Lecture 14: Protein structure and function

Question 1

What is a protein?

Answer 1

A chain of amino acids linked by peptide bonds - polypeptide

Question 2

Describe the structure of an amino acid

Answer 2

A central carbon atom bonded to an amine (NH2) group and a carboxyl (COOH) group and a hydrogen and a R group

Question 3

What is a zwitterion?

Answer 3

The ion form of an amino acid where the H from carboxyl group is donated to the amine group

Question 4

What is a condensation reaction?

Answer 4

Formation of peptide bond forming a H2O molecule

Question 5

What are the properties of peptide bonds?

Answer 5

• Cannot rotate due to resonance
• O-C-N-H of peptide bonds co-planar
• Rotation can occur at single bonds between carbons

Question 6

What are the two orientation of peptide bonds?

Answer 6

Cis- R groups on same side
Trans - R groups on opposite sides

Cis orientation is less stable due to steric repulsion of the side chains and is rare

Question 7

How many amino acids are there?

Answer 7

20

Question 8

What is the lock and key theory?

Answer 8

Protein structure determines function - the shape of the protein (enzyme) is specific to a substrate

Question 9

What is the induced fit theory?

Answer 9

Binding of substrate causes conformational change locking the molecule in

Question 10

What are the 4 stages of protein structure?

Answer 10

Primary
Secondary
Tertiary
Quaternary

Question 11

What is the primary structure of a protein?

Answer 11

The sequence of amino acids - formed from peptide bonds

Determined by DNA sequence of gene coding for protein

Question 12

What is the secondary structure of a protein?

Answer 12

Localised folding of the polypeptide due to hydrogen bonding between amino acids

Two types include Beta pleated sheet and alpha helix

Question 13

How do Beta pleated sheets form?

Answer 13

H bonding between amine group on one strand and a carbonyl (C=O) group on another strand

Two types: parallel and anti-parallel

Question 14

How do alpha helix form?

Answer 14

H bonding between a backbone amine group and carbonyl group 3 or 4 residues earlier

Question 15

Is it possible to predict the secondary structure of an amino acid?

Answer 15

Yes, certain amino acids favour one type of secondary structure due to their R group

Question 16

What is the tertiary structure of a protein?

Answer 16

The 3D shape of a protein - due to interactions of the side chains

Question 17

What are the bond types that form tertiary structure?

Answer 17

Hydrogen bonding - between polar R groups of amino acids
Disulphide bridge- covalent bond between R groups of amino acid cysteine
Ionic bonding - between charged portions of R groups
Van der waals
Hydrophobic interactions - when non-polar hydrophobic R groups orient themselves towards the inside of the protein molecule
Hydrophilic interactions - when polar R groups orient themselves towards the outside of the protein towards water

Question 18

What are co-factors or prosthetic groups?

Answer 18

Molecules which bind to part of the protein changing structure or activating the function of protein.

Question 19

What is the quaternary structure of a protein?

Answer 19

Binding together of multiple folded protein subunits due to interactions between groups of adjacent amino acids

Question 20

What are the two types of proteins with quaternary structure?

Answer 20

Homooligomers - same proteins binded together

Heterooligomers - different proteins bound together

Question 21

What are the types of protein?

Answer 21

Globular
Fibrous
Membrane proteins

Question 22

Are globular proteins and fibrous proteins soluble?

Answer 22

Globular proteins are soluble

Fibrous proteins are insoluble

Question 23

What are the functions of globular proteins?

Answer 23

Usually transport, enzymes, immune

Question 24

What are the functions of fibrous proteins?

Answer 24

Structural

Question 25

Describe the stability of fibrous and globular proteins?

Answer 25

Fibrous proteins are highly stable and globular proteins are lower stability

Question 26

What are the function of membrane proteins?

Answer 26

Signalling, receptors, transport, adhesion

Question 27

What is the Abbe's Diffraction limit?

Answer 27

Minimum resolution able to observed- half the wavelength of the medium of light used (0.2 micrometers)

Question 28

What are the two types of protein imaging?

Answer 28

X-ray crystallography | Cryo-electron microscopy

Question 29

What are the features of X-Ray Crystallography?

Answer 29

``` Sample must be crystallised Any size macromolecule Atomic resolution can be achieved Crystallisation can only occur with some proteins and the proteins could be damaged in the process Takes long ```

Question 30

What are the features of cryo-electron microscopy?

Answer 30

Frozen in its native state and observed via an electron microscope (small wavelength electron beam) Only large proteins can be observed Near-atomic resolution Fast preparation

Question 31

What is resolution?

Answer 31

Distance corresponding to the smallest observable feature

Question 32

What is Levinthal's paradox?

Answer 32

Very large number of degrees of freedom in an unfolded polypeptide chain e.g. 100 aa protein will have 3^198 different conformations