Microbial Metabolism and Genetics: Step-by-Step Study Guidance

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Q1. What are the net results of glucose being metabolized by glycolysis? (Consider what is made: ATP, NADH, final carbon compound)

Background

Topic: Glycolysis (Microbial Metabolism)

This question tests your understanding of the products generated during glycolysis, the first step in the breakdown of glucose for energy in cells.

Key Terms and Formulas

Glycolysis: The metabolic pathway that converts glucose (6C) into two molecules of pyruvate (3C each).
ATP: Adenosine triphosphate, the cell's energy currency.
NADH: Nicotinamide adenine dinucleotide (reduced form), an electron carrier.
Net yield: The total produced minus what is consumed during the process.

Step-by-Step Guidance

Start by recalling that glycolysis splits one glucose molecule (6 carbons) into two pyruvate molecules (3 carbons each).
Consider the ATP: Glycolysis uses some ATP in early steps and produces more later. Calculate the net gain by subtracting ATP used from ATP produced.
Think about the electron carriers: NAD+ is reduced to NADH during glycolysis. Determine how many NADH molecules are generated per glucose.
Identify the final carbon compound produced at the end of glycolysis.
Set up your answer by listing the net ATP, NADH, and the final carbon compound, but do not write the final numbers yet.

Try solving on your own before revealing the answer!

Final Answer:

The net results of glycolysis per glucose molecule are:

2 ATP (net gain)
2 NADH
2 pyruvate (3C each)

Glycolysis uses 2 ATP in early steps and produces 4 ATP, for a net gain of 2 ATP. Two NADH are produced as glucose is oxidized, and the final carbon compound is pyruvate.

Q2. Pyruvate (3C) is the starting point for the Krebs Cycle but only 2 carbons enter the cycle. What happened to the other carbon?

Background

Topic: Link between Glycolysis and Krebs Cycle (Microbial Metabolism)

This question examines your understanding of the fate of pyruvate carbons as they enter the Krebs cycle.

Key Terms and Concepts

Pyruvate: 3-carbon molecule produced from glycolysis.
Krebs Cycle: Also called the citric acid cycle; processes acetyl-CoA to generate energy carriers.
Decarboxylation: Removal of a carbon as CO2.

Step-by-Step Guidance

Recall that pyruvate (3C) must be converted before entering the Krebs cycle.
Think about what happens to pyruvate in the 'link reaction' (pyruvate dehydrogenase complex).
Identify which molecule is released during this conversion and what the remaining 2C fragment becomes.
Set up your answer by describing the fate of the third carbon atom.

Try solving on your own before revealing the answer!

Final Answer:

The third carbon of pyruvate is released as CO2 during the conversion of pyruvate to acetyl-CoA (the link reaction). Only the 2-carbon acetyl group enters the Krebs cycle.

Q3. During active metabolism, many more carbons enter the Krebs cycle than the number of carbons given off as CO2. What happens to all the carbon that doesn’t become CO2?

Background

Topic: Krebs Cycle and Cellular Biosynthesis

This question tests your understanding of how cells use carbon from metabolic pathways for purposes other than energy production.

Key Terms and Concepts

Krebs Cycle Intermediates: Compounds that can be siphoned off for biosynthesis.
Anabolism: Building cellular components from smaller molecules.
Precursor Metabolites: Intermediates used to make amino acids, nucleotides, etc.

Step-by-Step Guidance

Recall that not all carbon entering the Krebs cycle is oxidized to CO2.
Think about the cell’s need to build macromolecules (anabolism) and where the building blocks come from.
Identify how Krebs cycle intermediates can be diverted for biosynthetic pathways.
Set up your answer by explaining the fate of these carbons in the cell.

Try solving on your own before revealing the answer!

Final Answer:

The carbons that do not become CO2 are used as precursor metabolites for biosynthesis. They are withdrawn from the Krebs cycle to build amino acids, nucleotides, and other cellular components.

Q4. Electrons cannot run free in the cell. How are they handled by metabolism?

Background

Topic: Electron Carriers in Metabolism

This question tests your understanding of how cells manage electrons released during metabolic reactions.

Key Terms and Concepts

Electron Carriers: Molecules like NAD+, FAD, which temporarily hold electrons.
Redox Reactions: Oxidation-reduction reactions where electrons are transferred.
Electron Transport Chain (ETC): Series of proteins that transfer electrons to generate ATP.

Step-by-Step Guidance

Recall that electrons are released during oxidation of substrates (e.g., glucose).
Identify the molecules that accept these electrons (e.g., NAD+ becomes NADH).
Think about how these carriers deliver electrons to the electron transport chain.
Set up your answer by describing the role of electron carriers and the ETC.

Try solving on your own before revealing the answer!

Final Answer:

Electrons are transferred to electron carriers like NAD+ and FAD, forming NADH and FADH2. These carriers shuttle electrons to the electron transport chain, where they are ultimately transferred to a final electron acceptor (e.g., O2 in aerobic respiration).

Q5. Describe the role of chemiosmosis in the cell getting energy (ATP) during electron transport. Where is ATPase located in the cell?

Background

Topic: Chemiosmosis and ATP Synthesis

This question tests your understanding of how cells use the energy from electrons to make ATP and the cellular location of ATP synthase (ATPase).

Key Terms and Concepts

Chemiosmosis: The movement of ions (usually H+) across a membrane, generating ATP.
ATP Synthase (ATPase): Enzyme that synthesizes ATP using the proton gradient.
Proton Motive Force: The electrochemical gradient of H+ across the membrane.

Step-by-Step Guidance

Recall that as electrons move through the electron transport chain, protons are pumped across the membrane.
Think about how this creates a proton gradient (proton motive force).
Describe how protons flow back through ATP synthase, driving ATP production.
Identify the location of ATP synthase in prokaryotic cells (bacteria).

Try solving on your own before revealing the answer!

Final Answer:

Chemiosmosis uses the proton gradient created by the electron transport chain to drive protons back through ATP synthase, producing ATP. In bacteria, ATP synthase is located in the cell (plasma) membrane.

Q6. What is meant by phosphorylation? What is the main difference between substrate-level phosphorylation and oxidative phosphorylation?

Background

Topic: ATP Formation Mechanisms

This question tests your understanding of how phosphate groups are added to ADP to form ATP, and the two main mechanisms by which this occurs.

Key Terms and Concepts

Phosphorylation: Addition of a phosphate group to a molecule (e.g., ADP to ATP).
Substrate-level Phosphorylation: Direct transfer of phosphate from a substrate to ADP.
Oxidative Phosphorylation: ATP formation using energy from the electron transport chain and chemiosmosis.

Step-by-Step Guidance

Define phosphorylation in the context of cellular metabolism.
Describe how substrate-level phosphorylation occurs during glycolysis and the Krebs cycle.
Explain how oxidative phosphorylation is linked to the electron transport chain and chemiosmosis.
Set up your answer by comparing the two processes.

Try solving on your own before revealing the answer!

Final Answer:

Phosphorylation is the addition of a phosphate group to ADP to form ATP. Substrate-level phosphorylation transfers a phosphate directly from a substrate to ADP, while oxidative phosphorylation uses the energy from electrons moving through the electron transport chain to drive ATP synthesis via chemiosmosis.

Q7. How does anaerobic respiration differ from aerobic respiration in bacteria? (Hint: Where do the electrons end up?)

Background

Topic: Types of Respiration in Bacteria

This question tests your understanding of the differences between aerobic and anaerobic respiration, especially regarding the final electron acceptor.

Key Terms and Concepts

Aerobic Respiration: Uses O2 as the final electron acceptor.
Anaerobic Respiration: Uses other inorganic molecules (e.g., NO3-, SO42-, CO32-) as the final electron acceptor.
Electron Transport Chain: Pathway where electrons are transferred to the final acceptor.

Step-by-Step Guidance

Recall the role of the electron transport chain in both types of respiration.
Identify the final electron acceptor in aerobic respiration (O2).
List alternative electron acceptors used in anaerobic respiration.
Set up your answer by comparing where electrons end up in each process.

Try solving on your own before revealing the answer!

Final Answer:

In aerobic respiration, electrons are transferred to oxygen, forming water. In anaerobic respiration, electrons are transferred to other inorganic molecules such as nitrate (NO3-), sulfate (SO42-), or carbonate (CO32-), resulting in different end products.

Q8. In fermentation, what is used as the final electron acceptor? What carbon compounds result from this and what does the cell do with these compounds?

Background

Topic: Fermentation Pathways

This question tests your understanding of how cells regenerate NAD+ in the absence of an electron transport chain and what happens to the end products.

Key Terms and Concepts

Fermentation: Anaerobic process that regenerates NAD+ by transferring electrons to organic molecules.
Final Electron Acceptor: An organic molecule derived from pyruvate.
End Products: Ethanol, lactic acid, mixed acids, etc.

Step-by-Step Guidance

Recall that fermentation does not use an electron transport chain.
Identify what acts as the final electron acceptor in fermentation (hint: it's not O2 or an inorganic molecule).
List common carbon-containing end products of fermentation.
Describe what the cell does with these end products (e.g., excretion).

Try solving on your own before revealing the answer!

Final Answer:

In fermentation, the final electron acceptor is an organic molecule (often pyruvate or a derivative). The resulting carbon compounds (e.g., ethanol, lactic acid) are excreted from the cell as waste products.

Q9. Approximately how much energy in ATPs does a cell get from these metabolic processes starting with glucose?

Background

Topic: ATP Yield from Different Metabolic Pathways

This question tests your ability to compare the energy yield (in ATP) from aerobic respiration, anaerobic respiration, glycolysis alone, and fermentation.

Key Terms and Concepts

Aerobic Respiration: Complete oxidation of glucose using O2.
Anaerobic Respiration: Uses alternative electron acceptors.
Glycolysis: First step, yields small amount of ATP.
Fermentation: Only glycolysis, no Krebs or ETC.

Step-by-Step Guidance

Recall the ATP yield for each process:
- a) Aerobic respiration: Includes glycolysis, Krebs, and ETC.
- b) Anaerobic respiration: Similar pathways but less efficient than aerobic.
- c) Glycolysis alone: Only substrate-level phosphorylation.
- d) Fermentation: Only glycolysis, no ETC or Krebs.
List the approximate ATP yields for each process, but do not write the final numbers yet.

Try solving on your own before revealing the answer!

Final Answer:

a) Aerobic respiration: 32–36 ATP per glucose
b) Anaerobic respiration: Less than aerobic, but more than fermentation (variable, often 2–30 ATP)
c) Glycolysis alone: 2 ATP per glucose
d) Fermentation: 2 ATP per glucose (from glycolysis only)

Aerobic respiration is the most efficient, while fermentation yields the least ATP.

Q10. What process constitutes “replication”?

Background

Topic: DNA Replication (Microbial Genetics)

This question tests your understanding of how cells duplicate their genetic material.

Key Terms and Concepts

Replication: Making an exact copy of DNA.
DNA Polymerase: Enzyme that synthesizes new DNA strands.
Template Strand: The original DNA strand used for copying.

Step-by-Step Guidance

Recall the central dogma: DNA → RNA → Protein.
Identify which process copies DNA to make more DNA.
Describe the role of DNA polymerase in this process.
Set up your answer by defining replication.

Try solving on your own before revealing the answer!

Final Answer:

Replication is the process by which a cell makes an exact copy of its DNA, using DNA polymerase and the original DNA as a template.

Q11. What is “transcription”?

Background

Topic: Transcription (Microbial Genetics)

This question tests your understanding of how genetic information is transferred from DNA to RNA.

Key Terms and Concepts

Transcription: Synthesis of RNA from a DNA template.
RNA Polymerase: Enzyme that builds RNA strands.
mRNA: Messenger RNA, carries genetic code to ribosomes.

Step-by-Step Guidance

Recall the central dogma: DNA → RNA → Protein.
Identify which process makes RNA from DNA.
Describe the role of RNA polymerase in this process.
Set up your answer by defining transcription.

Try solving on your own before revealing the answer!

Final Answer:

Transcription is the process by which RNA is synthesized from a DNA template, using RNA polymerase.

Q12. What is “translation”?

Background

Topic: Translation (Microbial Genetics)

This question tests your understanding of how the genetic code in mRNA is used to build proteins.

Key Terms and Concepts

Translation: Synthesis of protein from mRNA template.
Ribosome: Molecular machine that assembles amino acids into proteins.
tRNA: Transfer RNA, brings amino acids to the ribosome.

Step-by-Step Guidance

Recall the central dogma: DNA → RNA → Protein.
Identify which process uses mRNA to build proteins.
Describe the role of ribosomes and tRNA in this process.
Set up your answer by defining translation.

Try solving on your own before revealing the answer!

Final Answer:

Translation is the process by which the sequence of an mRNA molecule is used to assemble a chain of amino acids, forming a protein, at the ribosome.

Q13. Distinguish between genotype and phenotype.

Background

Topic: Genotype vs. Phenotype (Microbial Genetics)

This question tests your understanding of the difference between an organism’s genetic makeup and its observable traits.

Key Terms and Concepts

Genotype: The genetic composition (DNA sequence) of an organism.
Phenotype: The observable characteristics or traits.

Step-by-Step Guidance

Define genotype in terms of DNA sequence.
Define phenotype as the result of gene expression.
Set up your answer by comparing the two concepts.

Try solving on your own before revealing the answer!

Final Answer:

Genotype refers to the genetic makeup (DNA sequence) of an organism, while phenotype is the set of observable traits resulting from gene expression.

Q14. What is meant by mutation? What is the spontaneous rate of mutation in bacteria? How can the mutation rate be increased to aid genetic research?

Background

Topic: Mutation and Mutation Rates (Microbial Genetics)

This question tests your understanding of genetic mutations, their natural frequency, and how scientists can increase mutation rates.

Key Terms and Concepts

Mutation: A heritable change in the DNA sequence.
Spontaneous Mutation Rate: The natural frequency of mutations during DNA replication.
Mutagen: An agent that increases mutation rate.

Step-by-Step Guidance

Define mutation in the context of genetics.
Recall the typical spontaneous mutation rate in bacteria (e.g., per base pair per generation).
List ways to increase mutation rate (e.g., exposure to mutagens).
Set up your answer by summarizing these points.

Try solving on your own before revealing the answer!

Final Answer:

A mutation is a heritable change in the DNA sequence. The spontaneous mutation rate in bacteria is about 1 in 107 to 109 base pairs per generation. Mutation rates can be increased by exposing cells to mutagens such as chemicals or radiation.

Q15. What are mutagens? Give some examples of physical, chemical, and biological mutagens.

Background

Topic: Mutagens (Microbial Genetics)

This question tests your understanding of agents that cause mutations and their types.

Key Terms and Concepts

Mutagen: An agent that increases the frequency of mutations.
Physical Mutagens: e.g., radiation.
Chemical Mutagens: e.g., base analogs, alkylating agents.
Biological Mutagens: e.g., transposons, viruses.

Step-by-Step Guidance

Define mutagen and its role in genetics.
List examples of physical mutagens (e.g., UV light, X-rays).
List examples of chemical mutagens (e.g., nitrous acid, ethidium bromide).
List examples of biological mutagens (e.g., transposons, some viruses).

Try solving on your own before revealing the answer!

Final Answer:

Mutagens are agents that increase the mutation rate. Physical mutagens include UV light and gamma rays; chemical mutagens include nitrous acid and base analogs; biological mutagens include transposons and certain viruses.

Q16. What are the 3 methods of genetic transfer among bacteria? What are their similarities and differences? Why is it called ‘horizontal transfer’?

Background

Topic: Horizontal Gene Transfer (Microbial Genetics)

This question tests your understanding of the main mechanisms by which bacteria exchange genetic material.

Key Terms and Concepts

Transformation: Uptake of naked DNA from the environment.
Conjugation: Direct transfer of DNA via cell-to-cell contact (sex pilus).
Transduction: Transfer of DNA by bacteriophages (viruses).
Horizontal Transfer: Gene transfer between cells of the same generation.

Step-by-Step Guidance

List the three main methods: transformation, conjugation, and transduction.
Briefly describe each method.
Compare similarities (all involve gene transfer) and differences (mechanism, requirement for contact, etc.).
Explain why these are called horizontal (not vertical) transfer.

Try solving on your own before revealing the answer!

Final Answer:

The three methods are transformation, conjugation, and transduction. All transfer genes between bacteria, but differ in mechanism: transformation involves naked DNA, conjugation requires cell contact, and transduction uses viruses. It's called horizontal transfer because genes move between cells of the same generation, not parent to offspring.

Q17. What is a sex pilus? What are plasmids? How do plasmids differ from the cell’s DNA genome?

Background

Topic: Plasmids and Conjugation (Microbial Genetics)

This question tests your understanding of bacterial structures and genetic elements involved in gene transfer.

Key Terms and Concepts

Sex Pilus: A structure used to connect donor and recipient cells during conjugation.
Plasmid: Small, circular DNA molecule separate from the chromosome.
Genome: The cell’s main DNA, containing essential genes.

Step-by-Step Guidance

Define sex pilus and its role in conjugation.
Define plasmid and its general features.
Compare plasmids to the main bacterial genome (size, essentiality, replication).
Set up your answer by summarizing these differences.

Try solving on your own before revealing the answer!

Final Answer:

A sex pilus is a structure that connects bacterial cells during conjugation. Plasmids are small, circular DNA molecules that replicate independently of the genome and often carry non-essential genes (e.g., antibiotic resistance), while the genome contains essential genes for survival.

Q18. Distinguish between an F-Factor and an R-Factor.

Background

Topic: Plasmid Types (Microbial Genetics)

This question tests your understanding of different types of plasmids and their roles in bacteria.

Key Terms and Concepts

F-Factor (Fertility Factor): Plasmid that enables conjugation (transfer of DNA).
R-Factor (Resistance Factor): Plasmid that carries antibiotic resistance genes.

Step-by-Step Guidance

Define F-Factor and its function in gene transfer.
Define R-Factor and its role in antibiotic resistance.
Compare the two types of plasmids.
Set up your answer by summarizing their differences.

Try solving on your own before revealing the answer!

Final Answer:

The F-Factor is a plasmid that enables bacteria to transfer DNA via conjugation, while the R-Factor is a plasmid that carries genes for antibiotic resistance. Both are plasmids, but they have different functions.

Q19. How does the DNA get from the donor cell to the recipient in each of the 3 methods of ‘transduction’?

Background

Topic: Mechanisms of Genetic Transfer (Microbial Genetics)

This question tests your understanding of how DNA is transferred between bacteria by different mechanisms, focusing on transduction.

Key Terms and Concepts

Transduction: Transfer of DNA by bacteriophages (viruses).
Generalized Transduction: Any bacterial gene can be transferred.
Specialized Transduction: Only specific genes near the prophage site are transferred.

Step-by-Step Guidance

Recall the three main methods of genetic transfer: transformation, conjugation, and transduction.
For transduction, describe how bacteriophages transfer DNA from donor to recipient.
Distinguish between generalized and specialized transduction.
Set up your answer by summarizing the DNA transfer process in each method.

Try solving on your own before revealing the answer!

Final Answer:

In transduction, bacteriophages (viruses) carry DNA from a donor cell to a recipient cell. In generalized transduction, any gene can be transferred; in specialized transduction, only specific genes near the prophage site are transferred.

Q20. What is the fate of the donor cell in the transfer process in each of the 3 methods?

Background

Topic: Outcomes of Genetic Transfer (Microbial Genetics)

This question tests your understanding of what happens to the donor cell after genetic material is transferred by transformation, conjugation, or transduction.

Key Terms and Concepts

Transformation: Uptake of naked DNA; donor cell is not directly involved.
Conjugation: Donor cell remains alive and can transfer DNA multiple times.
Transduction: Donor cell is usually lysed by the bacteriophage.

Step-by-Step Guidance

For transformation, consider whether the donor cell survives or is present during DNA uptake.
For conjugation, think about the fate of the donor cell after plasmid transfer.
For transduction, recall what happens to the donor cell when a bacteriophage is involved.
Set up your answer by summarizing the fate of the donor cell in each method.

Try solving on your own before revealing the answer!

Final Answer:

In transformation, the donor cell is not directly involved and may be dead. In conjugation, the donor cell survives and can continue transferring DNA. In transduction, the donor cell is typically lysed (destroyed) by the bacteriophage.