Photosynthesis, Nucleic Acid Structure, and DNA Replication

Vocabulary practice flashcards covering photosynthesis mechanisms and pathways from Chapter 8, alongside nucleic acid structure, replication mechanisms, and chromosome compaction from Chapter 11.

Photosynthesis

The biological process in which light energy is captured and used to synthesize carbohydrates according to the equation $CO_2 + H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + O_2 + H_2O$, where $CO_2$ is reduced and $H_2O$ is oxidized.

Heterotroph

An organism that must consume organic molecules from its environment to sustain life.

Autotroph

An organism that produces organic molecules from inorganic sources.

Photoautotroph

An autotroph that uses light as an energy source to synthesize organic molecules, such as green plants, algae, and cyanobacteria.

Chloroplast

The specialized organelle found in plants and algae that carries out photosynthesis.

Mesophyll

The internal tissue of a leaf where the majority of photosynthesis occurs, containing chloroplast-rich mesophyll cells.

Stomata

Microscopic pores on the surface of leaves through which carbon dioxide enters and oxygen exits.

Thylakoid Membrane

The third membrane system of a chloroplast that forms flattened sacs called thylakoids, encloses the thylakoid lumen, and contains photosynthetic pigment molecules.

Granum

A stack of thylakoid discs located within the chloroplast.

Stroma

The fluid-filled region of the chloroplast located between the thylakoid membrane and the inner membrane, serving as the site of the Calvin cycle.

Light Reactions

The first stage of photosynthesis, taking place in the thylakoid membranes, which utilizes light energy to produce $ATP$, $NADPH$, and $O_2$.

Calvin Cycle

The second stage of photosynthesis occurring in the stroma, which uses $ATP$ and $NADPH$ to incorporate carbon dioxide into carbohydrates.

Photon

A discrete particle of light electromagnetic radiation; shorter wavelengths correspond to photons carrying more energy.

Absorption Spectrum

A graphical representation of the specific wavelengths of light electromagnetic radiation absorbed by different photosynthetic pigments.

Action Spectrum

A graph depicting the rate of photosynthesis produced by a whole plant across specific wavelengths of light.

Photosystem II (PSII)

The initial photosystem complex in the thylakoid membrane that captures light, oxidizes water at a manganese cluster to generate $O_2$ and $H^+$, and releases energized electrons into an electron transport chain.

Photosystem I (PSI)

A photosystem complex in the thylakoid membrane that absorbs light to boost electrons to a higher energy level, with the primary role of producing $NADPH$ in the stroma.

Photophosphorylation

The process of synthesizing $ATP$ in chloroplasts driven by chemiosmosis through $ATP$ synthase using an $H^+$ electrochemical gradient across the thylakoid membrane.

Cyclic Photophosphorylation

A photosynthetic pathway where excited electrons from $PSI$ travel through ferredoxin, $Q_B$, the cytochrome complex, and plastocyanin before returning to $PSI$, generating an $H^+$ electrochemical gradient to produce only $ATP$.

Enhancement Effect

The phenomenon where simultaneous exposure to flashes of light at $680\,nm$ and $700\,nm$ more than doubles the rate of photosynthesis, providing evidence for the cooperation of two distinct photosystems.

Z Scheme

The zigzag progression of energy levels experienced by an electron as it moves from $PSII$ through $PSI$ to $NADP^+$ during noncyclic electron flow.

Rubisco

The enzyme that catalyzes the initial carbon fixation step of the Calvin cycle by adding $CO_2$ to ribulose bisphosphate ($RuBP$).

Photorespiration

A wasteful process occurring when rubisco functions as an oxygenase by adding $O_2$ to $RuBP$ and releasing $CO_2$; favored in hot, dry environments with low $CO_2$ and high $O_2$.

C4 Plants

Plants that minimize photorespiration by using $PEP$ carboxylase in mesophyll cells to fix $CO_2$ into a $4\text{-carbon}$ molecule (oxaloacetate) before shuttling malate into bundle-sheath cells for the Calvin cycle.

CAM Plants

Plants that utilize Crassulacean Acid Metabolism to temporally separate carbon capture and the Calvin cycle, opening stomata at night to store carbon as malate and closing them during the day to conserve water.

Bacterial Transformation

The process discovered by Frederick Griffith wherein genetic material is transferred from heat-killed virulent bacteria (type S) to live benign bacteria (type R), conferring a heritable capsule-secreting trait.

Genome

The complete complement of genetic material in an organism.

Purines

A class of double-ring nitrogenous bases found in nucleic acids, including adenine ($A$) and guanine ($G$).

Pyrimidines

A class of single-ring nitrogenous bases found in nucleic acids, including cytosine ($C$), thymine ($T$), and uracil ($U$).

Phosphodiester Bond

A covalent linkage in DNA and RNA that connects the phosphate group on the $5'$ carbon of one sugar to the $3'$ hydroxyl group of the adjacent sugar.

Chargaff's Rule

The biochemical observation that double-stranded DNA contains equimolar quantities of adenine and thymine ($A = T$) and equimolar quantities of guanine and cytosine ($G = C$).

Major Groove

A wide indentation on the exterior surface of the DNA double helix where regulatory proteins bind to affect gene expression.

Minor Groove

The narrower of the two spiral indentations on the surface of the DNA double helix.

Semiconservative Mechanism

The mechanism of DNA replication wherein each separated parental strand serves as a template, producing two double helices each composed of one original parental strand and one newly made daughter strand.

Conservative Mechanism

A rejected model of DNA replication predicting that replication produces one double helix with both original parental strands and another with two entirely new daughter strands.

Dispersive Mechanism

A rejected model of DNA replication predicting that segments of newly synthesized DNA are interspersed with parental DNA segments along each strand.

Origin of Replication

A specific site on a chromosome where DNA unwinds, forming a replication bubble flanked by two bidirectional replication forks.

DNA Helicase

An enzyme that binds to DNA and travels along one strand in the $5'$ to $3'$ direction, using $ATP$ to separate the double helix and advance the replication fork.

DNA Topoisomerase

An enzyme that travels slightly ahead of the replication fork to alleviate coiling and torsional strain caused by helicase unwinding.

Single-Strand Binding Proteins

Proteins that coat separated single strands of template DNA to prevent them from re-annealing into a double helix during replication.

DNA Primase

An enzyme that synthesizes short RNA primers complementary to template strands to initiate synthesis by DNA polymerase.

DNA Polymerase

An enzyme that covalently links deoxynucleoside triphosphates together to synthesize a complementary DNA strand in a $5'$ to $3'$ direction.

Leading Strand

The newly made DNA daughter strand that is synthesized continuously in a $5'$ to $3'$ direction toward the opening replication fork.

Lagging Strand

The newly made DNA daughter strand synthesized discontinuously in a $5'$ to $3'$ direction away from the replication fork as Okazaki fragments.

Okazaki Fragments

Short segments of DNA synthesized on the lagging strand that each begin with an RNA primer.

DNA Ligase

An enzyme that catalyzes the covalent joining of adjacent Okazaki fragments by forming phosphodiester linkages.

Telomere

A specialized region of repetitive nucleotide sequences located at the ends of eukaryotic chromosomes characterized by a $3'$ overhang.

Telomerase

A ribonucleoprotein enzyme that attaches multiple copies of repeated DNA sequences to the ends of eukaryotic chromosomes to prevent progressive shortening.

Nucleosome

The repeating structural unit of eukaryotic chromatin, composed of $146$ or $147$ base pairs of DNA wrapped around an octamer of eight histone proteins.

30-nm Fiber

A level of chromatin compaction where nucleosomes assemble into a three-dimensional zigzag array via histone H1 and other proteins, shortening DNA length $7\text{-fold}$.

Radial Loop Domains

Loops of $30\text{-nm}$ chromatin fibers anchored to protein fibers in the nuclear matrix.

Heterochromatin

Highly compacted, transcriptionally inactive regions of chromosomal chromatin.

Euchromatin

Less condensed regions of chromatin that are accessible for active gene transcription.