Lecture 16

What does 'Omics' refer to in biological studies?

study of a complete set of biological molecules in a cell, organism, or system

What is proteomics?

study of all the proteins in a system

what is bioinformatics?

use of computational tools to analyze sequence data, such as BLAST

what is phylogenetics?

study of building and interpreting evolutionary trees

what is genomics?

study of entire genome

what is the transcriptome?

all RNA transcripts

what is the proteome?

all proteins

what is the metabolome?

all the metabolites

What are the steps in the proteomic workflow?

protein extraction, denaturation/digestion/separation, and mass spec analysis

what is the goal and process of the protein extraction step?

get proteins out of cells/tissue by lysing cells and separating proteins from other components

What is the goal of the protein denaturation step?

unfold proteins from their 3D structures by using trypsin to cut proteins at specific amino acids to make a complex mix of peptides (separated using LC before analysis)

what is the goal of the mass spectrometry step?

measure the mass of peptides to identify them using MS/MS (measures mass-to-charge ratio of peptides from digestion, then selects a single peptide to break into smaller fragment ions, then the MS measures the ratio of the fragments)

what is the goal and the process of the data analysis step?

use MS/MS data to determine what proteins were in original sample by using computer algorithms to compare the fragment spectrum against a theoretical database of known protein sequences

What enzyme is commonly used for protein digestion in proteomics?

Trypsin

What is bioinformatics?

use of computational tools to organize, analyze, and interpret biological data

What does ORF stand for in genetic analysis?

ORF stands for Open Reading Frame, which is a stretch of DNA that can be translated into a protein - starts with a start codon (ATG) and ends with a stop codon (TAA, TAG, TGA)

What is the BLAST tool in bioinformatics?

a tool that compares a query sequence against a database to find similar sequences.

how does the BLAST score affect results?

the higher the better - measures overall alignment quality

how does the BLAST e-value affect results?

the lower the better - measures number of matches you could expect to find by chance (high score means match is random)

what are identities in BLAST?

percentage of bases/amino acids that are an exact match

what are gaps in BLAST?

places where a sequence has an insertion/deletion relative to another

What are homologs in phylogenetics?

genes that share a common evolutionary ancestor

what are orthologs in phylogenetics?

homolog genes in DIFFERENT SPECIES that have the same function and arose from speciation

what are paralogs in phylogenetics?

homolog genes in SAME SPECIES that have related but different functions and arose from gene duplication

What is a node in a phylogenetic tree?

represents a branch point indicating a common ancestor.

what is a clade in a phylogenetic tree?

group containing an ancestor and ALL descendants

what are two main methods of building phylogenetic trees?

parsimony and likelihood & bayesian

what is parsimony as a tree-building method?

find a tree with fewest evolutionary changes - can be confused by long branch attraction, and result in polytomy (node with 3 or more branches)

what is likelihood & byesian as a tree building method?

use statistical models of how DNA/proteins evolve - usually accurate but slow

What is bootstrapping in the context of phylogenetic trees?

method to assess confidence in branching patterns by resampling the data and building new trees - high value means that a specific clade showed up in the shuffled data set, which indicates high confidence (so higher is better)

How can the evolutionary history of proteins be reconstructed?

By combining phylogenetics, sequence alignment, and functional data.

What is the method for determining post-translational modifications in proteomics?

Analysis in the data analysis step to identify modifications in proteins based on matching fragment patterns.