Introduction to Bioinformatics

What type of amino acids are in group 1?

Non-polar

Which amino acids are in group 1?

Glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, and tryptophan

Are the group 1 amino acids hydrophobic or hydrophilic?

Hydrophobic

What types of R-groups do group 1 amino acids have?

Aliphatic or aromatic

What happens to globular proteins in aqueous solutions?

They will fold into a 3D shape to bury the hydrophobic side-chain in the protein interior

What is glycine's three letter code?

Gly

What is glycine's one letter code?

G

What is alanine's three letter code?

Ala

What is alanine's one letter code?

A

What is valine's three letter code?

Val

What is valine's one letter code?

V

What is leucine's three letter code?

Leu

What is leucine's one letter code?

L

What is isoleucine's three letter code?

Ile

What is isoleucine's one letter code?

I

What is proline's three letter code?

Pro

What is proline's one letter code?

P

What is phenylalanine's three letter code?

Phe

What is phenylalanine's one letter code?

F

What is methionine's three letter code?

Met

What is methionine's one letter code?

M

What is tryptophan's three letter code?

Trp

What is tryptophan's one letter code?

W

What makes proline different?

It is an imino acid, it has an imino and carboxyl group together

What type of amino acids are in group 2?

Polar, uncharged

What amino acids are in group 2?

Serine, cysteine, threonine, tyrosine, asparagine, and glutamine

What do most group 2 side-chains have?

At least one nitrogen, oxygen, or sulphur with electron pairs available for hydrogen bonding to water and other molecules

What is serine's three letter code?

Ser

What is serine's one letter code?

S

What is cysteine's three letter code?

Cys

What is cysteine's one letter code?

C

What is threonine's three letter code?

Thr

What is threonine's one letter code?

T

What is tyrosine's three letter code?

Tyr

What is tyrosine's one letter code?

Y

What is asparagine's three letter code?

Asn

What is asparagine's one letter code?

N

What is glutamine's three letter code?

Gln

What is glutamine's one letter code?

Q

What two amino acids contain sulphur?

Methionine and cysteine

What types of R-groups do asparagine and glutamine have?

Amide R-groups

Is tyrosine hydrophilic or hydrophobic?

Hydrophobic

What type of amino acids are in group 3?

Acidic

What amino acids are in group 3?

Aspartic acid and glutamic acid

What makes aspartic acid and glutamic acid acidic?

They both have carboxylic acid on their side-chain

What happens to aspartic acid and glutamic acid is aqueous solutions at physiological pH?

All three functional groups ionise making the overall charge -1

What are the ionic forms of aspartic acid and glutamic acid?

Aspartate and glutamate

What is aspartic acid's three letter code?

Asp

What is aspartic acid's one letter code?

D

What is glutamic acid's three letter code?

Glu

What is glutamic acid's one letter code?

E

What type of amino acids are in group 4?

Basic

What amino acids are in group 4?

Arginine, histidine, and lysine

What are arginine and lysine's overall charges at a physiological pH?

+1

Which amino acid has the most basic R-group and why?

Arginine as it has a guandio group on its side-chain

What type of bonds do arginine and lysine's side chains form?

Ionic bonds

What is arginine's three letter code?

Arg

What is arginine's one letter code?

R

What is histidine's three letter code?

His

What is histidine's one letter code?

H

What is lysine's three letter code?

Lys

What is lysine's one letter code?

K

Which amino acid usually makes up the active site of protein enzymes?

Histidine

Which amino acid has the largest side-chain?

Tryptophan

What is the protein's primary strucutre?

The amino acid sequence and the location of disulphide bonds

What do residue's refer to?

Amino acids linked by peptide bonds

What is the protein's secondary structure?

The regular, local structure of the protein backbone

What stabilises the secondary structure?

Intramolecular forces and sometimes intermolecular hydrogen bonding of amide groups

What are two main types of secondary strucutre?

Alpha helix and beta sheet

What is the most common secondary structure?

Alpha helix

What is the protein's tertiary structure?

The fold (3D shape) of the protein as a result of spatial arrangements of secondary structure elements

What holds the tertiary structure together?

Non-covalent bonding (hydrogen bonding, ionic interactions, van der Waals forces, and hydrophobic packing), disulphide bonds, and metal ion coordination

What is a protein's quaternary structure?

When some proteins form assemblies (units) with other molecules

What holds the quaternary structure together?

The same forces as the tertiary structure

What does PDB stand for?

Protein Data Bank

What is usually deposited in the PDB?

3D structure data of large biological molecules (proteins/ nucleic acids)

How is PDB data usually obtained?

Experimentally using either X-ray crystallography, NMR spectroscopy, or cryo-electron microscopy

How are PDB files visualised?

With PyMol

What is UniProt?

It is a key database for information about protein sequences and contains annotation data and other functional information

What is usually deposited into UniProt?

Data from genome sequencing projects

Where is UniProts' information about the biological function of proteins from?

Research literature

What is Ensembl

It is a genome browser that annotates and maps genomic features from gene sequences?

What is type of resource is Ensembl?

It is an 'added value resource' that brings together information from a wide range of other databases into a single site

What are Ensembl's features?

It gene builds for \> 300 species, gene trees, regulatory build (ENCODE), variation display and VEP, display of user data, BioMart (data export), programmatic access via the API's, and completely open source

What can Ensembl display?

The graphical alignment of genes against a reference genome

What is Ensembl Genomes used for?

Non-vertebrates (protists, plants, fungi, metazoa, and bacteria)

What types of data is on NCBI and EMBL-EBI?

Nucleotide data

What does the primary accession code from NCBI and EMBL-EBI provide?

A unique reference for the particular sequence

What is homology?

Similarly due to a common (relatively) recent ancestor.

Is homology binary or non-binary?

Binary, either two things are homologous or they are not

What is molecular evolution?

The mechanisms underlying evolution at a molecular level

What does molecular evolution provide?

The mutations provide genetic variation within a population.

What will most mutations do to the population?

They will be detrimental and purifying (negative) selection will act to eliminate them from the population

What is the impact of a neutral mutation?

They will be neutral in terms of the phenotype, some will be randomly accepted (neutral genetic drift)

What is the impact of a positive mutation?

They will be positive and adaptation (positive selection) will act to select these

What is a phylogenetic tree?

A graphical representation of the relationship between genes and shows the gene's history

What is an ortholog?

A subset of homology that refers to the same gene across different species.

What are orthologs likely to have?

A similar function which can be used to predict the functions/ structure of the other

What are paralogs?

A subset of homology that refers to genes related within the species with a common ancestor within its gene family

What are paralogs likely to have?

Diverging gene functions and so one cannot be used to predict the function of the other