BME 203 Cell Biology Exam 1 Vocabulary Flashcards

Vocabulary flashcards covering cytoskeletal elements, microscopy, macromolecules, enzyme kinetics, replication, repair, translation, CRISPR-Cas9, and PCR from the BME 203 study guide.

Microtubules

Cytoskeletal filaments with a diameter of $\sim 25\,\text{nm}$ (thickest) made of tubulin subunits that function as transport tracks for organelles and vesicles, form the mitotic spindle, and structure cilia/flagella.

Intermediate filaments

Cytoskeletal filaments with a diameter of $\sim 10\,\text{nm}$ composed of variable protein subunits (e.g., keratin, lamin) that provide mechanical strength and structural support to cells.

Actin filaments

Cytoskeletal filaments with a diameter of $\sim 7\,\text{nm}$ (thinnest) composed of actin subunits that drive cell motility, cell shape, and contraction.

Phase-contrast microscopy

A microscopy technique that uses differences in refractive index to visualize live, unstained cells.

Transmission electron microscopy (TEM)

An electron microscopy method providing high resolution (down to $\sim 2\,\text{nm}$) to view the internal ultrastructure of thin tissue sections.

Scanning electron microscopy (SEM)

An electron microscopy technique in which a sample is coated with heavy metal to collect reflected electrons, producing a 3D image of surface topography.

Phospholipid

An amphipathic molecule composed of a hydrophilic polar head group (phosphate attached to glycerol) and two hydrophobic fatty acid tails.

Adenosine triphosphate (ATP)

A high-energy nucleotide consisting of an adenine base, a ribose sugar, and three phosphate groups linked by phosphoanhydride bonds.

Saturated fatty acid

A fatty acid chain containing no carbon-carbon double bonds, producing a straight tail structure.

Unsaturated fatty acid

A fatty acid chain containing one or more carbon-carbon double bonds, creating a kinked tail structure.

Deoxyribose

The five-carbon sugar with the molecular formula $\text{C}_5\text{H}_{10}\text{O}_4$ present in DNA nucleotides.

Ribose

The five-carbon sugar with the molecular formula $\text{C}_5\text{H}_{10}\text{O}_5$ present in RNA nucleotides.

Primary protein structure

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

Secondary protein structure

Local backbone folding patterns, such as alpha helices and beta sheets, stabilized by hydrogen bonds.

Tertiary protein structure

The overall 3D folding pattern of a single polypeptide chain driven by side-chain interactions.

Quaternary protein structure

The structural arrangement formed by the assembly of multiple polypeptide subunits into a functional complex.

Loss of function (LOF) mutation

A mutation that causes a gene product to lose activity, be produced in reduced amounts, or fail to be synthesized.

Gain of function (GOF) mutation

A mutation that causes a gene product to become hyperactive, active at inappropriate times, or incapable of being inactivated.

Vmax

The maximum velocity of an enzymatic reaction achieved when all enzyme active sites are fully saturated with substrate.

Km

The substrate concentration at which the reaction rate reaches half of $V_{\max}$, representing a measure of the enzyme's apparent affinity for its substrate.

Competitive inhibitor

An inhibitor that competes with the substrate for binding to the active site, increasing $K_M$ without changing $V_{\max}$.

Non-competitive inhibitor

An inhibitor that binds to an allosteric site rather than the active site, decreasing $V_{\max}$ without significantly altering $K_M$.

Transition state

The high-energy, unstable intermediate configuration at the peak of a reaction's energy barrier.

Antibody

A protein made of two identical heavy chains and two identical light chains connected by disulfide bonds, featuring variable domains for antigen recognition and constant domains.

Phosphatase

An enzyme class responsible for removing phosphate groups from substrates.

Kinase

An enzyme class responsible for adding phosphate groups to substrates.

DNA helicase

An enzyme that unwinds and opens the double-stranded DNA helix ahead of the replication fork.

Primase

An RNA polymerase enzyme that synthesizes short RNA primers required for DNA synthesis.

Single-strand binding protein

A protein that binds to exposed single-stranded DNA (ssDNA) to prevent premature reannealing during replication.

Nonhomologous end joining (NHEJ)

An error-prone DNA repair mechanism that directly ligates broken ends of double-strand DNA breaks without using a homologous template.

Homologous recombination

An accurate double-strand break repair pathway that uses a homologous DNA template (such as a sister chromatid) to restore sequence integrity.

rRNA

Ribosomal RNA molecules that form the core structure of ribosomes and catalyze peptide bond formation during protein synthesis.

tRNA

Transfer RNA molecules that serve as adaptors matching mRNA codons with specific amino acids.

miRNA

MicroRNA molecules that regulate gene expression post-transcriptionally by degrading target mRNA or repressing translation.

snRNA

Small nuclear RNA molecules involved in RNA splicing as integral components of the spliceosome.

siRNA

Small interfering RNA molecules that mediate RNA interference to protect cells against viral nucleic acids.

Ribosomal binding sites (E, P, A sites)

The three functional tRNA binding sites on the ribosome: A site (aminoacyl), P site (peptidyl), and E site (exit).

Polyribosome

A complex formed when multiple ribosomes simultaneously translate a single mRNA molecule.

Cas9

An RNA-guided endonuclease used in Type II CRISPR systems to create targeted double-strand breaks in DNA.

tracrRNA and crRNA processing

In Type II CRISPR systems, tracrRNA pairs with pre-crRNA to recruit RNase III for maturation into functional crRNA-tracrRNA guides.

PCR Denaturation

The first step of PCR where double-stranded DNA is heated to break hydrogen bonds and yield single-stranded templates.

PCR Annealing

The second step of PCR where the mixture is cooled to allow short DNA primers to hydrogen-bond with complementary template regions.

PCR Elongation

The third step of PCR where the temperature is adjusted to the optimal level for Taq Polymerase to synthesize new complementary DNA strands.

CRISPR accuracy vs precision

Accuracy: does the Cas9 complex cut DNA at the correct location in the genome?
Precision: Does the process create the desired edit?

Gel electrophoresis

• DNA fragments move through a matrix with a microscopic network of pores (the gel).
• DNA is negatively charged (phosphate backbone), so fragments migrate toward the positive
electrode — not the negative one.
• Fragments are separated by size (smaller fragments move farther).
• Visualization requires a stain or label (e.g., ethidium bromide, SYBR dyes) DNA isn't visible
unaided.