Biology Exam 3: Cell Signaling, DNA Replication, and Gene Expression

Vocabulary practice flashcards covering cell signaling pathways, historical DNA discovery experiments, DNA structure, replication enzymes, and transcriptional/translational gene expression based on lecture notes.

Direct Intercellular Signaling

A signaling mechanism where cell junctions allow signaling molecules to pass directly from one cell to another, such as gap junctions in cardiac muscle cells that propagate electrical signals.

Contact-Dependent Signaling

A signaling mechanism requiring direct contact between cells, where membrane-bound molecules on one cell surface act as signals to incoming cells, such as in immune cells.

Autocrine Signaling

A signaling mechanism where a cell secretes molecules that bind to receptors on its own surface or on nearby cells of the same type, such as insulin signaling on beta cells in the pancreas.

Paracrine Signaling

A signaling mechanism where secreted molecules do not affect the secreting cell itself, but influence neighboring target cells, such as in neuron signaling and blood clotting.

Endocrine Signaling

A long-distance, slower-acting, and longer-lasting signaling mechanism where hormones travel through the bloodstream to elicit a response in any cell with the corresponding receptor.

Second Messengers

Intracellular signaling molecules, such as cAMP, that relay and amplify signals inside the cell, speeding up cellular processes by activating downstream targets.

Reception

The first step of signal transduction in which an extracellular signaling molecule (ligand) binds to a specific receptor on the cell surface or inside the cell, triggering a conformational change.

Signal Transduction

The second stage of cell signaling where an activated receptor converts an extracellular signal into an intracellular molecular message via relay molecules, second messengers, and protein kinases.

Cellular Response

The final stage of signal transduction that triggers cellular activity, such as gene expression shifts, metabolic changes, cytoskeletal rearrangements, cell division, secretion, or apoptosis.

Ligand-Gated Ion Channels

Cell surface receptors that form closed channels until a ligand binds, opening the gate to allow ions such as calcium or sodium to cross the plasma membrane and alter the electrochemical gradient.

G Protein-Coupled Receptors (GPCRs)

Common eukaryotic cell surface receptors containing 7 transmembrane segments that, upon ligand binding, prompt an associated G protein to exchange GDP for GTP and dissociate.

Protein Kinase A (PKA)

An enzyme activated by cAMP that phosphorylates and activates several downstream proteins, leading to a specific cellular response.

Phosphorylation

The chemical process of covalently adding a phosphate group to a molecule or organic compound.

Apoptosis

Programmed cell death that can be initiated intrinsically or extrinsically to eliminate damaged cells, prevent the propagation of DNA damage, or stop infections.

Griffith's Bacterial Transformations (1920)

An experiment with Streptococcus pneumoniae showing that genetic material from heat-killed pathogenic type S bacteria was transferred to living harmless type R bacteria, transforming them into deadly bacteria.

Avery, MacLeod, and McCarty Experiment (1940s)

A study that separated and purified DNA, RNA, and protein from bacteria, concluding that only purified DNA stored and transferred the genetic information required for transformation.

Chargaff's Rule

The biochemical principle establishing that base amounts in DNA are not all equal, but the amount of adenine equals thymine ($A = T$) and guanine equals cytosine ($G = C$).

Double Helix

The antiparallel structure of DNA comprising two complementary nucleotide strands held together by hydrogen bonds, characterized by 10 base pairs per turn.

Phosphodiester Bond

The covalent bond that links the pentose sugar of one nucleotide to the phosphate group of another, forming the structural backbone of a single DNA strand.

Purines

Double-ringed nitrogenous bases comprising adenine and guanine.

Pyrimidines

Single-ringed nitrogenous bases comprising cytosine, thymine (in DNA), and uracil (in RNA).

Origin of Replication

The specific starting sequence where DNA replication initiates, opening into a replication bubble with two replication forks; bacteria possess a single origin, whereas eukaryotes have multiple origins.

DNA Helicase

An enzyme that binds to DNA and separates the two strands by breaking the hydrogen bonds between base pairs, unzipping the double helix.

DNA Topoisomerase

An enzyme that travels ahead of DNA helicase to relieve supercoiling, knots, and tension in the unwinding DNA strands.

Single-Stranded Binding Proteins

Proteins that coat the separated single strands of template DNA during replication to prevent them from reannealing or reforming hydrogen bonds.

DNA Primase

An enzyme that synthesizes a short RNA primer to provide a starting point for DNA polymerase during replication.

DNA Polymerase

An enzyme that synthesizes new DNA by joining dNTPs in the $5' \rightarrow 3'$ direction, requiring a preexisting RNA primer to extend.

DNA Ligase

An enzyme that covalently joins adjacent Okazaki fragments together on the lagging strand during DNA replication.

Leading Strand

The continuously synthesized DNA strand that elongates in the same direction as the moving replication fork.

Lagging Strand

The discontinuously synthesized DNA strand that is synthesized in the $5' \rightarrow 3'$ direction away from the replication fork as a series of Okazaki fragments.

Okazaki Fragments

Short stretches of DNA synthesized discontinuously on the lagging strand, each beginning with its own RNA primer.

Euchromatin

The loosely packed, accessible conformation of chromatin organized in radial loop domains present when a cell is not actively dividing.

Heterochromatin

The highly condensed, densely packed form of chromatin organized into visible chromosomes during cell division to ensure proper chromosome segregation.

Telomerase

An enzyme that attaches tandem DNA repeat sequences to chromosome ends (telomeres) to prevent them from progressively shortening with each replication cycle.

Transcription

The process occurring in the nucleus where the template strand of DNA is read by RNA polymerase to synthesize a complementary mRNA transcript.

Translation

The process taking place at the ribosome in the cytoplasm where an mRNA sequence is decoded into a polypeptide chain.

Central Dogma

The directional pathway of genetic expression: DNA is transcribed into RNA, RNA is translated into an amino acid chain, and the chain folds into a functional protein.

Introns

Non-coding intervening sequences within pre-mRNA that are excised and removed during RNA splicing.

Exons

The coding sequences of an RNA transcript that are spliced together and subsequently translated into protein.

Spliceosome

A large complex composed of small nuclear ribonucleoproteins (snRNPs) that recognizes splice sites and excises introns from eukaryotic pre-mRNA.

Alternative Splicing

A regulated process in higher eukaryotes where pre-mRNA exons are spliced in multiple combinations, enabling a single gene to encode multiple distinct polypeptides.

5' Cap

A modified guanosine cap added to the $5'$ end of eukaryotic pre-mRNA that facilitates export from the nucleus, assists ribosome binding, and prevents degradation.

Poly A Tail

A sequence of 100 to 200 adenine nucleotides added to the $3'$ end of eukaryotic pre-mRNA that enhances stability and increases longevity in the cytosol.

Aminoacyl-tRNA Synthetase

An enzyme that uses ATP to covalently attach the correct amino acid to its corresponding tRNA molecule.

Reverse Transcriptase

A specialized enzyme that uses an RNA template to synthesize a complementary DNA (cDNA) molecule.

Promoter

A regulatory DNA sequence where RNA polymerase binds to initiate transcription of a gene.

Terminator

A DNA sequence that signals RNA polymerase to cease transcription and detach from the DNA template.

Codon

A triplet sequence of nucleotides in mRNA that specifies a particular amino acid, start signal, or stop signal during protein synthesis.

Anticodon

A three-nucleotide sequence on a tRNA molecule that base-pairs complementarily with an mRNA codon.

A Site (Aminoacyl Site)

The ribosomal binding site that accepts an incoming charged aminoacyl-tRNA delivering the next amino acid for the growing polypeptide.

P Site (Peptidyl Site)

The ribosomal binding site that holds the initiator tRNA at initiation and subsequently holds the tRNA bearing the elongating polypeptide chain.

E Site (Exit Site)

The ribosomal site where an uncharged tRNA pauses before detaching and exiting the ribosome.

One Gene–One Polypeptide Hypothesis

The revised version of the 'one gene-one enzyme' hypothesis recognizing that not all proteins are enzymes, multi-subunit proteins comprise multiple polypeptides, and single genes can generate multiple polypeptides.

Origin of Replication

A specific genomic site where the DNA duplex unwinds to form an open replication bubble containing bidirectional replication forks. Bacteria contain a single origin, whereas eukaryotic chromosomes possess multiple origins.

Replication Fork

The Y-shaped active region within a replication bubble where the parental DNA duplex is unwound and new daughter strands are synthesized.

DNA Helicase

An enzyme that tracks along the parental duplex ahead of the replication fork, breaking hydrogen bonds between base pairs to separate the two strands.

DNA Topoisomerase

An enzyme that travels upstream of DNA helicase to relieve supercoiling and torsional strain generated during strand separation.

Single-Stranded Binding Proteins (SSBs)

Proteins that coat the exposed single-stranded template DNA to prevent the parental strands from prematurely reannealing.

DNA Primase

An RNA polymerase that synthesizes short, complementary RNA primers on single-stranded template DNA to establish a free $3'\text{-OH}$ starting end.

RNA Primer

A short stretch of RNA nucleotides laid down by DNA primase that provides the initial terminus necessary for DNA polymerase to begin elongation.

DNA Polymerase

An enzyme that synthesizes daughter DNA strands by adding complementary deoxynucleotide triphosphates (dNTPs) via phosphodiester bonds exclusively in the $5' \rightarrow 3'$ direction.

Leading Strand

The daughter DNA strand synthesized continuously toward the progressing replication fork in the $5' \rightarrow 3'$ direction.

Lagging Strand

The daughter DNA strand synthesized discontinuously away from the replication fork in the $5' \rightarrow 3'$ direction as a series of short segments.

Okazaki Fragments

Short, discontinuous segments of DNA synthesized on the lagging strand, each initiated by its own RNA primer.

DNA Ligase

An enzyme that catalyzes the formation of covalent phosphodiester bonds between adjacent Okazaki fragments, sealing gaps in the sugar-phosphate backbone.

Telomerase

A specialized enzyme that attaches repetitive non-coding DNA sequences to the ends of eukaryotic chromosomes (tel