Primary, Secondary, Tertiary & Quaternary Structure

Question 1

What does the primary structure of a protein describe?

Answer 1

The amino acid sequence in a polypeptide

Question 2

What does the secondary structure of a protein describe?

Answer 2

The local spatial arrangements of amino acids in the peptide chain

Question 3

What does the tertiary structure of a protein describe?

Answer 3

The organisation of the primary and secondary structures into the 3D protein shape

Question 4

What does the quaternary structure of a protein describe?

Answer 4

The arrangement of different subunits in a protein

Question 5

What determines the primary structure of a protein?

Answer 5

The gene that codes for the protein

1. the gene is transcribed to produce mRNA
2. the mRNA is translated on the ribosome

Question 6

What is so significant about the amino acid sequence of a protein?

Answer 6

This ultimately determines the structure and function of the folded protein

The unique properties of a protein is determined by the order of AAs and the R-groups they contain

Question 7

What forms a polypeptide chain?

Answer 7

many amino acids joined by peptide bonds

Question 8

How many amino acid residues are most natural proteins made up from?

Answer 8

50 - 2,000 amino acid residues

Question 9

What is the backbone of an amino acid chain?

Answer 9

The backbone runs along the centre of the chain

It is alpha carbon atoms, each connected to the next by a peptide bond

Question 10

What is meant by residues in an amino acid chain?

Answer 10

Amino acids within a polypeptide chain are residues

Question 11

What is meant by ‘side chains’ within a polypeptide chain?

Answer 11

The different R-groups of amino acids are the side chains

Question 12

What are the N-terminus and C-terminus within an amino acid chain?

Answer 12

The free amino group at one end is the N-terminus

The free carboxyl group at the other end is the C-terminus

This gives a polypeptide chain direction

Question 13

What type of bond is a peptide bond?

How is it formed?

Answer 13

It is an amide bond

A condensation reaction occurs on the ribosome, and a water molecule is released

Question 14

Why does the peptide bond not behave like a normal single covalent bond?

Answer 14

It resonates between 2 different structures

This means the C-N bond shows some double bond characteristics

Question 15

What is significant about the peptide bond resonating between 2 forms?

Answer 15

This makes the peptide bond quite rigid

There is very limited rotation around the peptide bond

Question 16

How are both forms of the secondary structure stabilised?

Answer 16

They are stabilised by hydrogen bonds arising between the O in the peptide bond, and the H atom attached to the N in another peptide bond

Question 17

What forms the helix of an alpha-helix?

Answer 17

The helix is formed by the backbone of the chain

The sidechains extend outside of the helix

Question 18

What type of helix is the alpha helix?

How many amino acid residues are there per turn?

Answer 18

The alpha helix is a right-handed helix

It has 3.6 residues per turn

Question 19

What type of hydrogen bonds are present in the alpha helix?

Answer 19

intrachain hydrogen bonds

these are bonds between different parts of the same chain

Question 20

Between which groups do the intrachain hydrogen bonds form in the alpha helix?

Answer 20

Hydrogen bonds between the N-H and the C=O groups of the main chain stabilise the helix

Question 21

What gives the alpha helix some elasticity?

Answer 21

The fact that all the hydrogen bonds lie parallel to the alpha helix

Question 22

How many strands make up the beta pleated sheet?

Answer 22

Polypeptide chains run alongside each other

There may be several strands making up a beta sheet

They may be different chains or different parts of the same chain

Question 23

Where are the side chains found on a beta pleated sheet?

Answer 23

The side chains lie above or below the plane of the sheet

Question 24

What types of hydrogen bonds stabilise the beta pleated sheet?

Answer 24

Hydrogen bonds between adjacent starnds

These may be intrachain or interchain

Question 25

What is the difference between intrachain and interchain hydrogen bonds?

Answer 25

Intrachain bonds are between 2 parts of the same chain Interchain bonds are between different amino acid chains

Question 26

What gives the strands of a beta pleated sheet a pleated appearance? How does this affect the properties of this secondary structure?

Answer 26

The tetrahedral angles separating the bonds on the carbon This means the bonds are quite rigid and the structure has little elasticity

Question 27

How do the strands in a beta pleated sheet run?

Answer 27

The strands may run parallel to one another, or may be antiparallel Loops and turns between the strands allow for a change in direction of the chain

Question 28

How is the arrangement of the tertiary structure described?

Answer 28

The structure is compact but there is some flexibility

Question 29

What amino acids tend to make up the interior of soluble proteins?

Answer 29

Hydrophobic amino acids e.g. Leu, Val, Met, Phe

Question 30

What amino acids tend to make up the exterior of soluble proteins?

Answer 30

Hydrophilic amino acids e.g. Arg, His, Lys, Asp, Gly

Question 31

Why is it significant that hydrophilic amino acids are on the exterior of the protein molecule?

Answer 31

Most proteins exist in a hydrophilic environment

Question 32

Why is the tertiary structure important?

Answer 32

It is important for the positioning of binding sites and active sites The residues which make these up are not located very close together

Question 33

When does a protein have a quaternary structure?

Answer 33

A protein only has a quaternary structure if it is composed of several individual polypeptide subunits

Question 34

What stabilises the packing of helices, sheets and different subunits in proteins?

Answer 34

Side chain interactions These may be covalent, but more often are non-covalent

Question 35

What is a disulphide bond?

Answer 35

A covalent bond between two cysteine amino acid residues This is because cysteine contains the -SH thiol group

Question 36

What happens when 2 cysteine residues are brought in close proximity?

Answer 36

When they are brought in close proximity within a folded protein, the thiol groups react to form a disulphide bond

Question 37

What is the role of disulphide bonds in a quaternary structure? What are some examples?

Answer 37

The disulphide bonds attach 2 different polypeptide chains to one another e.g. insulin and antibodies

Question 38

What causes electrostatic interactions?

Answer 38

Attractions between charged amino acid side chains

Question 39

What is meant by an ion pair and a salt bridge?

Answer 39

the tertiary and quaternary structure are stabilised by electrostatic interactions between oppositely charged side chains This is an ion pair and the interaction is a salt bridge

Question 40

What would happen if two similar charges were brought close together during the folding process?

Answer 40

They would repel each other This would destabilise the structure

Question 41

In which molecules do van der waals interactions occur?

Answer 41

Van der Waals interactions occur in electrically neutral molecules

Question 42

What is involved in formation of van der waals interactions? What makes them stronger?

Answer 42

They rely on the formation of dipoles (permanent or induced) of varying strength The stronger the dipole, the stronger the interaction

Question 43

What creates a polar molecule?

Answer 43

When atoms of different elements are joined by a covalent bond, the two atoms attract the shared pair of electrons to different degrees

Question 44

What creates a dipole?

Answer 44

Covalent bonds with unequal electron sharing A positive charge is concentrated towards one end and negative charge towards the other end

Question 45

What is a hydrogen bond?

Answer 45

An interaction between a hydrogen atom of a donor group and non-bonding electrons on an acceptor group

Question 46

What are examples of donor and acceptor groups?

Answer 46

Donor: -OH, =NH Acceptor: O=C-

Question 47

How many amino acids can form hydrogen bonds?

Answer 47

Most of the polar residues This is 12 out of the 20 amino acids

Question 48

What creates a temporary dipole?

Answer 48

Electrons may become temporarily unevenly distributed across a bond This creates regions of slightly negative and slightly positive charges

Question 49

What causes a temporary dipole to form? Is it constant?

Answer 49

It may occur by chance or be induced by the proximity of a charged atom The dipole is constantly changing and will disappear and reform

Question 50

What creates an induced dipole from a temporary dipole?

Answer 50

When it becomes close to another molecule, the slightly negative end of the molecule will repel electrons in the neighbouring molecule

Question 51

What is the most important effect in stabilising proteins?

Answer 51

The hydrophobic effect

Question 52

What is meant by the hydrophobic effect?

Answer 52

Polar amino acids are found on the surface of the protein or are hydrogen-bonded in the core Non-polar amino acids are buried in the core of the protein

Question 53

Why is it energetically most advantageous if non-polar molecules are found on the inside of proteins?

Answer 53

The presence of hydrophobic molecules interferes with hydrogen bonds between water molecules Being in the core means they will not prevent H bonding any more than is necessary