MICROBIO EXAM 2: 9-16

Chap 9 learning objective 1

What structural elements do viruses have?

How do we name and classify viruses?

Chap 9 learning objective 2

How do viruses multiply?

What are acute, latent, and persistent infections ?

Chap 9 learning objective 3

How do we study viruses?

Chap 9 learning objective 4

What are prions?

What is the structure of a virus? 

Viruses have a genome, protective layer, and spikes

Genomes carry the nucleic acid DNA, the protective layer is a capsid, and the spikes are for a way to get into a cell

What are the functions for spikes/glycoproteins in viruses

Allows binding of viruses to target cells to gain entry into cell

What does a capside do and whar are the types of virus capsids 

Capside protect the genome from damage to ensure DNA transfer to the host cell is complete

There is helical, wraps around genome. Icosahedral which creates many triangles around the genome, and complex

Helical Capsid - boundary

Rod shaped capsomeres wrapped around the nucleic acid. It is called nucleocapsid 

Icosahedral Capsid - boundary

Capsomeres create triangular shapes surrounding genome. Creating an icoasahedron

Envelope - boundary

Envelopes are optional for viruses, creates another layer of protection, and helps evade the immune system by stealing glycoproteins from host cell DNA

What are the different kinds of envelope boundaries?

Naked (Icosahedral and Helical) versus Envelope (Icosahedral and Helical)

What are the characteristics of internal - nucleic acids (genomes)?

Genomes within viruses may be RNA or DNA. They made be single or double stranded. Lastly, negative or postive sense RNA

What is the difference from negative and positive sense between internal nucleic acids 

Negative sense RNA has to be transformed to a positive sense first, then it translates. While a positive sense RNA can translate immediatley to mRNA

What if internally we need other substances? What does the virus do?

The virus will replicate or copy nucleic acids from polymerases. This is called RNA Dependent RNA Polymerase (RDRP) to produce necessary RNA or proteins.

Reverse transcriptase takes the RNA of the viral genome and translates it to DNA by negative sense to positive sense. This is brought over via capsid.

What are the different kinds of viral multiplication?

1. Attachment - virus binds to its receptors using spikes(glycoproteins)

2. Entry - virus enters the cell 

3. Replication - virus makes copies of its viral proteins 

4. Assembly - virus assembles components into virions

5. Release - virus leaves cell to infect others

Viral multiplication - attachment characteristics

Viral glycoproteins (spikes) determine the host range, which is the spectrum of hosts a virus can infect. These spikes recognize and bind to specific receptors on the host cell surface. Entry receptors help initiate viral entry

Viral multiplication - entry characteristics

There are 2 types of viral entry:

1. Endocytosis - Virus is engulfed by the cell through a vesicle. 

2. Fusion - The virus envelopes with the host cell 

Viral multiplication - replication and production 

In replication and production, the nucleic acid (genome) of the virus must be replicated and the viral proteins (capsids) must be made regardless. 

This will occur all in the nucelus of the cell and RNA viruses will be completed in the cytoplasm. 

What are three essential components of a virus 

Genome, capsid, and spikes

What shapes may the capsid be

Icoasahedral and helical 

purpose of an envelope? Do all viruses have an envelope?

No it is optional, purpose of an envelope is to create another layer of protection and disguise from host immune cells. No envelope means naked virus. 

What could a genome look like?

DNA, RNA, + / -, single and double stranded

What might a virus carry into the cell with them

Extra enzymes if needed, RNA and Retroviruses will bring in RDRP and RT

What are the steps of virual multiplication

Attachment, enter (endocytosis/fusion), replication of the genome structure, assembly, and release 

How do viruses enter and exit host cells

Entry, through endocytosis (vesicle engulfing) and fusion (virus merges with cell membrane). Virus exits by lysis (pressure bursts) and exocytosis (vesicles leaving) and budding (growing + being picked up naturally)

What are infection curves?

Acute, happens and dies. Persistent/chronic, happens and continues to live in body. Latent, happens, becomes dormant, and then if triggered again it infects in the body

How to study viruses outside of human hosts

Needs to be a living cell that will incubate the virus

What are prions

Misfolded proteins that keep misfolding proteins in a domino effect fucking up everything ane can only be killed by incineration. Very fatal, causes plaque leading to neuro diseases

Genome, gene, genotype, phenotype, structural, and regulatory genes

Genome, all genetic material. Gene, all genetic material required to make 1 protein. Genotype, genetic makeup. Phenotype, physical makeup. Structural, proteins that create structure of microbe. Regulatory, proteins that regulate expression of genes 

Replication

DNA to DNA

Transcription

DNA to RNA

Translation

RNA to protein

Splicing/stuttering

One gene making multiple proteins, resulting to benefits of gene variation

What is an operon

It is a gene that is regulated to work together

Induction and Repression

Induction, is the on state. RNA is transcribed (anabolic) !! Repressed, off state, NO RNA transcribed!! (catabolic)

How does the lactose operon in E. Coli work

The operon will be repressed, but if lactose is PRESENT it will be induced transcribing RNA 

Phase variation

A phenomenon where bacteria change their surface proteins to evade the immune response. This allows them to adapt and survive in different environments.

DNA recombination

To increase genetic variation, sharing DNA from donor to recipient

Conjugation

Donor gives DNA via pilus to reciepient

Transformation

Donor explodes and reciepient picks up dead donor DNA

Transduction

Donor cell infected with virus transfers DNA to recipient cells.

Transpons

USES 1 CELL ONLY, switching spots within cell to create different DNA

Mutations

Point mutation, addition, deletion, or substitution of a nucleotide

What causes mutations to occur

Spontaneous during replication of DNA or induced when a microbe is exposed to a mutagen ( UV Rays)

What is a mutation in DNA called

Point mutation

Missense, nonsense, silent, and frameshift definitions

Missense, amino acid swap. Nonsense, early stop codon in translation. Silent, codon different but produces same protein. Frameshift, deletion or addition which leads to different amino acid thread

What can restriction of endonucleases do

Recognize and cut dna in certain sites

Purpose of PCR

Make many copies of a gene

What do PFGE results tell us

If we are able to identify source of outbreak is from the SAME SOURCE

How do we use DNA Recombination to our advantage

By editing genes to create proper help within the body

Goal of gene therapy

To replace defective genes with a working copy

Different between gene addition and editing 

Addition is giving a functioning gene while gene editing is fixing a mutated gene, not removing or adding anything

Pros and Cons of viral vectors to deliver genes

Pros, can target specific cells. Cons, it can create an immune response trigger

Goals of clinical microbiology

Determine if a pathogen is present, identify pathogen correctly, and to characterize the pathogen 

Phenotypic, genotypic, immunologic assay

Gram stain, DNA/RNA, and immunologic is looking for antigeno r antibody

Indirect ELISA

Antibodies

Direct ELISA

Antigens

Sterlization

Everything is removed, prions and endospores

Disinfection

Kills all pathogens

Sanitization

Lowering # of microbes

Antisepsis

Disenfects living tissue too

-cide and -static

cide means to kill and static means to inhibitthe growth of microorganisms.

3 categories of control methods

Mechanical (barrier), physical (pump), and chemical (chemical)

What factors influence the effectiveness of control measures

Population size, composition, concentration, and temperature

What microbs are most resistant to least

Prions + endospores, least are enveloped viruses

How to test effectiveness

Phenol test or in-use tests (swapping location for growth)

How to differentiate 5 terms for antimicrobials

Broad spectrum, narrow spectrum, antibitoics, antimicrobrial, and prophylaxis

Kirby-Bauer and E-test purposes

KB - looking at susceptibility of a microbe and ET - looking at sensitivity of a microbe. Susceptible means it can kill the microbe while resistant has no effect

What is MIC? What is the therapeutic window?

Minimum amount of chemical needed to inhibit the genetic creation of a microbe. The therapeutic window is the range between the minimum effective dose and the minimum toxic dose of a drug.

Why might an antimicrobial treatment not work as intended?

It cannot reach the site of infection, the microbe may be resistant, or the dosage may be insufficient.

How od antimicrobial drugs work?

By attacking a specific microbe and destroying all of it so there is no survival 

Five main targets of antimicrobial drugs?

Cell wall synthesis, protein synthesis, nucleic acid synthesis, metabolic pathways, and cell membrane function.

B-Lactam affecting cell wall

B-Lactam antibiotics (penicillin) are more effective on gram-positive bactera than gram-negative bacteria due to the thicker peptidoglycan layer in their cell walls.

Vancomycin affecting cell wall

Prevents proper peptidoglycan production, important for treating methicillin-resistant (MRSA)

Quinolone antibiotics affecting nucleic acids

Inhibits DNA transcription and replication by inhibiting microbe-specific enzymes 

Drugs that affect target protein synthesis

Block successful translation at the ribsome/mRNA level

Drugs that target cytoplasmic membrane

Polymyxin interacts with phospholipids causing distortion and leakage of cell contents of the bacteria, leading to cell death.

Drugs that target folic acid synthesis

Folic Acid: An essential vitamin required for DNA synthesis and cell replication. Bacteria synthesizes folic acid. Sulfonamides are inhibited by blocking the enzymes required for folic acid synthesis

How should you consider treating fungi, protozoa, helminths, viruses, and biofilms?

If eukaryotic (fungi, protozoa) do not kill human cells, for helminths you need to kill all life cycle stages, for viruses target inhibition host cell pathways via vaccines, and for biofilms remove them or add antimicrobials to disrupt.

Five ways that microbs acquire drug resistance

1. Synthesis of new enzymes that inactivate the drug

2. A microbial cell does not let drug in

3. Drug is eliminated

4. Binding sites for drug are decreased 

5. Microbe uses an alternate pathway to bypass the drug's effects.

How do Beta-Lactamases work

They do not allow synthesization of the bacterial cell wall by breaking down beta-lactam antibiotics, rendering them ineffective against resistant bacteria.

MecA gene functions

MecA is an antibacterial resistance gene used by MSRA 

Penicillin attacks peptidoglycan by binding to its target (Penicillin-Binding Protein) 

MecA allows the bacteria to make another version of the target protein called PBP2a which penicillin can’t bind to 

How do populations of microbes acquire resistance?

1. A group of bacteria, some of which are resistant to antibiotics

2. Antibiotics kill bacteria causing the illness as well as good bacteria protecting the body from infection

3. Resistant bacteria now have preferred conditions to grow and take over 

4. Bacteria can transfer their drug-resistance to other bacteria, causing more problems

Common adverse reactions hosts have to antimicrobials

1. Toxicity to organs: Drug damages human organs

2. Allergic reactions: Drug triggers the immune system

3. Microbiome: Helpful microbes are killed 

What is a superinfection and how does this happen?

Superinfection: After destruction microbes which are usually present in small numbers overgrow and cause disease 

(i.e. - UTI becoming a yeast infection)

What is the microbiome/normal flora? How do they work?

Microbes colonize in/on a host that do not normally cause disease 

They work by having a host defense, influenced by enviornment/genetics and competing with harmful pathogens for resources.

Differences of colonization, infection, and disease 

1. Colonization: Act of microbes taking up long-term residence in a human host

2. Infection: The entry and multiplication of microbes in host tissues

3. Disease: Any deviation from health, including when a microbial infection damages or disrupts host tissues and organs 

+Microbial antagonism: Normal flora is colonized, normal flora creates a hostile environment for other organisms, and normal flora keeps each other in check

Opportunistic pathogen versus true pathogen

Opportunistic pathogens: Cause disease when host’s defenses are compromised

True pathogens: Capable of causing disease in healthy people with normal immune defences

• Pathogenicity: An organism’s potential to causes disease 

Stages of infection disease

1. Portals of entry

• The route of microbe entry into a host + infectious dose (ID) the minimum number of microbes required to establish infection

1. Attachment and interaction with microbiome

• Microbes need to gain stable foothold on host tissues via spikes

1. Surviving host defenses

• Host immune system recognizes “foreign microbes”  and attacks phagocytes

1. Causing disease

• Through enzymes/toxins (virulence factors), indirectly inducing host defenses and producing EXCESSIVE RESPONSE