Microbiology Exam 2

BIO2104 Weekly Review for Week 5

Reading

Chapter 10

Review Questions

1. Define the following terms:

a. Metabolism
All chemical reactions in a cell that maintain life.

b. Catabolism
Breaking down molecules to release energy.

c. Anabolism
Building molecules using energy.

2. Understand the basic structure and role of enzymes.
Structure – Made of proteins, has an active site where reactions occur
Role – Speed up chemical reactions by lowering activation energy
Specificity – Each enzyme works on a specific substrate (like a lock-and-key)

3. Distinguish between competitive and noncompetitive inhibition.
Competitive Inhibition-
Inhibitor competes with the substrate for the active site
Can be overcome by adding more substrate

Noncompetitive Inhibition -
The inhibitor binds elsewhere which changes the enzyme shape so the active site no longer accepts the substrate.
Cannot be overcome by adding more substrate.

4. Understand the metabolic control process and purpose of feedback inhibition.
A product will slow down or stop its own production by inhibiting an enzyme earlier in the pathway.
Helps regulate metabolism and prevent waste.

5. Know the basic reactions catalyzed by the following enzyme groups:
a. Oxidoreductase – Transfers electrons (oxidation and reduction reactions)
b. Transferase – moves functional groups between molecules
c. Hydrolase – Breaks bonds using water (hydrolysis).
d. Lyase – Breaks bonds without using water.
e. Isomerase – Rearranges atoms within a molecule to make an isomer.
f. Ligase – Joins two molecules together
g. Kinase – Transfers phosphate groups to molecules (often from ATP)
h. Phosphatase – Removes phosphate groups

6. Understand the roles that cofactors and coenzymes play in enzymatic reactions.
Cofactors – Non protein helpers (e.g. metal ions like Mg2, Fe2)
Coenzymes – Organic molecules that assist enzymes (e.g. vitamins like NAD+, FAD)

7. Explain the effect on enzyme activity due to changes in temperature, pH, and substrate
concentration.
Temperature – too high or low can denature (destroy) enzymes
pH – Extreme pH changes enzyme shape and function
Substrate Concentration – More substrate increases activity until enzymes are saturated

8. Explain how ATP is made through: substrate-level phosphorylation, oxidative phosphorylation, and
photophosphorylation.
Substrate-level phosphorylation
Direct transfer of a phosphate to ADP

Oxidative Phosphorylation
Uses electron transport chain (ETC) to. Make ATP

Photophosphorylation
Light-driven ATP production in photosynthesis

9. Know the basic processes of the glycolysis (focus on inputs and outputs).
a. How much ATP is used? 2 ATP
b. How much ATP is made? 4 (2net)
c. How much NADH is made? (2 NADH)
d. What is the starting molecule and the end products? Starting is glucose ending is pyruvate, ATP and NADH

10. What occurs during the transition reaction?
Converts pyruvate into Acetyl-CoA
Produces NADH and CO2

11. Know the basic steps of the Krebs cycle (focus on the inputs and outputs).
a. How much ATP is made? 2 ATP
b. How much NADH and FADH 2 are made?  6 NADH, 2FADH2
c. How much CO2 is generated? Why is it generated? 4CO2 because the carbons are a waste product after acetyl-coA is oxidized
d. What is the starting molecule and the end products? ACETYL COA STARTS, CO2, NADH, FADH2, ATP ENDS

12. Understand the basic set up and purpose of the electron transport system and how it drives
oxidative phosphorylation.
Uses NADH & FADH2 to generate ATP
Oxygen is the final electron acceptor, forming water
Drives oxidative phosphorylation to make about 34 ATP

13. Know the following metabolic intermediates and what important metabolites are made from them
(reference the lecture slides):
a. Dihydroxyacetone phosphate (DHAP)
Used in lipid metabolism

b. Acetyl-CoA
Enters Krebs cycle; used for fatty acid synthesis

c. Pyruvic acid (pyruvate)
Can be converted into Acetyl-CoA or used in fermentation

d. Glucose-6-phosphate
Used in glycolysis & pentose phosphate pathway

e. Phosphoglyceric acid
Intermediate in glycolysis

f. Phophoenolpyruvic acid
Helps make ATP in glycolysis

g. Oxaloacetatic acid
Key molecule in the Krebs cycle

h. α-ketoglutaraic acid
Krebs cycle intermediate; used for amino acid synthesis

14. State the importance of the Pentose Phosphate Pathway and the Entner-Doudoroff Pathway.
Pentose Phosphate Pathway – produces NADPH & ribose for DNA/RNA
Entner-Doudoroff Pathway – Alternate glycolysis used by some bacteria

15. Understand the process of fermentation and how much ATP is produced by the cell during this
process.
Converts pyruvate into waste products (e.g. alcohol, lactic acid)
Produces only 2 ATP per glucose (much less than respiration)

16. Compare and contrast the outputs of alcohol and acidic fermentation.
Alcohol fermentation – Produces ethanol & CO2 (e.g. yeast)
Acidic Fermentation – Produces lactic acid (e.g. muscle cells, bacteria)

17. Compare general amounts of ATP produced by aerobic respiration, anaerobic respiration, and
fermentation.
Aerobic Respiration – 28-38 ATP
Anaerobic Respiration – Varies but less than Aerobic (about 2-36 ATP)
Fermentation – 2 ATP per glucose (least efficient)

18. Know the final electron acceptor(s) for
aerobic respiration – O2
anaerobic respiration – NO3, SO4, and CO3
fermentation – pyruvate


19. Compare oxygenic and anoxygenic photosynthesis.
Oxygenic – Produces O2 (plants, cyanobacteria)
Anoxygenic – No O2 produced (some bacteria)

20. Briefly describe the Calvin Cycle and its importance.
Uses CO2, ATP and NADPH to make glucose
Essential for carbon fixation in plants

BIO2104 Weekly Review for Week 6

Reading:

Chapter 6 and 8

Review Questions:

1. Briefly describe the process of DNA replication in prokaryotic cells, including leading and lagging strands.
-Starts at the origin of replication (one per chromosome)
-Helicase unzips DNA ; SSB proteins keep the strands apart
-Primase lays down RNA primers
-DNA Polymerase III adds nucleotides in the 5’ to 3’ direction
-Leading strand is continuous synthesis toward the replication fork
-Lagging strand is sections of synthesis away from fork forming Okazaki fragments
-DNA polymerase I replaces the RNA primers with DNA
-DNA ligase joins the Okazaki fragments

2. Briefly explain the process of transcription/translation in prokaryotes and eukaryotes (Similarities?)
Both use RNA polymerase to make mRNA from DNA
Ribosomes translate mRNA into protein

(Differences?)
Prokaryotes – Transcription and translation happen simultaneously in the cytoplasm. No mRNA processing
Eukaryotes – Transcription occurs in the nucleus, translation in the cytoplasm. mRNA is processed (splicing, 5’ cap, poly-A tail).

3. Know the possible consequences of base substitution (point) mutations:

a. silent mutation
No change in the amino acid (due to codon redundancy)

b. missense mutation
Changes one amino acid, possibly altering protein function

c. nonsense mutation
Creates a stop codon prematurely, leading to a shortened non-functional protein.

4. Describe the consequences of a frameshift mutation.
-Insertion/deletion shifts the reading frame
-Changes every codon after the mutation
-Usually results in a non-functional protein

5. Draw an operon, including the:
promoter region – Binding site for RNA polymerase
operator region – Regulatory region where repressors bind
structure gene sequence(s)- Code for proteins (enzymes)

6. Describe the control mechanisms for the lac operon.
-No lactose  repressor binds operator, blocking transcription
-Lactose present  Lactose binds repressor, inactivating it  Transcription occurs
-Glucose present  Low cAMP, CAP doesn’t bind, low transcription

7. Describe the control mechanisms for the tryptophan operon.
-Low tryptophan  Operon is ON, enzymes make tryptophan
-High tryptophan  Tryptophan binds repressor  repressor blocks transcription

8. Describe the processes of transformation and transduction.
Transformation – Bacteria take up foreign DNA from environment
Transduction – Bacteriophage (virus) transfers DNA between bacteria

9. Compare conjugation between: F + x F - and Hfr x F-

10. Explain what transposons (jumping genes) are and how they can contribute to genetic changes.
-Mobile DNA sequences that move within genome
-Can insert into genes, disrupting functions

11. Explain how the following is used in a plasmid for gene cloning:

a. antibiotic resistance gene
Selects for transformed bacteria

b. LacZ
Helps identify successful recombinants

c. complementary DNA (cDNA)
Complementary DNA made from mRNA (no introns)

12. Briefly explain the purpose and use of restriction enzymes.
-Cut DNA at specific sequences (palindromes)
-Used in cloning, genome editing, DNA analysis

13. Briefly describe the processes of polymerase chain reaction (PCR).
-Denaturation: heat separates DNA strands
-Annealing: Primers bind to target DNA
-Extension: SNA polymerase adds nucleotides

14. Compare and contrast the following types of PCR:

a. Regular PCR
Amplifies DNA

b. RT-PCR
Converts RNA to DNA before PCR

c. Real-time (qPCR)
Measures DNA amplification in real-time

15. Understand the basic process and use of DNA sequencing.
-Determines the order of nucleotides
-Used in genetic research, forensics and diagnostics

16. State the difference between:
- Sanger sequencing uses labeled nucleotides; slow but accurate
-Next-Gen sequencing is high-speed, parallel sequencing
-RNA Seq sequences mRNA to analyze gene expression

BIO2104 Weekly Review for Week 7

Reading:

Chapter 13

Review Questions:

1. Explain how the microbiome can prevent the activity of pathogens.
-Competes for space and nutrients, making it harder for pathogens to grow
-Produces antimicrobial substances that kill or inhibit pathogens
-Stimulates the immune system to be more effective
-Lowers pH (e.g. in the gut or vagina) to create an unfavorable environment for pathogens

2. Compare and contrast different portals of entries for pathogens.
Similarities:
-all allow microbes to enter the body
-can lead to infection if the immune system is weak

Differences:
Skin – through cuts, insect bites or wounds
Mucous membranes- respiratory tract (inhalation), gastrointestinal tract (ingestion), urogenital tract (sexual contact).
Parenteral route – directly into the tissues via punctures, needles or surgery

3. Compare and contrast ID50 and LD50.
ID50 (infectious Dose 50) – number of microbes needed to infect 50% of the population
LD50 (lethal dose 50) – amount of toxin/pathogen needed to kill 50% of a population
Key Difference – iD50 measures infection potential, LD50 measures death potential

4. Explain the importance of virulence factors.
Help pathogens infect, spread and evade the immune system.

Give examples of virulence factors that:
a. Are enzymes
Coagulase (clots blood to protect bacteria)

b. Digest membrane components
Phospholipases (break down cell membranes)

c. Have both binding and enzyme activity
Hyaluronidase (breaks down connective tissue, helping bacteria spread)

d. Can lead to overstimulation of the inflammatory system
Superantigens (cause excessive immune response, leading to shock)

e. Can prevent phagocytosis
Capsules (hide bacteria from immune cells)

5. What is an endotoxin? How does it compare to an exotoxin? State specific examples of each.
Endotoxin -
Found in Gram-negative bacteria (LPS in outer membrane)
Released when bacteria die
Causes fever, inflammation and septic shock

Exotoxin -
Secreted by both Gram-positive & Gram-negative bacteria
Highly toxic, specific effects
Example: Botulinum toxin

6. State methods by which organisms can exit a host.
-Respiratory droplets (coughing, sneezing)
-Feces (gastrointestinal infections)
-Urine (UTIs)
-Blood (insect bites, needles)
-Skin (wounds, lesions)
-Sexual fluids (STIs)

7. Differentiate between the following stages of infectious disease:
incubation stage – no symptoms yet, pathogen is multiplying
prodromal stage – early, mild symptoms appear
acute phase – full-blown illness, most severe symptoms
convalescent period – symptoms fade, recovery begins
continuation period – some infections linger or cause long-term effects

8. Explain the difference between the following terms:
a. communicable and noncommunicable diseases
Communicable- spreads between people (flu)
Noncommunicable – Does not spread (tetanus)

b. Local, focal and systemic diseases
Local – Confined to one area (skin infection)
Focal – starts local and spreads (infected tooth leading to heart infection)
Systemic – Affects the whole body (sepsis)

c. acute, latent and chronic diseases
Acute – rapid onset, short duration (flu)
Latent – Dormant, can reactivate (herpes)
Chronic – long-lasting (tuberculosis)

d. Bacteremia, viremia, toxemia, septicemia/sepsis
Bacteremia – bacteria in the blood (not multiplying)
Viremia – Toxins in the blood
Septicemia- bacteria multiplying in blood, causing severe infection

e. Primary and secondary infection
Primary – Initial illness (flu)
Secondary – Happens after primary weakens the immune system (pneumonia after the flu)

9. Differentiate the methods by which transmission can occur:
a. Direct contact transmission – Physical touch (kissing, touching wounds)
b. Congenital transmission – from mother to baby (placenta, birth, breast milk)
c. Indirect contact transmission – touching contaminated objects (doorknobs, utensils)
d. Droplet transmission – respiratory droplets (coughing, sneezing)
e. Vehicle transmission – contaminated food, water, air
f. Vectors - differentiate between:
mechanical – carry pathogens without being infected (flies landing on food)
biological – Pathogens develop inside the vector (mosquito carrying malaria)

10. Explain the difference between a reservoir and a host and name the types of reservoirs.
Reservoir – Where a pathogen normally lives
Types:
-Human reservoir (carriers of disease)
-Animal reservoir (zoonotic diseases like rabies)
-Environmental reservoir (soil, water)
Host – Organism infected by the pathogen

BIO2104 Weekly Review for Week 8

Reading:

Chapter 14

Review Questions:

State the role of an epidemiologist.

Study how diseases spread and affect people. They collect and analyze data to find out why diseases

happen and how to prevent or control them and they help guide public health decisions and inform

people about staying healthy.

What are notifiable infectious diseases?

Illnesses that must be reported to health authorities when they are diagnosed period this helps track

outbreaks monitor public health and implement control measures to prevent the spread of disease

period examples include diseases like tuberculosis measles and COVID-19

State the difference between prevalence and incidence of a disease.

Prevalence refers to the total number of cases of a disease in a population at a specific point in time and

incidence refers to the number of new cases that develop during a certain time period

Explain the difference between sporadic, endemic, epidemic and pandemic diseases.

Sporadic occurs occasionally and irregularly.

Endemic regularly occurs within a specific geographic area or population at a consistent rate over time

period.

Epidemic is a sudden increase in the number of cases of a disease above what is normally expected in a

specific area or population.

Pandemic to the global outbreak of a disease that affects large numbers of people across multiple

countries or continents

Explain the difference between a point-source epidemic, a common-source epidemic and a

propagated epidemic.

Point source occurs when a group of people are exposed to the same source of infection at the

same time for example a single potato salad at a picnic

common source epidemic happens when people are exposed to the same infectious source over

a period of time causing a longer more gradual increase in cases an example would be the

McDonald's onion E coli outbreak

propagated epidemic is spread from person to person over time leading to a gradual rise in

cases that can last longer as the infection continues to spreadWhat is the purpose of the reproducibility rate? Explain how it is used along with case fatality ratios to

determine the need for a response to an outbreak.

The reproducibility rate or R0 measures how many people on average one infected person will spread

the disease too this helps assess how contagious the disease is a higher R0 indicates a more easily

spread illness for example if the R0 is five that means one infected person could potentially infect 5

susceptible people

The case fatality rate or CFR represents the percentage of people who die from the disease out of those

who are diagnosed with it

Together these two metrics guide the outbreak response R0 is high the disease could spread quickly

indicating a need for stronger control measures if the CFR is high it suggests the Disease is severe

reinforcing the urgency for a response

Both metrics help health authorities determine whether the outbreak requires urgent containment

actions to prevent widespread illness and death

Explain what a nosocomial infection or healthcare-associated infection is and how they occur. State

methods by which they can be avoided.

A nosocomial infection or healthcare associated infection is an infection that a patient acquires while

receiving treatment healthcare settings such as a hospital

How they occur:

Unsterile medical instruments

Prolonged hospital stays or invasive procedures such as catheters or ventilators

Improper hand hygiene of healthcare workers

Methods to avoid them:

Regular hand washing by healthcare workers and patients

Use of sterile techniques during procedures

Proper sterilization and disinfection of medical equipment

Isolating patients with contagious infections

Monitoring and controlling the use of antibiotics to present resistance prevent resistance

State what is meant by ‘emerging infection’. State factors that can contribute to the emergence of an

infectious disease.

A new or previously unknown infectious disease that is rapidly spreading or increasing in occurrence.

These infections can also include diseases that are reappearing after a period of decline

Contributing factors:

• Environmental changes (climate change, deforestation)

• Human behavior (urbanization or travel)

• Changes in pathogens (mutations or resistance to treatments)

• Globalization (increased movement of people or goods)• Antibiotic misuse (leading to resistant strains)

• Zoonotic transmission(diseases jumping from animals to humans)

Explain what a zoonoses are.

Diseases that can be transmitted from animals to humans such as rabies, tuberculosis, bird flu and Lyme

disease.

What are neglected tropical diseases?

A group of infectious diseases that primarily affect people living in poverty in tropical and subtropical

regions these diseases can be things like dengue fever, leprosy, trachoma and chagas disease