Biochem 384 Exam 1 Review

The first cloned mammal was created by transferring the nucleus of a somatic cell into an unfertilized egg. This accomplishment represented a significant advance in cloning technology, but there was concern that cloning animals using this method would result in animals that aged prematurely. What was the basis for this concern? (ch.3)

Every time a cell divides, the telomere length is reduced. Because somatic cells have little to no telomerase activity, these cells cannot restore telomere length, and older cells generally have shorter telomeres. Scientists feared that an embryo created from a somatic cell would have the telomere length, and therefore "age," of the somatic cell.

Random mutations occur in DNA at a high frequency, although most are repaired quickly and do not alter the DNA sequence in germ cells (sperm and egg cells). However, occasionally a DNA mutation will occur in the germ line and be passed on to the next generation through mating. Explain why most variations in DNA sequence between individuals of the same species are found outside of the protein-coding regions of genes. (ch.1)

Germ-line mutations occurring outside of protein-coding sequences can persist in the germ line if they do not affect genome stability or regulation; there are neutral mutations. However, germ-line mutations occurring in protein-coding sequences will be selected against by natural selection if they alter reproductive rates.

Which of the following are negatively charged amino acids at pH = 7? (HW3)

Glu, Asp

Hydrolysis of ATP is favorable (ΔG°′ = −30.5 kJ/mol), but the addition of inorganic phosphate (Pi) to glucose to yield glucose-6-phosphate (the first step in glycolysis) is unfavorable (ΔG°′ = +13.8 kJ/mol). Show how these two reactions can be coupled to favor formation of glucose-6-phosphate and allow glycolysis to proceed. Include the overall ΔG°′ value for the reaction. (ch.2)

Glucose+Pi <--> Glucose-6-phosphate ΔG°′=+13.8kJ/mol ATP <--> ADP+Pi ΔG°′=-30.5kJ/mol ------------------------ Glucose + ATP <--> Glucose-6-phosphate + ADP ΔG°′=-16.7kJ/mol

Which THREE of the following statements about autotrophs and heterotrophs on Earth are true? (HW1)

Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration. The majority of autotrophs on Earth require aerobic respiration in order to survive. Heterotrophs depend on autotrophs for conversion of light energy to chemical energy.

Identify the THREE conditions in the list below that BEST describe low energy charge in a cell. (HW1)

High AMP concentrations, Low ATP concentrations, The energy charge ratio is below 0.70

Name the four noncovalent interactions that occur within and between biomolecules that facilitate life processes at the molecular level. Which of these noncovalent interactions directly or indirectly involve H2O molecules? (ch.2)

(1) Hydrogen bonds, (2) ionic interactions, (3) van der Waals interactions, and (4) hydrophobic effects. Hydrogen bonds form directly between H2O and biomolecules and between H2O molecules themselves, whereas hydrophobic effects are indirectly caused by H2O due to "water-avoiding" interactions between nonpolar molecules.

What characterizes (a) secondary and (b) tertiary protein structure? (HW3)

(a) alpha helices/beta sheets; (b) zinc fingers

For the reaction A↔B, ΔG°' = -28.5 kJ/mol At steady-state in cells at 37 °C, [A] is 0.05 mM and [B] is 15 mM, calculate ΔG for the A↔B reaction. (Note: Use the alternative convention that the biochemical standard state is defined at 37C.) (HW1)

-13.8 kJ/mol

Consider a reaction consisting of 2 species D and M which interconvert according to the reaction D < == > 2M. Assume that at equilibrium, the concentrations are [D]eq = 4.8 x 10^-5 M and [M]eq = 4.0 x 10^-6 M . What is Keq for this reaction? (HW1)

0.00000033 M

What is the isoelectric point (pI) of lysine, which has pKa values of 2.1 for the α-carboxyl group, 9.7 for the α-amino group, and 10.5 for the side chain amino group? (HW2)

10.1

A histidine residue is in a hydrophobic environment in the interior of a protein. If the pKa of the imidazole group of this histidine is 5.5, what would be the ratio of deprotonated imidazole sidechain to protonated imidazole sidechain at pH 7? (HW2)

31.6/1

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is adenine? (HW2)

35%

Predict the complementary strand of the following DNA sequence: 5'-ATCTGAATCT-3' (HW2)

5'-AGATTCAGAT-3'

Using the pKas shown, what is the isoelectric point of the amino acid tyrosine? (HW3)

5.5

A 20 bp duplex with __________ content at __________ will have the highest absorbance at 260 nm. (HW2)

60 percent A-T; 50 degrees C

Calculate the linking number for a B-DNA strand that contains 735 total base pairs. (HW2)

70

Consider a pentapeptide with the sequence Lys-Tyr-Glu-Asn-His (K-Y-E-N-H). Using the pKa values in Table 4.3, make a table to show the approximate charges (if any) on the terminal groups and the side chain of each residue in the peptide at pH 7 and at pH 11. What would be the approximate net charge on this pentapeptide at pH 7 and at pH 11? (ch.4)

N-terminal amino group of chain: charge at pH 7 (+1), charge at pH 11 (0) C-terminal carboxyl group of chain: charge at pH 7 (-1), charge at pH 11 (-1) Side chain of Lys: charge at pH 7 (+1), charge at pH 11 (0) Side chain of Tyr: charge at pH 7 (0), charge at pH 11 (-1) Side chain of Glu: charge at pH 7 (-1), charge at pH 11 (-1) Side chain of Asn: charge at pH 7 (0), charge at pH 11 (0) Side chain of His: charge at pH 7 (0), charge at pH 11 (0) Net charge on peptide: charge at pH 7 (0), charge at pH 11 (-3)

If a cell is placed in a hypotonic solution, then (HW1)

None of these answers are correct.

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace? (HW3)

None of these answers are correct. Correct answer NCCNCC

Which two of the following processes are driven by the hydrophobic effect? (HW1)

Separation of oil and water Sequestration of hydrophobic groups to the interior of a folder protein

Which FOUR statements are true regarding β sheets? (HW3)

Stabilized by H-bonds between -NH and -CO groups; Found in globular proteins; An extended conformation of the polypeptide chain; the stability is affected by amino sequence

Red blood cells are placed into a solution of unknown solute concentration. After an hour they have all burst open. The best explanation is that the solution (HW1)

had no solutes

Limonene is a nonpolar molecule. The water molecules around it forms (HW1)

hydrogen bonds with itself and entropy decreases.

The interior stacking of the DNA bases in the double helix provides stability through (HW2)

hydrophobic and van der Waals interactions

As DNA unwinds and denatures, absorbance is predicted to (HW2)

increase

What mediates the binding of histone proteins to DNA? (HW2)

ionic attractions

Choose the ONE best response to complete this sentence: "A protein in solution is more likely to maintain its native conformation when (HW3)

it s hydrophobic residues are largely buried in the protein interior

The points in the Ramachandran plot are derived by (HW3)

measuring the phi and psi angles in an experimentally determined protein crystal structure.

What would be the expected orientation of an amphipathic alpha helix occurring in a globular protein in aqueous solution? (HW3)

A soluble protein will have lots of hydrophilic amino acids on its surface, so the helix will be arranged to have the hydrophilic side facing toward the outside of the protein.

Which of the of four amino acids residues listed in the choices below are all most likely to be buried in the interior of a water soluble protein? (HW3)

Ala, Val, Leu, Ile

How does the second law of thermodynamics apply to energy conversion systems in a living organism? (ch.2)

All natural processes in the universe tend toward dispersal of energy (entropy) in the absence of energy input. Many biochemical reactions are maintained at a steady state far from equilibrium; to do this, they are using chemical energy to limit entropy and avoid reaching equilibrium with the environment (death).

What is the dominant secondary structure found in hair keratin? (HW3)

Alpha helices

Which two functional groups are involved in producing a peptide bond? (HW1)

Amino and carboxyl

Fatty acids are important for cell membrane formation because they are (HW1)

Amphipathic.

Explain why amylose and cellulose, both polymers of glucose, are not of equal nutritional value to humans. Explain why horses, which have similar digestion enzymes encoded in their genomes to those of humans, can live on cellulose-based foods for long periods of time and humans cannot. (ch.1)

Amylose is a glucose polymer with α(1→4) glycosidic bonds that can be cleaved by the human enzyme amylase. Cellulose is a glucose polymer with β(1→4) glycosidic bonds, cleaved by cellulase, an enzyme not found in humans. Horse's intestines have bacteria that secrete cellulase, which aids the horse to digest plant material.

A titratable group is in the active site of an enzyme and must be protonated for the enzyme to function. Assume that the group has a pKa of 6.5 and that the activity is proportional to the fraction of molecules in the protonated state. Which of the following are true? There are four correct answers. (HW1)

At pH 9.0 close to 100% of the enzyme molecules are inactive.At pH 6.5 the enyzme is 50% active. At pH 6.8 the enzyme is 66.6% inactive. At pH 7.2 there are about 5 inactive enzymes for every active enzyme.

Eduard Buchner is credited with discovering reaction conditions required for in vitro fermentation using protein extracts prepared from yeast. Louis Pasteur, at the urging of the local wineries in France, had also tried to reproduce fermentation in vitro using yeast cell extracts, but to no avail. Describe three things that Buchner did differently from Pasteur that are thought to have contributed to his success. (ch.1)

Buchner (1) used a different strain of yeast than Pasteur used, (2) prepared the yeast extract using quartz mixed with diatomaceous earth rather than glass, and (3) his extract buffer contained glucose, the carbon source for fermentation.

What charged group(s) are present in the amino acid Gly at a pH of 12? (HW3)

COO-

Pyruvate decarboxylase converts pyruvate into (HW1)

Carbon dioxide and acetaldehyde

Which THREE of the following biochemical relationships are correct statements illustrating the hierarchical organization of molecular life? (HW1)

Carbon, hydrogen, and oxygen are the most abundant elements in biomolecules. Metabolic pathways are considered more complex than biomolecules but less complex than ecosystems. Insects degrade organic materials on the forest floor and generate nitrogen compounds that are used by tree seedlings as nutrients.

In the closely packed interior of the tertiary structure of an enzyme, an alanine residue was changed by mutation to a valine, leading to a loss of enzyme activity, although that residue was not directly involved in the catalytic function of the enzyme. However, activity was partially regained when an additional mutation at a different position in the primary structure changed an isoleucine residue to a glycine. Based on the structure of the amino acid side chains of alanine, valine, isoleucine, and glycine, explain how the first mutation Ala→Val likely caused a loss of activity, and the second mutation in another region of the protein, Ile→Gly, resulted in a partial recovery of enzyme activity. (ch.4)

Changing an Ala to a Val would introduce a bulkier side chain, taking up more volume in the protein interior; the resulting structural adjustments in the tertiary structure must be serious enough to cause the enzyme to lose activity. The replacement of an Ile residue with a Gly allows a tertiary structure close enough to the original structure for partial enzyme activity.

If the concentration of aspartate in the cell decreased, what would be the predicted outcome? (HW1)

Decreased concentration of fumarate

Which stabilizing force in protein tertiary structures is a covalent bonding force? (HW3)

Disulfide bonding

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments? (HW2)

Gel electrophoresis

Choose the THREE most correct statements regarding interpretation of the gene expression microarray data shown above. The color code is represented by the following using a reference gene as the control; RED means higher level of gene expression, GREEN means lower level of gene expression, and YELLOW would mean that the expression is unchanged. (HW2)

Genes in the A group are initially expressed at the same level as the control genes, but have increased expression later in the time course. Genes in the B and C groups are differentially expressed at about the same time, but the pattern of expression is reciprocal. Genes in the D group are initially expressed at the same level as the control genes, but have decreased expression later in the time course.

A scientist can use a variety of bioinformatic tools to compare the DNA of individuals suffering from a genetic disease to the DNA of unaffected individuals. Why, then, do scientists try to identify the gene involved in the disease before searching for a specific mutation? (ch.3)

Human genomes contain many random mutations that have little to no effect on protein expression or function. Some are spontaneous, whereas SNPs and STRs are inherited. Simply comparing the DNA of two individuals would result in the identification of hundreds to thousands of differences. If the affected gene is known, then the sequence of that gene from an affected individual can be compared to unaffected individuals, including parents or siblings, in order to help eliminate inherited variations as potential disease-causing mutations.

Why does hydrogen bonding between base pairs contribute little to overall helix stability? (ch.3)

Hydrogen bonding occurs between bases within a DNA double helix, but when DNA strands are denatured, the hydrogen bonds are replaced by hydrogen bonds between bases and water that are similar in strength.

Phosphorylation of serine residues is a common way to regulate the activity of proteins. The source of phosphate for phosphorylation is ATP. Here are the two reactions involved: phosphoserine + H20 <==> serine + Pi ΔG°' = -10.3 kJ/mol ATP + H2O <==> ADP + Pi ΔG°' = -30.5 kJ/mol Using the information in the reactions above, which of the following are correct? (HW1)

Hydrolysis of ATP is an exergonic reaction

Peptide hormones, such as insulin and glucagon, are extracellular molecules that circulate in the blood and transmit signals to the inside of target cells by binding to transmembrane receptor proteins. Considering that both insulin and glucagon are secreted from the pancreas into the blood and have equal access to all cells in the body, explain why insulin activates signaling pathways in both liver cells and skeletal muscle cells, whereas glucagon activates signaling pathways in liver cells but not in skeletal muscle cells. (ch.1)

Liver cells and skeletal muscle cells both contain insulin receptors, but only liver cells contain glucagon receptors; skeletal muscle cells do not.

The K+ ion concentration in a DNA sample is increased from 50 mM to 100 mM. The Tm will (HW2)

Increase

How does a lack of introns in prokaryotic genes contribute to their faster growth? (ch.3)

Introns must be spliced out of mRNA before translation can occur. Because the majority of prokaryotic genes do not contain introns, the mRNA does not need to be processed and can be translated as it is transcribed, leading to faster cell division.

To study red blood cells without damaging them through osmotic shock, they should be kept in a solution which is (HW1)

Isotonic

For the reaction: A + B ↔ C + D, which of the following is correct? (HW1)

Keq = [C][D]/[A][B]

In the opening sequence of the video, a protein is "unraveled" down to an extended linear conformation. Which of the following statements accurately captures what is happening in this process? (HW3)

Linearizing the polypeptide destroys the spatial relationships that define secondary and tertiary structure

The amino acid sequence of a protein determines its 3D structure, which in turn determines its functions. The amino acid sequences of the bacterial and mouse ribonucleotide reductase proteins shown in figure 1.30a are about 20% identical, and both proteins have the same structure and function. Moreover, the amino acid sequences of the bacterial porin channel protein in figure 1.30b is about 10% identical to the amino acid sequence of the jellyfish green fluorescent protein, and although both have the same beta-barrel 3D structure, the functions of these two proteins are very different. Lastly, the two DNA-binding proteins shown in figure 1.30c have amino acid sequence identities of about 10% and have similar functions but very different 3D structures. based on these relationships, what could you predict about the structure and function of two proteins that were <20% identical in their amino acid sequences? What could

Not much can be predicted about amino acid sequences with <20% identity; they could have a similar protein structure, or a similar proteins function, or neither. In contrast, two proteins that are >80% identical are very likely to have the same structure and function.

Match each of the four building block biomolecules on the left with the ONE specific biomolecule on the right that best represents it (HW1)

Nucleotide ->cytidine monophosphate Simple sugar ->Ribose Amino acid-> aspartate Fatty acid-> Palmitate

Polycistronic genes that contain a coding sequence for proteins that are only involved in one biochemical process are called (HW2)

Operons

What is a difference between parallel and antiparallel Beta-sheet secondary structures? (HW3)

Parallel beta-sheets require a larger loop connecting together the individual peptide strands in the sheet.

Select the one TRUE statement below about membranes from the choices below. (HW1)

Phospholipids can have both lateral and rotational movement within fluid membranes.

Explain why plants at night can be thought of as animals in terms of the similarities in their bioenergetic needs. (ch.2)

Plants (at night) and animals (all of the time) metabolize nutrients (carbohydrates) by the process of aerobic respiration.

Currently, there is much interest in studying the different "omes". Which of the following "ome" is matched with its correct biomolecule? (HW1)

Proteome-proteins

How do plants, fungi, and bacteria avoid the damaging effects of a hypotonic environment? (HW1)

Rigid cell walls

What is a current hypothesis that explains the infectious nature of prion diseases? (HW3)

The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins.

How would the G-C content of a primer affect the annealing temperature used for PCR? (ch.3)

The G-C content of a primer contributes more to the Tm than the A-T content because G-C base pairs require more heat to disrupt the duplex. Therefore, the higher the G-C content, the higher the Tm and the annealing temperature.

The polarity of the solvent and other environmental factors can affect the pKa of a weak acid. Suppose the alpha-amino group of a protein has a pKa of about 8.0 when it is exposed to H2O on the outside of a protein. Would you expect the pKa to be higher or lower than 8.0 if the alpha-amino group were buried in the hydrophobic interior of the protein and why? (HW3)

The alpha-amino group would be uncharged at neutral pH, which is favorable and therefore it would be lower.

Which of the following is correct about protein folding? (HW3)

The amino acid sequence of a protein leads to a limited number of possible folding pathways.

The fluidity of a membrane depends on (HW1)

The degree of saturation of the phospholipids

Select the four TRUE statements below describing the standard free energy change (delta G) and the equilibrium constant (Keq). (HW1)

The equilibrium constant is the ratio of product and reactant concentrations at equilibrium. The value for the standard free energy change is constant for a given reaction. The value for the equilibrium constant can be experimentally determined for a given reaction. If the value of the equilibrium constant is known, the value for the standard free energy change can be determined.

Within a eukaryotic cell, the _________ is the organelle with highly invaginated membrane structures that sequester ribosomes for protein synthesis. (SW1)

endoplasmic reticulum

Eduard Buchner is considered the first modern biochemist because he proved that __________ are sufficient for alcoholic fermentation in the absence of live yeast - as long as a source of ___________ is provided. (HW1)

enzymes, sugars

Given the energy charge equation below, if a biological system has an EC = 0.8, what is true about the concentrations of ATP, ADP, and AMP in the system? (HW1)

There is more ATP in the system than ADP or AMP

Which of the following statements about Ramachandran plots is true? (HW3)

They show that beta-sheets and alpha-helices occupy different phi and psi angles.

The pKa for a typical long-chain fatty acid is ~5. Explain why long-chain fatty acids can form micelles in solutions with pH > 7 but are insoluble in solutions with pH < 5. (ch.2)

To form a micelle, the fatty acid must have a charged polar head group. This will only occur when the carboxyl group has ionized, which only occurs at pH values higher that the pKa.

Which one of the following amino acid residues would most likely be buried in the interior of a water-soluble protein? (HW2)

Trp, Lys, Ser, Arg, Asp

The reaction below is a step in glycolysis where a 6-carbon sugar (F-1,6-BP) is cleaved into 2 3-carbon compounds (DHAP and GAP). Fructose 1,6-bisphosphate (F-1,6-BP) ↔ DHAP + GAP ΔG°' = +23.9 kJ/mol If under cellular conditions the sign of ΔG for this reaction is negative, the reaction would proceed spontaneously in the forward direction (F-1,6-BP → DHAP + GAP). (HW1)

True

Two proteins have the same overall fold, but different amino acid sequences. These proteins likely derived from a common ancestor. (HW1)

True

Choose the one best statement that completes this sentence: "Two amphipathic α helices in a dilute aqueous solution are likely to: (HW2)

form a coiled coil structure with the polar amino acid side chains interacting with each other down the middle.

Explain the roles of urea and β-mercaptoethanol in Anfinsen's experiments on protein folding using the protein ribonuclease. What was the most important conclusion resulting from this experiment that earned Anfinsen the Nobel Prize? (ch.4)

Urea is a denaturing agent: It unfolds proteins by disrupting noncovalent interactions; β-mercaptoethanol is a reducing agent: It breaks disulfide bonds. With sufficient amounts of both urea and β-mercaptoethanol, ribonuclease protein was completely unfolded. The important conclusion was that the primary structure has all the information necessary to specify the tertiary structure.

Why is it important that plasmids contain antibiotic-resistance genes when they are used for cloning in a laboratory? (ch.3)

When a plasmid is transformed into a culture of bacterial cells, not every cell will take up the plasmid. The use of antibiotic selection prevents bacteria without the plasmid from growing, so a bacterial colony that is antibiotic resistant can be assumed to have taken up the plasmid successfully.

What is the biological rationale for having both sequence-dependent and sequence-independent DNA and RNA binding proteins in the cell? (ch.3)

Whether a protein binds to DNA or RNA in a sequence-specific manner or nonspecifically depends on the function of the protein. Histone proteins bind to any DNA in order to compact it into chromosomes; they recognize the negatively charged backbone that is present in any DNA sequence. By contrast, proteins such as transcription factors need to bind to specific nucleotide sequences to initiate transcription of particular genes.

Answer the following questions based on these four primary protein sequences: 1. Asp-Gln-Leu-Glu-Lys-Glu-Leu-Gln-Ala-Leu-Glu-Lys-Glu-Leu-Ala 2. Phe-Gln-Ile-Asp-Met-Glu-Leu-Lys-Val-Asn-Leu-Asp-Phe-Arg-Ala 3. Ala-Gln-Tyr-Gly-Pro-Asn-Leu-Phe-Ala-Val-Ile-Lys-Asn-Cys-Ala 4. Phe-Asn-Ser-Val-Leu-Gln-Asp-Ile-Glu-Gln-Phe-Met-Ser-Cys-Ala a. Which sequence looks as if it could include a β turn (reverse turn)? Explain your reasoning. b. Which sequence looks as if it could form a β strand, with one surface facing the interior of the protein and the other surface exposed to water? Explain your reasoning. c. Which sequence looks as if it could form an α helix that would participate in a coiled coil structure within a protein? Explain your reasoning. d. Using the helical wheel drawn in Figure 4.34, which sequence looks as if it could form an amphipathic α helix? Which amino acids form the hydrophobic and hydrophilic faces of thi

a. 3 (it is the oly one with a Gly-Pro sequence for a beta turn) b. 2 (it is the only one that contains alternating hydrophobic and phdrophilic side chains: Ile, MEt, Leu, Phe alternate with Asp, Glu, Lys, Asn, Asp, Arg) c. 1 (every third or fourth residue is Leu) d. 4 (Phe, Val, Leu, Ile, Phe, Met, Ala on the hyrdophobic surface; Asn, Ser, Gln, Asp, Glu, Gln, Ser, Cys on the hyrdophilic face)

The energy charge (EC) of a cell reflects the amount of phosphoryl transfer energy available from ATP. The levels of ATP, ADP, and AMP in a cell are maintained in part by the adenylate kinase reaction, which interconverts ATP + AMP ⇌ ADP + ADP (ΔG°′ ≈ 0). a. Calculate the energy charge in a cultured cancer cell line found to have the following adenylate concentrations: 1.25 mM ATP, 0.35 mM ADP, and 0.12 mM AMP. b. What is the Keq of the adenylate kinase reaction in this cancer cell line, assuming the reaction is at equilibrium under the growth conditions used? (ch.2)

a. EC= ([ATP]+0.5[ADP])/([ATP]+[ADP]+[AMP]) EC=0.83 b. Keq=[ADP][ADP]/[ATP][AMP] keq=0.81

The polarity of the solvent and other environmental factors can affect the pKa of a weak acid. Suppose the α amino group of a protein has a pKa of about 8.0 when it is exposed to H2O on the outside of a protein. a. Would you expect the pKa to be higher or lower than 8 if the group were buried in the hydrophobic interior of the protein? Explain. b. This same α amino group in the hydrophobic interior of the protein has the opportunity to form an ionic bond in that hydrophobic environment with a carboxylate group in the side chain of a charged Asp residue. Under these conditions, how would the pKa of this α amino group compare with the pKa of the α amino group in the hydrophobic interior of the protein without a nearby Asp residue to form this ionic bond? (ch.4)

a. It is energetically unfavorable for the α amino group to be charged in the hydrophobic interior, thus the pKa would be lower. The proton can be released, as H3O+, before the amino group enters the interior during the folding process because the strong electrostatic attraction between the lone pair electrons in the N atom and the proton is outweighed by the unfavorable condition of a charge in a hydrophobic environment. b. The pKa for this α amino group would increase relative to the example in (a), and would be close to the pKa of ∼8. This ionic bond neutralizes both the NH3+ charge and the COO− charge, reducing the effect of having a charged group in the hydrophobic environment. Ionic bonds are stronger in a hydrophobic environment because it is unfavorable to have unbalanced charges.

The total carbonate pool in blood plasma (blood without red blood cells) is 0.025 M and consists of both HCO3−HCO3− and CO2(aq). The pKa for the dissociation of H2CO3 to produce HCO- + H+ at 37°C is 6.1. Because H2CO3 is readily produced in blood from dissolved CO2(aq) + H2), in a reaction catalyzed by the enzyme carbonic anhydrase, CO2(aq) can be considered the conjugate acid and HCO3- the conjugate base in the bicarbonate buffering system. a. What is the ratio of HCO3- and CO2(aq) in blood at pH7.4? b. What are the individual concentrations of CO2(aq) and HCO3- under these same conditions? (ch.2)

a. pH=pKa + log ([A-]/[HA]) 7.4=6.1 + log ([HCO3-]/[CO2(aq)])=20 b. 0.025M = 2.5x 10^-2 M= [HCO3-] + [CO2(aq)] 92.5 x 10^-2 M)/(20+1) = [CO2(aq)] = 1.19x10^-3 M [HCO3-]=2.5x10^-2 M - 1.19x10^-3 M =2.38x10^-2 M

The change in free energy between reactants and products can be used to determine if a reaction is spontaneous. a. What is meant by the free energy terms ΔG°′ and ΔG? b. Write an equation that describes ΔG°′ when a reaction is at equilibrium. c. What effects are there on ΔG, ΔG°′, or Keq if an enzyme is present in the reaction? Explain. (ch.2)

a. ΔG°′, expressed in kilojoules (kJ), refers to the biochemical standard free energy change of a reaction. This is the change from initial reactant and product concentrations of 1 M each, to steady-state concentrations at equilibrium under physiological conditions (298 K, 1 atm, pH 7). ΔG refers to the actual free energy change in a reaction, calculated from its ΔG°′ value and the initial concentrations of reactants and products in a real system. b. when a reaction is at equilibrium, ΔG=0 and ΔG°' is described by ΔG=ΔG°'+RTln([B]actual/[A]actual)=0 ΔG°'=-RTln([B]eq/[A]eq) c. Enzymes are catalysts and only affect the rates of chemical reactions. ΔG, ΔG°′, and Keq are all unchanged in the presence of an enzyme.

Two new microorganisms, labeled X and Y, were isolated from an oil spill during a search for organisms that will degrade petroleum products. DNA was isolated from each, and the percent adenine was measured. Assume each organism contains normal double-stranded DNA. Organism X: 18.7% adenine Organism Y: 29.9% adenine a.) What percentage of thymine does organism X have? b.) What percentage of cytosine does organism Y have? c.) Which organism will have the higher melting DNA (require a higher temperature to denature)?

a.)18.7% b.)20.1% c.) organism x

A polypeptide has a high pI value. Which amino acids might comprise it? (HW2)

arginine and lysine residues

When Hsp70 binds ATP, it undergoes a conformational change that exposes hydrophobic residues. The exposed hydrophobic residues on Hsp70 (HW3)

bind to the hydrophobic residues on the misfolded protein.

Organisms on Earth are considered _________ life forms (HW1)

carbon

Identify the four building block biomolecules from the list to the right, and then match them with the best description of their primary cellular function. (HW1)

cell recognition: simple sugars Neurotransmission: amino acids Cell membranes: fatty acids Enzyme catalysts: Nucleotides

During eukaryotic DNA condensation, nucleosomes are packed together to form (HW2)

chromatin

When DNA is transcribed into RNA, the __________ strand has the same base sequences as the RNA transcript. (HW2)

coding

Calculate the total number of possible dodecanucleotides that can be synthesized using the four nucleotides found in RNA. What is the maximum number of peptide sequences that can be encoded by this collection of dodecanucleotides using all 20 amino acids? (Assume that none of the trinucleotides are termination codons.) (ch.1)

dodecanucleotides is 4^12. tetrapeptides is 20^4

Energy conversion in living systems is required for what three types of work? (HW1)

osmotic work, chemical work, mechanical work

A homopolymer of lysine residues (polylysine) can adopt an a-helical conformation or a random coil conformation depending on the pH of the solution. Predict whether the conformation of polylysine would be a-helical or random coil at a pH of 1, 7, and 11. Choose a total of THREE answers. Choose either helix or random coil for pH 1, pH 7, and pH 11. (HW3)

pH 1 - random coil pH 11- helix pH 7 - random coil

Type II topoisomerase enzymes are important in replication and transcription because they (HW2)

relieve the positive supercoiling.

When a gene sequence is cloned using mRNA, the mRNA is isolated from the cell and converted into a double-stranded sequence using which enzyme? (HW2)

reverse transcriptase

The amino acid with the neutral side chain at neutral pH is (HW3)

serine

Urea is a highly polar solvent that can be used to fold proteins through formation of Intramolecular hydrogen bonds (HW3)

β-mercaptoethanol was used to disrupt disulfide bonds of the native protein so refolding could occur under favorable conditions.