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
genome used as mRNA or
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
pick up oncogene and transfer it
alter protooncogenes
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
denaturing
annealing
extension
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
isolation and fragmentation of source DNA
Insertion of DNA fragment into cloning vector
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