MCDB6 Week 4: Introduction to Metabolism and Cell Cycle

Flashcards covering key definitions and concepts for Metabolism, Energy, Thermodynamics, Enzymes, and the Cell Cycle based on Week 4 lecture notes.

Metabolism

The totality of an organism’s chemical reactions or the sum of all chemical reactions needed for life; an emergent property arising from orderly interactions between molecules.

Catabolic pathways

Metabolic pathways that break down complicated molecules into simple constituents, such as cellular respiration where glucose is broken down into $CO_2$ and $H_2O$, releasing energy for cellular work.

Anabolic pathways

Metabolic pathways that manufacture complicated molecules from simple starting molecules, such as protein synthesis from amino acids; these are also known as biosynthetic pathways.

Bioenergetics

The study of how energy flows through living organisms.

Kinetic Energy

Energy associated with the motion of objects, such as water gushing through a dam.

Thermal Energy

Kinetic energy associated with the random movement of molecules which is transferred as heat.

Potential Energy

Stored energy or the potential to do work that matter possesses because of its location or structure, such as water in a dam at high altitude or the arrangement of electrons in chemical bonds.

Chemical Energy

A form of potential energy available for release in a chemical reaction.

Thermodynamics

The study of energy transformations that occur in a collection of matter.

1st law of thermodynamics

The principle of conservation of energy stating that energy can be transferred or transformed, but it cannot be created or destroyed.

2nd law of thermodynamics

The principle stating that every energy transfer or transformation increases the entropy of the universe.

Entropy

A measure of molecular disorder or randomness, representing dispersed energy in a system.

Spontaneous processes

Processes that occur without energy input and are energetically favorable; they can be fast or slow.

Free energy (Gibbs free energy)

The portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system; calculated as \text{\Delta G} = G_{\text{final state}} - G_{\text{initial state}}.

Exergonic reaction

A reaction that proceeds with a net release of free energy and is spontaneous (energetically favorable), where \text{\Delta G} is negative.

Cellular Respiration Reaction

$C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O$ with a \text{\Delta G} = -686\,kcal\,mol^{-1} ($-2,870\,kJ\,mol^{-1}$).

Endergonic reaction

A reaction that absorbs free energy from its surroundings and is nonspontaneous, where \text{\Delta G} is positive.

Energy coupling

The use of an exergonic process (such as ATP hydrolysis) to drive an endergonic process.

Adenosine triphosphate (ATP)

A molecule consisting of a ribose sugar, the nitrogenous base adenine, and three phosphate groups; it is used to drive cellular work and to make RNA.

ATP Hydrolysis Reaction

$ATP + H_2O \rightarrow ADP + P_i$ with a \text{\Delta G} = -7.3\,kcal\,mol^{-1} ($-30.5\,kJ\,mol^{-1}$).

Phosphorylation

The transfer of a phosphate group from ATP to another molecule, such as a reactant, to drive endergonic reactions or induce conformational changes in proteins.

Enzymes

Catalytic proteins that speed up reactions by lowering the activation energy ($E_A$) without being consumed or affecting the change in free energy (\text{\Delta G}).

Activation energy ($E_A$)

The initial investment of energy required to start a reaction by breaking bonds in the reactant molecules.

Induced fit

The change in shape of an enzyme's active site so that it binds more snugly to the substrate, brought about by chemical interactions between the substrate and the active site.

Genome

The totality of DNA in a cell, which can consist of a single DNA molecule in prokaryotes or a number of DNA molecules in eukaryotes.

Chromatin

The entire complex of DNA and proteins that is the building material of eukaryotic chromosomes.

Somatic cells

All body cells except the reproductive cells; in humans, they contain two sets of $23$ chromosomes.

Gametes

Reproductive cells (sperm and eggs) that have half as many chromosomes as somatic cells; in humans, they have one set of $23$ chromosomes.

Sister chromatids

Joined identical copies of the original chromosome, initially attached by cohesin, which are eventually separated and moved into two nuclei during cell division.

Centromere

A region made up of repetitive sequences in the chromosomal DNA where the two sister chromatids are most closely attached.

Mitosis

The division of the genetic material in the nucleus.

Cytokinesis

The division of the cytoplasm, which brings about the separation into two daughter cells.

Interphase

The period in the cell cycle when the cell is not dividing, consisting of $G_1$ (first gap), $S$ (synthesis), and $G_2$ (second gap).

S phase

The subphase of interphase during which DNA synthesis occurs and chromosomes are duplicated.

Mitotic spindle

A structure consisting of microtubules and associated proteins that controls chromosome movement during mitosis.

Kinetochores

Protein complexes that assemble on sections of DNA at centromeres and attach to spindle microtubules.

Cleavage furrow

A shallow groove in the cell surface near the old metaphase plate, which is the first sign of cleavage in animal cells during cytokinesis.

Cell plate

A membrane-bounded, flattened sac located at the midline of a dividing plant cell, inside which the new cell wall forms during cytokinesis.