Comprehensive Biology Review: Cellular Energy, Photosynthesis, Cell Communication, and Molecular Genetics

Comprehensive vocabulary flashcards covering cellular energy, enzymes, cellular respiration, photosynthesis, cell signaling mechanisms, and molecular genetics from university lecture notes.

Chemical Potential Energy

The potential energy stored within the covalent bonds between atoms of molecules (such as glucose and $\text{ATP}$), which can be released when bonds are broken and rearranged.

First Law of Thermodynamics

A fundamental law stating that energy cannot be created or destroyed, but can be transferred from one place to another and transformed from one type to another.

Second Law of Thermodynamics

A physical law stating that any transfer or transformation of energy increases the entropy (degree of disorder) of a system, reducing the usable energy available to do work.

Free Energy ($G$)

The usable energy in a system available to promote change or do work under constant conditions.

Exergonic Reaction

A spontaneous chemical reaction where products have less free energy than reactants, resulting in a negative free-energy change ($\Delta G < 0$) and the release of free energy.

Endergonic Reaction

A nonspontaneous chemical reaction where products have more free energy than reactants, characterized by a positive free-energy change ($\Delta G > 0$) and requiring an input of energy.

Activation Energy ($E_A$)

The initial investment of energy required to start a chemical reaction by stretching and straining original bonds to achieve the transition state.

Induced Fit

Conformational changes undergone by an enzyme upon binding substrates that clasp the substrates more tightly and strain their chemical bonds.

$K_M$ (Michaelis Constant)

The substrate concentration at which the velocity of an enzyme-catalyzed reaction reaches half of its maximal rate ($\frac{V_{\max}}{2}$); it reflects the enzyme's affinity for the substrate.

Competitive Inhibitor

A molecule that regulates enzyme activity by noncovalently binding directly to the active site, increasing apparent $K_M$ without altering $V_{\max}$.

Noncompetitive Inhibitor

A molecule that binds to an allosteric site rather than the active site, changing enzyme conformation to lower $V_{\max}$ without affecting $K_M$.

Prosthetic Group

A small non-protein molecule that is permanently bound to an enzyme or protein, such as the heme group found in hemoglobin.

Coenzyme

An organic molecule that participates directly in an enzyme-catalyzed chemical reaction but is regenerated and left unchanged after the reaction completes (such as $\text{NAD}^+/\text{NADH}$).

Feedback Inhibition

A biochemical regulatory mechanism where the final product of a metabolic pathway binds to an allosteric site on an early pathway enzyme to inhibit its activity and prevent overproduction.

Substrate-Level Phosphorylation

A method of generating $\text{ATP}$ occurring during glycolysis and the citric acid cycle by the direct chemical transfer of a phosphate group from an organic molecule to $\text{ADP}$.

Chemiosmosis

The synthesis of $\text{ATP}$ driven by the potential energy of an $\text{H}^+$ electrochemical gradient across a membrane pushing protons through $\text{ATP}$ synthase.

Anaerobic Respiration

A cellular respiration mechanism used by microorganisms in oxygen-lacking environments that utilizes an electron transport chain with an inorganic molecule other than $\text{O}_2$ (such as nitrate, $\text{NO}_3^-$) as the final electron acceptor.

Fermentation

The breakdown of organic molecules to produce $\text{ATP}$ solely via substrate-level phosphorylation without net oxidation, recycling $\text{NADH}$ back to $\text{NAD}^+$ by transferring electrons to organic derivatives like pyruvate or acetaldehyde.

Photoautotroph

An organism, such as a green plant, alga, or cyanobacterium, that synthesizes organic molecules from inorganic raw materials using light as its source of energy.

Stomata

Microscopic pores on the leaf surface that regulate gas exchange, allowing $\text{CO}_2$ to enter the leaf and $\text{O}_2$ to exit.

Absorption Spectrum

A diagram or graph plotting the relative wavelengths of electromagnetic radiation absorbed by specific photosynthetic pigments.

Action Spectrum

A graph showing the overall rate of photosynthesis across different visible light wavelengths for an intact plant, peaking at wavelengths strongly absorbed by chlorophylls and carotenoids.

Linear Electron Flow

The pathway in photosynthesis where electrons travel from water through Photosystem II, the electron transport chain, and Photosystem I to $\text{NADP}^+$, producing $\text{O}_2$, $\text{ATP}$, and $\text{NADPH}$.

Cyclic Photophosphorylation

A photosynthetic electron flow process involving only Photosystem I and an electron transport chain that generates an $\text{H}^+$ gradient to produce extra $\text{ATP}$ without making $\text{NADPH}$ or $\text{O}_2$.

P680

A specialized pair of chlorophyll molecules residing in the reaction center of Photosystem II that, when photoexcited, releases a high-energy electron to a primary electron acceptor and oxidizes water.

Z Scheme

The model of photosynthetic linear electron flow representing the zig-zag changes in electron free energy as it is excited by light in Photosystem II, travels down the electron transport chain, and is excited again in Photosystem I.

Rubisco

The primary photosynthetic enzyme (ribulose 1,5-bisphosphate carboxylase-oxygenase) that catalyzes the fixation of $\text{CO}_2$ to $\text{RuBP}$ in the first phase of the Calvin cycle.

Photorespiration

A wasteful metabolic process occurring in $C_3$ plants when rubisco incorporates $\text{O}_2$ instead of $\text{CO}_2$ during hot and dry conditions, releasing $\text{CO}_2$ and reducing photosynthetic efficiency.

$C_4$ Plants

Plants that avoid photorespiration by spatially separating carbon capture (in mesophyll cells via $\text{PEP}$ carboxylase into oxaloacetate) and the Calvin cycle (in bundle-sheath cells).

CAM Plants

Plants that minimize photorespiration and water loss by temporally separating carbon fixation, opening stomata at night to store $\text{CO}_2$ as malate and releasing it to the Calvin cycle during the day.

Direct Intercellular Signaling

A cell communication method in which signaling molecules travel directly through intercellular channels (such as gap junctions) between adjacent cell cytosols.

Contact-Dependent Signaling

Cell-to-cell communication in which membrane-bound signaling molecules on one cell surface bind to receptors on adjacent encountering cells.

Autocrine Signaling

A form of cell communication where cells secrete signaling molecules that bind to receptors on their own plasma membrane and that of nearby cells of identical type.

Paracrine Signaling

A local signaling mechanism in which a cell releases signaling molecules that travel short distances through extracellular fluid to affect target cells in the immediate vicinity.

Endocrine Signaling

Long-distance signaling in which cells secrete hormones directly into the bloodstream to reach distant target cells.

Dissociation Constant ($K_d$)

A numerical value ($\frac{k_{\text{off}}}{k_{\text{on}}}$) reflecting the ligand concentration at which half the receptors are occupied; an inverse measure of receptor affinity.

Enzyme-Linked Receptor

A plasma membrane receptor featuring an extracellular ligand-binding domain and an intracellular catalytic domain, typically functioning as a protein kinase that transfers a phosphate from $\text{ATP}$ to a protein.

G-Protein-Coupled Receptor (GPCR)

A cell surface receptor that interacts with an intracellular trimeric G protein, causing the exchange of $\text{GDP}$ for $\text{GTP}$ and dissociation of the $\alpha$ subunit from the $\beta/\gamma$ dimer.

Ligand-Gated Ion Channel

A transmembrane protein channel that opens in response to the binding of specific chemical ligands, allowing ions to diffuse down their electrochemical gradient.

Intracellular Receptor

A receptor protein located in the cytosol or nucleus that binds small, hydrophobic signaling molecules (such as estrogen) that can diffuse across the lipid bilayer.

Bacterial Transformation

The process discovered by Frederick Griffith in which genetic material transferred from dead virulent bacteria (Type S) confers a new, heritable phenotype to living nonvirulent bacteria (Type R).

Phosphodiester Bond

The covalent linkage formed between the $3'$ hydroxyl group of one nucleotide sugar and the $5'$ phosphate group of the adjacent nucleotide, creating the backbone of a nucleic acid strand.

Chargaff's Rule

The empirical finding that in double-stranded DNA, the percentage of adenine equals thymine ($\text{A} = \text{T}$) and the percentage of guanine equals cytosine ($\text{G} = \text{C}$).

Semiconservative Replication

The mechanism of DNA replication proven by Meselson and Stahl where parental double helices unwind and each parent strand serves as a template, producing two daughter helices containing one parental and one newly synthesized strand.

DNA Helicase

An enzyme that uses energy from $\text{ATP}$ hydrolysis to separate double-stranded DNA into single strands, traveling in the $5'$ to $3'$ direction.

DNA Topoisomerase

An enzyme that travels ahead of the replication fork to relieve supercoiling and torsional strain produced by the unwinding action of DNA helicase.

Single-Strand Binding Protein (SSB)

A protein that binds to exposed single-stranded DNA template strands to prevent them from prematurely reannealing into a double helix.

DNA Primase

An RNA polymerase that synthesizes short RNA primers ($10$ to $12$ nucleotides long) complementary to template DNA, providing a free $3'$ hydroxyl group for DNA polymerase.

Okazaki Fragments

Short discontinuous segments of DNA synthesized on the lagging strand that begin with an RNA primer and are extended in the $5'$ to $3'$ direction away from the replication fork.

DNA Ligase

An enzyme that catalyzes the formation of a phosphodiester bond between adjacent Okazaki fragments, covalently sealing nicks in the lagging strand backbone.

Nucleosome

The fundamental repeating structural unit of eukaryotic chromatin, consisting of an octamer of eight histone proteins wrapped with approximately $146$ to $147$ base pairs of DNA, measuring $11\,\text{nm}$ in diameter.

Loop Domain

A chromatin structural folding configuration generated when DNA wrapped in nucleosomes is passed through an SMC protein ring and stabilized at its base by CTCF proteins.

Topologically Associating Domain (TAD)

A conserved genomic loop domain spanning $100\,\text{kb}$ to $1\,\text{Mb}$ containing $1$ to $5$ genes, within which DNA sequences preferentially interact with one another rather than outside sequences.

Heterochromatin

Highly condensed, tightly packed regions of interphase chromatin that typically localize near the nuclear lamina and are transcriptionally inactive.

Euchromatin

Less compacted, open regions of interphase chromatin located toward the nuclear interior that contain actively transcribed genes.