Bioinformatics Exam 1 Review

Flashcards covering bioinformatics databases, translation, phylogenic trees, amino acid properties, restriction enzymes, and structure prediction methods.

GenBank and DDBJ

Public DNA sequence databases.

Protein Data Bank (PDB)

The public database for protein 3D structures.

Reading frame shift

A method used in translation where the first 3 reading frames are determined by shifting the base to the next one.

DND file

A file format used for representing phylogenic trees.

Glycine (Gly, G)

A small amino acid with a molecular weight of $57.05$.

Alanine (Ala, A)

A small amino acid with a molecular weight of $71.09$.

Serine (Ser, S)

A nucleophilic amino acid with a molecular weight of $87.08$ and a $pKa$ of $16$.

Threonine (Thr, T)

A nucleophilic amino acid with a molecular weight of $101.11$ and a $pKa$ of $16$.

Cysteine (Cys, C)

A nucleophilic amino acid with a molecular weight of $103.15$ and a $pKa$ of $8.35$.

Valine (Val, V)

A hydrophobic amino acid with a molecular weight of $99.14$.

Leucine (Leu, L)

A hydrophobic amino acid with a molecular weight of $113.16$.

Isoleucine (Ile, I)

A hydrophobic amino acid with a molecular weight of $113.16$.

Methionine (Met, M)

A hydrophobic amino acid with a molecular weight of $131.19$.

Proline (Pro, P)

A hydrophobic amino acid with a molecular weight of $97.12$.

Phenylalanine (Phe, F)

An aromatic amino acid with a molecular weight of $147.18$.

Tyrosine (Tyr, Y)

An aromatic amino acid with a molecular weight of $163.18$.

Tryptophan (Trp, W)

An aromatic amino acid with a molecular weight of $186.21$.

Aspartic Acid (Asp, D)

An acidic amino acid with a molecular weight of $115.09$ and a $pKa$ of $3.9$.

Glutamic Acid (Glu, E)

An acidic amino acid with a molecular weight of $129.12$ and a $pKa$ of $4.07$.

Lysine (Lys, K)

A basic amino acid with a molecular weight of $146.17$ and a $pKa$ of $10.79$.

Arginine (Arg, R)

A basic amino acid with a molecular weight of $156.19$ and a $pKa$ of $12.48$.

ClaI

A restriction enzyme with the recognition site ATCGAT.

EcoP15I

A restriction enzyme with the recognition sites CAGCAG and CTGCTG.

FokI

A restriction enzyme with the recognition site GGATG.

BspMI

A restriction enzyme with recognition sites ACCTG and TGGAC.

SduI

A restriction enzyme with the recognition site GD(G-A-T) GCH(A-C-T) C.

Eco571

A restriction enzyme with recognition sites CTGAAG and CTTCAG.

PmaCI

A restriction enzyme with the recognition site CACGTG.

BgII

A restriction enzyme with the recognition site GCCNNNNNGGC.

SacII

A restriction enzyme with the recognition site CCGCGG.

SfiI

A restriction enzyme with the recognition sites GGCNNNNNGGCC or GGCCNNNNNGCC.

AFIII

A restriction enzyme with the recognition sites ACRYGT, specifically ACGTGT or ACACGT.

Signal peptide

A short peptide present at the N-terminus of most newly synthesized proteins that are destined towards the secretory pathway.

Chou-Fasman method

A method used for RNA-secondary structure prediction.

Mfold (Zuker) method

A method specifically designated for RNA-secondary structure prediction.

DNA Fragment Assembly Overlap

A process where the overlap between fragments must be a minimum of 4 bases.