cardiff exam-style questions Flashcards
why is the bacterial DNA circular unlike eukaryotic DNA?
because in bacterial DNA, the 5’ end is attached to the 3’ end which forms the circular nature of bacterial DNA
what’s the difference between gram negative and positive bacteria
compare in terms of cell wall/plasma membrane/gram stain/lipid & protein content
how do you differentiate gram positive and gram negative?
via gram staining procedure:
- Gram-positive, the low lipid concentration is important for the retention of the complex iodine-crystal violet: the cells remain blue
- In Gram-negative, the high lipid concentration found in the outer layers of the cell wall is dissolved which facilitates the release of the iodine-crystal violet complex leaving the cell colourless.
what are the major amino acids that make up the cell wall of bacteria (peptidoglycan layer)?
- n-acetyl muramic acid
- n-acetyl glucosamine
how does the cell wall (peptidoglycan layer) form in bacteria?
penicillin binding proteins help in the final assembly of the outside membrane via the high molecular weight polymer of (n-acetyl muramic acid/glucosamine) attached to several amino acids attached to n-acetyl muramic acid molecules
what types of chemotherapeutic antibiotics are there?
- intracellular
- glycopeptides
- beta lactams (PBP inhibitors)
what are the types of beta lactam antibiotics
- penicillins
- cephalosporins
- monobactams
- penems
- carbapenems
- beta lactamase inhibitors
what is the chemical composition of plasma membrane of bacteria
40% lipid
60% protein
small amount of carbohydrates with no sterols
what is the function of the cytoplasmic membrane?
- Effective permeability barrier of the cell regulating the inflow and outflow of metabolites to, and from the protoplast.
- the proton motive force that generates adenosine triphosphate (ATP; energy)
what facilitates the release of iodine crystal violet complex in gram negative during gram procedure?
the high lipid concentration in the outer layer of the cell wall
what is the function of efflux proteins in bacteria’s cytoplasmic membrane?
use chemical energy to transport molecules
compare and contrast:
bacterial vs eukaryotic ribosomes
define plasmid
a short length of extrachromosomal DNA, they play an important role in the transfer of genetic material between bacteria.
true or false
The chromosome exists as a closed circle in all bacteria and is not surrounded by a nuclear membrane.
true
Many bacteria form and store granules in their cytoplasm in the form of high molecular weight polymers. what are they?
- glycogen: a storage form of both carbon and energy
- polymer of β-hydroxybutyric acid (storage form of both carbon and energy)
what molecules can be stores as inclusion granules in bacteria?
- phosphate as polymeric phosphate volutin
- protein crystals such as those of Bacillus thuringiensis
look at the different targets of each antibiotic
just look at them again
what is the function of flagella
enables movement and chemotaxis
what is Pili (fimbriae)?
very fine, hair-like, surface filaments, consist of protein sub-units wound around one another generating a hollow core.
Pili can be separated into a number of types based on their function, list its functions
- adherence: both to one another and to foreign cells (e.g. red blood cells)
- antigenic
- genetic exchange (gene transfer) by conjugation:
- attachment sites for bacteriophages
- Chemotaxis
- virulence: toxin
bacteria divide by binary fission in 4 steps
- elongation and DNA replication
- cell membrane and cell wall divide
- cross wall forms completely around DNA
- cell separation
in binary fission, the daughter cell is identical to ________ cell
mother cell
define bacterial growth
Change in the population rather than an increase in the size or mass of the individual bacterium
explain what happens in each phase of bacterial growth
explain what happens in the exponential growth phase in bacterial growth
One cell divides producing 2 (‘daughter’) cells.
Total population b at the end of a given period (starting with 1 cell)
b = 1 x 2n
a bioreactor to which fresh medium is continuously added, while culture liquid is continuously removed to keep the culture volume constant. What is the name of the bioreactor?
chemostat
what does a chemostat achieve?
- controlled growth rate
- optimised production
- continuous fermentation
- batch fermentation
what are the chemical and physical requirements for the growth of bacteria?
Chemical: oxygen, sulfur, phosphorus, ions,carbon,nitrogen,electrons
Physical: temperature, pH, high water activity
how do you prevent microbial growth
- extreme pH > 8
- -20C deep freeze of raw materials
- 8-12 syrups/eye drops
- 80C for WFI
low pH results in spoilage by ___________ e.g. fruit juice flavoured syrups
mould and yeast
Water activity of aqueous formulations can be lowered to decrease microbial growth to ________
Aw = 0.86
define sterile pharmaceutical products
Preparations required to be sterile on the dosage form and other preparations labelled sterile
what is considered a non-sterile pharmaceutical product
- topical products/resp products
- oral/rectal administration
- herbal medicines
- natural product/raw
what is a viable count?
The viable count referred as to the number of colony-forming units (cfu)
list the plate count methods
- pour plate
- spread plate
what type of filter is used for aqueous, oily and weakly alcoholic solutions in bacterial enumeration?
Cellulose nitrate filter (0.45 µm membrane filters)
what filter is used for strongly alcoholic solutions in bacterial enumeration?
Cellulose acetate
how do you get the total cell count/mass/density/activity?
- Cell count Directly by microscopy or electronic particle counter
- Cell mass Directly by weighing, measurement of cell nitrogen; measurement of dry weight (oven)
- Spectrophotometric measurement Measurements of turbidity, optical density
- Cell activity Indirectly by relating the degree of biochemical activity to the size of the population
what Rapid Microbiology Methods (RMM) are there?
- growth based methods
- direct measurement
- cell component analysis
what are examples of growth based RMM?
what are examples of direct measurement RMM
what is an example of cell component analysis RMM?
nucleic acid amplification technique (NAAT)
why are the classifications of life based on RNA
because rRNA is present in all living cells thus they can be classified into similar categories
what are the three domains of life
- eukaryotic
- prokaryotic
- archaea
staphylococcus aures
state the genus and the species
genus: staphylococcus
species: aures
what are the traditional and newer bacterial identification techniques?
traditional:
- cultivation growth: requirement
- selective agar
- biochemical profiling
- serological testing
New:
- nucleic acid techniques
- MALDI TOF
what are the rapid bacterial identification methods?
- serological testing
- nucleic acid techniques
- MALDI TOF
what is pure culture?
a culture containing a growth of a single kind of organism free from other organisms and is dependent on its growth requirements
what does pure culture help identify?
- Morphological characterisation
- Shape (cocci, bacilli, etc)
- Staining characteristics endospore production flagella capsule
what is selective media?
provide an example of a type of selective media
suppressing the growth of all bacteria while promoting the growth of only one selected type
e.g. MacConkey agar/ vogel johnson agar
what is biochemical profiling based on?
provide examples of biochemical profiling
- growth requirements of the organism
- enzymatic activities
e.g. sugar fermentation/oxidase production/hydrogen sulfide production
what are the positives and negatives of cultivation?
how does serological testing work? provide an example of a serological test
Uses highly specific antibody (Ab) antigen (Ag) interaction
e.g Enzyme Linked Immunosorbent Assay (ELISA)
how does Enzyme Linked Immunosorbent Assay (ELISA) work?
- Sensitive: signal amplified by conjugate enzyme
- Quantitative (linked to the concentration of antibodies (intensity of colour depend on antibody concentration)
what are the positives and negatives of serological testing?
what are Polymerase Chain Reaction (PCR)?
Polymerase Chain Reaction (PCR) based techniques allow amplification of a known gene of interest for nucleic acid sequencing, allows accurate identification of genus/species
how do PCRs work?
- Gene sequence is compared with online database e.g. NCBI (National Center for Biotechnology Information)
- BLAST tool finds regions of similarity between your sequence and those identified previously
- Gene sequence is then compared with online database e.g. NCBI (National Center for Biotechnology Information)
what are the positives and negatives of pcr tests
how do microarrays work in the identification of bacteria?
what does whole genome sequencing tell you?
- bacterial identification
- metabolism
- growth requirements
- pathogenecity
what does MALDI-TOF stand for
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry
how does MALDI TOF work?
- bacteria mixed with matrix material
- bombarded with laser pulses
- Sample is ionised and passed through electrostatic field (acceleration)
- Ions pass through flight tube before hitting detector
- Generates a unique mass spectrum for different bacteria
- check spectrum with database
what are the advantages and disadvantages of maldi tof
what species are capable of sporulation?
bacillus
clostridium
Spores enable the survival of the bacterium (genetic material) during harsh conditions such as ________
lack of food& water
chemical and physical stress
draw an endospore
define sporulation
the formation of spores
is sporulation a reproductive process?
NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
you’ll remember that for sure
what is germination
Germination is the process by which a spore reverts into a (vegetative) bacterium
Germination can be forced to occur using certain chemicals called germinants such as_______
D-alanine
talk about the stages of sporulation/germination
what are the properties of spores
- highly dehydrated
- no metabolic activity
- constituents (e.g. small acid soluble proteins, SASPs; dipicolinic acid)
- structure (lots of coats)
how are spores eliminated?
High-level disinfection: kill (99.999% reduction or 5 log10 reduction in viability) of micro-organisms including spores
what is the function of spore coats in an endospore?
barrier to biocides
what are the properties of inner membrane of endospores?
- highly compressed
- barrier to biocides
- barrier to rehydration
what does the spore core contain?
Small Acid Soluble Proteins (SASPs) that Protect nucleic acid and low water content 10-30%
process that kill all micro-organisms including spores
sterilization
The use of broad spectrum chemotherapeutic antibiotics is associated with an increased risk of developing ___________
C.diff associated disease (CDAD)
Chlamydia are obligate intracellular bacteria, what does that mean?
they lack the metabolic pathway to produce their own high-energy phosphate compounds (“energy parasites”)
what are the forms of chlamidya
- the small (300-400nm) extracellular infectious elementary body (EB)
- the larger (800-1000nm) intracellular non-infectious reticulate body (RB)
describe the structure of chlamidya
- internal and external membrane similar to Gram-negative bacteria
- no peptidoglycan layers
- lipopolysaccharide
- no flagella and non-piliated
how is chlamidya treated?
- Tetracyclines: doxycycline 100 mg bds; 7 days
- Macrolides: azithromycin 1g: single dose.
explain how chlamidya infections occur
- Elementary Body are metabolically inactive and represent the extracellular C. trachomatis growth form. EB are highly infectious
- Once ingested into a phagosome, fusion of the phagosome with the host lysosome is prevented
- The EB reorganizes within the phagosome into a metabolically active (not infectious) Reticulate body
mycobacteria is a gram positive bacteria
remember that
explain and draw the structure of mycobacteria
- highly hydrophobic cell wall (peptidoglycan connected to arabinogalactan) esterfied to mycolic acid structure
- 25% of the dry weight is free lipids located outside the outer layers
- cord factor (6,6”-dimycolate of trehalose)
what is mycolic acid found in mycobacteria
High-molecular-weight (60-90 carbons) 3-hydroxy fatty acid.
what lipids are there in mycobacteria
- waxes
- , species-specific mycosides (complex glycolipids and peptidoglycolipids
- lipopolysaccharides
- cord factor (6,6”-dimycolate of trehalose)
who are at risk of TB?
- close contact
- places where TB is common
- immunocompromised
- poor lifestyle factors
- young children/elderly
what are the first line of treatment for TB
isoniazid, rifampicin, pyrazinamide, ethambutol
why are Anti-TB drugs always prescribed in combination
to reduce the risk of the TB bacilli becoming resistant to one or more of them
why is It vital that TB medication is taken as prescribed
. Taking anti-TB medication in the wrong dose, intermittently or for too short a time can result in the development of drug resistance
why is necessary that a course of anti-TB drugs lasts for at least six months?
because the medicine is most effective against bacilli that are “awake” and growing.
define Infectious diseases
also known as transmissible diseases or communicable diseases comprise clinically evident illness, resulting from the infection, presence and growth of pathogenic biological agents in an individual host organism.
what are the determinant factors of an infectious disease?
- Adhere to colonise or invade the host.
- Multiply or complete its life cycle on or in the host or the host’s cells.
- Initially evade the hosts defence mechanism.
- Possess the mechanical, chemical, or molecular ability to damage the host.
what is an opportunistic pathogen
normal flora, able to cause disease at a time of immune compromise
what does asymptomatic carrier mean
pathogenic organisms that may be present in a large percentage of the population without causing disease (not microflora)
what bacteria can one be an asymptomatic carrier to
clostridium difficile
Methicillin resistant Staphylococcus aureus
the degree or intensity of pathogenicity of an organism is known as
virulence
a microbial (bacteria, fungi, protozoa…) product that contributes to virulence is known as
virulence factor
what are the virulence factors of E.coli
- Adhesin - colonization factor (CFA1, CFA2)
- Endotoxin- lipopolysaccharide (pyrogen)
- Exotoxin - heat-labile (LT) enterotoxin - Vero cytotoxin-producing E. coli (VTEC) e.g. E. coli O157
- Invasin (uropathogenic E. coli)
- Capsule - evade phagocytosis
is antibiotic resistance a virulence factor?
NOPE NOPE NOPE AND NOPE
define Toxin
substance produced by an organism to damage the host
what types of toxins are there and what’s the difference?
Exotoxin Usually proteins released by bacteria as it grows and divides. small amounts cause disease,antigenic, unstable
Endotoxin - Bound to bacterium and is released when the bacterium lyses - Gram-negative bacteria; lipopolysaccharide (lipid A)
what bacterial exotoxins are there?
- neurotoxins
- enterotoxins
- cytotoxins
how do exotoxins mediate their effects?
- membrane damaging
- membrane acting
- intracellular
provide examples of exotoxins and their mechanism of action
what are the properties of endotoxins?
- weakly immunogenic
- stable
- capable of producing general systemic effects
- toxic at high doses
what do the lipopolysaccharides of gram-negative bacteria constitute
- lipid A (responsible for toxicity)
- core polysaccharide (intermediate)
- o specific side chain (antigenic outermost)
what is capsule in bacteria?
Loose-fitting, gelatinous structure that surrounds some bacteria.
what is the function of bacterial capsule?
- prevents phagocytosis
- water protects against dessication
- protection against detergents
where are the virulence genes located within the bacteria?
chromosomes / plasmids
what is the function of virulence genes in plasmids?
- export of virulence factors directly into cells
- Confer a variety of virulence traits (e.g. cell adherence, cell entry, toxins)
- radical changes in bacterial-host interactions
list all 22 antibiotic classes
a comparison of the amount of a therapeutic agent that causes the therapeutic effect to the amount that causes death (in animal studies) or toxicity (in human studies)” is known as
Therapeutic index/therapeutic dosage level
Therapeutic index = TD50 / ED50
what is td50 and ed50
TD50: dose that produces a toxicity in 50% of the population ED50: minimum effective dose for 50% of the population
Higher the therapeutic index, the more effective and less toxic the antibiotic
yes
provide examples that are NOT contraindicated in penicillin allergy
Amikacin
Minocycline
Azithromycin
Moxifloxacin
Chloramphenicol
Nitrofurantoin
Ciprofloxacin
what antibiotics are high risk of causing CDAD
list bacteria that have developed resistance
what’s the difference between intrinsic and acquired resistance?
intrinsic resistance: natural property of a micro-organism
Acquired resistance: can be transferred between bacteria
what are the mechanisms by which bacteria confer resistance to antibiotics?
intrinsic: a natural property of the microorganism
Acquired resistance: can be transferred between bacteria
what are examples of intrinsic bacterial resistance?
- impermeability barrier (change in permeability)
- efflux
- enzymatic inactivation
what are examples of acquired bacterial resistance?
- decreased uptake/permeability
- decreased accumulation (efflux)
- enzymatic inactivation
- duplication & overproduction of targets
- modification of target site
- bypass of a metabolic pathway/enzyme
which domain of life do fungi belong to
eukaryotes
what are the properties of fungi?
eukaryotic
spore-bearing
absorptive nutrition
no chlorophyll
reproduce sexually and asexually
cell wall made of chitin (polysaccharide)
what’s the difference between saprophytes and parasites?
Saprophytes: live on dead plant and animal material
Parasites: live on/in living material
name 3 types of fungal metabolism
- Aerobic (e.g. generate ATP from glycolysis)
- Facultative anaerobes-fermentation (make ethyl alcohol from glucose)
- Obligate anaerobes (rumen of cattle)
90,000 fungal species -only approx. 50 cause human diseases
Read that again, 50
define mycoses
a disease caused by infection with a fungus, such as ringworm or thrush
who are the risk patients of fungal infections?
- immunocompromised
- chemotherapy/radiotherapy
- indwelling catheters
- corticosteroid treatments
- surgery
name two opportunistic fungal pathogens
aspergillus fumigatus
candida albicans
name a systemic fungal disease and its pathogen
Blastomycosis caused by → Blastomyces dermatitidis
what type of fungal infection is athlete’s foot and what fungus causes it
it is a cutaneous fungal infection caused by trichophyton rubrum
what causes Black piedra and what type of mycosis is it?
superficial, affecting the scalp, and caused by Piedraia hortae
what is candidiasis
a systemic fungal infection
how do fungal infections spread?
Fungal spores (moulds) - Inhaled - Cut or wound
Direct contact (yeast)
what are mycotoxins?
naturally occurring toxins produced by certain moulds (fungi) and can be found in food.
what are the outcomes of mycotoxins
- intoxication (digestion)
- allergies
- infection
provide examples of contagious cutaneous dermatomycoses
and non-contagious subcutaneous dermatomycoses
contagious: Tinea pedis, Tinea capitis, Tinea corporis
non-contagious: sporotrichosis, chromomycosis,
list some Non-contagious systemic infections
- aspergillosis
- blastomycosis
- cryptococcosis
- histoplasmosis
- sporotrichosis
describe oral thrush
- White deposit on the tongue, oral cavity
- Most common: acute pseudomembranous candidiasis
- Asymptomatic lesions
how is candida diagnosed
- Identification of clinical signs and symptoms
- Presence of candida on direct examination
- Biopsy examination showing hyphae in the epithelium
- Positive culture
- Serological tests
how is candida albicans cultured?
on a Sabouraud glucose agar, 25°C
candida albicans is an opportunistic pathogen, what makes it manifest as a disease?
disruption of microflora
candida albicans is dimorphic, what does that mean?
Can change from yeast form to mycelial, depending on environmental factors: nutrients, CO2 ,temperature
true or false
candida albicans are strict aerobes
true
what is chitin (cell wall of fungi)
natural polymer of n-acetyl glucosamine
how much of the cell wall does chitin make up?
80%
why is chitin a good antifungal therapy target?
because chitin is absent in mammalian cells, meaning the drug (caspofungin) will not be toxic to human cells
what is the function of ergosterol in fungal cells?
it is synthesized for incorporation in plasma membrane that limits the permeability of the membrane
this makes the cytoplasmic membrane sensitive to antimicrobial agents which either block the synthesis of ergosterol (e.g. azoles) or bind specifically to the ergosterol (e.g. polyene antifungals)
how does yeast reproduce?
by budding, producing daughter diploid cells that are identical to mother cell with no genetic diversity
what species of aspergillus are the most common causes of aspergillosis?
aspergillus fumigatus
aspergillus flavus
what is pulmonary aspergillosis?
opportunistic infection that gains entry through the respiratory tract that may cause an allergic response (mycotoxins), it can spread to other organs
who is at risk of aspergillosis
- immunocompromised
- neutropenia
- leukemia
- chemotherapy
- corticosteroid treatment
Hyphae can be _______ or crossed walled-septa
continuous
define hyphae
Long branched thread-like filaments of cells
when do yeast reproduce sexually and asexually
when starved: sexual (fusion)
when there’s plentiful food supply: asexually (budding)
what makes antifungal therapy difficult?
Similarity to human
Drugs tend to be more toxic
Repeated applications
Lengthy treatments
are the drug targets for antifungals?
ergosterol
chitin
b-1,3 glucan synthase
membrane sterols
what is the mechanism of action of itraconazole
inhibits cytochrome P450 14α-demethylase (P45014DM), Enzyme required in the sterol biosynthesis pathway, prevents lanosterol methylation to ergosterol, thus lessening the amount of ergosterol in cell wall leading to membrane instability, growth inhibition, and cell death
what is the mechanism of action of amphoterecin B
binds ergosterol, the dominant sterol in fungal cells, increasing membrane permeability by formation of pores allowing escape of intracellular potassium, magnesium, sugars, and metabolites
what are the toxicity problems caused by amphoterecin b
cardiovascular
renal
hepatic
what are the properties of protozoa
- eukaryotic
- unicellular
- heterotrophic
- parasitic (commensal)
- live in aqueous environments
provide 3 examples of protozoal diseases and their pathogenic cause
Giardiasis → Giardia intestinalis
Amoebiasis → Entamoeba histolytica
malaria → plasmodium vivax
what are the Plasmodium-ameboid intracellular parasites
P. vivax, P. falciparum, P. malariae
how is malaria prevented?
- mosquito control
- prophylaxis drugs and exposure
- rapid identification
what drugs can be used for prophylactic treatment of malaria?
- Chloroquine
- Mefloquine
- Doxycyline
- Malarone
what types of treatments are there for malaria?
- Artemisinin-based combination therapy (ACT)
- co-formulated drugs (Malarone or riamet)
For P. falciparum two or more drugs with different modes of action in combination are now recommended, why?
Combination therapy to prevent malaria parasite’s resistance from developing
what are companion drugs of ACT
lumefantrine, mefloquine, amodiaquine
what do Artemisinin derivatives include
dihydroartemisinin
artesunate
artemether
define co-formulated drug
one in which two different drugs are combined in one tablet
what is the mechanism of action of malarone?
Proguanil interferes with two different pathways involved in biosynthesis of pyrimidines (cytosine, thymine, uracil) required for nucleic acid replication.
Atovaquone -Inhibit electron transport chain
what is the mechanism of action of riamet?
Interferes with the ability of the malaria parasites to convert heme into hemozoin.
Causes levels of the toxic heme to rise, which kills the blood stages of the malaria parasites
how is Cryptosporidiosis transmitted?
fecal-oral route
how is Cryptosporidiosis diagnosed?
stool sample
how do you treat Cryptosporidiosis
- Fluid and electrolyte replacement
what are the symptoms of Cryptosporidiosis
abdominal pain
diarrhea
nausea
what organism causes Cryptosporidiosis
Cryptosporidium parvum, hominis
who is a risk patient for severe Cryptosporidiosis
HIV patients
what organism causes Amoebiasis
Entamoeba histolytica
describe amebiasis
- range from mild diarrhea to dysentery with blood and mucus in the stool.
how is Amoebiasis transmitted?
fecal-oral route
how is Amoebiasis diagnosed
stool sample
what are the forms of severe Amoebiasis
- Invasion of the intestinal lining causes amoebic dysentery or amoebic colitis.
- Parasite reaching the bloodstream and becoming systemic, most frequently ending up in the liver where it causes amoebic liver abscesses
how do you treat amoebiasis?
- Metrodinazole
- Tinidazole
- Diloxanide fluorate (Asymptomatic patients)
what are helminths?
Parasitic worms
what are the transmission routes for helminths
Schistosome or hookworm larvae directly penetrate the skin from infected water or soil
Filarial worms (e.g. Onchocerca) transmitted by insect vectors
what are examples of helminthic infections
- Schistosomiasis (bilharzia)
- Cysticercosis
- Lymphatic filariasis (elephantiasis)
- Onchocerciasis (river blindness)
what is a major risk for developing helminth infections
inadequate sanitation
what are the general symptoms of helminthic infections
- asymptomatic (a few roundworms). \
- reduced nutritional uptake
- intestinal obstruction or bleeding
- rectal prolapse
- presence of a worm within vomit or stools.
how do tapeworms gain entry to human body
ingestion of uncooked meat (eggs)
talk about the life cycle of helminths
name two antihelmintic drugs and their mechanism of action
Praziquantel: Increases membrane permeability to calcium ions, paralyzing the parasite
Mebendazole: Inhibits the synthesis of microtubules, glucose uptake
true or false
viruses are acellular, they are only carriers of genetic material (RNA/DNA)
true
how are viruses classified?
enveloped
nonenveloped
viruses are obligatory intracellular parasites, what does that mean?
they require a host for replication
true or false
viruses cause diseases in all living organisms, including bacteria
true
what is the viral envelop?
surrounds the viral capsid, derived from portions of the host cell membranes
true or false
enveloped viruses can survive longer when mixed with fomites (blood/mucus)
true
what is the viral capsid
s the protein shell that encloses the nucleic acid. It is built of structure units known as capsomeres
what forms of capsid are there
icosahedral
helical
define viral receptors
Glycoproteins (virus encoded) on the surface of the envelope or protruding from the capsid serve to identify and bind to receptor sites on the host’s membrane
how do viruses gain entry to the host cell
endocytosis
fusion
describe the properties of the viral genome
Either RNA or DNA but can be single or double stranded, circular or linear
describe the steps in the virus life cycle
- attachment and penetration
- uncoating and macromolecular synthesis of nucleic acids
- assembly of progeny virions and release into host cells
define antigenic shift
Process by which two or more different strains of a virus, or strains of two or more different viruses, combine to form a new subtype having a mixture of the surface antigens of the two or more original strains
what types of influenza reassortment are there
antigenic drift
antigenic shift
define antigenic drift
Small changes (mutations) in the virus that happen continually over time, Difficult to immunise/vaccinate for long term protection
what is herpes virus latent infection
when it persists in a quiescent but persistent form in the neural ganglia
how does HSV infect the mucosal epithelia?
- Productive replication, production of progeny virions and virions spread to infect additional epithelial cells
- Virus enters innervating sensory neurons, and nucleocapsids are transported to the neuronal cell body
- Viral DNA is released into the neuronal nucleus and circularizes
- Circular viral DNA persists in the neuronal cell nucleus
how is HSV reactivated
- Initiation of viral lytic gene expression
- Newly formed capsids are transported to the axonal termini
- Infectious virus is released from the axon and infects epithelial cells leading to recurrent infection and shedding
what type of viruses are coronaviruses
Enveloped, positive-sense RNA viruses
true or false
coronaviruses are responsible for up to 30% of common colds
true
Coronaviruses use a viral__________________ enzyme to synthesize mRNA
RNA-dependent RNA-polymerase
_________ mediates RNA proofreading and regulate replication fidelity
Viral RNA exonuclease
why are coronaviruses able to produce new strains that often cause pandemics?
Combination of RNA recombination, high polymerase error, and regulated replication fidelity appears to favor the generation of recombinant and highly diverse populations of viruses with the potential to cross species and subsequently adapt to new hosts
how does RNA-RNA recombination occur?
“jump” across an RNA template or between two different templates
SARS-CoV is a zoonotic virus likely derived from _____
bats
what does MERS-COV stand for
Middle East respiratory syndrome
_____________ may be a major reservoir host for MERS-CoV
Dromedary camels
SARS-COV-2 resulted in a pandemic in the year of ______
r u serious? 2020
what are the properties of HIV
- retrovirus
- infects CD4+ and destroys them
- severely weakens immune system
define AIDS
Defined as an HIV infection with either a CD4+ T cell count below 200 cells per µL
or
the occurrence of specific diseases associated with HIV infection
how is HIV transmitted
Unprotected sex
Sharing needles, syringes or other injecting equipment
Transmission from mother to baby during pregnancy, birth or breastfeeding
primary HIV is asymptomatic or associated with _________
acute retroviral syndrome
describe the stages of HIV
To design a drug, one needs to understand virus life cycle.
describe the life cycle of HIV
what do antivirals target
virus specific enzymes
life cycle processes
what is the aim of HIV antiviral therapy
reduce viral levels (viral load < 50copies/ml) and reduce AIDS-related illnesses
what is the mechanism of action of zidovudine
zidovudine is nucleoside reverse transcriptase inhibitor, which acts as a nucleoside analogue , it prevents any more DNA from being made - by blocking further extension of the growing DNA chain.
it does so by inserts a molecule of zidovudine rather than a nucleoside, This terminates the DNA chain and no more can be appended to
what is the mechanism of action of non nucleoside reverse transcriptase inhibitors? provide an example of an NNRTI
NNRTIs attach to the reverse transcriptase and affect the activity of the enzyme by restricting its mobility and making it unable to function
Example: Efavirenz
what is the function of viral protease
an enzyme that cleaves peptide/polypeptide/protein chains
what is the mechanism of action of protease inhibitors
HIV protease inhibitors binds to enzyme active site. HIV virus is therefore unable to process proteins
what is viral integrase
an enzyme that allows the transfer of HIV cDNA to cellular DNA
what is the mechanism of action of integrase inhibitors?
provide 2 examples of integrase inhibitors
Dolutegravir
Raltegravir
define Fusion inhibitor, provide an example
an enzyme that prevent HIV envelope fusion
Enfuvirtide
a protein on the surface of white blood cells that is involved in the immune system as it acts as a receptor for chemokines (chemotactic cytokines.) this is known as
C-C chemokine receptor type 5, also known as CCR5 or CD195
what is the function of viral DNA polymerase
enzyme that creates DNA molecules by assembling nucleotides – essential for viral DNA synthesis
what drug is used to treat HSV? and what is its mechanism of action?
Acyclovir is converted by viral thymidine kinase to acyclovir monophosphate which is then converted by host cell kinases to acyclovir triphosphate (ACV-TP)
ACV-TP competitively inhibits and inactivates HSVspecific DNA polymerase
what is the mechanism of action of Neuraminidase inhibitors
prevent the release of the virions
what does prodrug mean?
an inactive drug that needs to be hydrolysed in the liver to function
oseltamivir → oseltamivir carboxylate
what makes viral diagnosis difficult?
Viruses have to be cultured in the presence of the host cell
how does plaque assay of viruses work
- Grow a lawn of host cells on dish
- Add virus
- Virus replicate and lyse host cells
- Viral Plaques: cytopathic effect
what is plaque forming units (PFU)
measure of infectivity not number of viruses
what are immunodiagnostics
Detection of host antibodies against virus
what is hemaegglutination
causing red blood cells to stick together
Presence of anti-virus _______ in patient serum can inhibit reaction
antibodies
what does Haemagglutinin Inhibition Assay (HI Test) - Inflluenza do?
- Measure how well antibodies bind to (and thus inactivate) influenza viruses
- RBCs (turkey, guinea pigs) in a solution will sink to the bottom of the assay well and form a red dot at the bottom
- When an influenza virus is added to the RBC solution, the virus’ haemagglutinin surface proteins bind to multiple RBC and keep RBCs suspended
what methods of molecular biology are used to diagnose viruses
o Viral DNA hybridisation with labelled probes
o Sequencing of portions of the viral genome
o Polymerase chain reaction
according to the baltimore classification system, list the 6 virus classes
- Double stranded DNA
- Single stranded DNA
- Double stranded RNA
- Single stranded RNA
- Single stranded RNA
- Double stranded DNA
what are the subviral agents
satellites
viroids spongiform encephalopathies
list the dsDNA viruses
Poxviruses
adenoviruses
Herpes
list the dsDNA viruses
Poxviruses
adenoviruses
Hepres
list ssDNA viruses
parvovirus
what class of viruses is Rotaviruses
dsRNA viruses
list ssRNA viruses
Togaviruses
Orthomyxoviruses
Rhinoviruses
Paramyxoviruses
Picornaviruses
what viruses are considered retroviruses
hepatitis B
HIV
what are reverse transcriptase viruses
there is an RNA intermediate before viral proteins can be manufactured.
true or false
Group VII can first transcribe their DNA into RNA, then transcribe it back to DNA (using reverse transcriptase) before it is inserted into the host DNA
true
what is the function of reverse transcriptase in retroviruses
The enzyme is responsible for transcription of the viral RNA to produce a dsDNA that can be inserted into the host genome
where is the normal flora located
stomach
small intestine
large intestine
urethra
vagina
nasopharynx
what is the metabolic function of microbiome
- Provide vital biochemical pathways for the metabolism of non-digestible carbohydrates (cellulose, hemicellulose, pectins, and gums), some oligosaccharides, unabsorbed sugars, alcohols and host-derived mucins
- Synthesis of vitamins - Enteric bacteria secrete Vitamin K and Vitamin B12
- Stimulate the development of certain tissues (Caecum; caecum of germ-free animals is enlarged, thin-walled, and fluid-filled)
what is the immune function of the microflora
- Produce antimicrobial compounds - Fatty acids and peroxides to highly specific bacteriocins.
- Compete for nutrients and sites of attachment in the gut lining, preventing colonization by pathogens (barrier or competitive-exclusion effect)
- intestinal epithelium is the main interface between the immune system and the external environment
- Exposure to intestinal bacteria is also implicated in the prevention of allergy
- The normal flora stimulates the production of cross-reactive antibodies.
what is the function of the gut brain axis
- Bidirectional communication system that integrates neural, hormonal, and immunological signalling between the gut and the brain.
- Stress influences the composition of the gut microbiota
- Stress influences the integrity of the gut epithelium and alter peristalsis, secretions, and mucin production.
what is the function of mucins
Glycoproteins that are expressed in cells
Signal transduction
Regulation of gene expression
Cell proliferation
Embryogenesis
Cell differentiation
Immunity
Apoptosis
Cancer
what is irritable bowel syndrome
Gut microbiota alteration linked to low-grade intestinal inflammation (inflammatory Bowel Disease)
what is obesity as a metabolic disease
alteration of Firmicutes/Bacteroidetes ratio in the gut microbiota
true or false
diabetes type 2 impacts the composition of intestinal microbiota
true
what are probiotics
Probiotics are microorganisms that are believed to provide health benefits when consumed.
The inflammation of the colon is pseudomembranous colitis and is generally caused by________
antibiotic associated diarrhea
C. difficile normally are indigenous bacteria, able to proliferate when most of the normal intestinal flora killed by the ________
antibiotic
why does eukaryotic DNA forms a helix?
The nucleobases in DNA have the ability to form hydrogen bonds between themselves, the poly nucleotide chain of DNA coils into a helix, which gets bonded to another helical strand by hydrogen bonds between the appropriate base pairs
what are the base pairs of DNA
In DNA, the base pairs are A-T (2 hydrogen bonds) and C-G (3 hydrogen bonds)
what is DNA made up of
long unbranched chain of oligonucleotides, which are linked via a phosphate group that joins the sugar unit with the nucleobase
The ester linkage between nucleotides is often a __________
phosphodiester bond.
phosphate group in nucleotides is attached via a ________
phospho ester linkage
nucleobase is linked to the sugar unit through an ___________ bond at C1.
N-glycoside
purines are linked through ______ while pyrimidines are linked through ________
N9
N1
what are nucleotides?
polymers of nucleic acids that are structurally made up of a heterocyclic base, sugar, phosphate
what is the most notable difference in DNA & RNA
deoxyribose in DNA and ribose in RNA
what is a nucleoside?
nucleotide lacking a phosphate group
what types of bases are there?
- monocyclic pyrimidines: cytosine, thymidine, uracil
- bicyclic purines: adenine, guanine
what type of sugar is the one in DNA/RNA
Pentoses
They are D-ribose in RNA and 2-deoxy-D-ribose in DNA
describe the structure of DNA
- bases are directed inwards to allow hydrogen bonding (base pairing)
- sugar units and the phosphodiester bonds will of the main chains form the outside part of the double helix
- The helix makes a complete turn every 10 bases
- The chains are antiparallel
how do the minor/major grooves form
because the glycoside bonds between the sugars and bases of a particular base pair are not directly opposite to each other, grooves along the outside of the double helix array are unequal in with giving rise to what is known as the minor groove and major groove
DNA replication proceeds in 3 enzymatically mediated steps known as
- initiation
- elongation
- termination
DNA replication is initiated in DNA regions known as ______
origins
what is the function of helicases in DNA replication
break the hydrogen bonds that ‘bind’ the DNA stands together
DNA synthesis is catalyzed by __________ enzyme
DNA polymerase
how is termination achieved in DNA replication
blocking the replication fork and this is often achieved by DNA replication terminus site binding proteins
The precursors for the synthesis of new DNA strands are___________
nucleoside triphosphates
triphosphate anhydrides are susceptible to nucleophilic attack from _______
hydroxyl groups
true or false
DNA chain extension is simply an esterification reaction of the 3’-hydroxyls using the triphosphate anhydrides that have the diphosphate as a good leaving group
true
how does RNA differ from DNA?
- . The sugar in RNA is ribose while in DNA its deoxyribose.
- Thymine is replaced by uracil in RNA.
- RNA is usually single stranded.
- DNA stores genetic information and RNA participate in the processes by which this information is used.
what are the three major forms of RNA found in prokaryotic cells
- mRNA
- tRNA
- rRNA
It’s the sequence of bases along one DNA strand which provides information for the synthesis of proteins in an organism. this is known as?
the coding strand
what is template strand
a complementary strand to the coding strand
DNA segment that contains the information necessary for the synthesis of one protein.
who am i?
gene
a sequence of 3 nucleotides
codons
true or false
Every amino acid is designated 2 or 3 specific triplet codons
true
what are stop codons
Three different codons which stop the translation process
Describe the stereochemistry of amino acids
Almost all amino acids contain a chiral centre on the alpha carbon. All naturally occurring amino acids have L-stereochemistry, i.e. they have the same configuration as the reference compound glyceraldehyde. D-amino acids are very rare, and are the product of biosynthesis
Explain what is unusual about the stereochemistry of glycine. Explain your answer
Glycine has no chiral centre and therefore cannot exist in L/D-forms. The alpha carbon does not have four non-identical groups attached, two are hydrogen (i.e. identical)
Provide a concise definition of a peptide
A small protein containing 50 or less amino acid residues
Briefly describe the nomenclature of peptides
. Peptides should be named, using three letter or single letter amino acid abbreviations starting from the N-terminal residue and listing sequentially to the C-terminal. Abbreviations separated by dashes
Consider the decapeptide (below) and answer the following questions: Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp
a) Name the N-terminal amino acid.
b) Name the C-terminal amino acid.
a) lysine
b) asparatic acid
State the side chain property of each amino acid in the peptide
Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp
Lys – basic;
Ala, Val, Leu and Ile – hydrophobic;
Ser – polar;
Asp – Acidic
Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp
Would you predict this peptide to be water soluble? Briefly explain your answer.
Will have some water solubility, although mostly non-polar amino acids there are three polar aa’s, two of which form a salt. OR – will not be soluble in water as 7 non-polar aa’s versus 3 polar.
) Describe the structure of a globular protein
Compact (tightly folded), roughly spherical, structurally complex, comprised of many elements of secondary structure, e.g. alpha helix, beta sheet, often clearly defined active site / cleft, internal bonding to maintain structure, e.g. disulfide bridges etc etc
Give an example of a globular protein.
trypsin (any enzyme)
Describe the general properties of a globular protein
c. Hydrophobic interior, hydrophilic exterior, water soluble, often function as catalysts
Describe how the three dimensional structure of a globular protein is maintained
ionic interactions, hydrogen bonding, hydrophobic interactions, covalent crosslinks
why isn’t the alpha helix considered a double helix?
The alpha helix is a single peptide backbone coiled around itself and stabilised by intra-strand H-bonds. [By contrast, DNA is an example of a double helix – two chains stabilised by inter-strand H-bonds]
why does the peptide bond usually adopts a trans conformation
Cis-amide bonds force unfavourable steric interactions between aa side chains and are not commonly found in proteins
why are antiparallel beta sheets more stable than parallel beta sheets
because the network of inter-strand H-bonds are better aligned and more stable in the anti-parallel type.
what is Native conformation.
biologically active form of the protein
what are Non-essential amino acids
An amino acid that can be biosynthesized with the body and therefore is not essential in the diet. E.g. Ala, Gly, Pro, Ser etc. It requires energy and raw materials to synthesize aa’s so in practice these are obtained from diet whenever possible
what is a Cyclic peptide.
A polypeptide joined via an amide (peptide) bond between the N and C terminal amino acids creating a continuous cyclic peptide backbone. Have pharmaceutical use. E.g. ciclosporin, a microbial cyclic peptide that contains non-coding biosynthesized amino acids. When non-amino acid groups are incorporated known as a pseudo-peptide
. Very briefly describe how enzymes function as catalyst
…by lowering the activation energy barrier to the reaction. Achieved by precise orientation of the substrate in the active site in a reactive conformation and provide missing functional groups or cofactors for the reaction. Enzymes provide the reaction ‘template’
Briefly describe how enzymes are named and classified. Illustrate your answer with suitable examples
Two methods, trivial and systematic. Trivial – name associated with the function or substrate (or both) is suffixed with –ase. E.g. L-dopa decarboxylase or DNA polymerase. Systematic system (enzyme commission: EC) assigns a unique serial number comprised of 4 digits. First digit is one of the six classes (list them) followed by two sets of sub classes and finally the unique identifier, e.g. alcohol dehydrogenase = EC1.1.1.1.
Many enzymes require cofactors for their biological function. Discuss this statement using alcohol dehydrogenase and another enzyme of your choice to illustrate your answe
. The 20 amino acids that occur naturally in proteins have limited functional groups / chemistry in their side chains. Co-factors, which can be metal ions or organic molecules (co-enzymes) supply this chemistry. Alcohol dehydrogenase uses two co-factors, a zinc ion and a NAD+ coenzyme. The zinc aligns the substrate in the active site to the –OH group. The NAD+ contains a functional group that accepts a proton (i.e. dehydrogenation)
e L-Dopa decarboxylase. The enzyme uses a co-enzyme (pyridoxal phosphate/vitB6) to facilitate the removal of a carboxylic acid. The co-enzyme contains an aldehyde functional group – not found in amino acids – to form an intermediate (imine) with the substrate etc etc.
Briefly discuss the importance of metals in protein function. Give one example of a protein that requires a metal atom to function
Proteins containing metal ions are known as metalloproteins or metalloenzymes if they have a catalytic function. The 20 amino acids that occur naturally in proteins have limited functional groups / chemistry in their side chains. Co-factors, which can be metal ions or organic molecules (co-enzymes) supply this chemistry. Metals are important in transport proteins (e.g. haemoglobin, Fe required to bind, store then release O2, four Fe atoms held in 4 prosthetic haem groups etc etc). Alcohol dehydrogenase and Zn etc etc
mRNA synthesis also known as transcription is mediated by the enzyme _______
RNA polymerase
The synthesis of mRNA from the DNA template is called _______
Transcription
Ribosomes are made up of 2 subunits termed S50 and S30, which are combinations of ________and proteins
rRNA
