Protein Biochemistry and Proteomics

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Questions and Answers

What is the typical range of amino acids in most proteins?

10-100

100-1000 (correct)

1000-5000

5000-10000

What is the main focus of this lesson?

Assessment details of the module

General properties and structure of proteins (correct)

Introduction to Eduvos (Pty) Ltd

Registration certificate of the institution

Which type of protein is linked to the membrane through a covalent bond to a lipid molecule?

Peripheral protein

Lipid-linked protein (correct)

Transmembrane protein

Integral membrane protein

Which of the following chapters are mentioned in this lesson?

Chapters 5, 6, and 9 Signup and view all the answers

What is the registration certificate number of Eduvos (Pty) Ltd?

2001/HE07/008 Signup and view all the answers

What is the process by which a denatured protein returns to its native structure?

Renaturation Signup and view all the answers

What is the term for the non-polar, hydrophobic amino acids?

Hydrophobic Signup and view all the answers

What is the name of the Act under which Eduvos (Pty) Ltd is registered?

Higher Education Act, 101, of 1997 Signup and view all the answers

What is the purpose of mentioning the page numbers of the chapters?

To highlight the difference in page numbers between book editions Signup and view all the answers

Which type of protein spans the entire width of the membrane?

Transmembrane protein Signup and view all the answers

What is the name of the institution that is registered with the Department of Higher Education and Training?

Eduvos (Pty) Ltd Signup and view all the answers

What is the term for the process by which a protein loses its native structure, often due to changes in temperature, pH, or solvent composition?

Denaturation Signup and view all the answers

What is the average length of an alpha helix in amino acids?

3.6 Signup and view all the answers

How many residues are present in each turn of an alpha helix?

3.6 Signup and view all the answers

What is the direction of the helical twist in an alpha helix?

Right handed Signup and view all the answers

What type of bond supports the helical twist in an alpha helix?

Hydrogen bond Signup and view all the answers

Where are the hydrogen bonds that support the helical twist found in the structure of an alpha helix?

Between C=O and N-H of every 4th residue Signup and view all the answers

What is the pitch of an alpha helix?

5.4 Å Signup and view all the answers

How many intra-chain hydrogen bonds are present in an alpha helix?

The number of residues per turn Signup and view all the answers

What is the direction of the Cα atoms in an alpha helix?

In a spiral arrangement Signup and view all the answers

What percentage of double bond character does the peptide group have?

40 % Signup and view all the answers

What is the conformation of peptide bonds where Cα atoms are on the same side?

Cis conformation Signup and view all the answers

What is the angle between the Cα and C atoms in the polypeptide backbone?

Psi (ψ) Signup and view all the answers

What is the main reason for the planar structure of peptide groups?

Double bond character Signup and view all the answers

What is the conformation of peptide bonds where Cα atoms are on opposite sides?

Trans conformation Signup and view all the answers

What is the term for the rotation of the polypeptide backbone around a bond?

Torsion angle Signup and view all the answers

What is the effect of steric interference of adjacent peptide groups?

It destabilizes the peptide bond Signup and view all the answers

What is the characteristic of the peptide group that makes it planar and rigid?

Double bond character Signup and view all the answers

What is the effect of increased hydropathy on a protein?

The protein becomes more nonpolar and hydrophobic Signup and view all the answers

Which of the following factors can influence the denaturation of proteins?

All of the above: heat, pH variations, detergents, and chaotropic agents Signup and view all the answers

What is the purpose of the activity in Lesson 3?

To research and understand protein purification techniques Signup and view all the answers

What is the main topic of Week 1, Lesson 3?

Protein purification and analysis Signup and view all the answers

What is the purpose of chaotropic agents in protein denaturation?

To denature proteins and disrupt their structure Signup and view all the answers

What is the outcome of increased hydropathy on a protein's hydrophobicity?

The protein becomes more hydrophobic Signup and view all the answers

What is the purpose of protein assays in protein purification?

To quantify the amount of protein present Signup and view all the answers

What is the outcome of the activity in Lesson 3?

A group understanding of protein purification techniques Signup and view all the answers

Study Notes

General Properties and Structure of Proteins

Proteins have 100-1000 amino acids.
Amino acids are classified into hydrophobic, nucleophilic, acidic, basic, and aromatic.
Greek alphabet and symbols are used to represent amino acids.

Levels of Protein Structure

Peptide bonds assume a trans conformation, which is a rigid, planar structure with 40% double bond character.
The peptide bond has Cα atoms on opposite sides in the trans conformation and on the same side in the cis conformation.
The extended conformation of polypeptide backbone has torsion angles Phi (ϕ) and Psi (ψ) for Cα-N and Cα-C bonds respectively.
Steric interference occurs between adjacent peptide groups.
The α helix is a type of secondary structure with properties such as left or right handedness, amount of polypeptides, and amount of residues per turn.
The α helix has an average length of 3.6 residues per turn and is supported by hydrogen bonds between C=O and N-H of the (N+4)th residue.
The α helix has a pitch of 5.4 Å and is right-handed.

Hydrophobic and Hydrophilic Tendencies

Hydrophobic and hydrophilic tendencies are measured by hydropathy, which increases with the nonpolar nature of the molecule.
Hydrophobic and hydrophilic interactions affect protein stability.

Factors that Influence Protein Stability

Factors that influence protein stability and denaturation include heat, pH variations, detergents, and chaotropic agents.
Chaotropic agents denature proteins by disrupting the hydrophobic and hydrophilic interactions.

Denaturation and Renaturation of Proteins

Proteins can be denatured and renatured, as shown in the process diagram of RNase A.
Denaturation and renaturation involve the disruption and reformation of hydrogen bonds, ionic interactions, and disulfide bonds.

Protein Purification and Analysis

Protein purification involves strategies to separate and purify proteins from a mixture.
Factors to control in protein purification include protein concentration, pH, and ionic strength.
Protein assays are used to quantify protein concentrations.
Different protein purification techniques include salt precipitation, ion exchange chromatography, size exclusion chromatography, affinity chromatography, and electrophoresis.

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Test your knowledge on protein biochemistry and proteomics, including concepts and techniques in this field of study.