MITES Biochemistry

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Name _________________________________

Practice Midterm Exam 200 points total – 75 minutes

Multiple Choice (3 pts each – 30 pts total) – Mark your answers in the space to the left:

____________ 1. Amphipathic molecules have regions that are:

a) polar b) nonpolar c) hydrophilic d) hydrophobic e) all of the above

____________ 2. Eukaryotic cells have:

a) a cell membrane b) a nucleus c) complex organelles d) all of the above e) none of the above

____________ 3. The pKa values for phosphoric acid are 2.14, 6.86, and 12.4. The pKb values are: a) 2.14, 6.86, and 12.4 b) 16.14, 20.86, and 26.4 c) -2.14, -6.86, and -12.4 d) 1.60, 7.14, and 11.86 e) 1.13, 2.04, and 6.54

____________ 4. Which of the following weak noncovalent forces would NOT be present

in an aqueous solution of a charged polar compound: a) Van der Waals interactions b) Hydrogen bonds c) Hydrophobic interactions d) Ionic interactions

____________ 5. There are ________ nucleotides per turn, each ________ Å (Distance) apart in the naturally occurring ______ form of double helical DNA. a) 11, 34, B b) 10.5, 3.4, A c) 10.5, 34, Z d) 12, 26, A e) 10.5, 3.4, B

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____________ 6. Shown below are four possible base pairing schemes between the bases guanine (G) and uracil (U). Remember that G-U base pairs form in RNA. X represents C1’ of ribose. Which base pairing scheme exhibits valid hydrogen bonding?

N C

CC

N

N

C

C

N

O

N

H

X

H

H

H

H

NC

CN

O

CC

O

X

H

H

G Ua)

N C

CC

N

N

C

C

N

O

N

H

X

H

H

H

NC

CN

O

CC

O

H

X

H

H

G

U

b)

N

C

C

N

O

C

C O

H

X

H H

N C

CC

N

N

C

C

N

O

N

H

X

H

H

H

G

U

c)

N

C

C

N

OC

C

O H

XH

H

N C

CC

N

N

C

C

N

O

N

H

X

H

H

H

G

U

d)

____________ 7. What is the tripeptide shown below?

NH3

+

C

C

NH

C

C

NH

C

C

O O

O

O

CH2CH

2S CH

3

CH2C

O

NH2

CH2

OH

a) Phe-Gln-Met b) Phe-Asn-Met c) Tyr-Gln-Met d) Tyr-Asn-Met e) none of the above

____________ 8. Which of the amino acids below has a side chain that is polar and

charged? a) alanine b) tyrosine c) aspartate d) threonine e) none of the above

____________ 9. Which of the amino acids below has a side chain that is nonpolar and charged? a) alanine b) phenylalanine c) glutamate d) histidine e) none of the above

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____________ 10. Which of the amino acids below has a side chain that is aromatic?

a) phenylalanine b) tyrosine c) tryptophan d) all of the above e) none of the above

True/False (3 pts each – 30 pts total) – Please mark your answers in the space to the left: ____________ 11. Monosaccharides and polysaccharides are types of proteins. ____________ 12. Water’s low specific heat is a direct result of hydrogen bonding. ____________ 13. At the half-equivalence point of a monoprotic acid titration curve,

[HA] = [A¯] and pH = pKa. ____________ 14. A 0.01-M solution of HCl would have pH = 1. ____________ 15. Hydrophobic interactions occur between lipid molecules. ____________ 16. In the titration of 100 mL of a 0.1-M phosphoric acid solution, 5 mL of a

2-M NaOH solution would be one equivalent. ____________ 17. All amino acids contain an amino group and a hydroxyl group. ____________ 18. Only L-amino acids are used in biologically produced proteins. ____________ 19. The zwitterionic form of lysine has a charge of +1. ____________ 20. Serine and methionine both contain sulfur atoms. Short Answer Please show your work--partial credit will be given. (55pts)

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21. A base titration curve of maleic acid (pKas = 2.00, 6.26) is shown below. Fill in the empty

boxes on the x- and y-axes with numerical values. (6pts)

Titration of Maleic Acid

0

0 2

Molar Equivalents of NaOH

pH

22. Give one example of a protein and one example of a nucleic acid. (2pts)

protein:_________________________ nucleic acid:________________________

23. On the molecules below, fill in labels to identify the functional groups. (6pts)

O

OH OH

HH

CH2

H H

OPO

O

O

N N

NN

O

NH2

H

C C

H

NH3

+O

OCH

2

SH

24. For each molecule below, write the total number of chiral centers and circle each one. (5pts)

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C

C

C

C

CH2OH

OHH

OHH

OHH

OH

ribose

___________

C

O O

OH HH

O C

CH2

C

O

O

chorismate

__________ 25. Circle and label the functional groups on the two molecules below. Note: “carbonyl” is

insufficient; please be more specific. (6pts)

O

OO

OPO

O

O

O

H

NH2

OH

26. Complete the table below. For the two biological polymers listed below, give the general name for the monomer and polymer of each. (4pts)

Protein Nucleic Acid Carbohydrate

Monomer

Polymer Polypeptide Nucleic Acid

27. Which two weak noncovalent interactions will occur between hydrophilic molecules? (4pts)

___________________________________ _____________________________________

28. Identify whether amino acids below are in the L or D form. (6pts)

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C

H

NH3

+COO

CH2

CH

CH3CH

3

_

_____________________

CH

NH3

+

COO

CH2

NH

N

_

___________________

29. Determine whether the following molecules S or R stereoisomers (12 pts):

____________

______________

_____________

30. In no more than two sentences, describe the main purpose behind the use of RNA interference (RNAi) in molecular biology today? (4pts)

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Problems – Please show your work—partial credit will be given. (85pts)

31. (7 pts) For each pair of molecules listed below, state whether hydrogen bonding will occur between the two molecules and if so show how this would occur.

Molecules H-bonding? (Y/N) If Yes, show H-bonding a) ____ b) ____ c) ____

32. (8 pts) pKa data for glycine are shown below.

pKa1 Carboxyl 2.34

pKa2 Amino 9.60

a) A buffer is prepared by combining 1 mole of fully-protonated glycine (NH3+-CH2-COOH)

and 0.5 mole NaOH in 1 L of water. What is the pH of the buffer?

N

H

O

CH3CH

3

O

CH3CH

3

N O

CH3CH

3

H

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b) 1 L of a 1M NaOH solution is added to this buffer. What is the new pH?

33. (15 pts) Using only H2PO4¯ and PO43— how many moles of each would you add to prepare 1

L of a 0.11 M buffer at pH 7.9? H3PO4 + H2O H2PO4

− + H3O+ (Rxn1) pKa1 = 2.1 H2PO4

− + H2O HPO42− + H3O+ (Rxn2) pKa2 = 6.9

HPO42− + H2O PO4

3− + H3O+ (Rxn3) pKa3 = 12.4

[A-] + [HA] = .11 7.9 = 6.9 + log ([A-]/[HA]) [A-] = .1 [HA] = .01 H2PO4- = .06 HPO4 = .05

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34. (20 pts) The structure of arginine and its Ka values are given below. Draw an schematic titration curve, identifying the axis with appropriate scale, pK’s, pI, and draw the specie that predominates at each endpoint, along with the net charge for each.

Ka1 (carboxyl) 10-2

Ka2 (amino) 10-9

KaR (side chain) 10-12

C

H

NH3

+COO

CH2

CH2

CH2

NH

C

NH2

NH2

+

_

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35. Draw a polypeptide chain containing the following amino acid sequence: Asn-Cys-Glu-Lys-Tyr. Circle the peptide bonds and mention the functional group they represent. What is the net charge of the polypeptide at pH = 1.0, 5.0, 7.0, 9.5, 13? (20pts)

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36. Draw a sequence of 3 DNA nucleotides: ACG. Circle the phosphodiester bonds and draw out the bases. Please state the directionality of the strand. (15pts)

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Supplementary Material

pKa1: 2.29 pKa2: 9.7 pKa1: 2.33 pKa2: 9.7 pKa1: 2.32 pKa2: 9.8

pKa1: 2.13 pKa2: 9.3 pKa1: 2.20 pKa2: 9.3

pKa1: 2.46 pKa2: 9.4

pKa1: 2.35 pKa2: 9.9 pKa1: 2.35 pKa2: 9.8 pKa1: 1.95 pKa2: 10.5

pKa1: 2.19 pKa2: 9.2 pKa1: 2.09 pKa2: 9.1 pKa1:1.6 pKa2:1.9 pKaR:10.7

pKa1: 2.17 pKa2: 9.1 pKa1: 2.14 pKa2: 8.4

pKa1:2.2 pKa2:9.2 pKaR:10.5

pKa1:2 pKa2:9.9 pKaR:3.9 pKa1:2.9 pKa2:9.5 pKaR:4

pKa1 1.8 pKa2 9.3 pKaR 6

pKa1:1.8 pKa2:9 pKaR:12.5 pKa1:2 pKa2:9.1 pKaR:10.54

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