KING ABDULAZIZ UNIVERSITY

FACULTY OF SCIENCES
DEPARTMENT OF BIOLOGICAL SCIENCES
GENOMICS AND BIOTECHNOLOGY SECTION

INTRODUCTION TO PROTEOMICS (Bio 405)

Final exam, summer 2011

Student Name : -------------------------------------------------------------------

Student Number : -----------------------------------------------------------------

B- Write if the True or False in the sentences :

1 The word " proteome " is derived from PROTEins expressed by genome and it refers to all the
Protein produced by an organism .
T

2 The large increase in protein diversity is thought to be due to alternative splicing and post- T
translational modification of proteins.

3 The proteome differs from cell to cell and is constantly changing through its biochemical T
interactions with the Genome and the environment.

4 One organism has different protein expression in different parts of its body . T

5 proteomics is the low scale study of protein , particularly their structure and functions . F

6 Group II : amino acids with neutral ( hydrophilic ) polar side chains , and consists of serine , T
theonine , cysteine , glutaming , and asparagine .

7 Gel based method are used including differential staining of gels with fluorescent dyes T
(difference gel electrophoresis).

8 The structural proteomics are high- throughput determination of protein structures in three- T
dimensional space.

9 All proteins are modified from their pure translated amino acid sequence , called post T
translational modification.

10 Protein are short chains of amino acids linked together by peptide bonds with positively and F
negatively charged.

11 In the question 10, negatively charged like carbonyl group at the other end. T

12 In the structure of amino acids, R can be H, in the case of glycine, an alkyl group or heterocyclic ring. T

13 All amino acids except glycine, will be chiral asymmetrical compounds. T

14 Amino acids are very soluble in water and high melting points in excess of 200 oC. T

15 All proteomics technology rely on the ability to separate a complex mixture of proteins so that F

1
 individual proteins are more difficult processed.

16 Two amino acids , glutamic acid and aspartic acid , have carboxyl groups in their side chains in T
addition to the one present in all amino acids .

17 Amino acids are joined to form unbranched polypeptides by a peptide bond. T

18 Peptide bond: covalent bond between the carboxyl group of one amino acid and amino group of T
the next amino acid.

19 In a protein, many amino acids (usually more than a hundred ) are linked by peptide bonds to T
form a polypeptide chain.

20 There are two levels of protein structure. F

21 Tertiary structures of proteins are subunits in the quaternary structure. T

22 Proteomics is the direct equivalent of transcriptomics. T

23 Gel Electrophoresis is the process molecules can be separated according to size and electrical T
charge by applying electric current to them.

24 A first common electrophoresis procedure is known as isoelectric focusing (IEF). T

25 The protein of the secondary structure is the first step in specifying the three dimensional F
structure of a protein.

26 An example of the power of structural proteomics was discussed by Shapiro & Harris (2000) using the T
proteins hemoglobin and myoglobin.

27 The resolution of the 2DGE was improved to increase the chance of detecting rare proteins T

28 The process " Edman Degradation method " is the manual sequencing method used . T

29 The m RNA molecule is translated into a mixture of radioactive proteins, which can be separated by gel T
electrophoresis and visualized by autoradiography.

30 The sequence of a peptide containing 100 to 200 residues can easily be determined by this method in F
about 30 minutes.

31 Two related techniques (HRT) and ( HART) are used to identify the translation product encoded by a T
cloned gene.

32 HRT (hybrid-release translation) and HART (hybrid-arrest translation) are used to identify the translation T
product encoded by a cloned gene.

33 The cloned gene's translation product is, therefore, identified as the protein that is absent from the T
autoradiograph.

34 Variants also have been produced that favor aminolysis ( synthesis ) over hydrolysis in aqueous solvents. T

35 The first stage of proteome scale analysis, Three dimensional electrophoresis for protein profiling F
.

36 Sequence analysis is sufficient to annotate all orphan genes. F

37 The yeast two-hybrid system, initially described by Fields & Song (1989), is the prototype of a range of T

2
 related techniques in which protein interactions are assayed in vivo.

38 All DNA sequences are made of the same four nucleotides and hence behave similarly in term of their T
chemical properties.

39 Protein arrays are emerging as a useful closed system for proteome analysis. T

40 Protein arrays are different to DNA arrays. F

41 The principles of molecular recognition (hybridization between complementary base pairs) apply to all T
sequences.

42 An alternative approach to directed evolution is gene shuffling. T

43 After a short period of primer extension, The DNA is subjected to a round of melting, annealing ,and T
extension.

44 The improved variant can be subjected to further rounds of mutagenesis and selection, a process known T
as directed evolution.

45 Hybridization again occurs between the c DNA and m RNA counterpart , but in this case the unbound m F
RNA is discarded

46 Sources of variants, different protein with the different activity may be found in other organisms, but the F
gene and protein sequences will be same.

47 In gene shuffling method of original method, The genes are digested with DNase to generate fragments to T
be recombined.

48 In previous question 47, about random chimeragenesis on transient template or ( RACHITT) , The gene T
fragments are generated from one strand of all but one of the parental DNAs

49 In the original ITCHY process, The incremental truncation was performed using timed exonulease T
digestions.

50 One drawback of ITCHY libraries is that they contain only two crossover per gene . F