Unit 1 Exam Recall Q's

Question 1

Differentiate between prokaryote and eukaryote cells

Answer 1

• Prokaryotes are always unicellular, while eukaryotes are often multi-celled organisms.
• DNA in eukaryotes is stored within the nucleus, while DNA is stored in the cytoplasm of prokaryotes
• prokaryotes undergo transl. and transcript. in cytoplasm while eukaryotes do so in nucleus then cytoplasm

Question 2

Demonstrate an understanding of the relatedness of living organisms
based on phylogeny

Question 3

Understand and define features of prokaryotic cells

Answer 3

• Prokaryotic cells are much smaller than eukaryotic cells
• have no nucleus, and lack organelles.
• encased by a cell wall
• have capsule or slime layer made of polysaccharide
• move by flagella
• ribosomes complex (30s & 50s)
• can become bacterial endosperm

Question 4

Differentiate between Gram positive and Gram negative bacteria

Answer 4

Gram-negative bacteria
- thin peptidoglycan cell wall
- outer membrane containing lipopolysaccharide.
- have Lipid A (part of LPS) is embedded in the OM (its an endotoxin)
- Core has O-specific polysaccharide

Gram-positive bacteria
- lack an outer membrane
- surrounded by layers of peptidoglycan many times thicker than is found in the Gram-negatives.
- Lipotechoic acids (LTA) are a major component of Gram positive cell walls..recognized by components of the innate immune system in higher eukaryotes

Question 5

Understand basic bacterial ribosome structure and function

Answer 5

• Bacterial ribosomes are composed of two subunits with densities of 50S and 30S
• protein synthesis
• ribosomes are synthesized in the cytoplasm through the transcription of multiple ribosome gene operons.

Question 6

Identify bacterial organelles and processes involved in endospore
formation

Answer 6

• Endospores are dormant alternate life forms produced by the genus Bacillus (resistant, dormant survival form of the organism)
• live in soil
• Under conditions of starvation, especially the lack of carbon and nitrogen sources, a single endospores form within some of the bacteria. The process is called sporulation
• resistant to high temperatures (including boiling), most disinfectants, low energy radiation, drying, etc
• can then survive until a variety of environmental stimuli trigger germination , allowing outgrowth of a single vegetative bacterium

Question 7

Where and how do bacteria store DNA?

Answer 7

DNA is contained in a single circular molecule, bacterial chromosome. The chromosome, along with several proteins and RNA molecules, forms an irregularly shaped structure called the nucleoid. This is in the cytoplasm.

Question 8

How does one distinguish between a chromosome and a plasmid? What experiment could be done?

Answer 8

Remove the plasmid, see if it regenerates or divides and if it does then its chromosome.

Note:
- plasmid DNA only contains extra genes that are not really necessary for the organism existence, but chromosomal DNA carries all of the information needed for the growth of the organism, development of the organism, and reproduction.

Question 9

Why can’t we use antibiotics on viruses?

Answer 9

They do not have cell walls or peptidolycan

Question 10

Why do microbes adapt fast?

Answer 10

Want resources and to exploit host, evolution is about survival

Question 11

Why is iodine used in gram stain?

Answer 11

interacts w crystal violet to make bigger/obvious, retains purple, affinity

Question 12

If polar localization of flagella, where would ‘sensing’ machinery be?

Answer 12

It should be on front of cell or leading edge..meanwhile signal transduction is back where flagella are

Question 13

Describe bacterial genetic elements required for gene expression (basic genetics)

Answer 13

• Initiation of translation in bacteria involves the assembly of the components of the translation system, which are: the two ribosomal subunits (50S and 30S subunits)
• Transcription initiation in bacteria requires proteins known as sigma factors (σ); essential for proper promoter recognition by RNA polymerase.
• a promoter, the correct translation initiation sequence such as a ribosomal binding site and start codon, a termination codon, and a transcription termination sequence.

Question 14

Describe the prokaryotic operon structure

Answer 14

• Operons are regulatory complexes that control and coordinate protein synthesis based on cell requirements.
• The operon genes occur continuously on the DNA and are controlled by a single promoter.
• The promoter is in turn regulated by regulatory elements based on the cell’s metabolic need.
• The main constituents of the operon are a promoter sequence, operator sequence, and structural genes.
• They participate in gene regulation by inducing or repressing genes.
• The regulatory proteins are either repressors or activators that bind to the operator gene and determine the fate of the operon.

Question 15

What are the roles of transcriptional activators and repressors?

Answer 15

• Activators recruit coactivators = gene activation
• Repressors recruit corepressors = transcriptional repression.

Question 16

Describe bacterial flagellar ultrastructure

Answer 16

The filamentous part that extends from the cell membrane is called the axial structure and consists of three major parts…

(1) filament
(2) hook, and rod,
(3) basal body

Question 17

Apply knowledge of the transcriptional organization using the paradigm of flagellar genes

Question 18

Why does sigma 28 interact with FlgM if it prevents expression of class 3 genes?

Answer 18

FlgM must be removed from system for Sigma28 to activate class 3 gene expression, but both are expressed under same transcriptional control (middle genes)

Question 19

What are antibiotics and where do they come from?

Answer 19

• are chemicals that kill or inhibit the growth of bacteria
• used to treat bacterial infections.
• produced in nature by soil bacteria and fungi
• chemically synthesized based on the structure of the natural products.

Question 20

Identify what cellular features are targeted by antibiotics and their basic mechanism of action

Answer 20

Three main antibiotic targets in bacteria:
(1) The cell wall or membranes that surrounds the bacterial cell.
(2) The machineries that make the nucleic acids DNA and RNA.
(3) The machinery that produce proteins (the ribosome and associated proteins)

Antibiotics disrupt essential processes or structures in the bacterial cell. This either kills the bacterium or slows down bacterial growth.

Question 21

How do bacteria develop
resistance to antibiotics?

Answer 21

• Through mutation and selection, bacteria can develop defense mechanisms against antibiotics.
• Mutations in their genes allow some bacteria to survive these antibiotics, and they pass these genes along to their descendants. This is how antibiotic-resistant strains of bacteria are formed.

Question 22

Describe bacterial community and
biofilm structure

Answer 22

• the ability to form communities called biofilms embedded in an exopolysaccharide matrix is one of the mechanisms of resistance used by bacteria to survive in the presence of an antibiotic

Question 23

What makes a relevant and appropriate target for inhibition?

Answer 23

Bacterial features that are unique (cell wall, outer membrane, protein translation and DNA replication - ribosomes, lipids, etc)

Question 24

Would flagella be a suitable target for inhibition?

Answer 24

No, only effective when flagella are expressed. Cell wouldn’t be able to swim.

Question 25

what are the four classes of antibacterial compounds?

Answer 25

methicillans, protein synthesis inhibitors, DNA/RNA and peptides

Question 26

Describe the mechanism of Beta-Lactam antibiotics?

Answer 26

• Block cell wall biosynthesis by inhibiting the transpeptide linkage to peptidoglycan.
• Causing weakened cell wall.
• Easier for immune response to kill bacteria.

Question 27

How do bacteria ‘fight back’ against beta-lactam antibiotics? And how do Chemists respond to that?

Answer 27

Bacteria use b-lactamases
- Enzymes that are secreted by bacteria to cleave the b-lactam ring compounds
- drug ineffective
- Population (density) effects are beneficial! more can take up effects

Chemists respond w/ Clavulinic acid
- b-lactamase inhibitor compound that is added to antibiotics
- $$$$

Question 28

List the four ways in which bacteria can develop antibiotic resistance.

Answer 28

1. Spread of resistance genes through genetic transfer events (Plasmids and conjugation)
2. Transformation (via competence)
3. Conjugation
4. Mutation

(and Lateral gene transfer through viruses aka bacteriophages)

Question 29

Name some ‘acquired’ genetic traits 
or phenotypes bacteria can receive

Answer 29

• Antibiotic resistance genes
• Amino acid biosynthesis genes
• Pilus (fimbrae) genes (attachment features helping to
• Unique or specific gene encoding a particular functional protein..Leading to a new trait (e.g sugar metabolism, virulence)

Question 30

Explain Lederberg and Tatum Experiments (1946)

Answer 30

• found that bacteria could transfer genetic material from one cell to another
• Conjugation was discovered…It was mainly used for transfer of genetic material between bacterial cells by a direct connection. It is a method of horizontal gene transfer.
• Two colonies alone couldn’t grow but together they synthesized amino acids and exchanged info for their progeny.

Question 31

What is combination therapy? Why is this used to treat bacteria?

Answer 31

• Treating w/ multiple antimicrobial agents to reduce the occurrence of surviving antibiotic resistant bacterial strains
• The probability of two independent mutations occurring in the same host (in a short time frame) is less likely

Question 32

Describe the following bacterial strains: MRSA, VRE and XDR (conjunction w/ HIV)

Answer 32

1. Methicillin resistant Staphylococcus aureus - A major issue in hospitals and in the community as it is community acquired (CA-MRSA)
2. Vancomycin Resistant Enterococci (VRE) - strains are very promiscuous with their DNA, naturally competent and many conjugative plasmids..hard to clear infection.
3. Multidrug and extremely resistant M. tuberculosis (XDR) strains - pressing issue in developing countries especially for immuno-compromised individuals, latent (dormant) phase results in carrier state..co-infection w/ HIV

Question 33

What is the importance of virulence factors for bacterial pathogenicity?

Answer 33

help bacteria to (1) invade the host, (2) cause disease, and (3) evade host defenses

Question 33

Differentiate between the concepts of infection, colonization, and disease

Answer 33

Infection - viruses, bacteria, etc enter your body and begin to multiply
Colonization - germs are on the body but do not make you sick (asymptomatic)
Disease - cells in your body are damaged as a result of infection (symptoms show)

Question 34

Identify the traditional classes of virulence factors

Answer 34

1. Extracellular enzymes
   - Function outside of bacterial cell to damage the host cell or tissue
   - promote colonization or spreading
2. Exotoxins
   – Proteins that are secreted to exert subversive functions on host
   cells (deliberate and very specific)
3. Endotoxins
   – Bacterial products that typically have functions for bacterial survival (structural or biochemical) but can still result in a diseased condition for the host
   - Effects are more acute with higher bacterial number (more material to
   initiate signalling)

Question 35

What are genetic pathogenicity islands

Answer 35

• distinct genetic elements on the chromosomes of a large number of bacterial pathogens. PAIs encode various virulence factors and are normally absent from non-pathogenic strains of the same or closely related species.
• play a pivotal role in the virulence of bacterial pathogens of humans and are also essential for virulence in pathogens of animals and plants.
• discrete DNA segments of ∼10 to >100 kbp that encode virulence factors and other accessory proteins, but no essential proteins. They reside within larger genetic units, usually the chromosomes, occasionally within plasmids or bacteriophages

Question 36

Recognize the burden of human disease severity associated bacterial persistence in the environment
(focus on Gram negative pathogens)

Answer 36

• Cholera toxin is of the AB type
• Toxin co-regulated pilus (by means of intestinal cell attachment and toxin secretion)
• combined effect promotes bacterial numbers (replication) and causes massive host diarrhea…Sheds (releases) copious amounts of ‘new’ bacteria into the environment

Question 37

How can E. coli be part of our normal flora and yet still cause such devastating morbidity and mortality?

Answer 37

• aids digestion and protects us from other harmful microbes.
• Certain strains of bacteria that are dangerous (or pathogenic) are introduced or evolve alongside virulence factors (toxins, pili to attach, etc)

Question 38

Recall Koch’s four postulates

Answer 38

1. Pathogen must be in all cases of disease and absent from healthy animals.
2. Suspected pathogen must grow in pure culture.
3. Cells from pure culture of suspected pathogen myst cause disease in healthy animal.
4. Suspected pathogen must be re-isolated and shown to be same as original.

Question 39

Does HIV cause AIDS?

Answer 39

HIV (human immunodeficiency virus) is a virus that attacks the body’s immune system. If HIV is not treated, it can lead to AIDS (acquired immunodeficiency syndrome).

Question 40

Demonstrate a detailed understanding of how certain pathogens subvert eukaryotic cellular pathways (cellular microbiology)

Answer 40

• evolved specific effectors and toxins to hijack host cell machinery for their own benefit
• Signaling molecules are preferentially targeted by pathogens because they globally regulate many cellular processes.
• ex: internalin (Inlb), ActA, LLO

Question 41

Recognize the global burden of respiratory disease associated with
Mycobacterium tuberculosis

Answer 41

• Extremely low infectious dose (highly infectious)
• Endemic where population levels are higher and medicine is less available
• Drug resistant strains are appearing
• Treatment of infected individuals is a long process often with failure
• Co-infection with M. tuberculosis and HIV is the major issue worldwide

Question 42

Understand etiology of syphilis and historical context of specific clinical studies

Answer 42

• sexually transmitted infectious (STI) disease
• bacterium Treponema pallidum
• Chronic disease progression (3
  stages) that includes latency (minor
  or no symptoms)
• Treatable with penicillin
• US gov withheld treatment to experimented black peoples over 40 yr period

Question 43

What are 3 main processes of Listeria

Answer 43

1. internalin (Inlb)
2. ActA
3. LLO

Question 44

Describe the processes of each: internalin (Inlb), ActA, LLO

Answer 44

(1) Induces internalization, binds to cell surface protein Met, Clathrin mediated endocytosis is used to acquire nutrients and recycle membrane

(2) a host actin modulating protein, creates Listerio-pod (Actin based motility) mediates directed
intracellular ‘push’ for eventual intercellular movement, gets double membrane
– Upon invasion of Listeriopod into an
adjacent cell, LLO is activated again

(3) Pore forming toxin, Replication in cytoplasm after internalization, active at pH 6 (phagosome) and less so within
the host cell cytoplasm (pH7, neutral)

Question 45

Provide 3 examples of pathologies (diseases) of E.coli that are observed in humans and other animals.

Answer 45

urinary tract infection, abdominal and pelvic infection, pneumonia, meningitis, vomiting, stomach cramps

Question 46

Distinguish between Listeria, E.coli, cholera and syphllius

Answer 46

Listeria:
- food borne
- bacterium Listeria monocytogenes
- targets pregnant women, elders, weakened immune systems
- flu like symptoms, meningitis, gastroenteritis, mother-child
- Gram positive bacterium

E. coli
- Shiga toxin-producing (STEC)
- Infection contaminated food or water
- UTI, vomiting, meningitis, stomach cramps

Cholera
- contaminated water
- Death in 48 hours without treatment
- Massive dehydration, diarrhea (rice water), ion imbalance, low tissue damage, results in organ failure

Syphllius
- sexually transmitted infection (STI)
- bacterium Treponema pallidum
- treatable with peniclin
- chronic disease progression
- 3 stages: sores, organ dysfunction & lesions, nervous & cardiovascular dysfunction

Question 47

Explain what a tubercule is? What is it composed of? What does it do? Why become dormant?

Answer 47

• associated TB disease
• granuloma that exists after M. tb
  replication within a macrophage (phagosome)
• made of recruited T cells, bacteria and
  macrophage
• some survive in a latent (dormant) form

Why?
- Avoid an ‘active’ immune response
- Carrier, asymptomatic, in ‘equilibrium’ with host
- Can be ‘activated’ and then become infectious again (once immunocompromised)

Question 48

Describe AB toxin subunits? What is their goal?

Answer 48

A subunit
- heterodimer (composed of A1&A2)
- ADP ribosylating activity (A1) modifies a host protein blocking its function
- Alpha helix (A2) sometimes requires activation by a host cellular protein

B subunit:
- homopentamer (five sub-units)
– Binds to host cell receptor (glycoprotein)
- Specificity and highly specialized
- targets AB5 toxins

Goal: abrogate normal cellular activity (inhibit protein synthesis via phosphorylation of eukaryotic elongation factor)

Question 49

Name three horizontal gene transfer mechanisms. How do they function?

Answer 49

transformation - a bacterium takes up a piece of DNA floating in its environment

transduction - DNA is accidentally moved from one bacterium to another by a virus

conjugation - DNA is transferred between bacteria through a tube between cells

Question 50

Explain how genetic mutations can be helpful or harmful

Answer 50

• Random mutations in combination with selective pressure (Bacteria that thrive spread and replicate better than competitors and then become the dominant form of bacteria in the environment)
• Mutation in ribosome genes results in protein synthesis inhibitors not being effective
• Mutation in DNA gyrase prevents fluoroquinolones from
  working

Question 51

Describe mechanisms of Colicins (antibiotic compound secreted by bacteria)

Answer 51

• proteins poke holes in membranes
• bind to bacterial membrane
  proteins, get internalized
• intracellular nuclease action on DNA,
  rRNA, or tRNA
• forms depolarizing and de-energizing ion-conductive channels in the CM
• prevents cell wall synthesis

Question 52

What makes a relevant and
appropriate target for inhibition? Give examples. (antibiotic targets)

Answer 52

• Bacterial features that are unique like protein translation, cell wall, outer membrane, DNA replication
• ex: Ribosomes, PG, lipids

Question 53

What happens when an individual misses antibiotic doses or has an irregular regimen??

Answer 53

Inconsistency gives these bacteria, alongside selective pressure, time to select mutations building resistance

Question 54

What are efflux pumps? Describe new and old purpose?

Answer 54

• Bacteria have evolved methods to remove toxic compounds from the cell thereby promoting survival

New Use:
- Multicomponent protein channels located in the bacterial membrane that serve to expel toxic compounds from the cytoplasm

Old use:
- pump out heavy metals and other chemicals

Question 55

What does ‘bacterial genes can be co-
expressed’ mean? Do bacteria have introns?

Answer 55

• A single promoter can control the expression of multiple genes, (not observed in eukaryotes)
• Bacterial genes do not have introns (no gene splicing), and transcription/translation occur in the same cellular compartment

Question 56

Explain transcriptional regulation in bacteria & sigma factors

Answer 56

• Bacterial gene expression is a tightly
  controlled process that involves many
  levels of complexity. It is a mechanism for the cell to control its genes based on its immediate environment.
• sigma Factors: proteins that bind to RNA pol and DNA sequences to
  promote gene transcription and specificity under appropriate conditions

Question 57

Explain bacterial flagellum

Answer 57

• Extracellular ‘hair-like’ structure anchored to the cell surface.
• Reversible rotary structure
• Considerable energy and resources
• Energy-driven by sodium ion pump

Question 58

What is FlhC2/FlhD2 complex? “Early genes?”

Answer 58

• Two proteins that form a tetrameric complex acting as entry level regulator for the beginning of flagellar biogenesis
• flhCD gene expression is controlled by catabolite repression, cell state sensors, temperature, inorganic
  salts, nutrients
• Early checkpoint – key event to express or repress flagellar
  expression

Question 59

What role do Class 2 (middle genes) play?

Answer 59

• Encode structural components of the hook basal body structure (think of a building foundation)
• FlhC2D2 acts as an activator…Binds to DNA and RNA polymerase (cis-specificity)
• A specialized ‘flagella specific’ sigma factor is encoded from class 2 genes

Question 60

Explain relationship between sigma28 and FlgM…process of class 3?

Answer 60

-Sigma28 would be present but not active
- FlgM must be removed from the system for Sigma28 to activate class 3 gene expression
- all class 2 gene mutations prevent
flagella from being formed (34 independent mutations)

Note:
- mutations would prevent basal body/rod structure from being made.
- Same effect as having FlgM ‘trapped’ in the cell

Question 61

How is FlgM secreted? What does this lead to?

Answer 61

• FlgM is removed from the cell by being secreted through the basal body/rod structure (once done)
• Class 3 gene expression is repressed until the basal body/rod structure is complete
• FlgM ‘senses’ the developmental state of the growing flagellar structure

Question 62

Differentiate between Archaea and Eukaryotes

Answer 62

Archaea:
- Prokaryotic
- Single celled organisms with diverse ecological niches
- Similar protein translation and transcriptional paradigms to eukaryotes
- Incredible biotech and industrial uses
- No introns and a single chromosome (like bacteria)(generally)

Eukaryotes:
- High order cellular functionality
- Larger in size
- Specialized organelles
- Single and multicellular
- Specialized cell types (immune, organ cells, blood cells etc)
- Yeast and other fungi
- Plants and Animals

Question 63

How do you detect spores generally?

Answer 63

• Dipicolinic acid
• Binds calcium, promotes dryness within the core
• Cortex (dried PG and peptides)