Lecture 11
Lecture 11 Evolution, Function, and Classification of Proteins
•The Nature of Protein Sequences •Homology •Protein Phylogeny •Conjugated Proteins and Prosthetic Groups •The Biological Functions of Proteins
Nature of Protein Sequences • Sequences and composition reflect the function of the protein - form follows function • e.g. membrane proteins have more hydrophobic residues, fibrous proteins (particularly collagen) may have atypical sequences • The similarity of one protein sequence to another is called homology
Phylogeny of Cytochrome c • The number of amino acid differences between two cyt c sequences is proportional to the phylogenetic difference between the species from which they are derived • This observation can be used to build phylogenetic trees of proteins molecular evolution
Cytochrome c
Functionally Related Proteins Often Share a Common Origin • e.g. the oxygen transport proteins myoglobin (in muscle) and hemoglobin (in erythrocytes) • Remember hemoglobin is a2b2 • Hemoglobin a and hemoglobin b: 64 common residues • Hemoglobin a and myoglobin: 38 common residues
Conjugated Proteins - when 20 just isn’t enough • Proteins that comprise only amino acids are simple proteins • Some include additional non-amino acid chemical functionality - conjugated proteins • The non-protein component is the prosthetic group • Allows for chemical (eg redox, hydride transfer) and structural (eg molecular recognition) properties not covered by the common amino acids
Glycoproteins • • • •
Proteins containing carbohhydrate May be a little, e.g. immunoglobulin G Or a lot, e.g. procaryotic cell wall proteoglycans Often extracellular proteins
Lipoproteins • • • •
igG
Proteins containing lipids (fats) May be as little as a single fatty acid, e.g. protein kinase A Or a lot, e.g. plasma lipoproteins (75% lipid by weight) Plasma lipoproteins are primarily for lipid transport
Nucleoproteins • Proteins conjugated to nucleotides • e.g. ribosomes • Flavoproteins contain flavin nucleotides covalently bonded to the protein • In contrast NAD+/NADH proteins have the nucleotide non-covalently associated
And… • Metalloproteins • Hemoproteins • Phosphoproteins – often signalling proteins – phosphorylation at ser, thr, tyr OH groups
Biological Functions of Proteins Proteins are the agents of biological function • Enzymes - phosphoglucose isomerase, trypsin • Regulatory proteins –Hormones, eg insulin, enkephalins, endorphins, GSH –Transcription Factors, eg zinc fingers, GCN4 –Kinases and phosphatases • Transport proteins - hemoglobin, VDAC • Structural proteins - collagen, intermediate filaments • Contractile proteins - actin, myosin • Exotic proteins - antifreeze proteins, venoms
•The Nature of Protein Sequences •Homology •Protein Phylogeny •Conjugated Proteins and Prosthetic Groups •The Biological Functions of Proteins
Nature of Protein Sequences • Sequences and composition reflect the function of the protein - form follows function • e.g. membrane proteins have more hydrophobic residues, fibrous proteins (particularly collagen) may have atypical sequences • The similarity of one protein sequence to another is called homology
Phylogeny of Cytochrome c • The number of amino acid differences between two cyt c sequences is proportional to the phylogenetic difference between the species from which they are derived • This observation can be used to build phylogenetic trees of proteins molecular evolution
Cytochrome c
Functionally Related Proteins Often Share a Common Origin • e.g. the oxygen transport proteins myoglobin (in muscle) and hemoglobin (in erythrocytes) • Remember hemoglobin is a2b2 • Hemoglobin a and hemoglobin b: 64 common residues • Hemoglobin a and myoglobin: 38 common residues
Conjugated Proteins - when 20 just isn’t enough • Proteins that comprise only amino acids are simple proteins • Some include additional non-amino acid chemical functionality - conjugated proteins • The non-protein component is the prosthetic group • Allows for chemical (eg redox, hydride transfer) and structural (eg molecular recognition) properties not covered by the common amino acids
Glycoproteins • • • •
Proteins containing carbohhydrate May be a little, e.g. immunoglobulin G Or a lot, e.g. procaryotic cell wall proteoglycans Often extracellular proteins
Lipoproteins • • • •
igG
Proteins containing lipids (fats) May be as little as a single fatty acid, e.g. protein kinase A Or a lot, e.g. plasma lipoproteins (75% lipid by weight) Plasma lipoproteins are primarily for lipid transport
Nucleoproteins • Proteins conjugated to nucleotides • e.g. ribosomes • Flavoproteins contain flavin nucleotides covalently bonded to the protein • In contrast NAD+/NADH proteins have the nucleotide non-covalently associated
And… • Metalloproteins • Hemoproteins • Phosphoproteins – often signalling proteins – phosphorylation at ser, thr, tyr OH groups
Biological Functions of Proteins Proteins are the agents of biological function • Enzymes - phosphoglucose isomerase, trypsin • Regulatory proteins –Hormones, eg insulin, enkephalins, endorphins, GSH –Transcription Factors, eg zinc fingers, GCN4 –Kinases and phosphatases • Transport proteins - hemoglobin, VDAC • Structural proteins - collagen, intermediate filaments • Contractile proteins - actin, myosin • Exotic proteins - antifreeze proteins, venoms
