What are the chemical elements that

form most of living biological matter?

The chemical elements that form most of the molecules of living beings are oxygen (O), carbon (C), hydrogen (H) and nitrogen (N). 

• Glucose and fructose are examples of

A. double sugarsB. disaccharidesC. single sugarsD. polysaccharides

• What are described as the "building blocks of Protein"?

A. FiberB. LipidsC. Amino AcidsD. Nutrients

• (CH2O)n is the molecular formula for which type of macromolecules?

A. ProteinsB. LipidsC. CarbohydratesD. Nucleic Acid

• Which macromolecule does not dissolve in water?

A. proteinsB. lipidsC. carbohydratesD. nucleic acids

• What type of organic substances are fats?

A. nucleic acidB. carbohydrateC. proteinD. lipids

• What are the monomers of lipids?

A. Amino acidsB. Simple sugarsC. Fatty acids and glycerolD. Nucleic acids

• Which of the following is a polymer?

A. nucleic acidB. fatty acidC. Amino acidD. Glycerol

• Proteins are ____ made of amino acid ____ .

A. monomers; polymersB. polymers; polypeptidesC. polymers; monomersD. monomers; molecules

• Which of the following is NOT a polysaccharide?

A. GlycogenB. StarchC. SucroseD. Cellulose

• What are used in animals as a source of quick energy that can be stored in the liver and muscles ？

A. ProteinsB. Nucleic acidsC. CarbohydratesD. Lipids

• Fats that have fatty acids with only single covalent bonds in their carbon skeletons are

A. saturatedB. unsaturatedC. found in plants instead of animalsD. liquid at room temperature

• Sugars, starches, and cellulose belong to which major class of biological molecules?

A. Nucleic acidsB. carbohydratesC. lipidsD. polypeptides

• Plants like sugar cane and sugar beets store the energy as simple sugars. Other plants, like corn and potatoes, store the energy as more complex sugars called?

A. carbohydratesB. caloriesC. starchesD. cellulose

• This biological macromolecule is responsible for controlling the activity of the cell, and it stores and transports genetic information.

A. CarbohydrateB. Nucleic acidC. WaterD. Glucose

• In this type of structure, most of carbonyl groups of peptide bonds forms a hydrogen bond with the amide nitrogen of another peptide bond four amino acids further down the polypeptide chain:

A. Alpha-helixB. Beta-sheetC. Beta-turnD. Quaternary

• Lipids are used by the body to perform all of the following functions EXCEPT:

A. membrane structural material.B. enzyme action.C. insulation.D. a rich energy source.

• What is the constitutional unit of proteins?

• What is the primary structure of a protein?

• The constitutional units of proteins are the amino acids.

• The primary protein structure is the linear sequence of amino acids that form the molecule.

What is the secondary structure of a

protein?

• The secondary protein structure is generated by the manner its amino acids interact through the inter-residue bond. These interactions create a spatial conformation of the polypeptide filament. The two most studied secondary conformations of proteins are the alpha-helix and the beta-sheet.

• The isoelectric point of an amino acid is defined as the pH

A. where the molecule carries no electric chargeB. where the carboxyl group is unchargedC. where the amino group is unchargedD. of maximum electrolytic mobility

• When the amino acid alanine (R-group is CH3) is added to a solution with a pH of 7.3, alanine becomes

A. a cationB. nonpolarC. a zwitterionsD. an anion

Isoelectric point of alanine

is 6.00

• The term “SALTING IN” refers to?

A. Changes in an amino acid’s isoelectric point.B. Increasing the solubility of a protein in solution by adding ions.C. The use of a liquid bridge in an electrochemical cell.D. The ionization of a strong acid.

Salting Out (by solubility)• Most proteins are less soluble at high salt concentrations, an effect

called salting out. • The salt concentration at which a protein precipitates differs from

one protein to another. Hence, salting out can be used to fractionate proteins.

• Dialysis can be used to remove the salt if necessary.

• The local spatial arrangement of a polypeptide’s backbone atoms without regard to the conformation of its side chains can be called as

A. Primary structureB. Secondary structureC. Tertiary structureD. Quaternary structure

• Which of the following amino acids are more likely to be found in a protein’s interior away from aqueous solvent molecules?

A. Val, Leu, Ile, Met, and PheB. Ser, Thr, Asn, Gln, and TyrC. Arg, His, Lys, Asp, and GluD. All of the above.

• Which of the following is (are) true of -turns in proteins?

A. It is a 180º turn of four amino acids.B. Glycine and proline are frequently found there.C. Are used as connecting turns of -helixD. All of the above.

• The primary stabilizing force of protein secondary structure is:

• A Ionic bonds.• B Covalent bonds.• C Van der Waals forces.• D Hydrogen bonds

• Two types of -pleated sheets can be called:

• A parallel and antiparallel

• B left-handed and right-handed.

• C and • D α and β

• Which of the following is NOT a characteristic of a globular protein?

• A Polypeptide chain in extended, long sheets

• B Polypeptide chains are folded in a spherical shape.

• C Contains several types of secondary structure

• D Typical for regulatory proteins.

• Which of the following statements regarding ligand binding is NOT correct?

A. Some proteins require ligands in order to perform their functionB. Enzymes with their attached ligands are called holoenzymesC. Ligands are synonymous with prosthetic groupsD. The heme group on hemoglobin is an example of a tightly bound ligand

• The alpha helix found in myoglobin can best be described as

A. Primary structureB. Secondary structureC. Tertiary structureD. Motif structure

• Some parts of a protein that have a specific chemical structure and function are called protein

A. chemicalsB. domainsC. subunitsD. enzymes

• One of the following is NOT usually a force that helps to hold the monomer units of a quaternary protein together?

A. Peptide bondsB. Disulfide bondsC. Salt bondsD. Hydrophobic interactions

What is the quaternary structure of a protein?

Do all proteins have quaternary structure?

• The quaternary protein structure is the spatial conformation due to interactions among polypeptide chains that form the protein.

• Only those proteins made of two or more polypeptide chains have quaternary structure.

What is protein denaturation? Is there any change in the primary structure when a protein is de

natured? What are some factors that can lead to protein denaturation?

• Secondary, tertiary and quaternary structures of proteins are spatial structures. Denaturation is modification in any of these spatial structures that makes the protein deficient or biologically inactive.

• After denaturation the primary protein structure is not affected.

• Protein denaturation can be caused by temperature variation, pH change, changes in the concentration of surrounding solutes. Most proteins denature after certain elevation of temperature or when in very acid or very basic solutions.

• Which of the following terms describes hemoglobin but not myoglobin?

A. The protein contains hydrogen bondsB. The protein contains a hydrophobic pocket that contains hemeC. Imidazole groups stabilize the ferrous ionD. The protein contains alpha and beta chains

• Of the following states of hemoglobin (Hb), which is least likely to bind the next molecule of oxygen (O2)?

A. HbB. Hb (O2)C. Hb (O2)2D. Hb (O2)3

• If a person breathes into a paper bag, you would expect their blood CO2 to

A. decrease and their blood pH to increaseB. decrease and their blood pH to decreaseC. increase and their blood pH to increaseD. increase and their blood pH to decrease

• The quaternary structure of a protein is

A. the sequence of amino acids in the polypeptideB. the coiling or folding of the polypeptideC. the intertwining of two or more polypeptidesD. the 3-dimensional appearance of the polypeptide

• The action of disrupting the three-dimensional shape of a protein is termed

A. dehydrationB. denaturationC. deaminationD. hydrolysis

Sample questionsSample questions

• At a pH >pI of a given protein, that protein becomes ______, at the pH<pI of that same protein, it becomes _______.

The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge.

negatively charged (an anion)positively charged (a cation)

Sample questionsSample questions

• What is the prosthetic group that hemoglobin and myoglobin's oxygen binding ability depend on?

• Define cooperativity relative to binding oxygen

• What are the two states of the hemoglobin quaternary structure? And what are their characteristics?

Heme

binding of oxygen at one site increases chances of binding oxygen at the other sites; loss of anoxygen at one site increases the chances of losing oxygen at the other sites

T state = taut (deoxy form)R state = relaxed (oxygenated form)

Sample questions

• The imino acid found in protein structure

• (a) Arginine

• (b) Proline

• (c) Histidine

• (d) Lysin

• The bonds in protein structure that are not broken on denaturation.

• (a) Hydrogen bonds

• (b) Peptide bonds

• (c) lonic bond

• (d) Disulfide bonds

• Which of the following is not considered a pyrimidine?

A. C B. T C. U D. G

• What type of sugar is found in the nucleotides of DNA?

A. deoxyriboseB. riboseC. glucoseD. none of the above

• What is the role of hydrogen bonds in the structure if DNA?

A. to code for proteinsB. to synthesize proteinsC. to separate the strandsD. to connect the base pairs

Which type of chemical bond maintains the

pairing of each chain in the DNA molecule?

• To form the DNA molecule, purine bases bind to pyrimidine bases by intermolecular bonds called hydrogen bonds. Hydrogen bonds occur when there is hydrogen near one of these electronegative elements: oxygen or nitrogen.

Sample questions for the nucleic acid section

Nucleoside is a pyrimidine or purine base

• A.covalently bonded to a sugar• B.ionically bonded to a sugar• C.hydrogen bonded to a sugar• D.none of the above

The sugar in RNA is ______ , the sugar in DNA is _____

• A.deoxyribose, ribose• B.ribose, deoxyribose• C.ribose, phosphate• D.ribose, uracil

Sample questions for the nucleic acid section

In gel electrophoresis, what fragments will move most quickly through a gel?

• A.Large fragments• B.Small fragments• C.Large genome• D.None of these

Nucleotide bases and aromatic amino acids absorb light respectively at

• A.280 and 260 nm• B.260 and 280 nm• C.270 and 280 nm• D.260 and 270 nm

Sample questions for the nucleic acid section

Which of the following is found on RNA but not DNA?

• A.Uracil• B.Deoxyribose• C.Phosphate• D.Adenine

Which is true about the pairing of bases in the DNA molecule?

• A. purines always pair with pyrimidines

• B. a single ring base pairs with another single ring base

• C. a double ring base pairs with another double ring base

• D. purines pair with purines and pyrimidines with pyrimidines

Sample questions for the nucleic acid section

A messenger acid is 336 nucleotides long, including the initiator and termination codons. The maximum number of amino acids in the protein translated from this mRNA is:

• A 999• B 630• C 330• D 111• E 110

With what mRNA codon would the tRNA in the diagram be able to form a codon-anticodon base pairing interaction?

• A. 3'-AUG-5'• B. 3'-GUA-5'• C. 3'-CAU-5'• D. 3'-UAC-5'• E. 3'-UAG-5'

Sample questions for the nucleic acid section

• Of what units are nucleic acids constituted? What are the chemical entities that compose that unit?

• What is the rule for the pairing of nitrogenous bases in the DNA molecule? And in the RNA?

• For each of the following structures identify: the carbohydrate (ribose or deoxyribose)?; nucleoside or a nucleotide? DNA or a RNA system?

Sample questions

What is the function of enzymes within living systems? • A) structural elements • B) neurotransmitters • C) catalysts • D) hormones

Enzymes have names that • A) always end in -ase • B) always end in -in • C) can end either in -in or -ase • D) can end in either -in or -ogen

Sample questions

The protein portion of a conjugated enzyme is called a(n) • A) apoenzyme. • B) coenzyme. • C) holoenzyme. • D) cofactor.

Which of the following could be a component of a conjugated enzyme? • A) coenzyme • B) cofactor • C) apoenzyme • D) more than one correct response • E) no correct response

Sample questions

Enzyme cofactors that bind covalently at the active site of an enzyme are referred to as _________.

• (a) cosubstrates. • (b) prosthetic groups. • (c) apoenzymes. • (d) vitamins

Sample questions

Which of the following statements concerning the effect of temperature change on an enzyme-catalyzed reaction is correct?

• A) An increase in temperature can stop the reaction by denaturing the enzyme.

• B) An increase in temperature can increase the reaction rate by increasing the speed at which molecules move.

• C) An increase in temperature to the optimum temperature maximizes reaction rate.

• D) more than one correct response • E) no correct response

Sample questions• A catalyst can promote product formation during a chemical reaction

by _____. • (a) lowering the activation energy barrier. • (b) stabilizing the transition state. • (c) positioning reactants in the correct orientation. • (d) bringing reactants together. • (e) all of the above

Which of the following is characteristic of an enzyme catalyst? • (a) It positions reactants in the correct orientation. • (b) It lowers the activation energy barrier. • (c) It binds the transition state tighter than the substrate. • (d) all of the above

Sample questions

An enzyme active site is the location in the enzyme where • A) protein side groups are brought together by bending and folding

to form a site for interactions with substrates • B) the catalyst interactions with the enzyme • C) catalyst molecules are generated • D) the substrate creates the catalyst molecules

An enzyme active site is the location in an enzyme where substrate molecules

• A) are generated. • B) become catalysts. • C) undergo change. • D) more than one correct response • E) no correct response

• For the enzyme reaction A+ B = C + D, Delta Go' = + 1 kcal/mol. This reaction will proceed spontaneously in a forward direction if:

A. The concentration of C is increased one-hundred foldB. The concentration of A is increased one-hundred foldC. The concentration of B is lowered one-hundred foldD. The concentration of both A and D are increased one-hundred fold

• Which of the following statements about enzymes or their function is true?

A. Enzymes do not alter the overall change in free energy for a reactionB. Enzymes are proteins whose three-dimensional form is key to their functionC. Enzymes speed up reactions by lowering activation energyD. All of the above

• What is the optimal temperature range for the majority of enzymes?

A. 40-55 ℃ B. 35-40 ℃C. 25-30 ℃ D. 15-20 ℃

• An allosteric activator

A. increases the binding affinityB. decreases the binding affinityC. stabilizes the R state of the proteinD. both (a) and (c)

• Reactants of an enzyme-catalyzed reaction are known as

A. productsB. substratesC. proteinsD. complex

• The location on an enzyme where binding occurs is known as the

A. action pointB. enzymeC. binding locationD. active site

• Enzymes catalyze reactions by

A. Increasing the free energy of the system so that the change in free energy is positiveB. Increasing the free energy of the substrate so that it is greater than the free energy of the productC. Changing the equilibrium constant for the reactionD. Decreasing the free energy of activation

• An apoenzyme 

A. Includes non-protein compounds such as metal ionsB. Consists of complex organic structures which may be classified as activation-transfer coenzymes or oxidation-reduction coenzymesC. Is the protein portion of the enzyme without the cofactorsD. None of the above

• NAD+, FAD, and FMN are all cofactors for:

A. OxidoreductasesB. TransferasesC. HydrolasesD. Ligases

• At the end of a chemical reaction

A. an enzyme's structure is alteredB. an enzyme is detached from the product, has its original structure, and can catalyze more chemical reactionsC. the enzyme loses its ablity to catallyze other chemical reactionsD. the enzyme remains attached to the products

Sample questions

The rate of a second order reaction depends on the concentration of _________.

• (a) one substrate • (b) two substrates • (c) three substrates • (d) none of the above

Rate constant (k) measures how rapidly a reaction occurs

A B + Ck1

k-1

Rate (v, velocity) = (rate constant) (concentration of reactants)

v= k1 [A] 1st order reaction (rate dependent on concentration of 1 reactant)

v= k-1[B][C]2nd order reaction (rate dependent on concentration of 2 reactants)

Zero order reaction (rate is independent of reactant concentration)

Rate constants and reaction order

• On the following plot, N represents the curve for an allosteric enzyme with no allosteric activators or inhibitors added. If an allosteric activator was added, which curve would one obtain?

A. Curve AB. Curve BC. Curve CD. Curve D

• Which of the following statements about allosteric enzymes is CORRECT?

A. The binding of substrate to any active site affects the other active sitesB. The plot of initial velocity vs. substrate concentration is a straight lineC. The Keq of the reaction is increased when allosteric activator is boundD. The enzymes contains only one polypeptide chain

Enzyme kinetics

Sample questions

Which of the following kinetic parameters best describes how well suited a specific compound functions as a substrate for a particular enzyme?

• (a) Km • (b) Vmax • (c) kcat

• (d) kcat/Km

Short summary

• Km substrate specificity; substrate binding

• kcat, the turnover number

• kcat/Km the catalytic efficiency

Sample questions

The rate-determining step of Michaelis Menten kinetics is• A.the complex formation step• B.the complex dissociation step to produce product• C.the product formation step• D.Both (a)and(c)

• A competitive inhibitor of an enzyme works by

A. fitting into the enzyme's active siteB. fitting into the allosteric site of the enzymeC. attaching itself to the substrate, thereby preventing the enzyme from making contact with substrateD. increasing the activation energy of the enzyme-catalyzed reaction

• If an enzyme is described by the Michaelis-Menten equation, a competitive inhibitor will:

A. decrease the Km and decrease the VmaxB. decrease the Km, but not the VmaxC. always just change the VmaxD. increase the Km but not change the Vmax

• The most likely effect of a non-competitive inhibitor on an Michaelis-Menten enzyme is to

A. Increase the Vmax

B. Decrease the Vmax

C. Increase both the Vmax and the KmD. Decrease both the Vmax and the Km

• Competitive inhibitor: Vmax stays the same, but Km increases• Non-competitive inhibitor decreases the turnover number of the enz

yme rather than preventing substrate binding- Vmax decreases but Km stays the same. This cannot be overcome with an increase in substrate concentration.

Sample questions

Which of the following binds to an enzyme at its active site? • A) irreversible inhibitor • B) reversible competitive inhibitor • C) reversible noncompetitive inhibitor • D) more than one correct response • E) no correct response

An uncompetitive inhibitor binds to _____. • (a) E • (b) ES • (c) P • (d) a and b • (e) a and c

Sample questions

A reversible inhibitor that can bind to either E alone or the ES complex is referred to as a _____.

• (a) competitive inhibitor. • (b) non-competitive inhibitor. • (c) uncompetitive inhibitor. • (d) suicide inhibitor. • (e) irreversible inhibitor.

Sample questions

A competitive inhibitor of an enzyme is usually• A.a highly reactive compound• B.a metal ion such as Hg2+ or Pb2+

• C.structurally similar to the substrate.• D.water insoluble

The enzyme inhibition can occur by• A.reversible inhibitors• B.irreversible inhibitors• C.Both (a) and (b)• D.None of these

Sample questions

In a Lineweaver-Burk Plot, competitive inhibitor shows which of the following effect?

• A.It moves the entire curve to right• B.It moves the entire curve to left• C.It changes the x-intercept• D.It has no effect on the slope

Sample questions

Non-competitive inhibitor of an enzyme catalyzed reaction

• A.decreases Vmax

• B.binds to ES• C.both (a) and (b)• D.can actually increase reaction velocity in rare cases

Sample questions

A classical uncompetitive inhibitor is a compound that binds• A.reversibly to the enzyme substrate complex yielding an inactiv

e ESI complex• B.irreversibly to the enzyme substrate complex yielding an inacti

ve ESI complex• C.reversibly to the enzyme substrate complex yielding an active

ESI complex• D.irreversibly to the enzyme substrate complex yielding an activ

e ESI complex

Enzyme regulation

Sample questions• Two curves showing the rate versus substrate concentration are sho

wn below for an enzyme‐catalyzed reaction. One curve is for the reaction in the presence of substance X. The other curve is for data in the absence of substance X. Examine the curves and tell which statement below is true.

• A) The catalysis shows Michaelis‐Menten kinetics with or without X.• B) X increases the activation energy for the catalytic reaction.• C) X could be a competitive inhibitor.• D) X is an activator of the enzyme.

Sample questionsAllosteric enzymes are• A.similar to simple enzyme• B.smaller than simple enzyme• C.larger and more complex than simple enzyme• D.smaller than simple enzyme but not complex

Which statement is false about allosteric regulation?• A. It is usually the mode of regulation for the last step in reaction pathways s

ince this step produces the final product.• B. Cellular response is faster with allosteric control than by controlling enzy

me concentration in the cell.• C. The regulation usually is important to the conservation of energy and mat

erials in cells.• D. Allosteric modulators bind non-covalently at sites other than the active sit

e and induce conformational changes in the enzyme.

Sample questions

Allosteric modulators seldom resemble the substrate or product of the enzyme. What does this observation show?

• A) Modulators likely bind at a site other than the active site.

• B) Modulators always act as activators.• C) Modulators bind non-covalently to the enzyme.• D) The enzyme catalyzes more than one reaction.

Sample questions

• Some enzymatic regulation is allosteric. In such cases, which of the following would usually be found?

• A) cooperativity• B) feedback inhibition• C) both activating and inhibitoryactivity• D) an enzyme with more than one subunit• E) the need for cofactors

Sample questions

• Describe allosteric regulation of enzyme activity?

An allosteric enzyme is one in which the activity of the enzyme can be controlled by the binding of a molecule to the “allosteric site”, somewhere other than the active site. Thus allosteric control of an enzyme can be classed in two ways. A positive allosteric regulation is the binding of a molecule to the enzyme which increase the rate of reaction. The opposite is a negative allosteric regulation. An example for this is phosphofructokinase, which is promoted by a high AMP concentration, and inhibited by a high ATP concentration. 

• This small protein can have dramatic effects on the activities of enzymes in response to changes in intracellular calcium ion concentration:

A. CalcitoninB. CalsequestrinC. CalmodulinD. Calcitriol

Non-covalent InteractionsProtein-Protein Interactions

• Calmodulin (CALcium MODULted proteIN)

– Binding of Ca++ to calmodulin changes its shape and allows binding and activation of certain enzymes

Sample questions

• Which statement is false about covalent modification?• A) It is reversible.• B) It is slower than allosteric regulation.• C) It is irreversible.• D) Phosphorylation is a common covalent modification.

Sample questions

Protein kinases are enzymes that act on other enzymes by adding phosphates groups. When the enzyme is phosphorylated, it changes its activity (it becomes more or less active, depending on the enzyme). This regulatory mechanism of enzymatic activity is called:

• A) Allosteric Control• B) Competitive inhibition• C) Covalent Modification• D) Isozymes Modification • E) Zymogen activation

Glycolysis

Sample questions• Glycolytic pathway regulation involves• A. allosteric stimulation by ADP• B. allosteric inhibition by ATP• C. feedback, or product, inhibition by ATP• D. all of the above

• Why does the glycolytic pathway continue in the direction of glucose catabolism?

• A. There are essentially three irreversible reactions that act as the driving force for the pathway

• B. High levels of ATP keep the pathway going in a forward direction• C. The enzymes of glycolysis only function in one direction• D. Glycolysis occurs in either direction

Sample questions

The released energy obtained by oxidation of glucose is stored as

A. a concentration gradient across a membrane

B. ADP

C. ATP

D. NAD+

A kinase is an enzyme that

A. removes phosphate groups of substrates

B. uses ATP to add a phosphate group to the substrate

C. uses NADH to change the oxidation state of the substrate

D. removes water from a double bond

Sample questions• For every one molecule of sugar glucose which is oxidized __________

molecule of pyruvic acid are produced.• A.1• B.2• C.3• D.4

• The enzymes of glycolysis in a eukaryotic cell are located in the• A.intermembrane space• B.plasma membrane• C.cytosol• D.mitochondrial matrix

Sample questions• Which of the following is not true of glycolysis?• A.ADP is phosphorylated to ATP via substrate level phosphorylation• B.The pathway does not require oxygen• C.The pathway oxidizes two moles of NADH to NAD+ for each mole of glu

cose that enters• D.The pathway requires two moles of ATP to get started catabolizing ea

ch mole of glucose

• ATP is from which general category of molecules?• A.Polysaccharides• B.Proteins• C.Nucleotides• D.Amino acids

Sample questions

• Which of the following regulates glycolysis steps?• A.Phosphofructokinase• B.Hexose kinase• C.Pyruvate kinase• D.All of these

Sample questions• Which of the following is not a mechanism for altering the flux of metab

olites through the rate-determining step of a pathway?• A. Allosteric control of the enzyme activity• B. Block active sites• C. Genetic control of the enzyme concentration• D. Covalent modification of the enzyme

• Phosphofructokinase, the major flux-controlling enzyme of glycolysis is allosterically inhibited and activated respectively by

• A.ATP and PEP• B.AMP and Pi• C.ATP and ADP• D.Citrate and ATP

• Where does glycolysis occur?

A. inner membrane of mitochondriaB. matrix of mitochondriaC. stroma of chloroplastD. cytoplasm

• Sports physiologists wanted to monitor athletes to determine at what point their muscles were functioning anaerobically. They could do this by checking for a buildup of which of the following compounds?

A. oxygenB. ATPC. lactateD. carbon dioxide

gluconeogenesis

Sample questions

• There are four enzymes of gluconeogenesis that circumvent the irreversible steps in glycolysis.  When starting with the substrate pyruvate or lactate they are

• A. Hexokinase, phosphofructokinase-1, phosphofructokinase-2 and pyruvate kinase

• B. Pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase, and glucose-6-phosphatase

• C. Glycerol kinase, glycerol-3-phosphate dehydrogenase, fructose-2,6-bisphosphatase, and glucose-6-phosphatase

• D. Amino transferase, phosphoenolpyruvate carboxykinase, fructose-2,6-bisphosphatase, and glucose-6-phosphatase

Sample questions

• The enzymes that remove phosphate groups during the process of gluconeogenesis and circumvent two of the three irreversible reactions of glycolysis are

• A. Pyruvate kinase and glycerol kinase• B. Phosphoenolpyruvate carboxykinase and glycerol kin

ase• C. 3-Phosphoglycerate kinase and fructose-1,6-bisphosp

hatase• D. Fructose-1,6-bisphosphatase and glucose-6-phosphat

ase

Glycolysis <-> gluconeogenesis

Gluconeogenesis is not the reversal of glycolysis !!!

Glycolysis: in the cytosol

Gluconeogenesis: major part in cytosol-> 1st step in mitochondria -> shuttle

Reverse reaction of glycolysis thermodynamically not favorable !!!

Biotin: prosthetic group -> carrier for CO2

112

Sample questions• The most important control step in gluconeogenesis is fructose-1,6-

bisphosphatase.  All of the following statements are true EXCEPT

• A. Fructose-1,6-bisphosphatase converts fructose-2,6-bisphosphate to fructose-6-phosphate

• B. During times when insulin is high, fructose-1,6-bisphosphatase is inhibited by fructose-2,6-bisphosphate

• C. During a fast or exercise when glucagon and/or epinephrine are high, fructose-1,6-bisphosphatase is active because of the absence of fructose-2,6-bisphosphate

• D. Glycolysis or gluconeogenesis cannot be active at the same time.  If they were is would be a futile cycle

Sample questions• In the liver, glucagon will activate• A. Glycolysis and glycogen synthesis• B. Gluconeogenesis and glycogenolysis• C. Gluconeogenesis and glycogen synthase• D. Gluconeogenesis and glycogen synthesis

• Which of the following statements about hormonal levels during different states is true?

• A. During the time you are eating a high carbohydrate mixed meal, the insulin to glucagon ratio will decrease

• B. When passing from the fed to fasting state, insulin and glucagon usually decrease

• C. When playing basketball, epinephrine is usually low and insulin is high• D. After running for 20 miles, epinephrine and glucagon are high and insulin

is low

Sample questions

• All of the following will result in activation of glycogen phosphorylase in skeletal muscle EXCEPT

• A. Increased concentrations of AMP from contraction of muscle

• B. Increased epinephrine and cAMP• C. Increased cytosolic [Ca++]• D. Increased protein phosphatase• E. Increased activity of glycogen phosphorylase kinase

• All of the following statements concerning glycogen synthesis and glycogenolysis are true EXCEPT

A. High blood glucose and high insulin will activate glycogen synthesis and inhibit glycogen phosphorylaseB. A low insulin to glucagon ratio will activate glycogen phosphorylase and inhibit glycogen synthaseC. Being hit in the head with a bat will activate glycogen synthesis and inhibit glycogen phosphorylaseD. Taking this test will activate glycogen phosphorylase and inhibit glycogen synthase

Lipid metabolism

Sample question

• Atherosclerosis can cause blood• A. thinning• B. blockage• C. thickening• D. none of these

Sample question

• Ketosis is ascribed in part to:– A. Slowdown in fat metabolism– B. An insufficient intermediates of TCA cycle– C. An underproduction of acetyl-CoA– D. An inhibition of glycogen synthesis

Sample question

• In the intestine, the dietary fats are hydrolyzed by• A.triacylglycerol lipase• B.adenylate cyclase• C.pancreatic lipase• D.protein kinase

Sample question

• In eukaryotes fatty acid breakdown occurs in• A. mitochondrial matrix• B. cytosol• C. cell membrane• D. endoplasmic reticulum

Sample question

• Fatty acid synthesis takes place in• A. mitochondria• B. cell membrane• C. cytosol• D. endoplasmic reticulum

Sample question

• Chylomicrons are synthesized in• A. blood• B. liver• C. intestine• D. pancreas

Sample question

• VLDLs are synthesized in• A. blood• B. liver• C. intestine• D. pancreas

Sample question

• Cholestrol is the precursor of• A. steroid hormones• B. vitamin A• C. bile salts• D. both (a) and (c)

Oxidative phosphorylation

Sample Questions• A biological redox reaction always involves• A.an oxidizing agent• B.a gain of electrons• C.a reducing agent• D.all of these

• Coenzyme Q is involved in electron transport as• A.directly to O2• B.a water-soluble electron donor• C.covalently attached cytochrome cofactor• D.a lipid-soluble electron carrier

Sample Questions• FAD is reduced to FADH2 during• A. electron transport phosphorylation• B. lactate fermentation• C. Krebs cycle• D. glycolysis

• During glycolysis, electrons removed from glucose are passed to

• A. FAD• B. NAD+

• C. acetyl CoA• D. pyruvic acid

Sample Questions• Almost all of the oxygen (O2) one consumes in breathing

is converted to:• A.acetyl-CoA.• B.carbon dioxide (CO2).• C.carbon monoxide and then to carbon dioxide.• D.water.

• The carbon dioxide is primary a product of• A.Krebs cycle• B.glycolysis• C.electron transport phosphorylation.• D.lactate fermentation.

Sample Question

• Which of the following statements about the chemiosmotic theory is correct?

• A. Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane.

• B. It predicts that oxidative phosphorylation can occur even in the absence of an intact inner mitochondrial membrane.

• C. The effect of uncoupling reagents is a consequence of their ability to carry electrons through membranes.

• D. The membrane ATP synthase has no significant role in the chemiosmotic theory.

Sample Question

• Uncoupling of mitochondrial oxidative phosphorylation:

• A. allows continued mitochondrial ATP formation, but halts O2 consumption.

• B. halts all mitochondrial metabolism.• C. halts mitochondrial ATP formation, but all

ows continued O2 consumption.• D. slows the conversion of glucose to pyruv

ate by glycolysis.

Sample Questions

• Where does Oxidative Phosphorylation occur?

• In the reaction in which FADH2 transfers hydrogen atoms to Q, which molecule is oxidized and which is reduced?

the inner membrane of the cell mitochondria

• Cellular respiration takes place mostly in:

A. chloroplastsB. ribosomesC. nucleusD. mitochondria

• Which of the following is not present during the TCA cycle?

A. NADHB. O2

C. CO2

D. ATP

• Which of the following is a list of the stages in the correct order?

A. pyruvate oxidation, glyocolysis, the citric acid cycle, and oxidative phosphorylationB. oxidative phosphorylation, glyocolysis, the citric acid cycle, and pyruvate oxidationC. glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylationD. glycolysis, the citric acid cycle, pyruvate oxidation, and oxidative phosphorylation

• What are the products of the citric acid cycle?

A. NADH, ATP, FADH2, and CO2

B. O2, ADP, 1 FAD, and NAD+C. Glucose, ATP, O2, and NADHD. heat, H2O, NADH, and pyruvate

• Which of the following is NOT a way of producing ATP in humans?

A. Krebs CycleB. Alcohol FermentationC. Lactic Acid FermentationD. Glycolysis

• Which of the following is an aerobic product of pyruvate catabolic metabolism?

• A lactate• B ethanol.• C acetyl CoA• D glucose.

• Someone had hypoglycemic coma after he injected himself with a large dose of insulin.  All of the following contributed to his coma EXCEPT

A. Insulin inhibited gluconeogenesis in the liverB. Insulin activated glycogen phosphoryalse in the liverC. Insulin increased Glut4 in the muscle membraneD. Insulin inhibited the mobilization of free fatty acid from adipose and the entrance into liver mitochondria

• The insulin to glucagon ratio is low as it usually is in both Type I and Type II diabetics.  During and immediately after a high carbohydrate meal, you would expect

A. The storage of glucose in muscle to be less than normal for type 2 patients but normal for type 1 patientsB. The storage of glucose in muscle to be less than normal for type 1 patients but normal for type 2 patientsC. The storage of glucose in muscle and liver to be less than normalD. The storage of glucose in muscle and liver to be greater than normal

• All other things being constant, an increase in glucagon would result in an increase in

A. Fatty acid synthesis in adipose tissueB. β-oxidation in liverC. Protein synthesis in muscleD. Glycogenolysis in muscle

• The pathway for the synthesis of glycogen from portal blood glucose in the liver:

A. Is inhibited by glucoseB. Is inhibited by insulinC. Uses activated glycogen phosphorylaseD. Is inhibited by high cAMP

• Epinephrine:

• A stimulates the synthesis of glycogen in liver cells.

• B has no effect on cAMP in muscle cells• C has a direct effect on the glucose tran

sporter in muscle cells.• D stimulates the degradation of glycoge

n in muscle cells.

• The TCA cycle:

A. Is found in the cytosolB. Is controlled by the ADP/ATP ratio and the NADH concentrationC. Is also called the Cori cycleD. Produces most of the water made in humans

• The Krebs Cycle begins when pytuvic acid produced by glycolsis enters the

A. cytosolB. airC. mitochondrionD. nuclear

• During the fasting state, the release of fatty acids from adipose tissue is increased. At least part of the signal for this release is carried by

A. insulin from beta-cells of the pancreasB. epinephrine from alpha-cells of the pancreasC. epinephrine from the adrenal medullaD. glucagon from the adrenal medulla

• In aerobic organisms growing in the presence of oxygen, the NADH produced by glycolysis ultimately donates its high-energy electrons to .

A. electron transport chains in the mitochondriaB. ATPC. pyruvateD. glucose

• Cellular respiration takes place mostly in:

A. chloroplastsB. ribosomesC. nucleusD. mitochondria

• The main purpose of the electron transport chain is to:

A. Use high energy electrons from other cycles to convert ADP into ATPB. Maintain a stable balance of high energy electronsC. Constantly distribute electrons throughout the cellD. Tell the cell when glycolysis should stop or start

• Oxidative phosphorylation:

A. Is anaerobicB. Requires AMPC. Requires the electron transport systemD. Is not dependent upon development of a proton gradient

• Where are the proteins of the electron transport chain located?

A. cytosolB. mitochondrial outer membraneC. mitochondrial inner membraneD. mitochondrial matrix

• The ATP synthase responsible for most of the ATP synthesis in the body is located:

A. On the outer side of the outer mitochondria membraneB. On the inner side of the outer mitochondria membraneC. On the outer side of the inner mitochondria membraneD. On the inner side of the inner mitochondria membrane

• In the electron transport chain, the final electron acceptor is

A. oxygenB. a molecule of carbon dioxideC. a molecule of waterD. ADP

• A mitochondrion is producing ATP at a constant rate and, then, a chemical uncoupler is added. Compared to before the uncoupler was added:

A. Less heat would be producedB. Less water would be producedC. More NADH would be oxidizedD. The proton gradient across the membrane would be increased

With uncoupler present, there is no pH or . G for H+ ejection is zeroG for e transfer coupled to H+ ejection is maximal (spontaneous). Respiration proceeds in the presence of an uncoupler, whether or not ADP is present.

Matrix

H+ + NADH NAD+

+ 2H+ 2H+ + ½ O2 H2O

2 e I Q III IV

4H+ 4H+ 2H+ H+ Intermembrane Space

cyt c

uncoupler

• A direct inhibitor of the ATP synthase (i.e. the ability to make ATP) in the presence of active electron transport:

• A. would increase the membrane potential.

• B would decrease the membrane potential.

• C would increase electron transport rates

• D would decrease the pH gradient.

• During chemiosmosis,

A. energy is released as H+ ions move across mitochondrial membranesB. H+ do NOT play any role in the production of ATP moleculesC. a concentration gradient is generated when large numbers of H+ ions are passively transported from the matrix of the mitochondrion to the mitochondrion's intermembrane spaceD. ATP is synthesized when H+ ions move through a channel in ATP synthase

• The chemiosmotic theory holds all of the following EXCEPT:

A. The cytosol has a higher pH than the matrixB. In the absence of a proton motive force, ATP will not be synthesizedC. The electrochemical potential comes from both the electrical potential and the proton concentration gradientD. Electrons are passed from one carrier to the next as protons are pumped across the inner mitochondrial membrane

• During REDOX reactions in cellular respiration, glucose undergoes _____ while oxygen undergoes______

A. reduction ..... oxidationB. oxidation ..... reductionC. no change ..... oxidationD. none of the above

• Anemia, hemorrhage, and chronic obstructive pulmonary disease can all cause metabolic acidosis. The best explanation is that the lack of oxygen causes

A. a decrease in insulin that, in turn, increases anaerobic glycolysis in the brainB. a decrease in oxidative phosphorylation so the cells have to rely upon anaerobic glycolysisC. a decrease in the removal of CO2 from the blood. The resulting decrease in pH causes an increase in glycolysis in most cellsD. an increase in glycolysis in red blood cells

• Hydrolysis of a triglyceride produces

A. many amino acidsB. different types of nucleotidesC. fatty acids and glycerolD. monosaccharides

• Free fatty acids are able to travel from adipose tissue to muscle or liver 

A. As independent water soluble compounds in the bloodB. By using receptors on red blood cellsC. Bound to serum proteinsD. By using enzymes that modify them

• When the concentration of epinephrine or glucagon is high, they bind to receptors on adipose cell membrane and all of the following can be expected to occur EXCEPT

A. Triacylglycerol is hydrolyzed to free fatty acids and glycerolB. Free fatty acids are carried to most tissues of the body by albuminC. Fatty acids are activated, enter the mitochondria, and are oxidized by β-oxidation and the TCA cycleD. Increased β-oxidation increases glycolysis in resting muscle

Amino acid metabolism

Sample question

• The site of amino acid catabolism is the:A. StomachB. Small intestineC. Large intestineD. Liver

Sample question

• The first step in the catabolism of most amino acids is

• A. Removal of carboxylate groups• B. Enzymatic hydrolysis of peptide bonds• C. Removal of the amino group• D. Zymogen cleavage

Sample question

Which of the following is true of urea?  • A. more toxic to human cells than ammonia • B. the primary nitrogenous waste products of

humans. • C. insoluble in water • D. the primary nitrogenous waste product of

most aquatic invertebrates

Sample question

A glucogenic amino acid is one which is degraded to

• A. keto-sugars• B. either acetyl CoA or acetoacetyl CoA• C. pyruvate or citric acid cycle intermedia

tes• D. none of the above

Sample question

Transamination is the process where

• A. carboxyl group is transferred from amino acid

• B. α-amino group is removed from the amino acid

• C. polymerization of amino acid takes place• D. none of the above

Sample question

Transamination is the transfer of an amino

• A. acid to a carboxylic acid plus ammonia• B. group from an amino acid to a keto acid• C. acid to a keto acid plus ammonia• D. group from an amino acid to a carboxylic a

cid

Nucleic acid metabolism

Sample Question

•  In inherited deficiency of hypoxanthine guanine phosphoribosyl transferase

(A) De novo synthesis of purine nucleotides is decreased(B) Salvage of purines is decreased(C) Salvage of purines is increased(D) Synthesis of uric acid is decreased

Sample Question

• Which of the following is a required substrate for purine biosynthesis ?

(A) 5- methyl thymidine(B) Ribose phosphate(C) PRPP(D) 5-Fluoro uracil

Sample Question

• The conversion of Inosine mono phosphate

(A) To Adenosine mono phosphate (AMP) is inhibited by Guanosine mono phosphate (GMP)(B) To AMP requires uridine mono phosphate (UMP)(C) To GMP requires GMP kinase(D) To GMP requires Glutamine

HN

N N

N

O

Ribose-P

N

N N

N

NH

Ribose-P

COO--OOC

HN

N N

N

O

Ribose-P

O

H

Adenylosuccinate xanthine monophosphate XMP

IMPIMP dehydrogenase

NAD+

NADH

A.S. synthetase

Aspartate + GTP

GDP

N

N N

N

NH2

Ribose-P

HN

N N

N

O

H2N

Ribose-P

A.S. lyase

fumarate

glutamine + ATP

Glutamate + AMP+ PPi

AMP GMP

Synthesis of adenineand guanine nucleotides

• Glutamine, NAD, ATP used in GMP production

• Aspartate, GTP used AMP production

IMP to AMP and GMP

DNA replication

Sample questions

• Both strands of DNA serve as templates concurrently in

• A. replication

• B. excision repair

• C. mismatch repair

• D. none of these

• Proofreading activity to maintain the fidelity of DNA synthesis

• A. occurs after the synthesis has been completed• B. is a function of the 3'-5' exonuclease activity of the

DNA polymerases• C. requires the presence of an enzyme separate fro

m the DNA polymerases• D. occurs in prokaryotes but not eukaryotes

• Which of the following repairs nicked DNA by forming a phosphodiester bond between adjacent nucleotides?

• A. Helicase• B. DNA gyrase• C. Topoisomerases• D. DNA ligase

• The replication of chromosomes by eukaryotes occurs in a relatively short period of time because

• A. the eukaryotes have more amount of DNA for replication

• B. the eukaryotic replication machinery is 1000 times faster than the prokaryotes

• C. each chromosome contains multiple replicons• D. eukaryotic DNA is always single stranded

• During which of the following process a new copy of a DNA molecule is precisely synthesized?

• A. Trasformation• B. Transcription• C. Translation• D. Replication

• Which of the following enzyme adds complementary bases during replication?

• A. Helicase• B. Synthesase• C. Replicase• D. Polymerase

• Which of the following enzymes unwind short stretches of DNA helix immediately ahead of a replication fork?

• A. DNA polymerases• B. Helicases• C. Single-stranded binding proteins• D. Topoisomerases

• Which DNA polymerase removes RNA primers in DNA synthesis?

• A. Polymerase I• B. Polymerase II• C. Polymerase III• D. none of these

DNA polymerases are specialized for different roles in the cell

• Enzyme, responsible for proofreading base pairing is

• A. DNA polymerase• B. Telomerase• C. Primase• D. DNA ligase

• DNA helicase is used to

• A. unwind the double helix• B. interact the double helix closely• C. break a phosphodiester bond in DNA strand• D. none of the above

• The synthesis of DNA by DNA polymerase occurs in the

• A. 3' to 5' direction• B. 5' to 5' direction• C. 5' to 3' direction• D. 3' to 3' direction

• The 5' and 3' numbers are related to the

• A. length of the DNA strand• B. carbon number in sugar• C. the number of phosphates• D. the base pair rule

• What is the main damaging effect of UV radiation on DNA?

• A. Depurination• B. Formation of thymine dimers• C. Single strand break• D. Dehydration

What is the function of DNA polymerase?Explain how a DNA molecule contains the

information necessary to produce copies of itself.

• DNA polymerase is an enzyme that catalyzes the reaction that adds nucleotides to a growing DNA strand while replication occurs. This enzyme also has a role in repairing errors in DNA molecules.

• Each strand of a DNA molecule serves as a template for the synthesis of a complementary DNA strand using base pair relationships. This makes it possible to produce an exact copy of a DNA molecule.

Transcription

Sample questions

• Which of the following enzyme is used for synthesis of RNA under the direction of DNA?

• A. RNA polymerase• B. DNA ligase• C. DNA polymerase• D. RNA ligase

• Which of the following is a product of transcription?

• A. mRNA

• B. tRNA

• C. rRNA

• D. all of these

• Recognition/binding site of RNA polymerase is called

• A. receptor

• B. promoter

• C. facilitator

• D. terminator

• An mRNA transcript of a gene contains

• A. a start codon

• B. a stop codon

• C. a terminator

• D. all of these

• The components found in all prokaryotic transcription terminators is

• A. a poly-U region

• B. Rho factor

• C. a hairpin structure

• D. none of these

• Where in the cell is the DNA transcribed into mRNA?

• A. Cytoplasm• B. Nucleus• C. Golgi• D. Cell cytoskeleton

• Which of the following does NOT happen during hnRNA processing?

• A. Introns are spliced out.• B. A 7-methylguanosine cap is added to the 5' end of the RNA.• C. A poly A tail is added.• D. Ribosomes bind and begin translation.

• Since the two strands of the DNA molecule are complementary, for any given gene:

• A. The RNA polymerase can bind to either strand.• B. Only one strand actually carries the genetic code for a

particular gene.• C. Each gene possesses an exact replica so that no

mutation occurs.• D. A gene transcribed in the 5’ to 3’ direction on one

strand can be transcribed in the 3’ to 5’ direction on the other strand.

Translation

Sample questions

• The site of protein synthesis is

• A. Ribosome

• B. Nucleus

• C. Endoplasmic reticulum

• D. Chromosome

Sample questions

• The structure in a bacterium that indicates an active site for protein synthesis is

• A. a chromosome.

• B. a cell membrane,

• C. a flagellum.

• D. a polysome.

Sample questions

• Which of the following is not necessary for protein synthesis to occur, once transcription is completed?

• A. tRNA• B. Ribosomes• C. mRNA• D. DNA

Sample questions

• During the process of translation:

• A. the peptide is ‘passed’ from the tRNA in the P-site to the tRNA in the A-site.

• B. incoming tRNAs must first bind to the E-site.• C. initiation begins with the binding of the ribosomal SSU to the pol

y-A tail of the mRNA.• D. the mRNA is translated by one ribosome at a time.

• The nucleolus of the nucleus is the site where:

• A. RNA processing occurs• B. rRNA is transcribed and ribosomal subunits are ass

embled• C. tRNA are charged with amino acids• D. mRNA is translated into protein

Ribosome Assembly: takes place largely in a specialized domain ofthe nucleus, the nucleolus

• The ribosomes are composed of

• A. proteins

• B. RNA

• C. both (a) and (b)

• D. lipids

• Which is required for protein synthesis?

• A. tRNA

• B. mRNA

• C. rRNA

• D. All of these

• In the genetic code there are:

• A. more tRNAs than codons.• B. more codons than amino acids.• C. more nucleotides than codons. • D. the same number of codons and amino aci

ds

• he anticodon of tRNA

• A. binds to rRNA• B. binds to an amino acid• C. binds to the Shine Dalgarno sequence• D. binds to an mRNA codon

• Initiation of eukaryotic translation begins when the:

• A. large and small subunits link together, then bind to the mRNA.

• B. ribosomal small subunit holding an initiator tRNA binds to the 5’ end of mRNA.

• C. ribosome binds to of the start codon and an initiator tRNA enters the ribosome.

• D. initiator tRNA binds to the start codon, followed by binding of the ribosome large subunit.

• On the ribosome, mRNA binds

• A. between the subunits• B. to the large subunit• C. to the small subunit• D. none of these

In addition to the APE sites there is an mRNA binding groovethat holds onto the message being translated

• The peptidyl transferase reaction occurs

• A. on the large subunit

• B. on the small subunit

• C. between the subunit

• D. none of these

• Ribosomes select the correct tRNAs

• A. based on the aminoacyl group

• B. solely on the basis of their anticodons

• C. depending on their abundance in the cytosol

• D. with the least abundant anticodons

• Which of the following amino acid starts all proteins synthesis?

• A. Glycine

• B. Proline

• C. Thymine

• D. Methionine

• The growing polypeptide chain is released from the ribosomes when

• A. a chain terminating codon is reached• B. a chain terminating tRNA binds to the ribosome• C. the 7-methyl guanosine cap is reached• D. the poly A tail is reached

What is a gene?

• A gene is a region of DNA whose final product is either a polypeptide or an RNA molecule

Gene regulation

Sample questions

• The lac repressor is a

• A. carbohydrate.

• B. DNA molecule.

• C. RNA molecule.

• D. protein molecule.

• What would be the effect of a mutation in the operator that blocked the lac repressor binding?

• A. The genes would be inducible by lactose.

• B. The lacZYA genes would be expressed constitutively.

• C. The lacZYA genes would not be expressed.• D. The lacZYA genes would be repressed by lactose.

• A regulatory site within the leader sequence of the tryptophan operon that controls this operon by diminishing transcription is called:

• A. operator• B. upregulator• C. repressor• D. transcriptor

• Which level of primary control in eukaryotic gene activity involves processing early RNA transcripts to mRNA and control of the rate at which mRNA leaves the nucleus?

• A. transcriptional control• B. translational control• C. posttranscriptional control• D. posttranslational control

• An enhancer site is

• A. part of an operon.

• B. found only in prokaryotes.

• C. located at a distance from the gene it affects.

• D. an attachment site for RNA polymerase.

Cell growth and carcinogenesis

Sample questions

• The event(s) which does not occur during interphase, is/are

• A. Chromatin condenses

• B. Protein Synthesis

• C. Organelles replication

• D. DNA replication

The Cell Cycle

• 2 major phases– Interphase– Mitosis

• At the center of the cell cycle control system is Cdk, a protein that

• A. is phosphorylated to become active

• B. binds to different cyclins

• C. is only active during mitosis

• D. manufactures growth factors

Sample questions

• An oncogene is

• A. a viral gene with no relation to the host cell's genes.

• B. a mutated form of a proto-oncogene.• C. a bacterial gene that causes cancer in the

host.• D. a gene that turns off cellular reproduction.

Questions that have been reviewed

The complementary sequence in the standard 5’ 3’ notation for GATCAA is _______

• TTGATC

List at least 3 non-covalent interactions in the biomolecules

• van der Waals• Hydrogen bonds• Ionic bonds• Hydrophobic interactions

Explain the hydrophobic interactions

• Hydrophobic interactions minimize interactions of non-polar components with aqueous solvent.

How are proteins separated by electrophoresis?

• The separation of proteins is done by charge. pH is kept higher then the isoelectric pH (pI). So, the proteins will have negative charge and so the proteins will move towards the positive electrode.

Explain the definition of domain of proteins.

• Fundamental functional & three dimensionFundamental functional & three dimensional structural units of proteins.al structural units of proteins.

What is the function of chaperones in protein folding? List at least one role.

• Assist foldingAssist folding• Protect Protect aggregation• Some times keep protein unfolded until sSome times keep protein unfolded until s

ynthesis is complete.ynthesis is complete.

Explain the difference between reversible denaturation and irreversible denaturation of proteins.

• Some proteins can refold upon removal of denaturant. Other can’t refold upon the removal of denaturant.

Molecules contain both a positive and a negative charged functional group is called _____

• zwitterion

Hemoglobin is an allosteric protein that can exist in two states: R (relaxed) and T (taut). ____ state binds oxygen tighter.

• R (relaxed)

The change in oxygen affinity with pH is known as the Bohr effect. Hemoglobin oxygen affinity is ____

(increased/decreased) as the acidity increases.

• Reduced or decreased

Proteins that recognize and bind to a particular antigen with very high specificity belong to a group of serum proteins called ______.

• Immunoglobulins or antibodies

What is the shape of the oxygen hemoglobin dissociation curve? How does the shape of the curve relate to

the cooperative binding of O2?

• Sigmoid or sigmoidal curve

• The small change of oxygen partial pressure results in a greater change of the hemoglobin binding affinity to oxygen.

How does the shape of oxygen–hemoglobin dissociation curve influence loading of oxygen at the lung and unloading of oxygen at the

tissue level? • There are a high oxygen partial pressure

in the lung and a low oxygen partial pressure in the other tissues. At high oxygen pressure, the hemoglobin tends to be saturated with oxygen while, at low oxygen pressure hemoglobin tends to unload all the oxygen molecules.

List at least 3 factors that influence the binding of hemoglobin to oxygen.

• carbon dioxide or CO2

• pH or acidity

• Oxidative state of Fe in the heme group

• 2,3-DPG or 2,3-BPG

• Carbon monoxide or CO

_____ are long polymers of nucleotides.

• Nucleic acids

The maximal UV absorbance of nucleic acids and proteins are at the wavelength of ___ nm and ___ nm, respectively.

• 260, 280

The sugar groups in the nucleic acids are ___ (D/L) ribose while the residues in the protein are ___ (D/L) amino acids.

• D, L

Polymer of nucleotides linked in a direction from ribose carbon ___ (3’/5’) to carbon ___ (3’/5’) by ______bonds.

• 5’, 3’, phosphodiester

List at least 3 types of RNA molecules in the biological system.

• ribosomal RNA or rRNA• messenger RNA or mRNA• transfer RNA or tRNA• microRNA or miRNA• small RNA or siRNA• long non-coding RNA• short non-coding RNA

Besides hydrophobic interactions, hydrogen bonding, and electrostatic interactions, nucleic acids have one more type of noncovalent i

nteraction that is called ____.

• Stacking interactions or base stacking (interactions between stacked bases)

What is DNA melting temperature?

• the temperature at which a DNA double helix dissociates into single strands

What is the purpose of using the polymerase chain reaction (PCR) in diagnosis or research?

• to rapidly amplify sequences of DNA

In the nucleosome, DNA wrapped around an octamer protein complex that are c

alled ____.

• histone

DNA binding proteins bind DNA in two ways: sequence-specific binding and non-sequence specific binding. Please list two example of non-sequence specific binding proteins.

• Single-stranded nucleic acid binding proteins (SSB)

• Exonucleases, RNase, or DNase • RNA polymerases or DNA polymerases• Topoisomerases

Define the enzyme active site.

• The active site of an enzyme represents as the small region at which the substrate (s) binds and participates in the catalysis

Feedback Inhibition is a type of allosteric regulation for enzyme. When does feedback inhibition occur?

• This occurs when an end-product of a pathway accumulates as the metabolic demand for it declines.

For every molecule of glucose that enters glycolysis, there is an initial investment of 2 molecules of ____ before the subsequent generation of ____ .

• ATP, ATP

What is the purpose of glucagon?

• It slows down glycolysis when blood sugar is low and stimulates the formation of more glucose.

An enzyme that catalyzes the phosphorylation of a molecule using ATP is called ____

• Kinase

Name two molecules that carries electrons from glycolysis and Krebs Cycle to the electron transport system.

• NADH and FADH2

Phosphofructokinase-1 (PFK-1) is an enzyme in glycolysis. It’s activity is controlled by a complex allosteric regulation.

What is the function of AMP in the PFK-1 regulation?

• AMP allosterically activates PFK-1

There are three irreversible reactions in the glycolysis. What are the corresponding enzymes that catalyze those reactions?

• Hexokinase or Glucokinase

• Phosphofructokinase 1 or PFK-1

• Pyruvate Kinase

Hexokinase is allosterically inhibited by its product Glucose 6 phosphate. The hexokinase in the liver is called glucokinase. However, glucokinase is not subject to product inhibition by glucose-6-phosphate. What the benefit of this characteristics of glucokinase?

• Liver will take up & phosphorylate glucose even when liver glucose-6-phosphate concentration is high.

During the Cori cycle, _____ is transported to the liver to regenerate glucose which is returned to muscle tissue.

• Lactic acid or lactate

Insulin is produced when blood glucose is high. How does insulin regulate the transcription of the glycolysis enzyme in liver,

glucokinase?

• Insulin activates of transcription of Glucokinase in liver.

In the liver, the most important coordinating modulator is fructose 2,6-bisphophate (F2,6BP). It is formed from F6P by the enzyme domain, phosphofructokinase-2 (PFK-2), and broken down by the same enzyme, but at a different domain called fructose 2,6-bisphosphatase (FBPase-2). How does the balance of PFK-2 to FBPase-2 activity controlled by glucagon?

• Glucagon causes the enzyme phosphorylation. Phosphorylation of the enzyme results in the inactivation of the phosphofructokinase-2 activity and activation of the fructose-2,6-bisphosphatase activity.

The last product of glycolysis is ____ while the first reactant of Krebs cycle is ____.

• Pyruvate, Acetyl Co-A

Briefly explain the Cori cycle which is a linked metabolic pathways.

• The glucose can enter the blood and be carried to muscles.

• Lactic acid is produced by anaerobic glycolysis in the muscles

• The lactic acid is sent in the blood to the liver which can convert it back to glucose through gluconeogenesis.

What is epinephrine’s role in glycogen and glucose metabolism?

• Epinephrine markedly stimulates glycogen breakdown and glycolysis.

Palmitic acid, CH3(CH2)14COOH, can maximally yield ____ acetyl-CoAs through ____ cycles of beta-oxidation.

• Eight, seven

Why can acetone be detected on breath of diabetic patients?

• Acetone breath in diabetics is caused by an excess production of ketone bodies.

• Glucose is abundant in blood, but uptake by cells in muscle, liver, and adipose cells is low. Cells, metabolically starved, turn to gluconeogenesis and fat/protein catabolism

• However, due to excess gluconeogenesis, oxaloacetate is low, so acetyl-CoA from fat/protein catabolism does not go to TCA, but rather to ketone body production.

High cholesterol diet leads to ____ (promotion/repression) of LDL receptor synthesis.

• repression

Chylomicrons are vesicles found in the blood and lymphatic fluid where they serve to transport lipid from the intestine to the liver and to adipose tissue. Of what are the chylomicrons composed? List at least 3 components.

• Triglycerides

• Cholesterols

• lipoproteins

• phospholipids

• Cholesteryl ester

What is the effect of epinephrine and glucagon on triglyceride metabolism?

• Epinephrine and glucagon trigger the mobilization of stored triglycerides

What is oxidative phosphorylation?

• Answer1: Oxidative phosphorylation transfers energy from NADH to ATP. (via chemiosmosis)

• Answer2: Oxidative phosphorylation is the process of converting this high redox potential into energy-rich ATP molecules.

Oxidative phosphorylation is accomplished via two separate systems in the mitochondrion. What are those two systems?

• Electron transport chain system and ATP synthesis system.

ATP synthesis is driven by proton motive force. What are the two types of gradient associated with proton motive force?

• a proton gradient or pH gradient

• a electrical gradient or ion gradient

Metabolism of amino acids differs, but all of them require the removal of amino groups. What are the two types of reactions to remove amino groups?

• Transamination

• Deamination

Disposal of ammonia from amino acid metabolism as _____ in most tissues especially in the brain and kidneys, as _____ in the liver, and as _____ in the skeletal muscles.

• Glutamine, urea, alanine

Based on the catabolic fates of carbon skeleton of amino acids, the amino acids can be classified as ____ or _____.

• Glucogenic, ketogenic

Dietary nucleotides _____ (do/do not) contribute energy as an energy source material and _____ (are/are not) incorporated into RNA or DNA.

• Do not, are not

The purine nucleotides are synthesized via two pathways in the body. One is ____ synthesis pathway while the other is ____ pathway.

• De novo, salvage

The purine synthesis is _____ by PRPP, _____ by IMP, _____ by AMP, and _____by GMP. Fill the blank with activated or inhibited.

• Activated, Inhibited, Inhibited, Inhibited,

What are the carbohydrate and fat metabolic events occurred in liver during fasting?

• The liver first starts glycogen degradation, then gluconeogenesis to maintain blood glucose levels.

• The fatty acid oxidation and ketone body production are increased.

Insulin promotes the translocation of ______ to the plasma membrane.

• GLUT or glucose transporter

Why do we say that DNA replication is semiconservative?

• The new strands composed of one original strand and one daughter strand

DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3’ end. Therefore, a short _____ is required to initiate nucleotide synthesis.

• RNA primer

Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends called ______.

• telomeres

Why is DNA replication semi- discontinuous?

• DNA strands are antiparallel. And, replication process obeys the principle that DNA is synthesized from the 5´ end to the 3´end.

• Leading strand synthesized continuously while lagging strand synthesized discontinuously

replication transcription

template double strands single strand

substrate dNTP NTP

primer yes no

Enzyme DNA polymerase RNA polymerase

product dsDNA ssRNA

base pair A-T, G-C A-U, T-A, G-C

List at least 3 differences between replication and transcription.

The whole genome of DNA needs to be replicated, but only small portion of genome is transcribed

• Template, coding

During transcription, one of the DNA strands called ______ strand is the strand from which the RNA is actually transcribed. The other strand called _____ strand is the strand whose base sequence specifies the amino acid sequence of the encoded protein.

• Only the template strand is used for the transcription, but the coding strand is not.

• The transcription direction on different strands is opposite.

5'

3'

3'

5'

What is asymmetric transcription?

The mRNA start codon is ___ in most cases.

• AUG

Deoxyribonucleotides are formed from their corresponding _____.

• ribonucleotides

• During splicing, introns are removed from the strand, and the exons that remain are assembled into a finished strand of mRNA that is ready for translation. 

Explain mRNA splicing

What is the consequence of frameshift mutation?

• Frameshift mutations result in all subsequent reading frames (codons) being shifted by one or two nucleotides. These shifted frames will code for different amino acids than before, and will result in the creation of a malfunctioning protein.

The GUU GUA transition still codes for Val and it therefore called to be ______ mutation.

• nonsense

The insertion or deletion of a nucleotide into a gene results in a _____ mutation.

• frameshift

An incoming aminoacyl-tRNA enters the ribosome at the ___ site.

• A

____ are synthesized as inactive precursors that require proteolysis for activation.

• zymogen or proenzyme

In the operon system, tryptophan acts as a ____ by binding the trp repressor.

• Co-repressor