Week 2

What is the difference between an acute, chronic and latent viral infection? Which one is most likely to spread when the host is asymptomatic?

Acute-comes on suddenly then goes away, short infectious virions Chronic- Long infectious virions after no more symptoms Latent- temperate virus where DNA becomes part of your chromosome and can be reactivated

Scientists were unable to culture bacterium X from a soil sample even though DNA sequence data indicated that the bacterium was present. Why?

Bacterium X has complex nutritional requirements. Bacterium X can only grow in the presence of certain other bacterial species. Lab techs placed the culture plates at the wrong temperature.

Why are microbes generally more resistant to antibiotics and disinfectants when growing in a biofilm?

Can work as community in biofilms, work together

What is the difference between an enveloped and non-enveloped virus? What is the envelope composed of and where do viruses obtain an envelope?

Enveloped virus contains extra lipid bilayer obtained from host cell

What is EPS? What does it do?

Extra polymeric substance created by planktonic, creates biofilm, allows microbes to live in biofilm together

What does the term "planktonic" mean?

Free roaming bacteria in nature that creates biofilms

What is an example of a human disease caused by reactivation of a latent virus?

Scarlet fever

What is the difference between lytic and temperate phages?

Temperate phage can go into latent state- where viral genome is inserted into host cell genome and both host and viral genomes are replicated

Why are viruses usually specific for a single cell type and/or single host species?

The virus binds to specific receptors on host cell

What does the term "generation time" mean? How can the total number of cells in a population be calculated if the generation time is known? (What is the formula and can you use it?)

Time it takes for bacterial population to double N0(# of cells at time beginning) x 2^n(# of generations-# of doublings) = Nt(# of cells at end)

Why are there relatively few antiviral drugs (as opposed to antibacterial drugs)?

Viruses have no cell wall, no ribosomes and therefore do not have protein synthesis, use host ribosomes and nutrients

lac operon

a gene system whose operator gene and three structural genes control lactose metabolism in E. coli, only turned on when glucose is not available

phase induction

a prophage is excised and enters lytic cycle

proton motive force

energy formed by electrochemical gradient established by electron transport chain

oxidative phosphorylation

energy of proton motive force drive the reaction

repressible

enzyme who's synthesis can be turned off in certain conditions

constitutive

enzymes synthesized constantly; ex enzymes of glycolysis

inducible

enzymes that are synthesized when needed

How are viruses classified?

genome structure (type of nucleic acid and strandedness) and hosts they infect

The protein receptor molecules on a host cell to which viruses attach by their spikes are

glycoproteins

facultative anaerobes

grow better if O2 is present but can also grow w/o it, use aerobic respiration if O2 is available

complex

have nucleocapsid head, tail spikes and tail

precursor

intermediate of catabolism that exit "deconstruction line" of breakdown process when cells use glucose to make amino acids; carbon skeletons

What are the phases of the growth curve? What is happening during each phase? How might bacterial growth in pure culture be different than growth in a natural setting?

lag- transcribing and translating bacterial genes, no division exponential growth/log- division, towards end is production of endospores Stationary- decrease nutrients and space increase waste, endospore production, some bacteria producing antibiotics, net 0=cells are dividing at the rate they are dying Death phase/prolonged decline- bacteria not able to recycle any more nutrients, waste buildup

amphipathic

like soap; A molecule that has both a hydrophilic region and a hydrophobic region.

transition step

links glycolysis to the TCA cycle.

4 biological macromolecules necessary for cellular structures

lipids, carbohydrates, proteins and nucleic acids

If bacterial cell is growing slowly because of nutrient limitation, then a _____ infection is more likely to occur

lysogenic

ATP

main energy of cells, ribose, adenine, and 3 phosphate groups; produced by adding inorganic phosphate group to ADP

sandwiched between the nucleocapsid and the envelope in enveloped viruses is the..

matrixes protein

Soap generally does not destroy all microbes but it aids in their

mechanical removal

terminal electron acceptor

molecule with high affinity (wants electrons), O2

energy source

molecules with low electron affinity (wants to give up electrons), glucose

Is there a cure for prion disease?

no

Chemoorganotrophs

obtain energy by degrading organic compounds to make other organic compounds. take potential energy of chemical bonds to create other ones. dependent on photosynthetic organisms; use substrate-level phosphorylation and oxidative phosphorylation to make ATP

What is an example of a way in which microbes can cooperate in a biofilm?

one microbe might break down polysaccharides while another microbe uses the waste as energy

generalized transduction

result of packaging errors during assembly stage of phage replication

photophosphorylation

use sun's energy and an electron transport chain to create proton motive force

Latent infection

viral infection in which viral genome is present but not active, so new viral particles are not being produced

Lytic infection

viral infection of host cell with subsequent production of more viral particles and lysis of cell

transcription

RNA polymerase enzyme synthesizes single-stranded RNA molecule from DNA template; 5' to 3' direction

temperate phage

bacteriophage that can either become integrated into the host cell DNA as a prophage or direct a productive infection that leads to cell lysis

Lysogen

bacterium that carries phage DNA (prophage) integrated into its genome

Glutaraldehyde

because of toxicity of this sterilant, treated items must be thoroughly rinsed with sterile water before use

translation

decoding information carried in mRNA to synthesize specified protein; requires mRNA, ribosomes and tRNA

elongation of translation

empty tRNAs leave ribosome via E-site, peptide bond formed between amino acids on adjacent tRNAs, tRNAs carrying amino acids occupy A-site and P-site of ribosome

substrate-level phosphorylation

energy release in exergonic reaction is used to add phosphate to ADP

Describe the structure of the SARS-CoV-2 virus. In basic terms, how does it replicate?

genetic instructions to make millions of copies of itself, infected cell reads RNA and translates into many kinds of virus proteins

What is a chemoorganoheterotroph? A photoautotroph?

get energy from organic compounds, Able to create own energy by sun

3 central metabolic pathways that oxidize glucose to CO2

glycolysis, pentose phosphate pathway, and Krebs cycle

What is the difference between an acidophile and a neutrophile? Which one would grow in a jar of pickles?

most microbes are neutrophils (pH 5-8); acidophils, not a lot of microbes can live in it therefore

TCA cycle

oxidizes 2 acetyl groups from transition step and releases two precursor metabolites, two CO2 and 2 ATP

mRNA

temporary copy of DNA, composed of nucleotides, cells decode mRNA into amino acids, 3 nucleotides (codon) to one amino acid

promoter

the DNA sequence to which RNA polymerase binds and initiates transcription

what processes are required for production of virus particles in a host cell?

translation of viral genes, transcription of viral genes, replication of viral genome

signal transduction

transmission of info form outside to inside of cell, allows cells to monitor and react to environmental conditions

formaldehyde

used to kill bacteria and inactivate viruses in vaccines; also used to preserve biological specimens

retrovirus

uses revers transcriptase to make DNA copy form its RNA genome like HIV

cellular respiration

uses the reducing power of NADH and FADH2 generated in glycolysis, the transition step, and the TCA cycle to synthesize ATP

photosynthetic organisms

using energy of sunlight, synthesis organic compounds from CO2. Convert kinetic energy of photons to potential energy of chemical bonds

productive infection

viral infection in which more viral particles are produced

filamentous phages

-single stranded DNA phages that look like long fibers, cause infections but process doesn't kill host cell- 1. Phage attaches to the F pilus of a bacterial cell and injects its single-stranded DNA 2. Phage DNA replicates; phage capsomeres are synthesized and embedded in the host membrane 3. split and have two carrier cells -M13 phage is useful in certain recombinant DNA procedures

Two types of transduction

1. generalized 2. specialized

catabolism of glucose steps

1. oxidizing glucose molecules to generate ATP, reducing power and precursor metabolites; accomplished in series of reactions called central metabolic pathways 2. transferring electrons carried by NADH and FADH2 to terminal electron acceptor, done by cellular respiration or fermentation

Why would an infection involving a biofilm be difficult to treat? Why might the microorganisms be difficult to identify?

Infection could be causes by more than one microorganism present in biofilm, some species cannot be cultured

Why does the research described in "An Irresistible Newcomer" represent a breakthrough discovery?

New way to grow bacterial and new antibiotic

Can viroids infect humans? Where do viroids cause significant disease?

No, are infectious for plants

When a bacterium is in a state of lysogenic conversion, why does it express a different protein(s)---often a toxin? What does this mean for the pathogenicity of the bacterium?

Phenotype is changed by lysogenic phase,

What factors could influence growth rate in vivo? (in the body)

Presence of competing microorganisms host immune system host genetics

elongation of RNA transcript

RNA polymerase denatures DNA exposing new region so elongation can continue and single-stranded RNA molecule is synthesized

obligate aerobes

absolute requirement of O2, use O2 in aerobic respiration

An antiviral drug that binds to a viral spike protein would directly prevent:

attachment

fastidious organisms

bacteria that require growth factors and specific nutrients

halophile

bacteria that require high concentration of salt

obligate anaerobes

cannot grow if O2 is present, killed by O2,

nucleocapsid

capsid- protein coat made up of subunits called capsomeres and nucleic acid

What are two enzymes that obligate aerobes and facultative anaerobes make that protect the cells from reaction oxygen species (ROS)?

catalase and superoxide dismutase

fermentation

cells break down glucose via glycolysis and use pyruvate or derivative as terminal electron acceptor, ATP generated comes from substrate-level phosphorylation during glycolysis

glycolysis

central metabolic pathway that splits glucose and oxidizes it to form molecules of pyruvate

Lysogenic conversion

change in properties of bacterium conferred by prophage

psychrophile

cold arctic regions

What is a way in which microbes can compete in a biofilm?

compete for space and nutrients, some might produce antibiotics

Virion

complete virus in its inert non-replicating form viral particle

thermophile

compost heat

Why is salt a good preservative?

creates a lot of dissolved solute outside of cell so water will flow from in to out of the cell causing cytoplasmic membrane to pull away from cell wall (plasmolysis)

mesophile

human body

If microorganism has temperature optimum close to boiling point of water, is it considered a

hyperthemophile extremophile

aerotolerant anaerobes/obligate fermenters

indifferent to O2, use fermentation

viroid

infectious agents of plants that consists only of RNA, lacks capsid

Prion

infectious protein that causes neurodegenerative disease

What directs corporation of phage DNA into bacterial chromosome

integrase

Viroids are known to infect:

plants

antigenic variation

process by which routine changes occur in a microbial surface antigen

specialized transduction

produces defective phage particles, transfers phage DNA and adjacent host genes, results form errors in excision of the prophage

lytic or virulent phages are ______ infections

productive; exit host at end of infection cycle by lysing cell

endergonic reaction

products have more free energy than starting compounds, requires input of energy

nuclease

protein in T4 lytic cycle that degrades bacterial DNA

chaperones

proteins that fold polypeptides so they become functional

psychrotroph

refrigeration

Enzymes are grouped according to type of _____ that controls their ____

regulation synthesis

microaerophiles

require small amounts of O2

autotroph

requires only carbon dioxide as sole carbon source

metabolic pathway

series of chemical reactions that converts a starting compound to an end product; linear, branched or cyclical

lysogenic conversion

some pathogenic bacteria produce toxins that are encoded on prophage DNA

How do viruses attach to cells?

spike proteins

exergonic reaction

starting compounds have more free energy than products; energy is released

electron carriers

step between energy source and terminal electron acceptor; NAD+/NADH NADP+/NADPH FAD/FADH2

Ribosome

string amino acids together to make polypeptide

reduced/hydrogenation

substance that gains electrons (addition of hydrogen atom)

Oxidized/dehydrogenation

substance that loses electrons (removal of hydrogen atom)

Why organisms use fermentation

suitable inorganic terminal electron acceptor is not available; they lack electron transport chain

antigenic shift

two different strains of a segmented virus enter the same cell, reassortment of the gene segments occur

phase variation

the routine switching on and off of certain genes

In contrast to phage replication, eukaryotic viruses...

the whole protein is encapsulated by the cell

A bacterial species was isolated from the middle of a compost pile where the temperature was 55-65oC. The group that best describes this microorganism would be:

thermophile

tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome, has anticodon

2 major microorganism groups found on skin

transient- from environment, stay on skin for short time, # reduced by hand washing resident(microbiota)- associated with sweat and sebaceous glands, not removed easily

What is the human "phageome"? How is this distinct from the virome?

virome- collection of all viruses in and on human body Phageome- collection of all phages that infect bacterial cells vs. Viruses- that infect host cells

Icosahedral

virus shape, 20 flat triangles arranged like soccer ball

helical

virus shape, appear cylindrical, spiral staircase

Bacteriophage/ phage

virus that infects bacteria