Peptide bond and Proteins

Question 1

side chain

Answer 1

Most important in determining reactivity of the amino acid.

Question 2

trans form

Answer 2

more space

Question 3

cis form

Answer 3

sterically hindered

Question 4

what’s so special about the peptide bond ??

Answer 4

The position of the double bond is not fixed over time.

Has a partial double bond character on the C-N bond.’

Resonates back and forth and conceptually it is the average of several structures.

Question 5

Consequences of resonance in the peptide bond - 1

Answer 5

It increases the polarity of the peptide bond

Question 6

Consequences of resonance in the peptide bond - 2

Answer 6

It restricts movement of the atoms in the bond.

Double bonds locked in position; single bonds free to rotate.

Question 7

The Four Levels of Structure

Answer 7

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

Question 8

Primary structure

Answer 8

The order of the amino acids in a polypeptide

Has Direction
N-terminal ——-> C-terminal end of the protein

Question 9

Secondary structure

Answer 9

Local folding of the polypeptide chains into regular patterns - helix, sheet

Question 10

Core secondary structures

Answer 10

Alpha Helix
Beta Sheet

Hydrogen bonding between the amine hydrogen and one AA and the carbonyl oxygen of another AA lead to formation of these structures.

Question 11

Alpha Helix

Answer 11

formation leads to the polypeptide

R-groups extend away from the axis

a typical a-helix has 11AA

Question 12

Beta Pleated Sheet

Answer 12

R-group trans: above and below the plane of the sheet.

these ‘sheets’ can line up next to each other

TWO TYPES
Parallel
Anti-parallel

Question 13

Parallel

Answer 13

direction of AA chain the same

N-termini of successive strands in the same direction

The N-terminus of one strand is adjacent to the N-terminus of the next strand.

Question 14

Anti-parallel

Answer 14

direction of AA chain opposite

Successive b-strands alternate directions

N-terminus of one strand is adjacent to the C-terminus of the next

H-bonds linear —-> strong

Question 15

Type I AA3

Answer 15

any AA

Question 16

Type II AA3

Answer 16

Glycine
(R-group=H, so small)

Question 17

super-secondary structures

Answer 17

can be assembled into more complex motifs

Certain substructures are found commonly in proteins
e.g. helix-loop-helix (top)
e.g. beta-alpha-beta (bottom)

Question 18

Tertiary structure

Answer 18

Overall folding of a single polypeptide chain

Question 19

Disulphide bonds (aka disulphide bridge)

Answer 19

Covalent link between two the -SH groups of two cysteine residues.

Important for stabilisation of the overall structure and flexibility.

Question 20

Tendencies in Tertiary structure

Answer 20

Charged & polar R-groups on the protein surface.
> interact with water

Non-polar R-groups tend to be buried in the cores of proteins.

Question 21

Quaternary structure

Answer 21

more than one polypeptide

A dimer is the most simple form

Tetramer
Hexamer

Question 22

Normal CFTR Channel

Answer 22

moves chloride ions to the outside of the cell.

Question 23

Mutant CFTR Channel

Answer 23

does not move chloride ions, causing sticky mucous to build up on the outside of the cell.

Question 24

REMEMBER!!

Answer 24

Proteins have a specific three dimensional conformation, which is essential for their function.

Maintaining the correct structure is essential to maintain correct function.

Question 25

Resonance

Answer 25

A peptide bond is shifting back and forth between different states and the average is usually observed.

Question 26

four levels of structure

Answer 26

Primary —- sequence
Secondary — local folding
Tertiary —- global folding
Quaternary — proteins binding together