Proteins

Question 1

What does it mean if a cell is polarised?

Answer 1

It means that each end of the cell has a different function.

Question 2

How is a prokaryotic cell different to a eukaryotic cell?

Answer 2

It has no distinct nucleus, it has fewer organelles and it has a cell wall as well as a plasma membrane.

Question 3

What is a monomeric unit? And what forces are involved in the making of a macro molecular complex?

Answer 3

It is a simple molecule. These are joined together by covalent bonds to form macromolecules which then combine to form macro molecular complexes. The complexes are held together by weaker non-covalent interactions.

Question 4

List the four types of weak interaction (non-covalent).

Answer 4

Hydrogen bonds (between dipoles on neutral groups)
Ionic interactions (between charged particles)
Hydrophobic interactions (exclusion of water)
Van dear waals forces.

Question 5

What must a molecule be able to form in order to be soluble?

Answer 5

Hydrogen bonds. This means soluble molecules often contain large numbers of OH groups or =O. Non polar molecules cannot form hydrogen bonds, and therefore are insoluble.

Question 6

What is an amphipathic molecule?

Answer 6

A molecule which has both polar and non polar regions

Question 7

What type of molecules form micelles and why?

Answer 7

Amphipathic molecules form micelles because the hydrophobic groups cluster together to exclude water and water surrounds the hydrophilic parts of the molecules.

Question 8

What is the fluid mosaic model for a plasma membrane?

Answer 8

This is where the phospholipid molecules form a bilayer with their hydrophobic tails pointing inwards and the hydrophilic heads pointing outwards.

Question 9

If cells all have the same DNA, how can we get different specialised cells?

Answer 9

Different cells have different proteins expressed and therefore carry out different functions.

Question 10

What is a protein?

Answer 10

A protein is a polypeptide. A polymer of covalently bonded amino acids.

Question 11

How does the amino acid sequence affect the protein function?

Answer 11

The amino acid sequence affects the way in which the protein folds, and therefore ultimately its shape. The shape of the protein determines it’s function.

Question 12

What is the structural state of an amino acid in water in the body?

Answer 12

Amino acids are dissolved in water in the body and so they are in their zwitterion form.

Question 13

What charge does an amino acid have?

Answer 13

Amino acids can act as both a base and an acid depending on their environment. The NH2 amine group can accept protons whilst the COOH group can donate protons.

Question 14

What determines the acid base behaviour of a protein?

Answer 14

The R groups. All the COOH and NH2 groups are contained within the peptide linkages which form when the protein forms.

Question 15

What are the three classes of amino acids?

Answer 15

Non-polar amino acids
Polar uncharged amino acids
Polar charged amino acids

Question 16

How can we estimate the effect that a mutation will have on a protein?

Answer 16

Look at the size and structure of the change in R groups. Large changes will have a bigger effect than small ones.

Question 17

What is pK and what does it tell us?

Answer 17

pK is how likely a group is to dissociate and donate a proton.

If pK pH : the group accepts a proton - is protonated

Question 18

What are the key properties of a peptide bond?

Answer 18

The peptide bond is C-N. This is a planar bond with the H and R groups above and below the plane. Electrons dissociate into the bond from C-O and this gives it partial double bond properties, preventing rotation.

Question 19

What is the Isoelectric point of a protein?

Answer 19

This is the point where there is no overall charge.

Question 20

Will a basic protein contain mostly positively or negatively charged amino acids?

Answer 20

Positively charged.

The basic protein has already accepted protons, and now it can act as an acid and donate protons.

Question 21

In what state will a protein be if pH

Answer 21

Protonated, because if pH is lower then it will of acted as a base and accepted a proton.

Question 22

What is an oligopeptide?

Answer 22

A peptide of only a few amino acids in length.

Question 23

What is the secondary structure of a protein and what two forms can it take?

Answer 23

The secondary structure is the spatial arrangement of the polypeptide backbone. This can take the form of either an a helix or a B sheet.

Question 24

What is the tertiary structure of a protein?

Answer 24

It is the 3D arrangement off all the atoms in the polypeptide.

Question 25

What is the quarternary structure of a protein?

Answer 25

It is the arrangement of multiple subunits within space.

Question 26

Describe the secondary protein structure: a helix

Answer 26

It is a right handed helix with 3.6 amino acid residues per turn. Hydrogen bonds form between every fourth amino acid residue.R groups are all on the outside of the helix and have no impact on formation.

Question 27

Can all polypeptides form a helixes?

Answer 27

No. Those will small R groups form strong helixes because these do not interact, however Proline acts as a helix breaker because the bond angles are impossible.

Question 28

What is a B sheet?

Answer 28

This is the fully extended conformation for a protein with R groups lying alternately on either side of the chain.

Question 29

What is the difference between a parallel and an anti-parallel B sheet?

Answer 29

In a parallel B sheet all strands run in the same direction, whilst in an anti parallel sheet they run in opposite directions. It is also possible to have mixed sheets.

Question 30

What are the three functions of a fibrous protein?

Answer 30

Support, shape, protection

Question 31

Give two properties of a fibrous protein.

Answer 31

They tend to have long strands or sheets and are made from a single repeating secondary structure.

Question 32

What type of proteins are involved in catalysis and regulation?

Answer 32

Globular

Question 33

What is a domain? (Think proteins)

Answer 33

A domain is a polypeptide chain which folds into a specific shape and has a functional role.

Question 34

What is a motif? (Think proteins)

Answer 34

A motif is a folding pattern which contains multiple secondary structures, for example a BaB loop.

Question 35

Where are hydrophobic R groups normally found when a protein folds?

Answer 35

They are normally buried within the protein to protect them from water.

Question 36

Between which amino acids do covalent disulphide bonds form and what type of proteins do these tend to be?

Answer 36

They are found between Cys residues. They tend to occur in proteins to be secreted. Particularly in the gut because here strong bonds are needed due to uncontrollable conditions.

Question 37

What are reasons for protein denaturation and why?

Answer 37

Heat due to increased vibrational energy
pH due to altered ionisation states
Solvents disrupt hydrophobic interactions.

Question 38

In protein folding, what is a Chaperone?

Answer 38

It holds the protein molecule to prevent misfolding.

Question 39

Define an amyloidose.

Answer 39

It is a disease that occurs due to the misfolding of proteins. Amyloid fibres form when normally soluble proteins are insoluble.

Question 40

What is the relationship between H+ and pH?

Answer 40

[H+] = 10^(-pH)

Question 41

What is the equation for pH which includes pKa?

Henderson-Hasselbalch equation.

Answer 41

pH = pKa + log([base]/[acid])