• The topology of a membrane protein is a specification of the number of transmembrane segments and their orientation across the membrane
• A hydropathy plot uses the hydrophobicity assigned to each amino acid to examine each amino acid in a protein as a function of hydrophobicity

1. The transitions are always endothermic; heat is absorbed as the temperature increases through the transition
2. Particular phospholipids display characteristic transition temperatures (Tm). Tm increases with chain length, decreases with unsaturation, and depends on the nature of the polar head group
3. For pure phospholipid bilayers, the transition occurs over a narrow temperature range
4. A volume change is usually associated with phase transitions in lipid bilayers

• Simple diffusion 
• Facilitated Diffusion
• Primary Active Transport
• Ionophore medicated ion transport
• Ion Channel/Ligand Channel
• Secondary Active Transport 

• Nonpolar compounds only
• down concentration gradient 
• slow

• Down electrochemical gradient 
• Facilitated diffusion rates display saturation behavior

• down electrochemical gradient 
• Ionophores are organic molecules that increase the permeability of membranes to ions

• Since ionophores passively permit ions to diffuse across a membrane in either direction, their effect can only be to equilibrate the concentrations of their selected ions across the membrane

• There are two types of ionophores:

1. Carrier ionophores increase the permeability of membranes to their selected ion by binding it, diffusing through the membrane, and releasing the ion on the other side
2. Channel-forming ionophores form transmembrane channels or pores through which their selected ions can diffuse

Ion Channels are gated

gating is controlled by what four channels?

• Mechanosensitive channels
• Ligand-gated channels
• Signal-gated channels
• Voltage-gated channels 

1. Mechanosensitive channels 

1. open in response to local deformations in the lipid bilayer. Consequently, they respond to direct physical stimuli such as touch, sound, and changes in osmotic pressure

1. Ligand-gated channels 

1. open in response to an extracellular chemical stimulus such as a neurotransmitter

1. Signal-gated channels 

1. open on intracellularly binding a Ca²⁺ ion or some other signaling molecule

1. Voltage-gated channels 

• Down electrochemical gradient
• may be gated by a ligand or ion

• against electrochemical gradient 
• driven by ATP
• solute accumulation is directly coupled to an exergonic chemical reaction such as conversion of ATP to ADP + P_i

• Secondary active transport: (2)

• Against chemical gradient
• driven by ion moving down chemical gradient
• Occurs when endergonic (uphill) transport of one solute is coupled to the exergonic (downhill) flow of a different solute that was originally pumped uphill by primary active transport

• Pumps that utilize ATP
• They hydrolyze ATP to create conformational changes in the in structure that stimulates movement of the ion or molecule 

1. P-type ATPases

1.  undergo phosphorylation as they transport cations such as Na⁺, K⁺, and Ca²⁺ across the membrane

1. F-type ATPases 

1. ABC transporters 

• Specificity
• Amplification
• Modularity
• Sensitivity
• Integration
• Localized Response

General Features of Signal Transduction:

Specificity

General Features of Signal Transduction

Amplification 

General Features of Signal Transduction

Modularity

General Features of Signal Transduction

Sensitivity

General Features of Signal Transduction

Integration 

General Features of Signal Transduction

Localized Response 

• G protein coupled receptor
• Receptor enzyme (tyrosine kinase)
• Gated ion channel

• Three essential components define signal transduction through GPCRs:
• 
  
  

• A plasma membrane receptor with seven transmembrane helical segments
• A G protein that cycles between active (GTP-bound) and inactive (GDP-bound) forms
• An effector enzyme (or ion channel) in the plasma membrane that is regulated by the activated G protein

The GTPase Switch

4 basic steps

The GTPase Switch in Context

Epinephrine pathway 7 steps

1. The β-adrenergic response will end when the concentration of epinephrine in the blood drops below the K_d for its receptor (hormone then dissociates from the receptor and the receptor assumes its inactive conformation)
2. A second means of ending the β-adrenergic response is the hydrolysis of GTP bound to the G_α subunit (catalyzed by the intrinsic GTPase activity of the G protein)

• The rate of G_S inactivation depends on the GTPase activity, which is very low for isolated G_α
• GTPase activator proteins (GAPs) strongly stimulate G_α GTPase activity, thereby causing rapid inactivation of the G protein

3. A third mechanism to end the β-adrenergic response is to remove the second messenger

• cAMP is hydrolyzed to 5’-AMP (not an active second messenger) by cyclic nucleotide phosphodiesterase

• An extracellular signal such as epinephrine can have different effects on different tissues or cell types, depending on three factors

• The type of receptor in the tissue
• The type of G protein with which the receptor is coupled (G_S or G_I)
• The set of PKA enzymes in the cell

• Receptor Tyrosine Kinases (RTKs) are 

Insulin Signaling Cascade

(7 steps)

• The proteins Raf-1, MEK, and ERK are members of three larger families

1. ERK is in the MAPK family: (2)

• Mitogen-Activated Protein Kinases (MAPK)
• Phosphorylate specific Ser or Thr residues

The proteins Raf-1, MEK, and ERK are members of three larger families

2. MEK belongs to a family of kinases that activate MAPK enzymes :(2)

• MAPK Kinases (MAPKK)
• Phosphorylate both a Ser or Tyr residue

3. The proteins Raf-1, MEK, and ERK are members of three larger families
4. Raf-1 belongs to the family of kinases that activate MAPKK enzymes: (2)

• MAPKK Kinases (MAPKKK)
• Phosphorylate specific Ser or Thr residues

The Membrane Phospholipid PIP3 Functions at a Brand in Insulin Signaling

5 steps

Multivalent Adaptor Proteins and Membrane Rafts

• Two generalizations regarding signaling systems:

• Protein kinases that phosphorylate, and phosphatases that dephosphorylate, Tyr, Ser, and Thr residues are central to signaling by directly affecting the activities of a large number of protein substrates by phosphorylation/dephosphorylation

1. Protein-protein interactions brought about by the reversible phosphorylation of Tyr, Ser, and Thr residues in signaling proteins create docking sites for other proteins that bring about indirect effects on proteins downstream in the signaling pathway

• Many signaling proteins are multivalent: they can interact with several different proteins simultaneously to form multi-protein signaling complexes

Protein Modules Bind which Phosphorylated 3

Residues in Partner Residues

• Thermodynamics: 

Chemical Logic and Biochemical Reactions

• Most of the reactions in living cells fall into one of five general categories:

1. Reactions that make or break carbon-carbon bonds
2. Internal rearrangements, isomerizations, and eliminations
3. Free-radical reactions
4. Group Transfers
5. Oxidation-Reduction Reactions

• A covalent bond consists of a shared pair of electrons, and the bond can be broken in two general ways

• In homolytic cleavage, each atom leaves the bond as a radical, carrying one unpaired electron
• In heterolytic cleavage (more common), one atom retains both bonding electrons
• Carbanions, carbocations, and hydride ions are highly unstable, which contributes to the chemistry of these ions

• The three major classes of reactions involving C-C bond making or breaking are: 

aldol condensations,

Claisen ester condensations,

and decarboxylations

• A common type of cellular reaction is an intramolecular rearrangement in which (2)

• redistribution of electrons results in alterations of many different types without a change in the overall oxidation state of the molecule
• The conversion of glucose 6-phosphate to fructose 6-phosphate

• The hemolytic cleavage of covalent bonds to generate free radicals
• found in a wide range of biochemical processes

• The transfer of acyl, glycosyl, and phosphoryl groups from one nucleophile to another is common in living cells
• Acyl group transfer generally involves the addition of a nucleophile to the carbonyl carbon of an acyl group to form a tetrahedral intermediate
• Could proceed by an S_N1 or S_N2 pathway

• In many metabolic reactions, a phosphoryl group is transferred from ATP to an alcohol, forming a phosphate ester (or to a carboxylic acid to form a mixed anhydride)
• When a nucleophile attacks the electrophilic phosphorous atom in ATP, a relatively stable pentacovalent structure forms as a reaction intermediate

• In many biological oxidations, a compound loses two electrons and two hydrogen ions; these reactions are commonly called dehydrogenations and the enzymes that catalyze them are called dehydrogenases
• In some cases, a carbon atom becomes covalently-bonded to an oxygen atom. The enzymes that catalyze these reactions are generally called oxidases (oxygenases if the oxygen atom is derived from molecular oxygen, O₂)

• The hydrolytic cleavage of the terminal phosphoric acid anhydride (phosphoanhydride) bond in ATP separates one of the three negatively charged phosphates and thus relieves some of the internal electrostatic repulsion in ATP
• The P_i released is stabilized by the formation of several resonance forms not possible in ATP

• Thioesters, in which a sulfur atom replaces the usual oxygen in the ester bond, also have large, negative, standard free-energies of hydrolysis.
• why? (3)

• Thioesters undergo much less resonance stabilization than do oxygen esters
• The difference in energy between the reactant and its hydrolysis products, which are resonance-stabilized, is greater for thioesters than for comparable oxygen esters
• Orbital overlap between S and C atoms is poorer and provides little resonance stabilization

Summarizing Hydrolysis Reactions. 

• For hydrolysis reactions with large, negative, standard free-energy changes, the products are more stable than the reactants for one or more of the following reasons: (4)

1. The bond strain in reactants due to electrostatic repulsion is relieved by charge separation, as for ATP
2. The products are stabilized by ionization, as for ATP, acyl phosphates, and thioesters
3. The products are stabilized by isomerization (tautomerization), as for PEP
4. The products are stabilized by resonance, as for creatine released from phosphocreatine

• Realistic view of ATP hydrolysis: (3)

• ATP hydrolysis usually accomplishes nothing but the liberation of heat (cannot drive a chemical process in an isothermal system)
• A single reaction arrow almost invariably represents a two-step process in which part of the ATP molecules, a phosphoryl or pyrophosphoryl group, is first transferred to a substrate molecules or to an amino acid residue in an enzyme (becoming covalently attached and raising the free-energy content)
• In a second step, the phosphate-containing moiety is displaced

• The phosphate compounds found in living organisms can be divided into two groups based on their standard free energies
• 
  
  

• “High-energy” compounds have a ΔG’° of hydrolysis more negative than -25 kJ/mol
• “Low-energy” compounds have a ΔG’° of hydrolysis that is less negative