BIO130 Section 2 Definitions: Weeks 1-3

Cell Theory

The cell is the basic living unit of life; multicellular organisms are composed of many different cell types, each with their own unique form and function

Animal Cells

Made of things such as cytoplasm, nucleus, mitochondrion, actin filaments, vesicles, golgi apparatus, endoplasmic reticulum, etc; doesn't have cell walls but has lysosomes and an extracellular matrix

Plant Cells

Made up of many of the same things that make up animal cells (cytoplasm, nucleus, etc)

Cytoplasm

Contents of the cell outside the nucleus

Cytosol

Aqueous part of the cytoplasm

Lumen

The inside of organelles

Liposomes

Are artificial lipid bilayers; used to study lipid properties, membrane protein properties, and/or drug delivery into cells

Singer-Nicolson Model

The current model used, it describes the cell membrane as a fluid mosaic with proteins embedded in the bilayer

Phospholipid

A molecule with hydrophilic phosphate heads and hydrophobic lipid tails, forms bilayers in water

Hydrophilic

Substances that are attracted to water

Hydrophobic

Substances that are not attracted to water

Glycolipid

A sugar chain attached to a phospholipid

Glycoprotein

A sugar chain attached to a membrane protein

Sterol

Any of a group of naturally occurring unsaturated steroid alcohols, typically waxy solids

Cholesterol

Short, rigid lipid molecule present in large amounts in the plasma membranes of animal cells, where it makes the lipid bilayer less flexible

Flippase

This protein uses the energy of ATP hydrolysis to transfer specific phospholipids from one side of the bilayer to the other—including moving selected lipids from the monolayer facing the exterior space to that facing the cytosol

Floppase

An ATP-dependent transporter protein that moves lipids from the inner (cytosolic) leaflet to the outer (exoplasmic) leaflet of a biological membrane

Scramblase

A type of transporter protein that removes randomly selected phospholipids from one half of the lipid bilayer and inserts them in the other

Integral Proteins

Proteins directly attached to lipid bilayer, inserted into lipid bilayer or attached to a lipid which is inserted into lipid bilayer, extraction methods use detergents (lipid bilayer destroyed)

Peripheral Proteins

A protein that is found temporarily attached to the cell or mitochondrial membrane and are almost entirely hydrophobic or hydrophilic depending on which side of the membrane in which they are found

Single-Pass Transmembrane Proteins

Proteins in which the polypeptide chain only crosses the membrane only once and are generally receptors for extracellular signals

Multi-Pass Transmembrane Proteins

One or more of the membrane-spanning regions are amphipathic—formed from α helices that contain both hydrophobic and hydrophilic amino acid side chains

X-Ray Crystallography

Technique used to determine the three-dimensional structure of a protein molecule by analyzing the diffraction pattern produced when a beam of x-rays is passed through an ordered, crystalline array of the protein

Hydrophobicity Plots

Segments of 20-30 hydrophobic amino acids can span the lipid bilayer as an α-helix

Monolayer Associated Membrane Proteins

Proteins anchored on cytosolic face by an amphipathic α-helix

Lipid-Linked Membrane Proteins

Protein with a GPI anchor (glycosylphosphatidylinositol) can do synthesis in ER lumen and ends up on cell surface (non cytosolic face) while a protein with another lipid anchor (fatty acid, prenyl); cytosolic enzymes add anchor and directs protein to cytosolic face

FRAP (Fluorescence Recovery After Photobleaching)

A technique used to study the mobility of molecules, particularly proteins, within cells by measuring the rate at which fluorescence returns to a bleached area

GFP (Green Fluorescent Protein)

A protein from the jellyfish Aequorea victoria that exhibits bright green fluorescence when exposed to blue or ultraviolet light, used as a marker to visualize proteins and cells in living organisms

Phosphatidylcholine

Common phospholipid present in abundance in most cell membranes; uses choline attached to a phosphate as its head group

Saturated

No double bonds, has the maximum amount of hydrogens

Unsaturated

At least one double bond, doesn’t have the maximum amount of hydrogens

Porins

These allow the passage of small nutrients, metabolites, and inorganic ions across their outer membranes, while preventing unwanted larger molecules from crossin

Detergents

Soapy substance used to solubilize lipids and membrane proteins

Protein Domains

Functionally and structurally specialized region in the membrane of a cell or organelle; typically characterized by the presence of specific proteins

Artificial Bilayer

A layer which is impermeable to most water soluble molecules

Cell Transport

Membrane transport proteins to transfer specific molecule; facilitated transport

Permeable Molecules

Move via simple diffusion through the lipid bilayer from high concentration to low concentration, and tend to be small polar molecules which can get through easily and small uncharged polar molecules that can get through with a bit of difficulty

Impermeable Molecules

Larger uncharged polar molecules like amino acids, which rarely gets through and therefore require membrane proteins for transport

Transmembrane Transport Proteins

Create a protein-lined path across the cell membrane and transport polar and charged molecules such as ions, sugars, amino acids, nucleotides, and various cell metabolites

Channel

A protein that forms a hydrophilic pore across a membrane, through which selected small molecules or ions can passively diffuse

Transporter

Also known as a carrier protein, it facilitates transport by having the solute fit into the specific binding site and having a series of conformational change for transport that bind strongly

Active Transport

This type of transport goes against the concentration gradient and does directly require energy

Passive Transport

This type of transport goes down the concentration gradient and doesn’t directly require energy

Membrane Potential

The charge across the membrane; on opposite sides of

Non-Gated Ion Channels

These channels are always open

Gated Ion Channels

For these channels, some type of signalling is required for channel opening which means that only specific ions are transported

Mechanically-Gated Channel

An ion channel that allows the passage of select ions across a membrane in response to a physical perturbation

Ligand-Gated Channel

An ion channel that is stimulated to open by the binding of a small molecule such as a neurotransmitter; can be extracellular or intracellular

Voltage-Gated Channel

Channel protein that permits the passage of selected ions, such as Na+, across a membrane in response to changes in the membrane potential, and is found primarily in electrically excitable cells such as nerve/muscle cells

Uniport

Stands for “one solute," passive transport down its electrochemical gradient, and direction of transport is reversible

Gradient-Driven Pumps

Pump uses one solute down its gradient (energy) while the second moves against the gradient

ATP-Driven Pumps (ATPases)

Pump uses ATP hydrolysis (energy) and it moves against its gradient

Light-Driven Pumps

This pump is in bacteria and uses light energy and moves against the gradient

Symport

Two solutes moved in the same direction, free energy from the first solute moves down its electrochemical gradient, it’s used to transport the second solute against the electrochemical gradient

Antiport

Two solutes, but one moves in one direction, and the other moves in the opposite direction, also uses energy from the first solute to move the second solute against the electrochemical gradient

P-Type Pumps

These pumps use ATP and are phosphorylated during pumping cycle; many types

Electrochemical Gradient

A gradient of electrochemical potential, usually for an ion that can move across a membrane

ABC Transporter

Uses 2 ATP to pump small molecules across the cell membrane

V-Type Proton Pumps

These use ATP to pump hydrogen ions into organelles to acidify the lumen; they are in the lysosome and plant vacuoles

F-Type ATP Synthase

These use the H+ electrochemical gradient to produce ATP, they are the opposite of the V-type pump (basically), and they are in mitochondria, chloroplasts, and bacteria

Equilibrium

Resting membrane potential (varies from -20 mV to -200 mV in animal cells)

Pump

A transporter that uses a source of energy, such as ATP hydrolysis or sunlight, to actively move a solute across a membrane against its electrochemical gradient

Na+ Pump

Transporter found in the plasma membrane of most animal cells that actively pumps Na+ out of the cell and K+ in using the energy derived from ATP hydrolysis

Ca2+ Pump

An active transporter that uses energy supplied by ATP hydrolysis to actively expel Ca2+ from the cell cytosol

H+ Pump

A protein or protein complex that uses energy supplied by ATP hydrolysis, an ion gradient, or light to actively move protons across a membrane

Ion Channel

Transmembrane protein that forms a pore across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients

Selectivity Filter

Part of an ion channel that determines which ions the channel can transport; located in the region where the channel is narrowest

K+ Leak Channel

Ion channel permeable to K+ that randomly flickers between an open and closed state; largely responsible for the resting membrane potential in animal cell

Resting Membrane Potential

Voltage difference across the plasma membrane when a cell is not stimulated

Nernst Equation

An equation that relates the concentrations of an inorganic ion on the two sides of a permeable membrane to the membrane potential at which there would be no net movement of the ion across the membrane

Patch-Clamp Recording

Technique used to monitor the activity of ion channels in a membrane; involves the formation of a tight seal between the tip of a glass electrode and a small region of cell membrane

Membrane Domain

Functionally and structurally specialized region in the membrane of a cell or organelle; typically characterized by the presence of specific proteins

Cytosol

Contains many metabolic pathways, protein synthesis and the cytoskeleton

Chromatin

Genetic information that is contained inside the nucleus

Cytoplasm

A jelly-like substance that surrounds the organelles

Cytoskeleton

An internal network of fibres that helps to maintain the cell's shape

Golgi Apparatus

Modifies, sorts, and packages proteins from the endoplasmic reticulum for delivery

Mitochondria

The powerhouse of the cell, produces ATP, made up of cristae (folds in the inner membrane of mitochondria)

Naked DNA

Circular DNA in the nucleoid that isn't to surrounded by a nuclear membrane and isn't associated with proteins

Nuclear Pores

Channel through which selected large molecules move between the nucleus and the cytoplasm

Nucleoid

An irregularly shaped region in a prokaryotic cell that contains its genetic material

Nucleolus

The thing in the middle of the nucleus responsible for RNA synthesis

Nucleus

The control center of the cell that contains most of the cell's DNA

Organelle

A discrete structure or subcompartment of a eukaryotic cell that is specialized to carry out a particular function; most but not all are membrane-enclosed; "little organs"

Osmosis

Where water moves from regions with low solute to high solute concentrations and no energy is needed for this process; no energy is needed

Plasma Membrane

These control the entry and exit of substances, pumping some of them in by active transport

Rough Endoplasmic Reticulum

Makes proteins for the cell, and has ribosomes

Smooth Endoplasmic Reticulum

Produces fats and oils for the cell, and has no ribosomes

Thylakoids

Sacs inside the chloroplast that collects light energy from sun

Vacuole

A membrane-bound organelle that stores water used by the cell

Degradation Vacuole

This type of vacuole plays a similar role to lysosomes in animal cells

Storage Vacuole

This vacuole is responsible for storing small molecules and proteins

Vesicle

Small, membrane-enclosed organelle in cytoplasm of a eukaryotic cell that shuttles components back and forth in the endomembrane system

Hepatocyte

A very common liver cell that helps with detoxification

Cytosolic Protein

A protein without a sorting signal with its default location being in the cytosol

Signal Sequence

Specific signal of an amino acid that tells the cell where the protein will go; it is not added for separately but instead coded for by the mRNA and the genome

Peroxisome

They contain enzymes for oxidative reactions which helps to detoxify toxins, and break down fatty acid molecules

Post-Translational Sorting

The proteins are nuclear-encoded and fully synthesized in cytosol before sorting; can be folded like the nucleus or unfolded like the mitochondria

Co-Translational Sorting

Proteins are nuclear-encoded and have an ER signal sequence, and they are associated with ER during protein synthesis in the cytosol

Cotranslational Translocation (Soluble Protein)

1. Translation starts, N-terminal ER signal sequence emerges
2. Recognized by SRP, elongation arrest by SRP
3. SRP-ribosome complex → SRP receptor → Translocon
4. Translocon opens
5. Protein synthesis resumes with protein transfer into ER lumen
6. Signal peptidase cleaves ER Signal sequence (signal sequence is hydrophobic - in lipid bilayer)
7. Protein released into ER lumen
8. Translocon closes and the destination of soluble protein is the lumen of an endomembrane organelle or secretion at PM