Biochemistry Test 1

Name:  _____________________                                                                        February 17, 2017

Possible:  78 pts

1.   (12 pts)      Sketch the tripeptide, SerLeuGln.  Show the atoms in their usual ionization states at physiological pH, which is about 7.4.

Backbone:  3 pts

Side chains:  6 pts

Order (N ® C):  1 pt

Charges: 2 pts


2.   (5 pts)  Here is a polypeptide.  Using the table below, indicate the charge on each side chain at a pH of 5.




 -1    0   +1   0   +1

Table 4-1  pKa values of ionizable groups in polypeptides


3.   (8 pts)  Calculate the pH of 1 L of water to which is added 2.5 mL of 0.040 M NaOH.

Moles of H+ = 0.0025 L × 0.040 mol/L = 0.0001 mol OH            2 pts

The concentration of OH is mol/L = 0.0001 mol / 1.0025 L = 0.0001 mol/L (nearly) 2 pts

pOH = -log(0.0001) = 4   2 pts

pH = 14 – 4 = 10    2 pts

This Page:  25 pts

4.     (4 pts)  To which class of biomolecules does each of the following belong?



nucleotide                                                                lipid

5.   (6 pts)  The figure below represents a protein.  What is the name of the secondary structure represented by the wide arrows?  ß-sheet


      Based on the orientation of the arrows, what is the term that describes the “directionality” of this structure?  antiparallel

      What is the name of the secondary structure represented by the F04_18regions?  α-helix

6.   (2 pts)  How many domains are present in the following protein?  (Ignore the horizontal bar.)

Two domains are present.

7.   (3 pts)  Which one of the following represents a protein that is heterotetrameric?  

a)      α4                b)  ß4                       c)  αß                       d)   αß2                    e)  αß2δ

8.   (3 pts)  Where in the protein is the information stored that determines the protein’s tertiary structure?

All of the information required for a protein to obtain its final shape is contained in its amino acid sequence.

This Page:  18 pts

9.   (2 pts)  According to the textbook, which instrumental technique is used to determine the structure of proteins in crystals?

X-ray crystallography









10. (2 pts)  The figure above shows that regions of unfavorable solvation come together when a protein folds.  This process is thermodynamically favorable because

a)      Energy is released when the protein folds

b)      Energy is absorbed when the protein folds

c)      Entropy increases when some of the water molecules are released from the unfavorable solvation region.

d)      Entropy decreases when some of the water molecules are released from the unfavorable solvation region.

11. (2 pts)  The residues making up carbohydrates, such as starch and cellulose (but not other biopolymers), are called _______________ (several answers are accepted).  sugars or monosaccharides

12. (5 pts)  The Henderson-Hasselbalch equation is given below. 

      A buffer solution is made by mixing 25 mL of 2.0 M sodium acetate and 75 mL of 2.0 M acetic acid (pKa = 4.76).  The final volume of the solution is 100 mL.  What is the final pH of the solution?

Use the buffer equation, pH = pKa + log [A-]/[HA].  The ratio [A]/[HA] is just 25/75, or 1/3.  So, pH = 4.76 + log 1/3 = 4.28        -2 pts for 5.24 (used [HA]/ [A] instead of [A]/[HA])

13. (4 pts)  Draw a simple sketch of the structure of a micelle formed by SDS, shown below.


Micelle:  F02_10

This Page:  15 pts

14. (2 pts)  How quickly do ions diffuse through a vesicle (choose the best answer)?

a)      They don’t

b)      At about the same speed as nonpolar substances.

c)      Quickly.     

d)      Very quickly.

e)      Somewhat slowly

15. (3 pts)  What is the significance of the Urey-Miller experiment?

It suggests how biological monomers could have arisen from “prebiotic” (that is, non-living) compounds in the early Earth.

16. (2 pts)  Which of the following is not considered to be evidence that all life originated from a common ancestor?

a)    Nucleic acids—DNA and RNA—participate in the storage and transmission of genetic information in all organisms.

b)   Oxidation of glucose is an almost universal means for generating metabolic free energy.

c)    The citric acid cycle takes place in the mitochondria of all eukaryotes.

17. (3 pts)  In the structure of malate (on the right), what is the oxidation number of the carbon attached to the OH?  zero


18. (2 pts)  Alpha helices are stabilized primarily by:

a. hydrogen bonds between the main chain peptide bond component atoms. 

b. electrostatic interactions between R-groups.

c. hydrophobic interactions between the a-carbons of the main chain.   

d. hydrogen bonding between the R-groups.    

e. hydrophobic interactions between R-groups and the solvent water.

19. Thermodynamics gives the equation DG = DH - T DS.  The DG value at 37°C for the arginine kinase reaction was recently determined.  The DH value for the reaction is –8.19 kJ/mol, and the value of DS is 2.2 J/(mol∙K).

a)      (6 pts)  What is the value of D for the reaction?

D = D - T D     = –8.19 kJ/mol – (273 + 37)K ∙ 2.2 J/(mol∙K)

                                    = –8190 J/mol – 310K ∙ 2.2 J/(mol∙K)

                                    = –8872 J/(mol∙K)

                                    or –8.87 kJ/(mol∙K)

                                    -2 pts for -682 (didn’t convert DH from J to kJ)

b)      (1 pt)   Is the reaction exothermic or endothermic?   Exothermic

c)      (1 pt)   Under standard conditions, will the reaction tend to take place spontaneously?  Yes

This Page:  20 pts