MICROBIO EXAM 2

viruses most basic form

have a genome, a protective layer, and a way to get into the cell.

external virus structure

Spikes

boundary structures(capsid)

icosahedral and helical

caspids

protect the genome

envelope

another layer of protection and helps the virus evade the immune system(stolen form host cell plasma membrane)

2 types of boundaries

naked and enveloped

virus nucleic acids

RNA or DNA, negative or positive sense RNA

internal substances(not the nucleic acids)

RNA dependent RNA polymerase(RDRP) and Reverse transcriptase- RNA to DNA

Viral multiplication (viral “life” cycle)

1. attachment

2. entry

3. replication

4. assemble

5. release

attachment

viral spikes determine the host range

2 types of viral entry

1. endocytosis(virus is engulfed)

2. Fusion(virus envelope fuses)

what do viruses need to do for replication and production

1. make the nucleic acid(genome)

2. make the viral proteins(capsomeres etc.)

where do DNA viruses do replication and production

Nucleus

Where do RNA viruses do replication and production

cytoplasm

what type of RNA genomes are ready for translation

positive sense ssRNA Genomes because they are already in the correct orientation for ribosomes to translate 

what do +sense RNA have to do to replicate and produce

has to make a copy of its genome

what do you have to do to make a copy of RNA

make the other sense (ex to copy +RNA you need to make -RNA and then form that make +RNA)

why do +RNA not need RDRP

because they can immediately make protein they make RDRP in the cell so they dont need to bring it in with them

what does -RNA have to bring with it into the cell

RDRP(RNA-dependent RNA polymerase)

What do retroviruses need to bring with them into the cell

RT(reverse transcriptase)

3 main ways viruses leave

1. lyse

2. exocytosis

3. bud(specific to envelope viruses)

the host in infected, virus is cleared

Acute infection

the host in infected, but the virus is not cleared

Persistent(chronic) infection

genome

the sum of total genetic material in an organism (RNA or DNA)

virus protective layer

1. capsid(ex. icosahedral, helical)

2. envelope(only applies to some) is stolen form the plasma membrane of host cell

Spikes on virus

Determine what cells a virus can infect

host is infected and is mostly clear but remains

latent infection

the virus “immortalizes” cells

Cancer from viral infection

why are viruses tricky to study in lab

they require living cells

what is a prion

misfolded proteins but they can accumulate in the brain and cause serious diesease in humans and animals 

prions 3 things

1. extremely difficult to get rid of in the environment

2. transmissible

3. always fatal

prion transmission

once the misfolded protein is in the body, all of the normally folded proteins will fold incorrectly

informational packets that code for a specific protein or RNA molecule

gene

structural genes

code for proteins

regulatory genes

control gene expression

genotype 

an organism’s distinctive genetic makeup

phenotype

the expression of the genotype, as defined by traits

DNA bases

A, C, G, and T that make up the genetic code.

DNA read and written

read 3 to 5 written 5 to 3

RDRP has low fidelity(bad at catching its mistakes)

high mutation rates

DNA replication

DNA to DNA

Transcription

DNA to RNA

initiation

RNA polymerase binds to the “template strand” at recognized sites called promoters

Elongation

RNA polymerase builds a complimentary RNA strand in a 5 to 3 orientation using U(uracil) instead of T (thymine)

Termination

RNA polymerase recognizes a stop sequence and releases the mRNA strand 

RNA bases

A, C, G, U

3 types of RNA

mRNA, rRNA, tRNA

Translation

mRNA to protein

how many amino acids are there

20

Polyribosomal complex in bacteria

to speed up protein synthesis in bacterial cells, translation of mRNA begins while transcription is still occuring

retroviruses use the reverse transcriptase (RT) to…

make DNA from their RNA genomes

viral genomes(2)

segmented vs non-segmented

what can viruses do with their genes to control how the ribosome reads it

Splicing and stuttering

operon

multiple genes in a row and they are all regulated together

inducing and operon

turn on

repressing and operon

turn off

catabolic operon

presence of the substrate induces the operons expression

anabolic operon

they are usually “on” but can be repressed for certain circumstances

the lactose operon

catabolic- present in E. coli and its expression allows the bacteria to use lactose as a nutrient via fermentatation

3 components of lac operon

1. regulator

2. control locus

3. Structural locus

Phase variation

when bacteria turn off genes that lead to obvious phenotypic types

strains with phase variation….

are more likely to be pathogenic

DNA recombination(since they dont sexually reproduce)

a dinor bacterial cell transfers DNA to a recipient cell (Usually in the form of plasmids)

plasmid

non-essential DNA (can carry genes for antibacterial resistance)

bacteria must have a direct connection (pilus) to transfer genetic material

Conjugation

have genes for resisting antibiotics

Resistance(R) plasmids

a cell nonspecifically accepts small fragments of soluble DNA

Transformation

viruses pick up DNA from donor cells during viral assembly and release it during viral entry of recipient cell

Transduction

can move DNA within an organism(within 1 cell)

Transposons

changes to nucleotide sequence

Mutation

spontaneous mutation

 errors in replication

Induced mutations

exposure to knows mutagens (ex. UV rays)

point mutation

addition, deletion, or substitution of single bases

Missense mutation

different amino acid

Nonsense mutation

changes to a stop codon

silent mutation

changes nucleotide sequence but does not change the amino acid

Frameshift mutation

deletion or insertion of one or more base pairs which shifts the reading frame of the mRNA

why don’t cells figure out a way to stop mutations completely

mutations give microbes variation which is helpful for adaptation

altering genes to introduce new traits

Genetic engineering

Cut DNA at sites with a particular nucleotide sequence

restriction endonucleases

Works by making many copies of of genes present in a sample

Polymerase Chain reaction (PCR)

So sensitive that you dont need to culture microbes to detect them

Polymerase chain reaction (PCR)

DNA is negatively charged

Pulsed field gel electrophoresis (PFGE)

Restriction endonucleases cut the whole genome at certain sites

Pulsed field gel electrophoresis (PFGE)

each organism will have different lengths of DNA pieces

Pulsed field gel electrophoresis (PFGE)

Organisms with similar banding patterns are from the same “source”

Pulsed field gel electrophoresis (PFGE)

Nucleotide sequence is determined

DNA sequencing

By adding foreign DNA we can make cells do “foreign” things

Recombinant DNA technology

Goal: replace defective genes with working copies

Gene therapy

2 types of gene therapy

Gene addition + Gene editing

Non mutated genes are added to the cell with a mutated genome

Gene addition

The mutated gene is corrected in place (use CRISPR)

Gene editing

how do we deliver genes

viral vector

why do we use viruses to deliver genes

viruses can get to hard to reach areas but are specific for cell types

How do we diagnose infectious disease

Clinical microbiology

3 steps of clinical microbiology

1. determine if there is a pathogen present

2. identify

3. characterize

one of the most important steps towards identification

Specimen collection

3 types of methods(assays) for identification

1. phenotypic

2. genotypic

3. immunologic

microscopic, macroscopic, Physiological/biochemical

Phenotypic

catalase test

Phenotypic