BME 203 Exam 1 Study Guide

Microtubules diameter

~25 nm (thickest)

Microtubules subunit

Tubulin

Microtubules main job

Organelle/vesicle transport tracks, mitotic spindle, cilia/flagella

Intermediate filaments diameter

~10 nm

Intermediate filaments subunit

Varies (e.g., keratin, lamin)

Intermediate filaments main job

Mechanical strength, structural support

Actin filaments diameter

~7 nm (thinnest)

Actin filaments subunit

Actin

Actin filaments main job

Motility, cell shape, contraction

Plasma membrane

The outer boundary line of the whole cell.

Nuclear envelope

Double membrane surrounding the nucleus, often drawn with pores.

Cytosol

Fluid background filling space between organelles.

Golgi apparatus

Stack of curved, flattened membranes near the nucleus.

Endoplasmic reticulum

Extensive, winding membrane network continuous with nuclear envelope.

Mitochondrion

Oval/bean-shaped organelle with folded internal membranes (cristae).

Transport vesicles

Small round circles budding off the ER/Golgi.

Phase-contrast microscopy key clue

Uses differences in refractive index; good for live, unstained cells.

Bright-field microscopy key clue

Standard light microscope; thick tissue must be fixed and stained.

Fluorescence microscopy key clue

Two filter sets for excitation and emission wavelength filtering.

Confocal microscopy key clue

Scanning laser + pinhole → optical sections → 3D reconstruction.

Transmission electron microscopy (TEM) key clue

Highest resolution option (down to ~2 nm).

Scanning electron microscopy (SEM) key clue

Sample coated with heavy metal → 3D surface image.

TEM vs. SEM functional difference

TEM sees internal ultrastructure; SEM creates 3D image of metal-coated surface.

Phospholipid polar head group components

Phosphate + attached group + glycerol backbone (hydrophilic).

Phospholipid fatty acid tails property

Hydrophobic; can be saturated (straight) or unsaturated (kinked).

Nucleotide structure

Five-carbon sugar + phosphate group + nitrogenous base.

RNA vs. DNA sugar difference

RNA uses ribose (C₅H₁₀O₅), which has one more oxygen than DNA's deoxyribose (C₅H₁₀O₄).

Base pairing hydrogen bonds count

A-T/A-U has 2 H-bonds; G-C has 3 H-bonds.

DNA double helix orientation

Antiparallel strands (5′→3′ and 3′→5′) with sugar-phosphate backbone outside, bases inside.

Primary protein structure

The linear amino acid sequence.

Secondary protein structure

Local folding patterns (alpha helices, beta sheets) stabilized by backbone H-bonds.

Tertiary protein structure

Overall 3D folding of a single polypeptide driven by side-chain interactions.

Quaternary protein structure

Arrangement of multiple polypeptide subunits into one functional complex.

Protein denaturation

Loss of folded 3D shape, destroying protein function.

Loss of function (LOF) mutation

Gene product stops working, is made less of, or is not made.

Gain of function (GOF) mutation

Gene product becomes more active, active at wrong time, or locked on.

Mutation changing an enzyme off-switch

Disrupting self-deactivation locks the protein in the active 'on' state.

Enzyme kinetics Vmax definition

Maximum reaction rate reached when enzyme is fully saturated with substrate.

Enzyme kinetics Km definition

Substrate concentration at which reaction rate reaches half of Vmax.

Effect of increasing enzyme concentration on Vmax and Km

Vmax increases; Km stays unchanged.

Effect of competitive inhibitor on Vmax and Km

Km increases (lower affinity); Vmax remains unchanged.

Effect of non-competitive inhibitor on Vmax and Km

Vmax decreases; Km remains unchanged.

Ligand

Any substance that binds to a specific protein.

Substrate

The specific molecule an enzyme acts on and converts into product.

Active site

Region of an enzyme where substrate binds and reaction is catalyzed.

Transition state

High-energy intermediate at the peak of reaction pathway before product formation.

Antibody structure

Two identical heavy chains and two light chains joined by disulfide bonds.

Phosphatase function

Removes a phosphate group.

Kinase function

Adds phosphate groups.

Protease function

Hydrolyzes peptide bonds.

Ligase function

Joins two ends of DNA using ATP.

Polymerase function

Synthesizes polymers (RNA/DNA).

Isomerase function

Rearranges bonds within one molecule.

DNA helicase function

Opens the double helix ahead of the replication fork.

Primase function

RNA polymerase that lays down RNA primers.

DNA polymerase function

Adds nucleotides to the 3′ end of a growing DNA strand.

Single-strand binding protein function

Coats ssDNA to prevent reannealing before copying.

Meselson & Stahl experiment conclusion

DNA replication is semiconservative (each new double helix has one old and one new strand).

Nonhomologous end joining (NHEJ)

Directly joins double-strand DNA breaks without template; error-prone.

Homologous recombination

Double-strand break repair pathway using homologous template (sister chromatid) for accurate repair.

rRNA role

Forms core of ribosome and catalyzes protein synthesis.

tRNA role

Adaptor between mRNA codons and amino acids.

snRNA role

Used in RNA splicing as part of spliceosome.

miRNA role

Regulates gene expression by repressing translation or mRNA stability.

Polyribosome (polysome)

Cluster of multiple ribosomes simultaneously translating a single mRNA molecule.

Cas9 gene knockout mechanism

Cas9 makes double-strand break, repaired by error-prone NHEJ causing indels and frame shifts.

Cas9 Accuracy vs Precision

Accuracy is cutting at correct genomic location; precision is creating desired edit.

PCR Step 1: Denaturation

Heating DNA to relax H-bonds and separate double strands.

PCR Step 2: Annealing

Cooling reaction so short primers form H-bonds with ssDNA template.

PCR Step 3: Elongation

Heating to optimal temp for Taq Polymerase to add nucleotides onto primers.

Gel Electrophoresis migration direction

Negatively charged DNA fragments migrate toward the positive electrode.

Gel Electrophoresis size separation

Smaller DNA fragments move faster and farther through the gel matrix.