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.