Cell Metabolism, Redox Reactions, and Energy Production in Microorganisms

What is the definition of metabolism?

The total of all chemical reactions in the cell.

What is catabolism?

The breakdown of complex molecules that releases energy and generates precursors for biosynthesis.

What is anabolism?

The biosynthesis of complex molecules, which requires energy.

What are the three major types of cellular work?

Chemical work, transport work, and mechanical work.

What is the chemical equilibrium of a reaction?

The state where the rate of the forward reaction equals the rate of the reverse reaction.

What does the equilibrium constant (Keq) express?

The equilibrium concentrations of products relative to reactants.

What is the difference between exergonic and endergonic reactions regarding free energy?

Exergonic reactions have a negative ΔG°′, while endergonic reactions have a positive ΔG°′.

Why is ATP considered a coupling agent in metabolism?

Its exergonic breakdown is coupled with endergonic reactions to make them more favorable.

What is the LEO GER acronym for redox reactions?

Loss of Electrons = Oxidation; Gain of Electrons = Reduction.

In a redox reaction, what is a reducing agent?

An electron donor that gets oxidized.

In a redox reaction, what is an oxidizing agent?

An electron acceptor that gets reduced.

What is standard reduction potential (E0)?

A measure of a molecule's tendency to accept electrons.

How does the difference in E0 between a redox pair affect free energy?

As the difference in E0 increases, the amount of free energy made available increases.

Which electron carrier uses iron within a heme group?

Cytochromes.

What is the function of nonheme iron-sulfur proteins like ferredoxin?

They use iron to transport electrons without being part of a heme group.

What is the Electron Transport Chain (ETC)?

A series of protein complexes and molecules that transfer electrons via redox reactions to synthesize ATP.

What is the proton motive force?

An electrochemical proton gradient created by redox reactions that drives ATP synthesis.

Where is the ETC located in bacteria and archaea?

In the plasma membrane.

Where is the ETC located in Eukarya?

In the internal membranes of mitochondria and chloroplasts.

How are electron carriers organized in the ETC?

They are organized from the most negative E′0 to the least negative, allowing electrons to flow sequentially.

What is the primary energy storage molecule in cells?

Adenosine triphosphate (ATP).

What is the relationship between electron content and energy in a molecule?

The more electrons a molecule has, the more energy-rich it is.

How do phototrophs obtain energy?

They use light.

How do chemotrophs obtain energy?

They obtain energy from the oxidation of chemical compounds.

What is the electron source for lithotrophs?

Reduced inorganic substances.

What is the electron source for organotrophs?

Reduced organic compounds.

What is the carbon source for autotrophs?

Carbon dioxide.

What is the carbon source for heterotrophs?

Organic molecules.

What is the nutritional type of humans and most nonphotosynthetic microbes?

Chemoorganoheterotrophs.

What are the three basic needs of all organisms regardless of their energy source?

ATP, reducing power, and precursor metabolites.

What is the final electron acceptor in aerobic respiration?

Oxygen.

What are some examples of final electron acceptors in anaerobic respiration?

NO3-, SO4 2-, CO2, Fe3+, or SeO4 2-.

How is ATP primarily generated during fermentation?

Substrate-level phosphorylation.

What are the three common glycolytic pathways?

Embden-Meyerhof (EM), Entner-Doudoroff (ED), and Pentose phosphate pathway (PPP).

What is the net yield of the Embden-Meyerhof pathway per glucose molecule?

2 pyruvate, 2 ATP, and 2 NADH.

Where does the TCA cycle occur in eukaryotes?

In the mitochondrial matrix.

Where does the TCA cycle occur in bacteria and archaea?

In the cytoplasm.

What molecule is pyruvate converted into before entering the TCA cycle?

Acetyl-CoA.

What are the products of the TCA cycle per acetyl-CoA molecule?

2 CO2, 3 NADH, 1 FADH2, and 1 GTP or ATP.

What is the primary function of the electron transport chain (ETC)?

To oxidize NADH and FADH2 to generate ATP via oxidative phosphorylation.

What is the chemiosmotic hypothesis?

The theory that ATP production is driven by the proton motive force.

What constitutes the proton motive force (PMF)?

A combined chemical and electrical potential difference across a membrane.

What enzyme uses the proton motive force to synthesize ATP?

ATP synthase.

How many ATP are theoretically produced during aerobic respiration?

32 ATP.

Where is the ETC located in bacteria and archaea?

In the plasma membrane.

Why might bacterial ETCs be less efficient than mitochondrial ETCs?

They may be shorter, resulting in fewer protons pumped and less energy conserved.

How many ATP molecules are yielded by glycolysis under anaerobic conditions?

2 ATP molecules

List three factors that affect the total ATP yield in bacteria.

Shorter ETCs, environmental conditions, and the use of PMF for non-ATP purposes like flagella rotation or nutrient uptake.

Why does anaerobic respiration yield less energy than aerobic respiration?

The reduction potential of the alternative terminal electron acceptor is less positive than that of oxygen.

What is the process of dissimilatory nitrate reduction that produces nitrogen gas?

Denitrification

What is the primary metabolic role of fermentation regarding NADH?

The oxidation of NADH to regenerate NAD+.

Does fermentation involve an electron transport chain?

No, it does not involve an ETC or oxidative phosphorylation.

How is ATP formed during fermentation?

By substrate-level phosphorylation.

What is the difference between homolactic and heterolactic fermenters?

Homolactic fermenters reduce pyruvate directly to lactate, while heterolactic fermenters produce lactate, ethanol, and CO2.

What are the end products of alcoholic fermentation?

Ethanol and CO2.

What is the primary energy source for chemolithotrophs?

Inorganic molecules.

Why do chemolithotrophs need to oxidize large quantities of inorganic material?

Because inorganic molecules have more positive redox potentials, resulting in less available energy compared to glucose.

What is the role of nitrifying bacteria?

They oxidize ammonia to nitrate.

What is electron bifurcation?

A process where a flavoenzyme couples an endergonic reaction with an exergonic reduction to drive the former.

What are the two main stages of photosynthesis in photoautotrophs?

Light reactions (energy conversion) and dark reactions (CO2 fixation).

What is the electron source for oxygenic photosynthesis?

Water (H2O).

What is the main difference between oxygenic and anoxygenic photosynthesis regarding oxygen production?

Oxygenic photosynthesis generates O2, while anoxygenic photosynthesis does not.

What is the function of light-harvesting complexes (antennas)?

To capture light energy and transfer it to the reaction-center chlorophyll.

Which photosystems are involved in non-cyclic photophosphorylation?

Both Photosystem I and Photosystem II.

What is the primary electron source for anoxygenic photosynthesis?

Inorganic compounds such as H2, H2S, or S.

In which structures do anoxygenic phototrophs house their bacteriochlorophylls?

Membranous vesicles called chlorosomes.

What is the primary function of bacteriorhodopsin in rhodopsin-based phototrophy?

It functions as a light-driven proton pump to generate a proton motive force.

Does rhodopsin-based phototrophy utilize an electron transport chain?

No, it does not.

What is the definition of a photoheterotroph?

An organism that uses light for energy but does not perform carbon fixation.

What is the main purpose of the dark reactions in photosynthesis?

To use ATP and NADPH to fix CO2 and synthesize cell constituents.

What are the two purine bases found in DNA?

Adenine and guanine

What are the two pyrimidine bases found in DNA?

Cytosine and thymine

How many hydrogen bonds connect guanine and cytosine?

Three

How many hydrogen bonds connect adenine and thymine?

Two

What term describes the orientation of the two strands of a DNA double helix?

Antiparallel

What are the three main differences between DNA and RNA?

RNA uses uracil instead of thymine, contains ribose instead of deoxyribose, and is typically single-stranded

What does it mean that DNA replication is semiconservative?

Each daughter cell obtains one old (template) strand and one newly synthesized strand

What is a replicon?

A portion of the genome that contains an origin and is replicated as a unit

What protein binds to the bacterial origin of replication (oriC) to initiate strand separation?

DnaA

In which direction does DNA polymerase synthesize new DNA strands?

5' to 3' direction

What are the three requirements for DNA polymerase to synthesize a new strand?

A template, a primer, and dNTPs

What is the function of topoisomerases during DNA replication?

To relieve tension from rapid unwinding and prevent positive supercoiling

What is the specific role of DNA gyrase?

To transiently break one or two strands of DNA to change its structure without altering the nucleotide sequence

What is the function of single-stranded DNA binding proteins (SSB)?

To keep the separated DNA strands apart during replication

What is the role of primase in DNA replication?

To synthesize short RNA primers needed by DNA polymerase

What are Okazaki fragments?

Short, discontinuous fragments of DNA synthesized on the lagging strand

How does DNA polymerase III perform proofreading?

By using 3' to 5' exonuclease activity to remove mismatched bases

What is the function of DNA polymerase I?

To remove RNA primers and fill the resulting gaps with DNA

What is the role of DNA ligase?

To form a phosphodiester bond between the 3'-hydroxyl and 5'-phosphate of adjacent DNA fragments

Why do eukaryotic chromosomes require multiple origins of replication?

Because eukaryotic chromosomes are much larger than bacterial chromosomes, multiple origins speed up the overall replication process

What is the origin recognition complex (ORC)?

A complex of proteins that marks the initiation sites for DNA replication in eukaryotes

What are telomeres?

Protective complex structures at the ends of linear chromosomes that shorten with each replication cycle

What is the G-tail in a telomere?

A single-stranded section at the very end of the chromosome rich in guanosine bases

How do archaeal chromosomes compare to bacterial chromosomes?

They are similar in size and circular structure, but some archaea have histones associated with their chromosomes

Which family of DNA polymerases do both eukaryotes and archaea use?

B family DNA polymerases

What are the three components attached to the central carbon of an amino acid?

A carboxy group (C-terminal), an amino group (N-terminal), and a side chain.

What type of bond links amino acids to form proteins?

Peptide bonds.

How is a gene defined in molecular biology?

A nucleic acid sequence that codes for a polypeptide, tRNA, or rRNA.

What is the function of the promoter region in a gene?

It is the non-transcribed region where RNA polymerase binds to initiate transcription.

What are the specific recognition and binding sites within a bacterial promoter?

The -35 site (recognition) and the -10 site (Pribnow box, binding).