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Introduction to Biochemistry > Basic protein structure > Flashcards

Basic protein structure Flashcards

1
Q

What is the type of reaction that forms peptide bonds between amino acids ?

A

Condensation (dehydration) reaction.

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2
Q

What are the properties of the peptide bond ?

A
  1. Rigid
  2. Polar uncharged
  3. Resistant to denaturation
  4. Trans peptide bond
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3
Q

Why the peptide bonds polar and uncharged ?

A

Peptide bonds are polar because its groups can be involved in hydrogen bond formation and they are uncharged because CO and NH groups of the peptide bond are uncharged at physiological PH and the charge on the peptide come for the N terminal and C terminal and any ionized groups in the side chain.

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4
Q

The peptide bond can have more than one orientation. Discuss

A

Peptide bonds have 2 orientation :
Cis peptide bond : two bulky groups on the same side
Trans peptide bond : two bulky groups are on opposite sides

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5
Q

What is the predominant orientation of peptide bond and Why ?

A

Trans peptide bond is the predominant orientation as the the orientation of bulky chains on opposite side decrease the steric repulsive forces on the side chains

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6
Q

What are the two types of peptides?

A
  1. Proteins : one or more large peptide and it have specific biological function
  2. Biologically active peptides : less than 50 AA, they have specific function as chemical signalling compounds and they are not classified as proteins.
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7
Q

Examples of the biologically active peptides ?

A

A. Gultathione :

  1. Tripeptide ( Y-glutamate , cysteine and Glycine )
  2. Reducing agent
  3. Reduce toxic H2O2 inyo H20 in RBCs
  4. Protect the wall of the RBCs against the Toxic H2O2

B. Endorphins :

  1. Pentapeptide
  2. Chemical signaling peptides
  3. Natural painkillers
  4. Interact with receptors in the brain to inhibit of transimission of pain signals

C. Oxytocin:

  1. 9 amino acids
  2. Secreted from the posterior lobe of the pitutary gland
  3. Stimulate uterine contraction
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8
Q

What are the types of covalent bonds present in the protein structure ?

A

Peptide and disulphide bonds.

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9
Q

How are the disulphide bonds formed ?

A

They are formed through the oxidation of SH as in cysteine to form cystine.

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10
Q

What are the type of Di sulphide bonds ?

A
  1. Intrachain disulphide bonds : 2 SH in the same polypeptide chain
  2. Interchain disulphide bonds : 2 SH in 2 polypeptide chains.
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11
Q

What are the non covalent stabilizing structures in the protein ?

A
  1. Hydrogen
  2. Hydrophobic
  3. Vander Waal
  4. Electrostatic
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12
Q

Describe Hydrogen bonds.

A

Hydrogen bonds are weaker than covalent bonds but their presence in large numbers contribute stability of folded protein.

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13
Q

Where can the hydrogen bond occur ?

A
  1. between two amino acids.
  2. Between two polypeptide chains.
  3. Between AA and water in the surrounding environment.
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14
Q

When do hydrogen bonds increase the solubility of AA ?

A

When they are formed between polar groups on the surface of proteins and the aqueous solvents

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15
Q

How does hydrogen bonds help in protein folding ?

A

They are the main determinant in the secondary structure of proteins.

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16
Q

What is meant by electrostatic stabilization ?

A

the attraction force between a positively charged groupand negatively charged one in the protein
Similarly charged groups cause repulsion forces which also affect the protein conformation.

17
Q

What is the most important non covalent bond that drives the process of protein folding ?

A

Hydrophobic interactions as non polar molecules tend to cluster because they are insoluble in water and they are located in the interior of proteins.

18
Q

What are the Vander Waals forces

A

Is the sum of attractive or repulsive forces between
atoms at 3- 4 A⁰ apart (contact distance) , At shorter distance, a strong repulsive force between positively charged nuclei are predominant , They are very weak forces, but they are important to stabilize atoms in their positions

18
Q

What are the Vander Waals forces

A

Is the sum of attractive or repulsive forces between
atoms at 3- 4 A⁰ apart (contact distance) , At shorter distance, a strong repulsive force between positively charged nuclei are predominant , They are very weak forces, but they are important to stabilize atoms in their positions

Introduction to Biochemistry (7 decks)

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