SC-ACE Program Laboratory Training Glossary

Comprehensive vocabulary flashcards covering molecular biology, biochemistry, chemistry, pharmacology, and laboratory techniques as presented in the SC-ACE Program Laboratory Training Glossary.

Central Dogma of Molecular Biology

The fundamental principle describing how genetic information flows within a biological system: DNA is transcribed into RNA, which is translated into protein (DNA $\rightarrow$ RNA $\rightarrow$ Protein).

DNA (Deoxyribonucleic Acid)

A double-stranded helix carrying genetic instructions, composed of nucleotides containing deoxyribose sugar, a phosphate group, and nitrogen bases: adenine ($A$), thymine ($T$), cytosine ($C$), and guanine ($G$).

mRNA (Messenger RNA)

A type of RNA transcribed from a DNA template that carries the coding sequence for a single protein to be translated by ribosomes.

Nucleotide

The basic building block of DNA and RNA consisting of a five-carbon sugar, a phosphate group, and a nitrogenous base ($A, T, C, G$ in DNA; $A, U, C, G$ in RNA).

Codon

A sequence of three consecutive nucleotides on an mRNA strand that encodes a specific amino acid or signals the start or stop of protein synthesis; there are $64$ possible codons.

Transcription

The first step of gene expression where the enzyme RNA polymerase reads a DNA template strand to synthesize a complementary mRNA strand in the nucleus.

Translation

The process occurring in the cytoplasm where ribosomes decode mRNA sequence codons to assemble a corresponding chain of amino acids into a polypeptide.

RNA Polymerase

The enzyme that unwinds the DNA double helix, reads the template strand $3'$ to $5'$, and assembles the mRNA strand $5'$ to $3'$.

Promoter

A specific DNA sequence found upstream of a gene that signals where RNA polymerase should bind and begin transcription.

Transcription Factor

A protein that binds specific DNA sequences near a promoter to activate or repress the transcription of a gene.

Double Helix

The three-dimensional shape of DNA consisting of two antiparallel strands held together by hydrogen bonds between complementary base pairs ($A$ with $T$, $C$ with $G$).

DNA Replication

The process by which DNA polymerase unwinds the double helix and uses each strand as a template to synthesize a new complementary strand before cell division.

Genome

The complete set of genetic material in an organism; the human genome contains about $3 \times 10^9$ base pairs of DNA encoding $\sim 20,000-25,000$ protein-coding genes.

SNP (Single Nucleotide Polymorphism)

A variation at a single position in the DNA sequence among individuals, commonly used in genome-wide association studies (GWAS).

Amino Acid

The $20$ standard building blocks of proteins, linked by peptide bonds to form polypeptide chains.

Protein Structure — Primary

The linear sequence of amino acids in a polypeptide chain.

Protein Structure — Secondary

Local folding patterns like alpha helices and beta sheets arising from hydrogen bonding in the polypeptide backbone.

Protein Structure — Tertiary

The overall three-dimensional shape of a single polypeptide chain formed by side chain ($R$ group) interactions.

Protein Structure — Quaternary

The arrangement of multiple polypeptide subunits into a multi-subunit protein complex, such as hemoglobin.

Enzyme

A biological catalyst that speeds up chemical reactions by lowering the activation energy without being consumed.

Active Site

The region of an enzyme with a specific three-dimensional shape where the substrate binds and the chemical reaction occurs.

Receptor

A protein that binds to a specific signal molecule (ligand) to trigger a cellular response.

Epigenetics

The study of heritable changes in gene expression, such as DNA methylation or histone modification, that do not involve changes in the underlying DNA sequence.

DNA Methylation

The addition of a methyl group ($CH_3$) to cytosine bases in DNA, typically silencing gene expression.

Chromatin

The complex of DNA and histone proteins found in the nucleus; its state (open euchromatin vs. closed heterochromatin) determines gene accessibility.

Metabolism

The complete set of chemical reactions in an organism, divided into catabolism (releasing energy) and anabolism (consuming energy).

ATP (Adenosine Triphosphate)

The primary energy currency of the cell that stores energy in high-energy phosphate bonds.

Glycolysis

A cytoplasmic metabolic pathway that breaks down one glucose molecule into two pyruvate molecules, producing ATP and NADH without requiring oxygen.

Oxidative Phosphorylation

The major source of ATP in aerobic organisms, occurring in the inner mitochondrial membrane via the electron transport chain and ATP synthase.

Reactive Oxygen Species (ROS)

Highly reactive oxygen-containing molecules like superoxide and hydrogen peroxide that can cause oxidative stress and damage DNA at high levels.

Phospholipid Bilayer

The structural component of cell membranes consisting of two layers of phospholipids with hydrophilic heads and hydrophobic tails.

pH

A measure of hydrogen ion concentration; values below $7$ are acidic, above $7$ are basic, and $7$ is neutral.

Molarity (M)

A unit of concentration equal to the number of moles of solute per liter of solution; one mole contains $6.022 \times 10^{23}$ molecules.

Serial Dilution

A stepwise dilution method where each step dilutes the original solution by a constant factor (e.g., $1:10$).

PBS (Phosphate-Buffered Saline)

An isotonic buffer solution with a pH of $\sim 7.4$ used for washing cells and diluting samples.

Osmosis

The passive movement of water across a semipermeable membrane from low solute concentration to high solute concentration.

Redox

Chemical reactions involving the loss of electrons (oxidation) and the gain of electrons (reduction).

Centrifugation

A technique using centrifugal force to separate particles in a mixture based on density; force is measured in $xg$ or RCF.

Spectrophotometry

A technique measuring how much light of a specific wavelength is absorbed by a solution to determine substance concentration based on the Beer-Lambert Law.

Sterile / Aseptic Technique

Practices aimed at preventing contamination, including working in a biosafety cabinet and using autoclaved equipment.

Pharmacokinetics (PK)

The study of what the body does to a drug, summarized by ADME (Absorption, Distribution, Metabolism, and Elimination).

Bioavailability

The fraction of an administered drug that reaches the systemic circulation in an unchanged, active form; IV administration is $100\%$.

First-Pass Effect

The reduction in concentration of an oral drug before reaching systemic circulation due to metabolism in the gut wall and liver.

Half-Life ($t_{1/2}$)

The time required for the drug concentration in the bloodstream to decrease by half.

Pharmacodynamics (PD)

The study of what a drug does to the body, including its biochemical effects and mechanism of action.

EC50 (Effective Concentration 50)

The concentration of drug required to produce $50\%$ of the maximum possible effect; used to measure potency.

IC50 (Inhibitory Concentration 50)

The concentration of a drug required to inhibit a specific biological activity by $50\%$.

Therapeutic Window

The range of drug concentrations that provides benefit without causing unacceptable toxicity.

High-Throughput Screening (HTS)

An automated process testing thousands to millions of compounds against a target to identify hits.

Clinical Trials Phase I

First-in-human stage involving $20-100$ participants focused on assessing safety and maximum tolerated dose.

Clinical Trials Phase III

Large-scale randomized and controlled trials involving hundreds to thousands of patients to compare a new drug to the standard of care.

Mitochondria

Membrane-bound organelles responsible for ATP production via oxidative phosphorylation; they contain their own DNA and regulate apoptosis.

Endoplasmic Reticulum (ER)

A network where the rough ER (with ribosomes) synthesizes proteins and the smooth ER synthesizes lipids and detoxifies drugs.

Lysosome

An organelle with a low pH ($\sim 5$) containing digestive enzymes to break down waste and cellular debris.

Cell Cycle

The ordered sequence of events for cell growth and division: $G_1$ (growth), $S$ (DNA replication), $G_2$ (preparation), and $M$ (mitosis).

Apoptosis

A genetically controlled process of programmed cell death characterized by cell shrinkage and DNA fragmentation.

Necrosis

Uncontrolled cell death resulting from acute injury that triggers an inflammatory response by releasing cellular contents.

Signal Transduction

The process by which a signal molecule binding to a receptor converts into a specific cellular response through a cascade of events.

Phosphorylation

The addition of a phosphate group ($PO_4$) to a protein by a kinase, changing its activity or shape.

G Protein-Coupled Receptor (GPCR)

The largest family of cell-surface receptors, consisting of seven-transmembrane proteins that activate intracellular G proteins.

Receptor Tyrosine Kinase (RTK)

Cell-surface receptors that phosphorylating tyrosine residues on themselves; examples include EGFR and HER2.

Metastasis

The spread of cancer cells from a primary tumor to distant sites via the bloodstream or lymphatic system to form secondary tumors.

Oncogene

A mutated proto-oncogene that is permanently 'on,' promoting uncontrolled cell growth and division.

Tumor Suppressor Gene

A gene that normally restrains cell growth or promoted DNA repair; loss-of-function mutations in both copies contribute to cancer (e.g., $TP53$).

p53 (TP53)

Known as the 'guardian of the genome,' this tumor suppressor protein detects DNA damage to initiate repair or apoptosis; it is mutated in over $50\%$ of human cancers.

PCR (Polymerase Chain Reaction)

A technique that exponentially amplifies DNA segments through cycles of denaturation ($\sim 95\,^\circ C$), annealing ($\sim 55-65\,^\circ C$), and extension ($\sim 72\,^\circ C$).

Gel Electrophoresis

A method separating molecules by size and charge using an electric field; smaller DNA fragments travel farther through the porous gel matrix.

Western Blot

A technique detecting specific proteins by separating them via SDS-PAGE, transferring to a membrane, and incubating with specific antibodies.

ELISA (Enzyme-Linked Immunosorbent Assay)

A plate-based assay using antibodies and enzyme-linked signals to quantify proteins (antigens) in liquid samples.

Monoclonal Antibody (mAb)

An antibody produced by a single clone of B cells, ensuring identical antigen specificity and sequence across all molecules.

Flow Cytometry

A technique measuring properties of individual cells (size, granularity, fluorescence) as they pass single-file through a laser beam.

MTT Assay

A colorimetric assay where yellow MTT reagent is reduced to purple formazan by mitochondrial enzymes to measure metabolic activity/cell viability.

siRNA (Small Interfering RNA)

Double-stranded RNA molecules ($21-23$ nucleotides) that trigger the degradation of specific mRNA to 'silence' or 'knock down' genes.

Micropipette

A precision instrument transferring small volumes of liquid; common variations include P20 ($0.5-20\,\mu L$), P200 ($20-200\,\mu L$), and P1000 ($100-1000\,\mu L$).

CO2 Incubator

A chamber maintaining conditions for mammalian cell growth: $37\,^\circ C$, $5\%$ $CO_2$, and high humidity.

Autoclave

Equipment that sterilizes items using pressurized steam at $121\,^\circ C$ for $15-20$ minutes.

Hemocytometer

A specialized microscope slide with a grid used to count cells and calculate cell density in a defined volume.

NanoDrop

A spectrophotometer measuring nucleic acid concentration and purity ($260\,nm$/$280\,nm$) using a $1-2\,\mu L$ sample volume.

Primary Cell Culture

Cells isolated directly from a living organism; they resemble in vivo behavior but have a limited lifespan and cannot be passaged indefinitely.

Confluency

The percentage of a culture vessel surface covered by adherent cells; cells are usually passaged at $70-90\%$ confluency.

Trypsin

A serine protease used to detach adherent cells from a surface by cleaving anchoring proteins.

DMSO (Dimethyl Sulfoxide)

A solvent for water-insoluble compounds and a cryoprotectant (typically used at $10\%$) for freezing cells to prevent membrane rupture.

In Vitro

Experiments performed outside a living organism, such as in a laboratory dish or tube.

Knockout (KO) Mouse

A mouse genetically engineered to have a specific gene inactivated to study its biological function.

3Rs Principle

Ethical framework for animal research: Replace (use alternatives), Reduce (use minimum number), and Refine (minimize suffering).

Statistical Significance

A measure of the likelihood a result occurred by chance; a $p-value < 0.05$ is typically the threshold.

GFP (Green Fluorescent Protein)

A protein from jellyfish that emits green light when excited by blue light, used to visualize protein localization in live cells.

Adaptive (Acquired) Immunity

A specific immune response involving B cells (producing antibodies) and T cells that develops memory of pathogens.

Epitope

The specific part of an antigen that an antibody or T cell receptor recognizes and binds.