SFP2 - Review of protein structure

Question 1

What is the unit to measure proteins?

Answer 1

Daltons (1 Da = 1 amu)

Question 2

Proteome meaning?

Answer 2

A proteome is the complete set of proteins expressed by an organism

Question 3

Where on the zwitterion is the negative and positive charge?

Answer 3

Positive is on the Nitrogen with an extra hydrogen (proton), and the negative is from the oxygen missing a hydrogen.

Question 4

What is meant by amphoteric behaviour?

Answer 4

This means the zwitterion can act as a base or as an acid. They can act as a base by donating a proton, or act as an acid by receiving a proton.

Question 5

Which is the simplest amino acid?

Answer 5

Glycine

Question 6

What are the two different isomers of amino acids?

Answer 6

D and L isomers

Question 7

Which isomer is the constituent of proteins?

Answer 7

L-isomer. It should spell out CORN in when read down the hydrogen bond in 3D space.

Question 8

What does a residue mean?

Answer 8

An amino acid in a polypeptide

Question 9

Why does the planar structure of a peptide lock in place?

Answer 9

Residence of electrons around the carbon-nitrogen double bond. Gives weak dipole bonds across bond. The double bond character proposes there is no free rotation between the carbon and nitrogen.

Question 10

What is the trans and cis conformation?

Answer 10

Trans = 2 alpha carbons at either side of the C-N bond. Cis = 2 alpha carbons on the same side of the C-N bond. (carbon from nitrogen)

Question 11

Which is favoured between the trans and cis conformation?

Answer 11

Trans due to less repulsion between atoms connected to carbon

Question 12

What is the primary structure?

Answer 12

Amino acid sequence

Question 13

Secondary structure?

Answer 13

The regular, repeating patterns of folding or twisting that occur in localised regions of the protein chain, such as the alpha helices or beta sheets.

Question 14

Tertiary structure?

Answer 14

The overall 3D shape of the entire protein molecule. This structure is determined by interactions between amino acid side-chains, such as hydrophobic interactions, hydrogen bonding, and disulfide bonds.

Question 15

Quarternary structure?

Answer 15

More than one polypeptide working together to form a functional protein complex

Question 16

What type of bond is the peptide bond?

Answer 16

Covalent (strong)

Question 17

What are the four non-covalent bonds present in the 1-4 structure?

Answer 17

Electrostatic (attraction between anions and cations of -R groups). Hydrophobic (non-polar R groups repelled from water and forced together). Hydrogen bonds. Van der Waals (attraction between atoms which are very close together)

Question 18

What is a rare type of secondary structure?

Answer 18

Collagen fold (triple helix)

Question 19

Which type of bond stabilises the secondary structure throughout?

Answer 19

Hydrogen bonds involving the peptide bond groups

Question 20

What is meant by the ‘pitch’ in an alpha helices?

Answer 20

The distance between amino acids residues (0.54nm)

Question 21

How many amino acids are present per turn?

Answer 21

3.5

Question 22

Which hand is the alpha helix?

Answer 22

Right-handed because the the spiral follows a clock-wise rotation

Question 23

How can a beta sheet be parallel or antiparallel?

Answer 23

The beta strands can run alongside each other (parallel) or against each other (antiparallel)

Question 24

Which is more stable and why?

Answer 24

Antiparallel - Hydrogen bonds are aligned, resulting in stronger bonding and a more stable structure.

Question 25

What is the role of a turn in the secondary structure?

Answer 25

It connects two elements of a protein, such as an alpha helix and beta sheet

Question 26

Where do hydrophobic R-groups tend to sit?

Answer 26

They cluster together in the interior of the protein, away from the aqueous environment

Question 27

What about polar amino acids?

Answer 27

Hydrophilic R-groups tend to be exposed to the surface, where they can interact with water molecules

Question 28

How else can R-groups stabilise the tertiary structure?

Answer 28

They can form hydrogen bonds, ionic interactions, and VDWs with other nearby R-groups or with the protein backbone

Question 29

Which amino acid are disulfide bonds found between?

Answer 29

Cysteine residues

Question 30

How are the A and B chain in bovine insulin stabilised together?

Answer 30

Cystein no.7 in A and C7 in B form a disulphide bond. C20 in A and C19 in B too.

Question 31

Domains can fold independently to the rest of the protein. They are composed of one or more supersecondary structures and they have their own specific function. Protein domains with a similar structure often have similar functions