CMB405 Final (Exam 4)

proteasome

degrades bad proteins (ER-associated degradation); located in cytosol

calnexin

membrane protein/chaperone protein of the endoplasmic reticulum that facilitates the folding of glycoproteins

cis face

receiving side of golgi apparatus; faces ER

trans face

the "shipping" side of the golgi apparatus; further away from the ER

mannosidase II

enzyme found specifically in the *medial* cisternae of the golgi

nucleoside diphosphatase

enzyme found specifically in the *trans* cisternae of the golgi

glycosylation

• addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination
• sorting signal → tells cell where the protein needs to go

glycosyltransferases

enzymes that transfer sugars onto the ends of proteins

vesicular transport model

• cargo is shuttled from the CGN toward the TGN in vesicles (anterograde direction only)
• carrying glycosyltransferases, proteins being modified

anterograde

direction of movement from cis golgi face (ER side) to trans golgi face

retrograde

direction of movement from trans golgi face towards cis golgi face/ER

cisternal maturation model

• each cistern "matures" as it progresses from the cis face to the trans face → new cis face added, pushes previous cis face towards trans face
• vesicles moving in retrograde direction only
• carrying sugars and enzymes needed for next (newest) stack

COPII-coated vesicles

move materials from the ER "forward" to the ERGIC and Golgi complex (anterograde)

COPI-coated vesicles

• move materials from ERGIC and Golgi "backward" to ER, or from the trans Golgi to the cis Golgi cisternae (retrograde)
• transports escaped proteins back to ER
• binds to KKXX motif

clathrin-coated vesicles

move materials from the TGN (trans golgi network) to endosomes, lysosomes, and plant vacuoles

vesicle protein coat functions

• causes membrane to curve and form a vesicle (force budding from membrane)
• select the components (cargo) to be carried by the vesicle

SAR 1-GTP

initial protein that binds to ER and inserts itself into the membrane
↳ starts to curve membrane

adaptor proteins

• recognize ER export signal on cargo receptors
• interact with cargo receptors

SAR 1-GDP

• triggers disassembly of vesicle upon arrival at golgi complex
• produced from the hydrolysis of GTP → GDP

retention

resident molecules are excluded from transport vesicles

retrieval

"escaped" molecules move back to the compartment where they reside

lumen proteins

contain retrieval signal KDEL on C terminal end

membrane proteins (golgi)

contain retrieval signal KKXX on C terminal end

KDEL receptors

specific type of receptor (membrane protein) that contains the KKXX motif

lysosomal enzymes

• tagged with phosphorylated mannose residues (mannose-6-phosphate)
• recognized and captured by mannose-6-phosphate receptors

mannose-6-phosphate

lysosomal targeting sequence attached to peptides in the Golgi

outer lattice

(of clathrin-coated vesicles) composed of clathrin

middle shell

(of clathrin-coated vesicles) composed of protein adaptors

inner shell

(of clathrin-coated vesicles) composed of receptors

ARF-1 GTP

• similar to SAR1 (clathrin-coated vesicles)
• binds to membrane and begins to deform it

secretory proteins

aggregate in dense granules that emerge from the TGN

rabs

proteins that provide much of target specificity

V SNAREs

SNAREs incorporate into vesicles

T SNAREs

SNAREs located in the target membrane

docking

• T and V SNAREs interact with each other by twisting around each other's alpha helices in the cytoplasm
• form 4-strand alpha helix

transition state

SNAREs wind tightly around each other, bringing membranes close together

botox

• comes from Clostridium botulinum
• paralyzes muscle cells around injection site
↳ destroys SNARE proteins → vesicles can't bind and release neurotransmitters → no signal to muscle cells

flavoproteins

polypeptides bound to either FAD or FMN

cytochromes

contain heme groups bearing Fe or Cu metal ions

ubiquinone (coenzyme Q)

lipid-soluble, electron carrier molecule made up of five carbon isoprenoid units

uncoupling proteins

protein that allow protons to pass through inner mitochondrial membrane without passing through ATP synthase

spongy mesophyll

space for gas exchange

palisade cells

closely packed photosynthetic cells within leaves; where most photosynthesis happens

stomata

small openings on a leaf through which oxygen and carbon dioxide can move

chloroplast

organelle performing photosynthesis

stroma

• fluid portion inside the chloroplast space; outside of the thylakoids
• where **light-independent\** reactions occur

thylakoid

• flattened membrane sac inside the chloroplast, used to convert light energy into chemical energy
• where **light-dependent\** reactions occur

granna

stacks of thylakoids

porphyrin ring

light-absorbing "head" of molecule in chlorophyll

phytotail

embeds itself into the thylakoid membrane

blues/reds

light frequencies best absorbed by chlorophyll a and b

reaction center chlorophyll

• transfers electrons to an electron acceptor in photosynthesis
• only chlorophyll that can put electron into chemical bond

photosystem II

• boosts electrons from below energy level of water to a midpoint
• electrons start here

photosystem I

boosts electrons to a level above NADP+

oxygen evolving complex

splits water to extract electrons and passes them to P680 chlorophyll

NADP+ reductase

enzyme that reduces NADP+ → NADH

rubisco

• most abundant protein on Earth
• fixes carbon (very slow)

photorespiration

• reaction in which rubisco binds to oxygen instead of carbon dioxide (when stomata are closed)
• plant releases carbon dioxide instead of fixing it
• oxygen builds up

PEPC (PEP carboxylase)

• has affinity for carbon dioxide, but not much for oxygen
• does not undergo photorespiration → separate carbon fixation from RUBISCO
• results in a 4 carbon product (oxaloacetate)

C4 plants

• physical separation between light and dark reactions
• light reactions occur in mesophyll cells
• separated from bundle-sheath cells
• ex. grasses, corn

bundle sheath cells

• in C4 plants, a type of photosynthetic cell arranged into tightly packed sheaths around the veins of a leaf
• release carbon dioxide used in Calvin cycle

light-dependent reactions

set of reactions in photosynthesis that use light energy to produce ATP and NADPH

light-independent reactions

• set of reactions in photosynthesis that do not require light
• energy from ATP and NADPH is used to build sugar
• aka Calvin cycle/C3 pathway

CAM plants

• temporal separation of carbon dioxide fixation

• take in carbon at night for fixation by PEPC → sends to calvin cycle during day

• ex. pineapple, cacti, orchids

autocrine

cell makes and responds to its own signal

paracrine

signals diffuse to nearby cells

endocrine

signal travels long distances (ex. through bloodstream) and can affect different tissues

receptor

recruits proteins to intracellular domain

effector

enzyme that releases second messenger

signaling pathway

transmission of signal to next protein

kinases

phosphorylate other proteins

phosphatases

take phosphates off other proteins

transcription factor

binds to DNA and activates transcription of genes

extracellular messengers

includes: small molecules such as amino acids & derivatives; gases; eicosanoids; various peptides & proteins; light

eicosanoids

lipids derived from fatty acids

G protein coupled receptors (GPCRs)

• large family of integral membrane proteins involved in signal transduction
• characterized by their 7 transmembrane domains
• utilize heterotrimeric G protein to transmit signals to effector cells

turn off signal

• alpha subunit hydrolyzes GTP → GPD; inactivating itself

• phosphorylate receptors → arrestins compete with G proteins to bind GPCRs

phospholipases

• release 2nd messenger from the membrane
• can convert some phospholipids of cell membrane into 2nd messengers

troponin

regulatory protein that binds to actin, tropomyosin, and calcium

tropomyosin

covers myosin binding sites on the actin molecules

insulin

• turns on glycogen synthase
• released when blood sugar is ↑

glycogen

storage molecule for glucose

glucagon/epinephrine

• turns on glycogen phosphorylase
• released when blood sugar is ↓

glycogen phosphorylase

converts glycogen to glucose

protein kinase A (PKA)

kinase that inactivates glycogen synthase and activates glycogen phosphorylase

cholera toxin

• binds to G protein and constitutively activates adenylyl cyclase
• ↑ cAMP binds and activates CFTR → pumps Cl⁻ out
• water follows by osmosis (causing diarrhea and potentially death)

receptor tyrosine kinases (RTKs)

dimerize after ligand binds and trans-autophosphorylate tyrosine residues on intracellular domain

SH2/PTB

protein domains that bind to phosphorylated tyrosines

insulin receptor substrate (IRS)

• contains a PTB domain
• interacts with insulin receptor
• amplifies signal
• provides more tyrosine residues that can be phosphorylated by RTKs
• helps activate GLUT4

GLUT4

• glucose transport protein found in vesicles near membrane
• vesicles respond to insulin by bringing glucose transporters to the membrane so cell can take in glucose

extracellular matrix (ECM)

• glue that holds cells together; sticky; allows cells to adhere to surfaces
• unique for different tissues
• fibrous proteins + carbohydrates ("macromolecules")
• important for cell/tissue organization

collagen

• glycoprotein with high tensile strength
• made up of alpha chain trimer (forms triple helix)

hydroxyproline

• allows hydrogen bonds to form between collagen alpha chains
• vitamin C important for production

fibronectin

• RGD loops
• binds to many different ECM proteins; short; connects things together
• aids in cell migration

RGD

• binds integrins

• found on fibronectin

laminin

• binds to collagen and integrins/glycoproteins on the cell membrane
• short, connect things together
• aid in cell migration

proteoglycan

• protein-polysaccharide complex consisting of a core protein attached to glycosaminoglycans (GAGs)
• repeating disaccharide structure

glycosaminoglycans (GAGs)

• negatively charged → attracts cations, which attract water
• forms porous, hydrated gel (reduces friction, shock absorption)

basement membranes

• mechanical support and cell migration
• barrier for macromolecules/separate tissues
• cell survival signals
• high density of collagen, fibronectin, laminins

cancer cells

produce substances that break down basement membranes, allowing them to migrate throughout the body