exam 4 bio 302

cytosol

jellylike fluid in the cell

cytoplasm

aqueous compartment of the cell that consists of a jellylike fluid called the cytosol

nucleus

organelle of a eukaryotic cell that contains genetic information

nuclear envelope

double membrane of phospholipids that surrounds the nucleus

nuclear lamina

netlike array of protein filaments that lines the inner surface of the nuclear envelope and helps maintain shape

rough ER (RER)

ribosomes on the cytosolic surface that make secretory proteins which get feb into the ER

smooth ER (SER)

lack ribosomes and is the site of hormone and lipid synthesis, sequesters Ca2+ from cytosol

cisternae

flattened, membranous sacs

Golgi apparatus

an organelle in eukaryotic cells that modifies, stores, and routes products of the ER

cis face

receiving departments, near the ER

Trans face

shipping department

lysosomes

“garbage disposal” of animal sales

endosomes

compartments within the cell that contain endocoytosed materials

peroxisomes

small, round single-membrane organelles

endomembrane system

interconnected network of membranes made up of the nuclear envelope, ER, Golgi, Lysosomes, peroxisomes, and endosomes

mitochondria

organelles in eukaryotic cells responsible for making ATP through cellular respiration

chloroplasts

plant organelles that carry out photosynthesis

thylakoids

flattened, membranous sacs that contain machinery to convert light energy, a stack is called granum

stroma

dense fluid around thylakoids where DNA and enzymes are kept

signal recognition (SRP)

present in the cytosol and binds to ribosome and ER signal sequence as it emerges from the ribosome

SRP receptor

embedded in the ER membrane and recognizes the SRP

exocytosis

push molecules out of the cell

endocytosis

brings molecules into the cell

coated vesicles

distinctive protein coat on their cytosolic surface

coat protein or COP-coated vesicles

transfer molecules between the ER and Golgi and from one part of the Golgi to another

Rab proteins

the identification process depends upon a family of monomeric GTPases, on the vesicle surface are recognized by tethering proteins

SNAREs

transmembrane proteins firmly dock the vesicles in place

disulfide bonds

help to stabilize proteins formed by the oxidation of cysteine side chains are catalyzed by an enzyme in the ER lumen, they help stabilize proteins that may encounter degradative enzymes or pH changes

oligosaccharides

can protect a protein from degradation, hold tin the ER until it is folded, or serve as a transport signal for packing the protein into a vesicle

unfolded protein response (UPR)

triggered if the buildup is large enough

phagocytosis 

an endocytic process by which cells take up large particles, also known as cellular eating 

pinocytosis

form of endocytosis in which cells take up extracellular fluid and soluble molecules, known as cell drinking

receptor-mediated endocytosis

selective process by which molecules are taken up into the cell after binding to specific cell-surface receptors

endosomes

membrane-bound compartments that result from endocytosis mechanisms

endocrine signaling 

involves hormones traveling throughout the bloodstream, long distance signaling

paracrine signaling

involves local diffusion of signal molecules

autocrine signaling

involves a cell responding to its own signals

neuronal signaling

involves specific signaling between nerve cells through the release of neurotransmitters

contact-dependent signaling

involves physical interaction of cells 

transmembrane proteins

detect extracellular signals and relay the message across the membrane to the interior of the target cell

signal reception

first step in signal transduction

feedback regulation

can boost or weaken the response to a signal

positive feedback 

has a molecule in the pathway that enhances an earlier component continuing the signal

negative feedback

a molecule in the pathway that inhibits an earlier component stopping the signal

molecular switches

intracellular signaling proteins that toggle between active and inactive response to a signal

protein kinase

covalently adds a phosphatase

protein phosphatase

removes the phosphatase

trimeric GTP-binding protein

relays messages from GTP-binding proteins

monomeric GTPase

turned on by guanine nucleotide exchange factor (GEFs) and turned off by GTPase-activating proteins (GAPs), can remove their own phosphate group and shut themselves off

ion-channel-couple receptors

alter plasma permeability to certain ions, thus altering membrane potential or producing an elecrical current

G-protein-coupled receptors

activate membrane-bound GTP-binding proteins which activate or inhibit an enzyme or ion channel, resulting in a signaling cascade 

enzyme-coupled receptor

acts as enzymes or associate with internal enzymes, activating a variety of signaling pathways

GPCRs

undergo a conformational change upon binding a signal molecule that enables it to activate a G protein on the cytosolic side of the membrane

signal binding and G protein activation

causes the alpha subunit to decrease its affinity for GDP which gets exchanged for GTP

Cholera

caused by a bacterium that produces a toxin called cholera toxin in the intestine 

adenylyl cyclase

an enzyme that formation of cyclic AMP (cAMP) from ATP

cAMP phosphodiesterase

continuously active inside the cell, leading to rapid changes in cAMP concentration

activated PKA

catalyzed phosphorylation of serines or thrones on specific proteins

phospholipase C 

an enzyme associated with the plasma membrane that generates 2 second messenger in response to a signal 

cytosolic Ca2+

kept low allowing for a steep electrochemical gradient for intracellular messenger

calmodulin

a small protein that modifies that activity of many other proteins in response to Ca2+

ca2+/calmodulin-dependent protein kinases (CaM-kinases)

an important target of calmodulin that phosphorylate other proteins

CaM-kinases

important at synapses of neurons in the mammalian brain, thought to play an important role in learning and memory

Nitric oxide(NO)

a gaseous signaling molecule produced by GPCRs

Rhodopsin

a G-protein-coupled light receptor responsible for non-color vision in dim light, activates the protein transduction which activates a signal cascaded causes cation channels to close and change cell voltage

enzyme-coupled receptors

have one transmembrane segment that spans the bilayer as an alpha helix

receptor tyrosine kinases(RTKs)

largest class of enzyme-coupled receptors, are phosphorylated upon dimerization

Ras

a monomeric GTPase that is attached to the cytosolic side of the plasma membrane by a lipid tail, cycles between the GTP-bound active state and GDP-bound inactive state

when Ras is active

initiates a phosphorylation cascade through serine/threonine kinases

MAP-Kinases signaling module

relay involves a 3-kinase module

mitogen-activated protein kinase or MAP kinase

final enzyme in the chain for Ras

phosphorylates inositol phospholipids

in the plasma membrane that serve as docking site for intracellular signaling proteins

phosphoniositide 3-kinase (PI 3-kinase)

an important enzyme that RTKs activate to promote cell growth

Akt (protein kinase B, PKB)

a key set/thr kinase that inactivates its target

Bad

promotes cell survival

Tor

stimulates growth

Notch 

an important receptor in animals that acts as a transcription regular 

Notch cleavage

releases the cytosolic tail which moves to the nucleus to activate Notch-responsive genes

cytoskeleton 

intricate network of protein filaments that extend throughout the cytoplasm

intermediate filament proteins

fibrous monomers consisting of a central rod domain with globular regions at either end

tetramers

can pack together end to end, when 2 dimers line up they are formed

amyotrophic lateral sclerosis (ALS)

associated with abnormal accumulation of neurofilaments in the cell bodies and axons of motor neurons, contributing to neuronal degeneration and muscle weakness

Microtubules

extend throughou

polymers of actin

one of the most abundant proteins in most cell types, essential for maintaining cell shape and movement that involves the outer membrane

actin filaments

7 nm in diameter and consists of a twisted chain of identical globular actin monomers that point in the same direction

thymosin

binds to monomers to prevent polymerization

myosins

motor proteins that hydrolyze ATP to move

Myosin I

is in all cell types, the head binds ATP and it attached to actin filaments, but the tails vary between the types of myosin I and the cargo

Myosin II

also in all cell types and interacts with actin to form contractile rings, and makes muscles contract

Fibroblasts

extends flattened lamellipodia and thin filopodia from its surface, mostly from the leading edge

lamellipodia

have dense meshwork of actin with the plus end closest to the plasma membrane

filopodia

have loose bundles of 10-20 actin filaments with their plus ends pointing outward

formin dimers

attach to the growing end of an actin filament to promote filopodia growth

Rho proteins

small monomeric GTPases that control the reorganization of the actin cytoskeleton

actin

primarily at the cell cortex and microtubules are primarily organize the cell interior, giving a cell polarity

myosin filaments 

point in opposite directions, each bound to an actin filament that they slide past one another 

myofibril

a chain of tiny contractile units called sarcomeres that are made up if both actin and myosin filaments