SCPAA3 Protein Biochemistry and Proteomics PDF

Protein Biochemistry and Proteomics SCPAA3 Eduvos (Pty) Ltd (formerly Pearson Institute of Higher Education) is registered with the Department of Highe...

Protein Biochemistry and Proteomics SCPAA3 Eduvos (Pty) Ltd (formerly Pearson Institute of Higher Education) is registered with the Department of Higher Education and Training as a private higher education institution under the Higher Education Act, 101, of 1997. Registration Certificate number: 2001/HE07/008  Module Overview and Assessment Details Eduvos (Pty) Ltd (formerly Pearson Institute of Higher Education) is registered with the Department of Higher Education and Training as a private higher education institution under the Higher Education Act, 101, of 1997. Registration Certificate number: 2001/HE07/008 Week 1: Lesson 2 Introduction In this lesson, you will learn about the general properties and structure of proteins. Chapter 5 , Chapter 6 & Chapter 9 (Pages numbers for all chapters differ with the book edition)  What will be covered in today’s lesson? Week 1 General Properties and Structure of Proteins- Introduction Lesson 2 Levels of protein structure Factors that influence protein stability Factors That Allow a Protein to be Denatured and Explain the Renaturation Process Integral Membrane, Transmembrane, Lipid- linked and Peripheral Proteins  HYDROPHOBI SMALL C NUCLEOPHILI C Outcome 1 – Amino acids 5  Outcome 1 – Amino acids (cont.) AROMATI ACIDIC C AMIDE BASIC 6 Outcome 1 – Greek alphabet and symbols (future use) 7  Outcome 1 – Composition of proteins Most proteins have 100 – 1000 amino acids Table 5-1 © 2017 John Wiley & Sons, Inc. All rights reserved 8 Outcome 2 – Levels of protein structure 9 Figure 6-1 © 2017 John Wiley & Sons, Inc. All rights reserved  10 Figure 6-1 part 2 © 2017 John Wiley & Sons, Inc. All rights Outcome 2 – Peptide bonds assume trans conformation Peptide group: Rigid, planar structure 40 % double bond character Trans conformation – Cα atoms are on opposite side of the peptide bond Cis conformation - Cα atoms are on the same side of the peptide bond 11 Figure 6-2 © 2017 John Wiley & Sons, Inc. All rights reserved Outcome 2 – Extended conformation of polypeptide 12 Figure 6-3 © 2017 John Wiley & Sons, Inc. All rights reserved Outcome 2 – Torsion angles of polypeptide backbone Psi (ψ) – Cα - C Phi (ϕ) – Cα - N 13 Figure 6-4 © 2017 John Wiley & Sons, Inc. All rights reserved Outcome 2 – Steric interference of adjacent peptide groups 14 Figure 6-5 © 2017 John Wiley & Sons, Inc. All rights reserved  Outcome 2 – The α helix Properties: Left or right handed Amount of polypeptides Amount of residues per turn Average length in the amino acid – (how many turns) Bond that supports the helical twist Where are these bonds found in the structure Figure 3-7 © 2017 John Wiley & Sons, Inc. All rights reserved 15  Outcome 2 – The α helix Cα Cα Cα How many amino acid residues are in this Cα helix? How many intra-chain hydrogen bonds? Hydrogen bonds Cα Cα Cα Alpha helices have 3.6 Cα residues per turn H-bond between C=O and N-H Cα residue (N+4)th residue O Right handed C Cα Pitch of 5.4 Å N Cα H 16 Figure 6-7 © 2017 John Wiley & Sons, Inc. All rights reserved  Outcome 2 – The space filling model The backbone atoms are coloured according to type with C green, N blue, O red, and H white. The side chains (gold) project away from the helix. This α helix is a segment of sperm whale myoglobin. Figure 6-8 © 2017 John Wiley & Sons, Inc. All rights reserved 17 Outcome 2 – Interactions within a polypeptide 18 Outcome 2 – Globular proteins and Side chain location varies with polarity Globular proteins: usually have a spherical shape caused by tightly folded polypeptide chains. The chains are usually folded so that the hydrophobic groups are on the inside, while the hydrophilic groups are on the outside. This makes them water soluble. Eg. Transport proteins – such as haemoglobin, myoglobin and embedded trans-membrane proteins The amino acid side chains in globular proteins are spatially distributed according to their polarities: 1. The nonpolar residues Val, Leu, Ile, Met, and Phe 2. The charged polar residues Arg, His, Lys, Asp, and Glu 3. The uncharged polar groups Ser, Thr, Asn, Gln, and Tyr. 19 Outcome 2 – Side chain location varies with polarity Figure 6-27 © 2017 John Wiley & Sons, Inc. All rights reserved 20 Outcome 4 – Hydrophobic & hydrophilic tendencies: Hydropathy Increased hydropathy – the more nonpolar (hydrophobic) 21 Factors that influence the denaturing of proteins These forces include: 1. Heat 2. pH variations 3. Detergents 4. Chaotropic agents © 2017 John Wiley & Sons, Inc. All rights reserved 22 Outcome 5 & 6 – Chaotropic agents denature proteins © 2017 John Wiley & Sons, Inc. All rights reserved 23 Process diagram: Denaturation and renaturation of RNase A 24 Figure 6-38 © 2017 John Wiley & Sons, Inc. All rights reserved Week 1: Lesson 3 Introduction In this lesson, you will learn about protein purification and analysis, how proteins are quantified by assays and the purification strategy.  What will be covered in today’s lesson? Protein purification and Week 1 analysis introduction Lesson 3 Strategy for protein purification Factors to control Protein Assays  Activity 1. Form Groups: Divide yourself into groups of 3-4 students. 2. Assign Topics: Each group will be assigned one of the following protein purification techniques: 1. Salt Precipitation 2. Ion Exchange Chromatography 3. Size Exclusion Chromatography 4. Affinity Chromatography 5. Electrophoresis 3. Research: Spend 10-15 minutes researching your assigned topic. Use your course materials, assigned readings, and online resources to understand the principles of your assigned technique and when and why it is used in protein purification. What Happens Next? In your next lecturer led session you will learn about general properties of enzymes and activation energy Ensure that you engage with your week 2 myLMS content before the lecturer led session.