Class 1

Question 1

two common types of covalent bonds between amino acids in proteins

Answer 1

1. the peptide bonds that link amino acids together into polypeptide chains
2. disulphide bridges between cysteine R-groups.

Question 2

how is a peptide bond formed?

Answer 2

peptide bond is formed between the carboxyl group of one amino acid and the alpha amino group of another amino acid with the loss of water

Question 3

What is the backbone of the polypeptide?

Answer 3

NCCNCC

Question 4

residue

Answer 4

an amino acid is termed residue when it is part of a polypeptide chain.

Question 5

what do we know from thermodynamics about spontaneous reactions?

Answer 5

we know that free energy must decrease for a reaction to proceed spontaneously and that such a reaction will spontaneously move towards equilibrium.

Question 6

Proteolysis

Answer 6

also known as proteolytic cleavage

it is the hydrolysis of a protein by another protein.

The protein that does the cutting is known as a proteolytic enzyme or protease.

Question 7

Is proteolytic cleavage, a specific way of cleaving peptide bonds?

Answer 7

yes it is! Learn!

Many enzymes only cleave the peptide bond adjacent to a specific amino acid.

Question 8

an example of trypsin cleavage is….

Answer 8

the protease trypsin cleaves on the carboxyl side of the positively charged (basic) residues arginine and lysine.

Question 9

an example of chymotrypsin cleavage is…

Answer 9

chymotrypsin cleaves adjacent to hydrophobic residues such as phenylalanine.

Question 10

What is Cysteine?

Answer 10

Cysteine is an amino acid with a reactive thiol (sulfhydryl, SH) in its side chain.

The thiol of one cysteine can react with the thiol of another cysteine to produce a covalent sulphur-sulphur bond known as disulphide bond.

Question 11

Cystine Vs Cysteine

Answer 11

Once a Cysteine residue becomes disulphide-bonded to another cysteine residue , it is called cystine instead of cysteine.

Question 12

Which is more oxidized, the sulphur in cysteine or the sulphur in cystine?

Answer 12

The sulphur in cysteine is bonded to a hydrogen and a carbon; the sulphur in cystine is bonded to a sulphur and a carbon (two hydrogens removed in the reaction).

Hence the sulphur is cystine is more oxidized.

Question 13

antioxidants

Answer 13

Chemicals that prevent oxidation reactions

Question 14

The inside of cells is known as a reducing environment because cells possess antioxidants. Where would disulphide bridges be more likely to be found, in extracellular proteins, under oxidizing conditions, or in the interior of cells, in a reducing environment?

Answer 14

In a reducing environment, the S-S group is reduced to two SH groups. Disulphide bridges are found only in extracellular polypeptides,where they will not be reduced. Examples of protein complexes held together by disulphide bridges include antibodies and the hormone insulin.

Question 15

Primary structure :

Answer 15

The amino acid sequence

Question 16

Secondary Structure :

Answer 16

Hydrogen bonds between backbone groups

Question 17

Tertiary Structure :

Answer 17

Hydrophobic/ Hydrophilic interactions

Question 18

Quaternary Structure :

Answer 18

Various Bonds Between Separate Chains

Question 19

Denaturation

Answer 19

Denaturation refers to the disruption of a protein’s shape without breaking peptide bonds.

Question 20

What denatures proteins?

Answer 20

Urea - which disrupts hydrogen bonding interactions

Extremes of pH

Extremes of Temperature

By changes in salt concentrations (tonicity)

Question 21

Primary Structure description

Answer 21

• simplest level
• This is the linear ordering of amino acid residues
• Primary structure is the same as sequence
• The bond that determines the primary structure is the peptide bond

Question 22

Secondary Structure

Answer 22

-Refers to the initial folding of a polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups.

Question 23

What are the two most common secondary structures?

Answer 23

Alpha helix &

Beta-pleated sheet

Question 24

How does hydrogen bonding occur in the Beta pleated sheets?

Answer 24

Hydrogen bonding occurs between residues distant from each other in the chain or even on separate polypeptide chains.

Question 25

how many types of b-sheets are there?

Answer 25

There are two types of b-sheets -

1. one with adjacent polypeptide chains running in the same direction ( parallel b-pleated sheets)
2. One with adjacent polypeptide chains running in opposite direction ( anti-parallel b-pleated sheets)

Question 26

If a single polypeptide folds once and forms a b-pleated sheet with itself, would this be a parallel or antiparallel b-pleated sheet?

Answer 26

It would be antiparallel, since one participant in the b-pleated sheet would have a C to N direction, while the other would be running N to C

Question 27

What effect would a molecule that disrupts hydrogen bonding , e.g. urea have on protein structure?

Answer 27

Putting a protein in a urea solution will disrupt H-bonding, thus disrupting the secondary structure by unfolding alpha helices and b-sheets.

It would not affect the primary structure, which depends on the much more stable peptide bond.disruption of secondary, tertiary and quaternary structure without breaking peptide bonds is denaturation.

Question 28

Tertiary structure description

Answer 28

It concerns interactions between amino acid residues located more distantly from each other in the polypeptide chain.

Question 29

a reducing agent

Answer 29

B-mercaptoethanol

Question 30

ribonuclease has eight cysteine that form four disulphide bonds. What effect would a reducing agent have on its tertiary structure?

Answer 30

The disulphide bridges would be broken.

Tertiary structure would be less stable.

Question 31

If the disulphides serve only to lock into place a tertiary protein structure that forms first on its own, then what effect would the reducing agent have on correct protein folding?

Answer 31

The shape should not be disrupted if breaking disulphides is the only disturbance. Its just that the shape would be less sturdy.

Question 32

What happens if you allow disulfide bridges to form while the protein is still denatured?

Answer 32

If you allow disulphide bridges to form while the protein is still denatured, it will become locked into an abnormal shape.

Question 33

How can you denature a protein and then finally get the correct previous tertiary structure?

Answer 33

• You break the reinforcing disulphide bridges
• You denature the protein completely by disrupting H-bonds
• you allow the H-bonds to reform.

as stated in the text, normally the correct tertiary structure will form spontaneously if you leave the polypeptide alone.

• Now finally, the disulphide bridges are reformed, thus locking the structure into its correct form.

Question 34

Why is disulfide bridge not a great example of tertiary structure?

Answer 34

Because it is a covalent bond, not a hydrophobic interaction. However, because the disulphide is formed after secondary structure and before quaternary structure, it is usually considered part of tertiary folding.

Question 35

Hydrogen bonds between backbone amino and carboxyl groups is an example of _______

Answer 35

Secondary Structure

Question 36

Covalent disulphide bonds between cysteine residues located far apart on a polypeptide ——– This is an example of ………………

Answer 36

It describes the disulphide, which is considered to be tertiary because of when it is formed, despite the fact that it is a covalent bond.

Question 37

What is a quaternary structure basically?

Answer 37

Various bonds between Separate Chains

Question 38

Quaternary Structure

Answer 38

• The highest level of protein structure
• it describes the interaction between polypeptide subunits
• The arrangement of subunits in a multisubunit complex is what we mean by the quaternary structure.
• For example - mammalian RNA polymerase II contains twelve different subunits.

Question 39

A Subunit

Answer 39

A subunit is a SINGLE polypeptide chain that is part of a large complex containing many subunits ( a multisubunit complex)

Question 40

What are the forces stabilizing quaternary structure?

Answer 40

The forces stabilizing the quaternary structure are generally the same as those involved in secondary and tertiary structure - non-covalent interactions.

However covalent bonds may also be involved.

Question 41

What are the non - covalent interactions?

Answer 41

The hydrogen bond and the van der waals interaction