Final exam short answer prompts

Koch’s postulates (experiments and limitations)

Used to link a microbe to a disease. The microorganism must be present in every case of the disease but absent in healthy individuals. Must be isolated and grown in a pure culture. Same disease must result when inoculated into a healthy host. Same microorganism must be isolated from newly diseased organism. Limitations- asymptomatic individuals, some microorganisms cannot be independently grown, differing immune responses.

Know the difference between a capsule and a slime layer along with the term glycocalyx and how does it relate to capsules and slime layers.

Capsules are thick, structured and organized layers surrounding the cell wall. Slime layers are thin, loose, unorganized layers surrounding a cell wall. The glycocalyx is the general term for layers surrounding the cell wall. Capsules are associated with virulence while slime layers are associated with biofilm formation/adhesion.

S-layers and some capsules are composed of proteins. Know how these differ.

S-layers are sheets of repeating protein or glycoprotein subunits that self-assemble into a highly ordered lattice directly on the cell surface. They act like a molecular armor, offering mechanical protection, controlling permeability, and sometimes helping evade phagocytosis. Protein-based capsules, however, are thicker and more amorphous structures composed of protein polymers rather than repeating crystalline units. Capsules primarily function in immune evasion by blocking recognition or complement binding, whereas S-layers also have roles in structural stability and environmental resistance. The key difference is the ordered, lattice-like architecture of S-layers versus the irregular, gel-like nature of capsules.

Know the different stages for bacterial growth and be able to describe them.

The bacterial growth curve contains 4 phases, lag, exponential, stationary, death. In the exponential phase, cells are dividing more rapidly, making them more susceptible to antibiotics such as penicillin that disrupts cell wall synthesis. During an oil spill, different bacterial species dominate and grow exponentially depending on the oil makeup.

How do antibiotics work

Antibiotics inhibit bacteria by targeting essential processes such as cell wall synthesis, protein translation, nucleic acid replication, cell membrane integrity, or metabolic pathways. β-lactams like penicillin block cell wall synthesis leading to lysis. Macrolides and aminoglycosides inhibit ribosomal function by binding to the 50S or 30S subunits, stopping protein synthesis. Fluoroquinolones block DNA gyrase and topoisomerase IV, preventing replication fork movement.

Know the glycolytic pathways, EMP, EDP AND PPP. Be able to explain the steps and proteins along with inputs and outputs.

The EMP pathway is converts glucose to pyruvate producing 2 ATP and 2 NADH. The EDP is used by many Gram-negative bacteria and converts glucose to pyruvate yielding only 1 ATP but requiring fewer enzymes. The PPP generates NADPH and ribose-5-phosphate for biosynthesis and can operate alongside EMP or EDP to balance reducing power. Each pathway uses different key enzymes. Inputs are typically glucose, while outputs differ in ATP, NAD(P)H, and precursor metabolites.

Binary fission in bacteria

Binary fission begins with cell growth and replication of the chromosome at the origin of replication. The DNA replication forks move bidirectionally until termination, and the cell elongates while chromosomes segregate to opposite poles. The FtsZ protein then forms a contractile Z-ring at mid-cell, recruiting enzymes that build a division septum. New cell wall and membrane materials are inserted as the septum constricts. Finally, the septum closes completely, forming two genetically identical daughter cells.

How does termination of replication in E. coli differ from replication of linear chromosomes in B. burgdorferi bacteria

E. coli has circular chromosomes while B. burgdoferi has linear chromosomes. E. coli has one origin of replication, and replication stops when the fork reaches the termination site. The strand need to be temporarily broken to separate. Bacteria with linear chromosomes disguise chromosome ends with hairpin structures.

What is Quorum sensing? How do microorganisms communicate to each other. Describe benefits to different organisms that utilize quorum sensing.

Quorum sensing is a method of communication that microorganisms use. As population density increases, microorganisms secrete molecules to activate gene expression. They can trigger biofilm production, bioluminescence, virulence, etc. This communication increases the chances of survival of bacterial communities.

Discuss the three stages of CRISPR/Cas System. Name each stage and briefly describe what each stage does

The CRISPR–Cas system has three stages: adaptation, expression, and interference. During adaptation, the cell captures short DNA fragments from invading viruses and inserts them as new spacers into the CRISPR array. In the expression phase, the CRISPR array is transcribed into a long pre-crRNA and processed into individual guide RNAs that pair with Cas proteins. During interference, the crRNA-Cas complex scans for matching viral DNA and cleaves it, providing sequence-specific immunity. This creates a molecular memory that protects the cell from future infections by the same phage.

Be able to compare transduction, transformation, and conjugation. Give specific examples for each one

Transformation is the uptake of naked DNA from the environment. This can happen if a bacterium takes up the DNA of another that has lysed. Transduction involves a bacteriophage transporting DNA from one organism to another. Conjugation involves direct cell to cell contact, usually through a sex pilus. All three are examples of horizontal gene transfer.

Compare and contrast the presence of sugar (lactose or arabinose) versus the amino acid tryptophan. Be specific about what is inhibited and how they do it.

The lac operon and the ara operon are activated with the presence of lactose/arabinose. They are also both repressed by catabolite repression, meaning that they will only be activated in the absence of glucose and presence of lactose/arabinose. On the other hand, the trp operon is repressed in the presence of tryptophan. Tryptophan binds to the repressor, allowing it to bind to the operator. It also uses attenuation to prematurely stop transcription by forming a terminator hairpin.

Discuss Bacterial conjugation and what happens during mating. (be sure to include F+, F-, F’, and Hfr)

Bacterial conjugation is the transfer of genetic information through direct contact using a sex pilus. F+ F- conjugation results in two F+ cells. HFr conjugation transfers only a portion of the genome, making the resulting cells HFr and F-. F’ conjugation results in two F’ cells.

Review the Human Microbiome article and the question from the class activity. (Chap 24 Class Activity)

Climate change resulting from human activities such as greenhouse gasses are decreasing the soil microbe diversity. The soil microbiome is necessary for fertility and an imbalance will decrease nutritional value of plants. Chemicals used on plants to control disease can end up in humans and act as an antibiotic, decreasing biodiversity in our intestines. These factors result in malnutrition and can lead to several diseases.