Exam 3 Microbiology

energy

the capacity to do work or bring about change

what are the different forms of energy

heat, light, chemical, mechanical, electrical, nuclear, radiant

metabolism

all of the biochemical reactions that occur within the cells of a living organism

discuss the difference between catobolism and anabolism

• catabolism- breakdown of compounds (release energy, provide building blocks)- ex: starch is broken down into glucose.

• anabolism- building of compounds (requires energy, uses up building blocks) ex- amino acids are built to make proteins

describe a metabolic pathway

a series of linked enzyme-controlled reactions in a cell that begins with a particular reactant and ends with a specific product. one reaction leads to the next in a stepwise manner

coupling reaction

when energy from a catabolic reaction is used in an anabolic reaction

enzyme

reaction-specific protein catalysts that speed up the rate of a reaction. they are involved in but not used in chemical rxn.

in regards to enzyme functioning, define substrate

the reactants that binds to an enzyme

list the characteristics of an enzyme

• lowers AE

• not used up in reactions

• often end in the suffix “ase”

• over 4000 characterized enzymes in living organisms

in regards to enzyme functioning, what is the active site of an enzyme

specific site on an enzyme where substrates bind

In regards to enzyme functioning, how do enzyme-substrate complexes form

substrate binds to enzyme forming an enzyme-substrate complex. the reaction occurs and the substrate is transformed into products. then products are released and the enzyme is available to catalyze another reaction

In thinking about factors that influence enzymes, discuss the effect that mild changes in temperature can have on the rate of a chemical reaction.

Mild increases in temperature can speed up or slow down a chemical reaction because of enzyme and substrate motion. warm temps will speed up the enzyme-substrate contacts which speeds up the chemical reaction. Cool temps will slow down the enzyme substrate contacts, which will slow down the chemical reactions.

In thinking about factors that influence enzyme activity, discuss the effect that high temperatures can have on an enzyme and chemical reactions.

If the temp is too high, the enzyme will denature and no longer function.

In thinking about factors that influence enzyme activity, discuss the effect that pH can have on an enzyme and chemical reactions.

if the pH becomes too acidic or too basic the enzyme will denature and the chemical reactions will stop.

In thinking about factors that influence enzyme activity, discuss the effect that enzyme concentration can have on the rate of a chemical reaction.

Low enzyme concentration → slower reaction because fewer active sites

High enzyme concentration → faster reaction because more active sites

What is the difference between cofactors and coenzymes?*

• Cofactors are inorganic molecules essential for enzyme activity. Ions such as K+ or Ca2+ are common cofactors.

• Coenzymes are nonprotein organic molecules that bind to enzymes near the active site to form the functional enzyme. Many vitamins are coenzymes.

What is the difference between Apoenzyme and Holoenzyme?

An apoenzyme is an inactive enzyme without its required cofactor.

A holoenzyme is the active enzyme with its cofactor attached.

competitive inhibition

an inhibitor binds to the active site and competes it with the substrate, blocking it

noncompetitive inhibition

An inhibitor binds to a site other than the active site, changing the enzyme’s shape so it no longer works properly.

feedback inhibition

one of the products near the end pathway binds to an earlier enzyme and stops the pathway.

Describe the difference between an oxidation reaction and a reduction reaction

• Oxidation = loss of electrons

• Reduction = gain of electrons

What is a dehydration reaction?

a biological oxidation where there is a loss and gain of a hydrogen ion (proton) and an electron

What is ATP?

Adenosine triphosphate (ATP) is the cell’s energy molecule. It captures energy from reactions and provides it to processes that require energy.

List the three compounds that make up the structure of ATP.

1. Adenine (a nitrogenous base)

2. Ribose (a sugar)

3. Three phosphate groups (PO4)

What are the three ways ATP is generated?

1. Substrate-level phosphorylation

2. Oxidative phosphorylation

3. Photophosphorylation

Where is the chemical energy used by living organisms stored in the ATP molecule?

in the high-energy bond between phosphate groups

ATP has been called the rechargeable battery of the cell. Discuss why that statement is true.

ATP is like a rechargeable battery because it stores energy that can be released when a phosphate group is removed, forming ADP. ADP can then be “recharged” by adding a phosphate group back to make ATP again.

Give three general examples of when or where ATP is used

1. chemical work- synthesis of proteins and lipids.

2. transport work- active transport of substances through the plasma membrane

3. mechanical work- muscle contraction in organisms

aerobic respiration

O2 is the final electron acceptor at the end of the electron transport step

anaerobic cellular respiration

O2 is NOT the final electron acceptor at the end of the electron transport step, an oxygen-containing polyatomic ion is the electron acceptor.

fermenation

anaerobic only the first step of cellular respiration occurs and an organic molecule functions as a final electron acceptor.

What is the chemical equation for aerobic cellular respiration?

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP (energy)

glycolysis

splitting of sugar

For each step in aerobic cell respiration, Glycolysis, Krebs cycle, and Electron Transport discuss the following: What is used?

Glycolysis: Simple sugars such as glucose.

Krebs Cycle: Pyruvate

Electron Transport: Oxygen and the hydrogen carriers NADH and FADH2.

For each step in aerobic cell respiration, Glycolysis, Krebs cycle, and Electron Transport discuss the following: What is produced?

Glycolysis: Pyruvate, the hydrogen carrier NADH, and ATP

Krebs Cycle: Carbon dioxide, the hydrogen carriers NADH and FADH2, and ATP.

Electron Transport: Water and ATP

For each step in aerobic cell respiration, Glycolysis, Krebs cycle, and Electron Transport discuss the following:        Where does it occur?

Glycolysis: In the cytosol of both bacteria and eukaryotic cells.

Krebs Cycle: In the cytosol of bacteria and in the matrix of the mitochondria in eukaryotic cells.

Electron Transport: On the cell membrane of bacteria and the inner membrane of the mitochondria in eukaryotic cells.

For each step in (prokaryotic) aerobic cell respiration , Glycolysis, Krebs cycle, and Electron Transport discuss the following: How much ATP is produced?

Glycolysis: A net gain of 2 ATP

Krebs Cycle: 2 ATP

Electron Transport 34 ATP

What is the function of oxygen in aerobic cell respiration?

Oxygen is the final electron acceptor in the electron transport chain and forms water when it picks up two electrons and two hydrogen ions.

In Eukaryotic cells, what is the total amount of ATP that could be produced from one glucose molecule using aerobic cellular respiration?

38 ATP

In prokaryotic cells, what is the total amount of ATP that could be produced from one glucose molecule using aerobic cellular respiration?

36 ATP

What is fermentation and what are the pathways (steps)?

Fermentation is the production of ATP without using Oxygen or an oxygen containing polyatomic ion.

There are two steps, glycolysis and then the fermentation step.

Which step of aerobic cellular respiration is used in anaerobic fermentation?

glycolysis

In each pathway (step) of anaerobic fermentation, how much ATP is produced?

Glycolysis Net gain of 2 ATP and in the fermentation step 0 ATP

What are the three (main) products possible from fermentation?  

Organic acid, Alcohol, and/or CO2 Gas

What is the main importance of each pathway (step) in a anaerobic fermentation pathway?

Glycolysis Step - Production of ATP and NADH

Fermentation Step - The conversion of NADH back to NAD+, which allows glycolysis step to continue breaking down glucose.

What is the difference between lactic acid and alcohol fermentation?

Lactic acid fermentation: The first step is glycolysis. Next pyruvate is broken-down to lactic acid. Alcohol fermentation: The first step is glycolysis. Next pyruvate is broken down into acetaldehyde and CO2. Then acetaldehyde is converted to alcohol.

Why is anaerobic cell respiration important?

Anaerobic respiration is important because it allows organisms (like bacteria) to produce ATP without oxygen, still using ETC

What are lipids broken down to before they can be used in cellular respiration and where do they enter cell respiration?

Lipids are broken down into fatty acids and glycerol. The fatty acids are converted into acetyl-CoA and enter the Krebs cycle, while glycerol enters glycolysis.

What are proteins broken down to before they can be used in cellular respiration?

Proteins are brokendown to amino acids. Then the amino acids are next enzymatically converted to other substances which can enter cell respiration at several point, either glycolysis or the Krebs cycle.

What is an exoenzyme?

Enzymes released from the cell and are used outside of the cell to breakdown nutrients such as carbohydrates, proteins, and lipids.

Why do bacteria have to produce exoenzymes to break down proteins?

Bacteria are not able to ingest large macromolecules like proteins.

What role do biochemical tests have in the classification and identification of bacteria?

Biochemical tests identify bacteria by checking for specific enzymes and reactions. The presence or absence of growth or reactions creates a biochemical “fingerprint,” which is compared to known bacteria to determine the species.

Physical requirements, temperature. Describe the differences between bacteria that are psychrophiles, physcrotroph mesophiles, thermophiles, and extreme thermophiles.

Psychrophiles: 0–20°C (cold-loving)
Psychrotrophs: 0–30°C (can grow in cold, common in food spoilage)
Mesophiles: 20–45°C (moderate temperatures)
Thermophiles: 50–75°C (heat-loving)
Extreme thermophiles: 80°C+ (very high heat)

Physical requirements, pH. What is the difference between bacteria that are acidophiles, neutrophiles, and alkaliphiles?

Acidophiles - can grow in acidic environments (pH below 5.5)
Neutrophiles - can grow in environments near neutral pH (pH range of 5 to 8)
Alkaliphiles - can grow in basic environments (pH above 8.5)

Physical requirements, osmotic pressure tolerance. Explain the difference between the halophiles

Mild halophiles: require ~1–6% NaCl
Moderate halophiles: require ~6–15% NaCl
Extreme (obligate) halophiles: require ~15–30%+ NaCl
Halotolerant (facultative halophiles): grow in 0–15% NaCl (do not require salt)

Chemical requirements, what does CHONPS stand for?

Carbon - the "backbone" of all living matter (organic life).
Hydrogen &amp

Oxygen - both are found in all components of the cell.
Nitrogen - 14% dry mass of cell (Proteins and Nucleic Acids)
Phosphorus & Sulfur - 4% of the dry mass of cell (Cysteine (a.a.) &amp

Nucleic Acids)

Chemical requirements, describe the function of trace elements.

Small amounts of minerals. Important as cofactors for enzymes. Examples: iron, zinc, and copper.

Chemical requirements, describe the function of oxygen.

Essential as a final electron acceptor in respiration.

Chemical requirements, explain the difference between obligate aerobes, obligate anaerobes, and facultative anaerobes.

Obligate aerobes - oxygen necessary.
Facultative anaerobes - can use oxygen when present.
Obligate anaerobes - do not use oxygen. Oxygen is toxic to them.

Chemical requirements, organic growth factors. What are the functions of vitamins and amino acids?

Vitamins:
Act as coenzymes that help enzymes function.

Amino acids:
Used to build proteins; some bacteria must obtain them from the environment.

Culture media, discuss the difference between chemically defined, complex, selective, and differential media.

Chemically defined media:
Exact chemical composition is known.

Complex media:
Contains extracts, so exact composition is unknown.

Selective media:
Allows some bacteria to grow while inhibiting others.

Differential media:
Allows bacteria to grow but shows differences between them (appear differently).

Culture media, discuss some of the methods for culturing anaerobic bacteria.

Reducing media - depletes oxygen in the media.
Anaerobic jars

Culture media, what is the function of enrichment media?

A liquid medium that provides nutrients to help specific bacteria grow and increase in number.

Preserving bacteria, how is deep freezing used in preserving bacteria?

Quick freeze using liquid nitrogen, -194oC. Bacteria survive indefinitely.
Do not use slow freeze using a refrigerator freezer. Ice crystals form. Bacteria usually do not survive (Ice Crystals).

Preserving bacteria, how is lyophilization used in preserving bacteria?

Lyophilization - freeze drying. Quick freeze then vacuum dry. Bacteria are in a powder form and will survive indefinitely.

Preserving bacteria, how agar slants used in preserving bacteria?

The bacteria are grown on the slanted agar in a test tube, then the tube is sealed and stored in the fridge to slow their growth.

Bacterial growth, describe the process of bacterial binary fission.

1. DNA is copied

2. Cell grows and DNA separates

3. Cell splits into two cells.

Bacterial growth, list and describe each of the growth phases that bacteria in culture go through (lag, log, stationary, and death).

1. Lag phase - Little or no cell division. Period of synthesis
2. Log phase - Exponential growth phase. Generation time reaches a constant. Cells are most metabolically active and most sensitive to antibiotics.
3. Stationary phase - Death rate = Division rate. A constant number of cells. Run out of nutrients or pH change is occurring.
4. Death phase - Death rate greater than division rate. No nutrients or extreme pH.

Measurement of growth, discuss how Viable Plate Counts are used to determine the number of bacteria in a culture.

The sample is diluted, spread on agar, colonies are counted, and used to calculate the number of bacteria.

How is Filtration used in determining the presence of bacteria?

A water sample is filtered to trap and concentrate bacteria, then the filter is placed on nutrient media to see if bacteria grow.

Measurement of growth, discuss how the Most Probable Number method is used to estimate the number of bacteria in a stock culture.

The sample is diluted in broth, and growth results are compared to a table to statistically estimate bacterial numbers.

Measurement of growth, discuss how microscopy is used to estimate the number of bacteria in a stock culture.*

Bacteria are counted directly under a microscope using a counting chamber, then calculated to estimate total cells.

Measurement of growth, discuss how turbidity is used to estimate the number of bacteria in a stock culture.

A spectrophotometer measures light passing through a sample; more cloudiness means more bacteria.

Measurement of growth, discuss how metabolic activity is used to estimate the number of bacteria in a stock culture.

Measure the rate of cellular metabolism, such as CO2 or acid released,

Measurement of growth, discuss how dry mass is used to estimate the number of bacteria in a stock culture.

If you know the mass of one cell you can use the dry mass of all of the cells in the sample to determine the number of cells in the sample.

What is a bacterial biofilm?  How are they important in health care?

A community of bacteria that stick together and are held in a self-produced protective matrix.

Biofilms can cause infections because they are harder to remove and more resistant to antibiotics.

What is bacterial biofilm quorum sensing?

Bacteria send out chemical signals to detect population size and coordinate their behavior.

what virus caused COVID-19

SARS -CoV-2

When was COVID-19 first identified?

2019

What is the incubation period for COVID-19?

2-14 days

Which receptor does SARS-CoV-2 use to enter human cells?

ACE-2 receptor

Name three common symptoms of COVID-19.

Fever/cough/fatigue, loss of taste or smell, severe pneumonia-like symptoms

How can COVID-19 spread be reduced?

Masks, social distancing, hand hygiene, avoiding poorly ventilated spaces

Which animals are natural reservoirs for coronaviruses like SARS-CoV-2?

Bats

What causes cholera?

Vibrio cholerae

What is a classic symptom of cholera?

Rice water stool (watery diarrhea)

How is cholera mainly treated?

Oral Rehydration Therapy (ORT) to prevent dehydration

How is cholera transmitted?

Fecal-oral route via contaminated water or food

Who is John Snow and why is he important?

Linked cholera to contaminated water; helped start epidemiology

What is the mortality rate if cholera is untreated?

up to 50%

What strain of E. coli causes severe foodborne illness with bloody diarrhea?

E. coli O157:H7

What serious complication can occur in 5–10% of E. coli O157:H7 infections?

Hemolytic uremic syndrome (HUS), which can cause kidney failure

What are the main symptoms of E. coli O157:H7 infection?

Abdominal cramps, diarrhea (can become bloody), fever, vomiting

Name common sources of E. coli O157:H7 infection.

Undercooked beef, unpasteurized products, contaminated fruits/vegetables, sewage-contaminated water, petting zoos

How can E. coli O157:H7 infection be prevented?

Cook meat thoroughly (72 °C / 160 °F), avoid cross-contamination, drink pasteurized products, wash produce

About how many E. coli O157:H7 cells are needed to cause disease?

Only ~100 organisms

What famous outbreak was linked to undercooked hamburgers?

ack in the Box outbreak (1992–93), 732 infections and 4 deaths

What is the Kreb’s cycle also known as?

tricarboxylic acid cycle (TCA cycle) or citric acid cycle

lag phase

little or no cell division, period of synthesis

log phase or exponential growth phase

cells most metabolically active, most sensitive to antibiotics