Lab Act 1: Understanding HIV Infection and Evolution

Question 1

Human Immunodeficiency Virus (HIV) is the causative agent for

Answer 1

Acquired Immunodeficiency Syndrome (AIDS)

Question 2

HIV
> Part of the __ family
> __ -nm enveloped particles with a conical capsid
> Linear (+)ssRNA genome of __
> Thought to have evolved from the __;
> a distinct virus that infects humans
> Vaccines are currently being tested

Answer 2

• Retroviridae
• ~120
• ~9,700 bp (base pairs)
• simian immunodeficiency virus (SIV)

Question 3

the predominant subtype that causes HIV/AIDS

Answer 3

human immunodeficiency virus type 1 (HIV-1)

Question 4

stimulate other immune cells to mediate the host’s immune response.

Answer 4

CD4+ immune cells

Question 5

Materials (Per group)

Answer 5

• Laptop
• Internet connection
• Pop beads of three colors to represent:
  –> double-stranded DNA genome of host cell (40-50 beads)
  –> single-stranded RNA genome of the virus (5-10 beads)
  –> double-stranded DNA copy of the viral genome (10-20 beads)
• Nucleotide cutouts (4 pieces per nucleotide: A, T, G, C)
• Scissors
• Masking tape
• AZT cutouts

Question 6

Materials (provided by the Instructor)

Answer 6

Animation of the HIV Life Cycle

Question 7

HIV is a retrovirus carrying a __

Answer 7

single-stranded RNA genome

Question 8

A __ surrounds the viral genome.

Answer 8

capsid

Question 9

An outer membrane called an __ covers the capsid.

Answer 9

envelope

Question 10

The __ bind with a receptor and a co-receptor on the surface of the target host cell, mediating the __ with the host cell membrane and the subsequent entry of the HIV genome into the cell.

Answer 10

• viral envelope proteins
• fusion of the viral envelope

Question 11

consists of a complex of gp120 and gp41. gp120 determines viral tropism by binding to target-cell receptors, while gp41 mediates fusion between viral and cellular membranes.

Answer 11

Envelope glycoproteins

Question 12

convert its RNA into viral DNA

Answer 12

reverse transcriptase

Question 13

an enzyme that integrates viral DNA into the host genome.

Answer 13

integrase

Question 14

cuts up large precursor proteins into smaller proteins. These smaller proteins combine with HIV’s genetic material to form a new HIV.

Answer 14

protease

Question 15

a nucleic acid chaperone, which remodels nucleic acid structures so that the most thermodynamically stable conformations are formed. This activity is essential for virus replication and has a critical role in mediating highly specific and efficient reverse transcription.

Answer 15

nucleocapsid protein

Question 16

contains all the necessary information to synthesize all proteins for making new virions in the host cells.

Answer 16

RNA genome

Question 17

a conical shell that encases viral nucleoprotein complexes necessary for replication

Answer 17

capsid protein

Question 18

a structural protein critically involved in most stages of the life cycle of the retrovirus. It participates in the early stages of virus replication as well as in RNA targeting to the plasma membrane, incorporation of the envelope into virions and particle assembly.

Answer 18

matrix proteins

Question 19

allows assembly and budding at the plasma membrane of the infected cell.

Answer 19

lipid envelope

Question 20

describe the host genome

Answer 20

• Double-stranded DNA
• Relatively large

Question 21

describe the HIV genome

Answer 21

• Single-stranded DNA
• Relatively small

Question 22

describe the DNA Copy of HIV Genome

Answer 22

• Double-stranded DNA
• Relatively small

Question 23

Steps on how HIV replicates (10 steps)

Answer 23

A. Glycoprotein binding to host cell receptors
B. Fusion of virus envelope and host cell membrane
C. Reverse transcription
D. Viral genome integration into host DNA
E. Viral genome replication
F. mRNA transcription
G. Translation into viral proteins
H. Glycoprotein processing
I. Virus assembly
J. Virus budding

Question 24

1. __ on the surface of HIV bind to the primary cellular receptor CD4 and then to a cellular coreceptor. This triggers the cell membrane to fuse with the virus’s envelope, releasing the virus’s __ and viral proteins, including __ and __, into the cell’s cytosol.

Answer 24

• Glycoproteins
• (+)RNA genome
• reverse transcriptase
• integrase

Question 25

2. The viral __ transcribes the virus’s (+)RNA genome into __ in a process known as __. This is then used to make a __ of the virus’s genome. The DNA copy travels to the __ and is inserted into the cell’s genome by the __.

Answer 25

- reverse transcriptase - complementary DNA (cDNA) - reverse transcription - dsDNA copy - nucleus - viral integrase

Question 26

3. The viral genome is transcribed by the host machinery alongside the host genome. This produces more copies of the virus’s __, as well as __. The __ leave the nucleus and are translated into proteins by __ in the __ and on the __. __ are further modified through protein processing in the __, then are transported to the cell membrane.

Answer 26

- (+)RNA genome - mRNAs; mRNAs - ribosomes - cytosol - endoplasmic reticulum (ER) - HIV glycoproteins - ER-Golgi network

Question 27

4. Viral genomes and proteins assemble into new viruses at the cell surface, which leave the cell through a process known as __. This process surrounds the virus in a piece of the cell membrane containing viral proteins, which becomes the virus’s __.

Answer 27

- budding - envelope

Question 28

treatment combination: > __ is a medication used to delay the onset of AIDS (acquired immunodeficiency syndrome) in HIV-infected patients (Rogers, 2008). > has a structure similar to that of the nucleoside __, can connect with a phosphate group to generate a nucleotide that can integrate into a developing nucleic acid chain. - interferes with an enzyme called __, which is used by HIV-infected cells to make new viruses. > Since this inhibits, or reduces the activity of this enzyme, this drug causes HIV-infected cells to produce fewer viruses (Thackzuk, 2014).

Answer 28

- AZT (azidothymidine; Zidovudine) - thymidine - reverse transcriptase (RT)

Question 29

AZT is a synthetic dideoxynucleoside in which azido group is present in place of __

Answer 29

3′- hydroxyl group of thymidine

Question 30

When AZT is incorporated into the DNA chain, it terminates further __. This is because AZT lacks a ___ necessary for the formation of a __ with the next nucleotide, effectively stopping __. This termination prevents the virus from replicating its genetic material, thereby inhibiting its ability to infect new cells and replicate within the host.

Answer 30

- DNA synthesis - 3'-OH group - phosphodiester bond - DNA replication

Question 31

AZT therapy may cause __, including the __. AZT reduces the formation of: 1) 2) 3) Resulting in: 1) 2) 3)

Answer 31

- muscle tissue damage; heart 1) red blood cells 2) Neutrophils 3) other bone marrow cells 1) Fatigue 2) Malaise 3) Anemia

Question 32

NRTIs stands for

Answer 32

nucleoside/nucleotide reverse transcriptase inhibitors