L22 Functional genomics 2: Proteomics

Question 1

What is functional genomics?

Answer 1

The study of gene functions and interactions using various high-throughput techniques that analyse global gene expression, protein interactions, and effects of gene mutations.

Question 2

How do traditional methods of gene expression analysis differ from genome wide analysis?

Answer 2

Traditional methods focus on a limited number of predetermined genes, while genome-wide analysis allows for the study of all genes simultaneously, revealing unknown gene responses.

Question 3

What is a DNA microarray?

Answer 3

A DNA microarray is a tool that contains small, solid supports where individual DNA samples representing all genes in an organism are spotted, allowing for the analysis of gene expression levels across the entire genome.

Question 4

Describe the principle of hybridization in DNA microarrays.

Answer 4

DNA samples (cDNA) are hybridised to the immobilised gene probes on the array and the binding of cDNA to the probes is quantified using fluorescent tags to analyse gene expression levels.

Question 5

What is chromatin immunoprecipitation (ChIP)?

Answer 5

It is a technique used to study protein-DNA interactions by cross-linking proteins to DNA, shearing the DNA, and using antibodies to isolate the protein-bound DNA fragments for analysis.

Question 6

What technologies can be utilised to analyse protein-DNA binding sites?

Answer 6

ChIP and ChIP-seq

Question 7

What is a gene knockout?

Answer 7

A genetic technique where a specific gene is deliberately disrupted or deleted to study its function and the resulting phenotypic changes in an organism.

Question 8

What purpose do knockout mice serve in research?

Answer 8

They are models to study human genetic disease by mimicking various genetic disorders and allowing researchers to analyse the effects of gene inactivation.

Question 9

How does RNA interference (RNAi) work in gene knockdown?

Answer 9

RNAi utilised small interfering RNA’s (siRNAs) to suppress target mRNA translation, effectively reducing gene expression without permanently affecting the gene itself.

Question 10

What methods allow for genome-wide RNA knockdown analysis in organisms like C. elegans?

Answer 10

A feeding library of E.coli engineered to express specific dsRNA can be used to achieve RNA knockdown across the genome of C.elegans affecting gene expression in all cells of the organism.

Question 11

Explain how a standard ChIP procedure works.

Answer 11

It involves cross-linking DNA-binding proteins to DNA, lysing cells, shearing chromatin, inmmunoprecipitating with specific antibodies, reversing cross-links, and analysing the bound DNA via PCR or other methods.

Question 12

What is the significance of using fluorescent labelling in microarray analysis?

Answer 12

Fluorescent labelling allows for the simultaneous comparison of two different cDNA populations (eg normal v diseased) by enabling the visualisation and quantification of differential gene expression.

Question 13

How can DNA microarrays be used to detect genetic disorders?

Answer 13

Comparative genomic microarrays analyse genomic DNA to detect gains or losses of genetic material that may be associated with genetic disorders and can identify SNPs relevant to disease susceptibility.

Question 14

What are the advantages of RNA-Seq over DNA microarrays?

Answer 14

it offers the ability to dectect novel transcripts and splice variants, and it quantifies RNA levels more accurately, making it suitable for comprehensive expression profiling.

Question 15

What role do molecular barcodes play in yeast gene knockout studies?

Answer 15

They facilitate the identification of individual yeast strains in genome-wide experiments involving mixed pools of delation mutants, enabling more efficient gene function analysis.

Question 16

What are the limitations of traditional 2D gel electrophoresis in proteomics?

Answer 16

Limitations include: low reproductivity, difficulty in quantifying protein spots, clustering of proteins leading to signal overlap, and challenges in analysing membrane proteins.

Question 17

What is the purpose of 2D Difference Gel Electrophoresis (DIGE)?

Answer 17

DIGE improves on traditional methods by allowing the simultaneous comparison of multiple samples on the same gel, thereby reducing the variability due to handling and gel differences.

Question 18

How does SILAC work to quantify protein expression?

Answer 18

It uses stable isotope-labelled amino acids in cell culture, allowing mass differences to distinguish between proteins from different samples during analysis via mass spectrometry for quantification (Light and heavy).

Question 19

What methodology is used for peptide identification in proteomics?

Answer 19

It typically involves enzymatic digestion of proteins (e.g. tryptic digestion), followed by separation and quantification using liquid chromatography couples with tandem mass spectrometry(LC-MS/MS).

Question 20

Why is gene expression analysis important for understanding disease mechanisms?

Answer 20

It provides insights into how different genes respond to environmental stimuli, how they are regulated, and how alterations in their expression can contribute to disease processes, aiding in the development of targeted therapies.

Question 21

What is the isoelectric point (pI) of a protein, and why is it significant in proteomics?

Answer 21

The isoelectric point (pI) at which a protein has a net zero charge. It is significant because proteins migrate based on their charge during electrophoresis, and at pI, they stop moving, allowing their separation based on charge.

Question 22

How to membrane proteins typically behave in 2d gel electrophoresis, and what is the suggested method to analyze proteins instead?

Answer 22

Membrane proteins aggregate and precipitate together in 2d GE, making them difficult to analyse. Instead, methods like DIGE are suggested, as they allow for the simultaneous analysis of multiple protein samples using fluorescent labelling.

Question 23

Describe the role of trypsin in the mass spectrometry analysis of proteins.

Answer 23

Trypsin is a common protease that cleaves proteins at lysine and arginine residues.This creates a reproducible pattern of peptides that can be analysed through mass spectrometry to identify and quantify proteins based on their mass and fragmentation patterns.

Question 24

What is SILAC, and how does it facilitate protein quantification in cell populations?

Answer 24

Stable Isotope Labeling with amino Acids in Cell culture. SILAC uses metabolically incorporated stable isotope-labelled amino acids in cell cultures to differentiate protein levels. Proteins from light and heavy isotope-labelled populations are mixed, digested (by trypsin), and analysed by mass spectrometry to quantify differential changes in proteome

Question 25

Explain how LC-MS/MS works and its advantage in analysing protein samples.

Answer 25

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Delete Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS) is a powerful analytical technique widely used in biochemistry and molecular biology for the qualitative and quantitative analysis of proteins, peptides, and other biomolecules. Sample Preparation: The first step usually involves preparing the protein sample by digesting it into smaller peptides, commonly using an enzyme like trypsin. Ensuring the sample is in a suitable form (e.g., soluble in the mobile phase) is crucial for the following steps. Liquid Chromatography (LC): The prepared sample is loaded onto a liquid chromatography column. In LC, the sample components are separated based on their interactions with the column matrix and the mobile phase (solvent). This separation is typically performed on a reversed-phase column where hydrophobic peptides are retained longer than hydrophilic ones. a. Elution: As the peptides are gradually eluted from the column with a solvent gradient, they enter the mass spectrometer. Mass Spectrometry (MS): Once the peptides exit the LC column, they are ionized and introduced into the mass spectrometer. Common ionization techniques include Electrospray Ionization (ESI) and Matrix-Assisted Laser Desorption/Ionization (MALDI). a. Ionization: Peptides are converted into charged particles (ions) to be analyzed. b. Mass Analysis: The mass spectrometer measures the mass-to-charge ratio (m/z) of the ions. This information allows for the identification of the peptides based on their mass. Tandem Mass Spectrometry (MS/MS): In this step, selected ions (precursor ions) can be fragmented into smaller pieces (product ions) through collision-induced dissociation (CID). The fragments are then analyzed in a second mass spectrometer stage. a. Fragmentation: The fragmentation pattern provides structural information about the peptide, enabling its identification and characterization. b. Data Analysis: The resulting tandem mass spectra can be matched against protein databases to identify the proteins present in the sample. High Sensitivity: LC-MS/MS is highly sensitive and can detect low-abundance proteins, making it suitable for complex biological samples. Quantitative Analysis: This technique allows for reliable quantification of proteins and peptides, which is crucial for biomarker discovery and comparative studies. Specificity: The use of tandem MS provides highly specific analysis by confirming the identity of proteins through fragmentation patterns. Multi-Analyte Capability: LC-MS/MS can analyze a wide range of proteins simultaneously, providing a comprehensive profile of the proteome. Minimal Sample Preparation: Compared to other methods, LC-MS/MS requires less tedious sample preparation, especially when using techniques like isotopic labeling or affinity enrichment. Dynamic Range: The method can handle a wide dynamic range of protein concentrations, allowing the analysis of samples with varying peptide concentrations. Reliability in Post-Translational Modifications (PTMs): LC-MS/MS is effective in identifying and characterizing PTMs, such as phosphorylation or glycosylation, which are critical for protein function. Automation and High Throughput: Advances in LC-MS/MS technology have enabled high-throughput analysis, making it suitable for large-scale studies, such as proteomics. In summary, LC-MS/MS is an indispensable tool in modern protein analysis due to its sensitivity, specificity, and capability for both qualitative and quantitative assessments, making it ideal for a wide range of biological and clinical applications. Copy Humanize Summarize Delete Detectable IconAI TEXT DETECTED Don't get accused of using AI. Click here to bypass AI detectors. thats too much information. i need to fit it on a flash card Delete Sure! Here's a condensed version suitable for a flashcard: LC-MS/MS Overview What it is: A technique combining Liquid Chromatography and Tandem Mass Spectrometry for analyzing proteins and peptides. How it Works: Sample Prep: Proteins are digested into peptides. Liquid Chromatography: Peptides are separated based on properties. Mass Spectrometry: Peptides are ionized, measured for mass, and identified. Tandem MS: Selected peptides are fragmented for structural information. Advantages: High sensitivity for low-abundance proteins. Accurate quantitative analysis. Specific identification through fragmentation. Analyzes multiple proteins simultaneously. Effective for post-translational modifications. High throughput for large-scale studies.