Protein Structure

Question 1

What is the general structure of an amino acid?

Answer 1

A central carbon has an amino group, carboxyl group, a hydrogen atom and an R group covalently bonded to it

Question 2

In what state are amino acids usually present as?

Answer 2

Zwitter Ions

Question 3

What is an amino acid residue?

Answer 3

What remains of an amino acid after it has been joined by a peptide bond to form a protein

Question 4

If an amino acid has a high PKA value what does that indicate?

Answer 4

It is a basic amino acid

Question 5

What is pKa?

Answer 5

pKa tells you the strength of an acid, so how likely the groups are to lose or gain protons

Question 6

If the pH is less than then pKa value what will happen to the side group?

Answer 6

The group is more likely to be protonated

Question 7

What is the primary structure of a protein?

Answer 7

The amino acid sequence of the polypeptide chain

Question 8

What is the secondary structure?

Answer 8

The way the chains fold into conformations like helices etc

Question 9

What is the tertiary structure?

Answer 9

The overall 3D shape

Question 10

What is the quaternary structure?

Answer 10

The association between different polypeptides to form a multi-subunit protein

Question 11

In what type of reaction are peptide bonds formed?

Answer 11

A condensation reaction so a molecule of water is released

Question 12

What does it mean by saying that peptide bonds are planar?

Answer 12

The atoms all lie in the same plane

Question 13

Why can’t peptide bonds rotate?

Answer 13

Electrons from the C=O bond of the carboxyl group move between the central carbon and nitrogen from the amino group giving it double bond properties (resonance)

Question 14

Why do peptide bonds also have trans conformations?

Answer 14

By having the central carbon on opposite sides of the peptide bonds, the R groups will be further apart so won’t repel

Question 15

Why is the amino acid sequence important?

Answer 15

It determines the physical characteristic and the way in which the protein folds

Question 16

What is the ISO electric point of a protein?

Answer 16

The pH at which there is no overall net charge

Question 17

What happens if the pH is less than pI?

Answer 17

The amino acids will be protonated

Question 18

What are conjugated proteins?

Answer 18

Proteins that are covantely linked to other chemical components as well as amino acids e.g. Glycoproteins

Question 19

What binds hold the alpha helix structure together

Answer 19

Hydrogen bonds between the amino group and the carboxyl group

Question 20

What 2 arrangements can be made from proteins with a beta sheet secondary structure?

Answer 20

Antiparallel and parallel sheets

Question 21

Why are parallel beta sheets weaker than antiparallel sheets?

Answer 21

As the beta strands are running in the same direction the hydrogen bonds are at an angle and so are weaker

Question 22

What is the domain of a globular protein?

Answer 22

Where part of a polypeptide chain folds into a distinct shape and often has a specific role

Question 23

What are the 2 different types of tertiary structure?

Answer 23

Fibrous and Globular

Question 24

How can amino acids be classified?

Answer 24

By whether they are:

• hydrophilic/hydrophobic
• polar/non-polar
• basic/acidic/neutral
• aliphatic/aromatic

Question 25

If an amino acid has a charge will it be hydrophobic or hydrophilic

Answer 25

Hydrophilic

Question 26

What does it mean if the pKa is equal to pH?

Answer 26

There will be equal amounts of protonated and deprotonated forms

Question 27

What is the Henderson-Hasselbach equation?

Answer 27

pH = pKa + log(base/acid)

Question 28

What bonds hold the tertiary structure together?

Answer 28

Ionic, H bonds, covalent, Van der Walls and hydrophobic and disulphide bonds

Question 29

Between which amino acid residues do disulphide binds form?

Answer 29

Cystine

Question 30

What properties do disulphide bonds give to proteins

Answer 30

The binds help keep the structure better so they can withstand hostile environments

Question 31

Between what groups do electrostatic interactions occur

Answer 31

Oppositely charged groups

Question 32

What is the hydrophobic effect?

Answer 32

Interactions between hydrophobic side chains result in the exclusion of water

Question 33

What determines how a protein folds?

Answer 33

Primary sequence

Question 34

How do proteins fold?

Answer 34

There is localised folding to form stable conformations

Question 35

What is amyloidosis

Answer 35

A condition when their are deposits of amyloid fibres (misfolded, insoluble protein)