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Wstęp: biochemia i rewolucja genomowa,

Ewolucja biochemiczna, Struktura i funkcja białek

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B

IOCHEMIA

I

–

ĆWICZENIA

LISTA 1

do wykładu dr. hab. inż. P. Dobryszyckiego

W s t ę p : b i o c h e m i a i r e w o l u c j a g e n o m o w a

E w o l u c j a b i o c h e m i c z n a

S t r u k t u r a i f u n k c j a b i a ł e k [ f r a g m e n t ]

1. RNA differs from DNA because RNA:

(a) is usually single stranded.
(b) often base-pairs with itself (intrastrand pairing).
(c) uses deoxyribose instead of ribose.
(d) uses uracil instead of thymine.
(e) forms a triple helix instead of a double helix.

2. The distinguishing feature of the Eukarya is that:

(a) they are all multicellular.
(b) they have tough cell walls around each cell.
(c) they have a well-defined nucleus within each cell.
(d) they are more primitive than the Archaea or the Bacteria.

3. For the bonds or interactions in the left column, indicate all the characteristics in the right column that

are appropriate.

(a) electrostatic interaction

(1)

requires nonpolar species

(b) hydrogen bond

(2)

involves charged species only

(c) van der Waals bond

(3)

requires polar or charged species

(d) hydrophobic interaction

(4)

involves either O and H or N and H atoms

(5)

involves polarizable atoms

(6)

is also called a salt bridge

(7)

exists only in water

(8)

is optimal at the van der Waals contact distance

(9)

typically has an energy between 3 and 7 kcal/mol

(10)

typically has an energy of around 1 kJ/mol

(11)

is weakened in water

4. As will be seen in succeeding chapters, enzymes provide a specific binding site for substrates where one

or more chemical steps can be carried out. Often these sites are designed to exclude water. Suppose that
at a binding site, a negatively charged substrate interacts with a positively charged atom of an enzyme.

(a) Using Coulomb’s equation, show how the presence of water might affect the interaction. What sort of

environment might be preferable for an ionic interaction? Note that a numerical answer is not required
here.

(b) How would an ionic interaction be affected by the distance between the oppositely charged atoms?

5. Which of the following statements is correct? The entropy of a reaction refers to

(a) the heat given off by the reaction.
(b) the tendency of the system to move toward maximal randomness.
(c) the energy of the transition state.
(d) the effect of temperature on the rate of the reaction.

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Wstęp: biochemia i rewolucja genomowa,

Ewolucja biochemiczna, Struktura i funkcja białek

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6. The Second Law of Thermodynamics states that the entropy (disorder) of a system and its surroundings

always increases for a spontaneous process. So why do proteins fold up spontaneously? It is evident that
protein folding moves from a disorderly state (randomly unfolded proteins) to an orderly state (folded
proteins). Explain.

7. Osmosis tends to equalize concentrations on both sides of a membrane. Any living cell will have protein

and nucleic acid inside, which "draws" water inward. To prevent bursting, concentration of something
inside the cell has to be made lower than the concentration outside. Concentration of what? How is this
adjustment made?

8. What is the ratio of base to acid form at pH 0.8, 1.8, 2.3, 2.8, and 3.8 for the carboxylic group of

histidine? What physicochemical parameter regarding histidine do you need to know in order to
complete the required calculations? Find the appropriate value in the textbook.

9. Examine the four amino acids given below:

A

B

C

D

Indicate which of these amino acids are associated with the following properties:

(a) aliphatic side chain

(b) basic side chain

(c) three ionizable groups

(d) charge of +1 at pH 7.0

(e) pK ~10 in proteins

(f) secondary amino group

(g) designated by the symbol K

(h) in the same class as phenylalanine

(i) most hydrophobic of the four

(j) side chain capable of forming hydrogen bonds

(k) Name the four amino acids.

(l) Name the other amino acids of the same class as D.

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Wstęp: biochemia i rewolucja genomowa,

Ewolucja biochemiczna, Struktura i funkcja białek

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10. Calculate the net charge of histidine at pH 6.5. What can you say about the buffering capacity of

histidine at pH 7,6?

11. Draw the structure of cysteine at pH 1.

12. Which of the following amino acids have side chains that are negatively charged under physiologic

conditions (i.e. near pH 7)?

(a) Asn

(d) Glu

(b) His

(e)

Cys

(c) Trp

13. How many different dipeptides can be made from the 20 L amino acids? What are the minimum and

the maximum number of pK values for any dipeptide?

14. For the pentapeptide Gln-Met-Arg-Thr-Glu,

(a) name the carboxyl-terminal residue.
(b) give the number of charged groups at pH 7.
(c) give the net charge at pH 1.
(d) write the sequence using one-letter symbols.
(e) draw the peptide bond between the Thr and Glu residues, including both side chains.

15. A dimeric protein is composed of identical polypeptides having 400 amino acid residues each. What is

the approximate molecular mass of the protein?

(a) 22 000 Da

(c) 88 000 Da

(b) 44 000 Da

(d) 196 kDa