Unit 4 & 5

Describe general acid-base catalysis. What is the general purpose of acid/base catalysis ? Identify the amino acid side chains that can function as acid-base catalysts (draw the proton donor and proton acceptor form of each)

General acid-base catalysis: proton transfers mediated by weak acids and bases other than water -Many biochemical reactions occur through the formation of unstable charged intermediates that tend to break down rapidly to their constituent reactant species, impeding the forward reaction -Charged intermediates can often be stabilized by the transfer of protons to form a species that breaks down more readily to products -GABC is crucial in active site of an enzyme, where water may not be available as proton donor/acceptor -Several amino acid side chains take on the role of proton donor/acceptor: Glu, Asp; Lys, Arg; Cys; His; Ser; Tyr -donor when protonated -acceptor when deprotonated

C -Positive values indicate hydrophobic regions; negative values indicate hydrophilic regions -Typically, membrane‑spanning regions have values above 1.6.

Identify which segment or segments of the polypeptide characterized in the hydropathy plot below could belong to a transmembrane region of a protein. How can you tell?

FLIP FLIP FLIP -green: peripheral -yellow: integral -blue: lipid‑linked -pink: integral -orange: peripheral

Label each of the proteins as one of the following: -peripheral membrane protein -integral membrane protein -lipid‑linked (anchored) protein-

Describe the evolution of protein families

-A gene in a hypothetical organism might occasionally, by accident, be copied twice during DNA replication, such that the organism has two full copies of the gene, one of which is superfluous -Over many generations, as the DNA with two genes is repeatedly duplicated, rare mistakes occur, leading to changes in the nucleotide sequence of the superfluous gene and thus of the protein that it encodes -In a few very rare cases, the altered protein produced from this mutant gene has acquired a new capability, which may allow the cell to survive in an ecological niche -Sometimes, duplicate gene is mutated such that it becomes inactive, becoming a pseudogene -If no gene duplication precedes mutation, the original function of the gene product is lost

Distinguish between a "flippase", a "floppase", and a "scramblase"

-All 3 facilitate transbilayer movement (translocation) of individual lipid molecules -flippase: catalyze translocation of the aminophospholipids from the extracellular to the ctyoplasmic leaflet of plasma membrane, contributing to the asymmetric distribution of phospholipids -consume about one ATP per molecule translocated -floppase: move plasma membrane phospholipids and sterols from the cytoplasmic to the extracellular leaflet ATP-dependent (like flippase) -scramblase: move any membrane phospholipid across the bilayer down its concentration gradient -Not ATP-dependent; some require Ca2+ -leads to controlled randomization of the head-group composition on the two faces of the bilayer

The structures of many integral membrane proteins have been determined. Make some generalizations about these structures in terms of α-helices and β-sheets

-Alpha helices traverse the bilayer roughly perpendicular to the plane of the membrane (hydrophobic) -Planar beta sheets are not on the membrane -Beta barrels are present - transmembrane segments form beta sheets that line a cylinder -Tyr, Trp residues at interface between lipid and water -Serve as membrane interface anchors -Positive-inside rule: positively charged Lys and Arg residues in the extramembrane loop of membrane proteins occur more commonly on the cytoplasmic face of plasma membranes

Discuss the effect of a positive or negative microenvironment on the pK of the following amino acid side chains: -aspartic acid -histidine

-Aspartic acid -Positive microenvironment: positive charges around --> favor deprotonated (negative form) --> decrease pK -Negative microenvironment: negative charges around --> favor protonated (neutral form) --> increase pK -Histidine -Positive microenvironment: positive charges around --> favor deprotonated (neutral form) --> decrease pK -Negative microenvironment: favor protonated (positive form)--> increase pK -favor a favorable rxn -avoid a disfavorable rxn

Discuss the importance of binding energy, ΔGB, in enzyme catalyzed reactions

-Binding energy: the energy derived from noncovalent enzyme-substrate interaction -Stickase example: The increase in free energy required to draw the stick into a bent and partially broken conformation is offset by the weak interactions that form between the enzyme and substrate in the transition state -Formation of each weak interaction in the ES complex is accompanied by release of a small amount of free energy that stabilizes the interaction -Summation of unfavorable positive activation energy and favorable negative binding energy results in a lower net activation energy -Binding energy gives an enzyme its specificity; if an active site has functional groups arranged optimally to form a variety of weak interactions with a particular substrate in the transition state, the enzyme will not be able to interact to the same degree with any other molecule

Discuss how the two components of the electrochemical potential affect the movement of a permeant ion across the membrane

-Chemical gradient: difference in solute concentration -Net movement of electrically neutral solute is toward side of lower solute [ ] until equilibrium reached -Electrical gradient (Vm): difference in electrical potential across the membrane -Net movement until gradient is neutralized (Vm = 0) -Net movement of an electrically charged solute is dictated by a combination of the electrical potential (Vm) and the ratio of chemical concentrations (C2/C1) across the membrane -Net ion movement continues until electrochemical potential reaches zero

Describe covalent catalysis. What is the purpose of covalent catalysis?

-Covalent catalysis: a transient covalent bond is formed between the enzyme and substrate -In the presence of a covalent catalyst (an enzyme with nucleophilic group X:) the hydrolysis of A and B becomes: A--B + X: --> A--X + B --> A + X: + B -Formation and breakdown of a covalent intermediate creates a new pathway for the rxn, but catalysis results only when the new pathway has a lower activation energy than the uncatalyzed pathway -Both of the new steps must be faster than the uncatalyzed reaction -several amino acid side chains and the functional groups of some enzyme cofactors can serve as nucleophiles

Discuss how detergents "solubilize" membranes and membrane proteins

-Detergents disrupt hydrophobic interactions with the lipid bilayer and form micelle-like clusters around individual protein molecules

Discuss the kinetic properties of allosteric enzymes.

-Differ from Michaelis-Menten kinetics -Do exhibit saturation with the substrate when [S] is sufficiently high, but for allosteric enzymes, plots of V0 vs. [S] usually produce a sigmoid saturation curve, rather than the hyperbolic curve typical of nonregulatory enzymes -On the sigmoid saturation curve, we can find a value of [S] at which V0 is half-maximal but we cannot refer to it with the designation Km because the enzyme does not follow the hyperbolic M-M relationship -Instead the symbol [S]0.5 or K0.5 is often used to represent the substrate concentration giving half-maximal velocity of the reaction catalyzed by an allosteric enzyme

List two reasons why enzyme activity is affected by pH

-Enzymes have an optimum pH or pH range at which their activity is maximal 1) Amino acid side chains in the active site may act as weak acids and bases only if they maintain a certain state of ionization 2) Less common: titration of a group on the substrate - pH range over which an enzyme undergoes changes in activity can provide a clue to the type of residue involved

What kind of linkage joins the fatty acids to the glycerol part of the molecule? What kind of linkage joins the phosphate to the glycerol part of the molecule?

-Ester -Ether

FLIP FLIP FLIP 1. X and Zβ2; Yα and Yβ; Yα and Zβ1; Zβ1 and Zβ2 2. Yα and Zα; X and Zβ2; Yα and Zβ1; X and Yα 3. Yα and Yβ; Zβ1 and Zβ2; Zα and Zβ2

-Given this diagram 1. Name 4 pairs of homologs 2. Name 4 pairs of orthologs 3. Name 3 pairs of paralogs

Discuss the regulation of glycogen phosphorylase by covalent modification

-Glycogen phosphorylase catalyzes the following reaction: (Glucose)n + Pi --> (glucose)n-1 + glucose 1-phosphate -glycogen phosphorylase is not a kinase because it does not utilize ATP as a phosphoryl donor -Two forms: more active phosphorylase a and less active phosphorylase b -Phosphorylase a has 2 subunits, each with a specific Ser residue that is phosphorylated at its hydroxyl group -Phosphorylase b is covalently transformed into active phosphorylase a by phosphorylase kinase, which catalyzes the transfer of phosphoryl groups from ATP to the hydroxyl groups of the two specific Ser residues in phosphorylase b -Phosphoryl groups are added and removed by different enzymes, and the processes can therefore be separately regulated -Phosphoryl groups of phosphorylase a are hydrolytically removed by phosphoprotein phosphatase 1 (PP1)

Describe the structure of ATCase. How does ATCase differ from hemoglobin with respect to the types of subunits?

-Has 2 stacked catalytic clusters, each with 3 catalytic polypeptide chains, and 3 regulatory clusters, each with 2 regulatory polypeptide chains -Regulatory clusters form the points of a triangle surrounding the catalytic subunits -Binding sites for allosteric modulators are on the regulatory subunits -Hb only has one type of subunit

Distinguish between integral, peripheral, and amphitropic membrane proteins.

-Integral: proteins firmly bound to a membrane by interactions resulting from the hydrophobic effect -Firmly embedded within the lipid bilayer and are removable only by agents that overcome hydrophobic interactions -Peripheral: proteins loosely bound to a membrane by hydrogen bonds or electrostatic forces; generally water-soluble once released from the membrane -Can be released from their membrane association by relatively mild treatments that interfere with electrostatic interactions or that break hydrogen bonds -Amphitropic: proteins that associate reversibly with the membrane and thus can be found in the cytosol, in the membrane, or in both places -Affinity results in some cases from the protein's noncovalent interaction with another membrane protein or lipid; other cases from the presence of one or more covalently attached lipids

Name and describe the experiment typically used to measure the rate of lateral diffusion of lipids and proteins in membranes.

-Lateral diffusion can be shown experimentally by attaching fluorescent probes to the head groups of lipids and using fluorescence microscopy to follow the probes over time -A small region of a cell surface with fluorescence-tagged lipids is bleached by intense laser radiation so that the irradiated patch no longer fluoresces when viewed with nonbleaching light in fluorescence microscope -Within milliseconds, the region recovers its fluorescence as unbleached lipid molecules diffuse into the bleached patch and bleached lipid molecules diffuse away from it -FRAP: rate of fluorescence recovery after photobleaching - measure of the rate of lateral diffusion of the lipids

Many enzymes require metal ions for activity. Describe two functions of these metal ions.

-Metals can participate in catalysis 1) Ionic interactions between an enzyme-bound metal and a substrate can help orient the substrate for reaction or stabilize charged reaction transition states -Can contribute to enzyme-transition state complementarity 2) Metals can also mediate oxidation-reduction reactions by reversible changes in the metal ion's oxidation state

Discuss the structures of bilayers, vesicles (liposomes), and micelles. What is the major driving force for formation of these structures?

-Micelles: hydrophobic chains of fatty acids are sequestered at the core of the sphere -Virtually no water in hydrophobic interior -individual units are wedge shaped (cross-section of head greater than that of side chain) -Bilayer: in an open bilayer, all acyl side chains except those at the edges of the sheet are protected from interaction with water -Individual units are cylindrical (cross section of head equals that of side chain) -Vesicle: when a 2D bilayer folds on itself, it forms a closed bilayer, a 3D hollow vesicle enclosing an aqueous cavity ---------------------- -when amphipathic lipids are mixed with water -hydrophobic effect: reduces amount of hydrophobic surface exposed to water

Given the total number of carbons, draw the structure of a straight-chain fatty acid

-Nomenclature: 16-carbon saturated = 16:0 -18-carbon with one double bond = 18:1 -positions of any double bonds, designated delta, are specified relative to C1 (carboxyl carbon) by a superscript number indicating lower-numbered C in the double bond -Ex: oleic acid with double bond between C-9 and C-10

Discuss the "RNA world" scenario

-One of the earliest stages of biological evolution was the chance formation of an RNA molecule that could catalyze the formation of other RNA molecules of the same sequence - a self-replicating, self-perpetuating RNA 1. Prebiotic formation of simple compounds, including nucleotides, from components of Earth's primitive atmosphere or gases in undersea volcanic vents --> 2. Production of short RNA molecules with random sequences --> 3. Selective replication of self-duplicating catalytic RNA segments --> 4. Synthesis of specific peptides, catalyzed by RNA --> 5. Increasing role of peptides in RNA replication; coevolution of RNA and protein --> 6.Primitive translation system develops, with RNA genome and RNA-protein catalysts --> 7. Genomic RNA begins to be copied into DNA --> 8. DNA genome, translated on RNA-protein complex (ribosome) with RNA and protein catalysts

List several types of covalent modification

-Phosphorylation -Adenylylation -Acetylation -Myristoylation -Ubiquitination -ADP-ribosylation -Methylation

Discuss the three major classes of regulatory enzymes in metabolic pathways clearly distinguishing between each class

-Regulatory enzymes: an enzyme with regulatory function, through its capacity to undergo a change in catalytic activity 1. Allosteric enzymes: function through reversible, noncovalent binding of a specific metabolite at a site other than the active site -Tends to be multisubunit proteins, and in some cases the regulatory site(s) and the active site are on separate subunits 2. Covalent Modification: reversible -Tends to be multisubunit proteins, and in some cases the regulatory site(s) and the active site are on separate subunits 3. Regulation by Proteolytic Cleavage: peptide segments are removed -unlike effector-mediated regulation, this is irreversible -several types of regulation may occur in a single regulatory enzyme

Describe the 2° and 3° structure of chymotrypsin. Name the three residues in the "catalytic triad" and discuss their position in the 1° and 3° structure

-Secondary: consists of 3 polypeptide chains linked by disulfide bonds -Tertiary: Active-site amino acid residues are grouped together in the 3D structure -Hydrophobic pocket where aromatic amino acid side chain of substrate is bound

Name the three amino acid side chains on which both protein kinases and phosphatases types act. What functional group do these three side chains have in common?

-Serine -Threonine -Tyrosine -all have an OH group

In a cell, what is the key advantage of any enzyme with sigmoid versus hyperbolic kinetics? -Review the meaning of homotropic and heterotropic allosteric control

-Sigmoid kinetic behavior reflects cooperative interactions between multiple protein subunits -Changes in the structure of one subunit are translated into structural changes in adjacent subunits, an effect mediated by noncovalent interactions at the interface between subunits -Cooperative interactions are beneficial in general because further substrates can bind more easily -Homotropic: when substrate and modulator are identical -Heterotropic: when modulator is a molecule other than the substrate

Explain why some regulatory enzymes use several regulatory mechanisms

-The control of catalysis is critical to life -if all possible reactions in a cell were catalyzed simultaneously, macromolecules and metabolites would quickly be broken down to much simpler chemical forms -Instead, cells catalyze only the reactions they need at a given moment -When chemical resources are plentiful, cells synthesize and store glucose and other metabolites -When chemical resources are scarce, cells use these stores to fuel cellular metabolism -Chemical energy is used economically, parceled out to various metabolic pathways as cellular needs dictate -The availability of powerful catalysts, each specific for a given reaction, makes the regulation of these reactions possible

Walk through the steps of the mechanism of action of chymotrypsin. Draw each step. -What interactions stabilize the oxyanion intermediates? -What is the name of the region where these interactions occur?

-The oxyanion intermediates are stabilized by hydrogen bonds -Region: oxyanion hole

When the primary sequence but not the structure of a membrane protein is known, how can a model of the structure be made?

-The relative polarity of each amino acid can be determined by measuring the free-energy change accompanying movement of that AA side chain from a hydrophobic environment into water --> hydropathy index -To scan a polypeptide sequence for potential membrane-spanning segments, you can calculate the hydropathy index for successive segments (windows) of a given size -Plot average hydropathy index vs. residue number --> a region with more than 20 residues of high hydropathy index is presumed to be a transmembrane segment

In the mechanism of action of chymotrypsin, what is the role of each of the residues in the "catalytic triad" in the overall mechanism?

-When a peptide substrate binds to chymotrypsin, a subtle change in conformation compresses the hydrogen bond between His57 and Asp102, resulting in a stronger interaction, called a low-barrier hydrogen bond -this enhanced interaction increases the pKa of His57, allowing the His residue to act as an enhanced general base that can remove the proton from the Ser195 hydroxyl group -Deprotonation prevents development of a highly unstable positive charge on the Ser195 hydroxyl and makes the Ser side chain a stronger nucleophile -At later reaction stages, His57 also acts as a proton donor, protonating the amino group in the displaced portion of the substrate (the leaving group)

Explain how chymotrypsinogen is activated? How are proteolytically activated enzymes inactivated?

-Zymogen: an inactive precursor of an enzyme -Chymotrypsin is initially synthesized as chymotrypsinogen -Specific cleavage causes conformational changes that expose the enzyme active site -Chymotrypsinogen (inactive) --trypsin--> pi-chymotrypsin (active) --autolysis--> alpha-chymotrypsin (active) -------------------- -This type of activation is irreversible, and additional regulation requires a different mechanism -A previously activated protease is inactivated by inhibitor proteins that bind very tightly to the enzyme active site

Give a general description of the structure of cholesterol

-amphipathic: polar head group (hydroxyl group)and a nonpolar hydrocarbon body -about as long as a 16-C fatty in its extended form -Steroid nucleus, consisting of 4 fused rings: three with 6 carbons and one with 5 -Almost planar; relatively rigid - fused rings do no not allow rotation

Name the three residues in the "catalytic triad" and discuss their position in the 1° and 3° structure

-catalytic triad: a hydrogen-bonding network -Ser195 is linked to His57 and Asp102 -Per residue numbers, they are not that close to each other in primary structure -But, they are brought closer together in 3D structure via protein folding -Located on the inside of the enzyme

Is cholesterol present in eukaryotic or prokaryotic membranes? Identify the eukaryotic membrane in which cholesterol is most prominent.

-eukaryotes -plasma membrane

Define the following terms: -genome -homolog -paralog -ortholog -alignment -pseudogene

-genome: the complete set of genes, composed of DNA -homolog: when 2 genes share readily detectable sequence similarities, the proteins they encode are homologs; the members of protein families are called homologs -paralog: if 2 proteins in a family (2 homologs) are present in the same species, they are referred to as paralogs -ortholog: Homologs from different species are called orthologs -alignment: In bioinformatics, a way of arranging the sequences of DNA, RNA, protein to identify regions of similarity that may be a consequence of functional, structural or evolutionary relationships between the sequences -pseudogene: A mutation in a gene that makes in inactive

Compare allosteric enzymes to others in terms of structure

-in addition to active sites, allosteric enzymes often have one or more regulatory/allosteric sites for binding to each heterotropic modulator -Just as active site is specific for substrate, each regulatory site is specific for its modulator -enzymes with several modulators generally have different specific binding sites for each -Tends to be multisubunit proteins, and in some cases the regulatory site(s) and the active site are on separate subunits

What is the effect of unsaturated fatty acids on the fluidity of a membrane? What is the relationship between fatty acid length and fluidity?

-kinks in unsaturated fatty acids (due to double bond) interfere with tight packing, so interactions are weaker -favor Ld state -make more fluid ----------------------- -long chain: liquid ordered --> less fluid -shorter chain: liquid disordered --> more fluid

Distinguish between the liquid-disordered and the liquid-ordered states

-liquid-ordered state (Lo): gel-like; all types of motion of individual lipid molecules are strongly constrained -below normal physiological temperatures -liquid disordered state (Ld): individual hydrocarbon chains of fatty acids are in constant motion produced by rotation about the C-C bonds of the long acyl side chains and by lateral diffusion of individual lipid molecules in the plane of the bilayer -above physiological temperatures

Detergents, including soaps (i.e. ionized fatty acids), form micelles and phospholipids form bilayers. Discuss the difference in structure that could account for the formation of micelles vs bilayers?

-micelle formation is favored when the cross-sectional area of the head group is greater than that of the acyl side chain(s) -bilayer formation is favored if the cross-sectional areas of the head group and acyl side chain(s) are similar

The asymmetric distribution of lipids between the two sides of the bilayer is presumably created by flippases of different specificity. What is the significance of this?

-phosphatidylethanolamine and phosphatidylserine primarily in the cytoplasmic leaflet -sphingolipids and phosphatidylcholine in the outer leaflet -keeping phosphatidylserine out of the EC leaflet is important: its exposure on the outer surface triggers apoptosis and engulfment by macrophages

Name the class of enzymes that attaches phosphoryl groups to specific amino acids. Write a balanced chemical equation for the reaction catalyzed by this class of enzyme.

-protein kinases: attach phosphoryl groups to specific amino acid residues of a protein 2ATP + phosphorylase b --> 2ADP + phosphorylase a

Discuss the evolution of eukaryotic cells

-the earliest eukaryote, an anaerobe, acquired endosymbiotic purple bacteria, which carried with them their capacity for aerobic catabolism and became, over time, mitochondria -when photosynthetic cyanobacteria subsequently became endosymbionts of some aerobic eukaryotes, these cells became the photosynthetic precursors of modern green algae and plants

Which of the following are true characteristics of allosteric enzymes? 1. They tend to have a sigmoidal (S‑shaped) curve of V0 vs. [S]. 2. They may have binding sites for regulatory molecules that are separate from active sites. 3. They conform to Michaelis-Menten kinetics. 4. They are generally small single subunit proteins. 5. They interconvert between a more active form and a less active form.

1 2 5

Arrange the fatty acids from highest melting point to lowest melting point. 1. CH3(CH2)16COOH 2. CH3(CH2)5CH=CH(CH2)7COOH 3. CH3CH2(CH=CHCH2)3(CH2)6COOH 4. CH3(CH2)10COOH Select the statements about fatty acid melting points that are true. 1. A saturated fatty acid with a greater molar mass has a higher melting point than a saturated fatty acid with a lower molar mass. 2. A saturated fatty acid with a greater molar mass has a lower melting point than a saturated fatty acid with a lower molar mass. 3. A saturated fatty acid has a higher melting point than an unsaturated fatty acid. 4.A saturated fatty acid has a lower melting point than an unsaturated fatty acid.

1 4 2 3 ------- 1 3

Place the sentences in order according to how life on Earth may have arisen from terrestrial origins. Only four sentences will be used. 1. Simple inorganic compounds were exposed to energy in the form of light, heat, and lightning. 2. Organic molecules self‑assembled into more complex molecules and polymers. 3. Larger organic molecules became enclosed within a membrane‑like structure. 4. Meteorites that impacted Earth ~4 billion years ago contained traces of 18 amino acids. 5. Simple organic molecules, such as amino acids, formed from precursors exposed to energy.

1 5 2 3

For each of the following, point out whether the interacting groups must be precisely aligned to get significant binding and whether the distance between interacting groups is critical for binding 1. Electrostatic interactions 2. Hydrogen bonds 3. van der Waals forces 4. Hydrophobic interactions -What is a general rule to remember this?

1. Electrostatic: Distance important -Force of ionic interactions depends on distance between the charged groups (only over short distances) 2. Hydrogen: Precise alignment and distance both important -strongest when the hydrogen atom and the 2 atoms that share it are in a straight line -if too far apart, can't sense each other 3. VDW: distance important -the 2 dipoles weakly attract each other, bringing their nuclei closer 4. Hydrophobic: distance important -nonpolar regions cluster together to present smallest hydrophobic area to aqueous solvent -Rule: distance important for all; alignment only for H-bonding

Sort each of the following into a)Membrane‑spanning α helix b)Membrane‑spanning β strands c)Lipid‑anchored membrane protein or d)Peripheral membrane protein: 1. can usually be released from membrane by concentrated salt solutions 2. often contain a residue with covalently attached glycosyl phosphatidylinositol 3. membrane attachment depends upon electrostatic interactions with membrane phospholipid head groups 4. amino acid sequence pattern: nonpolar R group, polar R group (repeats) 5. composed of about 20 hydrophobic residues

1. Peripheral membrane protein 2. Lipid‑anchored membrane protein 3. Peripheral membrane protein 4. Membrane‑spanning β strands 5. Membrane‑spanning α helix

Differentiate between the different types of transport

1. Simple diffusion: nonpolar compounds only; down [ ] gradient 2. Facilitated diffusion: down electrochemical gradient -Uniport: transport that carries only one solute 3. Primary active transport: against electrochemical gradient; driven by ATP -Energy released by ATP hydrolysis drives solute movement against an electrochemical gradient 4. Secondary active transport: against electrochemical gradient; driven by ion moving down its gradient -Symport: cotransport of solutes across a membrane in the same direction -Antiport: cotransport of two solutes across a membrane in opposite directions -A gradient of an ion has been established by primary active transport; movement of ion down its electrochemical gradient now provides the energy to drive contransport of a second solute against its electrochemical gradient 5. Ion channel: down electrochemical gradient; may be gated by a ligand or ion 6. Ionophore-mediated ion transport: down electrochemical gradient

What is the purpose of the "hydrophobic pocket" in the mechanism of action of chymotrypsin?

1. When substrate binds, the side chain of the residue adjacent to the peptide bond to be cleaved nestles in a hydrophobic pocket on the enzyme, positioning the peptide bond for attack -Side chain will be FYW (large, bulky, aromatic)

Categorize each of the following as a) acid-base catalysis b) covalent catalysis c) metal ion catalyis or d) all 1. a covalent bond forms between enzyme and substrate 2. catalysts may participate in oxidation‑reduction reactions by changes in the oxidation state 3. lowers the energy or stabilizes the transition state or intermediate 4. may take part in interactions involving Fe2+ 5. uses a nucleophilic functional group 6. a proton is transferred between enzyme and substrate 7. may use amino acids such as aspartate or lysine for protonation or proton abstraction 8. two part catalytic process (for example, the chymotrypsin mechanism) 9. catalyst retains its original form after reaction occurs 10. a Zn2+ cofactor may properly orient the substrate in the active site through ionic interactions

1. covalent 2. metal ion 3. all 4. metal ion 5. covalent 6. acid-base 7. acid-base 8. covalent 9. all 10. metal ion

Classify each of the following as describing a) kinase b) phosphatase c) neither or d) both: 1. catalyze phosphorylation reactions 2. PKA (protein kinase A) is an example 3. remove phosphoryl groups from proteins 4. in eukaryotes, transfer phosphoryl groups to acidic amino acids 5. turn off signaling pathways triggered by kinases 6. catalyze reactions that are the reverse of dephosphorylation reactions 7. regulate the activity of other proteins 8. may use ATP as a phosphoryl group donor

1. kinase 2. kinase 3. phosphatase 4. neither 5. phosphatase 6. neither 7. both 8. kinase

Which of the choices best describes a biological membrane? 1. a bilayer containing lipids with hydrophilic head groups pointing inward and hydrophobic tail groups oriented toward the solvent (extracellular fluid and cytosol) 2. a bilayer containing lipids with hydrophobic head groups oriented toward the solvent (extracellular fluid and cytosol) and hydrophilic tail groups pointing inward 3. a bilayer containing lipids with hydrophilic head groups oriented toward the solvent (extracellular fluid and cytosol) and hydrophobic tail groups pointing inward Which of the choices are components of biological membranes? 1. proteins 2. nucleic acids 3. lipids

3 ----- 1 3

FLIP FLIP FLIP top right

The small section of lipid bilayer (very top left) is shown consisting of membrane lipids and integral (intrinsic) proteins represented by red and yellow shapes. According to the fluid mosaic model, which of the bottom four images is most likely after several hours have passed?

-How does a negative effector affect the sigmoidal velocity curve of an allosteric enzyme? Draw the curves of the modified and unmodified enzyme -Assume that this is a positively cooperative enzyme. What would happen to [T]/[R] if substrate concentration is decreased?

[T]/[R] would increase

Name the class of enzymes that removes phosphoryl groups. Write a balanced chemical equation for the reaction catalyzed by this class of enzyme.

protein phosphatases: remove phosphoryl groups from these same target proteins phosphorylase a + 2H20 --> phosphorylase b + 2Pi

What have liposomes been used to study?

receptors, lipid permeability, and lipid interactions