Exam Flashcards

Question

Why is the balance between mitochondrial fusion and fission crucial for cellular homeostasis?

Answer 1

Mitochondrial fusion and fission are essential for maintaining mitochondrial health and cellular function. Fusion allows for the exchange of genetic material, while fission divides mitochondria. Excessive fission can lead to fragmentation and impaired function, while excessive fusion can create detrimental elongated networks. The balance between these processes is critical for cellular homeostasis.

Answer 2

Peptidoglycan biosynthesis begins in the cytoplasm with the synthesis of UDP-NAG from activated sugars. UDP-NAG is then converted to UDP-NAM, and amino acids are sequentially added to form UDP-NAM-pentapeptide. Outside the cell, the removal of a terminal amino acid provides the energy to link the disaccharide-pentapeptide to the existing peptidoglycan chain. Penicillin-binding proteins (PBPs) are enzymes that catalyse the cross-linking of the peptidoglycan layer, ensuring the integrity of the bacterial cell wall.

Answer 3

Lipid A anchors the lipopolysaccharide (LPS) to the outer membrane of Gram-negative bacteria. The synthesis of Lipid A involves several steps: First, a fatty acid is esterified to UDP-NAG. Then, the acetyl group is removed, and a second esterification occurs with the help of ACP. UDP is hydrolysed, and two of the esterified glucosamine molecules are linked. Further esterifications lead to the formation of Lipid A, which then integrates into the outer membrane. Finally, core sugars are added.

Answer 4

Bacterial flagella are tubular structures composed of flagellin, a globular protein. The flagellum is divided into three parts: the filaments (made of flagellin), the hook (a more rigid protein structure connecting the filaments to the basal body), and the basal body itself which contains protein rings that anchor the flagellum to the cell wall. In Gram-negative bacteria, two sets of rings are required because of the outer membrane. Flagella can be arranged in different ways: monotrichous (single flagellum), lophotrichous (multiple flagella at one end), amphitrichous (flagella at both ends), and peritrichous (flagella distributed over the entire cell surface).

Answer 5

FtsZ is a highly conserved protein that plays a central role in bacterial cell division. It assembles at the mid-cell to form a ring, which constricts the cell membrane and initiates septum formation. The MinE protein signals FtsZ to form this ring at the center of the cell by recruiting other proteins. Mutations in ftsZ result in a filamentous phenotype, where cells cannot complete division. Mutations in min genes cause FtsZ to bind randomly, leading to asymmetrical cell division.

Answer 6

Drug resistance refers to a microorganism’s ability to withstand the effects of a specific drug. Multiple Drug Resistance (MDR), on the other hand, is when a microorganism is resistant to several structurally and functionally unrelated drugs, often due to mechanisms that affect multiple drugs simultaneously. MDR is a more complex phenomenon than simple drug resistance, often involving efflux pumps, altered drug targets or other mechanisms that affect different drugs.

Answer 7

Hfq is a protein that acts as a chaperone, facilitating the binding of sRNAs to their target mRNAs. This binding can lead to mRNA degradation, translational repression, or translational activation. To demonstrate the direct binding of sRNA to Hfq, a gel-mobility shift assay (EMSA) could be performed. In this assay, labelled sRNA is mixed with purified Hfq protein. If they interact, the complex will migrate slower than the sRNA alone in a gel.

Answer 8

Alternative sigma factors are proteins that bind to RNA polymerase and direct it to transcribe specific sets of genes by recognising specific promoter sequences. In E. coli, sigma-70 is the major sigma factor, responsible for transcribing housekeeping genes. Sigma-N is involved in the transcription of genes related to nitrogen limitation, and sigma-S is associated with the stationary phase. Each sigma factor recognises a different consensus sequence in the promoter region: sigma-70 recognises -35 and -10 elements while sigma-N (54) recognizes -24 and -12.

Answer 9

Protein ubiquitination is a process where ubiquitin, a small protein, is attached to a target protein. This process involves multiple steps and enzymes including ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). Ubiquitination can lead to proteasomal degradation, altered protein function or localisation and in the context of the general stress response, ubiquitination primarily targets damaged or misfolded proteins for degradation.

Answer 10

The transcription factors Msn2 and Msn4 are key regulators of the general stress response (GSR) in yeast, upregulating a wide range of genes involved in processes such as carbohydrate metabolism, redox reactions, protein folding and degradation, DNA repair and intracellular signalling. These transcription factors are activated in response to a variety of stress conditions. When stress occurs, Msn2 and Msn4 are rapidly phosphorylated, leading to their nuclear accumulation and activation of target genes.

Answer 11

Quorum quenching is the process of interfering with QS to disrupt bacterial communication and prevent coordinated group behaviours. The three main strategies include: 1) Blocking AHL synthesis, preventing the production of the signalling molecules. 2) Interference with signal receptors, using molecules that bind more strongly to the receptor than the autoinducers, blocking the receptor. 3) AHL inactivation by employing enzymes like lactonases to degrade the autoinducer molecules.

Answer 12

A sensor protein (typically in the plasma membrane or cell wall), a response regulator protein (usually in the cytoplasm), and a signal. The sensor detects environmental changes and transmits the signal via conformational changes.

Answer 13

The sensor protein detects a stimulus, leading to its autophosphorylation. The phosphate group is then transferred to the response regulator, which can then bind to DNA and alter gene expression.

Answer 14

Quorum sensing is a communication mechanism used by bacteria to coordinate group behaviours based on population density. It involves the production and detection of signalling molecules called autoinducers.

Answer 15

Gram-negative bacteria typically use acylated homoserine lactones (AHLs) as autoinducers, which are membrane permeable. Gram-positive bacteria use secreted peptides as autoinducers, requiring ABC transporters for secretion.

Answer 16

sRNAs are short RNA molecules that do not code for proteins but regulate gene expression. They can act by binding to mRNA, affecting translation or stability.

Answer 17

RyhB is negatively regulated by the ferric uptake regulator (Fur). In iron-limited conditions, Fur repression of RyhB is alleviated. RyhB then suppresses genes involved in iron storage and iron-using proteins, making more iron available.

Answer 18

It is a conserved, initial response to various stresses, aiming to protect critical cell functions until a specific response can be activated.

Answer 19

Chaperones are proteins that bind to other proteins to protect them from denaturation. The main classes include: Small HSPs (HSP12-42), Intermediate HSPs (HSP60-90), Large HSPs (HSP100).

Answer 20

Msn4 is a transcription factor that is induced to activate the general stress response. It binds to specific sequences in the promoter region of genes like SOD1.

Answer 21

SOD1 is a superoxide dismutase that converts superoxide radicals into hydrogen peroxide, which is then broken down by catalases. It is part of the cell's defense against oxidative stress.

Answer 22

Alternative sigma (σ) factors are proteins that direct RNA polymerase to specific sets of promoters. They enable the polymerase to recognize promoter regions, allowing for the transcription of specific genes in response to various conditions.

Answer 23

The heat shock response is triggered by a sudden increase in temperature, which can lead to protein denaturation. It involves the increased expression of chaperones and proteases. Sigma factors such as σ32 (encoded by rpoH) are key regulators of this response.

Answer 24

σE is complexed with an anti-sigma factor, RseA, which sequesters σE in the cytoplasm. When outer membrane stress is detected, RseA is degraded, releasing σE, which can then activate its regulon.

Answer 25

A biofilm is a community of microorganisms attached to a surface, encased in a self-produced matrix of extracellular polymeric substances (EPS). Steps include: 1. Attachment to a surface 2. Accumulation of signalling molecules that activate biofilm formation genes 3. Development of structures and channels 4. Detachment of cells to colonize new locations.

Answer 26

Advantages: Increased resistance to antibiotics and host defenses, increased access to nutrients, and enhanced cell-to-cell communication. Disadvantages: Can lead to chronic infections, biofouling of medical devices, and increased difficulty in eradication.

Answer 27

Bacteria produce signalling molecules that accumulate as the cell population increases. When a threshold concentration is reached, these molecules activate genes involved in biofilm formation.

Answer 28

Quorum quenching is the process of disrupting or inhibiting quorum sensing. This can be achieved by degrading the autoinducers, blocking their receptors, or inhibiting their synthesis.

Answer 29

Gram-positive bacteria have a thick peptidoglycan layer and lack an outer membrane. Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane containing lipopolysaccharides (LPS).

Answer 30

LPS is composed of three parts: Lipid A: Anchors LPS to the outer membrane. Core: A repeating sugar unit attached to Lipid A. O-antigen: A repeating sugar structure linked to the core, unique to each bacterial strain.

Answer 31

Both are types of glycocalyx composed of exopolysaccharides (EPS). Capsules are tightly attached, organized matrices that exclude small particles, while slime layers are loosely attached, easily deformed, diffuse layers.

Answer 32

FtsZ is a protein essential for cell division. It assembles at the division site between segregated chromosomes, forming a ring that constricts the cell membrane.

Answer 33

A flagellum consists of: Filament: composed of flagellin, Hook: a rigid structure connecting the filament to the motor, Basal body: the motor of the flagella, inserted into the plasma membrane.

Answer 34

1. Rhizobia stimulate root hair growth, and are captured in curled root hairs. 2. Infection threads form, allowing bacteria to enter cortical cell layers. 3. Nodule primordium forms and bacteria are released into the plant cytoplasm. 4. Bacteria differentiate into bacteroids which fix nitrogen.

Answer 35

Nod factors are lipochitooligosaccharides secreted by bacteria which are specific to the plant they are infecting. They are recognized by receptors on plant cells, triggering a response that activates nod genes in the bacteria.

Answer 36

MDR transporters are efflux pumps that actively transport drugs out of the cell, reducing their intracellular concentration. This is a common resistance mechanism against many structurally and chemically different compounds.

Answer 37

ABC Transporters: Utilize ATP hydrolysis to drive transport (active transport). MFS Transporters: Utilize the electrochemical gradient of protons (H+) across the membrane (secondary active transport).

Answer 38

Mechanisms include: Mutations in drug target proteins, Overexpression of target proteins, Efflux of the drug via MDR transporters, Metabolic tolerance to the drug.

Answer 39

5-FC is a prodrug that is converted into 5-FU inside the pathogen. 5-FU disrupts DNA and protein synthesis.

Answer 40

Azoles target Erg11p, an enzyme required for ergosterol biosynthesis in fungal cell membranes.

Answer 41

Lipid rafts are tightly packed platforms formed by sphingolipids and sterols. They serve as sorting and segregation devices for proteins, particularly in the plasma membrane.

Answer 42

Markers include chromosome condensation, DNA fragmentation, ROS generation, exposure of phosphatidylserine, and loss of membrane integrity.

Answer 43

Apoptosis in unicellular organisms allows the population to function as a multicellular-like system, with damaged or aged cells sacrificing themselves for the benefit of the collective.

Answer 44

Ubiquitination is involved in tagging proteins for degradation. In the general stress response, it helps remove damaged or misfolded proteins.

Answer 45

Indirect Methods: Expression studies to identify genes that are affected by the presence or absence of the TF. Direct Methods: More rigorous methods to determine direct binding including: Chromatin Immunoprecipitation (ChIP): Determines TF binding sites in vivo. Electrophoretic Mobility Shift Assay (EMSA): Identifies protein-DNA interactions in vitro. DNase Footprinting Assay: Identifies specific DNA regions bound by proteins in vitro.

Answer 46

Transcription factories are discrete sites in the nucleus where multiple active RNA polymerases are concentrated. Actively transcribed genes can be located at the same location, allowing for efficient transcription.

Answer 47

Oxidative stress induces the formation of disulphide bonds in cysteine residues of Yap1, causing conformational changes that prevent its export from the nucleus and leading to nuclear accumulation and activation of MDR genes.

Answer 48

PDR5, SNQ2 and YOR1 which encode for efflux pumps.

Answer 49

Virulence factors include pili (CblA), flagella, siderophores, lipases, haemolysin, melanin, zinc metalloproteases, a type III secretion system, quorum sensing systems, lipopolysaccharide (LPS), and exopolysaccharide (EPS) such as cepacian.

Answer 50

Cepacian is a virulence factor produced by Bcc bacteria that forms a protective layer and contributes to biofilm formation. EPS-negative mutants are less virulent.

Answer 51

The bce gene clusters are responsible for producing exopolysaccharide (EPS), including cepacian. These clusters include genes involved in nucleotide sugar biosynthesis, polymerization, and export of EPS.

Answer 52

The LD50 (lethal dose 50) is the amount of a pathogen required to kill 50% of the hosts in a test group. A lower LD50 indicates higher virulence.

Answer 53

This process involves the attachment of ubiquitin to target proteins in a multi-step process involving: Ubiquitin-activating enzyme (E1), Ubiquitin-conjugating enzyme (E2), Ubiquitin ligase (E3).

Answer 54

FNR system cooperates with the NarQ/NarP and NarX/NarL systems to activate the fumarate reductase and nitrate reductase as part of a newly formed respiratory chain.

Answer 55

DNA binding domain, transactivation domain and a dimerization domain.

Answer 56

A TCRS consists of a sensor histidine kinase (HK), such as BfmS, and a response regulator (RR), such as BfmR. The BfmS sensor protein detects a signal and autophosphorylates. The phosphate group is then transferred to the BfmR regulator, which can then bind to DNA and alter gene expression. The system is activated by a structural change that aligns a conserved histidine residue with the ATP binding site of the kinase.

Answer 57

An experiment could involve creating a mutant strain of A. baumannii with a non-functional bfmS gene and comparing the phosphorylation state of BfmR in this mutant versus a wild-type strain. If BfmR phosphorylation is reduced or absent in the bfmS mutant, it would indicate that BfmS is required for BfmR activation. Another approach would be to use purified BfmS and BfmR proteins and assess the transfer of a phosphate from BfmS to BfmR in vitro, confirming a direct interaction.

Answer 58

Quorum sensing is a regulatory mechanism where bacteria communicate via autoinducers to coordinate gene expression based on population density. The AbaI protein synthesizes the autoinducer N-hydroxy-dodecanoyl-L-homoserine.

Answer 59

A TCRS responds to a stimulus through a sensor histidine kinase (HK) and a response regulator (RR). Upon stimulus detection, the HK autophosphorylates, transferring the phosphate to the RR, which then alters gene expression. HK activation can occur via: ◦ Conformational Changes: Large structural shifts in the protein expose a conserved histidine residue to the ATP binding site, enabling phosphate transfer. ◦ Helix Sliding: A helix containing the histidine slides within the dimerization domain to facilitate the phosphate transfer.

Answer 60

This experiment would use purified BfmS and BfmR proteins, and would include the following: ◦ Incubation: Mix purified BfmS with ATP and purified BfmR in a reaction buffer and incubate. ◦ Controls: ▪ BfmS with ATP, but without BfmR. ▪ BfmR with ATP, but without BfmS. ▪ BfmS and BfmR without ATP. ◦ Detection: Use phospho-specific antibodies against phosphorylated BfmR to detect the transfer of a phosphate from BfmS to BfmR.

Answer 61

Both are LuxI/LuxR homologs. ◦ LasI/LasR: LasI synthesizes an autoinducer that, upon binding to LasR, activates the expression of several virulence genes, including lasB, lasA, toxA, and aprA, as well as lasI itself (positive feedback). ◦ RhII/RhIR: The LasR-autoinducer complex induces the expression of rhIR. RhIR, when bound to its autoinducer, activates some of the same target genes as the Las system, such as lasB and aprA, but also unique targets like rpoS and rhlAB.

Answer 62

Quorum quenching disrupts bacterial communication, which can reduce virulence and biofilm formation. ◦ Autoinducer Degradation: Enzymes that degrade AHLs (autoinducers in Gram-negative bacteria) can be used. For example, AHL lactonases can break down AHLs. ◦ Receptor Blocking: Molecules that bind to and block the autoinducer receptor but do not activate it, preventing the signal from being transduced. ◦ Inhibition of Synthesis: Drugs that inhibit autoinducer synthases such as AbaI and LasI can reduce the accumulation of the signalling molecules.

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