BIOB10

Fall 2022

Turnover Number

Turnover Number

maximum number of substrate molecules an enzyme molecule converts to product each second

Allosteric Enzyme

two or more binding sites

Positive Regulation

Binding of one ligand encourages binding of the second ligand

Negative Regulation

Binding of first ligand discourages binding of the second ligand

Signal Sequence

sequence on the N-terminus or in the middle of the chain specifying a location

Protein Targeting

using signal sequences to get proteins to their destinations

Co-Translational Translocation

import proteins to ER before completing protein synthesis

Post-Translational Translocation

cytosolic ribosomes complete protein synthesis before translocation

SRP

Signal Recognition Particle: protein that recognizes and binds to signal sequence, pauses translation

SRP Receptor

on ER membrane, binds to SRP

Translocator

channel on the membrane that allows proteins to pass through

BiP

Translocator accessory protein

Protein Glycosylation

adding oligosaccharide chains

Glucosyl Transferase

aka oligosaccharyl transferase, catalyzes protein glycosylation

Calnexin

membrane protein with affinity for the third glucose in oligosaccharide, pauses protein folding

Retrotranslocation

decomposition of an incorrectly folded protein

Mannosidase

removes mannose on core oligosaccharide tree

E3 ubiquitin ligase

attaches polyubiquitin tags to unfolded proteins

Proteasome

destroys proteins

N-glycanase

salvages oligosaccharide chain

Clathrin-coated

Golgi to plasma membrane and vice versa

COP1-coated

Golgi to ER

COPII-coated

ER to Golgi

Adaptor Protein

inner layer of clathrin

Uncoating

shedding clathrin coat

PIPs

binds to adaptor protein and changes conformation

BAR Domains

crescent-shaped domains that impose shape on vesicles

Dynamin

cytoplasmic protein that seals vesicles

GEFs

Guanine Nucleotide Exchange Factor: remove GDP and replace with GTP

GAPs

GTPase activating proteins

Rab Proteins

GTPases that help vesicles arrive at the correct target membrane

Rab-GDP Dissociation Inhibitor (GDI)

binds to Rab-GDP and keeps them soluble

trans-SNARE complex

1 v-SNARE and 3 t-SNARE

NSF protein

protein using ATP hydrolysis to dissociate trans-SNARE into v-SNAREs and t-SNAREs

Retrieval (Retrograde) Transport

escaped ER proteins returning to ER depending on ER retrieval signals (KDEL sequence)

cis Golgi Network

entry

trans Golgi Network

exit face

Mannose 6-phosphate

M6P groups, tags proteins that need to get to lysosomes

Endolysosome

Late endosome and lysosome

Constitutive Secretory Pathway

immediate and continuous delivery to cell surface

Regulated Secretory Pathway

secretory vesicles for later release

Regulated Secretory Vesicles

dense-core secretory granules (high cargo concentration)

Pinocytosis

material to be ingested is gradually enclosed by a small portion of the plasma membrane

ESCRT Complex

bringing ubiquitylated cargo to intralumenal vesicle

Transcytosis

recycling receptors to different plasma membrane domains

TOM Complex

transfer proteins to outer membrane

TIM Complex

transfer proteins to inner membrane

Micelle

hydrophobic clustering into a ball

Lipid bilayer

hydrophobic clustering into two layers

Transporters

Solute binding changes conformation to allow transfer

Channels

If open, continuous passive transfer

Passive Transport

movement of materials down the concentration gradient

Active Transport

movement against concentration gradient, requiring energy

Electrochemical Gradient

concentration and electrical gradient

Voltage-Gated Channel

gates open depending on charge gradient

Ligand-Gated Channel

binding of ligand changes conformation of channel to open/close gates

Mechanically Gated Channel

opens or closes from mechanical distortion

K+ leak channels

ion channels permeable mainly to K+ to maintain membrane potential

Uniporter

not coupled transporter

Coupled Transporter

Two molecules being transported, each going opposite directions of concentration gradient

Symport

both molecules move in the same direction of the bilayer

Antiport

molecules move in opposite directions of the bilayer

P-Type Pump

pumps ions

ABC Transporter

pumps small molecules

V-Type Proton Pump

pumps protons into organelles

F-Type ATP Synthase

uses proton gradient to drive ATP synthesis (opposite of V-Type Proton Pump)

Pyruvate

Derived from glucose and other sugars

Citric Acid Cycle

Produces Acetyl CoA, NADH and CO2

ETC

Electron Transport Chain, dependent on electrons from NADH

oxidative phosphorylation

Energy generated from electrons being transported through ETC are used to pump protons against their gradient, generating energy to synthesis ATP

Light Reactions

Photosynthetic electron transfer: generates ATP and NADPH

Dark Reactions

Carbon Fixation: uses ATP and NADPH to convert CO2 to sugar/amino acids/fatty acids

Protofilament

Putting tubulin subunits in a single file line

Microtubule

13 protofilaments

Tubulin GTP Hydrolysis

T form subunits binds to D form subunit and is hydrolyzed into D form subunit

Rescue

GTP cap grows faster than it shrinks

Catastrophe

GTP cap shrinks faster than it grows

γ-Tubulin Ring complex

nucleates microtubule

Centrosome

Microtubule-organizing center (MTOC) for animal cells

Kinesin

Microtubule motor protein, walks toward plus end

G-acting

globular actin

Treadmilling

Growth is faster on one end, hydrolysis is faster on the other end, maintaining actin length

Myosin Motor Proteins

Attaches and releases actin filament repeatedly through ATP hydrolysis to move down actin filament

Intermediate Filament

Made of 32 monomers = 8 tetramers

Adherens Junction

Adhesion Belts: connects actin to actin

Desmosomes

intermediate filament to intermediate filament

Actin-linked cell-matrix junction

actin filament to ECM

Hemidesmosome

intermediate filament to ECM

Junctional Complex

Adherens junction + desmosomes + tight junction

Tight junction

seals gap between epithelial centre

Cadherin

cell to cell

Integrin

cell to matrix

Collagen

major protein of the ECM, triple-stranded helix

Elastin

gives flexibility

Dynein

Microtubule motor protein, walks toward minus end