ch. 5 Organizing Principles: Lipids, Membranes, and Cell Compartments book notes

transporters:

Membrane proteins that move ions or other molecules across the cell membrane.

The Golgi apparatus has three primary roles:

(1) It further modifies proteins and lipids produced by the ER (2) it acts as a sorting station as these proteins and lipids move to their final destinations (3) it is the site of synthesis of most of the cell's carbohydrates.

vacuole:

A cell structure that absorbs water and contributes to turgor pressure.

endomembrane system :

A cellular system that includes the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, the plasma membrane, and the vesicles that move between them.

ribosome :

A complex structure of RNA and protein, bound to the cytosolic face of the RER in the cytoplasm, on which proteins are synthesized.

cell wall:

A defining boundary in many organism, external to the cell membrane, that helps maintain the shape and internal composition of the cell.

electrochemical gradient:

A gradient that combines the charge gradient and the chemical gradient of protons and other ions.

thylakoid membrane:

A highly folded membrane in the center of the chloroplast that contains light-collecting pigments and that is the site of the photosynthetic electron transport chain.

anchor:

A membrane protein that attaches to other proteins and helps to maintain cell structure and shape.

fluid mosaic model:

A model that proposes that the lipid bilayer is a fluid structure that allows molecules to move laterally within the membrane and is a mosaic of two types of molecules, lipids and proteins.

receptor:

A molecule on cell membranes that detects critical features of the environment. Receptors detecting signals that easily cross the cell membrane are sometimes found in the cytoplasm.

aquaporin:

A protein channel that allows water to flow through the plasma membrane more readily by facilitated diffusion.

enzyme:

A protein that functions as a catalyst to accelerate the rate of a chemical reaction; enzymes are critical in determining which chemical reactions take place in a cell.

integral membrane protein:

A protein that is permanently associated with the cell membrane and cannot be separated from the membrane experimentally without destroying the membrane itself.

peripheral membrane protein:

A protein that is temporarily associated with the lipid bilayer or with integral membrane proteins through weak noncovalent interactions.

vesicle :

A small membrane-enclosed sac that transports substances within the cell. form by budding off an organelle, taking with them a piece of the membrane and internal contents of the organelle from which they derive. They then fuse with another organelle or the plasma membrane, re-forming a continuous membrane and unloading their contents.

micelle:

A spherical structure in which lipids with bulky heads and a single hydrophobic tail are packed.

pilus (plural, pili) :

A threadlike structure that connects bacteria, allowing plasmids to be transferred between them.

carrier:

A transporter that facilitates movement of molecules.

channel:

A transporter with a passage that allows the movement of molecules through it depending on their shape/charge

bilayer:

A two-layered structure of the cell membrane with hydrophilic "heads" pointing outward toward the aqueous environment and hydrophobic "tails" oriented inward, away from water.

contractile vacuole:

A type of cellular compartment that takes up excess water and waste products from inside the cell and expels them into the external environment.

lysosome :

A vesicle derived from the Golgi apparatus that contains enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbohydrates.

primary active transport:

Active transport that uses the energy of ATP directly.

secondary active transport:

Active transport that uses the energy of an electrochemical gradient, not ATP directly, to drive the movement of molecules.

signal-recognition particle (SRP) :

An RNA-protein complex that binds with part of a polypeptide chain and marks the molecule for incorporation into the endoplasmic reticulum (eukaryotes) or the plasma membrane (prokaryotes).

signal sequence :

An amino acid sequence that directs a protein to its proper cellular compartment.

cholesterol:

An amphipathic lipid that is a major component of animal cell membranes.

liposome:

An enclosed bilayer structure spontaneously formed by phospholipids in environments with neutral pH, like water.

Describe an experiment that demonstrates that proteins move in membranes.

An experiment designed to show that proteins move in membranes can use the FRAP technique. FRAP stands for fluorescence recovery after photobleaching. First, the proteins embedded in the cell membrane are labeled with fluorescent dye molecules. A laser is then used to bleach part of the cell so that it no longer fluoresces. Eventually, the fluorescently labeled proteins from other parts of the cell move into the bleached area and cause it to fluoresce once again. If the proteins did not move in membranes, that area would stay bleached for the life of the cell.

chloroplast :

An organelle that converts energy of sunlight into chemical energy by synthesizing simple sugars

Lipids are the main component of cell membranes.

Carbohydrates can also be found in cell membranes, usually attached to lipids (glycolipids) and proteins (glycoproteins). Lipids freely associate with one another because of extensive van der Waals forces between their fatty acid tails & also rapidly rotate around their vertical axis, and individual fatty acid chains are able to flex, or bend.

selectively permeable:

Describes the properties of some membranes, including the plasma membrane, which lets some molecules in and out freely, lets others in and out only under certain conditions, and prevents other molecules from passing through at all.

facilitated diffusion:

Diffusion through a membrane protein, bypassing the lipid bilayer.

amphipathic:

Having both hydrophilic and hydrophobic regions.

In the absence of the sodium-potassium pump, the extracellular solution becomes hypotonic relative to the inside of the cell. Poisons such as the snake venom ouabain can interfere with the action of the sodium-potassium pump. What are the consequences for the cell?

If the sodium-potassium pump is made inactive by poison, the cell will swell and even burst, as the intracellular fluid becomes hypertonic relative to the outside of the cell and water moves into the cell by osmosis.

The degree of membrane fluidity depends on which types of lipid make up the membrane:

In a single layer of the lipid bilayer, the strength of the van der Waals interactions between the lipids' tails depends on the length of the fatty acid tails and the presence of double bonds between neighboring carbon atoms. The longer the fatty acid tails, the more surface is available to participate in van der Waals interactions. The tighter packing that results tends to reduce lipid mobility. Likewise, saturated fatty acid tails, which have no double bonds, are straight and tightly packed—again reducing mobility (Fig. 5.4a). The double bonds in unsaturated fatty acids introduce kinks in the fatty acid tails, reducing the tightness of packing and enhancing lipid mobility in the membrane

Describe how lipids with hydrophilic and hydrophobic regions behave in an aqueous environment.

In an aqueous environment, the polar hydrophilic head group readily interacts with the polar water molecules. In contrast, the nonpolar hydrophobic tail does not readily interact with water and instead interacts with other nonpolar tail groups or hydrophobic molecules. For example, a micelle forms when the polar head group of a lipid interacts with water and the hydrophobic tails of the lipids interact with each other, excluding the water. Lipids can also form bilayers and liposomes

plasmid:

In bacteria, a small circular molecule of DNA carrying a small number of genes that can replicate independently of the bacterial genomic DNA.

cytoskeleton :

In eukaryotes, an internal protein scaffold that helps cells to maintain their shape and serves as a network of tracks for the movement of substances within cells.

lumen :

In eukaryotes, the continuous interior of the endoplasmic reticulum; in plants, a fluid-filled compartment enclosed by the thylakoid membrane; generally, the interior of any tubelike structure.

nucleoid:

In prokaryotes, a cell structure with multiple loops formed from supercoils of DNA.

signal-anchor sequence:

In protein sorting, an amino acid sequence in a polypeptide chain that embeds the chain in the membrane.

lipid raft:

Lipids assembled in a defined patch in the cell membrane.

nuclear pore :

One of many protein channels in the nuclear envelope that act as gateways that allow molecules to move into and out of the nucleus and are thus essential for the nucleus to communicate with the rest of the cell.

peroxisomes :

Organelles in eukaryotic cells that contain many different enzymes and are involved in metabolic reactions.

Protein transporters that move in opposite directions are antiporters

Other transporters move two molecules in the same direction, and are referred to as symporters or cotransporters.

turgor pressure:

Pressure within a cell resulting from the movement of water into the cell by osmosis and the tendency of the cell wall to resist deformation.

Describe two types of association between proteins and membranes.

Proteins can associate with membranes in the following ways: (1) Integral membrane proteins are permanently associated with the membrane and cannot be removed without destroying the membrane itself. Most integral membrane proteins span the cell membrane, and therefore they have both hydrophilic and hydrophobic regions. (2) Peripheral membrane proteins are temporarily associated with the membrane and can easily be experimentally separated. These proteins can be associated with either the internal or external side of the membrane. They are mostly hydrophilic and interact with the polar heads of the lipid bilayer, or the hydrophilic regions of integral membrane proteins.

transmembrane proteins:

Proteins that span the entire lipid bilayer; most integral membrane proteins are transmembrane proteins

Secondary active transport:

Protons are pumped across a membrane by (a) primary active transport, resulting in (b) an electrochemical gradient, which drives (c) the movement of another molecule against its concentration gradient.

Most animal fats are solid at room temperature, whereas plant and fish oils tend to be liquid. Both contain fatty acids. Can you predict which type of fat contains saturated fatty acids, and which type contains unsaturated fatty acids?

Saturated fatty acids are less mobile within the membrane compared to unsaturated fatty acids. As a result, saturated fatty acids tend to be solid at room temperature, whereas unsaturated fatty acids tend to be liquid. Margarine and many other animal fats contain saturated fatty acids and are solid, whereas many plant and fish oils contain unsaturated fatty acids and are liquid at room temperature.

secondary active transport vs primary active transport:

Secondary active transport uses the potential energy of an electrochemical gradient to drive the movement of molecules; by contrast, primary active transport uses the chemical energy of ATP directly.

mitochondria (singular, mitochondrion) :

Specialized organelles that harness energy for the cell from chemical compounds like sugars and convert it into ATP.

active transport:

The "uphill" movement of substances against a concentration gradient requiring an input of energy. move substances from areas of lower concentration to areas of higher concentration.

homeostasis :

The active regulation and maintenance, in animals, organs, or cells, of a stable internal physiological state in the face of a changing external environment.

photosynthesis:

The biochemical process in which carbohydrates are built from carbon dioxide and the energy of sunlight.

nuclear envelope :

The cell structure, composed of two membranes, inner and outer, each is a lipid bilayer with associated proteins, that defines the boundary of the nucleus.

cytoplasm :

The contents of the cell other than the nucleus.

chlorophyll :

The major photosynthetic pigment contained in the thylakoid membrane; it plays a key role in the chloroplast's ability to capture energy from sunlight. Chlorophyll appears green because it is poor at absorbing green wavelengths.

plasma membrane:

The membrane that defines the space of the cell, separating the living material within the cell from the nonliving environment around it.

osmosis:

The net movement of a solvent, such as water, across a selectively permeable membrane toward the side of higher solute concentration. lower *solute* concentration to an area of higher *solute* concentration. high *water* concentration to low *water* concentration

endoplasmic reticulum (ER) :

The organelle involved in the synthesis of proteins and lipids.

Golgi apparatus :

The organelle that modifies proteins and lipids produced by the ER and acts as a sorting station as they move to their final destinations.

rough endoplasmic reticulum (RER)

The part of the endoplasmic reticulum with attached ribosomes. synthesizes transmembrane proteins, proteins that end up in the interior of organelles, and proteins destined for secretion

smooth endoplasmic reticulum (SER) :

The portion of the endoplasmic reticulum that lacks ribosomes. site of fatty acid and phospholipid biosynthesis

protein sorting :

The process by which proteins end up where they need to be in the cell to perform their function. directs proteins to the cytosol, the lumen of organelles, the membranes of the endomembrane system, or even out of the cell entirely.

endocytosis:

The process in which a vesicle buds off from the plasma membrane, bringing material from outside the cell into that vesicle, which can then fuse with other organelles.

exocytosis :

The process in which a vesicle fuses with the plasma membrane and empties its contents into the extracellular space or delivers proteins to the plasma membrane.

diffusion:

The random motion of individual molecules, with net movement occurring where there are areas of higher and lower concentration of the molecules. higher water concentration to regions of lower water concentration

cytosol :

The region of the cell inside the plasma membrane but outside the organelles; the jelly-like internal environment that surrounds the organelles.

cisternae (singular, cisterna) :

The series of flattened membrane sacs that make up the Golgi apparatus.

nuclear localization signal:

The signal sequence for the nucleus that enables proteins to move through pores in the nuclear envelope.

The sodium-potassium pump is a membrane protein that uses the energy stored in ATP to move sodium and potassium ions against their concentration gradients.

The sodium-potassium pump actively moves sodium out of the cell and potassium into the cell. This movement of ions takes energy, which comes from the chemical energy stored in ATP. (3 sodium out for every 2 potassium in)

Proteins produced on the rough ER end up in the lumen of the endomembrane system, secreted out of the cell, or as transmembrane proteins (These proteins are sorted as they are translated)

They begin translation on free ribosomes, but a specific signal sequence at their amino terminal end directs the ribosome to the rough ER and into a membrane channel that leads into the ER lumen.

Name three parameters that need to be stably maintained inside a cell.

Three parameters that need to be stably maintained inside a cell are pH, salt concentration, and volume.

A container is divided into two compartments by a membrane that is fully permeable to water and small ions. Water is added to one side of the membrane (side A), and a 5% solution of sodium chloride (NaCl) is added to the other (side B). In which direction will water molecules move? In which direction will sodium and chloride ions move? When the concentration is equal on both sides, will diffusion stop?

Water molecules move in both directions, but the net movement of water molecules is from side A to side B. Water moves from regions of higher water concentration to regions of lower water concentration. Likewise, sodium and chloride ions move in both directions, but the net movement of sodium and chloride ions is from side B to side A. Movement of water and ions results from diffusion, the random motion of substances. Even when the concentration of all molecules is the same on the two sides, diffusion still occurs, but there is no net movement of water molecules or ions.

isotonic solution:

equal, the same solute concentration

A proton electrochemical gradient is generated across the inner mitochondrial membrane, and the energy stored in the gradient is used to synthesize ATP for use by the cell. Mitochondria are the site of cellular respiration, and the oxygen that you take in with each breath is used by mitochondria to produce ATP.

mitochondira

hypertonic solution:

one with a higher solute concentration than that inside the cell, water leaves the cell by osmosis and the cell shrinks. *more outside the cell*

hypotonic solution:

one with a lower solute concentration than that inside the cell) water moves into the cell by osmosis and the cell lyses, or bursts. *more inside the cell*

The major types of lipid found in cell membranes are ____________

phospholipids. phospholipids are made up of a glycerol backbone attached to a phosphate group and two fatty acids. The phosphate head group is hydrophilic ("water-loving") because it is polar, enabling it to form hydrogen bonds with water. By contrast, the two fatty acid tails are hydrophobic ("water-fearing") because they are nonpolar and do not form hydrogen bonds with water. This arrangement results from the tendency of polar molecules like water to exclude nonpolar molecules or nonpolar groups of molecules.

5.5 Mitochondria and chloroplasts are organelles involved in harnessing energy, and likely evolved from free-living prokaryotes.

• Mitochondria harness energy from chemical compounds for use by both animal and plant cells. • Chloroplasts harness the energy of sunlight to build sugars.

5.1 Cell membranes are composed of lipids, proteins, and carbohydrates.

• Phospholipids have both hydrophilic and hydrophobic regions. As a result, they spontaneously form structures such as micelles and bilayers when placed in an aqueous environment. • Membranes are fluid, meaning that membrane components are able to move laterally in the plane of the membrane. • Membrane fluidity is influenced by length of fatty acid chains, presence of carbon-carbon double bonds in fatty acid chains, and amount of cholesterol. • Many membranes also contain proteins that span the membrane (transmembrane proteins) or are temporarily associated with one or other layer of the lipid bilayer (peripheral proteins).

5.3 Cells can be classified as prokaryotes or eukaryotes, which differ in the degree of internal compartmentalization.

• Prokaryotic cells lack a nucleus and other internal membrane-enclosed compartments. • Prokaryotic cells include bacteria and archaeons and are much smaller than eukaryotes. • Eukaryotic cells have a nucleus and other internal compartments called organelles. • Eukaryotes include animals, plants, fungi, and protists.

5.2 The plasma membrane is a selective barrier that controls the movement of molecules between the inside and the outside of the cell.

• Selective permeability results from the combination of lipids and proteins that makes up cell membranes. • Passive transport is the movement of molecules by diffusion, the random movement of molecules. There is a net movement of molecules from regions of higher concentration to regions of lower concentration. • Passive transport can occur by the diffusion of molecules directly through the plasma membrane (simple diffusion) or be aided by protein transporters (facilitated diffusion). • Active transport moves molecules from regions of lower concentration to regions of higher concentration and requires energy. • Primary active transport uses energy stored in ATP; secondary active transport uses the energy stored in an electrochemical gradient. • Animal cells often maintain size and shape by protein pumps that actively move ions in and out of the cell. • Plants, fungi, and bacteria have a cell wall outside the plasma membrane that maintains cell size and shape.

5.4 The endomembrane system is an interconnected system of membranes that includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, and plasma membrane.

• The nucleus, which is enclosed by a double membrane called the nuclear envelope, houses the genome. • The endoplasmic reticulum is continuous with the outer nuclear envelope and manufactures proteins and lipids for use by the cell or for export out of the cell. • The Golgi apparatus communicates with the endoplasmic reticulum by transport vesicles. It receives proteins and lipids from the endoplasmic reticulum and directs them to their final destinations. • Lysosomes break down macromolecules like proteins to simpler compounds that can be used by the cell. • Protein sorting directs proteins to their final destinations in or out of the cell. • Proteins synthesized on free ribosomes are sorted after translation and proteins synthesized on ribosomes associated with the rough endoplasmic reticulum are sorted during translation. • Proteins synthesized on free ribososomes are often sorted by means of a signal sequence and are destined for the cytosol, mitochondria, chloroplasts, or nucleus. • Proteins synthesized on ribosomes on the rough endoplasmic reticulum have a signal sequence that is recognized by a signal-recognition particle. These proteins end up as transmembrane proteins, in the interior of various organelles, or secreted.