INTRODUCTION TO PROTEOMICS (Bio 405)

Final Exam 1434-1435 (2013-2014)

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I : Choose the correct answer:

1- Unlike the genome of an organism, the proteome …………………. from cell to cell.
a) Differs
b) Is similar

2- The number of genes in human genome versus the number of proteins in the human
proteome is:
a) 20,000-25,000 genes vs. 1,000,000 proteins
b) 1,000,000 genes vs. 20,000-25,000 proteins

3- The procedure for low-throughput sequencing through Edman degradation is called:

a) Protein quantification
b) Protein separation
c) Protein sequence analysis
d) Protein identification

4- The procedure for protein or peptide matching through protein databases is called:
a) Protein quantification
b) Protein separation
c) Protein sequence analysis
d) Protein identification

5- The high-throughput sequencing determines the …………………. structures of a protein

a) 1-D b) 2-D c) 3-D d) 4-D

6- …………………. methods includes differential staining with fluorescent dyes.

a) Gel-free b) Gel-based

7- According to the classification of amino acids based on their polarity:

a) 20 different amino acids occur in living cells
b) Four chemical groups (composition of the R group)
c) Number of acidic amino acids is two & basic amino acids is three
d) All of the above

8- Subunits in the quaternary structure is considered:

a) Primary structure
b) Secondary structure

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 c) Tertiary structure
d) Quaternary structure

9- …………………. involves the sharing of pairs of electrons in two atoms.

a) Covalent bond
b) Noncovalent bond
c) van der Waals force

10- …………………. is the sum of the attractive or repulsive forces between two molecules.
a) Covalent bond
b) Noncovalent bond
c) van der Waals force

11- The differences in function of different body tissues are caused by:
a) Chromosome crossover
b) Differences in gene expression
c) Mutations

12- The general method allows the visualization of all cellular proteins, separated according to
their:
a) Charge
b) Molecular weight
c) Charge and molecular weight

13- In the specific method of protein characterization, we use:

a) mRNA b) antibodies

14- The reaction of a specific antibody-protein reaction indicates gene ……………….

a) size b) location c) expression d) sequence

15- HRT and HART are used for:

a) Gene amplification
b) Identification of translation product encoded by a cloned gene

16- Both HRT and HART work best when the gene being studied has been obtained as:
a) DNA b) cDNA c) mRNA d) tRNA

17- In HART, the missing band indicates:

a) wrong results b) DNA loss c) the proper protein

18- An example of the power of structural proteomics was discussed by Shapiro & Harris
(2000) using the following:
a) Hemoglobin b) myoglobin c) cleft shape d) a & b.
19- Higher resolution characterization (…….……) may be possible by matching the shape of
the cleft to a library of small molecular shapes.
a) circulator b) size c) superfolds d) cleft shape

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20- The final component of the yeast system is a reporter gene that is activated specifically by
the ………………… transcription factors.
a) two b) three c) four d) five

21- Improved variant can be subjected to further rounds of mutagenesis and selection known as
a) Protein sequencing b) transcription c) directed evolution d) transformation

22- An alternative approach to directed evolution is

a) Gene shuffling b) gene shifting c) protein shuffling d) protein shifting

23- Different polymorphic gene of interest might exist naturally in:

a) Haploid organisms b) diploid organisms c) single organism d) tetraploid
organism

24- Genes are digested with ……….. to generate fragment to be recombined

a) RNase b) proteinase c) DNase d) all of the above

25- The more cycles of extension, melting and annealing, the …………….... the variability
that can be produced
a) greater b) fewer

26- Gene shuffling relies on the annealing of mismatched DNA sequencing during
a) gel electrophoresis b) PCR c) spectophotometer d) none of the above

27- The labeling of proteins is ……………… variable and labeling/attachment to a substrate

could interfere with protein binding, either by affecting the way the protein folds or by
blocking the binding site.
a) More b) less

28- Protein array device can contain any type of………..…. and is used to assay protein–
protein interactions and protein interactions with other molecules.
a) Protein b) DNA c) RNA d) enzymes

29- A number of ligand classes are equally attractive for the production of high-affinity, high-
specificity target binders. These include the following:
a) Polyclonal antibodies b) Monoclonal antibodies c) Phage display antibodies
d) all of the above

30- The principle of phage display is the expression of fusion proteins in such a way that a
foreign peptide sequence is “…………..” on the bacteriophage surface.
a) created b) removed c) displayed d) none of the above

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II: Put (True) or (False) in front of the following sentences:
The word “proteome” is derived from PROTEins expressed by genome and it refers to
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all the proteins produced by an organism.
The large increase in protein diversity is thought to be due to alternative splicing and
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post-translational modification of proteins.
The proteome differs from cell to cell and is constantly changing through its
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biochemical interactions with the genome and the environment.
4 One organism has different protein expression in different parts of its body.
5 Proteomics is the low scale study of protein, particularly their structure and functions.
Group II amino acids with neutral (hydrophilic) polar side chains, and consists of serine,
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theonine, cysteine, glutaming and asparagine.
Gel based method are used including differential staining of gels with fluorescent dyes
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(difference gel electrophoresis).
The structural proteomics are high- throughput determination of protein structures in
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three dimensional space.
All proteins are modified from their pure translated amino acid sequence, called post
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translational modification.
Protein are short chains of amino acids linked together by peptide bonds with positive
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and negative charges
11 In the question 10, negatively charged protein is like carbonyl group at one end.
In the structure of amino acids, R can be H, in the case of glycine, with an alkyl group or
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heterocyclic ring.
13 All amino acids except glycine, are chiral asymmetrical compounds.
14 Amino acids are very soluble in water and high melting points in excess of 200oC
All proteomics technology rely on the ability to separate a complex mixture of proteins
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so that individual proteins are more difficult to be processed.
Two amino acids, glutamic acid and aspartic acid, have carboxyl groups in their side
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chains in addition to the one present in all amino acids.
17 Amino acids are joined to form unbranched polypeptides by a peptide bond.
Peptide bond is covalent bond between the carboxyl group of one amino acid and amino
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group of the next amino acid.
In a protein, many amino acids (usually more than a hundred) are linked by peptide
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bonds to form a polypeptide chain.
20 There are two levels of protein structure.
21 Tertiary structures of proteins are subunits in the quaternary structure.
22 Proteomics is the direct equivalent of transcriptomics.
Gel Electrophoresis is the process where molecules can be separated according to size
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and electrical charge by applying electric current.
A first common electrophoresis procedure in 2-D gel is known as isoelectric focusing
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(IEF).
The protein of the secondary structure is the first step in specifying the three
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dimensional structure of a protein.
An example of the power of structural proteomics was discussed by Shapiro & Harris
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(2000 ) using the proteins hemoglobin and myoglobin.
The resolution of the 2DGE was improved to increase the chance of detecting rare
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proteins.

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28 The process "Edman Degradation method" is the manual sequencing method used.
The mRNA molecules are translated into mixture radioactive proteins, which can be
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separated by gel electrophoresis and visualized by autoradiography.
The sequence of a peptide containing 100 to 200 residues can easily be determined by
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this method in about 30 minutes.
Two related techniques (HRT) and (HART) are used to identify the translation product
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encoded by a cloned gene.
HRT (hybrid-release translation) and HART (hybrid-arrest translation) are used to
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identify the translation product encoded by a cloned gene.
The cloned gene's translation product is identified as the protein that is absent from the
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autoradiograph.
Variants have been produced by gene shuffling that favor aminolysis (synthesis) over
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hydrolysis in aqueous solvents.
35 The first stage of proteome scale analysis is 3D electrophoresis for protein profiling.
36 Sequence analysis is sufficient to annotate all orphan genes.
The yeast two-hybrid system, initially described by Fields & Song (1989), is the
37 prototype of a range of related techniques in which protein interactions are assayed in
vivo.
All DNA sequences are made of the same four nucleotides and hence behave similarly
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in term of their chemical properties.
39 Protein arrays are emerging as a useful closed system for proteome analysis.
40 Protein arrays are different from DNA arrays.
The principles of molecular recognition (hybridization between complementary base
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pairs) apply to all sequences.
42 An alternative approach to directed evolution is gene shuffling.
After a short period of primer extension, The DNA is subjected to a round of melting,
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annealing and extension.
The improved variant can be subjected to further rounds of mutagenesis and selection, a
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process known as directed evolution.
Hybridization occurs between the cDNA and mRNA counterpart, but in this case the
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unbound mRNA is discarded.
Sources of variants, different protein with the different activity may be found in other
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organisms, but the gene and protein sequences will be same.
In gene shuffling method of original method, the genes are digested with DNase to
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generate fragments to be recombined.
In previous question 47, about random chimeragenesis on transient template or
48 (RACHITT), the gene fragments are generated from one strand of all but one of the
parental DNAs
In the original ITCHY process, the incremental truncation was performed using timed
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exonulease digestions.
50 One drawback of ITCHY libraries is that they contain only two crossover per gene.