Cell Bio
For each of the following statements, indicate for which coated vesicle the statement is true: clathrin- (C), COPI- (I), or COPII-coated (II). Each statement may be true for one, several, or none (N) of the coated vesicles discussed in this chapter.
(a) Binding of the coat protein to an LDL receptor is mediated by an adaptor protein complex. Clathrin (C) (b) Fusion of the vesicle (after dissociation of the coat) with the Golgi membrane is facilitated by specific t-SNARE and Rab proteins. COPII (c) Has a role in bidirectional transport between the ER and Golgi complex. COPI (d) Has a role in sorting proteins for intracellular transport to specific destinations. Clathrin, COPI, COPII (e) Has a role in transport of acid hydrolases to late endosomes. Clathrin (f) Is essential for all endocytic processes. None (g) Is important for retrograde traffic through the Golgi complex. COPI (h) Is involved in the movement of membrane lipids from the TGN to the plasma membrane. Clathrin (i) The basic structural component of the coat is called a triskelion. Clathrin (j) The protein coat dissociates shortly after formation of the vesicle. Clathrin, COPI, COPII (k) The protein coat always includes a specific small GTP-binding protein. COPI, COPII
Each of these statements is an experimental observation concerning the reassembly of tobacco mosaic virus (TMV) virions from TMV RNA and coat protein subunits. In each case, carefully state a reasonable conclusion that can be drawn from the experimental finding.
(a) When RNA from a specific strain of TMV is mixed with coat protein from the same strain, infectious virions are formed. TMV virions self-assemble spontaneously without the input of energy or information, which means that all of the information necessary to direct their assembly must be already present RNA and/or proteins (b) When RNA from strain A of TMV is mixed with coat protein from strain B, the reassembled virions are infectious, giving rise to strain A virus particles in the infected tobacco cells. The strain specific assembly of TMV in vivo is determined by the RNA, not the coat protein. (c) Isolated coat protein monomers can polymerize into a virus like helix in the absence of RNA. The information necessary to direct self-assembly in TMV virions appears to be reside in the coat protein monomers. (d) In infected plant cells, the TMV virions that form contain only TMV RNA and never any of the various kinds of cellular RNAs present in the host cell. The self-assembly of TMV virions is specific for TMV RNA. (e) Regardless of the ratio of RNA to coat protein in the starting mixture, the reassembled virions always contain RNA and coat protein in the ratio of three nucleotides of RNA per coat protein monomer. The most stable conformation for TMV virions is achieved by the 3:1 ratio of nucleotides and coat protein monomers and is therefore the product formed upon self-assembly regardless of the starting ratio of nucleotides and monomers.
Primary Structure - amino acid sequence of a protein
1st protein to have its primary structure (complete amino acid sequence) determined
You have measured the concentrations of reactants and products of a chemical that reached equilibrium. If the concentrations of reactants and products are 1 milli mol/L and 10 micro mol/L respectively, the Keq of this reaction at 25oC will be ---------------------. 1) 10 2) 1.0 3) 0.1 4) 0.01 5) 0.5
0.01
In a reversible reaction at equilibrium, the concentration of R (the reactant) is 3.0 mol/L and the concentration of P (the product) is 0.9 mol/L. At 25°C, what would be the K ? 37.5 1.0 3.0 1.5 0.3
0.3
Depending on their relative affinities to water amino acids will be localized either in the interior or on the exterior of globular proteins. For each of the following pairs of amino acids, choose the one that is more likely to be found in the interior of a globular protein and explain why:
1) Alanine; (Interior, More Nonpolar)Glycine 2) Tyrosine; Phenylalanine (Interior, Hydrophobic and nonpolar) 3) Glutamate; (Interior, More hydrophobic, because of the extra methyl group) Aspartate 4) Methionine;- (Interior, More hydrophobic, because of internal �S�) Cysteine
What are the 4 major criteria for a macromolecule to be the genetic material. Describe how Watson and Crick model of DNA structure satisfactorily explained DNA as the genetic material.
1. Should store information; stable Double helical structure and phosphate backbone protect interior bases which encode information 2 Self replicate Antiparallel and complementarity of bases aid this 3.Ability create variation and evolve Antiparallel and complementarity of bases aid this; changes in one strand copy to the other 4. Should be able to encode and control functional information Antiparallel and complementarity of bases helps to copy the message encoded in DNA to RNA
possible stereoisomers
2^n n= # of asymmetric "C"
Which of the following is not a fundamental property of carbon? 1) Carbon-containing molecules are diverse. 2) Carbon-containing molecules form stereoisomers. 3) Carbon atoms are most likely to form ionic bonds with one another. 4) Carbon-containing molecules are stable. 5) Carbon has a valence of 4.
3) Carbon atoms are most likely to form ionic bonds with one another.
Imagine the reaction A --> B with a negative G value under experimental conditions. Which of the following statements is true about this reaction? 1) The reaction is energetically unfavorable. 2) The reaction proceeds spontaneously and rapidly under these conditions. 3) Increasing the concentration of B molecules would increase the Î"G value (toward more positive values). 4) The reaction would result in a net decrease in the entropy (disorder) of the universe. 5) The reaction cannot proceed unless it is coupled to another reaction with a positive value of Î"G.
3) Increasing the concentration of B molecules would increase the Î"G value (toward more positive values).
What is the maximum number of stereoisomers that may exist for heptose? 64 32 8 16 4
32
Which of the following is not an example of posttranslational processing? 1) glycosylation 2) protein folding 3) 5' CAP formation 4) signal sequence removed 5) all but choice C
5' CAP formation
The endoplasmic reticulum is a site for _____________ 1) drug detoxification by catalase 2) N-linked glycosylation of polypeptides. 3) addition of lipid residues. 4) potassium storage in muscle cells. 5) both B and C
5) both B and C
Ribose has five carbon atoms, of which three are asymmetric. What is the maximum number of stereoisomers that may exist for ribose? 16 3 6 9 8
8
The following questions are based on sickle cell anemia, a striking example of a genetic disease caused by single amino acid substitution that drastically affects the structure and function of hemoglobin.
A) Given the chemical nature of glutamate and valine, why substitution of valine at position 6 of the b chain of hemoglobin is deleterious? The amino acid glutamate is hydrophilic and ionizes at cellular pH, whereas valine is hydrophobic and nonionic. Substitution of the latter for the former is likely to change the chemical and structural nature of the part of the protein to affect the function. B) What are other amino acids that would be much less likely than valine to cause impairment of hemoglobin function if substituted for glutamate at position 6 of the b chain? Aspartate is another acidic amino acid and is therefore conserving the charge, structure and function of the hemoglobin. Others that are unlikely to have major effects are the polar but uncharged amino acids serine, threonine, tyrosine and cysteine. C) Explain why, in some cases, two proteins could differ at several points in their amino acid sequence and still be very similar in structure and function? Yes, if substitutions of amino acids are always of like-for-like amino acids in terms of chemical properties, it will become a chemically conservative changes, therefore, polypeptide could maintain the structure.
Correct each of the following false statement and explain why it was false:
A) Proteins, nucleic acids, polysaccharides, and lipids are polymers synthesized by condensation of monomer units. Proteins, nucleic acids, polysaccharides are synthesized from monomers through condensation reaction, but not lipids. B) The amino acid proline is not found in a helices because its R group too large to fit into the a helix. The amino acid proline is not found in a helices because its R group is covalently bonded to the amino nitrogen. Once the peptide bond is formed involving proline, its amino nitrogen has no available hydrogen for forming a hydrogen bond within an a-helix. C) While a protein can be denatured by high temperature, extremes of pH generally have no effect on tertiary structure. Both high temperature and extreme pH denature protein and hence the tertiary structure. D) a-D-glucose and b-D-glucose are stereoisomers. a-D-glucose and b-D-glucose are isomers differing in the position of the hydroxyl group attached to carbon atom 1, but they are not stereoisomers (mirror images). D-glucose and L-glucose are stereo isomers. E) Fatty acids are important component of all cellular lipids. Fatty acids are important components of the phospholipids found in all cellular membranes. However, there are many other cellular lipids that do not contain fatty acids. F) It is easy to predict the final folded structure of a protein from its amino acid sequence using today�s powerful super computers. Although a polypeptide�s primary sequence determine its final folded (tertiary) structure, because there are limitless ways in which even a small protein can fold, it is still not possible to predict this structure from primary sequence.
In each statement below indicate how the property of carbon atom contributes its role as the most important atom in biomolecules.
A) The carbon atom has a valance of four. Because of valance of 4, C can form multiple covalent bonds with either other atoms or with C atoms itself to form greater diversity. B) The C-C bond has a bond energy that is above the energy of photons of light in the visible range (400 � 700 nm). Stability, visible light, cells can survive C) A carbon atom can bond simultaneously to two other carbon atoms Long chain C atom compounds as well as ring structures D) Carbon atoms can bond readily to H, N, and S atoms. Diversity E) Carbon-containing compounds can contain asymetric carbon atoms. Structural diversity in the form of stereoisomers
If a cell in mitosis is cooled to 0°C, the microtubules in the spindle depolymerize into tubulin subunits. The same is true for microtubules made from pure tubulin in a test tube; they assemble readily at 37°C, but disassemble at low temperature. In fact, many protein assemblies that are held together by noncovalent bonds show the same behavior: they disassemble when cooled. This behavior is governed by the basic thermodynamic equation ΔG =ΔH-TΔH, where ∆H is the change in enthalpy (chemical-bond energy), ∆S is the change in entropy (disorder of the system), and T is the absolute temperature.
A) The change in free energy (∆G) must be negative for the reaction (tubulin subunits → microtubules) to proceed at high temperature. At low temperature, ∆G must be positive to permit disassembly; that is, to favor the reverse reaction. Decide what the signs (positive or negative) of ∆H and ∆S must be, and show how your choices account for polymerization of tubulin at high temperature and its depolymerization at low temperature. (Assume that the ∆H and ∆S values themselves do not change with temperature.) Both ΔH and ΔS should be positive for polymerization to be proceed at high temp. In this condition, -TΔS will be larger than ΔH term, resulting in a negative ΔG. When ΔH and ΔS are positive depolymerization will be promoted at lower temperature and depolymerization to proceed at low temp. Under such condition, the -TΔS becomes smaller because ΔH become too big and ΔG will be positive B) Polymerization of tubulin subunits into microtubules at body temperature clearly occurs with an increase in the orderliness of the subunits. Yet tubulin polymerization occurs with an increase in entropy (decrease in order). How can that be? Tubulin polymerization seems to contradict the 2nd law of thermodynamics if we consider the polymerization of tubulin monomers in isolation. During polymerization, water molecules attached to tubulin monomers are released which interact then interacts with surrounding water molecules to increase the disorder within the whole system (universe).
Decide whether each of these statements about water is TRUE (T) or FALSE (F). For each true statement indicate a possible benefit to living organism.
A) Water is a polar molecule, hence an excellent solvent for polar compounds, T, Living organisms are essentially aqueous solutions containing many kinds of molecules, most of which are polar and are readily soluble in water. B) Water can be formed by the reduction of molecular oxygen (O2.) T, Oxygen is the ultimate electron acceptor in cellular respiration with H20 as product C) The density of water is less than the density of ice. F, the density of ice is less than the density of water, thereby ensuring that ice will readily float on the surface body of water, where it will readily melt if the temperature of the surrounding air rises above the freezing point. D) The molecule of liquid water is extensively hydrogen-bonded to one another. T, high specific heat and high heat of vaporization and hence the capacity of water to buffer cells and organisms against temperature changes E) Water does not absorb visible light. T, this property of water allows light to penetrate readily so that submerged photosynthetic organisms can survive. F) Water is odorless and tasteless. X, the lack of odor or taste is probably not a strategic advantage to most organisms. G) Water has high specific heat. T, Effectively buffer cells under temperature changes H) Water has high heat of vaporization. T, Organisms can be effectively cooled by evaporation of perspiration or other forms of liquid water from skin or other surface of organisms
Glycogen and amylopectin are common examples of branched-chain storage polysaccharides in cells. Both are degraded exolytically, which means by stepwise removal of terminal glucose units.
A) What is the advantage of storage polysaccharides to have a branched-chain structure instead of a linear structure? Compared to a linear molecule, a branched-chain polymer has more termini for addition or hydrolysis of glucose units per unit volume of polymer, thereby facilitating both the deposition and mobilization of glucose by providing more sites for enzymatic activity. B) Can you foresee any metabolic complications in the process of glycogen degradation? How cell handle this? Every branch point will have an α(1→6) glycosidic bond that will have to be hydrolyzed. This is handled by the presence of an additional enzyme specific for the α(1→6) bond. C) Why cells that degrade amylose instead of amylopectin have enzymes capable of both exolytic and endolytic (internal) cleavage of glycosidic bonds? Endolytic cleavage breaks the molecule infernally, creating additional ends for exolytic attack and thereby allowing the mobilization of more glucose per unit time. D) Why the structural polysaccharide cellulose does not contain branches? Cellulose molecules are rigid, linear rods that aggregate laterally into microfibrils. Branches in the molecule would generate side chains which would almost certainly make it difficult to pack the cellulose molecules into microfibrils, thereby decreasing the rigidity and strength of the microfibrils.
The following questions are based on permanent hair styling, which change the shape of the hair by rearranging the extensive disulfide bonds of keratin.
A) What is the chemical basis of permanent? Be sure to include the use of a reducing and a oxidizing agent in your explanation. Hair proteins are first treated with a sulfhydryl reducing agent to break disulfide bonds and thereby destroy much of the natural tertiary structure and shape of the hair. After being �set� in the desired shape, the hair is treated with an oxidizing agent to allow disulfide bonds to re-form, but now between different cysteine groups, as determined by the positioning imposed by the curlers. These unnatural disulfide bonds then stabilize the desired configuration. B) Why do you suppose a permanent isn�t permanent? (Explain why the wave or curl is gradually lost after permanent.) There are two reasons for the lack of permanence: (1) Disulfide bonds occasionally break and re-form spontaneously, allowing the hair proteins to return gradually to their original, thermodynamically more favorable shape. (2) Hair continues to grow, and the new α-keratin molecules will have the natural (correct) disulfide bonds. C) Can you suggest an explanation for naturally curly hair? There is probably a genetic difference in the positioning of cysteine groups and hence in the formation of disulfide bonds.
Describe the source or sources of energy needed for unidirectional translocation across the membrane in
A) cotranslational translocation into the endoplasmic reticulum (ER); The energy source for cotranslational translocation comes from the translation process itself�in other words, the nascent chain is pushed through the translocon channel. Please note, however, that as translation is completed a portion of the newly synthesized protein still resides within the translocon. This portion is drawn into the ER lumen rather than being pushed. (B) post-translational translocation into the ER; In post-translational translocation, the newly synthesized polypeptide chain is drawn through the translocon by an energy input from ATP hydrolysis by BiP. BiP is luminal protein of the ER and is a member of the Hsc70 family of molecular chaperones. BiP-ATP activates by binding to the Sec63 complex that in turn binds to the Sec61 translocon complex. Activated BiP is enzymatically active and cleaves ATP to ADP plus Pi. It is BiP-ADP that binds to the entering, unfolded nascent chain. Sequential binding of BiP-ADP to the nascent chain serves to block any sliding of the chain back and forth in the translocon and to ratchet the nascent chain through the translocon. (C) translocation into the mitochondrial matrix. Translocation into the mitochondrial matrix occurs through a bipartite Tom/ Tim complex in which Tom is the outer membrane translocon and Tim is the inner membrane translocon. Three energy inputs are required. First, ATP hydrolysis by a cytosolic Hsc70 chaperone keeps the newly synthesized mitochondrial precursor protein unfolded in the cytosol. Second, ATP hydrolysis by multiple ATP-driven matrix Hsc70 chaperones may serve to pull the translocating protein into the matrix. Matrix Hsc70s interact with Tim44 and hence may be analogous to the BiP/Sec63 interaction at the ER membrane. Third, energy input from the H+ electrochemical gradient or proton-motive force is required. The inside-negative membrane electric potential may serve to electrophorese the amphipathic matrix-targeting sequence toward the matrix.
Which of the following could be an ER retention signal? 1) arg-Arg (R-R) 2) lys-asp-glu-leu (KDEL) 3) lys-x-lys (KXK) 4) A and B 5) A, B and C
A, B and C
Indicate whether each of the following statement is true of the G1 phase of the cell cycle, the S phase of the cell cycle, the G2 phase or the M phase. A given statement may be true of any, all or none of the phases.
A. The amount of nuclear DNA in the cell doubles. - S B. The nuclear envelops breaks into fragments. - M C. Sister chromatids separate from each other. - M D. Cells that will never divide again are likely to be arrested in this phase. - G1 E. The primary cell wall of a plant cell forms. - M F. Chromosomes are presented as diffuse, extended chromatin. - G1, S, G2 G. Mitotic cyclin is at its lowest level. - M H. A Cdk protein is present in the cell. - G1, S, G2, M I. A cell cycle checkpoint has been identified in this phase. - G1, S, G2, M J. This phase is a part of interphase. - G1, S, G2
Identify CORRECT statement. 1) Many cellular processes except cell survival are coordinated with cell-cell and cellmatrix adhesion. 2) Proteaoglycans rich in hyaluronate are cement cell-cell junctions. 3) Plakoglobulin is one of adhesion molecules is which cements two cells together. 4) Adherens junctions are exclusive to plant cells. 5) Adhesive junctions are dynamic in response to cellular signals.
Adhesive junctions are dynamic in response to cellular signals.
What R group structural feature is common to phenylalanine, tyrosine, tryptophan, and histidine?
All four have rings that are attached to the core via a -CH2 group
What structural feature is common to alanine, serine and cysteine?
All three have a single carbon in their R groups.
Living systems are so complex and intricately ordered. Do you think living system violates, the second law of thermodynamics, which states that the disorder (entropy) in the universe will increase as systems changes spontaneously. Explain your results.
Although living system are open (exchange energy and matter with envt), they still follow 2nd law of thermodynamic that been developed using experiments in a closed system. Living organism grow by taking food and energy to form more ordered structure; they release the waste products and excess energy in to the envt which are more disordered than the ordered structure that they create.
Why wouldn't your blood and other fluids become significantly acidic after you drink a half gallon of orange juice or soda?
Although the orange juice is acidic, your body contains buffers that absorb these excess hydrogen ions and preserve the neutral pH of your blood
Which of the following has the greatest number of glycosidic bonds? DNA Amylopectin Vitamin A glucose triacylglycerol
Amylopectin
Identify the INCORRECT statement. 1) Some small molecules could move through basal lamina. 2) An abundant source of lamins are basal lamina. 3) Basal lamina contains proteoglycans, laminins, collagen type IV, and elastin. 4) Basal lamina provide adhesive and structural support to epithelium. 5) Migration of cells in certain areas of the body are regulated by basal lamina.
An abundant source of lamins are basal lamina.
polar hydrophillic charged
Aspartic acid (-) Glutamic Acid (-) Lysine (+) (K) Arginine (+) (R) Histidine (+) (H)
Why do polar substances such as NaCl dissolve so readily in water? a) The sodium ions repel the negative end of the water molecule. b) NaCl is a very dry powder, and the water is able to soak into the salt. c) Spheres of hydration form between the water and the ions. d) The charged ends of the water molecules are able to surround the oppositely charged salt ion. e) Both C & D
Both C & D c) Spheres of hydration form between the water and the ions. d) The charged ends of the water molecules are able to surround the oppositely charged salt ion.
What structural feature is common to isoleucine and threonine
Both have an asymmetric carbon in their R group
Which of the following bond(s) is/are present in the third/vapor state of water? a) Covalent b) Hydrogen c) Ionic d) Both A & B e) Both B & C
Covalent
Phosphoanhydride bonds store majority of the energy in ATP
Hydrolysis of ATP is favorable mainly because electrostatic repulsion created by 4 closely spaced negative charges on ATP4 - is partially relieved by hydrolysis
Suppose life has been discovered on Mars and shown to contain a new type of macromolecule, named marsalive. You have been hired to study this new compound and want to determine whether marsalive is a structural or an informational macromolecule. What features would you look for?
Determine whether the macromolecule is made up of a series of monomeric units, if so, determine the arrangement of monomers. A repetitive pattern consisting of one or two different monomers suggests that it is structural, otherwise, it is informational.
The statement, "The total amount of energy in the universe is constant," is a tenet of entropy enthalpy the second law of thermodynamics. the first law of thermodynamics. thermodynamic spontaneity.
the first law of thermodynamics.
Your company has developed a new anticancer drug, but it will not cross through the membrane of target cells because it is large and contains many polar functional groups. Can you design a strategy to get this new drug into the cancer cells?
Encapsulate within a nonpolar lipid soluble vescicle (liposome) that will readily absorbed by the cell.
Enzymes are the cells catalyst crew. They make the life of the cell possible by carrying out various reactions with astounding performance. Which of the following is NOT true regarding cellular enzymes? 1) Enzymes lower the activation energy of the reactions that they catalyze. 2) Enzymes can specifically drive substrate along certain reaction pathways. 3) Enzymes can push energetically unfavorable reactions forward by coupling them to energetically favorable reactions. 4) Enzymes are proteins, but RNA catalysts, called ribozymes, also exist. 5) Enzymes can change the equilibrium point for reactions that they catalyze.
Enzymes can change the equilibrium point for reactions that they catalyze.
Which of the following cell populations in our body has the highest mitotic index? 1) Neurons 2) Hepatocytes 3) Red blood cells 4) Fibroblasts 5) Skeletal myocytes
Fibroblasts
What amino acid has the shortest carbon chain in its R group?
Glycine. It has no carbon in its R group.
The following questions are based on the properties of lipids discussed:
In what sense is the operational definition different from that of proteins, nucleic acids, or carbohydrates? A lipid is a molecule that is preferentially soluble in an organic solvent rather than in water. This definition is therefore based on the solubility properties of the molecule rather than on the chemical nature of the subunits or the bond that links subunits together, as is the case for proteins, nucleic acids, and carbohydrates. B) Arrange the following lipids in the order of decreasing polarity: Cholesterol, estradiol, fatty acid, phosphatidyl choline, and triglycerides. Explain your reasoning. Phosphatidyl choline > Fatty acid > Triacylglycerol > Estradiol > Cholesterol. C) Which would you expect to resemble sphingomyelin molecule more closely: a molecule of phosphatidyl choline containing two molecules of palmitic acid as its fatty acid side chains or phosphatidyl choline molecule with one molecule of palmitate and one molecule of oleate as its fatty acid side chains? Explain your answer? The presence of an oleate will introduce a bend in one of the side chains that will closely approximate the shape of sphingomyelin, because the latter also has a double bond and hence a bend. D) Assign each of the following melting temperature to the appropriate fatty acid and explain your answer. Melting temperature: -11, 5, 16, 63, 70, and 76.5. Fatty acids: arachidic, linoleic, linolenic, oleaic, palmitic, and stearic acids. �11�C: Linolenic acid +63�C: Palmitic acid +5�C: Linoleic acid +70�C: Stearic acid +16�C: Oleic acid +76.5�C: Arachidic acid E) For each of the following amphipathic molecules, indicate which part of the molecule is hydrophilic: phosphatidyl serine, sphingomyelin, cholesterol, and triacylglycerol. Phosphatidyl serine: the phosphoserine group Sphingomyelin: the phosphocholine group Cholesterol: the hydroxyl group (only slightly hydrophilic) Triacylglycerol: the ester bonds between glycerol and the fatty acids. F) What does partial hydrogenation of cooking oils accomplish chemically? and physically? Partial hydrogenation results in the partial reduction of C=C double bonds to C�C single bonds in the fatty acyl chains of the triglycerides. Become more solid at room temperature. G) Why would it be misleading to say that the shortening is �made from 100% polyunsaturated oils�? Although the ingredients for making the shortening may be 100% polyunsaturated oils, to convert them into solid, they must be hydrogenated and thus become saturated fats in the final product.
Which of the following is more directly driven by active M-Cdk? 1) Centrosome maturation 2) Centrosome duplication 3) Nuclear envelope reassembly 4) Inactivation of APC/C 5) Cell cleavage
Inactivation of APC/C
What function does the SRP receptor have in protein targeting? 1) It ensures that proteins enter mitochondria in an unfolded state. 2) It reactivates protein synthesis once a ribosome attaches to the ER membrane. 3) It forms a channel that permits proteins to enter peroxisomes. 4) It helps proteins that enter chloroplasts fold into their proper shape. 5) It inhibits protein synthesis in ribosomes not attached to the ER.
It inhibits protein synthesis in ribosomes not attached to the ER.
The First Law of Thermodynamics
Law of conservation of energy Energy can't be created or destroyed, however, can be convert from one form to another Internal Energy: E = Total energy stored within a system ΔE = Change in internal energy during transformation ΔE = Efinal- Einitial For Chemical system - ΔE = Eproducts- Ereactants For biological system change in heat content (or Enthalpy) is more relevant H = E + PV (change in heat is depend on change in energy, pressure and volume In biological system negligible change in pressure and volume Δ H = Δ E + Δ PV; Since ΔPV = 0 Δ H = dΔE or Δ H = Hproducts- Hreactants
Which amino acid has the longest straight chain of carbons in its R group?
Lysine. It has 4. Leucine and isoleucine have 4 but their chains are branched
Which amino acid is most likely to be found in the core of a protein? a) E b) T c) S d) N e) M
M
According to bioenergetics 1) Matter does not accompany energy as it enters the biosphere, but it does flow with energy from the biosphere. 2) Matter and energy flow sometimes in cycles and sometimes unidirectionally. 3) Energy flows as organic molecules are reduced to inorganic molecules, but matter does not. 4) Energy flows from chemotrophs to phototrophs, whereas matter flows from phototrophs to chemotrophs. 5) Matter flows in cycles, whereas energy flows in one direction.
Matter flows in cycles, whereas energy flows in one direction.
Roughly, how long would it take a single fertilized human egg to make a cluster of cells weighing 70 kg by repeated divisions, if each cell weighs 1 nanogram just after cell division and each cell cycle take 24 hrs? Why does it take much longer than this to make a 70-kg adult human?
Mode of cell population increase = exponential Weight of cell cluster after N cell division = 2^N x 10-9 g Number of cycles needed for 70 kg =2^N = (70 x 103 )/10-9 = 70x1012 N = ln(70x1012)/ln(2) = 46 cell cycle or 46 days It take much longer than 46 days to make 70-kg adult human because 1) as a result of terminal differentiation exponential division would not happen in vivo and 2) tissue homeostasis is maintained by cell death and apoptosis.
Identify the smallest? 1) ribosome 2) E. Coli bacteria 3) Covid-19 virus 4) Peptidyl tranferase enzyme 5) Hemoglobin protein
Peptidyl tranferase enzyme
Quaternary Structure Level of protein structure involving interactions between two or more polypeptide chains to form a single multimeric protein
Pyruvate dehydrogenase complex ___ 3 individual enzymes
Tertiary Structure Conformation of the entire protein
Result of interaction between R group Neither repetitive nor predictable Fibrous proteins: extensive repetitive secondary structure Silk fibroin, Keratin Globular Proteins: polypeptides are folded into compact structures Ribonuclease Protein Domains A discrete, locally folded unit of tertiary structure that usually has a specific function
In the reaction 2 Na + Cl2 → 2 Na+ + 2 Cl-, what is being oxidized and what is being reduced? How can you tell.
Rewrite the reactions as follows: 2 Na → 2 Na+ + 2 e- (Na is oxidized, because it loose electrons) 2 e-+ Cl2→ 2 Cl- (it accept electrons, Cl is reduced)
Which of the following is true of fatty acids? a) Fatty acids are synthesized by the stepwise addition of three carbon units. b) Saturated fatty acids have no double bonds between carbons. c) Fatty acids with 24 carbons are most common. d) Unsaturated fatty acids are usually branched. e) Laurate is an unsaturated fatty acid.
Saturated fatty acids have no double bonds between carbons.
Glyceraldehyde Phosphate Dehydrogenase
Sickle Cell Anemia Hemoglobin - E6V Alter the solubility of Hemoglobin - crystalize And alter the shape of Red blood cells
The organic chemical reactions is special because (i) it occurs in hydrophilic conditions and (ii) it achieve very complex reactions in a cell. Compare and contrast organic reactions in vitro in a lab and inside a cell.
Similarities includes both in vitro and in vivo organic reactions results in same products and intermediates. Differences: in vitro organic reactions takes place in non-polar solvents where as in vivo organic reactions take place in hydrophilic environment. In vivo reactions use enzymes; have higher specificity, and proceed at a faster rate. Multiple organic reactions can take place without cross talk in vitro but not in vitro
Why DNA has Thymine instead of Uracil as its pyrimidine base?
Suppose if uracil is incorporated in DNA, a mutation (deamination of cytosine will create uracil) would confuse DNA repairing enzymes, whether the original nucleotide was either Uracil or Cytosine. The additional CH3 residue on Thymine would avoid this confusion.
Which of the following statements is TRUE regarding reactions involving oxidation and reduction? 1) The carbon atom is more oxidized in formaldehyde (CH2O) than in methanol (CH3OH). 2) Oxidation of food in all organisms requires oxygen. 3) A molecule is oxidized if it gains an electron (plus a proton) in a reaction. 4) A dehydrogenation reaction is a reduction. 5) In an organic molecule, the number of Câ"H bonds increases as a result of oxidation.
The carbon atom is more oxidized in formaldehyde (CH2O) than in methanol (CH3OH).
Water can absorb and store a large amount of heat while increasing only a few degrees in temperature. Why? a) The heat must first be used to break the hydrogen bonds rather than raise the temperature. b) The heat must first be used to break the ionic bonds rather than raise the temperature. c) The heat must first be used to break the covalent bonds rather than raise the temperature. d) An increase in temperature causes an increase in adhesion of the water. e) An increase in temperature causes an increase in cohesion of the water.
The heat must first be used to break the hydrogen bonds rather than raise the temperature.
Which of the following statements is TRUE regarding cellular metabolism? 1) A living organism decreases the entropy in its surroundings. 2) During catabolism, heat is generated, and the cell uses this heat to perform work during anabolism. 3) The heat released by an animal cell as part of its metabolic processes comes from the bond energies in the foodstuffs that are consumed by the animal. 4) Living organisms defy the second law of thermodynamics, but still obey the first law.
The heat released by an animal cell as part of its metabolic processes comes from the bond energies in the foodstuffs that are consumed by the animal.
In a chemical reaction, the standard free energy change (ΔG°') is calculated to be -3.67 cal/mol. What can be said of the chemical reaction? a) The reaction is not spontaneous under standard conditions. b) The reaction is spontaneous under standard conditions. c) There can be no reaction. d) The reaction is at equilibrium under standard conditions. e) Reactants predominate over products at equilibrium under standard conditions.
The reaction is spontaneous under standard conditions.
Secondary Structure: Local conformation of the protein stabilized by hydrogen bonds
Two main types 1) Alpha Helix and 2) β-pleated sheets Alpha Helix 3.6 residue / turn The CO group of n residue form hydrogen bond with n+4 residue Residues 2 and 4 are at a distance can't form interactions Hydrogen bonding always intramolecular β-pleated sheets Several segments of a polypeptide assumes b-pleated structure and connected by hydrogen bonds Hydrogen bonding can be intra and inter Molecular Parallel and anti parallel b-sheet β−strands are extended - resist pulling Eg., Silk fibroin motif: Small segments of a-helix and/or b-sheets connected by a loop region
polar hydrophobic uncharged
Tyrosine (Y) Asparagine (N) Glutamine (Q) Serine (S) Threonine (T) Cysteine (C)
Which of the following is a nonpolar (hydrophobic) amino acid? Y D K V S
V
Which of the following statements about the polymerization of macromolecules is false? 1) The polymer chain usually has two different ends. 2) A monomer is usually activated by the coupling of the monomer to a carrier. 3) Often the energy needed for polymerization is supplied by ATP. 4) Macromolecules are synthesized by the stepwise addition of monomers. 5) Water is added to join the monomers of the macromolecules.
Water is added to join the monomers of the macromolecules.
The oxidation of glucose to carbon dioxide is given by C6H12O6 + 6O2 ↔6CO2 + 6H2O. The enthalpy change for this reaction ΔH = -673 kcal/mol and ΔG= -786 kcal/mol at 25oC.
What do ΔH and ΔG mean? What does the negative sign mean in each case? DH: This is the measure of the difference in heat content between the products and reactants of the reaction. A -DH means excess heat is released into the environment as reaction proceeds. DG : This is teh measure of the difference in free energy between the products and the reactants of the reaction. Therefore, a - DG means free energy is released into the environment as reaction proceeds. B) What does it mean to say that the difference between the ΔG and ΔH values is due to entropy? The DG (change in free energy), is the algebraic sum of the change in enthalpy (DH) and the change in entropy (DS) that occur as reactants are converted into products under specified conditions. C) Without doing any calculation do you think entropy (ΔS) will be positive or negative In the break down of glucose, a large organic molecule (glucose) combine with six O2 to get 12 simpler molecules (6CO2 and 6H20), which increases randomness to results in a positive entropy change. D) Now calculate ΔS for this reaction and compare it to the answer of "C" DG = DH - T DS DS = (DH - DG )/T = (-673-[-786])/(25+273) = +113/298 = +0.3791 = 379.1 cal/mol-K The sign DS agrees with the prediction in part C E) What are the values of ΔG, ΔH, and ΔS for the reverse of the above reaction as carried out by a photosynthetic algal cells that is using CO2 and H2O to make C6H12O6? Since the reverse reaction of glucose break down is photosynthesis, the values of DS, DH, and DG in photosynthesis will have same magnitude with opposite signs.
ΔH = ΔG + TΔS where ΔH = change in Enthalpy ΔG = change in Free Energy T = Temperature in Kelvin ΔS = Change in entropy Total energy change is equal to sum of the change in useful energy (ΔG) and the energy that is unavailable to do further work. ΔG = ΔH - TΔS - this will measure the spontaneity of a particular process, predicts directionality of reaction ΔG < 0 = (-ΔG) reaction thermodynamically favored - Exergonic Reaction ΔG > 0 = (+ΔG) Spontaneous reaction not favored - Endergonic Reaction
While negative ΔG predicts whether reaction will be spontaneous, It can't say whether reaction will happen ΔG negative: Reaction thermodynamically feasible. Work can be done under the reaction conditions ΔG positive: Reaction is not feasible. Energy must be supplied to drive the reaction Δg = zero: Reaction is at equilibrium No work can be done Nor energy is required
What kind of organism reaches equilibrium? a prokaryote a eukaryote a dead organism one with a low metabolic rate one that is actively metabolizing
a dead organism
Which of the following would be most likely to dissolve in olive oil? 1) a polar molecule 2) a nonpolar molecule 3) a hydrophilic molecule 4) A and C 5) B and C
a nonpolar molecule
What bond is responsible for the branch points in glycogen and amylopectin? 3'-5' phosphodiester linkages b(1->6) glycosidic linkages a(1->6) glycosidic linkages b(1->4) glycosidic linkages a(1->4) glycosidic linkages
a(1->6) glycosidic linkages
What type of protein secondary structure is characterized as being highly extensible because of its coiled structure? A + C A + B a-helix double helix ß-pleated sheet
a-helix
Which of the following is a nucleotide? None of the above adenine + sugar + phosphate sugar + nitrogenous base adenine + deoxyribose phosphate + ribose
adenine + sugar + phosphate
Bioenergetics can be simply defined as applied thermodynamics. holding constant the variables in the universe. the application of biological principles to physics. subdivision of biology. the units in which energy is expressed.
applied thermodynamics.
For proteolytic cleavge of the nuclear protein Lamin A carried out by ------------------ 1) caspase-2 2) caspase-3 3) Caspase-8 4) Caspase-9 5) IAPs
caspase-3
Two water molecules can bond to each other by _________ bonding; this is an example of __________. 1) hydrogen; adhesion 2) covalent; adhesion 3) covalent; cohesion 4) non-covalent; cohesion 5) hydrogen; cohesion
hydrogen; cohesion
Mutant Saccharomyces cerevisiae cells that lack the gene encoding securin can divide more or less normally by mitosis, without significant chromosome segregation defects. Cells harboring a nondegradable version of securin, on the other hand, arrest in metaphase as expected, since they cannot activate separase to enter anaphase. Similarly, cells lacking Cdc20 arrest in metaphase, since they cannot activate APC/C. Finally, cells lacking both securin and Cdc20 arrest in anaphase: they manage to separate sister chromatids, but do not progress much further. These results suggest that in wild-type cells 1) degradation of securin is necessary to trigger sister-chromatid separation. 2) degradation of securin is sufficient to trigger sister-chromatid separation. 3) Cdc20-APC/C is NOT necessary for sister-chromatid separation. 4) Cdc20-APC/C is NOT necessary for later events in anaphase. 5) All of the above.
degradation of securin is necessary to trigger sister-chromatid separation.
Proteins are often composed of two or more distinct modules that fold up independently of one another. They often represent parts of a protein that function in a semi-independent manner. These modules are called ______. All of the above dominoes domains functionals protein motifs
domains
_________ can bind to dynein and kinesin motor proteins and allow movement along the microtubules. 1) sec23 2) sec23p 3) copII 4) dynactin 5) All of the above
dynactin
Which eukaryotic initiation factor binds to the 5' cap of the eukaryotic mRNA? 1) eIF4E 2) eIF4A 3) eIF4G 4) eIF2 5) eIF2A
eIF4E
Which of the following is defined as change "heat content"? enthalpy energy output heat loss entropy solar radiation
enthalpy
Non-polar hydrophobic uncharged
glycine (G) analine (A) phenylalanine (F) Valine (V) Leucine (L) Isoleucine (I) Tryptophan (W) Proline (P) Methionine (M)
Disulfide bond
product of an oxidation reaction between 2 cysteines links 2 sulfur groups to one another Cysteines can be from same or different polypeptide chains broken by reducing Agents Insulin is a 2 chain protein connected by a disulfide bond
Which of the following is NOT a type of vesicle coat protein? 1) rab 2) clathrin 3) COPI 4) COPII 5) all of the above are coat proteins
rab
Disulfide bonds are often found to stabilize which of the following levels of protein structure? none of the above all of the above primary secondary tertiary
tertiary
The first orbital shell of an atom can hold ___ electrons.
two
A covalent bond is formed when: 1) two non-polar molecules associate with each other in a polar environment. 2) a positively charged particle is attracted to a negatively charged particle. 3) one atom gives up electrons to another atom. 4) two atoms share electrons. 5) two polar molecules associate with each other in a non-polar environment.
two atoms share electrons
