Molec Cell Exam One

DNA

2'-deoxy-ribonucleic acid, the genetic material of the cell, which is synthesized in the $5'$ to $3'$ direction.

mRNA

Messenger RNA, a single-stranded RNA molecule transcribed from DNA that serves as the template for protein translation.

Transcription

The enzymatic process of synthesizing an RNA molecule (such as mRNA) from a DNA template in the $5'$ to $3'$ direction.

Translation

The cellular process in which the genetic code in mRNA is read to synthesize a specific chain of amino acids into a protein.

Golgi complex

An organelle that modifies, sorts, and packages proteins and lipids received from the endoplasmic reticulum for secretion or delivery to other organelles.

Mitochondria

Double-membrane eukaryotic organelles responsible for cellular respiration and ATP energy production.

Peroxisome

A membrane-bound organelle containing enzymes involved in metabolic processes, including fatty acid breakdown and oxidation.

Cytoskeleton

A network of protein filaments within the cytosol that maintains cell shape, enables movement, and arranges organelles.

Reverse transcription (RT)

The enzymatic synthesis of complementary DNA (cDNA) using an RNA template.

Polymerase chain reaction (PCR)

A laboratory technique used to rapidly make millions of copies of a specific DNA sample.

RT-PCR

A method combining reverse transcription of RNA into cDNA followed by PCR amplification of the target cDNA.

Plasmid/cloning vector

A small, circular DNA molecule used as a vehicle to artificially carry foreign genetic material into a host cell for replication or cloning.

Expression vector

A plasmid designed specifically for gene expression in cells to produce the protein encoded by the inserted gene.

cDNA/cDNA library

Complementary DNA synthesized from mature mRNA templates representing expressed genes, or a collection of such cloned cDNA fragments.

Restriction enzyme

An enzyme that cuts double-stranded DNA at specific nucleotide recognition sequences.

Gel electrophoresis

A technique used to separate macromolecules such as DNA, RNA, or proteins based on their size and electrical charge.

Transformation/bacterial transformation

The process by which bacterial cells take up foreign DNA from their extracellular environment.

Transfection/tissue culture transfection

The process of deliberately introducing foreign nucleic acids into cultured eukaryotic cells.

Immunofluorescence/Fluorescence immunostaining

A technique where smaller fluorescent molecules are chemically conjugated to antibodies to visualize specific target proteins within cells.

GFP-fusion protein or RFP-fusion protein

A recombinant protein created by fusing GFP or RFP to a target protein; note that antibodies are not typically fused with GFP, but smaller fluorescent molecules can be conjugated to antibodies.

Centrifugation (rate-zonal & differential)

Techniques that utilize centrifugal force to separate cellular components based on their density, size, and shape.

SDS-PAGE gel electrophoresis

An analytical technique used to separate proteins according to their molecular weight using a denaturing polyacrylamide gel.

Western blot

A technique used to detect specific proteins in a sample following gel electrophoresis, using primary and secondary antibodies.

In situ hybridization

A molecular technique using labeled complementary nucleic acid probes to locate specific DNA or RNA sequences directly within tissue or cell samples.

DNA microarray

A collection of microscopic DNA spots attached to a solid surface used to measure expression levels of large numbers of genes simultaneously.

Proteomics

The large-scale, comprehensive study of proteomes, including protein expression, structure, and function within a cell type.

X-ray crystallography

An experimental technique used to determine the precise 3D arrangement of atoms within a crystallized protein or macromolecule.

Gene knock-out

A genetic engineering procedure in which a target gene is rendered completely inactive or deleted.

Gene knock-in

A genetic technique involving the targeted insertion of a specific gene or sequence into a defined locus in the host genome.

Transgene/transgenic animal

An animal whose genome has been stably modified by the deliberate introduction of foreign DNA (a transgene).

RNAi

RNA interference; a biological sequence-specific mechanism in which non-coding RNA molecules suppress gene expression by degrading target mRNA.

CRISPR

A targeted genome-editing tool used to precisely alter DNA sequences and modify gene expression.

Transmission electron microscopy (TEM)

A high-resolution imaging technique where a beam of electrons passes through an ultra-thin sample to view internal cellular structures.

Scanning electron microscopy (SEM)

An imaging technique that scans the surface of a sample with electrons to produce detailed 3D surface topography images.

Nucleotide

The structural monomer of nucleic acids, consisting of a nitrogenous base, a pentose sugar (ribose or 2'-deoxyribose), and one or more phosphate groups.

Purine

Adenine and Guanine found in DNA

Pyrimidine

Cytosine, thymine, and uracil, found in DNA and RNA.

Peptide bond

The covalent amide bond formed between the carboxyl group (C-terminus) of one amino acid and the amino group (N-terminus) of another.

Disulfide Bond

A covalent linkage formed between the thiol groups of cysteine residues that stabilizes higher-order protein structures.

Hydrophobic Effects

The physical interaction causing nonpolar molecules or side chains to aggregate together in aqueous solution, driving proper protein folding.

alpha-helix

A coiled secondary structure motif in proteins stabilized by hydrogen bonding along the polypeptide backbone.

beta-sheet

A protein secondary structure consisting of adjacent extended polypeptide strands linked laterally by hydrogen bonds.

beta-turn

A short protein secondary structure consisting of four amino acids that reverses the direction of the polypeptide chain.

Primary structure

The specific linear sequence of amino acids joined by peptide bonds in a polypeptide chain.

Secondary structure

Local backbone folding patterns within a polypeptide, primarily alpha-helices, beta-sheets, and beta-turns, stabilized by hydrogen bonds.

Tertiary structure

The full three-dimensional, folded spatial arrangement of a single polypeptide chain, mediated by side-chain ('R' group) interactions.

Quaternary structure

The structural organization and assembly formed by the association of multiple polypeptide subunits into a functional protein complex.

Structural motif

A specific, recurring combination of secondary structural elements (such as helix-turn-helix) found across different proteins.

Domain

A distinct, independently folding functional or structural unit within a protein's tertiary structure.

Conformation

The specific three-dimensional spatial arrangement of atoms in a folded macromolecule or protein.