Lecture 11 - Protein structure

Question 1

What are the monomers of proteins?

Answer 1

amino acids

Question 2

All amino acids have two common groups. What?

Answer 2

Amine - NH2
Carboxyl - COOH

Question 3

Amino acids contain an amino acid side chain. R group. It is known as…

Answer 3

a variable side chain

Question 4

Side chains may be…

Answer 4

• maybe a single hydrogen or contain 9 carbons with their associated hydrogen atoms
• side chains may be non-polar, polar but not ionized or polar ahdn ionized.

Question 5

Draw the general formula of an amino acid.

Answer 5

Question 6

What atom in an amino acid is an alpha carbon?

Answer 6

the carbon next to the carboxylic acid group is the alpha carbon

Question 7

Most amino acids are chiral. What does this mean. Which is the only achiral amino acid?

Answer 7

• stereogenic centre, 4 different groups attached to the alpha carbon
• glycine is the only achiral amino acid.

Question 8

What are proteogenic amino acids?

Answer 8

The name given to the 20 naturally occurring amino acids found in proteins. These amino acids are alpha amino acids and have the general formula that we know and understand.

Question 9

How do amino acids form peptides?

Answer 9

The N terminus/ amine group of one amino acid react with the C terminus/carboxyl group of the next in a condensation reaction- covalent peptide bonds form between the amino acids

Question 10

Draw the condensation reaction between two amino acids, showing the two isomers.

Answer 10

Question 11

Define the primary structure of a protein

Answer 11

The sequence of amino acids in a polypeptide chain.

Question 12

What is the primary structure of a protein determined by?

Answer 12

1. the number of amino acids in the polypeptide chain
2. the specific sequence of different amino acids.

Question 13

Peptide bonds form the …………. of the polypeptide chain

Answer 13

backbone

Question 14

What is the sequence of a backbone of a protein

Answer 14

N-C(alpha)-C-N-C(alpha)-C

Question 15

How do peptide bonds break? Give an example.

Answer 15

broken by hydrolysis to yield individual amino acids- e.g. when we digest protein from the food we eat.

Question 16

The peptide bonds is flat- aka…

Answer 16

planar

Question 17

There is an equilibrium between the two isomers of the peptide bonds which results in…

Answer 17

• partial double bond characteristic/planar bond
• a reasonably stable bond
• the nitrogen and carbonyl are less reactive than you would think.

Question 18

The double bond/peptide bond prevents….

Answer 18

rotation

Question 19

There can be different isomers of the peptide. Which are more energetically favourable and why?

Answer 19

Trans - the groups are on opposite sides which reduces repulsion.

Question 20

2 arrangements in secondary structure

Answer 20

• alpha helix
• beta pleated sheet

Question 21

How does the secondary structure come about?

Answer 21

hydrogen bonds form between the polypeptide chain.

Question 22

What are hydrogen bonds?

Answer 22

A hydrogen bond forms between an electronegative atom covalently bonded to a hydrogen atom and an electronegative atom with lone pair of electrons.

non-covalent

Question 23

What is an alpha helix?

Answer 23

Non-covalent interactions between residues close together in primary sequence. Helixes are stabilised by hydrogen bonds between the backbone amine of one amino acid and the backbone carbonyl of the amino acid four residues earlier.

Question 24

Alpha helix have a ……… arrangement

Answer 24

regular

Question 25

What is a beta pleated sheet?

Answer 25

Hydrogen bonds form between residues of the primary sequence that are far away from each other.
B pleated sheets are stabilised by backbone hydrogen bonds between carbonyl on one strand and amine of the next.

Question 26

Beta pleated sheets are not as ………. as alpha helix

Answer 26

regular

Question 27

In beta pleated sheets the chains run ……………. or …………… . Which is the most common?

Answer 27

• parallel
• antiparallel
  antiparallel is most common

Question 28

Beta sheet maximises…

Answer 28

hydrogen bonding between the polypeptide chain

Question 29

the secondary structure only involves …………. atoms

Answer 29

backbone

Question 30

Secondary structure is held together by ………… ………………… interactions

Answer 30

non covalent

Question 31

What is tertiary structure?

Answer 31

Non-covalent amino acid interactions of a single polypeptide chain that are not included in the secondary structure.
- Include all interactions between protein sidechains or between protein sidechains and the backbone.
- Tertiary structure often involves interactions between residues that are far apart in terms of primary sequence.

Question 32

What is quaternary structure?

Answer 32

• The interactions holding multiple polypeptide chains together in one protein.

Question 33

Each polypeptide chain in quaternary structure is referred to as….

Answer 33

a subunit

Question 34

Subunits are held together by…?

Answer 34

the same non-covalent interactions as the tertiary structure.

Question 35

protein with two subunits in their quaternary structure are called…?

Answer 35

dimers

Question 36

protein with three subunits in their quaternary structure are called…?

Answer 36

trimers

Question 37

protein with four subunits in their quaternary structure are called…? give an example

Answer 37

tetramers. Haemoglobin.

Question 38

Give the non-covalent interactions we find in the tertiary and quaternary structure.

Answer 38

• hydrophobic interactions
• hydrogen bonds
• salt bridges (pairs of acid and basic amino acids close together in structure- interactions between permanent positive and negative charges AND also repulsive interactions)
• van der Waals interactions- interactions between either permanent or transient charges
• Disulphide bridges- a covalent S-S bond between the side chains of two cysteines close together in space.

Question 39

How are protein structures broken?

Answer 39

heat, extreme pH, detergents, chemical modification.