Biology Exam 2 March 7, 2014
Chapter 6: Cell Membranes
Section 1: What is the Structure of a Biological Membrane?
• Organization of biological membranes depend on lipids, proteins, and carbohydrates:
Lipids maintain physical state of membrane and controls what passes through membrane
Lipids as a “lake” where protein “floats”
Fluid Mosaic Model:
1. Proteins are embedded into bilayer by hydrophobic regions, but hydrophilic regions are exposed
2. Membrane proteins move materials across membrane or receive chemical signals
3. Carbohydrates are attached to lipids or protein molecules. They are located on outside of cell and interact with external
substances. Recognize specific molecules.
• Hydrophilic Region : Phosphorouscontaining “head” of phospholipid > electrically charged and polar
• Hydrophobic Region : Long, nonpolar fatty acid “tails” of phospholipid> nonpolar
• Saturated: Single bond (just long and straight) > cholesterol is a saturated fatty acid.
• Unsaturated: Double of triple bond with a lot of kinks
• Membrane Fluidity :
1. Lipid composition: Longchain saturated fatty acids leave little room for movement because they are tightly packed.
Shorter chain fatty acids and unsaturated fatty acids > more fluidity
2. Temperature: Lower temperatures cause molecules to move slower and fluidity decrease. Organisms will just change
lipid composition of membranes when they get cold and replace saturated with unsaturated fatty acids.
• Transmembrane Protein : Protein that extends through bilayer and protrudes on both sides
• Peripheral Membrane Proteins : Located on one side of membrane or another
• MembraneAssociated Carbohydrates :
1. Glycolipid: Carbohydrate covalently bonded to a lipid
Serves as recognition signal for interactions between cells
Carbohydrates on glycolipids will change when cells become harmful
2. Glycoprotein: One or more short carbohydrate chains covalently bonded to a protein
Proteogylan is a heavily saturated glyocoprotein> Has more carbohydrate molecules and chain is longer
Function in cell recognition and adhesion
Section 2: How is the Plasma Membrane Involved in Cell Adhesion and Recognition?
• Sponge cells can be separated and will stick together a couple hours later to reform its original shape because of cell
• Cell Recognition is done by proteoglycans that carry 2 kinds of carbohydrates:
1. Small and binds to membrane components, keeping proteoglycan attached to cell
2. Larger, sulfated polysaccharide
• Cell adhesion occurs because of interactions between carbohydrates
• Homotypic: Adhesion of same molecule sticking out of different cells
• Heterotypic: Adhesion between two different molecules on different cells
• Cell Junctions : Additional membrane structure formed by material of binding cells> cell adhesion and intercellular
1. Tight Junctions: Prevent things from moving through spaces between cells. Maintain distinct faces of a cell within
tissue by restricting migration of membrane proteins
2. Desmosomes: holds neighboring cells together. Mechanical stability for tissues
3. Gap Junctions: channels that run between membrane pores in adjacent cells, allowing substances to pass between cells.
• Integrin (transmembrane protein) mediates attachment of epithelial cells to extracellular matrix. Binding is noncovalent
and reversible. When cell moves, part of it is detached from extracellular matrix while other moves in direction of
movement, forming new attachments. The integrin is brought into cytoplasm by endocytosis and it is recycled. Section 3: What are the Passive Processes of Membrane Transport?
• Crossing Processes:
Selective Permeability: Allows membrane determine what substances get to enter or leave cell
1. Passive Transport: Do not require chemical energy to drive them
Energy comes from concentration gradient (difference between concentration on one side of membrane to the other)
Two Types of Diffusion:
A. Simple diffusion through phospholipid bilayer
B. Facilitated diffusion via channel proteins or carrier proteins
2. Active Transport: require chemical energy (metabolic energy)
• Rate of diffusion depends on :
1. Diameter of ions: Smaller means faster
2. Temperature of solution: Higher temp means faster diffusion because ions have more energy
3. Concentration gradient: Greater gradient, the more rapidly
• Diffusion Types :
1. Within Cells and Tissues: Small volume> solutes distribute themselves rapidly.
2. Across Membranes: properties of membrane affect movement of solutes. Membrane is permeable if solutes can cross
it easily, but impermeable if substances cannot move across it.
• Simple Diffusion : Does not involve direct energy or assistance by carrier protein
More lipidsoluble molecules diffuse faster through the membrane bilayer
Electrically charged cannot pass easily because they are not soluble and form many Hbonds with water and ions in
aqueous environment. Many Hbonds prevent it from moving to hydrophobic interior of membrane.
• Osmosis : movement of water across differently permeable membrane where water potential is more negative> Uses no
metabolic energy and depends on concentrations of molecules on each side of membrane.
1. Hypertonic: Higher solute concentration than solution
A. Animal cell Cell loses water and shrinks
B. Plant cell Cell shrinks (wilting)
2. Isotonic: Equal solute and solution concentrations
A. Animal cell Rate of water movement in and out are equal
B. Plant cell Rate of water movement in and out are equal
3. Hypotonic: Lower solute concentration than solution
A. Animal cell Cell takes up water, swell and bursts
B. Plant cell Cell stiffens, but cell retains shape> Turgor pressure (pressure within cell that keeps plants upright)
• Facilitated Diffusion (passive movement involving protein, not concentration gradient):
1. Channel proteins: membrane proteins that form channels across membrane through which substances cross
A. Ion channels: Usually gated, but opened when a stimulus changes 3D shape of channel.
B. Ligandgated channels are controlled by stimulus that involves binding of chemical signal a.k.a ligands.
C. Voltagegated channel is stimulated to open or close by change in voltage.
D. Ions pass based on charge and size of ion.
E. Aquaporin: transport protein through which water passes in osmosis
2. Carrier proteins: Bind substances and speed up their diffusion through phospholipid bilayer
A. Transport polar molecules such as sugars and amino acids
B. Binds to protein, brings it to membrane, changes shape, and releases into cytoplasm.
C. Concentration gradient matters to a point> rate of increase slows after diffusion rate becomes constant which is
when all carrier molecules have a solute molecule. This is called “saturated”
Section 4: What are the Active Processes of Membrane Transport?
• Active Transport requires energy (usually ATP) to drive against gradient concentration
• Three kinds of membrane proteins that carry out active transport:
1. Uniporter: Moves single substance in one direction, either outside cell or inside.
2. Symporter: Moves two substances in the same direction.
3. Antipoter: Moves two substances in opposite directions, one into cell and other out of cell.
Symporters and antiporters are known as coupled transporters because they move two substances at once
• Primary Active Transport: Direct hydrolysis of ATP Example: Sodiumpotassium pump. Pump is an integral membrane gly+oprotein that breaks down a +olecule of ATP to
ADP and P (phosphate ion) and uses energy released to bring K ions into cell and export Na ions. This is an example of
• Secondary Active Transport: Does not use ATP directly. Energy supplied by an ion concentration gradient established by
ATP driven active transport.
Uses energy “regained” by letting ions move across membrane with concentration gradients. Example, once sodium
potassium pump establishes concentration, passive diffusion of Na back into cell provides energy for secondary active
transport of glucose back into cell. Occurs when glucose is absorbed into the bloodstream from digestive track.
Helps in uptake of amino acids and sugars
Coupled transport proteins are used for this
Section 5: How do Large Molecules Enter and Leave a Cell?
• Endocytosis : Group of processes that bring small molecules into eukaryotic cell. Plasma membrane folds inward to form a
small pocket around materials form environment. Pocket deepens to form vesicle that separates from membrane and
migrates into interior of cell.
1. Phagocytosis: “cellular eating” part of membrane engulfs large particles or even entire cells. Unicellular protists use
this method to feed.
2. Pinocytosis: “cellular drinking” small vesicles are formed to bring fluids and dissolved substances into cell.
3. ReceptorMediated Endocytosis: Molecules at the cell surface recognize and trigger the uptake of specific materials
Used by animals to capture specific macromolecules
Depends on receptor proteins (proteins that can bind to specific molecules within or outside the cell
Receptors are integral membrane proteins located at regions on the membrane called coated pits because they have
slight depressions in the plasma membrane. The cytoplasmic surface is coated by clathrin.
When receptor protein binds to specific ligand, its coated pit deepens to form a vesicle. Clathrin molecules strength
and stabilize vesicle that carries it into the cytoplasm.
Once inside, vesicle loses clathrin coat, and it might be fused with a lysosome so products are released into
Because of specificity, this is an efficient method of taking low concentration substances
Also method by which cholesterol is taken up.
• Exocytosis: Process by which materials packaged in vesicles are secreted from cell when vesicle membrane fuses with
Fusing makes opening to the outside of a cell where contents are released. Vesicle membrane slowly becomes
reincorporated into plasma membrane.
Vesicle touches cell membrane and a pore forms that releases vesicle’s contents. No membrane fusion.
Chapter 7: Cell Communication and Multicellularity
Section 1: What are signals and how do cells respond to them?
• Signal Transduction Pathway: Sequence of molecular events and chemical reactions that lead to a cell’s response to a
• Pathway involves signal, receptor and response
• Signals are present in tiny concentrations and differ in sources and mode of delivery:
a. Autocrine Signals : Diffuse to and affect the cells that make them. Example: Tumor cells that reproduce uncontrollably
because they both make and respond to signals that stimulate cell division.
b. Juxtacrine Signals : Affect only cells adjacent to the cell producing the signal. Common during development
c. Paracrine Signals : Diffuse to and affect nearby cells. Example is a neurotransmitter made by a cell and then diffuses to
a nearby cell to stimulate it.
d. Hormones : Signals that travel through circulatory systems of animals or vascular systems of plants
• Only cells with appropriate receptors can respond.
• Response involves enzymes and transcription factors:
Activities of specific enzymes and transcription factors are regulated: Either activated or inactivated to bring about
Activity of protein can also be regulated by mechanisms that control its location in the cell
• Crosstalk: interactions between different signal transduction pathways Pathways will branch: receptor/enzyme will active enzymes or transcription factors in multiple pathways, leading to
multiple responses to a single stimulus
Multiple signal transduction pathways converge on a single transcription factor, allowing transcription of a single gene to
be adjusted in response to several different signals
Crosstalk results in the activation of one pathway and the inhibition of another.
Section 2: How do Signal Receptors Initiate a Cellular Response?
• Receptor Protein recognizes signal very specifically.
Specific chemical signal molecule fits into 3D site of protein receptor
Ligand: any molecule that binds to a receptor site of another molecule
Binding of signaling ligand causes receptor protein to change 3D shape, which initiates another cellular response
Ligand does not contribute to this response. It is not even metabolized into a useful product.
• Sensitivity of cell to a signal determined by affinity of cell’s receptors for signal ligand likelihood that receptor will bind
Binding: R (receptor) +L (ligand) > RL (Rate constant K ) 1
Dissociation: RL> R + L (Rate constant K ) 2
Usually binding is favored because equilibrium point is far right.
Rate of Binding: K [1 [L]
Rate of Dissociation: K [2 ]
[K ]/[K ]= K
2 1 D
• Dissociation Constant, K , Deasure of affinity of receptor for ligand.
The lower this value, the higher the binding ability of the ligand for receptor, meaning it can bind to ligands
at very low ligand concentrations.
Inhibitor can also bind to receptor protein, instead of normal ligand.
• Two Locations for Receptors :
1. Membrane Receptors: Large or polar ligands cannot cross lipid bilayer. Has to bind to a transmembrane receptor with
an extracellular binding domain.
2. Intracellular Receptors: Small or nonpolar ligands that diffuse across lipid bilayer of plasma membrane and enter the
cell. Binds to receptor inside cell.
• Plasma Membrane Receptors :
1. Ion Channels: GateOpening mechanism is an alternation in the 3D shape of channel protein upon interaction with a
signal. Ion channels respond to specific signal.
Acetylcholine receptor is a sodium channel that binds to acetylcholine, a neurotransmitter, a chemical signal
that is released from neurons.
Two molecules bind to receptor which opens, allowing for Na to rush into cell and change gradient
2. Protein Kinase Receptors: When they are activated, they catalyze the phosphorylation of themselves and/or other
proteins, which causes a change in shape and function.
Example: Receptor for insulin. When insulin binds to receptor, receptor becomes activated and phosphorylates itself
and insulin response substrates which initiate other cellular responses.
3. G ProteinLinked Receptors: Seventransmembrane domain receptors.
Light Detection (Photoreceptors)
Odor Detection (Olfactory Receptors)
Regulation of mood and behavior
Seven domains pass through phospholipid bilayer and are separated by short loops that extend outside or inside the
Ligand binding on extracellular side changes shape of cytoplasmic region, exposing site that binds to mobile
membrane protein (G protein)
G protein is partially inside lipid bilayer and partially exposed on membrane
Can bind to receptor, GDP and ATP, or an effector protein
GTP binding causes change in G protein. GTPbound subunit separates from rest of the G protein, diffusing through
bilayer until it encounters effector protein to which it binds to and then an effect is caused
After activation of effort protein, GTP bound to the G protein is hydrolyzed to GDP. Now inactive G protein subunit
separates from effector protein and binds with two other G protein subunits in membrane.
When 3 components of G protein are reassembled, protein is capable of binding to activated receptor Activated receptor exchanges GDP on G protein for GTP and cycle begins again
• Intraceullar Receptors : Located inside and respond to physical signals or chemical signals
Many are transcription factors (proteins that assemble on chromosome, allowing RNA polymerase II
to perform transcription
Usually located in cytoplasm until they are activated. After binding to ligands, transcription factors
move to nucleus to bind to DNA and alter expression of genes
Some are located in nucleus and their ligands have to enter nucleus before binding
Example: Receptor (which is usually bound to chaperone protein that that blocks it from entering
nucleus) for steroid hormone cortisol. Binding with hormone causes receptor to change shape so
chaperone is released. Release allows receptor to enter nucleus and affect DNA transcription
Chapter 8: Energy, Enzymes, and Metabolism
Section 1: What Physical Principles Underlie Biological Energy Transformations?
• Chemical Reaction occurs when atoms have energy to combine or change bonding partners
• C H O (sucrose)+ H O > C H O (glucose) + C H O (fructose)
12 22 11 2 6 12 6 6 12 6
• Metabolism: Sum total of all chemical reactions, which involves energy changes.
• Energy : Capacity for change. Usually associated with changes in chemical compositions and properties of molecules.
• Forms of Energy:
1. Potential Energy: Energy of state of position or stored energy. Stored in chemical bonds, as a concentration gradient or
as an electric charge imbalance
2. Kinetic Energy: Energy of movement. Energy that does work, that makes things change.
• Anabolic Reactions (Anabolism): Link simple molecules to form complex molecules. Requires an input of energy that is
captured (as potential energy) in the chemical bonds that are formed. Increase complexity (order) in cell.
• Catabolic Reactions (Catabolism): Break down complex molecules into simpler ones and release energy stored in
chemical bonds. Released energy may be recaptured in new chemical bonds or used as kinetic energy. Decrease
complexity (generate disorder).
• Catabolic and anabolic reactions are often linked. Energy released in catabolic reactions drive anabolic reactions.
• Law of Thermodynamics :
1. Energy is neither created nor destroyed
2. After energy transformations, some energy becomes unavailable to do work
Entropy: Measure of disorder in system (S)
To instill order in the system, energy needs to be applied first.
Total energy = usable energy + unusable energy
Total Energy: Enthalpy (H)
Usable Energy: Free Energy (G). This is what cells require to do chemical reactions such as growth, cell division and
Unusable Energy: Entropy (S) x Absolute Temperature (T)
∆ G = ∆ H –T ∆ S
∆ Greaction ∆ Gproducts ∆ G reactants
If products have more free energy than reactants, there must be input of energy into reaction
If ∆ G is negative, free energy is released
If ∆ G is positive, free energy is consumed
If free energy is not available, reaction does not occur. Sign and magnitude oG depends on:
1. ∆ H: Total amount of energy added to system ( ∆ H >0) or released (∆ H Free Energy + Small Molecules
• Anabolic reactions may single product (ordered substance) out of smaller reactants (less ordered). This consumes free
energy ∆ G making it an endergonic (endothermic) reaction. Free Energy + Small Molecules > Complex Molecules • Chemical Equilibrium: Balance between forward and reverse reactions. State when ∆ G = 0.
• Chemical equilibrium is related to free energy so the further toward completion the point of equilibrium lies, the more free
energy is released
• Value of ∆ G depends on beginning concentrations of reactants and products, temperature, pressure, pH
• Large, positive ∆ G means it barely proceeds to right.
• ∆ G value near zero means it is readily reversible because reactants and products have almost same free energies
Section 2: What is the Role of ATP in Biochemical Energetics?
• Cells rely on ATP to capture and transfer free energy to do chemical work.
• ATP releases a relatively large amount of energy when hydrolyzed to ADP and P
• ATP can phosphorylate many different molecules, which gain some of the energy that was stored in the ATP
• ATP: Adenine (nitrogenous base) + Ribose + 3 Phosphate Groups
• ATP + H 2 > ADP + P + free energy is exergonic
• ATP hydrolysis is an exergonic reaction. ATP can be hydrolyzed either to ADP and P or to adenosine monophosphate
AMP and a pyrophosphate ion. Two characteristics of ATP account for the free energy released by the loss of one or two
of its phosphate groups:
1. Phosphate groups are negatively charged and repeal each other, meaning it takes energy to get them together and form
the covalent bond between them. Energy is stored as potential energy.
2. Free energy of P~O bond is higher than energy of OH bond. (~ : indicates higher energy bond)
• Cells use energy released by ATP hydrolysis to fuel endergonic reactions, for active transport, and for movement
• Bioluminescence: Production of light by living organisms. Example of endergonic reaction driven by ATP hydrolysis that
involves chemical > light energy.
• ADP + P + free energy > ATP + H O is endergonic
• Cellular Respiration is the most important exergonic reaction that provides energy to convert ADP to ATP.
• EnergyCoupling Cycle: Reuse of energy. Example: ADP picks up energy from exergonic reactions to become ATP, which
then donates energy to endergonic reactions.
• Processes that require energy from hydrolysis of ATP:
1. Active transport across a membrane
2. Condensation reactions that use enzymes to form polymers
3. Modification of cell signaling proteins by protein kinases
4. Motor proteins that move vesicles along microtubules
• ATP is synthesized and used up very rapidly because of enzymes.
Section 3: What are Enzymes?
• Exergonic reaction needs a catalyst to overcome the energy barrier between reactants and products
• Transition State: Reactive condition of the substrate after there has been sufficient input of energy (activation energy, E )
to initiate the reaction.
• Ea is energy needed to change the reactants into unstable molecular forms called transitionstate intermediates.
• Transitionstate intermediates have higher free energies than reactants and products.
• Ea comes from kinetic energy of molecules.
• Enzymes and ribozymes lower energy barrier by bringing reactants closer together.
• Catalysts increase rates of chemical reactions. Nonbiological ones are nonspecific and biological ones are highly specific
• Enzymes and ribozymes recognize and bind to only one or a few closely related reactants and catalyzes only a single
• Substrates: Reactants of an enzymecatalyzed reaction.
Bind to particular site on enzyme (active site) where catalysis takes place call an EnzymeSubstrate Complex (ES)
Specificity of enzyme results in exact 3D shape and structure of its active site
• Enzyme Names: Function + “ase”
• EnzymeSubstrate Complex (ES) is held together by Hbond, electron attraction, temp. covalent bonding
• E + S > ES > E + P (product) • Lower K Dalue means tighter bonding, favors formation of ES.
• When reactants are bound to enzyme, forming enzymesubstrat