Lecture 1: Basic Principles Flashcards
Prokaryote Characteristics (6)
- single circular DNA
- no Nuclear Membrane
- no Mitochondria
- no golgi bodies
- no ER
- has complex cell wall
Examples of prokaryotes
- bacteria
- blue green algae
examples of eukaryotes
- animals
- plants
- fungi
- protozoa
- algae
Eukaryote characteristics
- diploid genome
- organelles
- membrane-bound nucleus
methods to classify bacteria (5)
- growth characteristics
- cell morphology
- gram stain characteristics
- external structures
- spore formation
examples of growth characteristics (9)
- color
- size
- shape
- smell
- nutrients
- antibiotic resistance
- fermenation
- hemolytic properties
- lipid hydrolysis
Cell morphology examples (6)
- coccus
- bacillus
- spirillum
- fusiform bacillus
- vibrio
- spirochete
Gram stain procedure
- crystal violet
- iodine
- alcohol wash
- safranin
characteristics of Gram (+) cells
- thick peptidoglycan layer with teichoic and lipoteichoic acids
characteristics of Gram (-) cells
- thin peptidoglycan layer and outer membrane with LPS, phospholipids, and proteins
What is a techoic acid?
a water-soluble polymer of repeating ribitol phosphate units
what is a lipiteichoic acid?
a polymer with a fatty acid that is anchored in cytoplasmic membrane by diacylglycerol
what can techoic and lipoteichoic acids do?
- distinguish bacterial serotypes and promote adherence
- can be virulence factors
Components of the gram (-) cell wall
- outer membrane
- periplasmic space
- no teichoic acids
function and components of the gram (-) cell outer membrane
- maintains structure, permeability barrier
- provides protection from adverse environmental conditions, such as digestive system
- phospholipid inner leaf
- lipopolysaccharide
- outer leaf
- porins
what is LPS, and how does it affect the body?
lipopolysaccharide
- endotoxin that stimulates immune response–> shed into media and host, activates B cells and macrophages, induces macrophages and dendritic cells to release IL1, IL6, TNF, which induces fever and causes shock
what are the purpose of porins
porins allow diffusion of hydrophilic molecules <700Da, allows passage of metabolites and small hydrophilic antiobiotics
3 structural components of LPS
O antigen
- linear polysaccharide
- 50-100 repeating sugar units
- differs between serotypes
core polysaccharide
- branched, 9-12 sugars
- contains phosphorylated KDO
- essential for bacterial viability
- same for each species
Lipid A
- **endotoxin
- phosphorylated glucosamine disacchardie with fatty acids
- phosphates connect LPS units into aggregates
- Essential for bacterial viability
what is KDO and what does it do?
1-deoxy-D-manno-oct-2-ulosonic acid
used by bacteria in synthesis of lipopolysaccharides
examples of external structures for bacteria
- capsules
- Flagella
- fimbriae
- spore formation
What is a capsule?
- composed of polysaccharide or protein layers
- its a “slime layer”, loosely adherent and non-uniform
- aka glycocalyx
what kind of capsule does Bacillus anthracis have?
polypeptide capsule
what properties of a capsule allow it to help bacteria persist in their host?
- poorly antigenic
- antiphagocytic
- major virulence factor
- barrier against abx and host defense
adherence
properties and uses of flagella
- essentially propellers, though not all are motile
- coiled flagellin protein subunits
- anchored in membrane through hook and basal body
- important in motility (chemotaxis)
- -> swim straight then tumble, depending on which way flagellum spins
- antigenic and strain determinants
physical characteristics of fimbriae (4)
- aka pili
- hairlike structures
- composed of pilin protein subunits
- not coiled
- several hundred over entire surface of bacterium
how do fimbriae help the bacteria persist in the host
- adherence
- virulence factor for colonization and infection
- DNA transfer via f pili
what is the f pili and what is it used for?
- the sex pili
- a tube that binds to other bacteria to transfer bacterial DNA
- -> allows plasmids or chromosomes to jump into the new bacterium
unique product of corynebacterium and nocardia ?
- mycolic acid lipids
unique characteristics of mycoplasma
- no peptidoglycan, incorporates steroids from host into membrane
unique characteristics of mycobacteria
- peptidoglycan layer intertwined with an arabinogalactan polymer, surrounded by wax-like lipid coat of mycolic acids
- acid-fast stain
- viruence and antiphagocytic
name two bacteria that utilize spore formation
- bacillus
- clostridium
what do spores enable bacteria to do?
- convert from vegetative to dormant state under harsh environmental conditions
what do spores contain?
- chromosome
- minimum proteins and ribosomes
- calcium bound to dipicolinic acid
how are spores formed?
- spore septum begins to isolate newly replicated DNA and a small portion of cytoplasm
- paslma membrane starts to surround DNA, cytoplasm, and membrane isolated in step 1
- spore septum surrounds isolated portion forming the forespore
- peptidoglycan layer forms between membranes
- spore coat forms
- endospore is freed from the cell.
overview of spore formation
DNA replication, spore septum begins to isolate new DNA, plasma membrane forms, peptidoglycan layer forms between membranes, spore coat forms, endospore released from cell
overview of bacterial genetics
haploid chromosome
- one chromosome, one copy of each gene
plasmids
- extrachromosomal genetic elements
bacteriophages
- bacterial viruses (?)
Central Dogma of Genetics
DNA –> mRNA –> protein
Genetic mutations
- silent
- missense
- nonsense
- insertion
- deletion
- null
What changes will a silent mutation have
no change
what changes will a missense mutation have?
substitution of a different amino acid –> may or may not have an effect
silent to severe effect
what changes will a nonsense mutation have?
a premature stop –> non-functional protein
almost always severe effect
what changes will an insertion mutation have?
frameshift –> amino acids after shift are affected
usually severe since protein is typically nonfunctional
what changes will a deletion mutation have?
frameshift –> amino acids after shift are affected
usually severe since protein is typically nonfunctional
what changes will a null mutation have?
complete destruction of protein function through extensive insertion, deletion, or rearrangement
types of genetic repair
- direct DNA repair
- excision repair
- recombinational repair
- SOS response
- Error-prone repair
how does direct DNA repair work?
enzymatic removal of damage
how does excision repair work?
excision of damage, followed by synthesis of new DNA strand
how does recombinational repair work?
retrieval of missing info by genetic recombination when both DNA strands are damaged
how does the SOS response work?
induction of ~15 genes after DNA damage or interruption of replication
how does the error-prone repair work?
last resort
- fills in gaps with random sequences when DNA template is not available for accurate repair
types of bacterial genetic transfer
- transformation
- transduction
- conjugation
- transposition
what is transformation?
take up fragments of naked DNA and incorporate into their genome
donor cell undergoes cell lysis –> release of DNA fragments –> DNA enters recipient cell and integrates into DNA
what is transduction
transfer from one bacteria to another by bacteriophage
transducing phage containing donor genomic DNA undergoes cell lysis –> release of phages –> phage infects recipient cell; donor DNA integrates into recipient DNA
what is conjugation
quasi-sexual exchange of DNA
free plasmid moves from donor to recipient cell via sex (f) pilus –> integrated plasmid (episome) promotes transfer of genomic DNA, which integrates into recipient DNA
what is transposition
“jumping” of DNA elements between DNA molecules
transposed DNA from the donor jumps into the sequence of the recipient
What makes a virus a virus? (11)
- filterable
- obligate intracellular parasite
- cannot make energy or proteins independently
- RNA or DNA
- naked capsid or envelope
- components are assembled in order to construct the virus
- viruses are NOT “alive”
- must be infectious to endure
- must be able to use host cell processes
- must encode anything not provided by cell
- must have self-assembling components
what is an orphan virus?
one that does not have an associated disease
ex: reovirus is a virus of either the respiratory or enteric systems that does not have an associated disease.
Viral classification overview
no consistent classification system
- DNA or RNA genome
- has been based off of viral characteristics
- has been based on the tissue affected or disease produced
- has been based off of the geographic location it was found in
- has been based on virus characteristics
What is the Baltimore System of viral classification
the most consistent and current classification; is by
- physical and biochemical characteristics (size, morphology, type of genome, means of replication
T/F viruses are the same size.
False
Viruses can be different sizes
Types of genetic material in viruses
DNA genome
- single or double stranded
RNA genome
- + or - sense, or ambisense (both)
MAY BE SEGMENTED)
T/F the outer layer of a virus can be a capsid or an envelope.
true
T/F the capsid is obtained by the host and the envelope is encoded by the virus
false
capsid is encoded by the virus
envelope is obtained by the host
what functions do glycoproteins serve for viruses?
viral attachment and entry
fusion, enzyme functions (neuraminidase), immune response
structure and capability of a naked capsid virus (8)
- composed of protein
- environmentally stable
- released by cell lysis
- spread easily by fomites, P2P, dust, droplets
- retains infectivity when dry
- survives gut
- resistant to detergents
- antibody response may be sufficient for immunoprotection
structure and capability of a naked capsid virus (8)
- composed of protein, lipid, glycoprotein
- environmentally labile
- released by budding or lysis
- spread by large droplets, secretions, organs, blood
- must stay wet to endure
- cannot survive gut
- detergents destroy infectivity
- antibody and cell-mediated immune response, inflammation, hypersensitivity
T/F all RNA-viruses are enveloped
true
what can the envelope of a virus be composed of?
- host membrane
- viral proteins
- viral glycoproteins
what is tegument?
the space between the capsid and envelope, it contains enzymes, proteins, and mRNA
viral replication of a naked capsid virus
- recognition
- attachment.
- penetration/entry
- uncoating
- macromolecular synthesis
- assembly
- release
viral replicatoin of an enveloped virus
- recognition
- attachment
- penetration/entry
4/ uncoating - macromolecular synthesis
- assembly
- budding
- release
in terms of viral replication, where do enveloped and naked viruses differ?
enveloped viruses require budding before release (this is where they integrate the host’s membrane into their structure). naked viruses do not need to undergo budding before release.
In viral replication, what occurs during recognition?
viral attachment proteins (VAPs) identify specific host cells
In viral replication, what occurs during attachment?
- VAPs bind to cell receptors
- receptors can be proteins or carbohydrates
- determines host range and tissue tropism
In viral replication, what occurs during penetration/entry?
- non-enveloped viruses enter by receptor-mediated endocytosis
- enveloped viruses enter by fusion of viral and cellular membranes
In viral replication, what occurs during uncoating?
- capsid/envelope is removed
- DNA delivered to nucleus, RNA to cytoplasm
In viral replication, what occurs during macromolecular synthesis?
- synthesis of viral mRNA
- most DNA viruses use cell RNA polymerase II
- most RNA viruses encode enzymes for transcription and replication
- all viruses depend on host ribosomes, tRNA, and post-translational mechanisms
In viral replication, what occurs during assembly?
- 3D interlocking self-assembling puzzle
- DNA in nucleus
- RNA and pox in cytoplasm
In viral replication, what occurs during budding?
- occurs in enveloped viruses only!
- viral glycoproteins delivered to cell membranes
- capsid interacts with glycoprotein-membrane and surrounds capsid
- budding occurs from plasma membrane, ER, golgi, or nuclear membrane
In viral replication, what occurs during release?
- lysis–> naked capsids usually lyse cell for release
- budding–> most enveloped viruses release from membrane WITHOUT killing cell
- exocytosis–> viruses that bud into cytoplasm remain cell-associated and released by exocytosis or lysis or nuclear membrane
T/F viral mutations occur constantly.
true
T/F RNA viruses have a lower mutation rate than DNA viruses
false
Why do RNA viruses have a higher mutation rate than DNA viruses?
RNA viruses have no proof-reading capability
Types of viral mutations
- lethal
- deletion
- plaque mutants
- host range mutants
- attenuated mutants
- conditional mutants
what is a lethal mutation?
virus cannot replicated and dies without replicating
what is a deletion mutation?
loss or selective removal of function
what is a plaque mutant
a viral mutation that differs from wild type
what is a host range mutant
a viral mutation that differs in target tissue or the species infected
What is an attenuated mutant
a viral mutation that causes less serious disease
what is a conditional mutant
a mutation that allows virus production only under certain conditions (temperature sensitivity for example)
viral recovery genetic processes
- recombination
- integration
- reassortment
- complementation
- marker rescue
- pseudotype virus
viral recombination
occurs readily between related viruses; exchange of genetic sequences
viral integration
retroviruses and some tumorigenic viruses integrate into host genome; causes mutation of host
viral reassortment
segmented viruses exchange segments when >1 strain infects a cell
viral complementation
replication of a virus or expression of gene provides missing function in defective virus
viral marker rescue
repair of a mutation with wild type sequence
viral pseudotype virus
proteins/capsid from one virus and genome of different virus
T/F recombination (both homologous and nonhomologous) only occurs in bacteria
false;
homologous and nonhomologous recombination can occur in both bacteria and viruses
T/F we can utilize genetic engineering to engineer bacteria to help humankind.
True
ex: E. coli can produce insulin; there are yeast that present hepatitis B surface proteins for use in vaccines
T/F animals, insects, humans, birds, the environment, etc. are all separate
False
all are connected through the ecosystem
What is the One Health Initiative?
a coordinated effort between the AMA, AVMA, American Society of Tropical Med, CDC, USDA, US National Environmental Health Association, scientists, physicians, vets, acknowledging that human health, animal health, and ecosystem health are inextricably linked.
Why did we see such a decrease in the more prominent diseases in the 70s and 80s?
vaccine development and changes in attitude toward vaccine use
increased use –> increased herd immunity
why was there a slight uptick in TB cases?
drug resistance and immunocompromised hosts (HIV/AIDS victims)
Why are some vaccination protocols working and some aren’t?
high variety of serotypes?
