Microbial Metabolism and Genomics Flashcards

Vocabulary flashcards based on the MCB 2010 lecture covering genomics, DNA/RNA structures, metabolism, glycolysis, the TCA cycle, ETC, and fermentation.

Ribose

The sugar component used in RNA, which is oxygenated at the $2'$ carbon.

Diploid

Having two copies of every chromosome in a cell.

Extrachromosomal DNA

DNA located outside of an organism's primary chromosome(s), such as in mitochondria, chloroplasts, or plasmids.

Plasmids

Mobile extrachromosomal genetic elements in bacteria that can encode toxins and antibiotic resistance.

First Law of Thermodynamics

The law stating that energy can neither be created nor destroyed, only transferred from one form to another.

Anabolism

Metabolic processes that require or store energy (non-spontaneous/endergonic) to build larger building blocks and cellular structures.

Catabolism

Metabolic processes that release energy (spontaneous/exergonic) by breaking down complex nutrients.

Autotrophs

Organisms that convert inorganic $\text{CO}_2$ into organic molecules.

Heterotrophs

Organisms that consume organic molecules as an energy source.

Energy & Carbon source of Chemoautotrophs

Chemical; inorganic

Energy & Carbon source of Chemoheterotrophs

Chemical; Organic compounds

Energy & Carbon source of Photoautotrophs

Light; inorganic

Energy & Carbon source of Photoheterotrophs

Light; organic compounds

Organotrophs

Chemotrophs that use organic compounds as electron sources.

Lithotrophs

Chemotrophs that use inorganic compounds as electron sources ("litho" = rock).

Reduction

The addition of electrons to an atom or system.

Oxidation

The removal of electrons from an atom or system.

Enzyme

A protein catalyst that starts or assists chemical reactions by lowering the required activation energy.

Entner-Doudoroff (ED) Pathway

An alternative prokaryotic glycolytic pathway used by organisms such as Pseudomonas aeruginosa.

Pentose Phosphate Pathway (PPP)

An ancient prokaryotic glycolytic pathway involved in glucose breakdown.

Bridge Reaction

The metabolic reaction connecting glycolysis to the TCA cycle by converting pyruvate into acetyl $\text{CoA}$.

TCA Cycle

The tricarboxylic acid (or Krebs) cycle; a closed-loop metabolic pathway that is both anabolic and catabolic, processing acetyl $\text{CoA}$ to yield ATP and electron carriers.

Substrate-Level Phosphorylation / “Energy Investment Phase”

Direct synthesis of ATP by transferring a phosphate group from an intermediate substrate molecule to ADP, occurring during glycolysis.

Oxidative Phosphorylation

The synthesis of ATP driven by the transfer of electrons through an electron transport chain via proton motive force using $\text{NADH}$ and $\text{FADH}_2$.

Fermentation

An anaerobic metabolic process occurring without an electron transport chain, where $\text{NADH}$ is re-oxidized by reacting with pyruvate to form lactic acid.

Glycolysis

A cytoplasmic process that breaks down glucose into two pyruvate molecules, producing a net yield of $2\,\text{ATP}$ and $2\,\text{NADH}$

What is the goal of glycolysis?

to break down glucose (six carbons) into two pyruvate compounds

What is another name for the phase of substrate level phosphorylation?

Energy Investment Phase

What is the total generated from Glycolysis?

4 ATP and 2 NADH

How many times is the TCA cycle completed during a single respiration, and how much ATP does it directly yield?

completed twice, producing a total of 2 ATP

Where are the electron carriers recharged and how much is produced?

Glycolysis- 2 NADH

Bridge reaction- 2 NADH

TCA cycle- 6 NADH + 2 FADH2

What is the net yield of ATP in Respiration?

returns 40 ATP with a net yield of 38 ATP

What is the final electron acceptor in anaerobic respiration?

nitrate or nitrite

Complex 1 of the Electron Transport Chain

most negative redox potential in the ETC, oxidizes $\text{NADH}$, and translocates $4$ protons across the membrane.

Complex 2 of the Electron Transport Chain

oxidizes $\text{FADH}_2$, pairs with Coenzyme Q, and translocates no protons across the membrane.

Complex 3 of the Electron Transport Chain

oxidizes Complex 2 and Coenzyme Q (CoQ), translocating 4 protons across the membrane.

Complex 4 of the Electron Transport Chain

The ETC component that transfers electrons to oxygen as the final electron acceptor and translocates $4$ protons across the membrane.