Micro Unit 4

Virion

Extracellular complete virus particle; includes nucleic acid surrounded by a protein coat

nucleocapsid

nucleic acid, protein coat (capsid), maybe some additional components

helical symmetry

icosahedral symmetry

binal symmetry

T4 bacteriophage

positive sense virus

viral genome and mRNA are the same sequence

negative sense virus

viral genome and mRNA are compliments

Negative sense dogma

RNA genome --> mRNA --> protein

Positive sense dogma

1) genome used as mRNA
or
2) RNA --> DNA --> mRNA --> protein

viral envelopes

outer flexible membranous layer around the capsid that is usually host derived

Envelope proteins

spikes or peplomers for attachment to host, enzymatic activity, nucleic acid replication, identification

viral replication

attachment, entry, uncoating, synthesis, assembly, release

One step growth curve

bacteriophage characteristics

infect bacteria, diverse and structurally complex, contain dsDNA, naked

Virulent

lytic

temperate

lysogenic

Lytic cycle

multiplies immediately after entering the host, lyses host cell for release; ex: T4

lysogenic cycle

integrate with host genome and remain in the host cell without killing it, may switch to lytic at any time; ex: lambda

lysogeny

nonlytic relationship between host genome and integrated viral genome

prophage

integrated bacteriophage genome

lysogeny enzyme

integrase

lysogenic attachment sites

between galactose and biotin operons

lysogenic conversion

prophage changes the phenotype of hose

induction

when a phage switches from lysogenic to lytic cycle

What causes a drop in lambda repressor?

exposure to UV light or chemical mutagen that causes DNA damage

What is triggered by a drop in lambda repressor?

switch to the lytic cycle

excisionase

binds integrase enzyme and enables integrase to reverse integration process; SOS response

latent viral infection

virus stops reproducing and remains dormant for some time; ex: HSV

persistent viral infection

virus almost always detectable, clinical symptoms mild or absent for long periods; ex: hepatitus B, HIV

oncoviruses

1) pick up oncogene and transfer it
2) alter protooncogenes
3) incorporate directly into tumor suppressor gene and inactivate it

retroviruses

replicate through a DNA intermediate using reverse transcriptase, released by budding

SARS-CoV-2

positive sense, ssRNA, helical capsid symmetry, spike glycoprotein

Covid Infection and Transmission

spike protein attaches to host receptor on lung epithelial cells, fuses with cell membrane, virions released by exocytosis, zoonotic and person to person through droplets

nucleiod

location of bacterial chromosome and proteins

plasmid

small closed circular DNA that exist and replicate independently of the chromosome

gene

DNA segment that codes for a polypeptide, rRNA or tRNA

genotype

specific set of genes an organism possesses

phenotype

set of observable characteristics denoted with a + or -

wild type strain

strain isolated from nature

mutation

stable, heritable change in nucleotide sequence that alters the genotype, may or may not have an effect on the phenotype

forward mutation

wild type becomes mutant form

reverse mutations

mutant phenotype becomes wild type phenotype

auxotroph

lost the ability to synthesize essential compounds

prototroph

can synthesize essential compounds

screening

detects mutants via observation

selecting

placing organisms under conditions where the growth of those with a particular genotype will be favored

transformation

take up of DNA from a lysed donor cell

transduction

take up of DNA from a viral injection

conjugation

sharing of plasmid DNA between living cells

homologous recombination

DNA is nicked, single stranded binding protein and RecA complex formed, recipient DNA invaded, crossover leads to exchange which is then ligated to form two recombinant DNA molecules

RecA

gene required for homologous recombination

F+

contains the fertility plasmid

F-

does not contain the fertility plasmid

tra

encode for conjugation

ori

independent origin of replication

λdgal

carries genes for galactose utilization

generalized transduction

host DNA mistakenly packaged into phage head

specialized transduction

temperate phages with established lysogeny are incorrectly excised, host DNA exchanged for phage DNA and makes way into new phages

PCR

synthesis of large quantities of DNA

PCR Ingredients

target DNA, primers, taq polymerase (thermostable), dNTPs

PCR Steps

1. denaturing
2. annealing
3. extension
4. repeat

denaturing

denature target DNA with heat

annealing

primers bind to target DNA

Extension

copies of target DNA are synthesized

PCR Protocol

95 C for 1 min
30 cycles of
- 95 C for 30 sec
- 55 C for 1 min
- 72 C for 1 min
Hold at 4 C

Steps of Molecular Cloning

1. isolation and fragmentation of source DNA
2. Insertion of DNA fragment into cloning vector
3. Introduction of cloned DNA into host organism

restriction enzymes

cut DNA at specific sequences

plasmid vector

take up foreign DNA and replicate independent of chromosome

DNA ligase

joins DNA

why are plasmids good as cloning vectors?

easy to purify, small size, independent origin of replication, multiple copy number, presence of selectable markers, unique cloning sites

Locations of normal microbiota

surfaces and mucous membranes; eyes, ears, nose, mouth/throat, stomach, small intestine, large intestine, skin, urethra, vagina

Skin bacteria

inhospitable environment, both transient and resident, influenced by environment and host factors, cause acne and body odor

Mouth bacteria

antimicrobial enzymes in saliva, streptococcus colonize on teeth and gums, biofilm forming,

Stomach bacteria

hard to survive in acidic conditions, some survive if pass through quickly or ingested in food particles, helicobacter pylori

Intestinal bacteria

small- increasing pH has increasing microbes, E faecalis, lactobacilli
large- most microbes in body, obligate anaerobes, bacteroides, clostridium, produce vitamins and gas

respiratory bacteria

staphylcocci/streptococci in upper tract, no normal microbiota in lower tract, lysozyme in mucous

Urogenital bacteria

kidneys/ureter/bladder may have residential, few microbes in distal portions of urethra (E coli can cause UTI), lactobacilli in vagina

Infection vs disease

infection means there are bacteria present, disease means they are causing damage to host tissues

5 rings of infectous disease

agent, virulence, exposure, dose, susceptibility

direct disease transmission

infected host to susceptible host

indirect disease transmission

fecal-oral, airborne, fomites

vector disease transmission

through insect bites

reservoir disease transmission

animate or inanimate place pathogens reside or propagate

zoonosis

disease occurs primarily in animals but is occasionally transmitted to humans

common source curve

rapid rise to peak, moderately rapid decline

propagated cruve

slow, progressive rise and gradual decline

immune system

recognizes foreign substances or microbes and acts to neutralize or destroy them

immunity

ability of a host to resist a particular disease or infection

immunology

study of immune response

innate response

nonspecific natural response

adaptive response

specific and acquired-- cell mediated or antibody mediated

innate barriers to pathogen invasion

first line of defense, no memory, does not rely on previous exposure

phagocytes

engulfs and destroys foreign substances, results in inflammation

cell mediated immunity

T cells, mobile, require antigen binding to T cell receptors

antibody mediated immunity

B cells, not very mobile, activated by some binding but mostly need T cell triggering

Acquired immunity

Natural- active from being sick, passive from breast feeding
Artificial- active from vaccination, passive from nonhuman sources