Week 1 Flashcards
Name the three different types of capsids for viruses
Icosahedral
Helical
Complex
What are the three basic functions of a capsid?
Protect genetic material
Aid entry into cell
Package of viral enzymes
Icosahedral capsids are composed of repeating subunits Called ___. These subunits are each composed of 5-6 individual protein structures called ____
Capsomere
Protomer
What are ‘spikes’?
Glycoproteins embedded in the envelope of viruses that function to attach viruses to host cell membranes
What is tegument?
A layer of proteins between the envelope and capsid of enveloped viruses. It serves to attach the envelope to the capsid and can be involved with delivering viral genetic material/replication enzymes into cells.
It is polar
What is ambisense RNA?
Double stranded RNA that contains both positive and negative sense strands in the same dsRNA
True or false… positive sense RNA is oriented 3’-5’
False. It is oriented 5’-3’, meaning that it can be translated directly, thus is essentially mRNA
Which virus is more likely to contain RNA dependent polymerase? A virus containing negative sense RNA or positive sense RNA?
Negative sense
Under the ____ system of classification, viruses are grouped according to genetic material
Baltimore
Viruses have no means of locomotion, thus completely rely on ____ to reach cells
Collision
True or false… viruses often require coreceptors to enter a cell
True
Once the virus is inside of the cell is it considered to be in the ____ phase
Eclipse
Define uncoating
The process in which viral genetic material is placed into cells
What are the two different types of pathways in which enveloped viruses enter the cell? Also name three examples of viruses for each
Direct fusion: HIV 1, herpesviruses, paramyxovirus
Viropexis: influenza, rubella, rabies
In direct fusion, the ____ remains in the plasma membrane, allowing the ____ to enter the cytoplasm.
True or false… in direct fusion, the normal endocytic pathway doesn’t take place
Envelope
Nucleocapsid
True
Explain how viropexis works.
Basically receptor mediated endocytosis.
Here the envelope remains in fact as it crosses the plasma membrane. Once inside the cell the vesicles are in low pH environments then fuses with endosomal vesicles. (Normal endocytic pathway)
Describe how naked viruses enter the cell
Basically through viropexis except it must disrupt the endosomal vesicle because they have no envelopeto fuse with it.
The low pH in the vesicle will activate viral proteins which lyse the vesicles
What is a concatamer?
A series of repeated viral genomes. This is produced by the viral DNA folding in a way to allow replication to occur over and over again on the same DNA strand, allowing the generation of continuous RNA
What must occur to concatemers before viral genomic assembly?
Concatemers must be cleaved into single strand viral genomic DNA
List the steps for the parvirus (a DNA virus)
1) viropexis
2) host DNA polymerase 2nd strand synthesis
3) DNA replication within host cell cycle
4) mRNA generation via host RNA polymerase 2 during S phase
5) translation via host ribosomes
6) viral replication proteins return to the nucleus to pump up viral DNA replication and viral structural proteins
7) concatemers makes even more viral mRNA
8) concatemers breaks into single strand viral DNA
9) New progeny virus
Where do RNA + viruses typically reproduce?
In the cytoplasm
List the steps for a RNA + virus
1) RNA + virus enters cell and uses host ribosomes for direct translation of viral proteins
2) initial production of viral replication proteins and structural proteins in a large polyprotein precursor, which is cleaved into functional parts
3) viral RNA replication enzymes generate RNA - strand templates, which make more complementary viral RNA +
4) more viral structural proteins are transcribed
5) new progeny viruses are formed
How can RNA - viruses replicate in either the cytoplasm or the nucleus?
They bring their own enzymes (specifically RNA reverse polymerase, to form RNA +)
List the steps for RNA - virus
1) viral RNA - enters nucleus (or cytoplasm) and must utilize reverse RNA polymerase to create RNA + strands
2) complementary RNA + strands are produced using viral RNA reverse polymerase.
3) RNA + strands are either sent to the cytoplasm for translation in host ribosomes or retained and used as templates to replicate complementary viral RNA -
4) viral structural and replication proteins are transcribed
5) assembly of structural protein with RNA - (formation of new progeny viruses)
Describe the steps for a retrovirus
1) Viral RNA enters nucleus (or cytoplasm) and must use reverse transcriptase to create DNA from RNA template
2) viral RNA is reverse transcribed into DNA, using viral reverse transcriptase enzymes
3) viral DNA can replicate along with the normal cell cycle.
4) viral DNA is transcribed to form both viral mRNA and new viral RNA, using host cell machinery
5) viral mRNA is translated to form viral structural and replicative proteins
6) assembly of structural protein with viral RNA arising from reverse transcribed viral DNA
7) new virus progeny are formed
Define encapsidation
The insertion of individual viral genomes into individual capsids.
There is usually a site on the viral genome that codes for proteins intended to initiate assembly called ____
Packaging site
What is the most likely form of egression for naked viruses?
Cell apoptosis
What type of fungi is part of our normal flora?
Candida
Name three polysaccharides that make up the cell wall of fungi
Mannan
Chitin
B glucans
Instead of cholesterol, fungi have ____ in their membrane
Ergosterol
What drug destroys ergosterol?
Polyenes
What drug destroys the enzyme responsible for synthesizing ergosterol 14a-demthylase?
Azoles
What drug is responsible for targeting 1-3 B D glucan synthase in the fungal cell membrane?
Echinocandins
True or false…both yeasts and molds are always single cellular
False. Although yeasts are single cellular, molds are multicellular and filamentous
Describe what yeast colonies in culture look like
Single
Creamy, mucoid
Facultative anaerobes
Describe what mold colonies look like in culture
Fuzzy/velvety
Obligate aerobes
What is a blastoconidia?
A new bud that is budding off of a parent yeast cell
Strings of blastoconidia will form ____ whereas germ tubes will form ____.
Pseudohypha
Hypha
Usually yeast only form pseudohypha while mold form true hypha. What is the yeast that is the exception,
Because it can form both?
Candida
What are the two types of true hypha? Name a type of fungi of each type
Septate hypha - aspergillus
Nonseptate hypha - zygomycete
The sexual cycle in fungi is called ____
Sporulation
Yeasts reproduce by budding (asexual) only whereas molds can reproduce asexually and sexually. What is the term for the asexual state and the sexual state?
Asexual - anamorph
Sexual - telomorph
Describe asexual reproduction in fungi
Mitotic division of haploid nucleus
Yeast by budding
Molds by producing conidia, or by division of hypha elements
Describe sexual reproduction in fungi
Diploid nucleus divides by meiosis
Haploid nuclei of donor and recipient fertile cells fuse
Molds can also reproduce by producing spores
Define dimorphic fungi
Geographically restricted pathogens that exist as a mold at lower temperatures (environment) and a yeast at higher temperatures (body)
Name six dimorphic fungi species
Blastomyces dermatitidis Coccidiodes immitis Histoplasma capsulatum Paracoccidiodes brasiliensis Penicillium marneffei Sporothrix schenckii
Name sex examples of opportunistic fungi
Aspergillus spp. Candida spp. Cryptococcus neoformas Mucor spp. Rhizopus spp. Pneumocystis jirovecii
Name four examples of cutaneous fungi
Malassezia furfur
Epidermyophyton spp.
Microsporum spp.
Trycophyton spp.
What are the three immunity strategies to fight off fungi?
Natural barriers
Innate immunity
Cell mediated immunity
Note that antibodies are not helpful in fighting off fungi
What are the gram stain results for yeast?
Yeasts stain gram positive (violet)
What are the two most common species of candida?
Candida albicans Candida glabrata (note that this species is resistant to fluconazole)
True or false… candida species are part of our normal flora. If so, where are they found and what are some common infections?
What are some drug classes to treat candida diseases?
True
Skin, mouth, upper respiratory tract, bowels, vagina
Thrush, vaginitis, balanitis, diaper rash
Azoles (fluconazole), echinocandins (caspodungin), or polyenes (amphotericin).
Rhinocerebral zygomycosis (also referred to as mucormycosis) are rare infections from what three genus types? These thrive in high _____ and ____ environments
Mucor, rhizopus, rhizomucor
Glucose
Acidic
Rhinocerebral zygomycosis disease are ____ meaning that airborne spores are inhaled and can spread through vessels and facial planes
Angioinvasive
True or false… candida species are yeast. Mucor and rhizopus species are also yeast
The first part is true, the second is false. Mucor and rhizopus species are zygomycete species.
What is candidemia?
Systemic candidiasis
Define pancytopenia
Deficiency of all three blood types (RBCs, White blood cells, platelets)
Describe mycobacteria
Bacilli
Obligate aerobes
Cell wall - ‘waxy’ coat, high lipid content, mycolic acids, lipoarabinomannan
Acid fast bacilli (binds carbon fuchsin dye so that it is not removed by acid alcohol)
What does it mean to be acid fast?
Resistance to decolonization by acid
Name four tuberculous mycobacteria species
M. Tuberculosis (MTB)
M. Africanum
M. Bovis
M. Bovis bacille calmette-guerin (BCG)
Name four non-tuberculous slow growing mycobacteria species
M. Kansasii
M. Valium-intracellulare complex
M. Marinum
M. Scrofulaceum
Name two non-tuberculous mycobacteria rapid growing species, and one special grower
Rapid growers
M. Chelonae-abscesses complex
M. Fortuitum complex
Special grower
M. Leprae
True or false… mycobacterium tuberculosis is transmitted via the respirator route. The respiratory droplets can remain suspended in air for several hours
True
Which results in respiratory droplets being expelled the furthest and fastest, sneezing, coughing, or breathing?
Sneezing
T cells will wall off the tuberculosis infection into a structure called a ____. _____ necrosis occurs here
Granuloma
Casteating necrosis
TB remains in the latent phase but will go to the active phase usually about ___ years after exposure. When it becomes active, it will activate in the ___ portion of the lung
5-7
Superior apeces (because this is where the highest conc. Of oxygen exists).
What is a Ghon complex?
A calcified focus of infection and associate lymph node
In two step TST testing, what is the difference between the first and second test?
First test will test if the person has TB infection or not.
Second will test if the person has LTBI or not
Besides a TB skin test, what is another method for testing if the patient has TB or not? Explain how it works
Interferon-gamma release assay
The APC processes antigen, APC presents antigen to T cell, T cell produces IFN-gamma
In active TB, what is the difference between cavitation and milliary TB?
Cavitation is localized while milliary is spread
Name three clinical features of active TB
Cough and production of sputum as tissue necrosis is one of the earliest signs
Dyspnea (aka shortness of breath) - a later symptom indicating extensive involvement parenchyma)
Fever and weight loss reflecting systemic actions of IL-1 and TNF-a secreted by activated macrophages
True or false… the treatment and infection control measures for latent TB and active TB are the same
False, they are different
True or false… sterile tissue/body tissue can be used to diagnose TB. CSF, bone, pleural fluid, and blood culture can be used
False… all these can be used besides blood culture
True or false… AFB stains does not differentiate between MTB and NTM
True
True or false… nucleic acid amplification tests can be used directly from sputum
True
Describe the Ruyon classification system of NTM (non-tuberculous mycobacteria).
This is an old classification system, current identification by rRNA sequencing and/orMALDI-TOF MS
Groups based on rate of growth, production of yellow pigment, whether pigment is produced in the dark or only after exposure to light
Name the four Runyon classes?
runyon 1 - photochromogens (slow growth, yellow pigment only when exposed to light)
runyon 2 - scotochromogens (slow growth, yellow pigment in light or dark)
runyon 3 - nonchromogenic (slow growth, no pigment.
runyon 4 - rapid growers (colonies in 5 days, no pigment)
Where are rapid growers most likely to infect a host?
Skin and soft tissue as well as lung tissue
Note that these species are morphologically indistinguishable
What is a sporotrichoid?
Lymphocutaneous infection
Name two examples of Runyon class 4 species
M. Fortuitum
M. Chelonae-abcessus
Describe M. Marinum
A slow grower
Photochromogen
Grows best 30-32 C
Traumatized skin in contact with water
What is a scrofula?
Cervical lymphadenitis (slowly progressive)
What does it mean if cervical lymphadenitis is…
Acute/bilateral
Acute/unilateral
Subacute or chronic unilateral
Acute/bilateral - viral upper respiratory tract infection or streptococcal pharyngitis
Acute unilateral - streptococcal or staphylococcal infection
Subacute or chronic unilateral - bartonella (cat scratch disease), or MYCOBACTERIA infection
What runyon classification is M. Scrofulace?
Runyon 2
M. Kansasii and M. Marinum are under what runyon classification?
Runyon 1
Name some differences between lepromatous leprosy and tuberculoid leprosy
Lepromatous leprosy
Poorly demarcated, raised lesions. Sheets of foamy macrophages in the dermis containing very large numbers of bacilli (multibacillary)
Tuberculoid leprosy
Well demarcated lesions with central hypopigmentation and hypoesthesia. Granulmatous inflammation and rare acid-fast bacilli in the tissues (paucibacillary)
True or false… bacterial infections are on the rise. Why?
True
Increasing number of immunocompromised patients, increase spread of antibiotic resistant bacteria, increasing international travel.
True or false… bacteria are the oldest, most prevalent forms of life on earth
True
Define pleomorphic
Lacking a distinct shape
What is the bacteria morphology that is between vibrio and spirochete?
Spirillium
What are the four phases to binary replication?
Lag phase
Log phase
Stationary phase
Death phase
_____ ____ in biofilms allow bacteria to communicate
Quorum sensing
What is periplasmic space?
This is the space in gram negative bacteria between the cell membrane and the outer cell membrane
What bacteria do not have cell walls?
Mycoplasma
Acid-fast bacteria
Respiratory chains, secretion systems, and adhesins are located in the bacterial cell membrane, true or false
False. These are located in the cell WALL
Where would you find teichoic acid?
In the peptidoglycan cell wall of gram positive bacteria
Binding of peptidoglycan to ____ or _____ can stimulate inflammatory responses
Toll-like receptor 2 or pattern recognition receptor
In peptidoglycan, the peptide chains are attached to ____. Each peptide chain connects to another peptide chain by ____
NAM
Pentaglycine interbridge
The binding of LPS by _____ or ____ can stimulate an inflammatory response
Pattern recognition receptor
Toll-like receptor 4
The ____ on LPS is highly variable
O-chain
True or false… you will be able to see ureoplasma and mycoplasma species in gram stain
False. Because these species have no cell wall
If a bacterial species lacks a cell wall, what does it use to stabilize its cell membrane?
Sterols (cholesterol from hosts)
Note that these species will also be resistant to penicillin
Name six factors associated with bacterial cell walls
Electron transport chains Protein secretion systems Flagella Adhesins Capsules Spores
Describe facultative anaerobes
They prefer the presence of oxygen but can survive without it
The drawback to oxygen is that it can produce toxic byproducts. Name two enzymes that are used to counter this issue.
Superoxide dismutase
Catalase or peroxidase
What are secretion systems?
Usually found in gram negative species. They allow toxins or effector molecules to be injected into host cells or the environment.
How do type 3, 4, 6, and 7 secretion system work?
It actually punctures a hole in the host cell and directly injects toxins to alter host cellular pathways
How do type 1, 2, and 5 secretion systems work?
They deliver proteins like toxins or siderophores to the extracellular environment
Flagellin is highly antigenic. It is known as the ___ antigen
H antigen
What does lophotrichous mean?
This bacteria has a tuft of flagella on one side of the cell
Describe axial filaments
Flagella present within the periplasmic space of spirochetes. This allows them to corkscrew their way through dense tissue. They often pick up host proteases on the way to aid in their penetration
Bacterial ____ proteins are often associated with hair -like fibers called pili or fimbriae
Adhesin
Type ___ pili is involved in conjugation
4
True or false.. pili may be used for motility
True.
Describe capsules. Also known as the ___ antigen
Layer of polysaccharide or polypeptide associated with the bacterial surface. Provides protection against phagocytosis, detergents, and antimicrobial peptides.
K antigen
(Capsules are opsonic)
What is the difference between operons and regulons?
Operons are genes that code for multiple RNA.
Regulons regulate the transcription of operons
True or false… there are no exons or introns in bacterial genes
True. It is an open reading frame
Sigma factors are like transcription factors. Without them you will not get tight binding of ___ to the ___
RNA polymerase to the promoter
What two methods do bacteria use to increase genetic diversity?
Mutation
Horizontal gene exchange mechanisms
True or false.. regardless of the circumstances, bacteria do not change their ability to mutate
False. Some may become hypermutable in stressful environments
Out of the following bacteria,determine which are obligate aerobes, faculatative, microaerobes, or anaerobic. Neisseria Pseudomonas Legionella Mycobacterium Most gram - species Streptococcus Spirochetes Clostridium Bacteroides
Obligate aerobes: neisseria, pseudomonas, legionella, mycobacterium
Facultative anaerobes: most gram - negative rods, streptococcus
Microaerobes: streptococcus, spirochetes
Anaerobes: clostridium, bacteroides
Name some features of streptococcus pneumoniae
Gram positive cocci in pairs
Catalase negative Bile soluble (substrate dissolves them)
Name some features of Haemophilus influenzae
Gram negative pleomorphic
Only grows on chocolate agar
Requires X and V factors
Name some features of pseudomonas
Non fermenting gram negative bacilli
Smells like corn chips
Oxidase positive
Produces pyocyanin
Name some features of legionella species
Pleomorphic, gram negative bacilli
