I.1: how many carbons does Arachidic acid have? (20 carbons)2: how many double bonds does Arachidonic acid have? (4 double bonds)3: list two advantages that fats have over sugars as stored fuels (more energy gramfor gram; no hydration needed)4: where inside the cells are most of the phospholipids degraded (lysosomes)5: oligosaccharide head groups determine the blood type of an individual. How are they attached to the plasma membrane? (glycosphingolipids or lipids and surface proteins) 6: list at least one genetic disease that could result from abnormal accumulation of membrane lipids (Tay-Sachs, Sandhoff’s, Fabry’s, Gaucher’s, or Niemann-Pick diseases) 7: list the three main eicosanoids that produced from arachidonic acid (prostaglandins; thromboxanes; and leukotrienes).8: list one NASID you know (aspirin, ibuprofen, or acetaminophen or meclofenamate)9: list two fat-soluble vitamins (A, D, E, K)10: which vitamin can be derived from beta-carotene (A).11: which year was the fluid mosaic model proposed? (1972)12: why the thickness of most biological membranes is thicker than 3nm, the standard thickness of lipid bilayer? ( due to association of proteins to the membrane and carbohydrates on the membrane)13: Please define the transition temperature of the lipid bilayer (the temperature above which the paracrystalline solid changes to fluid)14: If a membrane protein has its N-terminus exposed to the outside of the cell while its C-terminus resides in the cytosolic compartment, is it a type I transmembrane protein ? (yes).15: How can you predict if a protein has a transmembrane domain? (hydropathy or hydropathy index, or hydropathy plot).16: Name the two cell surface receptors that HIV use to enter cells (CCR5 and CD4). 17: For the Na+ K+ ATPase, how many Na+ and K+ can it move across the membrane for the hydrolysis of one ATP (2 K+ in, 3 Na+ out).18: what drives F-type ATPases to synthesize ATP? (proton or proton gradients) 19: The acetylcholine receptor is a _____-gated channel (Ligand)20: The neuronal Na+ channel is a _____-gated channel (voltage)II.D and H(3 points) The antiparallel orientation of complementary strands in duplex DNA was elegantly determined in 1960 by Arthur Kornberg by nearest-neighbor analysis. In this technique, DNA is synthesized by DNA polymerase I from one (alpha-32P)-labelled and three unlabelled deoxynucleoside triphosphates. The resulting product is then hydrolyzed by a Dnase that cleaves phosphodiester bonds on the 3’ sides of all deoxynucleotides. For example, in the labeled dATP reaction,ppp*A + pppC + pppG +pppT --Æ …pCpTp*ApCpCp*ApGp*Ap*ApTp… -Æ …+Cp+Tp*+Ap+Cp+Cp*+Ap+Gp*+Ap*+Ap+TpT…If in the dATP labeled reaction the relative radioactivity of Tp*, Gp*, Cp* and Ap* is 0.2, 0.3, 0.4 and 0.1.In the labeled dGTP reaction, Tp* radioactivity will beA)0.1B)0.2C)0.3D)0.4E)0In the labeled dCTP reaction, Tp* radioactivity will beF)0.1G)0.2H)0.3I)0.4J)0(B)(1 point) A molecule of amylopectin consists of 1000 glucose residues and is branched every 25 residues. How many reducing ends does it have?A)0B)1C)25D)40E)41F)1000(1 point) (D)A mirror image ofB form DNA isA)Z-DNAB)A-DNAC)B-DNAD)does not exist in nature(1 point) (A)Which of the following statements is not true?A)all natural occurring DNA is in B formB)A-DNA probably does not exist in vivoC)Both major groove and minor grove of B-DNA are deepD)B-DNA is right handed, while Z-DNA is left handed.(1 point) (A)Lung fish has 100,000,000 kb (kb=1000 base pairs) for its haploid genome. The total length of this DNA isA)34 mB)3.4 mC)1 mD)17 mE) 1.7 mF) 34 mm(3 points?) (1.5 point) A, D, EBoth tubes X and Y contain the same DNA in 0.1 M NaCl solution. In tube X more NaCl is added and in tube Y some ethanol is added. Which of the following is (are) correct?A)tube X will have higher Tm than YB)tube Y will higher Tm than XC)tube X and Y will have the same TmD)tube X will have higher Tm than originalE)tube Y will have lower Tm than original(1 point) (D)Which of the following is NOT correct?A)Glycosaminoglycan chains are linearB)Glycosaminoglycan chains are acidicC)Glycosaminoglycans are composed of repeating disaccharide unitsD)Different glycosaminoglycans have the same disaccharide units(1 point) (C)The so-called table sugar or cane sugar is a disaccharide ofA)galactose and glucoseB)2 glucose unitsC)glucose and fructoseD)galactose and fructose(1 point) (A)Lactose is a disaccharide ofA)galactose and glucoseB)2 glucose unitsC)glucose and fructoseD)galactose and fructose(1 point) (B)Choose the INCORRECT statement. In dideoxy sequencing or Sanger’s method,A)the newly synthesized DNA is labeled while the template is notB)the template has to be labeledC)a primer has to be usedD)ddNTPs are used to terminate elongation(1 point) (B)Choose the INCORRECT statement. In Maxam-Gilbert sequencing or chemical method,A)the template is labeledB)a primer is neededC)enzyme is not neededD)nucleotide analogues are not used(1 point) (D)uv radiation in the solar light directly cause which kind of the following DNA damage?A)deaminationB)methylationC)DNA breakageD)pyrimidine dimer formationE)depurination(1 point) (C)RNA is sensitive to alkaline hydrolysis becauseA)RNA has uridine instead of thymidine in its sequenceB)RNA has hydroxyl group at 4th and 5th positions of its riboseC)RNA has hydroxyl group at 2nd and 3rd positions of its riboseD)RNA is mostly single strandedE)RNA forms three dimensional structure(1 point) (D)Which of the following is NOT a carbohydrateA)glucoseB)maltoseC)glycogenD)proteglycanE)glycosaminoglycan(3 points?)(1.5 point) C, E, FWhich of the following is (are) NOT branchedA)glycogenB)starchC)celluloseD)amylopectinE)amyloseF)chitin(1 point) (A)Shown on the right isA)AB)GC)TD)CE)U(1 point) (C)Shown on the right isA)AB)GC)TD)CE)UIII.1)The follows are the important features of signal transduction systems EXCEPT :A.AmplificationB.Desensitization/turn-offC.SpecificityD.SimplicityE.Integration2)Relative to the outside of a cell, calcium concentration inside the cell is:A.HigherB.LowerC.Approximately equal3)Hydrolysis of GTP to GDP is essential for the normal function of all the GTP-bindingproteinsA.TrueB.False4)cAMP-dept kinase (PKA) regulates only sugar metabolismA.TrueB.False5)The follows are among the intracellular second messengers EXCEPT:A.cAMPB.cGMPC.Ca2+D.IP3E.ATP6)How does IP3 work as a second messenger?A． By activating phaspholipase CB． By activating protein kinase CC. By activating Ca2+ channelsD. By activating GαS7)The insulin receptor has tyrosine kinase activity which phsophorylates severaldifferent proteins including itselfA.TrueB.False8)The insulin signal is amplified via the MAP kinase cascadeA.TrueB.False9)All signaling pathways are very unique and very specific, and they don’t talk to eachotherA.TrueB.False10)Which of the followings is UNIQUE to TGFβreceptors?A.transmembrane proteinsB.Ser/The receptor kinasesC.Ligand binding activity present in the extracellular domainD.Become activated upon ligand binding11)The activity of CDK proteins is tightly regulated by the following events EXCEPT :A.PhosphorylationB.DephosphorylationC.Cyclin bindingD.UbiquitinationE.CDK inhibitors12)Caspases play essential roles in apoptosis. The following are among their effectsEXCEPT:A.Activation of DNaseB.Activation of other caspasesC.Inducing cell shrinkageD.Stimulating gene expression13)Cancer can be a result of the following events EXCEPTA.Activation of mitogenic signalsB.Cell cycle arrestC.Inactivation of negative regulators for cell growthD.Blockage of cell apoptosis14)In 2002, the Nobel Price for Physiology or Medicine was awarded for the research onA.PhosphorylationB.Cell cycleC.ApoptosisD.G proteinE.OncogenesAnswers for Biosignaling:1) D2) A3) A4) B5) E6) C7) A8) A9) B10)B11)D12)D13)B14)CIV.1. Which of the following statement about 2,3-bisphosphoglycerate (BPG) is wrong: (d)(a) BPG binds at a site distant from the oxygen-binding site of hemoglobin.(b) BPG regulates the oxygen-binding affinity of hemoglobin in relation to the pO2 in the lungs.(c) BPG concentration in normal human blood at sea level is lower than that at high altitudes.(d) BPG greatly increases the affinity of hemoglobin for oxygen.2. Antibodies of the IgG class : (d)(a) consist of four subunits.(b) have noncovalent bonds and disulfide crosslinks.(c) are abundant in the blood.(d) All three choices are correct.3. ELISA allows for rapid screening and quantification of the presense of an antigen in a sample. Which of the following steps of ELISA is wrong: (a)(a) Proteins in a sample are adsorbed to an inert surface, and the surface is washed with a solution of specific protein similar to the protein of interest, to block proteins in subsequence steps from also adsorbing to these surfaces.(b) The sample was treated with a solution containing antibodies against the protein of interest. Unbound antibody is washed away, and the sample is treated with with a solution containing antibodies against the primary antibody.(c) These secondary antibodies have been linked to an enzyme that catalyzes a reaction that forms a colored product.(d) After unbound secondary antibody is washed away, the substrate of the antibody-linked enzyme is added and the product formation is proportional to the concentration of the protein of interest in the sample.4. The major proteins of muscle are: (c)(a) Myosin and hemoglobin(b) Actin and troponin(c) Myosin and actin(d) Myoglobin and actin5. Positive cooperative binding can be identified by (c)(a) a hyperbolic binding curve.(b) a Hill plot with a slope less than one.(c) a Hill plot with a slope greater than one.(d) Choices a) and b) are both correct.6. Which pair of amino acids absorbs the most UV light at 280 nm? (b)(a) Thr & His.(b) Trp & Tyr.(c) Phe & Pro.(d) Phe & Pro.7. The strong conclusion from Anfinsen's work on RNaseA was that: (b)(a) 100% enzyme activity corresponds to the native conformation.(b) the sequence of a protein determines its structure.(c) Cys-SH groups are not found in vivo.(d) disulfide bonds (S-S) in proteins can be reduced in vitro.(e) irreversible denaturation of proteins violates the "Thermodynamic Hypothesis".8. Which of the following statement about protein folding is wrong: (c)(a) Some proteins undergo assisted folding by chaperons.(b) Polypeptides fold rapidly by a stepwise process.(c) Misfolding may cause misfunctioning, but does not cause death.(d) A loss of 3-d protein structure sufficient to cause loss of function is called denaturation.9. Hydrogen bonds in a-helices are (d)(a) more numerous than Van der Waals interactions.(b) not present at Phe residues.(c) analogous to the steps in a spiral staircase.(d) roughly parallel to the helix axis.(e) about 5 Å in length.10. What is the appoximate molecular weight of a protein with 200 amino acid residues in a single polypeptide chain: (b)(a) 11000(b) 22000(c) 44000(d) 66000V.1. What are the two most striking characteristics of enzymes? (1 pt, 0.5 pt x 2)Answer:The two most striking characteristics of enzymes are their 1) catalytic power, 2) specificity.2．How does an enzyme gain its catalytic power? (2 pt, 1 pt x 2)Answer:1)Enzymes bring substrates together in an optimal orientation;2)They catalyze reactions by stabilizing transition states;3. Is the structure of the binding site of an enzyme complementary to its substrateor to transition state? Why? (1 pt, 0.5 pt x 2)Answer: An enzyme is in complementary in structure to the transition state of the substrate because the activation barrier is lowered during such a binding.4．How many general ways of regulations on enzyme Activity? (2 pts, 0.5 pt x 4) Answer:1) Feed-back Inhibition2) Regulatory Proteins3) Covalent Modification4) Proteolytic Activation5.List the common features of enzymes (2.5 pts, 0.5 pt x 5)Answer:1)The active site take up small volume compare with the entire protein volume;2)The active sites are composed of amino acid residues located in differentpositions on a linear sequence;3)An enzyme binds to its substrate via multiple weak interactions;4)Active sites are clefts or crevices;5)The specificity of binding depends on precisely defined arrangement of atomsin an active site.6. How many types of weak interactions involved in the binding of a substrate byan enzyme? (2 pts, 0.5 x 4)Answer:1)Electrostatic interactions; 2) Hydrogen bonds; 3) van der Waals forces; 4)Hydrophobic interactions.7. Write down the Michaelis-Menten equation (0.5 pt), what is the meaning of K m?(0.5 pt) Under which condition the K m is a measure of the affinity of the enzymefor the substrate? (1 pt), what is the meaning of V max? (0.5 pt) What is thephysical limit of the value of k3/k m? (1 pt)Answer:Michaelis-Menten equation: V = V max S/(S + K m)K m is equal to the substrate concentration at which the reaction rate is half itsmaximal rate value.K m is a measure of the enzyme’s affinity only when K2 >> K3 (i.e., thedissociation rate constant of ES is much greater than the catalytic rate constant)V max is reached when all the catalytic sites on an enzyme are saturated with substrate.The physical limit of the value of k3/k m is that the enzyme-catalyzed reactionrate is rate of diffusion of both the substrate and the enzyme.VI.The following statements are true (T) or false (F)?1. The biological system is an open system; living organisms are at equilibrium with their surroundings. 1.5False: The biological system is indeed an open system, able to absorb and exchange materials with the environment. However the living organisms use energy to, for example, keep their own concentrations of ions inside the cells, which are not necessarily of the same concentrations in the environment.2. Activation energy for a chemical reaction is t h e e n e r g y r e q u i r e d f o r a c h e m i c a lr e a c t i o n t o c o n v e r t t h e r e a c t a n t t o t r a n s i t i o n s t a t e,b u t d o e s n o t m e a s u r e t h e f r e e e n e r g yc h a n g e b e t w e e n t h e r e a c t a n t s a nd p r o d u c t s.1.5T r u e3.T h e m i t o c h o n d r i o n i s a n o r g a n e l l e t h a t f u n c t i o n s a s a n e n e r g y r e g e n e r a t i o np o w e r h o u s e,b u t d o e s n o t p a r t i c i p a t e i n t h e r e g u l a t i o n o f c e l l s u r v i v a l.1.5F a l s e:M i t o c h o n d r i a i n d e e d p l a y t h e m o s t i m p o r t a n t r o l e i n e n e r g y p r o d u c t i o n;h o w e v e r,t h e y a r e a l s o a k e y o r g a n e l l e i n t h e r e g u l a t i o n o f c e l l d e a t h.I n f a c t,m o s t c r i t i c a l a p o p t o t i c o r a n t i a p o p t o t i c f a c t o r s r e g u l a t e c e l ld e a t h t h r o u g h f u n c t i o n a l i n t e r a c t i o n w i t h m i t o c h o n d r i a.4. The Buchners’ discovery of fermentation supported the view, as asserted by Pasteur, that fermentation can take place only in l i v i n g c e l l s.1.5F a l s e:T h e B u c h n e r s’f i n d i n g t h a t f e r m e n t a t i o n c a n t a k e p l a c e i n y e a s t c e l le x t r a c t s d e m o n s t r a t e d t h a t c e l l-f r e e e x t r a c t s p o s s e s s a l l t h e e l e m e n t s f o rf e r m e n t a t i o n f r o m s u c r o s e t o a l c o h o l.P a s t e u r’s v i e w t h a t f e r m e n t a t i o n i s i n e x t r i c a b l y t i e d t o l i v i ng c e l l s w a s w r o n g.Thi s f i n d i n g h a s b e e n r e g a r d e da s o n e o f t h e e a r l i e s tb i oc h e m i c a l e x p e r i m e n t s.5.E n d o p l a s m i c r e t i c u l u m i s a p l a c e f o r p o s t t r a n s c r i p t i o n a l R N A p r o c e s s i n g,t r a n s l a t i o n,a n d p r o t e i n m o d i f i c a t i o n.1.5False: The ER is a place for protein synthesis (translation), protein modification such as glycosylation and signal peptide cleavage, but not for RNA processing.6. Carbohydrates function as structural components in nucleic acids, amino acids, and protein modification. 1.5E.False: Everything but amino acids7.T h e p r e s e n t d a y b i o c h e m i s t r y i s t h e i n t e r w e a v i n g p r o d u c t o f h i s t o r i c a l t r a d i t i o n s o fb i oc h e m i s t r y,c e l l b i o l o g y,m o l e c u l a r b i o l o g y a nd ge n e t i c s.1.5T r u e8.T h e y e a s t t w o h y b r i d m e t h o d i s u t i l i z e d t o i d e n t i f y p r o t e i n f a c t o r s t h a t b i n d t o a k n o w n p r o t e i n o f i n t e r e s t.1.5p o i n t sT r u eA n s w e r s:1.F2.T3.F4.F5.F6.F7.T8.T。