BioE 206 Exam 1

Vocabulary flashcards covering key topics in cellular biology, molecular interactions, DNA replication and repair, PCR, transcription, translation, and protein modifications.

Gene

A DNA segment carrying information for a functional product.

Genome

The complete genetic material of an organism.

Prokaryote

A single-celled organism lacking a membrane-bound nucleus, encompassing the domains Bacteria and Achaea.

Eukaryotic cell

A cell containing a nucleus and membrane-bound organelles.

Independent variable

The factor deliberately changed in an experiment.

Dependent variable

The measured outcome of an experiment.

Null hypothesis

An experimental model stating no effect or no difference.

Biological replicate

An independently prepared sample used to assess variation and reproducibility.

Cation

An atom or molecule that has lost electrons and carries a positive charge (PAW-sitive).

Anion

An atom or molecule that has gained electrons and carries a negative charge.

Covalent bond

A chemical bond where atoms share electrons, forming strong molecular backbones such as phosphodiester bonds.

Polar covalent bond

A chemical bond where electrons are shared unequally, creating partial charges and supporting water interactions.

Hydrogen bond

An interaction where a partially positive H attracts an N, O, or F bonded to another H, supporting water behavior and complementary DNA base pairing.

van der Waals attraction

Weak attraction between close nonpolar surfaces where many contacts can stabilize molecular fit and base stacking.

pH

A measure of hydrogen ion concentration calculated as $\text{pH} = -\log_{10}([\text{H}^+])$, where concentration is in $\text{mol/L}$.

Buffer

A solution containing a weak acid and its conjugate base that minimizes changes in pH.

Griffith experiment

Demonstrated that material from one bacterial population caused a heritable transformation in another, showing a transferable factor carries heritable information.

Avery MacLeod McCarty experiment

Showed that destroying DNA eliminated transforming activity while targeting RNA or protein did not, proving DNA was the transforming material.

Hershey Chase experiment

Showed that phage DNA labeled with phosphorus-32 entered bacteria while protein labeled with sulfur-35 did not, proving DNA carries viral genetic information.

Purines

Two-ring nitrogenous bases consisting of adenine and guanine.

Pyrimidines

One-ring nitrogenous bases consisting of cytosine and thymine.

Chargaff's pattern

The base ratio pattern for double-stranded DNA where $A = T$ and $G = C$.

Phosphodiester bond

A covalent bond connecting nucleotides within a single sugar-phosphate backbone.

Semiconservative replication

A replication pattern producing DNA molecules that contain 1 daughter strand and 1 parent strand.

Helicase

An enzyme that uses energy to separate parental DNA strands during replication.

Single-strand binding proteins

Proteins that keep exposed template strands from pairing again during DNA replication.

Primase

An enzyme that synthesizes short RNA primers to provide a free $3'\text{ OH}$ for DNA polymerase.

DNA Polymerase III

The primary bacterial enzyme that extends new DNA in the $5'$ to $3'$ direction.

DNA Polymerase I

The bacterial enzyme that replaces RNA primers with DNA during replication.

Sliding clamp

A protein structure that keeps DNA polymerase attached to the template strand to increase processivity.

Telomeres

Repetitive DNA at chromosome ends that protects useful genetic sequence and is extended using an internal RNA template.

Proofreading

A repair mechanism that detects and corrects many mismatches during DNA synthesis.

Mismatch Repair

A mechanism that fixes pairing errors remaining in newly replicated DNA.

Excision Repair

A DNA repair pathway where damaged bases or segments are removed, replaced, and resealed.

Denaturation (PCR)

The high-temperature step in PCR that breaks base-pair interactions to separate double-stranded template DNA.

Annealing (PCR)

The cooling step in PCR that allows artificial DNA primers to hybridize and define target boundaries.

Extension (PCR)

The PCR step where polymerase extends from each primer $5'$ to $3'$ to build new target copies.

cDNA

Complementary DNA synthesized from RNA by reverse transcriptase.

Transcription

The process of using DNA to make RNA, occurring in the cytoplasm in prokaryotes and in the nucleus in eukaryotes.

Translation

The process of using mRNA to make polypeptides, occurring in the cytoplasm or at the rough ER in eukaryotes.

mRNA

Messenger RNA; carries the coding message used by ribosomes to assemble proteins.

rRNA

Ribosomal RNA; forms the ribosome structure and catalyzes peptide-bond formation.

tRNA

Transfer RNA; pairs an anticodon with an mRNA codon and carries the corresponding amino acid.

Spliceosome

A complex including snRNPs that recognizes splice signals to remove introns and join exons together.

Introns

Non-coding pre-mRNA sequences that are transcribed and then removed during splicing.

Exons

Coding RNA sequences that are joined together in mature mRNA during splicing.

Codon

A 3-nucleotide sequence in mRNA read $5'$ to $3'$ specifying an amino acid or stop signal.

A-site

The Arrival site of the ribosome that accepts incoming aminoacyl tRNA.

P-site

The Peptide site of the ribosome that holds the tRNA carrying the growing polypeptide chain.

E-site

The Exit site of the ribosome that holds an empty tRNA before its release.

Signal sequence

An amino-acid sequence within a protein that directs its cellular localization.

Signal-recognition particle (SRP)

A complex that binds the ER signal peptide, pauses translation, and targets the ribosome and growing protein chain to the ER receptor and translocon.

Proteolysis

A post-translational modification where a protease cuts a polypeptide for signal removal, degradation, or maturation.

Phosphorylation

A reversible protein modification where a kinase adds a phosphate group and a phosphatase removes it to alter activity, binding, shape, or localization.

Glycosylation

The attachment and processing of sugars on proteins in the ER or Golgi, categorized as N-linked (asparagine) or O-linked (serine or threonine).

GPI anchoring

A modification where a glycolipid tethers a protein to the membrane surface without the protein spanning the bilayer.