Biochemistry Mastering Chapter 5 (5-L, 5-2)

e. Lysine f. N-terminal amine

Acetylating agents such as acetic anhydride react preferentially with primary amines, iodoacetate reacts preferentially with sulfhydryl groups, and ATP-dependent kinases preferentially add a phosphoryl group to side-chain hydroxyl or phenolic −OH groups. Which amino acid side chains, or main chain groups, in a polypeptide are most likely to be modified by treatment with: acetic anhydride a. Asparagine b. Glutamine c. Proline d. Arginine e. Lysine f. N-terminal amine

b. Threonine c. Serine e. Tyrosine

Acetylating agents such as acetic anhydride react preferentially with primary amines, iodoacetate reacts preferentially with sulfhydryl groups, and ATP-dependent kinases preferentially add a phosphoryl group to side-chain hydroxyl or phenolic −OH groups. Which amino acid side chains, or main chain groups, in a polypeptide are most likely to be modified by treatment with: kinase + ATP a. Glutamic Acid b. Threonine c. Serine d. Aspartic Acid e. Tyrosine

MFPSYPKDKKE

Assume the following portion of an mRNA. Find a start signal, and write the amino acid sequence that is coded for. 5'...GCCAUGUUUCCGAGUUAUCCCAAAGAUAAAAAAGAG...3'

Met-Set-Cys-His Before mRNA can be translated into an amino acid sequence, the mRNA must first be synthesized from DNA through transcription. Base pairing in mRNA synthesis follows slightly different rules than in DNA synthesis: uracil (U) replaces thymine (T) in pairing with adenine (A). The codons specified by the mRNA are then translated into a string of amino acids.

Before a molecule of mRNA can be translated into a protein on the ribosome, the mRNA must first be transcribed from a sequence of DNA. What amino acid sequence does the following DNA template sequence specify? 3′−TACAGAACGGTA−5′

1623.93 g/mol

Calculate the molecular weight of α-melanotropin, using data in the table below.

Answer attached

Draw the structure of the peptide DTLH, showing the backbone and side-chain atoms, at its isoelectric point.

Shown in the image.

Draw the structure of the peptide KSRYV, showing the backbone and side-chain atoms, at pH=7

a. Only statement 2 is correct. [Glycine is small, and proline is rigid.] Glycine is found at the surface of proteins because its side chain is hydrogen, which is very small. This imparts great flexibility to this amino acid. Proline is the only secondary amino acid and as such is very rigid. The geometrical limitations of this amino acid make it well suited for turns in proteins.

Glycine and proline are both non-polar amino acids, and both are very likely to be found at the surface of proteins. What physical characteristic of each is responsible for this observation? 1) Both glycine and proline are small. 2) Glycine is small, and proline is rigid. 3) The side chains of both these amino acids make favorable interactions with molecules near the surface of proteins. 4) Both amino acids make strong interactions with each other and therefore are likely to be found next to each other in a protein. a. Only statement 2 is correct b. Only statements 1 and 2 are correct c. Only statements 2, 3, and 4 are correct d. Only statements 1, 2 and 3 are correct

C. This ionic state, where the carboxylic acid is negative and the amine group is positive, is known as the zwitterionic state.

Select the generic nonpolar amino acid that is in the correct form at pH=7.0, or at physiological conditions. Pay close attention to the charges on the amino group and the carboxylic acid group. A, B, C, or D

a. Electrophoresis. d. Chromatography on a cationic column, at pH=7.

Suggest a method for separating the peptides produced by chymotrypsin treatment. a. Electrophoresis b. Chromatography on a anionic column, at pH=4 c. Size exclusion chromatography d. Chromatography on a cationic column, at pH=7

a. Statements 1 and 2 are correct. [The microenvironment around a residue can impact its pKa value. A positively charged amino acid must be in close proximity to this residue.] These two statements most accurately describe this result; the presence of a nearby positive charge is likely to decrease the pKa of the His side chain because two neighboring positive charges will repel each other. There is not enough information to draw any conclusion about the location of this residue within the protein structure.

The side chain of histidine has a typical pKa value in the range of 6.5-7.4. However, when analyzing the pKa values in a particular protein, scientists determined that one particular His residue has an unusually low pKa value of 4.8. Which of the following statements correctly explain this anomaly? 1) The microenvironment around a residue can impact its pKa value. 2) A positively charged amino acid must be in close proximity to this residue. 3) A negatively charged amino acid must be in close proximity to this residue. 4) This residue must be located on the surface of the protein. a. Statements 1 and 2 are correct. b. Statements 1 and 4 are correct. c. Statements 2, 3 and 4 are correct. d. Statements 1, 2 and 4 are correct.

110.76

Using the in table below, calculate the average amino acid residue weight in a protein of typical composition. This is a useful number to know for approximate calculations.

a. net charge = +2

What is the net charge on the following peptide at pH = 0? Peptide sequence: DSVK a. net charge = +2 b. net charge = +1 c. net charge = 0 d. net charge = -2

e. Selenocysteine

Which of the following modified amino acids is incorporated during translation rather than being modified post-translationally? a. γ-carboxyglutamate b. Phosphoserine c. N-ε-acetyllysine d. 4-hydroxyproline e. Selenocysteine

8.813

Calculate the pI (isoelectric point) of α-melanotropin.

True

In size exclusion chromatography, the smallest proteins are eluted last. True or false?

2; H-bond acceptor 3; H-bond donor

Place the 'H-bond acceptor' and 'H-bond donor' in the correct positions (either 1, 2, 3, or 4)

True

Protein biosynthesis uses only L-amino acids. True or false?

histidine

The side chain of ________ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis.

a. The disulfide bonds form after the final proteolytic cleavage to yield mature insulin. this is incorrect.

Which of the following statements about insulin is INCORRECT? a. The disulfide bonds form after the final proteolytic cleavage to yield mature insulin. b. The leader sequence is cleaved off after membrane transport. c. It is synthesized as a random coil single chain on membrane-bound ribosomes. d. It is stored in the pancreas in an inactive form. e. In the active form it has two polypeptide chains joined by disulfide bonds.

d. A knock-out mutation results in a total absence of the mutated protein. A knock-out mutation refers to the loss of a protein's function but not necessarily to its complete absence.

Which of the following statements about mutations is false? a. A deletion mutation results in the loss of a base in the DNA sequence. b. An addition mutation results in an added base in the DNA sequence. c. Addition and deletion mutations disrupt the primary structure of proteins. d. A knock-out mutation results in a total absence of the mutated protein.

c. At pH=pl, there is no net charge on the protein.

Which of the following statements is true about a protein that is in an aqueous solution that has a pH equal to the pI of the protein? a. At pH=pl, there is a net negative charge on the protein. b. At pH=pl, there is a net positive charge on the protein. c. At pH=pl, there is no net charge on the protein. d. There is not enough information to answer this question.

UGU AAU UGU AAA GCG CCC GAG ACC GCG CUU UGU CGC CGA CGA UGU CAA CAA CAU

Write one of a possible sequence for an mRNA segment coding for apamine (CNCKAPETALCARRCQQH). UGU AAU AAA GCG CCC GAG ACC CUU CGA CAA CAU AUU AUA

Asp-Arg-Val-Tyr-Ile-Met-Pro-Phe

A mutant form of polypeptide hormone angiotensin II has the amino acid composition (Asp, Arg, Ile, Met, Phe, Pro, Tyr, Val) The following observations are made: ⋅ Trypsin yields a dipeptide containing Asp and Arg, and a hexapeptide with all the rest. ⋅ Cyanogen bromide cleavage yields a dipeptide containing Phe and Pro, and a hexapeptide containing all the others. ⋅ Chymotrypsin cleaves the hormone into two tetrapeptides, of composition (Asp, Arg, Tyr, Val) and (Ile, Met, Phe, Pro) The dipeptide of composition (Pro, Phe) cannot be cleaved by either chymotrypsin or carboxypeptidase. What is the sequence of angiotensin II?

a. AC

A protein has been sequenced after cleavage of disulfide bonds. The protein is known to contain 3 Cys residues, located as shown below. Only one of the Cys has a free −SH group and the other two are involved in an −S−S- bond. The only methionine and the only aromatic amino acid (Phe) in this protein are in the positions indicated. Cleavage of the intact protein (i.e., with disulfide bonds intact) by either cyanogen bromide or chymotrypsin does not break the protein into two peptides. Where is the -S-S- bond a. AC b. BC c. AB

b. The positive charge on the peptide will be reduced.

Acetylating agents such as acetic anhydride react preferentially with primary amines, iodoacetate reacts preferentially with sulfhydryl groups, and ATP-dependent kinases preferentially add a phosphoryl group to side-chain hydroxyl or phenolic −OH groups. For each modification, consider. Would the chemical modification change the overall charge on the acetic anhydride at pH=7? a. The charge on the peptide will not change. b. The positive charge on the peptide will be reduced. c. The negative charge on the peptide will be increased. d. The positive charge on the peptide will be increased. e. The negative charge on the peptide will be reduced.

a. Cysteine

Acetylating agents such as acetic anhydride react preferentially with primary amines, iodoacetate reacts preferentially with sulfhydryl groups, and ATP-dependent kinases preferentially add a phosphoryl group to side-chain hydroxyl or phenolic −OH groups. Which amino acid side chains, or main chain groups, in a polypeptide are most likely to be modified by treatment with: iodoacetate a. Cysteine b. Serine c. Methionine d. Valine

glycine

All amino acids have a chiral α-carbon EXCEPT ________.

b. two disulfides

Apamine is a small protein toxin present in the venom of the honeybee. It has the sequence CNCKAPETALCARRCQQH If apamine does not react with iodoacetate, then how many disulfide bonds are present? a. one disulfide b. two disulfides c. three disulfides

e. A, B, and C.

Applications of mass spectrometry include: a. determination of the mass of a protein. b. determining the primary structure of proteins. c. detection of post-translational modifications on proteins. d. A and B. e. A, B, and C.

False

At pH=0, the net charge on a polypeptide will be negative. True or false?

c. Cytochrome c Thrombin will elute slowly at pH=6.4. You could change the buffer to elute the protein more quickly.

At pH=6.4, which protein(s) do you predict will remain bound to the column with minimal flow through CM-cellulose? a. Thrombin (wild type) b. Lactoglobin c. Cytochrome c

3.998

Calculate to three decimal places the charge on α-melanotropin at pH value of 1.

-1.827

Calculate to three decimal places the charge on α-melanotropin at pH value of 11.

2.104

Calculate to three decimal places the charge on α-melanotropin at pH value of 5.

Acidic; Glutamic Acid Neutral polar; Threonine Neutral nonpolar; Tyrosine, Valine, Tryptophan

Classify these amino acids as acidic, basic, neutral polar, or neutral nonpolar.

Basic; Arginine Neutral polar; Glutamine, Cysteine, Asparagine Neutral nonpolar; Alanine

Classify these amino acids as acidic, basic, neutral polar, or neutral nonpolar.

Basic; Lysine Neutral polar; Serine Neutral nonpolar; Proline, Methionine, Phenylalanine

Classify these amino acids as acidic, basic, neutral polar, or neutral nonpolar.

False

Conservative amino acid changes never affect stability or function of a protein. True or false?

SYSMEHFRWGKPV

Constants | Periodic Table The melanocyte-stimulating peptide hormone α-melanotropin has the following sequence: Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro-Val Write the sequence using the one-letter abbreviations.

b. The pI of the sickle-cell globin will be higher than the wild-type globin because the mutation replaces a negatively charged side chain with one that carries no charge.

Do you expect the pI for the sickle-cell β-globin to be higher or lower than the pI for wild-type β-globin? Explain. a. The pI of the sickle-cell globin will be higher than the wild-type globin because the mutation replaces an uncharged side chain with one that carries positive charge. b. The pI of the sickle-cell globin will be higher than the wild-type globin because the mutation replaces a negatively charged side chain with one that carries no charge. c. The pI of the sickle-cell globin will be lower than the wild-type globin because the mutation replaces a positively charged side chain with one that carries negative charge. d. The pI of the sickle-cell globin will be lower than the wild-type globin because the mutation replaces an uncharged side chain with one that carries negative charge.

a. Apamine does not have an N-terminal methionine, so at least some proteolytic cleavage must be involved in its synthesis.

Do you think apamine is synthesized in the form CNCKAPETALCARRCQQH, or is it more likely a product of proteolytic cleavage of a larger peptide? Explain. a. Apamine does not have an N-terminal methionine, so at least some proteolytic cleavage must be involved in its synthesis. b. When apamine is released from a ribosome following translation, its synthesis is finished. c. Synthesis of apamine involves proteolytic cleavage of its dimer.

L-aspartic acid is an amino acid that is frequently used in enzymes to perform chemical reactions.

Draw L-aspartic acid as it would occur at the pH of most body fluids.

The dipeptide form of glycine is called glycylglycine.

Draw the dipeptide that results when a peptide bond is formed between the two glycine molecules shown. Draw it as it would occur at the pH of most body fluids.

Shown in the image attached

Draw the structure of the peptide KHEDC, showing the backbone and side-chain atoms, at its isoelectric point.

Met-Ala-Arg-Lys An amino acid sequence is determined by strings of three-letter codons on the mRNA, each of which codes for a specific amino acid or a stop signal. The mRNA is translated in a 5' → 3' direction.

During translation, nucleotide base triplets (codons) in mRNA are read in sequence in the 5' → 3' direction along the mRNA. Amino acids are specified by the string of codons. What amino acid sequence does the following mRNA nucleotide sequence specify? 5′−AUGGCAAGAAAA−3′

-4

Estimate the net charge at pH=12. Assume the pKa values given in the table above.

c. The acid with the lower pKa value would increase the pKa value for the other acid. This is correct because the presence of one negative charge is likely to make the formation of a second negative in close proximity less favorable because of charge-charge repulsion. Nonetheless, it is not impossible to overcome this interaction, but it does affect the pKa value as indicated.

For an amino acid such as aspartic acid, what impact do you expect the two neighboring carboxylic acids to have on the pKa values for each? a. The acid with the higher pKa value would decrease the pKa value for the other acid. b. The acid with the lower pKa value would decrease the pKa value for the other acid. c. The acid with the lower pKa value would increase the pKa value for the other acid. d. The neighboring acids would have no impact on each other's pKa values.

c. The acid with the lower pKa value would increase the pKa value for the other acid. This is correct because the presence of one negative charge is likely to make the formation of a second negative in close proximity less favorable because of charge-charge repulsion. Nonetheless, it is not impossible to overcome this interaction, but it does affect the pKa value as indicated.

For an amino acid such as aspartic acid, what impact do you expect the two neighboring carboxylic acids to have on the pKa values for each? a. The acid with the higher pKa value would decrease the pKa value for the other acid. b. The neighboring acids would have no impact on each other's pKa values. c. The acid with the lower pKa value would increase the pKa value for the other acid. d. The acid with the lower pKa value would decrease the pKa value for the other acid.

-1

Given the following peptide SEPIMAPVEYPK... Estimate the net charge at pH=7. Assume the pKa values given in the table above.

a. Only statement 2 is correct. Glycine is found at the surface of proteins because its side chain is hydrogen, which is very small. This imparts great flexibility to this amino acid. Proline is the only secondary amino acid and as such is very rigid. The geometrical limitations of this amino acid make it well suited for turns in proteins.

Glycine and proline are both non-polar amino acids, and both are very likely to be found at the surface of proteins. What physical characteristic of each is responsible for this observation? 1) Both glycine and proline are small. 2) Glycine is small, and proline is rigid. 3) The side chains of both these amino acids make favorable interactions with molecules near the surface of proteins. 4) Both amino acids make strong interactions with each other and therefore are likely to be found next to each other in a protein. a. Only statement 2 is correct. b. Only statements 1 and 2 are correct. c. Only statements 2, 3 and 4 are correct. d. Only statements 1, 2 and 3 are correct.

a. Cyanogen bromide: 2 peptides b. Trypsin: no cleavage c. Chymotrypsin: 2 peptides

How many peptides would result if this peptide were treated with (1) cyanogen bromide, or (2) trypsin, or (3) chymotrypsin? a. Cyanogen bromide: _______ b. Trypsin: _________ c. Chymotrypsin: ________ options; 2 peptides no cleavage 5 peptides 4 peptides 3 peptides

c. Statements 1 and 2 are correct. These statements are the most likely to be true; in general, nonconservative changes often have a dramatic effect on the function of proteins, and the similarity of the two sequences clearly indicates the evolutionary connection between the two very distinct species.

Human and sperm whale myoglobin have very similar primary structures. Which of the following statements are correct? 1) The two proteins are very likely related evolutionarily. 2) The differences in the sequences in many instances represent a conservative change (such L for I). 3) The differences in the sequences in many instances represent a nonconservative change (such as D for A). 4) There is no correlation between the two proteins, since they originate from very different species. a. Statements 1, 2 and 4 are correct. b. Statements 1, 2 and 3 are correct. c. Statements 1 and 2 are correct. d. All of the listed statements are correct.

D-Asparagine

Identify each amino acid shown below in Fischer projection. Indicate whether the D- or L- enantiomer is shown. Spell out the full name of the amino acid.

D-Threonine

Identify each amino acid shown below in Fischer projection. Indicate whether the D- or L- enantiomer is shown. Spell out the full name of the amino acid.

D-Valine

Identify each amino acid shown below in Fischer projection. Indicate whether the D- or L- enantiomer is shown. Spell out the full name of the amino acid.

Arg-Val-Tyr

Identify the amino acids in the following tripeptide.

A. Deletion The original sequence has lost the base C.

If a DNA sequence is altered from TAGCTGA to TAGTGA, what kind of mutation has occurred? a. Deletion. b. Both addition and deletion. c. Addition. d. None.

c. An addition mutation and a deletion mutation. If the mutations occur within the same codon, only that codon (amino acid) will be altered.

If a mutated DNA sequence produces a protein that differs in one central amino acid from the normal protein, which of the following kinds of mutations could have occurred? a. A deletion mutation b. None c. An addition mutation and a deletion mutation d. An addition mutation

a. pI is lower in every case.

If so, is the pI of the modified peptide higher or lower than that of the untreated peptide? a. pI is lower in every case. b. pI is higher in every case.

c. Two The second and third codons in the new sequence are different from the original codons.

If the sequence ATGCATGTCAATTGA were mutated such that a base were inserted after the first G and the third T were deleted, how many amino acids would be changed in the mutant protein? a. Three b. None c. Two d. One

1. Cys 1 - Cys 3 2. Cys 11 - Cys 15

If trypsin cleavage gave two peptides, then where is(are) the S−S bond(s)? Cys 1 Cys 3 Cys 11 Cys 15 1. _________ - ________ 2. _________ - ________

4,7,9,10,12

If you sketch the titration curve for α-melanotropin (SerTyrSerMetGluHisPheArgTrpGlyLysProVal), near what pH values would you expect the curve to exhibit inflections? Assume the pKas of the N- and C-termini are 7.9 and 3.8, respectively. For side chains, assume the pKa values given.

This is the structure of L-alanine. Only L amino acids are found in proteins. At physiological pH (7.4), amino acids are zwitterions. That is, the carboxyl group loses its hydrogen atom to become −COO−, and the amino group is protonated to become −NH3+.

In the reaction shown here, two amino acids link together to form a dipeptide. The first amino acid, which becomes the N-terminal amino-acid residue, is glutamine. Draw the L form of the second amino acid in this reaction that would link with glutamine to form the given dipeptide.

a. add a buffer with pH = 8.0 d. increasing the ionic strength of the buffer

List two different ways you could change the buffer to elute the bound protein(s) and achieve proper separation of the proteins. a. add a buffer with pH = 8.0 b. add a buffer with pH = 5.0 c. decreasing the ionic strength of the buffer d. increasing the ionic strength of the buffer

a. 1:D;2:C;3:F;4:E;5:B;6:A

Match the amino acid (AA) with its correct side chain category: 1. proline 2. histidine 3. alanine 4. threonine 5. tryptophan 6. aspartic acid a. negatively charged polar AA b. nonpolar aromatic AA c. positively charged polar AA d. nonpolar AA e. polar AA f. nonpolar aliphatic AA Pick A, B, C, or D

c. 1:D; 2:C; 3:F; 4:E; 5:B; 6:A

Match the amino acid (AA) with its correct side chain category: 1. proline 2. histidine 3. alanine 4. threonine 5. tryptophan 6. aspartic acid a. negatively charged polar AA b. nonpolar aromatic AA c. positively charged polar AA d. nonpolar AA e. polar AA f. nonpolar aliphatic AA A, B, C, or D.

d. 1:F; 2:D; 3:B; 4:E; 5:C; 6:A

Match the codon with the amino acid it encodes: 1) UCA A) Stop 2) CUA B) Lys 3) AAG C) Start/Met 4) GUA D) Leu 5) AUG E) Val 6) UAG F) Ser a, b, c, or d.

c. 1:F;2:D;3:B;4:E;5:C;6:A

Match the codon with the amino acid it encodes: 1. UCA 2. CUA 3. AAG 4. GUA 5. AUG 6. UAG a. Stop b. Lys c. Start/Met d. Leu e. Val f. Ser A, B, C, or D

False

Most proteins have blocked amino and carboxyl terminals. True or false?

Shown in the image attached.

Repeat on Mastering; Draw the structure of the peptide KHEDC, showing the backbone and side-chain atoms, at its isoelectric point. (Mastering gave different structure correct answer?)

5.1

Support your answer with the calculation of the pI of the mutant at pH=5.5. Assume that the only factors impacting the change in the pI are the side chains of the mutant protein.

b. Ion exchange chromatography. The A chain contains no basic residues in comparison with the B chain, so ion-exchange chromatography should work well.

Suppose you had separated the A and B chains of insulin by disulfide reduction. Part complete What chromatographic method should make it possible to isolate pure A and B chains? a. Size exclusion chromatography. The differences in size between A and B are big enough for SEC to be effective. b. Ion exchange chromatography. The A chain contains no basic residues in comparison with the B chain, so ion-exchange chromatography should work well. c. Immobilized metal affinity chromatography. The strong interactions between a Ni2+, Zn2+, or Co2+ ion and histidine residues of B chain; thus, B chain will bind to the IMAC matrix.

b. The expect score for the shorter sequence is more likely to be closer to one (i.e., the shorter sequence is more likely to match many entries in the database).

Suppose you performed two BLAST searches, one on the peptide sequence FIDPWE, and another on the sequence KRTIAAVNSPLLEVATY. Which search do you predict will give you alignments with "expect scores" closer to one? Explain your reasoning. a. The expect score for the longer sequence is more likely to be closer to one (i.e., the longer sequence consists of greater variety of amino acids). b. The expect score for the shorter sequence is more likely to be closer to one (i.e., the shorter sequence is more likely to match many entries in the database).

d. Statements 1 and 2 are correct. [The microenvironment around a residue can impact its pKa value. A positively charged amino acid must be in close proximity to this residue.] These two statements most accurately describe this result; the presence of a nearby positive charge is likely to decrease the pKa of the His side chain because two neighboring positive charges will repel each other. There is not enough information to draw any conclusion about the location of this residue within the protein structure.

The side chain of histidine has a typical pKa value in the range of 6.5-7.4. However, when analyzing the pKa values in a particular protein, scientists determined that one particular His residue has an unusually low pKa value of 4.8. Which of the following statements correctly explain this anomaly? 1) The microenvironment around a residue can impact its pKa value. 2) A positively charged amino acid must be in close proximity to this residue. 3) A negatively charged amino acid must be in close proximity to this residue. 4) This residue must be located on the surface of the protein. a. Statements 2, 3 and 4 are correct. b. Statements 1, 2 and 4 are correct. c. Statements 1 and 4 are correct. d. Statements 1 and 2 are correct.

DSGPYK, MEHFR, WGSPPK

There is another melanocyte-stimulating hormone called β-melanotropin. Cleavage of β-melanotropin with trypsin produces the following peptides plus free aspartic acid. If you assume maximum sequence similarity between α-melanotropin and β-melanotropin, then what must the sequence of the latter be? WGSPPK, DSGPYK, MEHFR

a. 1. Lactoglobin 2. Thrombin (wild type) 3. Cytochrome c.

To characterize the thrombin in the sample, you must remove two proteins that interfere with the thrombin activity assay: cytochrome c and lactoglobin. You find some CM-cellulose and a phosphate buffer (pH=6.4) on the shelf in your lab. You decide to load the protein sample onto a column of CM-cellulose equilibrated in the pH=6.4 buffer. Predict the order of elution for the three proteins shown in the table below. a. 1. Lactoglobin 2. Thrombin (wild type) 3. Cytochrome c b. 1. Thrombin (wild type) 2. Lactoglobin 3. Cytochrome c c. 1. Cytochrome c 2. Thrombin (wild type) 3. Lactoglobin

False

True or false? A codon is a group of three bases that can specify more than one amino acid.

start/methionine; AUG stop codon; UAG, UGA, UAA amino acid; ACU, GCA, UGC, CAC, AUC, AAA Nearly every mRNA gene that codes for a protein begins with the start codon, AUG, and thus begins with a methionine. Nearly every protein-coding sequence ends with one of the three stop codons (UAA, UAG, and UGA), which do not code for amino acids but signal the end of translation.

Use the table to sort the following ten codons into one of the three bins, according to whether they code for a start codon, an in-sequence amino acid, or a stop codon. The three bins are; start/methionine, stop codon, and amino acid Options; AUG, UAG, UGA, UAA, ACU, GCA, UGC, CAC, AUC, AAA

a. A change of the A in the GAG codon for glutamate to a U would change the codon to GUG, which codes for valine.

Using the information in table, explain how a point mutation could change a codon for Glu to a codon for Val. a. A change of the A in the GAG codon for glutamate to a U would change the codon to GUG, which codes for valine. b. A change of the G in the GAG codon for glutamate to a C would change the codon to GUC, which codes for valine. c. A change of the A in the GAA codon for glutamate to a U would change the codon to GAU, which codes for valine.

b. E is the N-terminal residue; Y is the C-terminal residue.

What are the N-terminal and C-terminal residues for the following peptide sequence? Peptide sequence: EASY a. Aspartic acid is the N-terminal residue; tyrosine is the C-terminal residue. b. E is the N-terminal residue; Y is the C-terminal residue. c. Glutamic acid is the N-terminal residue; tryptophan is the C-terminal residue. d. Y is the N-terminal residue; E is the C-terminal residue.

SYSM, EHFRWGKPV

What peptides are expected to be produced when α-melanotropin (SerTyrSerMetGluHisPheArgTrpGlyLysProVal) is cleaved by cyanogen bromide?

SYS, MEHFRWGKP, V

What peptides are expected to be produced when α-melanotropin (SerTyrSerMetGluHisPheArgTrpGlyLysProVal) is cleaved by thermolysin?

SYSMEHFR, WGKPV

What peptides are expected to be produced when α-melanotropin (SerTyrSerMetGluHisPheArgTrpGlyLysProVal) is cleaved by trypsin?

False

When referring to the amino acid sequences of proteins, sequence homology is the same as sequence similarity. True or false?

The CHNH2 group α to the carboxylic acid is oxidized to a C=O group by the transaminase.

When transaminated, the three branched-chain amino acids (valine, leucine, and isoleucine) form compounds that have the characteristic odor of maple syrup. An enzyme called α-keto acid dehydrogenase converts these compounds into CoA esters. Give the structure of the valine-derived compound that smells like maple syrup.

b. One addition and one deletion mutation. This combination results in no net change in the number of bases, so the reading frame would eventually be restored.

Which mutation(s) would not change the remainder of the reading frame of a gene sequence that follows the mutation(s)? a. One addition and two deletion mutations. b. One addition and one deletion mutation. c. One addition mutation. d. One deletion mutation.

Proline and Aspartic Acid

Which of the following amino acids would most likely be found on the surface of a protein? Phenylalanine Valine Proline Leucine Aspartic acid

a. Only statements 1 and 3 are correct. [The bond is planar. There is substantial double-bond character to this bond.]

Which of the following characteristics are true about a typical peptide (amide) bond? 1) The bond is planar. 2) There is free rotation about the carbonyl carbon and nitrogen bond. 3) There is substantial double-bond character to this bond. 4) There is a net negative charge on nitrogen and net positive charge on oxygen. a. Only statements 1 and 3 are correct. b. Only statements 1, 2 and 4 are correct. c. Only statements 2 and 3 are correct. d. All of the listed statements are correct.

b. Only statements 1 and 3 are correct.

Which of the following characteristics are true about a typical peptide (amide) bond? 1) The bond is planar. 2) There is free rotation about the carbonyl carbon and nitrogen bond. 3) There is substantial double-bond character to this bond. 4) There is a net negative charge on nitrogen and net positive charge on oxygen. a. Only statements 1, 2 and 4 are correct. b. Only statements 1 and 3 are correct. c. Only statements 2 and 3 are correct. d. All of the listed statements are correct.

c. Each of the three stop codons can also encode rare modified amino acids.

Which of the following is FALSE when considering the standard genetic code? a. AUG serves as the translation start codon in most cases. b. Three separate codons encode translation stop signals. c. Each of the three stop codons can also encode rare modified amino acids. d. Apart from methionine, the only other amino acid with a single codon is tryptophan. e. There are 64 possible codons to represent 20 common amino acids.

b. The negative charge on the peptide will be increased.

Would the chemical modification change the overall charge on the ATP-dependent kinases at pH=7? a. The positive charge on the peptide will be increased. b. The negative charge on the peptide will be increased. c. The negative charge on the peptide will be reduced. d. The charge on the peptide will not change. e. The positive charge on the peptide will be reduced.

e. The negative charge on the peptide will be increased.

Would the chemical modification change the overall charge on the iodoacetate at pH=7? a. The positive charge on the peptide will be increased. b. The positive charge on the peptide will be reduced. c. The negative charge on the peptide will be reduced. d. The charge on the peptide will not change. e. The negative charge on the peptide will be increased.

b. Yes. Loss of a (+)-charged side chain will increase the (-) charge density on the protein, making it less likely to bind to the CM cellulose.

You are surprised to observe that the patient's thrombin flows through the CM-cellulose column at pH=6.4 faster than expected based on its pI. Confident in your technique, you suspect the patient's thrombin is different from wild-type thrombin. Using a different buffer system, you manage to purify some of the patient's thrombin and you submit the purified sample for amino acid sequencing. The sequence analysis shows that the patient's thrombin contains a mutation in the enzyme active site. A lysine residue in the wild type has been mutated to an asparagine in the patient's thrombin. Does this mutation explain the anomalous CM-cellulose binding behavior you observed? a. No. Loss of a (+)-charged side chain would not affect the (-) charge density on the protein. b. Yes. Loss of a (+)-charged side chain will increase the (-) charge density on the protein, making it less likely to bind to the CM cellulose. c. No. Loss of a (+)-charged side chain will decrease the (-) charge density on the protein to have the same overall charge.

c. The pI of the mutant protein predicted to be less than the pI of the normal protein.

You have discovered a novel protein that has a pI=5.5. To study the functional properties of this new protein, your research group has made a mutant that contains two amino acid changes-namely, a surface Phe residue in the normal protein has been replaced by His (side chain pKa=6.1), and a surface Gln has been replaced by Glu (side chain pKa=4.2). Is the pI of the mutant protein predicted to be greater than, less than, or the same as the pI of the normal protein? a. The pI of the mutant protein predicted to be the same as the pI of the normal protein. b. The pI of the mutant protein predicted to be greater than the pI of the normal protein. c. The pI of the mutant protein predicted to be less than the pI of the normal protein.