2013 Final

List two ligand-gated channels we have discussed in class. Specify the names of the channels, ligands and molecules being transported.

1. Acetylcholine Receptor Coupled Channels: Ligands- Acetylcholine Molecules- Na+ and K+ 2. IP3 Receptor Ligands- IP3 Molecules- Ca2+

Receptor tyrosine kinases (RTK)s are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Receptor tyrosine kinases have been shown not only to be key regulators of normal cellular processes, but also to have a critical role in the development and progression of many types of diseases. The following statements are about receptor tyrosine kinases:

1. Receptor tyrosine kinases will move across cell membranes upon binding of ligands. 2. Receptor tyrosine kinases will undergo conformational changes upon binding of ligands. 3. Receptor tyrosine kinases cannot only phosphorylate themselves (called autophosphorylation) but also phosphorylate other proteins/enzymes based on what we discussed in class. 4. Receptor tyrosine kinases phosphorylate one or more specific tyrosine residues, but not all tyrosine residues of a particular protein.

List five different mechanisms of enzymes/ protein activation in signaling transduction. Provide one example we have discussed in class for each activation mechanism.

1. ligand and receptor binding (insulin and insulin receptor) 2. autophosphorylation (insulin receptor or EGF receptor) 3. protein-protein interaction (Sos and Ras) 4. binding of GTP (G protein and Ras) 5. phosphorylation (MEK) 6. dephosphorylation (glycogen synthase)

Assuming that one enzyme of any proteases can convert 100 substrates to 100 products. Activation of one enteropeptidase can eventually lead to formation of ______ π- chymotrypsin proteins and one chymotrypsin formation from chymotrypsinogen requires breakage of _________ peptide bonds.

10,000 4

Gap junctions are the proteins that provide metabolic connections between two animal cells. Nutrients, such as sugars and amino acids, can be transported from one cell to another cell through gap junctions. Gap junctions can be opened or closed in response to changes in Ca2+ concentration and pH. How many 32 kDa proteins does one gap junction contain? Are Gap junctions able to regulate neurotransmission?

12 yes

(SEE DIAGRAM #47-PG18) What percent of labeled cells are in M phase at 2 hours after exposure to labeled thymidine?

20

(SEE DIAGRAM #45-PG17) A sample of cells with a total receptor concentration of 50 μM was incubated with a ligand concentration of 100 μM. Following the incubation period, the concentration of unbound receptors was determined to be 15 μM. What is the Kd for the receptor-ligand interaction? Kd = [Ligand][Receptor]/[Ligand-Receptor]. To establish the optimal conditions to measure the specific binding of the hormone to its receptor, the experiment was repeated using a constant amount of membrane but varying the concentration of isotope labeled 3H-hormone. Which of the following graphs best depicts the expected results?

28 μM B

Aspartate transcarbamoylase (ATCase) catalyzes the reaction of reactants to carbamoylaspatate. Its activity is allosterically regulated by CTP and ATP. ATCase has ___________ catalytic subunits and ____________ regulatory subunits. Carbamoylaspatate is the first product of nucleotide metabolic pathway and the final product of this pathway is ______________ .

6 12 CTP

If the membrane preparation is incubated prior to the assay with GTP or GTP-γS (a non hydrolyzable analog of GTP), the binding affinity decreases. The decrease of binding affinity means that a higher concentration of hormone is needed to obtain identical amount of specific binding. Which of the following best explains these results? a) A G protein modulates the affinity of the receptor for the hormone b) Hydrolysis of GTP causes decreased affinity of the receptor for the hormone c) A GTP-dependent protease is present in the preparation d) The receptor directly interacts with adenylyl cyclase

A

Phosphorylated forms of phosphatidylinositol are called phosphoinositides and play important roles in cell signaling, lipid signaling and membrane trafficking. The following diagram shows the reactions involved in insulin and Ca2+ signaling pathways. PIP3 <=X/Y=> PIP2 =Z=> DAG or IP3 A. X: lipid phosphatase Y: PI3K Z: phospholipase C B. X: phospholipase C Y: PI3K Z: lipid phosphatase The correct letter for enzymes X, Y and Z is? The enzymatic reactions in the diagram above will regulate _____________ .

A Ca2+ signaling and insulin signaling

(SEE DIAGRAM #44-PG16) Which of the following additional pieces of experimental information would be most useful in elucidating the mechanism of action of glucagon on enzyme X? A. Rate of transcription of the gene for enzyme X B. Rate of covalent incorporation of isotope 32Pi into enzyme X C. Rate of covalent incorporating of isotope 35S methionine into enzyme X D. Translational efficiency of the mRNA for enzyme X E. Binding constant of H-8 for purified enzyme X F. Binding constant of D-2 for purified enzyme X

A and B only

Lactose permease is an example of active transporters. ____________ functions in __________ to cause a conformational change in order for a bacterial cell to transport lactose from the outside to the inside.

A proton gradient transfering H+ to a Glu residue of lactose permease

(SEE DIAGRAM #39-PG14) Blood clots are formed by a proteolytic cascade. Use the following diagram to show the steps of intrinsic and extrinsic pathways in the process of blood clotting. What molecules are the letters A, B and C represented? How many different active proteases in total are involved in intrinsic pathway and extrinsic pathways based on the diagram above?

A: Prothrombin B: Thrombin C: XIIIa 8

(SEE DIAGRAM #40-PG14) Blood clots are dissolved when the bleeding is healed. What molecules are the letter A, B, and C represented in the following diagram? How many active protease(s) and active serine protease(s) is(are) in the following diagram respectively?

A: Tissue Plasminogen Activator B: Plasminogen C: Plasmin 2 , 2

(SEE DIAGRAM #34-PG12) The following diagram illustrates the cycle of G-protein activation and inactivation. The letters A, B and C represent _______ . Which of the subunit(s) of G protein is(are) lipid anchored protein?

A: αβγGDP B: βγ C: αGTP α and γ, but not β

A. One ATP binds to the N domain of Ca2+ ATPase B. Two Ca2+ bind to Ca2+ ATPase C. Phosphorylation of Asp351 of the P domain of Ca2+ ATPase D. ADP is released to trigger a conformational change of Ca2+ ATPase E. Hydrolysis of phosphorylated Asp351 F. Two Ca2+ ions are released The correct sequence of Ca2+ transport process is?

B A C D F E

Ca2+ is an ion that acts as some types of cellular signal in nearly all cells. Ca2+ ions are sequestered inside vesicles called sarcoplasmic reticulum (SR) in human muscle cells. Ca2+ ATPase/pump functions in transporting Ca2+ between SR and cytoplasm. Transmembrane region of the ATPase/pump contains _____ and extramembrane domains have _________.

Ca2+ binding sites an ATP/ADP binding site

Muscle cells contain protein filaments that slide past one another, producing a contraction that changes both the length and the shape of the cell. Nearly all of the calcium ions are sequestered inside vesicles called sarcoplasmic reticulum (SR) in human muscle cells. Changes in Ca2+ concentrations are critical for muscle cell contraction. Ca2+ will be transported from sarcoplasmic reticulum to cytoplasm by ___________ and Ca2+ will be transported from cytoplasm to sarcoplasmic reticulum by ___________ .

Ca2+ channel Ca2+ pump

Both sugars and amino acids contain chiral carbon(s). Therefore majority of them exist D- and L-forms. _____________ are most common in nature.

D-sugars and L-amino acids

Enhanced cAMP cellular level will lead to the events of _____________ in the cells with mutation A and the events of _____________ in the cells with mutation B compared to the activity of glycogen synthase and phosphorylase at their normal cAMP cellular level respectively. A. Stronger activation of glycogen phosphorylase B. Stronger activation of glycogen synthase C. Stronger inhibition of glycogen phosphorylase D. Stronger inhibition of glycogen synthase E. No change of glycogen phosphorylase F. No change of glycogen synthase activity

E and F E and F

The correct sequence for the hormone-activated enzymatic cascade that leads to activation of certain enzymes and proteins. A. Activation of protein kinase A B. Phosphorylation of CREB C. Activation of adenylyl cyclase D. Phosphorylation of glycogen phosphorylase E. Activation of G-protein F. Activation of G-protein coupled receptor G. Phosphorylation of glycogen phosphorylase kinase The correct order of the activation events from the beginning to the end of G-protein and cAMP signaling pathway in response to change of cellular glucose level.

F E C A G D B

(SEE DIAGRAM #46-PG18) The reason it takes approximately one hour before the first radioactively labeled mitotic cells are observed is that?

G2 lasts 1 hr

Growth factors initiate cell proliferation & differentiation. Some factors affect many tissues and some are tissue specific. Growth factors are produced by a number of different cell types involved in the inflammatory response (WBC, platelets, endothelial cells, epithelial cells, fibroblasts smooth muscles cells, etc). Growth factors are mitogenic for tissue cells of ~all types, and they are also stimulating factors that suppress proliferation & tissue development. Growth factors bind to target cell receptors and elicit intracellular signals to induce gene transcription & may promote entry into the cell cycle. Epidermal growth factor (EGF) involves a number of sequential protein activation steps either through an enzymatic (phosphorylation, dephosphorylation, etc) reaction or a protein - protein interaction or both. Activation of ____________ is through a protein - protein interaction while ____________ of the signaling proteins are activated by an enzymatic reaction in EGF signaling.

Grb-2 and Sos MEK

Blood type is determined by specific O/H, A and B antigens that are examples of glycoproteins found in red blood cells. An A-type blood person has A antigen in the blood and has enzyme A. One of the substrates for enzyme A is ___________ . Enzyme A is found only in A-type or AB-type blood people, but not in O-type and B-type people because of __________ .

H antigen transcriptional regulation

(SEE DIAGRAM #48-PG18) If the length of G2 were increased by one hour, which of the following statements would be true regarding the slope of the line from the point of the first appearance of labeled mitotic cells were labeled?

It would stay the same

Membrane proteins constitute one of the three main protein classes, with the other classes being the fibrous and globular proteins. Membrane proteins are attached to, or associated with the membrane of a cell or an organelle. These proteins are specifically targeted to different types of biological membranes. In an α-helical protein that spans a cell membrane, _____ would likely be in the center of the membrane while _____ would likely be associated with the polar head groups and _____ would likely be associated with the aqueous environment. If polar amino acids are found in a membrane spanning α-helical region, they are most likely _____.

Leu Gln Asp hydrogen-bonded to other polar amino acids to prevent interaction with the membrane lipids

All cells acquire the molecules and ions they need from their surrounding extracellular fluid. There is an unceasing traffic of molecules and ions. Both Na+/K+ ATPase and ABC ATPase require ATP for transporting ions or molecules. However, ____________ has a phosphorylated form while ____________ does not involve a protein phosphorylation step. Na+/K+ ATPase transports 3 Na+ from the _________________ of a cell and 2 K+ from the _________________ of a cell by using energy of hydrolysis of one ATP molecules.

Na+/K+ ATPase ABC ATPase inside to the outside outside to the inside

_____________ most likely contain(s) a SH2 domain because its/their interacting protein(s) has/have ____________. A. G protein B. Grb-2 C. IRS D. PDK1 E PI3K F. Ras G. Sos

Only B, C and E phosphotyrosine site(s)

_________________ most likely contain(s) a PH domain because it/they has/have _________________ binding site(s). A. G protein B. Grb-2 C. IRS D. PDK1 E PI3K F. Ras G. Sos

Only D phosphatidylinositol 1,4,5-triphosphate(s)

(SEE DIAGRAM #2A-PG21) Draw out the structure of a tetrasaccharide with four glucose molecules and the linkage between glucose molecules are specified in the following diagram.

SEE KEY PG 21

An enzymatic reaction is used as part of a large biochemical process. The reaction is the typical: S->P where S is the substrate and P is the product. Derive Michaelis-Menten equation. E + S <=(k1/k-1)=> ES ES <=(k2/k-2)=> E + P 1. Assume substrate concentration high enough to quickly and entirely convert enzyme to ES form, therefore the second step of the reaction from ES to E + P becomes rate limiting 2. initial velocity monitored, thus ignore the reverse reaction of E+P going to ES 3. steady state assumption says that ES formation rate is equal to its rate of breakdown.

SEE KEY PG 22-23

(SEE DIAGRAM #1C-PG20) Identify the enzymes X, Y and Z in the following diagram.

X: Adenylyl cyclase Y: Phosphodiesterase Z: NMP kinase

(SEE DIAGRAM #2B-PG22) What are the molecules in the following diagram? Specify the difference between molecule Y and Z. Explain the activation of molecule X.

X: CaM Kinase Y: Apo CaM or inactive form of CaM Z: Holo CaM or active form of CaM It requires 1. the activation of its interacting protein CaM by Ca2+ bind and 2. then specific interaction between CaM and CaM kinase

Polysaccharide is an important class of biological polymers. Their function in living organisms is usually either structure- or storage-related. A polysaccharide consists of many covalently linked monosaccharides. These structures are often linear, but may contain various degrees of branching. Glycogen is a polymer of ______________ with branches of ______________ . A glycogen without branching is treated with dimethyl sulfate, which adds a methyl group to every free OH group. Next, the molecule is hydrolyzed to break all the glycosidic bonds between glucose residues. The reaction products are then chemically analyzed. How many different major types of methylated glucose molecules are obtained?

[glucose α-1,4 glucose]n glucose α-1,6 glucose; 3

The human body requires that the blood glucose level is maintained in a very narrow range. Glucose homeostasis is normally regulated by hormones. Secretion of glucagon and epinephrine are sensitive to low blood glucose level. Glucagon, a peptide hormone, is synthesized from α cells of human pancreas. Epinephrine, ______________ and is synthesized and secreted from adrenal gland. Epinephrine can function as a hormone, ______________ .

an organic compound and also a neurotransmitter

Ca2+ plays an important role in regulating a number of signal transduction pathways. For example, elevated level of Ca2+ concentration triggers muscle contraction and neurotransmission; Ca2+ also involves other biochemical functions, such as enzyme functions, antibody production. The followings are the events in Angiotensin II-Angiotensin II receptor signaling. A. Activation of a transcription factor B. Activation of a ligand gated receptor C. Activation of protein kinase by cofactor binding D. Activation of protein kinases by protein - protein interaction E. Activation of second messengers by an enzymatic reaction Angiotensin II-Angiotensin II receptor signaling regulates ____ .The correct sequence of Angiotensin II-Angiotensin II receptor signaling most likely is?

blood pressure E C B D A

Enzyme activity can be regulated by a number of ways: A. Allosteric regulation B. Isozymes C. Regulation by modulator proteins D. Protein phosphorylation E. Proteolytic activation If a particular enzyme has been regulated by one of the regulatory mechanisms listed above from A to E, it ___________ be regulated by a different regulatory mechanism listed above from A to E. ___________ of the regulatory mechanisms above is/are most likely a reversible process and can either activate or inhibit enzyme activity/protein function.

can only A, B, C, and D

Isozymes are enzymes with slightly different subunits in structure and catalytic function. Lactate dehydrogenase, an example of isozyme, has two different isoforms H and M. The tetramer, H4 expressed in heart, has the highest catalytic activity to convert lactate to pyruvate for the fuel of the ____________. An excess of the H type of lactate dehydrogenase in serum indicates a heart problem. In contrast, the tetramer, M4 expressed in muscle, has the highest catalytic activity to convert pyruvate to lactate since NAD+ is generated for continuing carbon metabolism. Different isoforms of lactate dehydrogenase are present in different ratio in different cell types because of _____________ .

citric acid cycle/TCA transcriptional regulation

The protein α-antitrypsin inhibits the action of the proteolytic enzyme: ______ in lung tissue. Smokers' lungs are often damaged by this enzyme because the α-antitrypsin is inactive. The best explanation for this effect is that tobacco smoke contains oxidants that chemically oxidize ______ .

elastase Met

(SEE DIAGRAM #42-PG15) Transcription of gene X is controlled by transcription factor A. Gene X is only transcribed when transcription factor A is phosphorylated. Data on tissue distribution of transcription factor A and activities of a protein kinase and a protein phosphatase specific for the transcription factor A are presented in the table below. Of these five tissues, gene X will be transcribed in ______ and its transcriptional level is regulated in _______ .

heart and kidney only kidney only

The neurotransmitters can be divided into five families: cholinergic agents, catecholamines, amino acids and their derivatives, peptide neurotransmitters and gaseous neurotransmitters. Different synapses utilize specific neurotransmitters. Processing defects of particular types of neurotransmitters during neurotransmission will cause neurological disorders. For example, defects of catecholamine process are responsible for the symptoms of clinical depression and parkinsonism. Diisopropyl-phosphofluoridate (DIPF), an acetylcholine esterase inhibitor by covalently attaching to the Ser residue acetylcholine esterase. Thus, DIPF will ______ the level and duration of action of the neurotransmission. Cocaine (benzoylmethylecgonine) is a crystalline tropane alkaloid that is obtained from the leaves of the coca plant. Cocaine increases alertness, feelings of well-being and euphoria, energy and motor activity. The most extensively studied effect of cocaine on the central nervous system is the blockade of the transporter protein of neurotransmitter dopamine. Injection of cocaine will __________ dopamine concentration in synapses.

increase increase

(SEE DIAGRAM #43-PG16) It can be inferred from these results that glucagon most likely acts to ________ and the changes or part of the changes in activity of enzyme X are most likely mediated by __________ .

increase the catalytic efficiency of enzyme X not through protein kinase A stimulate transcription of the gene for enzyme X

Caffeine is a bitter, white crystalline xanthine alkaloid and a stimulant drug. Caffeine is a central nervous system and metabolic stimulant, and is used both recreationally and medically to reduce physical fatigue and to restore alertness when drowsiness occurs. It produces increased wakefulness, faster and clearer flow of thought, increased focus, and better general body coordination. Drinking a caffeinated beverage would ___________ phophodiesterase activity, and ___________ GABA neurotransmission.

inhibit inhibit

Blood clotting must be precisely regulated. Specific inhibitors are critical for the regulation of clotting proteins. The most important is antithrombin III that _____ . This inhibitory action of antithrombin III is stimulated by heparin, a polysaccharide. Thus, heparin functions in inhibiting blood clotting cascade __________.

inhibits thrombin activity with an extrinsic signal or an intrinsic signal

A disaccharide is the carbohydrate formed when two monosaccharides undergo a condensation reaction which involves the elimination of a small molecule, such as water, from the functional groups only. The glycosidic bond can be formed between any hydroxyl group on the component monosaccharide. So, even if both component sugars are the same (e.g., glucose), different bond combinations (regiochemistry) and stereochemistry (alpha- or beta-) result in disaccharides that are diastereoisomers with different chemical and physical properties. The correct order of the disaccharides is _______ . ___________ has/have β type of linkage between two monosaccharides.

lactose, cellobiose, sucrose lactose and cellobiose

Each signaling pathway must be strictly regulated by the entire process from its initiation to termination. How is insulin signaling terminated after blood glucose level is returned to the normal level? A. Intrinsic GTPase activity of Ras converts Ras-GTP to Ras-GDP. B. Phosphorylation of one specific Ser residue of G-protein coupled receptor leads to the binding of β-arrestin that further diminishes the downstream signaling cascades. C. Phosphorylation of one specific Thr residue of G-protein coupled receptor leads to the binding of β-arrestin that further diminishes the downstream signaling cascades. D. Phosphorylation of one specific Ser and one specific Thr of G-protein coupled receptor leads to the binding of β-arrestin that further diminishes the downstream signaling cascades.

none

Glucose is an essential substrate for metabolism of most cells. Because glucose is a polar molecule, transport through biological membranes requires specific transport proteins. GLUT4 is one of glucose transporters. GLUT4 become associated with ______________ upon the activation of Akt in response of insulin signaling, and transport glucose to cytoplasm from blood vessel. GLUT4 is primarily found in muscle cells and ______________ .

plasma membranes adipose tissue

Vitamins are organic compounds required as essential nutrients in trace amounts by human. Vitamin K is required for the process of _______ and vitamin C is required for the biosynthesis of ________ .

prothrombin biosynthesis collagen

Potassium channel is specific for transport of potassium ion. The conserved K+ binding site of potassium channel contains unique amino acid sequence: Thr-Val-Gly-Tyr-Gly. One potassium channel has specific sites to bind maximal four K+ ions. Close to open of K+ channel is regulated by _____________ and K+ can rapidly shift from one binding site to another one farther up the channel because of charge repulsion. The interactions between potassium ions and K+ channels are mediated by _____________ .

rotation of one positively charged subunit of K+ channel polar - polar interactions

As temperatures grow colder with the onset of winter, animals will adapt by changing the fatty acid composition of cell membranes. What characteristics of fatty acids will be seen? This change in fatty acid composition to adapt the cold weather will ___ Tm of the phase transition.

shorter chains with greater unsaturation decrease

Hemagglutinin and neuraminidase are influenza proteins. Influenza, commonly known as the flu, is an infectious disease of birds and mammals caused by ssRNA virus. Hemagglutinin binds _______________ of glycoprotein on the surface of a host cell through _____________. Neuraminidase cleaves glycosidic bonds to free the pathogen to infect the cell.

sialic acid noncovalent bond interactions

Nerve cells contain high levels of _____________ . Neurotransmission is an electrical movement from one neuron to its adjacent neuron. From initiation to termination of neurotransmission requires a sequential activation of a number of channels, pumps and proteins/enzymes. The channels, pumps and proteins involved in neurotransmission are: A. Enzymatic reaction catalyzed by acetylcholine esterase B. Activation of acetylcholine receptor coupled K+ channel C. Activation of acetylcholine receptor coupled Na+ channel D. Activation of SNARE E. Ca2+ channel F. Na+/K+ pump

sphingomyelin E, D, C, B, F, A

cAMP binds to the regulatory subunits of protein kinase A (PKA) allowing the tetramer to dissociate into _______________ .

two active monomers and an inactive dimer

Gram negative bacteria are different from gram positive bacteria in that gram negative bacteria contain one peptidoglycan layer and ________. Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that form a mesh-like layer, forming the cell wall. The sugar portion of peptidoglycan is polymers of ______________ .

two lipid bilayer membranes [NAM β-1,4 NAG]n

Fibrin (also called Factor Ia) is a fibrous, non-globular protein involved in the clotting of blood. It is formed from fibrinogen by thrombin, and is then polymerized to form a homeostatic plug or clot (in conjunction with platelets) over a wound site. Fibrino-peptides are largely negatively charged to keep fibrinogen molecules separated. The composition of fibrin monomer is _____ and one fibrin monomer can interact with _____ other fibrin monomers to form a fibrin polymer, the blood clot.

α2β2γ2 4

Porins typically control the diffusion of small metabolites like sugars, ions, and amino acids in bacterial cells. Bacteriorhodopsin is an active transporter. Bacterial porin and bacteriorhodopsin are two examples of integral membrane proteins, which utilize ____________ and ___________in their transmembrane regions respectively. Bacteriorhodopsin captures light energy and uses it directly to generate _____________ .

β sheet α helices proton gradient