BIOL005A: Introduction to Cell and Molecular Biology - Exam Review Flashcards

Comprehensive practice flashcards defining key biological vocabulary across energy metabolism, cellular respiration, photosynthesis, DNA structure and replication, the cell cycle, mitosis, meiosis, and Mendelian genetics.

First Law of Thermodynamics

The law of conservation of energy stating that energy cannot be created or destroyed, only transferred or transformed.

Second Law of Thermodynamics

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

Exergonic Reaction

A spontaneous chemical reaction that releases free energy, characterized by a negative change in free energy ($\Delta G < 0$).

Endergonic Reaction

A nonspontaneous chemical reaction that absorbs and consumes free energy, characterized by a positive change in free energy ($\Delta G > 0$).

Energy Coupling

The use of an exergonic process (such as $\text{ATP}$ hydrolysis) to drive an endergonic one in cellular work.

Activation Energy ($E_A$)

The initial investment of energy required to contort reactant molecules so that chemical bonds can break and start a reaction.

Induced Fit

The conformational change that occurs when a substrate enters an enzyme active site, causing the enzyme to fold more closely around the substrate via weak chemical interactions.

Competitive Inhibitor

A substance that reduces enzyme activity by binding directly to the active site in place of the substrate; this inhibition can be overcome by increasing substrate concentration.

Noncompetitive Inhibitor

A substance that binds to an enzyme at a site other than the active site, changing the enzyme shape so that the active site functions much less effectively; cannot be overcome by high substrate concentrations.

Purines vs. Pyrimidines

Purines (Adenine and Guanine) contain two fused rings, whereas pyrimidines (Cytosine, Thymine, and Uracil) contain one ring.

Starch vs. Cellulose

Starch is a coiled polymer composed of $1-4$ linkages of $\alpha$-glucose monomers used for storage; cellulose consists of straight, flat chains of $1-4$ linkages of $\beta$-glucose monomers forming rigid structural microfibrils.

Chitin

An animal structural polysaccharide made of N-acetylglucosamine monomers (glucose linked to an acetyl amine group) found in the exoskeletons of arthropods.

Valine

A nonpolar amino acid characterized by a branched, hydrophobic hydrocarbon side chain ($-\text{CH}(\text{CH}_3)_2$).

Oxidation

The complete or partial loss of electrons from a substance in a redox reaction, accompanied by an increase in positive charge.

Reduction

The complete or partial gain of electrons by a substance in a redox reaction, accompanied by a decrease in positive charge.

Reducing Agent

The reactant that donates electrons in an oxidation-reduction reaction and consequently becomes oxidized.

Oxidizing Agent

The reactant that accepts electrons in an oxidation-reduction reaction and consequently becomes reduced.

Substrate-Level Phosphorylation

The enzymatic formation of $\text{ATP}$ by direct transfer of a phosphate group from a phosphorylated metabolic intermediate to $\text{ADP}$.

Glycolysis

A 10-step anaerobic metabolic pathway occurring in the cytosol that splits one molecule of glucose into two molecules of pyruvate, producing a net yield of $2\,\text{ATP}$ and $2\,\text{NADH}$.

Phosphofructokinase (PFK)

The key regulatory enzyme in step 3 of glycolysis that transfers a phosphate from $\text{ATP}$ to fructose-6-phosphate to yield fructose-1,6-bisphosphate; allosterically inhibited by high levels of $\text{ATP}$.

$\text{NAD}^+$ (Nicotinamide Adenine Dinucleotide)

A coenzyme and dinucleotide electron carrier that accepts two electrons and one proton to form $\text{NADH}$ during cellular respiration.

Pyruvate Oxidation

The step catalyzed by the pyruvate dehydrogenase complex in the mitochondrial matrix that converts each pyruvate into acetyl $\text{CoA}$, releasing one $\text{CO}_2$ and forming one $\text{NADH}$.

Coenzyme A (CoA)

A sulfur-containing helper compound derived from vitamin $B_5$ (pantothenate) that binds an acetyl group to its sulfhydryl ($-\text{SH}$) group, delivering it to the citric acid cycle.

Citric Acid Cycle

An 8-step metabolic cycle in the mitochondrial matrix that oxidizes acetyl $\text{CoA}$, producing per turn: $2\,\text{CO}_2$, $3\,\text{NADH}$, $1\,\text{FADH}_2$, and $1\,\text{ATP}$ (or $\text{GTP}$) via substrate-level phosphorylation.

Oxidative Phosphorylation

The production of $\text{ATP}$ using energy derived from the redox reactions of an electron transport chain coupled with chemiosmosis.

Proton-Motive Force

The potential energy stored in an electrochemical gradient of hydrogen ions ($\text{H}^+$) established by the electron transport chain pumping protons across the inner mitochondrial membrane into the intermembrane space.

ATP Synthase

A channel protein complex that uses the energy of protons flowing down their electrochemical gradient to synthesize $\text{ATP}$ from $\text{ADP}$ and inorganic phosphate ($\text{P}_i$).

Lactic Acid Fermentation

An anaerobic pathway in which pyruvate is reduced directly by $\text{NADH}$ to form lactate, regenerating $\text{NAD}^+$ without producing $\text{CO}_2$.

Thylakoid

A flattened, membranous sac inside a chloroplast whose membrane contains photosynthetic pigments and electron transport chains; stacked into structures called grana.

Stroma

The dense fluid within the chloroplast surrounding the thylakoid membranes, serving as the site of the Calvin cycle.

Chlorophyll a

The primary photosynthetic pigment containing a light-absorbing porphyrin ring that absorbs blue and red wavelengths while reflecting green light (around $550\,\text{nm}$).

Photosystem II (PS II)

A light-capturing complex with a $P680$ reaction-center chlorophyll a that uses light energy to excite electrons, transferring them to pheophytin, and replenishes lost electrons via the photolysis of water.

Photolysis

The enzymatic splitting of water molecules ($\text{H}_2\text{O} \rightarrow 2\,\text{H}^+ + \frac{1}{2}\,\text{O}_2 + 2\,\text{e}^-$) in Photosystem II, releasing oxygen and providing electrons for the light reactions.

Photosystem I (PS I)

A light-capturing complex with a $P700$ reaction-center chlorophyll a that accepts electrons from the PS II electron transport chain and re-energizes them to reduce $\text{NADP}^+$ to $\text{NADPH}$ via ferredoxin and $\text{NADP}^+$ reductase.

Chemiosmosis

An energy-coupling mechanism that uses energy stored in the form of a hydrogen ion gradient across a membrane (inner mitochondrial membrane or thylakoid membrane) to drive the cellular work of $\text{ATP}$ synthesis.

Calvin Cycle

The light-independent reactions occurring in the stroma of chloroplasts that use $\text{ATP}$ and $\text{NADPH}$ to convert $\text{CO}_2$ into the carbohydrate glyceraldehyde-3-phosphate (G3P).

Carbon Fixation

The initial incorporation of inorganic carbon from $\text{CO}_2$ into an organic molecule (RuBP) catalyzed by the enzyme RuBisCO.

RuBP (Ribulose-1,5-bisphosphate)

A 5-carbon sugar containing two phosphate groups that acts as the initial carbon dioxide acceptor in the Calvin cycle.

RuBisCO

Ribulose bisphosphate carboxylase-oxygenase; the most abundant enzyme on Earth, which catalyzes carbon fixation but has a slow turnover rate ($3-10\,\text{CO}_2$ per second) and mistakenly fixes $\text{O}_2$ in about $25\%$ of reactions.

Glyceraldehyde-3-Phosphate (G3P)

A three-carbon carbohydrate produced directly by the Calvin cycle that serves as the starting material for synthesizing glucose, sucrose, starch, and cellulose.

Transformation

A change in genotype and phenotype due to the assimilation of external DNA by a cell, first demonstrated in Streptococcus pneumoniae by Frederick Griffith in 1928.

Hershey-Chase Experiment

A 1952 experiment using bacteriophage T2 labeled with $^{35}\text{S}$ (protein) and $^{32}\text{P}$ (DNA) that showed only viral DNA enters host cells during infection, proving DNA is the genetic material.

Chargaff's Rules

The biochemical observation that DNA base composition varies among species and that within a species, the percentage of adenine equals thymine ($\%A = \%T$) and the percentage of guanine equals cytosine ($\%G = \%C$).

Antiparallel

The arrangement of the two sugar-phosphate backbones in a DNA double helix, running in opposite directions ($5' \rightarrow 3'$ relative to $3' \rightarrow 5'$).

Meselson-Stahl Experiment

A 1958 experiment using $^{15}\text{N}$ and $^{14}\text{N}$ isotopes and density-gradient centrifugation in E. coli that demonstrated DNA replicates semiconservatively.

Origin of Replication

A specific sequence of DNA where replication is initiated, opening up a replication bubble with two outward-moving replication forks.

Helicase

An enzyme that unwinds and separates parental double-stranded DNA at the replication forks by breaking hydrogen bonds between base pairs.

Primase

A specialized RNA polymerase that synthesizes short complementary RNA primers using parental DNA as a template, providing a free $3'\text{-OH}$ group for DNA polymerase.

DNA Polymerase III

The primary bacterial enzyme responsible for elongating new DNA strands by adding deoxyribonucleotides complementary to a template strand strictly in the $5' \rightarrow 3'$ direction.

DNA Polymerase I

The bacterial enzyme that removes RNA nucleotides from the $5'$ end of RNA primers and replaces them with DNA nucleotides added to the adjacent $3'$ end.

DNA Ligase

An enzyme that joins the sugar-phosphate backbones of DNA fragments (such as Okazaki fragments or repaired segments) by catalyzing the formation of phosphodiester bonds using $ATP$.

Leading Strand

The new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory $5' \rightarrow 3'$ direction.

Lagging Strand

A discontinuously synthesized DNA strand that elongates away from the replication fork by means of short segments called Okazaki fragments.

Okazaki Fragments

Short segments of DNA synthesized on the lagging strand template during replication, each initiated with an RNA primer and eventually joined together by DNA ligase.

Nucleotide Excision Repair

A DNA repair system in which a nuclease cuts out damaged or distorted segments of DNA, a DNA polymerase fills in the gap, and DNA ligase seals the nick.

Polymerase Chain Reaction (PCR)

An in vitro technique developed by Kary Mullis in the 1980s that exponentially amplifies a specific target DNA region through repeated cycles of denaturation, primer annealing, and extension.

Taq Polymerase

A heat-tolerant DNA polymerase isolated from the thermophilic bacterium Thermus aquaticus that remains active during the high-temperature denaturation step ($95^\circ\text{C}$) and elongates DNA at $72^\circ\text{C}$.

Ploidy

The number of complete sets of chromosomes in a cell; diploid cells contain two sets ($2n$) and haploid cells contain one set ($n$).

Centromere

The constricted region of a duplicated chromosome where sister chromatids are joined together and where kinetochore microtubules attach during cell division.

Sister Chromatids

Two identical copies of a duplicated chromosome produced during the S phase of interphase and held together at a centromere.

Cell Cycle

An ordered sequence of cellular events consisting of interphase (divided into $G_1$, $S$, and $G_2$ phases) alternating with the mitotic (M) phase (mitosis and cytokinesis).

Mitosis

A division of the eukaryotic cell nucleus that precisely segregates duplicated chromosomes into two genetically identical daughter nuclei.

Metaphase (Mitosis)

The mitotic stage during which condensed chromosomes align along the equatorial plane (metaphase plate) of the cell midway between the spindle poles.

Anaphase (Mitosis)

The mitotic stage where centromeres divide and sister chromatids separate into individual daughter chromosomes that are pulled toward opposite spindle poles.

Cytokinesis

The division of the cytoplasm to form two separate daughter cells; accomplished via a cleavage furrow in animal cells and a cell plate in plant cells.

Homologous Chromosomes

A pair of chromosomes of the same length, centromere position, and gene loci—one inherited from each parent—that may carry different alleles.

Synapsis

The pairing and physical association of duplicated homologous chromosomes during prophase I of meiosis.

Crossing Over (Recombination)

The reciprocal exchange of genetic material between nonsister chromatids during prophase I of meiosis, occurring at visible sites called chiasmata.

Meiosis I

The first division of meiosis, termed the reductional division ($2n \rightarrow n$), in which homologous chromosome pairs separate into two haploid daughter cells.

Meiosis II

The second division of meiosis, termed the equational division ($n \rightarrow n$), in which sister chromatids separate without an intervening round of DNA replication, producing four haploid gametes.

Fertilization

The union of two haploid gametes ($n + n$) to produce a diploid single-celled zygote ($2n$).

Particulate Inheritance

The genetic model proposed by Gregor Mendel asserting that parents pass on discrete, heritable units (genes) that retain their identities in offspring without blending.

True-Breeding

Describing organisms that produce offspring of the same phenotype over many generations of self-pollination or self-fertilization.

Law of Segregation

Mendel's first law stating that the two alleles for a heritable character separate during gamete formation and end up in different gametes.

Law of Independent Assortment

Mendel's second law stating that each pair of alleles segregates independently of any other pair of alleles during gamete formation, applying to genes located on different chromosomes.

Monohybrid Cross

A breeding experiment tracking the inheritance of a single character, yielding an $F_2$ phenotypic ratio of $3:1$ and a genotypic ratio of $1:2:1$.

Dihybrid Cross

A breeding cross between organisms that are heterozygous for two distinct characters, producing an $F_2$ phenotypic ratio of $9:3:3:1$ when alleles assort independently.