Proteins and Human Disease
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Questions and Answers

Which gene/protein is targeted by Alirocumab?

  • PCSK9 (correct)
  • C/EBPβ
  • IL1B
  • Spi-1

    • Which gene/protein is associated with inflammation and targeted by anakinra, rilonacept, and canakinumab?

  • C/EBPβ
  • IL1B (correct)
  • PCSK9
  • Spi-1

    • Which molecule can theoretically dock to the Spi-1 DBD pocket, blocking C/EBPβ binding?

  • PCSK9
  • Alirocumab
  • LDL cholesterol
  • L-Arginine (correct)

    • Which software platform integrates visualization, modeling, and simulations for drug discovery?

    <p>MOE (Molecular Operating Environment)</p> Signup and view all the answers

    What are the three aspects along which gene functions are classified in the Gene Ontology framework?

    <p>Molecular function, Cellular component, Biological process</p> Signup and view all the answers

    What is the main use of Gene Ontology in Enrichment Analysis?

    <p>Identifying overrepresented or underrepresented GO terms for a set of up-regulated genes under certain conditions</p> Signup and view all the answers

    What is the EC system used for in the functional assignment of enzymes?

    <p>Classifying enzymes into different categories based on their activities</p> Signup and view all the answers

    What is the impact of single amino acid substitutions on protein structure?

    <p>They can dramatically alter protein structure</p> Signup and view all the answers

    How is protein secondary structure determined?

    <p>By amino acid side chains</p> Signup and view all the answers

    What is the key role of the Protein Data Bank (PDB)?

    <p>It is a key repository for protein structures</p> Signup and view all the answers

    Which software platform is mentioned in the text for integrating visualization, modeling, and simulations for drug discovery?

    <p>MOE</p> Signup and view all the answers

    Which gene/protein is targeted by anakinra, rilonacept, and canakinumab?

    <p>IL1B</p> Signup and view all the answers

    What is the theoretical molecule that can dock to the Spi-1 DBD pocket, blocking C/EBPβ binding?

    <p>L-Arginine</p> Signup and view all the answers

    What is the function of the Bioinformatics software mentioned in the text?

    <p>Modeling the interactions between molecules to predict active site binding</p> Signup and view all the answers

    Which software platform is mentioned in the text for integrating visualization, modeling, and simulations for drug discovery?

    <p>MOE (Molecular Operating Environment)</p> Signup and view all the answers

    Which gene/protein is targeted by anakinra, rilonacept, and canakinumab?

    <p>IL1B</p> Signup and view all the answers

    What is the main function of Alirocumab?

    <p>Targeting the PCSK9 gene/protein</p> Signup and view all the answers

    What is the theoretical molecule that can dock to the Spi-1 DBD pocket, blocking C/EBPβ binding?

    <p>L-Arginine</p> Signup and view all the answers

    What is the impact of single amino acid substitutions on protein structure?

    <p>Significant impact on protein function</p> Signup and view all the answers

    What is the focus of differential expression analysis?

    <p>Genes that are transcribed and eventually translated in particular cells</p> Signup and view all the answers

    In what ways is gene expression regulated?

    <p>By region, in development, and in the dynamic response to environmental signals</p> Signup and view all the answers

    What does differential expression analysis help in understanding?

    <p>The link between genotype, environment, and phenotype</p> Signup and view all the answers

    What does FPKM stand for in the context of gene expression analysis?

    <p>Fragments Per Kilobase of Transcript per Million mapped reads</p> Signup and view all the answers

    What is the main purpose of comparing differential expression between samples in gene expression analysis?

    <p>To test for statistically significant differences in expression between isoforms</p> Signup and view all the answers

    What is the first step when you do not have an assembly for gene expression analysis?

    <p>Make an assembly</p> Signup and view all the answers

    What is the measure of gene expression that is biased by gene length and library depth?

    <p>Total number of fragments</p> Signup and view all the answers

    What are the two main methods for gene expression analysis mentioned in the text?

    <p>Microarrays and RNAseq</p> Signup and view all the answers

    Which step is crucial in microarray data analysis according to the text?

    <p>Biological confirmation</p> Signup and view all the answers

    What is the goal of the RNAseq pipeline mentioned in the text?

    <p>Achieving high correlation coefficients between replicates</p> Signup and view all the answers

    What is the measure of gene expression that is biased by gene length and library depth?

    <p>Fragments Per Kilobase of Transcript per Million mapped reads (FPKM)</p> Signup and view all the answers

    In gene expression analysis, what is the main purpose of comparing differential expression between samples?

    <p>To understand differences that affect phenotype</p> Signup and view all the answers

    What is the first step when you do not have an assembly for gene expression analysis?

    <p>Making an assembly</p> Signup and view all the answers

    What does FPKM stand for in the context of gene expression analysis?

    <p>Fragments Per Kilobase of Transcript per Million mapped reads</p> Signup and view all the answers

    What is the focus of differential expression analysis in gene expression?

    <p>Testing for statistically differences in expression between isoforms</p> Signup and view all the answers

    What is the main purpose of normalizing the estimated expression of genes and transcripts in gene expression analysis?

    <p>To account for the bias introduced by gene length and library depth</p> Signup and view all the answers

    What is the primary goal of comparing differential expression between samples in gene expression analysis?

    <p>To identify statistically significant differences in gene expression between conditions</p> Signup and view all the answers

    What is a key step in the data analysis of gene expression once the raw data is converted to expression values for each gene?

    <p>Preprocessing to clean up data</p> Signup and view all the answers

    What is the impact of the total number of fragments being biased by gene length and library depth in gene expression analysis?

    <p>It introduces bias that needs to be accounted for during normalization</p> Signup and view all the answers

    What is the main focus of gene expression analysis when comparing differential expression between samples?

    <p>Identifying genes with statistically significant differences in expression</p> Signup and view all the answers

    What is the main purpose of normalizing the estimated expression of genes and transcripts in gene expression analysis?

    <p>To account for the bias introduced by gene length and library depth</p> Signup and view all the answers

    What is the focus of differential expression analysis in gene expression?

    <p>To identify genes with significantly different expression levels between samples</p> Signup and view all the answers

    What is the key role of the Protein Data Bank (PDB)?

    <p>To provide 3D structural data for proteins and nucleic acids</p> Signup and view all the answers

    What is the theoretical molecule that can dock to the Spi-1 DBD pocket, blocking C/EBPβ binding?

    <p>Theoretical molecule A</p> Signup and view all the answers

    What are the three main approaches to data analysis of gene expression mentioned in the text?

    <p>Preprocessing, inferential statistics, clustering analysis</p> Signup and view all the answers

    What is the measure of gene expression that is biased by gene length and library depth?

    <p>FPKM (Fragments Per Kilobase of Transcript per Million mapped reads)</p> Signup and view all the answers

    What is the main use of Gene Ontology in Enrichment Analysis?

    <p>To identify overrepresented functional terms in a set of genes</p> Signup and view all the answers

    What is the impact of single amino acid substitutions on protein structure?

    <p>It can lead to changes in protein folding and function</p> Signup and view all the answers

    Study Notes

    Proteins and Human Disease: Insights and Applications

    • Understanding the pathways that impact phenotype is crucial after identifying a specific gene linked to disease.
    • Diseases such as cystic fibrosis (CFTR), sickle-cell anemia (hemoglobin beta), "mad cow" disease (prion protein), and Alzheimer's disease (amyloid precursor protein) are influenced by proteins.
    • Single amino acid substitutions can dramatically alter protein structure, such as the DF508 mutation in CFTR and the E6V mutation in hemoglobin beta.
    • Modeling protein structure, function, and interactions is essential for understanding disease phenotypes, risk, and drug targets.
    • Websites like ExPASy and ISREC provide resources for analyzing protein properties, but their accuracy varies.
    • Protein secondary structure is determined by amino acid side chains, with examples including a-helices in myoglobin and b-sheets in thioredoxin.
    • Prediction algorithms like Chou and Fasman's and modern methods use multiple sequence alignments and machine learning techniques to predict secondary protein structure.
    • Approaches for determining tertiary protein structure include experimental methods (X-ray crystallography, NMR) and prediction methods like comparative modeling and ab initio prediction.
    • The Protein Data Bank (PDB) is a key repository for protein structures, containing 97,000 entities in 2014.
    • The CATH Hierarchy of Structure and tools like VAST and JMol provide access to structure data and comparisons of protein structures.
    • More complex models have been developed to model molecular interactions, including protein-protein and protein-DNA interactions.
    • Drug discovery involves identifying compounds that can alter protein interactions, with steps including finding genomic regions associated with disease and determining the effect on protein structure and function.

    Gene Expression Analysis: Microarrays and RNAseq

    • Gene expression analysis involves comparing RNA samples from different conditions, such as normal colon and colon tumor.
    • Two main methods for gene expression analysis are microarrays and RNAseq, with the latter being genome-wide and measuring all RNA transcripts.
    • Microarrays involve short oligonucleotide probes representing exons and fluorescence-labeled cDNA hybridization, followed by image acquisition and data analysis.
    • The seven main steps for differential gene expression on microarrays include experimental design, RNA extraction, hybridization, image analysis, data analysis, biological confirmation, and depositing in databases.
    • Key considerations in microarray analysis include the importance of biological replicates, RNA and cDNA quality, and the impact of technical artifacts on results.
    • Microarray data analysis involves statistical analysis to determine differentially expressed RNA transcripts, as well as clustering and classification to identify meaningful biological patterns.
    • Biological confirmation of microarray results is crucial, typically using methods such as Northern blots, Western blots, RT-PCR, or RNAseq.
    • Two main repositories for microarray data are the Gene Expression Omnibus (GEO) at NCBI and ArrayExpress at the European Bioinformatics Institute, with specific requirements for experimental information (MIAME).
    • GEO Datasets allow users to search and analyze RNA transcript expression across experiments, perform statistical tests, and create heatmaps and gene expression clusters.
    • RNAseq involves isolating RNAs, converting to cDNA, sequencing, mapping to the genome, and downstream analysis of differential gene expression.
    • RNA studies require complex design due to technical and biological replicates, and the need to account for variation within cells, individuals, and environmental factors.
    • RNAseq pipeline includes steps like read alignment, transcript compilation, gene identification, and differential expression, with the goal of achieving high correlation coefficients between replicates.

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    Week 13 Functional analysis, clinical applications, drug discoveryv2.pptx
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    Description

    Test your knowledge of proteins and their role in human disease with this insightful quiz. Explore the impact of specific genes on diseases like cystic fibrosis and Alzheimer's, the influence of single amino acid substitutions, and the essential role of protein modeling in understanding disease phenotypes and drug targets. Dive into protein structure, prediction algorithms, and the Protein Data Bank as you expand your understanding of proteins and their applications in disease research.

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