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Bi 1 “The Biology and Biophysics of Viruses”. Lecture 1 Monday March 29, 2010 Organization of the Course. Topic for Bi 1 since 2007: “The Biology and Biophysics of Viruses”. Goal: Introduce biological concepts from a quantitative, molecular, chemical and biophysical perspective.

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Bi 1 the biology and biophysics of viruses l.jpg

Bi 1“The Biology and Biophysics of Viruses”

Lecture 1

Monday March 29, 2010

Organization of the Course

Topic for bi 1 since 2007 the biology and biophysics of viruses l.jpg

Topic for Bi 1 since 2007:“The Biology and Biophysics of Viruses”

Goal: Introduce biological concepts from a quantitative, molecular, chemical and biophysical perspective.

No memorization (open book problem sets, exams).

Focus on a topic critical to human health: viruses (HIV in particular).

An opportunity to use what you’ve learned to address a real world problem.

Important to ask questions (PJB Office hours Wednesday after class or by appointment).

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By the end of the course, students will gain a basic understanding of many issues affecting today’s world; e.g.,


Recombinant DNA technology, biotechnology

Stem Cell Research

Gene therapy

Viral outbreaks (e.g., swine flu)

Why biology needs physics, math, chemistry, computer science, engineering, etc. and why these fields needs biology

Possible careers in fields that use biology

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What we will NOT cover understanding of many issues affecting today’s world; e.g.,

Clinical aspects of AIDS and other viral diseases, social/political issues surrounding HIV/AIDS

Many interesting fields of biology

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Head TA: Helen Bermudez understanding of many issues affecting today’s world; e.g.,

Office Hours:Tuesdays 2pm; 153 Broad

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The Bi 1 homepage: understanding of many issues affecting today’s world; e.g.,


List of TAs, office hours

A glossary

Links to relevant websites

Lecture notes, problem sets

Course information, announcements, policies

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Moodle understanding of many issues affecting today’s world; e.g.,

  • Weekly homework surveys

  • To join Bi1 class, you’ll need the codeword:


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Clickers understanding of many issues affecting today’s world; e.g.,

We will use “clickers” (interactive response pads) to assess success in conveying key concepts.

We will NOT use clickers to take attendance.

Your responses are anonymous -- will not affect your grade.

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Clicker question: understanding of many issues affecting today’s world; e.g.,

My major is (or will probably be)

1. Chemistry

2. Math

3. Physics

4. Engineering

5. Geology

6. Computer Science

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Clicker question: understanding of many issues affecting today’s world; e.g.,

I have had taken one or more Biology courses in high school.

1. YES, ≥2 years in high school including AP Biology.

YES, 1 year in high school.

NO, but I took Biology in junior high.


Which is correct 1 rna dna protein 2 protein rna dna 3 dna rna protein 4 dna rna protein l.jpg

Clicker question: understanding of many issues affecting today’s world; e.g.,

Which is correct?

1. RNA --> DNA --> Protein

2. Protein --> RNA --> DNA

3. DNA --> RNA --> Protein

4. DNA <--> RNA --> Protein

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Clicker question: understanding of many issues affecting today’s world; e.g.,

HIV and other viruses are susceptible to antibiotics.

1. True

2. False

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Plagues and pestilence understanding of many issues affecting today’s world; e.g.,

History shaped by epidemics

Bubonic plague in 14th century killed 1/3 of Asian and 1/2 of European population (20 million deaths).

16th century Conquistadors conquered America with measles and small pox.

1700s: European navigators introduce syphilis, tuberculosis and whooping cough to South Pacific Islands. Population of Hawaii reduced by almost 90% by 1860.

Flu epidemic in 1918-19 killed 20-40 million (more than died in WWI).

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Ignorance/blame about disease is nothing new… understanding of many issues affecting today’s world; e.g.,

Christians blamed Jews for bubonic plague outbreaks in 14th century.

15-16th centuries: Italians called syphilis “The French Disease”. French called it “The Italian Disease”.

1930s: Cholera in New York was blamed on the Irish.

Early 20th century: Polio in US said to be caused by Italian immigrants.

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CDC* definition of AIDS understanding of many issues affecting today’s world; e.g.,

A = Acquired = a virus received from someone else

I = Immune = an individual’s natural protection against disease-causing microorganisms

D = Deficiency = a deterioration of the immune system

S = Syndrome = a group of signs and symptoms that together define AIDS as a human disease

* (Centers for Disease Control and Prevention; Atlanta, GA)

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What is AIDS? understanding of many issues affecting today’s world; e.g.,

HIV infection is not AIDS (is “HIV disease”)

AIDS is umbrella term for 26 known diseases and symptoms

AIDS diagnosis if meet three conditions:

Have one or more of known diseases/symptoms

CD4 T cell count <200/µL

What is CD4? What are T cells?

Test positive for HIVWhat do HIV tests detect?

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HIVs (there are many) are related to Simian Immunodeficiency Viruses (SIV)


  • Three groups of HIV-1 M = Main O = Outlier N = New

  • Group M HIV-1 is responsible for 99% of AIDS cases worldwide. M is divided into ~10 clades.

  • HIV-2 (related to SIVsm): less prevalent than HIV-1.

  • We will concentrate on Group M HIV-1.

  • HIV-1 is related to SIVcpz. SIV is relatively benign, whereas HIV is lethal.





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HIV-1, HIV-2, and SIVs Viruses (SIV)In nature:HIV-1 and HIV-2 infect humans.HIV-1-related CPZ viruses infect chimps.SIVs infect African monkeys. In laboratories:HIV-1 infects chimpanzees, but does not cause disease. HIV-1 does not infect old world monkeys.Asian macaques infected by some SIV and HIV-2 strains develop AIDS-like disease.

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World-wide prevalence of HIV (July 2008) Viruses (SIV)

People living with HIV/AIDS: ~33 million

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Estimated number of adult and child deaths Viruses (SIV)

due to AIDS globally, 1990–2007




























This bar indicates the range around the estimate


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Early history of HIV/AIDS Viruses (SIV)

1884-1924 -- (New) estimate for when SIVcpz crossed into humans

1959 -- Earliest known AIDS case: a Bantu man in the Republic of Congo

1981 -- first AIDS cases reported among homosexual males in US

1982 -- AIDS in hemophiliacs, transfusion patients, IV drug users

1983 -- AIDS in US heterosexuals; majority of AIDS in Central Africa affects heterosexuals

1983 -- Virus causing AIDS isolated by groups led by Luc Montagnier (France) and Robert Gallo (US)(SARS virus isolated in 2 weeks in 2003 by international consortium of 13 labs)

1985 -- Blood test to detect HIV

1987 -- AZT licensed for use in AIDS patients

1996 -- anti-HIV drugs (HAART*) reduce AIDS death rates

*Highly Active Anti-Retroviral Therapy

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Impact of AIDS on life expectancy in five African countries, 1970–2010






South Africa



at birth




















Source: United Nations Population Division (2004). World Population Prospects: The 2004 Revision, database.


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What is a virus? 1970–2010

Viruses are small* (compared with bacteria) infectious replicating objects that can cause disease in plants, animals, humans. [*5x108 rhinoviruses (common cold) will fit on the head of a pin.]

Viruses are parasites -- they live inside cells of their host animal or plant and reproduce by forcing their host to make new viruses.

Newly-made viruses leave host cell and infect similar cells.

All viruses have a protein coat that encloses genetic material (DNA or RNA). Some also have a membrane (envelope) around the protein coat.

Viruses use host cell machinery to make their components (proteins, carbohydrates, membranes), so they are harder to target with drugs than such as bacteria or fungi (self-sufficient pathogens).

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Why don’t antibiotics work against viruses? 1970–2010

  • Antibiotics interfere with metabolic processes in bacteria. Metabolic processes in bacteria (prokaryotes) and in us (eukaryotes) are different.

  • Example: penicillin interferes with the production of bacterial cell walls. Eukaryotic cells don’t have cell walls (neither do viruses).

  • Viruses use host cell machinery to undergo metabolic processes -- hard to specifically target a viral metabolic process.

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DNA viruses follow the 1970–2010“Central Dogma”

DNA --> RNA --> Protein

transcription translation

Most RNA viruses also follow part of the Central Dogma

RNA --> Protein

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HIV is a Retrovirus 1970–2010Retroviruses do NOT follow the Central Dogma

Retroviruses: a subset of RNA viruses that reverse usual flow of genetic information within host cell

Reverse transcription of viral RNA into viral DNA

RNA --> DNA --> RNA --> Protein

Three subfamilies of retroviruses

Oncoviruses (cause cancer)

Feline leukemia virus, Rous Sarcoma Virus, Mouse Mammary Tumor Virus

Lentiviruses (slow viruses)

HIV-1 & HIV-2, Feline Immunodeficiency Virus (cats), Visna virus (sheep), caprine arthritis-encephalitis virus (goats), SIV (nonhuman primates)

Spumavirus (not associated with human disease)

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( 1970–2010For exogenous retrovirus start here)



Membrane Fusion

Overview of





Reverse Transcription



Membrane Targeting

Nuclear transport


(For endogenous retrovirus start here)

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Some believe that HIV does not cause AIDS 1970–2010

~1987 to present: Peter Duesberg (UC Berkeley) believes there is no single causative agent of AIDS, but disease is a collection of non-infectious deficiencies associated with drug use, malnutrition, parasitic infections, other specific risks. (

~2000-2002: South African President Thabo Mbeki made statements that HIV does not cause AIDS, and that AIDS does not exist (>5 million people in South Africa are HIV-positive).

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HIV causes AIDS 1970–2010

See also Durban declaration (signed by >5000 HIV/AIDS scientists and physicians, released in July 2000) for evidence that HIV causes AIDS: few compelling facts:

Data from matched groups of homosexual males and hemophiliacs shows that only those infected with HIV develop AIDS.

Only HIV-positive mothers transmit HIV to fetuses and only HIV-positive newborns develop AIDS. HIV-negative newborns from HIV-positive mothers do not develop AIDS.

Laboratory and health-care workers with no known risk factors have developed AIDS after exposure to HIV.

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Koch’s postulates have been satisfied 1970–2010

Causative agent must be found in all cases of the disease.

It must be isolated from the host and grown in pure culture.

It must reproduce the original disease when introduced into a susceptible host.

It must be found in the experimental host so infected.

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Why study HIV? 1970–2010

“The Human Immunodeficiency Virus (HIV) epidemic has spawned a scientific effort unprecedented in the history of infectious disease research. This effort has merged aspects of clinical research, basic molecular biology, immunology, cell biology, epidemiology, and mathematical modeling in ways that have not been seen before. The ever unfolding discoveries of novel aspects of HIV-host interaction have been accompanied by (and often have resulted from) novel interactions among researchers in the disparate disciplines.”

Coffin, J.M. 1999. Molecular Biology of HIV. In The Evolution of HIV, ed. K.A. Crandall. Baltimore: Johns Hopkins University Press.

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Extra slides 1970–2010

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Figure 9-12 the US

Number of HIV cases worldwide at end of 2002

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Worldwide, HIV has spread to 70 million people, killed 30 million and is estimated to infect 40 million more in the next decade.

Consider Africa….

Sub-Saharan Africa has ~67% of world’s HIV/AIDS cases but only 10-11% of world’s population -- home to 87% of 2.3 million children living with HIV/AIDS.

South Africa has highest number of people living with HIV/AIDS in the world (5.5 million in May 2006) and almost one in five South African adults are HIV positive.

National HIV prevalence rate in Swaziland is 33%, the highest in the world.

Fact Sheet: The Global HIV/AIDS epidemic (May 2006)

Kaiser Family Foundation;

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Figure 9-22 million and is estimated to infect 40 million more in the next decade.

Opportunistic infections and malignancies in AIDS patients

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Symptoms of AIDS million and is estimated to infect 40 million more in the next decade.(each symptom can be caused by another disease; can’t rely on symptoms to diagnose AIDS)

Rapid weight loss

Dry cough

Recurring fevers, night sweats

Unexplained fatigue

Swollen lymph glands

Diarrhea that lasts more than a month

White spots on tongue, in mouth, or throat (thrush)


Red, brown, pink or purplish blotches on skin or inside mouth, nose, or eyelids (Kaposi Sarcoma)

Memory loss, depression, other neurological disorders

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Killing viruses million and is estimated to infect 40 million more in the next decade.

  • Can inactivate viruses using physical and chemical agents

    • Heat (e.g., boiling water) alters structures of proteins and nucleic acids

    • UV radiation crosslinks thymines in nucleic acids (more in problem set 1)

    • Formaldehyde combines with free amino groups on nucleic acids

    • Metals and phenol react with proteins in the viral capsid

    • Chlorine combines chemically with viral nucleic acid

    • Detergents denature viral proteins

    • Antiviral drugs (rare because they can interfere with essential chemical reactions in the host)