Like all viruses, HIV must infect a host cell to replicate.  Name the five steps of the viral replication cycle in order. Step 1: Step 2: Step 3: Step 4: Step 5:

TB infections usually start in the lungs as the bacteria is spread through aerosols and droplets.  This transmission method is similar to caused by .  For full credit include the complete genus and species name of the bacteria.

In order to analyze RNA-seq data you must have an annotated genome.  Describe the process for identifying and annotating an open reading frame (ORF).  (5 sentences max) For full credit be sure to: Identify all search characteristics for identifying the location of the ORF. Explain how the ORF is annotated.

Data from Figure 2 was generated by performing bacterial growth curves.  Name the 4 stages of a typical bacterial growth curve in order. Phase 1: Phase 2:  Phase 3: Phase 4:

Below are two images of bacterial envelopes.  Identify the envelopes as Gram positive or Gram negative. A: B:

Robert Koch won the Nobel Prize in 1905 for establishing the Germ Theory of Disease when he used postulates to discover that the bacteria Mycobacterium tuberculosis caused tuberculosis (TB).  Which of the following are included in Koch’s postulates?  Choose all that apply.

HIV is a naked virus.

TB infections are often diagnosed by collecting sputum samples from the patient’s lungs and staining the cells to view under the microscope (Figure 5).  Based on the microscopic image, what is the morphology of M. tuberculosis? Figure 5: Microscopic image of M. tuberculosis in a sputum sample.  M. tuberculosis cells are stained pink and labeled with arrows.

Describe how VapBC expression is regulated on a molecular level.  (6 sentences max) For full credit be sure to: Name and describe the function of all proteins involved in the regulation. Describe what is happening on a molecular level when the genes are transcribed. Describe what is happening on a molecular level when the genes are not transcribed.

TB can also be diagnosed through a skin test.  During a TB skin test, patients are exposed to tuberculin (a purified protein from M. tuberculosis) via an injection on the inner forearm.  The sight of injection is observed after 48-72 hours.  If the patient has been infected with M. tuberculosis, a large raised hard area of swelling will appear (Figure 6).  This is the result of… Choose all that apply. Figure 6: TB skin test.  Inoculation method (left) and positive result (right).