Genetics, Microbiome, Pathogenesis & Virology Study Guide

What single chemical difference explains why DNA is used for long-term storage while RNA is used for short-term transfer?

DNA uses 2'-deoxyribose while RNA uses ribose.

What was the main aspect of Watson and Crick's DNA model, and what was based on Rosalind Franklin's research?

Watson and Crick proposed the double-helical structure with antiparallel strands and specific base pairing, relying on Rosalind Franklin's X-ray diffraction images.

How do replication and transcription rely on complementary base pairing?

Specific hydrogen bonding determines base pairing; in DNA replication, Adenine pairs with Thymine and Cytosine pairs with Guanine; in transcription, Adenine pairs with Uracil.

Why is DNA → mRNA called 'transcription' while mRNA → Protein is called 'translation'?

DNA → mRNA is transcription because it rewrites information in nucleic acid form, while mRNA → Protein is translation because it converts genetic code into amino acids.

What is true regarding the E. coli Isocitrate Dehydrogenase gene?

It has been identified within the E. coli genome, and its full sequence is available in public databases.

How do the human and E. coli genomes compare regarding strandedness?

Both humans and E. coli have double-stranded DNA (dsDNA) genomes.

How does horizontal gene transfer occur, and how does it relate to antibiotic resistance?

Bacteria swap genetic material via conjugation, transformation, or transduction, leading to antibiotic resistance in human pathogens.

Why are culture-independent sampling methods superior to culture-dependent methods?

Over 99% of environmental and human microbes cannot be grown using standard laboratory culture media.

Which gut bacteria are considered 'good' symbionts vs. 'bad' pathobionts regarding oxygen relationships?

Good symbionts are obligate anaerobes, while potential pathobionts are facultative anaerobes.

How do dietary fiber, symbionts, SCFAs, pathobionts, and terminal electron acceptors interact in dysbiosis?

Undigested carbohydrates feed symbionts, which ferment them into SCFAs, while inflammation allows pathobionts to overgrow.

What are 3 key facts about Short-Chain Fatty Acids (SCFAs)?

1. Butyrate fuels colon epithelial cells. 2. They lower gut pH and suppress inflammation. 3. They regulate immune responses.

What does a higher Lethal Dose 50% (LD50) in a gene mutant strain indicate?

A higher LD50 means more microbes are needed to kill 50% of host animals, indicating the deleted gene encodes a virulence factor.

How does Vibrio cholerae cause disease, and why is it termed 'non-invasive'?

It colonizes the intestinal mucosa and produces cholera toxin without invading cells.

How do Yersinia pestis and Salmonella enterica survive inside host macrophages?

They prevent the initial phagosome from fusing with host lysosomes.

What determines whether Mycobacterium tuberculosis causes active dissemination or latent infection?

The state and strength of the host's immune system.

What is LTBI, and what are the 'unlucky 10%' and 'lucky 90%' in tuberculosis?

LTBI stands for Latent Tuberculosis Infection.

What does the unlucky 10% refer to?

Infected individuals who develop active disease over their lifetime.

What are the two distinct morphological forms of Chlamydia trachomatis?

The infectious, extracellular elementary body (EB) and the non-infectious, intracellularly replicating reticulate body (RB).

What does 'obligate intracellular pathogen' mean?

The organism cannot replicate or survive outside of a host cell because it relies on host cell energy (ATP) and metabolic machinery.

How does Helicobacter pylori survive in acidic stomach environments?

It produces urease, breaking down urea into ammonia (NH3) and CO2, which neutralizes stomach acid.

How can Salmonella cause long-term chronic carriage?

It colonizes the gallbladder and forms resilient biofilms on gallstones, causing periodic asymptomatic shedding in feces.

Why is Listeria monocytogenes a master at crossing physiological barriers?

It uses Listeriolysin O (LLO) to escape phagosomes and ActA to spread cell-to-cell.

Why is Listeria monocytogenes considered self-limiting?

Healthy immune systems resolve the resulting gastroenteritis without systemic spread.

Why is Listeria monocytogenes a major concern for the food industry?

It can multiply at refrigeration temperatures (4°C) and withstand high salt conditions.

What is the distinction between the core and dispensable genome of Staphylococcus aureus?

The core genome contains essential survival genes shared by all strains; the dispensable genome contains strain-specific mobile elements.

Why is Staphylococcus epidermidis an opportunistic pathogen?

It causes infection mainly in compromised hosts by forming biofilms on medical implants and exhibiting multidrug resistance.

What are the 6 standard steps of the viral replication cycle?

1. Attachment 2. Entry 3. Uncoating 4. Biosynthesis 5. Assembly 6. Release.

What is the basis of the Baltimore classification system for viruses?

How the virus generates its messenger RNA (mRNA) from its viral genetic material.

Which cellular receptors do SARS-CoV-2 and Influenza target?

SARS-CoV-2 Spike protein targets ACE2; Influenza Hemagglutinin (HA) targets Sialic acid.

What makes a virus-specific antibody 'neutralizing'?

They directly block viral surface proteins to prevent cellular attachment.

Why do SARS-CoV-2 variants arise?

Mutations in spike genes alter receptor binding site shapes, rendering existing antibodies ineffective.

Why does Influenza have a broad host range?

Its segmented genome allows for antigenic shift and drift.

How does HPV cause cancer through epithelial cell differentiation?

HPV infects basal epithelial cells and uses oncogenes E6 and E7 to force host cells to continually divide.

Why are HPV vaccines referred to as 'genome-less virions'?

They use Virus-Like Particles (VLPs) made solely of empty capsid protein shells.

How does Rotavirus cause severe illness in children?

It destroys absorptive enterocytes and secretes NSP4 enterotoxin, causing severe watery diarrhea.

How does HIV differ from other RNA viruses?

It uses Reverse Transcriptase to copy its RNA genome into DNA.

How does HIV cause AIDS?

By progressively destroying CD4+ T helper cells.

What makes HIV an 'evil genius'?

The integration step (via Integrase), which permanently inserts viral DNA into the host genome.

What are the infection phases of HIV?

Early phase involves entry and integration; late phase involves gene expression, assembly, and release.

Why are anti-HIV drugs described as 'suppressive'?

They stop active replication and reduce viral load but cannot clear integrated proviral DNA.

How does a COVID-19 mRNA vaccine differ from a live attenuated Rotavirus vaccine?

COVID-19 mRNA vaccines deliver synthetic instructions for Spike protein; live attenuated vaccines use weakened whole viruses.