BIOL 4004 Exam 2

TOM complex

This mitochondrial outer membrane translocator imports nearly all nucleus-encoded proteins from the cytosol into the mitochondrial intermembrane space

Nucleoporins

Have eight-fold rotational symmetry and enable bidirectional transport between nucleus and cytosol

Rough endoplasmic reticulum

Membranous tubules and sacs specialized for protein production and folding, have ribosomes attached

Peroxisomes

Organelles that contain oxidative enzymes

Sec61

SRP receptor passes ribosomes to this translocator that provides a channel for the emerging polypeptide to cross the membrane from the cytosol into the lumen of the ER

Topologically equivalent

Effectively continuous spaces; compartments through which material can transfer without crossing a membrane

Scramblase

Creates a hydrophilic path for phospholipids to passively and non-selectively transfer between ER monolayers

Biomolecular condensates

Membrane-less organelles in which a scaffold (protein or nucleic acid) binds to client molecules, concentrating specific factors that perform specialized cellular functions

Signal peptidase

Enzyme that removes a signal sequence after sorting

Lumen

The interior cavity of a tubular organelle or organ

Ran GTPase

Determines the directionality of nuclear transport by binding nuclear import or export receptors

Chaperones

Bind polypeptides to prevent aggregation of hydrophobic domains and promote protein folding

Signal sequence

A linear amino acid sequence "address" that directs a protein to a specific cellular compartment

Smooth endoplasmic reticulum

Membranous tubules and sacs specialized for lipid biosynthesis and Ca2+ storage, no ribosomes attached

TIM23 complex

The inner mitochondrial membrane translocator (from intermembrane space into the mitochondrial matrix)

GTPase activating proteins (GAP)

Regulatory proteins that bind to activated GTPases and stimulate their ability to hydrolyze GTP into GDP

Co-translational translocation

Transfer that occurs during translation with polypeptide elongation moving the protein across the ER membrane

Signal recognition particle (SRP)

Binds the ribosome to slow translation, and has a hydrophobic binding pocket that recognizes the signal sequence as it emerges from the ribosome

Oligosaccharyl transferase

Enzyme that transfers a precursor oligosaccharide to asparagine residues

Karyopherins

Nuclear transport receptors that bind proteins with nuclear export (NES) or localization signals (NLS)

Polyribosomes

A ribosome/mRNA structure that occurs free in the cytosol or attached to the ER membrane

Proteasomes

A cytosolic complex that degrades ubiquitylated proteins

Unfolded protein response

ER accumulation of misfolded proteins upregulates factors that promote protein folding and degradation

Flippase

Transporters that use ATP to unidirectionally transfer specific phospholipids between membrane bilayers

Peroxins

Translocate proteins from the cytosol into peroxisomes

Post-translational translocation

After translation, ATP is used to power movement of a completed polypeptide across the ER membrane

Endosymbionts

Organelles likely derived from bacteria trapped in cells

Glycosylphosphatidylinositol (GPI)

A membrane anchor added to proteins in the ER lumen

N-linked glycosylation

Attaching an oligosaccharide to an asparagine residue in a protein, its trimming is used as a protein folding timer

Guanine nucleotide exchange factor (GEF)

Regulatory proteins that stimulate an inactive GTPase to release GDP so that it binds GTP to become activate

Cristae

Folded structures of the mitochondrial inner membrane

Coat-recruitment GTPases

A family of proteins that inserts into the membrane and binds coat proteins and cargo during COPI-, COPII-, and retromer-coated vesicle formation; includes Sar1

COPI-coated vesicles

Coated vesicles that transport material from the Golgi back to the ER

Dynamin

Forms a spiral around the neck of a clathrin-coated bud, regulates membrane fusion, vesicle release

Autophagy

"Self eating", when a cell engulfs components of its own cytoplasm for degradation in lysosomes

ESCRTs

Protein complexes that regulate membrane budding including intralumenal vesicle formation and cytokinesis

Rab

A family of small GTPases; controls vesicular traffic by recruiting effector proteins that define membrane identity and function, mediate vesicular docking and fusion

Clathrin-coated vesicles

Coated vesicles that transport material endocytosed at the plasma membrane and within endosomal compartments

Cis face of the Golgi

Side of the Golgi stack at which material enters

Golgi reassembly and stacking proteins (GRASPs)

Structural proteins that create a scaffold between adjacent cisternae to form the Golgi stacks

SNAREs

Mediate vesicle docking and fusion to specific target membranes by winding into stable 4-helix complexes

Lysosomes

Membrane-bound organelle which contains digestive enzymes most active at low pH

Macropinocytosis

"Cell drinking", when a cell non-specifically traps extracellular fluid and material

Phosphoinositides (PIPs)

Variable phosphorylation of the 3', 4', and 5' position of this phosphilipid's sugar head group recruits different proteins to create functionally distinct membrane domains

ER exit sites

COPII-coated vesicles bud from this specialized region of the ER that is devoid of ribosomes

Mannose-6-phosphate (M6P)

This modification identifies acid (lysosome) hydrolases, formed by trimming GlcNAc from N-linked glycosylation

Complexin

Binds to SNAREs to prevent them from fully assembling, holds the complex in a frozen, "primed" metastable state

Receptor-mediated endocytosis

Clathrin complexes with a transmembrane receptor at the plasma membrane during this process

Cis Golgi Network (CGN)

This part of the Golgi includes fused vesicular clusters that arrive from the ER containing proteins and lipids that need sorting and processing

Endocytosis

General term for taking material into the cell through invagination and internalization of the plasma membrane

KDEL

The sequence that recruits soluble ER resident proteins into COPI retrieval vesicles for recycling back to the ER

Trans face of the Golgi

Side of the Golgi stack at which material exits

NSF

Uses ATP to separate a stable SNARE complex; this use of energy to put SNAREs in an unwound, less stable conformation creates force when SNAREs fuse

Golgins

Coiled-coil domain proteins that form long tethers with Rab binding sites, distinct at each Golgi stack level

Cisternae

Flattened, membrane-enclosed Golgi compartments

Caveolae

Deeply invaginated plasma membrane structures that organize lipid rafts, they are clathrin independent

Exocytosis

General term for the release material out of the cell by fusion of vesicles with the plasma membrane

ER retrieval

This process recovers ER resident proteins with KKXX or KDEL signals from the Golgi using COPI coated vesicles

COPII-coated vesicles

Coated vesicles that transport material from the ER to the Golgi apparatus

Trans Golgi Network (TGN)

Name for the Golgi stacks where proteins complete sorting and are released

GlcNAc phosphotransferase

Recognizes a signal patch on acid (lysosome) hydrolases and adds the sugar GlcNAc-phosphate to N-linked glycosylation, the first step in creating the M6P signal

Phagocytosis

Cargo-triggered ingestion of large extracellular particles such as dead cells or microorganisms

Rab cascade

Ordered recruitment of sequentially acting GTPases, typically through recruitment of effector proteins that are GEFs or GAPs, reprograms the compartment as in endosome maturation

Vesicular tubular clusters

Form after ER-derived vesicles shed their COPII coats and fuse. They bud COPI-coated vesicles back to the ER and are delivered to the cis face of the Golgi

Synaptotagmin

A Ca2+ sensor that binds to primed SNAREs and allows complex formation to complete upon Ca2+ influx at the presynaptic terminal; triggers neurotransmitter release

Hedgehog pathway

Components of this signaling pathway are held in close proximity due to their localization in the primary cilium.

Receptor tyrosine kinase (RTK)

Transmembrane proteins with encoded or associated kinase activity; ligand binding induces dimerization that brings the kinase domains together to activate them.

Src homology 2 (SH2) domains

Sequence in an intracellular signaling protein that binds to phosphotyrosines on the cytosolic tail of a receptor.

PI 3-kinase

The enzyme that phosphorylates inositol phospholipids at the 3 carbon position in the inositol ring head group.

Autocrine signaling

When a cell responds to a signal it produces because it expresses the receptor

Paracrine signaling

Short-range, limited diffusion of a signal molecule affects nearby cells that express the receptor.

SMADs

Latent transcriptional regulatory proteins activated by transforming growth factor-β (TGFβ) signaling.

Pleckstrin homology (PH) domains

Protein domain used by intracellular signaling proteins to dock at PIP3 in the membrane.

Protein Kinase C

A kinase that is activated by increased Ca2+

Phospholipase C- (PLC-)

Acts on the phosphoinositide PI(4,5,)2 to produce IP3 (inositol 1,3,5-trisphosphate) and diacylglycerol.

Wnt pathway

This signaling pathway triggers dissociation of the "destruction complex", stabilizing -catenin which transfers to the nucleus where it regulates transcription.

Calmodulin

A Ca2+ binding protein without enzymatic activity that activates target proteins (including kinases) to produce a cellular response to increased cytosolic Ca2+

Ras

A small, plasma membrane-anchored GTPase that uses the adaptor protein Grb2 to respond to receptor tyrosine kinase activation.

JAK-STAT

Cytokine receptors are associated with this kinase and transcription factor that transmit their intracellular signal

Heterotrimeric G protein

Has ⍺, β, and γ subunits, ⍺ and γ are membrane anchored. Binding of a receptor (GEF) triggers activation and dissociation of G⍺ (GTPase) from Gβγ.

Ca2+-Calmodulin Kinase II (CaMKII)

Has twelve individual kinase domains with inactive and "popped" active conformations that allow this complex to serve as a ratcheting frequency detector.

Guanalyl cyclase

Converts GTP to cGMP in response to photoactivation of the GPCR rhodopsin.

Mitogen activated protein (MAP) Kinase cascade

A series of kinases that relay and amplify the signal from Ras, ending by phosphorylating effector proteins

Ɣ-secretase

Performs the third, intracellular cleavage of the Notch receptor, releasing the cytoplasmic tail to act as a transcription factor.

G protein coupled receptor (GPCR)

Seven pass transmembrane receptor proteins that bind and regulate membrane anchored heterotrimeric G proteins that transmit the signal.

CREB

A protein phosphorylated by Protein Kinase A (PKA) that binds to DNA elements and activates transcription in response to cAMP.

Src homology 3 (SH3) domains

Proline-rich motifs that allow intracellular proteins to interact, typically found in adaptor proteins

Endocrine signaling

Signals secreted into the bloodstream are circulated throughout the body, any cell with a receptor responds

Phosphatase

The type of enzyme that removes phosphate groups.

Diacylglycerol

A simple lipid produced by Phospholipase C that remains in the membrane; activates Protein Kinase C when it binds along with Ca2+

TGF signaling

Local mediators including activin that bind single-pass transmembrane receptors with serine/threonine kinase activity, phosphorylate Smads.

Scaffold

A protein that binds other proteins that work together in series, like kinases, facilitating their sequential use and reducing cross-talk between pathways.

Adenylyl cyclase

A membrane associated enzyme that converts ATP to the second messenger cAMP.

Protein Kinase A (PKA)

Most of the effects of cAMP are mediated by activating this kinase that phosphorylates target proteins like CREB.

Kinase

The type of enzyme that adds phosphate groups.

Notch pathway

Contact-dependent signaling. The ligand and receptor are transmembrane proteins; upon activation, the receptor is processed to produce a transcription factor.

Effector proteins

The targets at the end of signaling pathways that implement an appropriate cellular change.

Phosphatidylinositol phosphates (PIPs)

Phophoinositides that are variably phosphorylated on carbons 3, 4, and 5 of the inositol head group.

Gq

Activates PLC-β

Gs

Activates adenylyl cyclase