BIO (PDF)

Bio Viruses and Human Disease

3/25/15 5:13 PM

Ch 1 Overview
Definitions:
• Virus
o An obligatory intracellular parasite that carries a nucleic acid
genome enclosed by a protein coat
• Enveloped Viruses
o Viruses that have additional lipid membrane surrounding the
protein coat
• Virions
o Also called virus particles. A virion refers to a physical
particle, whereas a virus is a more general term
Resolution of a microscope
o Ability to distinguish two objects as separate entities
• Bacteriophages
o Viruses that infect bacterial cells
Objectives
• Understand the relative size ranges of molecules, viruses, bacteria,
and eukaryotic cells, as measured by the appropriate units:
o Micron (1 micron= 1 micrometer)
§ Bacteria and eukaryotic cells in this range (10-100
micrometers)
§ A filter with 0.2 micron-sized pores will effectively
remove bacterial contamination by trapping them in the
filter
o Nanometer (nm)
§ Viruses are in this range
§ 20-100 nm is the typical range of diameters for viruses
§ The same filter mentioned above will not remove most
viruses
o Angstrom (A)
§ Molecules in this range
§ A nanometer= 10 angstrom
• Understand the difference between light microscopes and electron
microscopes
o Sources of illumination are different: photons (light) vs.
electrons
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o Level of resolution
o Different types of EM techniques (TEM, SEM, cryoEM, EM
tomography)
Know the viral causes of some common diseases
o Common cold (rhinovirus)
o Flu (influenza virus)
o Warts (human papillomavirus 1, 2, 4)
o Cold sores (herpes virus)
o Diarrhea (enterovirus)
o AIDS (HIV)
o Poliomyelitis (Poliovirus)

o Hemorrhagic fever (Ebola, dengue)
o SARS (coronavirus)
Ch 2 Virus Entry
• Definitions:
o Transmembrane Protein
§ A protein that spans across the membrane lipid bilayer,
at least once
o Viral Receptor
§ A cell surface molecule that is bound by a virus to
mediate its entry into host cells
o Tropism
§ The phenomenon that viruses are capable of infecting
certain cell types but not others
o Endocytosis
§ Cellular uptake of materials from extracellular space,
using membrane-bound vesicles called endosomes
o Highly pathogenic avian influenza (HPAI)
§ Avian flu virus that has crossed over from waterfowl to
domestic birds and causes high rate of death in the
latter population
• Objectives
o Understand the general steps of a virus life cycle
§ Entry, this includes receptor-binding all the way to
membrane penetration

Replication of viral genomes, which requires the
expression of replication enzymes
§ Viral assembly and exit, which requires the expression
of structural proteins
o Understand the structure of biological membranes
§ Lipid bilayer with embedded Transmembrane proteins
§ A barrier that viruses must cross to deliver its genome
into the cells
o Understand the importance of studying viral receptors
§ Elucidation of viral tropism
§ Help predicting viral pathogenesis
§

§ Reveal drug targets for therapy
o Know the 4 possible routes of viral entry, following receptorbinding
§ Pore formation at the cell surface (neutral pH)
§ Membrane fusion at the cell surface (neutral pH)
§ Pore formation in the endosomes (acidic pH)
§ Membrane fusion in the endosomes (acidic pH)
Ch 3 Genome Replication
• Definitions:
o Nucleic Acid
§ A polymer made up of repeating units of nucleotides,
can be either DNA or RNA
o Semiconservative Replication
§ During DNA replication, each daughter DNA contains
one strand of parental DNA and one strand of new DNA
o Reverse Transcriptase
§ The enzyme that uses RNA as template to produce
DNA. BY in large absent from the host cells and has to
be carried in by the virions
o RNA-Dependent RNA Polymerase
§ The enzyme that uses RNA as a template to produce
RNA. By in large absent from the host cells, it has to be
either carried in by the virions or encoded by the viral
genome
• Objectives

o Know the 7 types of viral genes
§ dsDNA viruses
ú DNA (+/-)
§ ssDNA viruses
ú DNA (+)
§ dsRNA viruses
ú RNA (+/-)
§ ssRNA viruses (+)
ú RNA (+)
§ ssRNA viruses (-)
ú RNA (-)
ssRNA-RT viruses
ú RNA (+)
§ dsDNA-RT viruses
ú DNA (+/-)
§ Notice the lack of double-stranded genome type with
one strand of DNA and one strand of RNA. These
molecules are physically unstable
o Understand why viruses are successful despite having limited
coding capacity in their genomes
§ Host provides much of the service
§ Viral genomes are more efficient in carrying information
(e.g., overlapping reading frames)
o RNA viruses have a much higher mutation rate, why?
§ The enzymes used to copy RNA genomes have low
fidelity during replication (make more mistakes).
§ These include the reverse transcriptase and RNAdependent RNA polymerase.
§ The DNA polymerases, which the host cell and DNA
viruses use, have much higher fidelity
o Understand the general scientific principles of reconstructing
extinct viruses
§ Obtain viral genome sequence and use it to synthesize
a “man-made” genome
ú 1. Find preserved viral genome in frozen body
tissue
§

2. Extract the RNA and obtain sequence of the
complete genome
ú 3. Synthesize genome
ú 4. Grow virus in cell culture
ú 5. Test virus in mice
o Understand the difference between positive-sense and
negative-sense RNA genomes
§ Positive-sense RNA directly spells out the code for
protein translation
§ Negative-sense RNA needs to be converted to positivesense RNA (via the base-pair rule) to spell out the code
ú

for protein translation. As a result, negative-sense RNA
viruses need to carry their own RNA
Ch 4 Virus Assembly
• Definitions:
o Icosahedron
§ A common shape adopted by viruses. It is characterized
by having 20 faces and three types of symmetries (5fold, 3-fold, and 2-fold)
o Packaging Signal
§ A piece of viral DNA/RNA sequence that is necessary
and sufficient for incorporations into virions. It is unique
for each virus
o Metastable State
§ A long-lived stable state that is less stable than the
most stable (lowest energy) state.
o Envelope Proteins
§ Virus-encoded proteins displayed on the membrane
surface of the virion. These proteins are typically
glycoproteins (having sugars added to them)
o RNA Secondary Structure
§ Partially double stranded structures; common motifs
include stem loops, hairpins, and kissing loops
• Objectives
o Understand the general consideration of viral assembly and
the two general shapes of viruses

Should be able to use very simple (single) repeating
protein units
§ The structure needs to close
§ Virions should be mobile (easy to roll: helical and
icosahedron)
§ Should be amenable to scaling up
o Know the basic characteristics of an icosahedron
§ 20 faces and 3 types of symmetry
§ Sphere-like properties and readily scalable
o Understand the three modes of virus assembly
§ Self-assembly
§

Capsid protein does it all by itself, even without
the genome.
ú Self-assembled empty “virus-like particles” can
serve as vaccines (HBV and HPV vaccines)
§ Assisted assembly
ú Chaperone proteins make sure the correct shapes
such as pentamers and hexamers are formed
ú Protein scaffolds have to build first for very large
virions (herpes virus)
§ Assembly followed by maturation (virion maturation)
ú The maturation process of HIV virions is a target
of the “cocktail therapy” (the protease inhibitors)
o Understand the different ways that assembled virions exit
from the host cell
§ Cell lysis
§ Budding out at the plasma membrane
§ Exocytosis (the reversal of endocytosis)
Ch 5 Virus-Host Interactions I: A Virus Hijacks a Cell
• Definitions:
o Cytoskeleton
§ A network of interconnected filaments and tubules that
extends throughout the cytosol, from the nucleus to the
inner surface of the plasma membrane. The three major
components are MT, MF, and IF
o Exocytosis
ú

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•

The reverse of endocytosis. The cellular pathway for
secreting proteins to the outside of the cell via
membrane-enclosed vesicles

Objectives
o Understand the difference between in vitro and in vivo studies
of viral infection
§ In vitro: outside a body and in cultured cells
§ In vivo: in the body of a living organism
o Understand the difference between primary cells and
immortalized cell lines
§ Primary cells are directly isolated from organisms, short
lived
§ Cell lines grow forever but are usually altered from the
original cell type in many aspects
o Know the four levels of biosafety containment
§ BSL-1: no known hazard
ú Ex: Recombinant DNA involving non-infectious
materials
§ BSL-2: Moderate hazards. Lab coats, gloves, and
biosafety cabinet required
ú Ex: cancer cell lines and many viruses
§ BSL-3: Serious or potentially lethal agents. Restricted
access. Solid-front gown, shoe cover, negative pressure
ú Ex: Virulent avian flu, rabies, smallpox
§ BSL-4: Extremely hazardous infectious agents
ú Ebola, Marburg
o Understand the following examples of normal functions of
viral receptors (see photos)
§ Signal transduction

§

Cell junction
formation

§

Receptor-mediated endocytosis

Understand the similarities between exocytosis and virus exit
o Require membrane-bound secretory vesicles
o Travels from the center of the cell (endoplasmic reticulum) to
the outer edge of the cell (plasma membrane)
Ch 6 Virus-Host Interactions II: The Cell Fights Back
• Definitions:
o PAMP
•

Pathogen associated molecular patterns. Examples
include dsRNA and viral proteins
o PRR (pattern recognition receptor)
§ Host proteins that detect PAMPs and activate cellular
responses
o Seroconversion
§ The point when antibodies against a virus become
detectable in a patient’s blood
Objectives
o Understand the multiple layers of host defense against
infections
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Primary barrier and chemical defense
ú Skin: largest organ of the body
• Viruses cannot penetrate skin unless there
is a cut
• So they are died up, washed away, or killed
by secreted chemicals
ú Chemical defense helps in areas not covered by
skin
• Tears: eyes
• Mucus: respiratory tract
• Acid pH: gastrointestinal tract
Intrinsic cellular response
ú Highly conserved mechanism found in all
organisms
ú Response is not specific to any virus or pathogen,
but requires recognition of “non-self”
Innate immunity
ú Rapid response such as the inflammatory
response
ú Involves dendritic cells, macrophages, and natural
killer cells
Adapted immunity
ú Slower response, specific to pathogen
ú Involves antibodies and cytotoxic T cells
ú Has memory and is the basis for vaccination