intro

Introduction to Computational Science (1999) CZ1103, Tutorial V (Computational Biology)
1. What is the function of the following cell component (scientifically called organelle)?
            Nucleus
            Ribosome
            Lysosome
            Golgi apparatus

Nucleus : DNA storage, DNA and RNA synthesis, Ribosomal subunit assembly
Ribosomes : Protein synthesis.
Lysosomes : Digestion of food, bacteria, and damaged cell components.
Golgi apparatus : Modification, tempprary storage, and transport of macromolecules.

Formation of lysosomes and transport vesicles.

2. Describe the difference between organ and organ system, give one example for each.

Organ system: A group of related body components that perform a specific type of function.
Organ: Functional group of organ system.
Example: Organ system => Central nervous system. Organ => Brain.

3. List major type of cell molecules.

Protein, DNA, RNA, Polysaccharides, Lipids, Sugar, and other chemical compounds such as hormones, neural transmitters etc.

4. Why are large molecules in cells called polymers? What are the two processes for making and breaking these polymers?

These molecules are called polymers because they are made in cells by joining together smaller organic molecules.
The two processes are dehydration synthesis (making a polymer) and hydrolysis (breaking a polymer).

5. What is the definition of population in biology?

A group of interbreeding individuals of one species.

6. What is the function of the following type of protein?
            Receptor
            Enzyme
            Ion channel

Receptors: Receiving and processing external signals.
Enzymes: Speed-up and control of chemical reactions.
Ion Channels: Responsible for the passage of signaling ions in and out of a cell.

7. What are the four levels of structural organization of proteins?

Primary structure, secondary structure, tertiary structure, quarternary structure.

8. What is the complementary sequence of the following DNA?
CGCGAATTCGCG (called Dickerson's dodecamer)
CTAGGCATTAAATCCGCG

GCGCTTAAGCGC
GATCCGTAATTTAGGCGC

9. Describe the three stages of protein making process.

Stage 1: Copy of genetic code from DNA to mRNA
Stage 2: mRNA moves to a designated location.
Stage 3: mRNA, tRNA (which is attached by an amino acid), and rRNA assemble in ribosome to make protein.

10. What kind of retrieval methods are used in biological databases?

11. What are the main features of biological databases?

Individule specialized database for sequence, structure, function, literature and others.
Cross-linking of related databases.
Mirro sites to enhance access speed.
Integrated search site that combines all information or links, search tools, and literature in one.

12. What are the applications of sequence alignment?

Homolog identification, gene identification and prediction

13. Describe the purpose of the following databases:
            The National Center for Biotechnology Information.
            Nucleic Acids Database.
            SWISS-PROT.
            Online Mendelian Inheritance in Man.
            AntiCancer Agent Mechanism Database.

The National Center for Biotechnology Information (NCBI).

Integrated ENTREZ retrieval software, BLAST search tools and databases for genetics, gene and protein sequences, 3D structures, and on-line PubMed library.

Nucleic Acids Database (NDB).

Structural and biological info for a set of 122 compounds with anticancer activity and reasonablly well known mechanism of action.

14. What is global alignment and what is local alignment?

Global alignment:
Uses entire sequences and counts penalties for end gaps.
Local alignment:
Begins with {a(i1), b(j1)} match and ends with the {a(ik), b(jk)} match. End gaps not counted.

15. What does BLAST stands for?

BLAST stands for Basic Local Alignment Search Tools.

16. Determine the total score for the following alignment:
Sequence a: AGC -ACACA
Sequence b: ACACAC -TA

Pair      Status              Scoring function
(A,A)    match             s=1, w=0
(G,C)    mismatch        s=-1, w=0
(C,A)    mismatch        s=-1, w=0
(-,C)      gap                 s=0, w=2
(A,A)   match              s=1,w=0
(C,C)     match             s=1, w=0
(A,-)     gap                  s=0, w=2
(C,T)    mismatch        s=-1, w=0
(A,A)    match             s=1, w=0

Total score = sum {s} - sum { w} = 1 - 4 =-3