BIO 114 — Exam II Lecture Notes

Comprehensive vocabulary flashcards reviewing molecular genetics, thermodynamics, enzyme kinetics, cellular respiration, and photosynthesis from the BIO 114 Exam II lecture notes.

Transformation

A change in genotype and phenotype caused by the assimilation of external DNA.

Chargaff's Rules

Analytical chemistry findings establishing that within DNA, the amount of adenine equals thymine ($A = T$) and the amount of guanine equals cytosine ($G = C$).

Semiconservative Replication

The mechanism of DNA replication in which parental strands separate and serve as templates to produce new complementary daughter strands.

Nucleosome

A fundamental subunit of chromatin consisting of DNA wound around a core complex of 8 histone proteins.

Kilobase (kb)

A unit of measurement for DNA length equal to $1000\text{ bp}$.

Megabase (Mb)

A unit of measurement for DNA length equal to $10^6\text{ bp}$.

Gene Expression

The cellular process by which DNA directs the synthesis of proteins, serving as the functional link between genotype and phenotype.

Transcription

The synthesis of an RNA molecule from a DNA template ($\text{DNA} \rightarrow \text{RNA}$), taking place within the nucleus.

Translation

The synthesis of a polypeptide specified by an mRNA template ($\text{RNA} \rightarrow \text{protein}$), occurring in the cytoplasm via ribosomes.

Codon

A specific sequence of 3 consecutive nucleotides in mRNA that specifies a particular amino acid.

Anticodon

A 3-nucleotide region on a tRNA molecule that base-pairs complementarily with a codon on an mRNA transcript.

Aminoacyl tRNA Synthetase

The enzyme responsible for attaching the appropriate amino acid to the $3'$ end of its corresponding tRNA molecule.

Polyribosome

A structure formed when a single mRNA transcript is translated simultaneously by multiple ribosomes.

Metabolic Pathway

A linked series of biochemical reactions where the product of one reaction becomes the specific substrate/reactant for the next.

Catabolic Pathways

Metabolic pathways that break down complex molecules into simpler compounds, releasing free energy.

Anabolic Pathways

Metabolic pathways that synthesize complex molecules from simpler ones, requiring an input of energy.

Energy Coupling

The biological mechanism where energy released by catabolic pathways is directly used to drive endergonic, anabolic processes.

First Law of Thermodynamics

The physical law stating that energy can neither be created nor destroyed; it can only be transferred or transformed.

Second Law of Thermodynamics

The physical principle stating that every energy transfer increases the total entropy of the universe and energy transfers are never $100\%$ efficient.

Entropy

A thermodynamic measure of disorder or randomness within a system.

Exergonic Reaction

A spontaneous chemical reaction that proceeds with a net release of free energy ($\Delta G < 0$), yielding products with less free energy than reactants.

Endergonic Reaction

A nonspontaneous chemical reaction that requires an input of energy ($\Delta G > 0$), yielding products with more free energy than reactants.

ATP (Adenosine Triphosphate)

The primary energy currency of cells, which releases energy via hydrolysis into $\text{ADP} + \text{P}_i$ to drive endergonic reactions.

Activation Energy ($E_A$)

The initial minimum amount of energy required to start a chemical reaction.

Catalyzed vs. Uncatalyzed Reaction Energy Profile

A reaction progress diagram illustrating that an enzyme accelerates a reaction by lowering the activation energy ($E_A$) without altering the net change in free energy ($\Delta G$).

Active Site

The specific localized pocket or groove on an enzyme where the substrate binds and catalysis takes place.

Induced Fit

The subtle conformational change an enzyme undergoes upon substrate binding to position catalytic groups more snugly.

Denaturation

The disruption of an enzyme's native 3D conformation caused by environmental extremes (such as temperature or pH), resulting in a loss of catalytic function.

Competitive Inhibitor

A substance that binds directly to an enzyme's active site, competing directly with the natural substrate for binding.

Noncompetitive Inhibitor

A substance that binds to a site other than the active site, altering the enzyme's conformation and reducing its catalytic effectiveness.

Cofactor

A non-protein, inorganic helper component (such as metal ions) required for proper catalytic enzyme activity.

Coenzyme

An organic molecule, frequently derived from vitamins, that assists an enzyme in performing its catalytic function.

Glycolysis

The anaerobic metabolic process occurring in the cytoplasm that splits one 6-carbon glucose into two 3-carbon pyruvates, yielding a net $2\text{ ATP}$ and $2\text{ NADH}$.

Pyruvate Oxidation

The mitochondrial matrix step converting each pyruvate into acetyl-CoA, accompanied by decarboxylation ($\text{CO}_2$ release) and the production of $\text{NADH}$.

Citric Acid Cycle

A cyclic metabolic pathway in the mitochondrial matrix that fully oxidizes acetyl groups, producing $6\text{ NADH}$, $2\text{ FADH}_2$, $2\text{ ATP}$, and $4\text{ CO}_2$ per glucose molecule.

Electron Transport Chain (ETC)

A series of protein complexes embedded in the inner mitochondrial membrane that transfers electrons from $\text{NADH}$ and $\text{FADH}_2$ to drive $\text{H}^+$ pumping across the membrane.

Chemiosmosis

The flow of protons ($\text{H}^+$) back across the inner mitochondrial membrane through ATP synthase to generate ATP from an established electrochemical gradient.

Fermentation

An anaerobic pathway that regenerates $\text{NAD}^+$ from $\text{NADH}$, permitting glycolysis to continuously generate ATP without oxygen.

Stomata

Specialized microscopic pores located on leaves through which $\text{CO}_2$ enters and $\text{O}_2$ exits the plant tissue.

Thylakoid

Flattened membranous sacs inside chloroplasts containing chlorophyll, which act as the site of light-dependent photosynthetic reactions.

Stroma

The dense fluid compartment of the chloroplast surrounding the thylakoid membranes, where the Calvin cycle reactions occur.

Photosystem II (PSII)

The first functioning light-harvesting photosystem in the thylakoid membrane, which absorbs light energy, splits $\text{H}_2\text{O}$, releases $\text{O}_2$, and generates a proton gradient.

Photosystem I (PSI)

The second photosystem in the light reactions that absorbs light to facilitate the enzymatic reduction of $\text{NADP}^+$ to $\text{NADPH}$.

Rubisco

The primary enzyme of the Calvin cycle that catalyzes carbon fixation by joining $\text{CO}_2$ to ribulose bisphosphate (RuBP).