Discussion Questions Unit 4/ Zoom Flashcards
Why might an organism that uses glycolysis and the citric acid cycle also need the pentose phosphate pathway?
PPP is an important source of metabolic intermediate to make nucleic acids and amino acids
Compare & contrast pentose phosphate pathway to glycolysis, Entner-Duodoroff pathway to glycolysis, pentose phosphate pathway to Entner-Duodoroff pathway.
Similar all three: start with glucose, some steps
Glycolysis: glucose -> pyruvate, +2 ATP, +2NADH
Entner-Duodoroff: 1 NADH, 1 ATP, 1 NADPH
Similar ED & PPP: precursor metabolites (6-phosphogluconate…), 1 NADPH
Pentose phosphate: 2 NADPH (any ATP made is when it cycles back into the end of glycolysis)
Compare & contrast aerobic respiration in prokaryotes vs. eukaryotes (include theoretical net ATP, location in the cell and end products.)
Similar:
- steps
- glycolysis in cytosol
- glycolysis yield 2 ATP + 2 NADH + pyruvate
- pyruvate -> acetyl CoA yields 2 NADH + 2 CO2
- TCA/Krebs yields 2 ATP + 6 NADH + 2 FADH2
- ETC/chemiosmosis
Prokaryotic aerobic respiration:
- transition step in cytosol (pyruvate -> acetyl- CoA)
- TCA/Krebs in cytosol
- ETC/Chemiosmosis in the CM -> 34 ATP
- Net yield: 38 ATP
Eukaryotic aerobic respiration:
- Transition step as it crosses mitochondrial membranes (use 2 ATP)
- TCA/Krebs in mitochondrial matrix
- ETC/Chemiosmosis in inner membrane of mitochondria -> 32 ATP
- Net yield: 36 ATP
Cyanide is a potent poison because it irreversibly blocks cytochrome a3. What effect would its action have on the rest of the electron transport chain?
What would be the redox state (reduced or oxidized) of ubiquinone in the presence of cyanide?
Cyanide blocks cytochrome a3, preventing electron transfer to oxygen, which halts the entire electron transport chain. In the presence of cyanide, ubiquinone would remain in its reduced state, as electrons cannot progress down the chain.
Explain why hyperthermophiles do not cause disease in humans.
Because they can only survive in high temperatures and the human body is too cold for it
In terms of its effects on human metabolism, why is a fever over 40°C often life threatening?
It can denature our proteins and disrupt our body’s functions
Giardia intestinalis and Entamoeba histolytica are protozoa that live in the colons of mammals and can cause life-threatening diarrhea. Interestingly, these microbes lack mitochondria. What kind of pathway must they have for carbohydrate catabolism?
Glycolysis and fermentation;
No mitochondria -> no aerobic respiration
Two cultures of a facultative anaerobe are grown in the same type of medium, but one is exposed to air, and the other is maintained under anaerobic conditions. Which of the two cultures will contain more cells at the end of a week? Why?
The one exposed to air because facultative anaerobes can grow in oxygen or without oxygen but the oxygen helps make ATP and the ATP helps it grow better and faster w/ energy (aerobic respiration)
Describe how bacterial fermentation causes milk to sour
Bacteria breaks down lactose into glucose and galactose. Both monosaccharides are catabolized into pyruvate then fermented into lactic acid … acids are sour in taste
Some desert rodents rarely have water to drink. How do they get enough water for their cells without drinking it?
Desert rodents get most of their water from breaking down food, especially fats, which produces water as a byproduct. They also conserve water by making very concentrated urine and dry feces, so they lose as little water as possible.
Photosynthetic organisms are rarely pathogenic. Why?
Photosynthetic organisms are rarely pathogenic because they produce their own food through photosynthesis and do not need to invade or harm other organisms to obtain nutrients.
A scientist moves a green plant in sunlight to a room with 24 hours of artificial green light. Will this increase or decrease the plant’s rate of photosynthesis? Why?
Decrease because green light would not be absorbed by plants because chl absorbs in the red and blue wavelengths of light;
How are photophosphorylation and oxidative phosphorylation similar? How are they different?
Similar: both make ATP by using an electron transport chain to create a proton gradient that powers ATP synthase; chemiosmosis
Different location:
- Photophosphorylation: chloroplasts
- Oxidative phosphorylation: mitochondria
Different energy sources:
- Photophosphorylation: sunlight; releases O2
- Oxidative phosphorylation: food molecules; consumes O2 (catabolism of sugars)
Mushrooms growing on dead fallen trees recycle organic & inorganic molecules such as ammonia.
Mushrooms are ______________.
Decomposers
Given a specific photo of a streak plate, identify the problem and how you would fix it next time.
Cross contamination: other bacteria’s in random places
- Fix: hold lid open small amount
Too much bacteria
- Fix: don’t gross over too much, don’t touch 4 to 1, sterilize with each step
- Fix: only dip once
What kind of pathways is NADH used with?
Catabolic pathways
What is the third membrane of chloroplasts?
Thylakoid membrane
What is anoxygenic?
Doesn’t produce oxygen
What are the lab tests for carbohydrate fermentation?
Durham Phenol red tests
MR-VP tests
TSI
Durham Phenol Red Tests
Durham Phenol Red Test
How It’s Done:
- Preparation: Inoculate a test tube containing phenol red broth (a pH indicator) with the organism being tested.
- Incubation: Incubate the tubes
- Observation: color change and gas production
Results:
- Color Change:
- Yellow: Indicates acid production, suggesting fermentation of the sugar present. This occurs when the pH drops below 6.8.
- Red: Indicates no acid production, suggesting no fermentation, with a pH above 6.8.
-
Gas Production:
- Gas Bubble in Durham Tube: Indicates gas production during fermentation.
- No Gas Bubble: Indicates no gas production.
TSI Tests
Triple Sugar Iron (TSI) Test
Differential test: gram-negative bacteria based on their ability to ferment sugars and produce gas and hydrogen sulfide (H₂S).
How It’s Done:
1. Preparation: Inoculate a TSI agar slant with the organism stab and streak
2. Incubation: Incubate the tube at 35-37°C for 24-36 hours (no more).
Results:
Color changes:
yellow butt: ferment glucose
yellow slant: ferment lactose
all yellow: ferment both lactose and sucrose (lac operon is on); acidic
red slant or butt: peptones deaminated
black anywhere: hydrogen sulfide production
all orange: none
Gas Bubble or Cracks: Indicates gas production (often CO₂) during fermentation
What lab tests for an enzyme that gets rid of toxic oxygen derivatives?
Catalase test
Catalase test:
Catalase Test
Used to determine whether an organism produces the enzyme catalase, which breaks down hydrogen peroxide (H₂O₂) into water and oxygen.
How It’s Done:
1. Place bacterial sample on a glass slide or in a test tube. Add a few drops of hydrogen peroxide (3% solution) directly onto the sample.
3. Watch for 2 min
Results:
- Bubbles Produced: Indicates a positive catalase test. Bubbles are oxygen gas released from the breakdown of hydrogen peroxide by catalase.
- Negative catalase: no bubbles, organism does not produce catalase
What is the lab test for aerobic respiration?
Oxidase test;
Presence of Cytochrome C oxidase
Oxidase test:
Oxidase Test
Used to determine whether an organism produces the enzyme cytochrome c oxidase
How It’s Done:
1. Place bacterial sample on q tip, Add a few drops of oxidase reagent directly onto the sample.
3. Watch for a color change
Results:
- Dark Purple/Blue Color: Indicates a positive oxidase test, suggesting the presence of cytochrome c oxidase.
- Negative Result: No color change (EC)
Chemiosmosis: Cellular respiration vs. Photosynthesis
ATP synthase; yes or no?:
Mitochondria: yes
Chloroplast: yes
Chemiosmosis: Cellular respiration vs. Photosynthesis
Electron transport chain:
Mitochondria: ETC
Chloroplast: Light reaction (ETC)
Chemiosmosis: Cellular respiration vs. Photosynthesis
Source of energy:
Mitochondria: Breakdown of food
Chloroplast: light
Chemiosmosis: Cellular respiration vs. Photosynthesis
Spatial organization; location:
Mitochondria: inner mitochondrial membrane
Chloroplast: thylakoid membrane
Chemiosmosis: Cellular respiration vs. Photosynthesis
Location of ATP formed from ATP synthase:
Mitochondria: matrix
Chloroplast: stroma
Joe Micro has isolated an unknown from a bog near his college. What growth, nutritional, or metabolic term(s) could he use to describe it if it:
Produces hydrogen sulfide from sulfates
Sulfur reducer
Joe Micro has isolated an unknown from a bog near his college. What growth, nutritional, or metabolic term(s) could he use to describe it if it:
Converts nitrate to nitrogen gas
Denitrifier
Joe Micro has isolated an unknown from a bog near his college. What growth, nutritional, or metabolic term(s) could he use to describe it if it:
Does not grow in the presence of oxygen
Obligate anaerobe
Joe Micro has isolated an unknown from a bog near his college. What growth, nutritional, or metabolic term(s) could he use to describe it if it:
Converts methane to H2 and CO2
Methanotroph
Joe Micro has isolated an unknown from a bog near his college. What growth, nutritional, or metabolic term(s) could he use to describe it if it:
Gets electrons from sulfates
Lithotroph
Joe Micro has isolated an unknown from a bog near his college. What growth, nutritional, or metabolic term(s) could he use to describe it if it:
Prefers to grow in temps about 10 C
Psychrophile
Decomposers are considered to be what?
Heterotrophs
Sulfur reducers make the soil more what?
Basic (reduce acidity)
What do nitrogen fixers do?
Convert N2 to ammonia
What do methanotrophs contribute to the atmosphere?
CO2
Comparison of Aerobic respiration, Anaerobic respiration, and Fermentation:
Oxygen required:
Aerobic respiration: yes
Anaerobic respiration: no
Fermentation: no
Comparison of Aerobic respiration, Anaerobic respiration, and Fermentation:
Type of phosphorylation:
Aerobic respiration: substrate-level and oxidative
Anaerobic respiration: substrate-level and oxidative
Fermentation: substrate-level
Comparison of Aerobic respiration, Anaerobic respiration, and Fermentation:
Final Electron (Hydrogen) Acceptor:
Aerobic respiration: oxygen
Anaerobic respiration: NO3-, SO4 2-, CO3 2-, or externally acquired organic materials
Fermentation: cellular organic molecules
Comparison of Aerobic respiration, Anaerobic respiration, and Fermentation:
Potential Molecules of ATP Produced per Molecule of Glucose:
Aerobic respiration: 38 prokaryotes
36 eukaryotes
Anaerobic respiration: 2-36
Fermentation: 2 (from glycolysis)
Where does PPP fit into the more familiar types of metabolism such as glycolysis?
What molecule does it begin with?
Glucose 6 phosphate
(Branches off from glycolysis)
Where does PPP fit into the more familiar types of metabolism such as glycolysis?
Does it occur early or late in catabolism?
Early (second step)
Where does PPP fit into the more familiar types of metabolism such as glycolysis?
What are its advantages?
To make predators for nucleic acids, amino acids, and sugars that feed back into glycolysis
Makes NADPH (biosynthetic) pathways make something (acids)
Where does PPP fit into the more familiar types of metabolism such as glycolysis?
Could PPP be considered anabolism as well as catabolism?
Anabolic because its used to make something
- cyclical vitamins
- nucleic acids
- amino acids
Cellular energy accounting Prokaryote an Eukaryote
Glycolysis
Prokaryote & Eukaryote: 2 ATP + 2 NADH
Cellular energy accounting Prokaryote an Eukaryote
Transition step
Prokaryote & Eukaryote: 2 NADH
But Eukaryotes: lose the 2 ATP to cross mitochondrial membranes
Cellular energy accounting Prokaryote an Eukaryote
TCA
Prokaryote & Eukaryote: 2 ATP, 6 NADH, 2 FADH2
Cellular energy accounting Prokaryote an Eukaryote
ETC
Prokaryote: 34 ATP
Eukaryote: 32 ATP (34-2)
Cellular energy accounting Prokaryote an Eukaryote
Total ATP
Prokaryote: 38
Eukaryote: 36
A scientist inoculates a bacterium into a complex nutrient slant tube using the stab and streak method. The bacterium forms only a few colonies on the slanted surface but grows prolifically in the depth of the agar. Describe the oxygen requirements of the bacterium.
Aerotolerant anaerobe;
Slant = aerobic
Butt of slant = anaerobic
A student has isolated a bacterium (MSA?). This bacterium grows best in the incubator (not as well as RT). It grew as well in the Gas Pak as it did outside the Gas Pak. What growth/nutritional terms could be used to describe this bacterium?
- Mesophile (RT)
- Aerotolerant
And because it ferments lactose we can assume:
- Chemotroph
- Organotroph
- Heterotroph
Grows and makes yellow zone of MSA and grows on CNA when incubated at 37C. Growth found at the top of the thioglycolate tube.
Chemoorganoheterotroph
possible Gram +
Halophile
Mesophile
Obligate aerobe
Grows as light beige large colonies on TSA, metallic green colonies on EMB when incubated at 60C. When grown in the Gas Pak, the colonies on TSA and EMB are small.
Chemoorganoheterotroph
possibly gram -
thermophile
facultative anaerobe
lactose fermenter
Grows best at 10C, has red growth on MacConkey as long as this medium is at pH 8.
Chemoorganoheterotroph
possible gram -
psychrophile
alkalinophile
Which metabolic process does not generate carbon dioxide as a by-product?
Oxidative phosphorylation
By-product: water
The PPP is used for the production of _______
Precursor metabolites for anabolic reactions such as nucleic acids
The ED pathway is an alternative to_____ and yields ___
glycolysis; ATP, NADH, NADPH, and metabolic intermediates
What is not a final electron acceptor in anaerobic respiration?
Oxygen (anaerobic)
Yes: nitrate, sulfate, iron
Does anaerobic respiration use a ETC?
Yes
Compare and contrast glycolysis + fermentation & aerobic respiration in prokaryotes
Similar:
- both use glycolysis in cytosol
- recycle NAD+
Prokaryotic glycolysis + fermentation:
- occurs in cytosol
- fermentation yields lactic acid (or other acids) or ethanol; recycles NAD+
- Glycolysis yields 2 ATP
-Final electron acceptor: organic molecule
Prokaryotic aerobic respiration:
- Transition step & TCA/Krebs in cytosol
- ETC/Chemiosmosis in CM
- Net yield: 38 ATP
- Final electron acceptor: Oxygen
