Cell Biology Lecture 34: Omics

(Omics Terms) The addition of "omics" to a molecular term implies what?

Comprehensive/global assessment

(Omics Terms) What is genomics?

Study of genes and their functions including disorders

(Omics Terms) What is transcriptomics?

Study of gene expression

(Omics Terms) What is proteomics?

Study of the proteome (All expressed proteins)

(Omics Terms) What is metabolomics?

Study of metabolites present (Substance used in metabolism)

(Genomics) What is a genome?

Entire DNA sequence of a particular species

(Genomics) What does genomics aim to understand?

Structure of genome

(Genomics) What are the ways the genome is studied in genomics?

1. Mapping genes

2. Sequencing DNA

3. Collecting variations

4. Organizing information in database

(Genomics) What do genomic studies provide a useful framework for studying?

Genetic variations related to disease

(Genomics) What is the process of determining the sequence of nucleotide bases in a piece of DNA?

DNA Sequencing

(Genomics) What is the most fundamental level of knowledge of a gene/genome?

Nucleotide sequence

(Genomics) What are the steps in DNA sequencing?

1. Break DNA into small pieces

2. Sequencing the pieces

3. Assembling sequences into a single consensus

(Genomics) How does illumina sequencing work?

Simultaneously identifying DNA bases using unique fluorescent signals and adding them to nucleic acid chain

(Genomics) Are all genetic conditions inherited?

No

(Genomics) What was the first major sequencing project?

Human Genome Project

(Genomics) What years did the human genome project last for?

1990 - 2003

(Genomics) How many genes were identified in the human genome project?

30,000

(Genomics) How many base pairs make up the human DNA?

3 billion

(Genomics) What does DNA sequencing allow us to detect?

Genetic predispositions to disease

(Genomics) What gene provides instructions on making a tumor suppressant protein?

BRCA1

(Genomics) What risk increases with the mutation of BRCA1 or BRCA2 genes?

Breast and ovarian cancer

(Transcriptomics) What is a transcriptome?

Set of all mRNA transcripts produced by a cell

(Transcriptomics) In what way does transcriptomics examine RNA levels?

1. Where transcripts are present (Qualitatively)

2. How much of transcript is expressed (Quantitively)

(Transcriptomics) What are the major types of RNA?

1. mRNA

2. rRNA

3. tRNA

(Transcriptomics) What is the function of mRNA?

Carrying information from DNA in the nucleus to the ribosomes of the cytoplasm for protein synthesis (Gene expression profiling)

(Transcriptomics) What is rRNA?

Structural components of ribosomes

(Transcriptomics) What is the function of tRNA?

Bring amino acids to ribosomes to be assembled

(Transcriptomics) What are the steps of studying the transcriptome (RNA Sequencing)?

1. Convert mRNA to cDNA

2. Sequence cDNA library

(Transcriptomics) What is RNA sequencing (RNA-seq) used to measure?

Expression across the transcriptome (transcriptional modulations)

(Transcriptomics) What are the limitations of RNA sequencing (RNA-seq)?

1. False positives (Need second confirmation)

2. Results may not be consistent among different strains

3. Upregulated transcription does not always means upregulated protein

(Proteomics) What is a proteome?

Proteins expressed by genome

(Proteomics) What does proteomics analyze in a protein?

1. Peptide abundance

2. Protein interactions

3. Protein modifications

(Proteomics) What are the types of proteomics?

1. Structural

2. Functional

(Proteomics) What is the goal of structural proteomics?

Define primary, secondary, and tertiary structure of proteins

(Proteomics) What is used to study protein functions in functional proteomics?

Information provided by structural genomics

(Proteomics) What technique is used to identify proteins in a sample?

Amino acid sequencing using Mass Spectrometry

(Proteomics) What procedure is used to identify proteins of interest?

Peptide mass fingerprinting

(Proteomics) How does mass spectrometry identify compounds?

Measuring mass of different molecules in a sample

(Proteomics) What biomolecules are identified using mass spectrometry?

1. Peptides

2. Lipids

3. Saccharides

(Proteomics) What is the process of measuring mass in mass spectrometry?

Production of ions by electron ionization of sample

(Proteomics) What are the ions characterized by in mass spectrometry?

1. Mass to Charge Ratio (m/z)

2. Ion Abundance

(Proteomics) What are the three functional units of mass spectrometry?

1. Ion source

2. Mass analyzer

3. Detector system

(Proteomics) What does the ion source do in mass spectrometry?

Ionize and transfer sample ions into gas phase

(Proteomics) What does the mass analyzer do in mass spectrometry?

Separate ions according to mass to charge ratio (m/z)

(Proteomics) What does the detector system do in mass spectrometry?

Measures relative abundance of ions

(Proteomics) What is the graph used in mass spectrometry?

Ion Abundance vs. Mass to Charge Ratio (m/z)

(Metabolomics) What is a metabolome?

Collection of all metabolites in an organism

(Metabolomics) What is a metabolite?

End products of gene expression

(Metabolomics) What are examples of metabolites?

1. Amino Acids

2. Fatty Acids

3. Carbohydrates

(Metabolomics) What is the process of metabolomics?

Comprehensive and simultaneous profiling and quantification of metabolites

(Metabolomics) What do metabolite levels and ratios reflect?

Metabolic function

(Metabolomics) If metabolite levels are out of range, what does it indicate?

Disease

(Metabolomics) What plays a key role in metabolic diseases?

Metabolic dysregulation

(Metabolomics) What non-metabolic diseases are affected by metabolic dysregulation?

1. Cancer

2. Cognitive disorders

3. Cardiovascular diseases

4. Respiratory pathologies

(Metabolomics) What can metabolomics be used to predict?

Cancer and cardiovascular events

(Microbiomics) What is studied in microbiomics?

Microbiota

(Microbiomics) What is microbiomics used to determine?

Microbiota correlated with diseases

(Microbiomics) Is the human mouth heavily colonized by microbes?

Yes

(Microbiomics) What does the accumulation of harmful microbes in the mouth lead to?

Inflammation and destruction of oral tissue

(Microbiomics) What kind of disease is periodontitis hypothesized to be?

Microbial-shift disease

(Microbiomics) What a protuberance that disrupts homeostasis that leads to oral disease?

Dysbiosis

(Microbiomics) What are the steps of profiling the microbiome?

1. Amplifying hypervariable regions

2. Sequencing hypervariable regions

3. Clustering sequences into operational taxonomic units

(Microbiomics) What can be used to distinguish close microbial species?

Shotgun metagenomics

(Microbiomics) What is bioinformatics used for?

Data analysis

(Microbiomics) What discipline allows storage and analysis of vast amounts of nucleic acid and protein sequence data?

Bioinformatics

(Microbiomics) What does bioinformatics provide?

Tools to make sense and predictions using other omics