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Molecular Genetics > Bioinformatics > Flashcards

Bioinformatics Flashcards

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Biology 101 flashcards
1
Q

What is transciptomics?

A

study of gene expression data

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2
Q

What is GenBank?

A

Large datasets of DNA sequence

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3
Q

What is in vivo?

A

traditional biological experiments within an organism

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4
Q

What is in vitro?

A

traditional biological experiments in an artificial environment

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5
Q

What is in silico?

A

On the computer

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6
Q

What is bioinformatics?

A

Application of computer science for the management and analysis of biological information

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7
Q

What are computers used for in bioinformatics?

A

GATHER biological data
STORE intelligently and efficiently
Provide TOOLS to allow extraction of meaningful biological information
MERGE information from several sources to increase understanding

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8
Q

What is a primary database?

A

information about e.g. DNA sequences

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9
Q

What is a secondary database?

A

contain results of analysis of primary resources e.g. sequence patterns or mutations

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10
Q

What are the three main nucleotide sequence databases?

A

GenBank (National Center for Biotechnology Information -NCBI)
EBI -EMBL (European Molecular Biology Laboratory)
DDBJ (DNA Data Bank of Japan)

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11
Q

What is easier to obtain protein or DNA sequences?

A

Protein sequences

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12
Q

What is UniProtKB

A

(Universal Protein Resource Knowledgebase) – Comprehensive catalogue of information about proteins.

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13
Q

What was the first protein to have its structure determined?

A

myoglobin

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14
Q

What is Protein Data Bank (RCSB PDB)?

A

a protein data bank that stores over 100,000 structures

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15
Q

How is bioinformatics used to annotate genomes?

A

identify genes, protein coding regions

predict structures and functions

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16
Q

True or False?

Bioinformatics is a new research tool which will replace the need for laboratory experiments in the future

A

False

Experiments will still be needed as proof

17
Q

True or False?

A bioinformatics database is an archive or store of biological data

A

True

18
Q

True or False?

This is a nucleotide sequence ACTRFCGTRECATCGNKL

A

False

Protein sequence

19
Q

True or False?

Protein structures are more difficult to determine than protein sequences

A

True

20
Q

What is BLAST?

A

commonly used bioinformatics tool for rapidly comparing new sequences with known sequences e.g. All known nucleotide sequences

21
Q

What can you find out if you have the complete sequence of a gene?

A

Gene name, organism, complete gene + protein sequences

Information about protein’s function, structure, evolution

22
Q

Even if you don’t have the complete sequence of the gene you can still find out stuff about it.
What can you find out and how?

A

function, evolution etc from looking at related sequences
Because similar sequences may
have similar structure and/or function
have evolved from common ancestor

23
Q

What can use to find out more about the human genome?

A

http://www.genecards.org/

24
Q

What is http://www.ensembl.org/ ?

A

A whole genome browser
“software system which produces and maintains automatic annotation on selected eukaryotic genomes”
Can browse genome at different levels: chromosome ->gene->exon->nucleotide

25
Q

What is sequence alignment?

A

‘line up’ sequences so that similar features are in same columns

26
Q

What are ClustalW2 and Clustal omega

A

Most commonly used multiple sequence alignment program
Can align DNA or protein sequences
Requires fixed format input e.g. file with sequences in FASTA format

27
Q

What is shotgun sequencing?

A

copy DNA many times
chop each up into many random fragments
sequence each little piece (“read”)
assemble fragments where they overlap

28
Q

What is functional annotation?

A

Finding out what genes are for by looking at what the proteins do

29
Q

Why would you rather use bioinformatics over experimental approaches to research functional annotation of genes?

A

Bioinformatics is a scaled up automatic approach making it much faster

30
Q

During functional annotations what should you find out about the proteins?

A

Are there related proteins? (BLAST search) – cautiously infer function from these
Search secondary databases (e.g. SMART) for functional domains
Predict 3D structure – help to determine function where sequences are only weakly related to known proteins

31
Q

What can you use genome sequencing for from a single genome?

A

What is necessary for life?
Genes that control economically important traits e.g. crops
Personalised medicine

32
Q

What can use genome sequencing for comparatively?

A

How have species evolved?

What makes humans unique? Only 1% of our genes have not been found in other species!

Molecular Genetics (4 decks)

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