Bioinformatics Final Exam || Complete
Questions & 100% Accurate Solutions
Conceptial Researchers
, Bioinformatics Final Exam || Complete
Questions & 100% Accurate Solutions
Bioinformatics - ANSWER - The technology that uses computers for storage,
retrieval, manipulation and distribution of information related to biological
macromolecules. (DNA, RNA, proteins, metabolites, lipids.)
Who is the mother of bioinformatics? - ANSWER - Margaret Dayhoff
What are the three main areas of bioinformatics? - ANSWER - - Molecular sequence
analysis
- Molecular structure analysis
- Molecular function analysis
Database - ANSWER - A digital archive used to store and organize data in such a
way that information can be retrieved easily using a variety of search criteria.
Biological databases - ANSWER - Libraries of the life sciences information, collected
through experimentation and analysis (Ex: UCSC, NCBI)
Store data that can be retrieved and queried for relationships.
Relational databases - ANSWER - A set of tables that have relationships between
them. Relationships are found through structured query language (SQL)
Flat file - ANSWER - A text file that contains pieces of data separated by a delimiter.
(Ex: comma, tab, space)
Databases at NCBI - ANSWER - 1. Genbank
2. Genome
3. GeneReviews
4. PubMed
5. OMIM
What are the three main sequence databases? - ANSWER - 1. Primary DNA
(DDBJ/EMBL/GenBank (ncbi)
2. Primary protein (GenPept/TrEMBL/UniProt)
3. Curated DB (RefSeq/UniProt)
Describe the Chou Fasman algorithm in detail - ANSWER - Measures propensity.
- uses observed frequencies in X-ray/NMR structures.
- ration of (x/m/(Y/N)
m: number of residues in a substrate (helix)
x: number of specific residue in a substrate (cytosine in a helix)
N: number of residues in all structures
Y: number of specific residues (cytosine in the whole structure)
, six residue scanning window for helices → 4 continuous residue P (propensity) > 1=
helix
Five-residue scanning window for strand→ 3 continuous residue P >1 = strand
Propensity - ANSWER - Probability of each AA residue to be present in a secondary
structure of helices or strand.
Describe the general properties of transmembrane domain proteins. - ANSWER - -
30% of all cellular proteins
- Various important functions: signal transduction, membrane transport etc.
- Alpha helices are common and Beta barrels are rare
- Hydrophobicity is required in transmembrane spanning region
- Structure is extremely difficult empirically
- Approximate 17-25 hydrophobic residues
- Residues flanking the transmembrane spans are hydrophilic loops of <60 residues
- The residues bordering the transmembrane spans on the cytosolic side are more
positively charged.
Positive inside rule.
Regarding transmembrane domain proteins in the context of cell surface receptors,
why are these proteins particularly important in drug design? - ANSWER - - Drugs
need to either get into the cell or target these proteins to initiate/block a signaling
cascade.
Homology modeling (tertiary structure prediction) - ANSWER - Builds structural
prediction based on known structure template WITH significant sequence similarity.
Threading (folding recognition)
(Tertiary structure prediction) - ANSWER - Builds structural prediction based on
known structure template WITH or WITHOUT any sequence similarity.
Ab intio (free modeling)
(tertiary structure prediction) - ANSWER - Based on molecular simulation and
predicts structures based on physiochemical principles WITHOUT structural
template.
Describe homology modeling in detail - ANSWER - Assumes two sequences with
high sequences similarity are likely to have similar 3D structures.
If the structure is known for one sequence then the structure can be inferred for the
similar sequence.
six steps:
1. Template selection: find a solved template structure with high sequence similarity
to the target sequence.
2. Sequence alignment (most critical step)
3. Backbone modeling
Questions & 100% Accurate Solutions
Conceptial Researchers
, Bioinformatics Final Exam || Complete
Questions & 100% Accurate Solutions
Bioinformatics - ANSWER - The technology that uses computers for storage,
retrieval, manipulation and distribution of information related to biological
macromolecules. (DNA, RNA, proteins, metabolites, lipids.)
Who is the mother of bioinformatics? - ANSWER - Margaret Dayhoff
What are the three main areas of bioinformatics? - ANSWER - - Molecular sequence
analysis
- Molecular structure analysis
- Molecular function analysis
Database - ANSWER - A digital archive used to store and organize data in such a
way that information can be retrieved easily using a variety of search criteria.
Biological databases - ANSWER - Libraries of the life sciences information, collected
through experimentation and analysis (Ex: UCSC, NCBI)
Store data that can be retrieved and queried for relationships.
Relational databases - ANSWER - A set of tables that have relationships between
them. Relationships are found through structured query language (SQL)
Flat file - ANSWER - A text file that contains pieces of data separated by a delimiter.
(Ex: comma, tab, space)
Databases at NCBI - ANSWER - 1. Genbank
2. Genome
3. GeneReviews
4. PubMed
5. OMIM
What are the three main sequence databases? - ANSWER - 1. Primary DNA
(DDBJ/EMBL/GenBank (ncbi)
2. Primary protein (GenPept/TrEMBL/UniProt)
3. Curated DB (RefSeq/UniProt)
Describe the Chou Fasman algorithm in detail - ANSWER - Measures propensity.
- uses observed frequencies in X-ray/NMR structures.
- ration of (x/m/(Y/N)
m: number of residues in a substrate (helix)
x: number of specific residue in a substrate (cytosine in a helix)
N: number of residues in all structures
Y: number of specific residues (cytosine in the whole structure)
, six residue scanning window for helices → 4 continuous residue P (propensity) > 1=
helix
Five-residue scanning window for strand→ 3 continuous residue P >1 = strand
Propensity - ANSWER - Probability of each AA residue to be present in a secondary
structure of helices or strand.
Describe the general properties of transmembrane domain proteins. - ANSWER - -
30% of all cellular proteins
- Various important functions: signal transduction, membrane transport etc.
- Alpha helices are common and Beta barrels are rare
- Hydrophobicity is required in transmembrane spanning region
- Structure is extremely difficult empirically
- Approximate 17-25 hydrophobic residues
- Residues flanking the transmembrane spans are hydrophilic loops of <60 residues
- The residues bordering the transmembrane spans on the cytosolic side are more
positively charged.
Positive inside rule.
Regarding transmembrane domain proteins in the context of cell surface receptors,
why are these proteins particularly important in drug design? - ANSWER - - Drugs
need to either get into the cell or target these proteins to initiate/block a signaling
cascade.
Homology modeling (tertiary structure prediction) - ANSWER - Builds structural
prediction based on known structure template WITH significant sequence similarity.
Threading (folding recognition)
(Tertiary structure prediction) - ANSWER - Builds structural prediction based on
known structure template WITH or WITHOUT any sequence similarity.
Ab intio (free modeling)
(tertiary structure prediction) - ANSWER - Based on molecular simulation and
predicts structures based on physiochemical principles WITHOUT structural
template.
Describe homology modeling in detail - ANSWER - Assumes two sequences with
high sequences similarity are likely to have similar 3D structures.
If the structure is known for one sequence then the structure can be inferred for the
similar sequence.
six steps:
1. Template selection: find a solved template structure with high sequence similarity
to the target sequence.
2. Sequence alignment (most critical step)
3. Backbone modeling
