Proteomics Proteomics is the study of protein structure and function. An organism’s proteome is its entire set of proteins. Proteomics is much more complicated than genomics. 1

Proteomics Versus Genomics Genomics tells us what kinds of proteins a given organism has the capacity for producing, but genomics tells us almost nothing about how those proteins function or when and in which cells those proteins are produced. Proteomics gives us a clearer picture of what roles the various proteins play in cells. Therefore, compared to genomics, proteomics allows us to better understand an organism. 2

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Four Levels of Protein Structure 4

DNA Signal Gene NUCLEUS Chromatin modification Chromatin Gene available for transcription Exon Intron Tail RNA Cap RNA processing Primary transcript mRNA in nucleus Transport to cytoplasm mRNA in cytoplasm Translatio n CYTOPLASM Degradation of mRNA Protein processing Polypeptide Active protein Cellular function Transport to cellular destination Degradation of protein Transcription 5

Regulation of gene expression trpE gene trpD gene trpC gene trpB gene trpA gene (b) Regulation of enzyme production (a) Regulation of enzyme activity Enzyme 1 Enzyme 2 Enzyme 3 Tryptophan Precursor Feedback inhibition 6

Polypeptide subunits that make up enzymes for tryptophan synthesis (b) Tryptophan present, repressor active, operon off Tryptophan (corepressor) (a) Tryptophan absent, repressor inactive, operon on No RNA made Active repressor mRNA Protein DNA mRNA 5 Protein Inactive repressor RNA polymerase Regulatory gene Promoter trp operon Genes of operon Operator Stop codon Start codon mRNA trpA 5 3 trpR trpE trpD trpC trpB ABC D E 7

(b) Lactose present, repressor inactive, operon on (a) Lactose absent, repressor active, operon off mRNA Protein DNA mRNA 5 Protein Active repressor RNA polymerase Regulatory gene Promoter Operator mRNA 5 3 Inactive repressor Allolactose (inducer) 5 3 No RNA made RNA polymerase Permease Transacetylase lac operon  -Galactosidase lacY lacZ lacA lac I lacZ 8

Enhancer TATA box Promoter Activators DNA Gene Distal control element Group of mediator proteins DNA-bending protein General transcription factors RNA polymerase II RNA polymerase II Transcription initiation complex RNA synthesis 9

Control elements Enhancer Available activators Albumin gene (b) Lens cell Crystallin gene expressed Available activators LENS CELL NUCLEUS LIVER CELL NUCLEUS Crystallin gene Promoter (a) Liver cell Crystallin gene not expressed Albumin gene expressed Albumin gene not expressed 10

Post-translational Modifications Phosphorylation Ubiquitination Methylation Acetylation Glycosylation 11

Local signaling Target cell Secreting cell Secretory vesicle Local regulator diffuses through extracellular fluid (a) Paracrine signaling(b) Synaptic signaling Target cell is stimulated Neurotransmitter diffuses across synapse Electrical signal along nerve cell triggers release of neurotransmitter Long-distance signaling Endocrine cell Blood vessel Hormone travels in bloodstream to target cells Target cell (c) Hormonal signaling 12

EXTRACELLULAR FLUID Plasma membrane CYTOPLASM Receptor Signaling molecule Relay molecules in a signal transduction pathway Activation of cellular response Reception TransductionResponse

Signaling molecule (ligand) Ligand-binding site  Helix Tyrosines Tyr Receptor tyrosine kinase proteins CYTOPLASM Signaling molecule Tyr Dimer Activated relay proteins Tyr P P P P P P Cellular response 1 Cellular response 2 Inactive relay proteins Activated tyrosine kinase regions Fully activated receptor tyrosine kinase 6 6 ADP ATP Tyr P P P P P P

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