MCB 104 Midterm

Vocabulary

Phospholipid bilayer (membrane)

Two layers of phospholipids (hydrophilic heads out, hydrophobic tails in) forming the basic structure of all cell membranes.

Chromosome

A single, long DNA molecule packaged with proteins, carrying genetic information.

Chromatid

One of two identical copies of a replicated chromosome, joined at the centromere.

Chromatin

DNA plus its associated packaging proteins (mainly histones).

Nucleosome

~147 bp of DNA wrapped around a histone octamer; the repeating unit of chromatin.

Histone

Small, positively charged proteins DNA wraps around to form nucleosomes.

Centromere

The chromosome region holding sister chromatids together; site of kinetochore assembly.

Telomere

Repetitive DNA capping the ends of linear chromosomes, protecting them from degradation.

Nucleolus

Non-membrane-bound region of the nucleus where rRNA is transcribed and ribosomal subunits assemble.

Nuclear envelope

The double membrane enclosing the nucleus, continuous with the ER, perforated by NPCs.

Enhancer

A DNA regulatory sequence bound by activator proteins to increase transcription of a target gene.

Activator protein

A transcription factor that binds an enhancer to increase gene expression.

Mediator

A protein complex bridging activators at enhancers to RNA Pol II at the promoter.

Chromatin remodeling complex

ATP-powered complex that slides, ejects, or restructures nucleosomes to change DNA accessibility.

TAD

A self-interacting chromatin loop within which enhancers/promoters contact each other frequently.

LAD

A chromatin region that physically docks onto the nuclear lamina at the periphery.

Lamin

Intermediate filament proteins forming the nuclear lamina.

Nuclear pore complex (NPC)

Large protein channel spanning the nuclear envelope that regulates nucleus-cytoplasm transport.

Histone tail

The unstructured region of a histone that protrudes from the nucleosome and is modified.

Post-translational modification (PTM)

Chemical modification of a protein after synthesis (e.g., acetylation, methylation, phosphorylation).

Nucleoporin

Individual protein subunits that build the NPC.

Nuclear localization sequence (NLS)

A short tag on a protein recognized by importins for nuclear import.

Importin (NIR)

Transport receptor that binds NLS-cargo and carries it into the nucleus.

Ran

A small GTPase whose GTP/GDP gradient drives directional nucleocytoplasmic transport.

GTPase

Enzyme that hydrolyzes GTP to GDP, acting as a molecular switch (active GTP-bound, inactive GDP-bound).

Ran-GAP

GTPase-activating protein for Ran; in the cytoplasm; triggers GTP hydrolysis, turning Ran off.

Ran-GEF (RCC1)

Guanine nucleotide exchange factor for Ran; in the nucleus; loads Ran with GTP, turning Ran on.

Molecular switch

A protein that toggles between active/inactive states (e.g., GTP vs. GDP bound) to control downstream events.

Exportin (NER)

Transport receptor that binds NES-cargo plus Ran-GTP in the nucleus and exports it to the cytoplasm.

RNA polymerase II

Enzyme that transcribes protein-coding genes into pre-mRNA.

5' cap

Modified guanine added to mRNA's 5' end; protects from degradation, needed for export/translation.

Poly-A tail

String of adenines added to mRNA's 3' end; protects from degradation, aids export/translation.

Intron

Non-coding sequence within a gene, removed during splicing.

Exon

Coding sequence retained in mature mRNA after splicing.

Cap binding protein (CBP)

Protein that binds the 5' cap; involved in mRNA export and translation initiation.

Endomembrane system

Interconnected network of ER, Golgi, lysosomes, endosomes, vesicles, and nuclear envelope.

Nascent chain

A polypeptide still being synthesized, not yet complete.

mRNA

Carries genetic information from DNA to the ribosome for translation.

Translocon

The protein channel (Sec61) in the ER membrane through which nascent chains pass.

Soluble (cytosolic)

Free-floating in the cytosol, not membrane-associated.

Chaperones

Proteins that assist proper protein folding and prevent aggregation.

Integral (membrane protein)

Permanently embedded in the lipid bilayer, usually via TM domains.

Peripheral (membrane protein)

Loosely associated with the membrane surface, not embedded in the bilayer.

N-terminus

The end of a polypeptide with a free amino group; made and exits the ribosome first.

C-terminus

The end of a polypeptide with a free carboxyl group; made and exits last.

ER signal sequence (START/STOP)

Hydrophobic amino acid stretch that initiates (START) or halts (STOP) translocation into the ER.

Signal peptidase

ER-lumenal enzyme that cleaves certain N-terminal cleavable signal sequences.

Transmembrane domain

A ~20-amino-acid hydrophobic stretch that spans the lipid bilayer.

Lumen

The interior space of a membrane-bound organelle (e.g., ER lumen).

Vesicle

Small membrane-bound sac that transports material between organelles/the plasma membrane.

Cytoskeleton

Network of protein filaments (microtubules, actin, intermediate filaments) providing structure and enabling movement.

Microtubules

Hollow polymers of tubulin involved in structure, transport, and the mitotic spindle.

Protofilament

A linear chain of tubulin dimers; ~13 form a microtubule.

Tubulin

The protein subunit of microtubules; exists as α/β heterodimers.

Tubulin subunit

An individual α- or β-tubulin monomer within the dimer.

MTOC

Microtubule-organizing center; nucleates microtubule growth, anchors the minus end.

MAPs

Microtubule-associated proteins that regulate microtubule stability/organization.

Dynamic instability

Microtubules stochastically switching between growth and rapid shrinkage.

Nucleation

Initial formation of a new polymer from free subunits.

Mitotic spindle apparatus

The microtubule machine built during mitosis to capture and segregate chromosomes.

G1 phase

Cell cycle gap phase after mitosis; cell grows, prepares for replication.

S phase

Cell cycle phase of DNA synthesis/replication.

G2 phase

Cell cycle gap phase after S; cell grows, checks replication is complete.

M phase

Mitosis and cytokinesis.

Prophase

Chromatin condenses, spindle begins forming; nuclear envelope still intact.

Prometaphase

Nuclear envelope breaks down; spindle attaches to kinetochores.

Metaphase

Chromosomes align at the spindle equator (metaphase plate).

Anaphase

Sister chromatids separate and move to opposite poles.

Telophase

Chromosomes decondense; nuclear envelope reforms.

Cytokinesis

Division of the cytoplasm into two daughter cells.

Kinase

Enzyme that adds phosphate groups to a substrate.

Phosphatase

Enzyme that removes phosphate groups.

Mitosis promoting factor (MPF)

The Cdk1–cyclin B complex; drives entry into mitosis.

Cyclin

Regulatory protein whose levels oscillate through the cell cycle, activating Cdks.

Cyclin B (M-cyclin)

The cyclin that peaks at M phase; partners with Cdk1 to form MPF.

Cyclin dependent kinase (Cdk)

A kinase only active when bound to its cyclin partner.

Cdk1

The Cdk that partners with cyclin B to drive mitosis.

Proteasome

Complex that degrades ubiquitin-tagged proteins.

Ubiquitin

Small protein tag marking targets for proteasomal degradation.

Ubiquitin ligase

Enzyme that attaches ubiquitin to target proteins (e.g., APC/C).

Kinetochore

Protein complex on the centromere that attaches the chromosome to spindle microtubules.

Sister chromatid

One of two identical copies of a replicated chromosome.

Sister chromatid cohesion (SCC)

The linkage (via cohesin) holding sister chromatids together from S phase to anaphase.

Cohesin

Ring-shaped complex holding sister chromatids together.

Condensin

Complex that compacts/condenses chromosomes for segregation.

Diploid (2n)

Having two complete sets of chromosomes.

Haploid (n)

Having one complete set of chromosomes.

n

Symbol for one full set of chromosomes.

Homologous chromosomes

A maternal/paternal chromosome pair with the same genes; pairs in meiosis I.

Chromosome axis

Proteinaceous core organizing meiotic chromatin into loops, forming the backbone for synapsis.

Meiotic bouquet

Stage where telomeres cluster at one region of the nuclear envelope, aiding pairing.

Synapsis

Intimate pairing of homologs along their length via the synaptonemal complex.

Synaptonemal complex (SC)

The protein structure that zips homologous chromosomes together.

Recombination

The process of exchanging genetic material between homologous chromosomes.

Crossover

The physical exchange event between non-sister chromatids of homologs.

Chiasmata

The visible structure marking where a crossover occurred.

Axis loop structure

Meiosis-specific loop-based chromatin organization along the chromosome axis.

Kleisin

Subunit that bridges/closes an SMC ring (cohesin/condensin); meiotic version is Rec8.

Separase

Protease that cleaves kleisin, releasing sister chromatid cohesion.

Aneuploidy

An abnormal chromosome number.