entry- Either the genome alone or whole virus particle enters the host  (virus dependent). Complex phage will inject genome alone into host  

Step 3 of animal virus infection

Biosynthesis- Involves making more viral genome and virus proteins

Step 4 of animal virus infection

Assembly/ Maturation-Puts Everything together, Build new virons, Done prior to release (sometimes will continue to mature during or post release) 

Step 5 of animal virus infection

Release (and transmission) -When the virus exits the host  

• May or may not kill host cell 

Early gene steps of biosynthesis

modify or alter hosts replication or transcription by making MORE viral DNA 

Late gene steps of biosynthesis

• proteins build phage tails, capsomeres, and lysozymes which are packaged for future infections  

• Expressed after transcription has been highjacked  

• Where protein production occurs  

Fusion

When they are fusing their envelope to with cell membrane at the cell surface (Plasma membrane)  

• MUST BE ENVELOPED  

Endocytosis

Viruses- host attachment triggers endosome formation and might fuse with host lysosome  

• ONLY OPTION FOR NON-ENVELOPED  

Apoptosis-

when they are non-enveloped, and their progeny accumulate inside the host cell, causing the cell to burst  

Budding-

virus pushes through host cell plasma membrane  

How do some viruses acquire an envelope?

Through budding where they push through a host cell and become wrapped in a piece of the host cells membrane  

How do viral proteins end up in the envelope? 

by being synthesized by the host cell and then inserted into a host cell membrane

Antigenic Drift

• Slow, small changes in the virus  

• Mistakes during VIRAL REPLICATION 

• Replicase (RdRP) and reverse transcriptase are more error prone 

Antigenic Shift-

A large, rapid change 

Why are some RNA viruses more prone to mutations and genetic changes?

their replication enzymes, like RNA-dependent RNA polymerase, generally lack a "proofreading" function that corrects errors during copying

What is viral latency? 

Virus remains dormant in host  

What is a provirus?  

• Forms from HPV  

• Alter host cells  

• Often DNA viruses or viruses that form a DNA intermediate  

• Can lead to increased or unregulated cell division and viral oncogenes  

How do some viral infections lead to cancer?  

Viral oncogenes are genes on the provirus that increase cell division and lead to host tumor formation  

Viroid (Infectious RNA) 

RNA is the entire infectious particle. Inhibit or change genes of host cells.There is NO PROTECTIVE CAPSID (no virions) . NOT IN HUMANS

Prions (only proteins)  

Prions are infectious agents made of only protein . No nucleic acid

Sterilize-

• Destruction of ALL living cell, spores, and/or viruses  

• Includes physical and chemical methods  

• Sterilant- Chemical agent used to sterilize (sometimes toxic to humans) 

Disinfect-

• Removal or elimination of most pathogens from inanimate surfaces 

• Includes physical or chemical methods  

Disinfectant-

a chemical (sometimes toxic) used on inanimate objects  

Antisepsis-

Removal or elimination of most pathogens from living tissues such as skin or mucous membrane.  

• Most often chemical methods are used  

Antiseptic 

chemical used to remove/ eliminate pathogens from living tissue 

Sanitize

Reduce microbe numbers to safe levels to meet some accepted . Minimal chances for disease transmission but not sterilized  

Preserve

delay spoilage of foods or perishable products  

Bacteriostatic-

Agents or methods inhibit bacterial growth

 Bactericidal-

Agents or methods kill bacteria 

Why is the number of microbes important to consider?

Higher number of cells require longer treatment 

What is D-value? 

D-value is tune required to kill 90% of cells at a particular temp  

Moist heat - (high temperature)  

Boiling, pasteurization and pressured steam

Boiling-  

kills most vegetative organisms and viruses  

• NOT endospores or hyperthermophiles  

• Some viruses resist

Pressured steam

Autoclave, pressure cooker, industrial canning – boiling point rises, so more effective. Standard parameters: 121*C at 15 psi for 20  

• Can Sterilize 

Pasteurization –

kills most spoilage bacteria without affecting the texture, color, or taste. Extends shelf life. Moderately high temp for short time  

Dry heat  

Incineration and Dry Ovens

Incineration-

Kills ALL organisms and viruses (destroys items) 

• Can sterilize  

Dry Ovens-

less effective, needs longer time to kill more organisms 

• Best for petri dishes, powders, and oils 

• Can Sterilize (if done properly)  

Filtration

Is useful for air and heat sensitive liquids or chemical additives 

• Includes face masks 

• Can sterilize  

Irradiation

• damages cells and DNA. Useful for heat and moisture sensitive items  

(UV and Ionizing radiation)

UV light-

only good for surface sterilization 

Ionizing Radiation

Can sterilize if does is strong and able to penetrate the material well  

• Not always approved for food  

• Viruses and Prions  

Which are able to sterilize? 

• Filtration 

• Dry Ovens 

• Ionizing radiation 

• UV light 

• Pressured steam 

• Incineration 

Narrow spectrum Drugs

targets one or a few bacteria  

• ORIGINAL PENICILLAN 

• Not as disruptive  

Broad spectrum

targets many groups of bacteria 

• Helpful if you don’t know what's wrong  

• Dysbiosis=disruption of normal microbiota  

Synergistic-

two drugs work better together (cocktail mixes) 

Antagonistic-

one drug inhibits the function of another  

Selective toxicity-

drug harms PATHOGEN not host  

• Therapeutic index-

Index at which we measure toxicity. 

•  Higher index = Less toxic 

Where do most antimicrobial drugs come from? 

From natural sources or modification of natural sources 

Why do we make semi-synthetic drugs 

To make the drugs more versatile, potent, and to combat drug resistance  

B-lactams & penicillin 

Inhibits enzymes that build peptide chains in PEPTIDIGLYCAN 

• Transpeptidase 

• Penicillin- binding proteins 

Macrolides 

Prevent peptidyl transferase activity and translocation  

 Gramicidin 

Targets Gram +’s by forming an ion channel in the membrane

 Polymyxins 

Target Gram -’s due to high affinity for LPS 

Quinolones-

Inhibit DNA Replication (DNA gyrase) 

• Affect Gram + and - 

Rifampin- 

Inhibits RNA Polymerase (transcription) 

• Affect Gram + and - 

Sulfonamides 

Inhibit folic acid synthesis by mimicking substrate 

AZT 

Targets reverse transcriptase (in many HIV drugs 

Paxlovid 

Inhibits protease (maturation)

Tamiflu 

Inhibits neuraminidase (release) 

 Triazoles 

Inhibits fungal ergosterol biosynthesis  

Why are viral, fungus, and protozoan pathogens harder to treat?

Because selective toxicity, they are eukaryotic, so they share a lot of similarities to host cells  

How do we measure resistance (disk diffusion and MIC) 

By measuring diameter of the clear zone around an antibiotic on a disk 

Intrinsic-

Due to inherent characteristics of that organism 

• Example: Gram negatives have outer membrane that prevents drug entry 

Acquired-

Developed drug resistance through mutations or new genes (HGT) 

What are the 4 general mechanisms of antimicrobial resistance? 

• Prevent entry  

• Prevent drug target binding  

• Dislodge antibiotic 

• Pump the antibiotic out 

How is resistance acquired and spread between bacteria (genetic mechanisms)? 

Through mutation and horizontal gene transfer  

How does antibiotic misuse promote the spread of antibiotic resistance? 

Reduced presence of drug allows things with a bit of resistance to survive and mutate  

Infection-

pathogen enters and begins to grow in host

Disease

Disruption of normal structure/ function that can be recognized by symptoms and signs 

• Occurs when the patient develops symptoms 

 infectious disease colonization-

Disease caused by a pathogen that can be transferred from host to host 

pathogenicity ( the how)-

Ability of an organism to cause disease 

 Pathogen (the who)- 

anything that causes disease in humans 

Parasite-

Microbes that cause harm inducing infections 

acute infections-

Symptoms develop and resolve rapidly

chronic infections-

Symptoms develop gradually and resolve slowly