Cell Bio Exam 3

eIF4E

initiation factor that recognzies 5’ 7-methylguanosine cap during cap-dependent translation

P site (peptidyl)

site where tRNA is attached to elongated polypeptide during translation

A site (aminoacyl)

site where aminoacyl tRNAs enter the ribosomes during translation elogation

IRES

nucleotide sequence in 5’ UTR that enable translation initiation without 5’ cap

E site (exit)

site on large ribosomal subunit where tRNA exits after delivering amino acids to the ribosome

RNA interference (RNAi)

the degradation of mRNAs by short complementary double stranded RNA molecules

short interfering RNA (siRNA)

short non coding double strand RNA that acts in the RNA interference pathway

micro RNA (miRNA)

naturally occurring short non coding RNA that acts to regulate gene expression

chaperones

proteins that facilitate correct folding of other proteins

amyloid

aggregate of misfolded protein

prion

misfolded protein capable of self replication

proteolysis

degradation of polypeptide chains

glycoprotein

proteins linked to oligosaccharides

GPI anchor

glycolipid that anchors proteins to the external face of plasma membrane

G proteins

family of cell signaling proteins regulated by guanine nucleotide binding

GEF factors

protein that acts on small GTP binding proteins and stimulates the EXCHANGE of GDP for GTP

GAP proteins

a protein that stimulates GTP hydrolysis (GTPase) to go from GTP—> GDP

protein kinase

catalyzes the phosphate in ATP to serionine, threonine, or tyrosine

protein phosphatase

enzyme that reverses protein kinases by removing phosphate groups from phosphorylated amino acids

proteasome

large protease complex that degrades proteins tagged by ubiquitin

outer nuclear membrane

part of nuclear membrane/envelope, membrane continuous with the ER

inner nuclear membrane

part of nuclear membrane/ envelope, adjacent to nuclear lamina

perinuclear space

luminal space between inner and outer membranes of nuclear envelope

lamin

intermediate filament protein that forms the nuclear lamina

nuclear pore complex

large structure forming a transport channel through the nuclear envelope

nuclear localization signal (NLS)

amino acid sequence that targets proteins from transportation FROM the cytoplasm TO the nucleus

nuclear transport receptor

protein that recognizes NLS and mediates transportation across nuclear envelope

Ran

a nuclear transport receptor

topologically associated domain (TAD)

region of RNA within a chromosome that are maintained in association with itself

nucleolus associated domain (NAD)

region of heterochromatin associated with the nucleolus

exportin

a karyopherin that recognizes nuclear export signals and directs transport FROM the nucleus TO the cytosol

nucelolus

nuclear site of rRNA transcription, processing, and ribosome assembly

FISH

method for detection of RNA or DNA molecules within cells hybridization with fluorescent probes

cajal body

nuclear body involved in assembly of snRNPs and other RNA-protein complexes

lamina associated domain (LAD)

region of heterochromatin associated with the nuclear lamina

small nucleolar RNA (snRNA)

small RNA in nucleolus that functions in pre rRNA processing

nuclear speckle

nuclear bodies in which snRNPs and machinery that carry out splicing are stored

nucleoporin

group of ~30 proteins that assemble to form nuclear pore complex

chromosome conformation capture (3C)

method which adjacent regions of chromosomes are identified by cross linking

nuclear export signal

amino acid sequence that targets proteins for transport from the nucleus to the cytosol

karyopherin

nuclear transport receptor (importins and exportins)

ER

extensive network of membrane-enclosed tubules and sacs involved in protein sorting and processing as well as in lipid synthesis

rough ER

region of ER covered in ribosomes and involved in protein metabolism

smooth ER

region of ER that is a major site of lipid synthesis in eukaryotic clls

secretory pathway

movement of secreted proteins from the ER to the golgi then secretory vesicles to the cell surface

signal sequence

hydrophobic sequence at the amino terminus of a polypeptide chain

bacteria: targets for secretion

eukaryotes: incorporation into ER

SRP receptor

protein on the membrane of ER that binds to SRP (signal recognition particle)

translocon

membrane channel through which polypeptide chains are transported into the ER

signal peptidase

enzyme that removes the signal sequence of a polypeptide chain by proteolysis

ER associated degradation (ERAD)

process in which misfolded protein in the ER are identified and returned to the cytosol for degradation by the ubiquitin-proteasome system

unfolded protein responses

excess of unfolded protein in the ER leads to…

1. general inhibition of protein synthesis

2. increased expression of chaperones

3. increased proteasome activity

flippase

a protein that catalyzes the translocation of lipids across the membrane of the ER

Golgi apparatus

involved in processing and sorting of proteins and lipids

cis

golgi cisterna closest to nucleus which RECIEVES transport vesicles from the ER

trans

golgi cisterna furthest from the nuceus

network: sorted and packaged to EXIT golgi

mannose-6-phosphate

targets proteins to lysosomes

apical domain

exposed free surface of a polarized epithelial cell

basolateral domain

surface region of a polarized epithelial cell that is in contact with adjacent cells or extracellular matrix

vesicle coat protein

COPI, COPII, or clathrin that drive vesicle budding

clathrin

coast the cytoplasmic surface of cell membranes and assembles into lattices to drive vesicle budding

COPII

vesicle coated in COPII that mediates transport from the ER to golgi

COPI

vesicle coated in COPI that mediates retrieval from the golgi to the ER

tethering factor

protein that mediates the initial interactions between transport vesicles and their target membranes

Rab

family of small GTP binding proteins that play a key role in vesicular transport

SNARE

transmembrane protein that mediates fusion of vesicle and target membranes

lysosomes

cytoplasmic organelle containing enzymes that breaks down biological polymers

endocytosis

uptake of extracellular material in vesicles formed from the plasma membrane

endosome

vesicular compartment involved in the sorting and transport to lysosomes of material taken up by endocytosis

authophagy

the degradation of cytoplasmic proteins and organelles by their enclosure in the cytoplasmic vesicles that fuse with lysosome

autophagosome

a vesicle containing internal organelles enclosed by fragments of cytoplasmic membranes that fuses with lysosomes

autolysosome

structured formed by the fusion of a lysosome and an autophagosome containing damages and/or old intracellular substances during the process of autophagy

autophagy related protein (Arp)

family composed approximately 20 proteins that function together to carry out autophagy

phagophore

an expanding double membrane structure docked at the ER in the early stage of autophagy

eIF2

binds initiator, methionyl-tRNA

• recognizes start codon

eIF4E

recognizes 5’ methyl cap

binds to 5’ methyl cap

inspects mRNA for tail and cap

eIF4A

unwinds secondary structures in the 5’ UTR

eEF2

required for translocation

eEF1 alpha

GTP binding protein, helps connect tRNA onto ribosome

• delivers tRNA

eIF5B

promotes ribosomal subunit, large and small binding

eIF2B

exchanges GDP for GTP on eIF2