Proteins

Question 1

What is the shape and structure of proteins determined by

Answer 1

The amino acid sequence

Question 2

What is a repeating sequence of atoms called

Answer 2

A polypeptide chain

Question 3

In a polypeptide chain what give the amino acid its unique properties

Answer 3

The side chains

Question 4

What chemical properties are given by side chains

Answer 4

Negative
Positive
Uncharged polar
Nonpolar

Question 5

What controls the folding of polypeptide chains

Answer 5

Weak iteractions 
Such as 
- Hydrogen bonds - requires hydrogen
- Ionic bonds - requires charge
- Van der Waals Forces - requires hydrophobicity

Molecular chaperones help proteins to fold

Question 6

How many different amino acids are there

Answer 6

20

There are 20 different r groups

Question 7

When proteins are denatured, what happens to their shape once the denaturing element is removed

Answer 7

They do not return to their original shape

Urea is an example of a solvent used to denature/ unfold proteins–> Creates a flexible polypeptide chain with no shape

Removal can cause spontaneous protein refolding or renaturation –> This tends to be in small proteins

Question 8

What impact does folding have on the amino acid

Answer 8

This is a very particular process. Folded one by one to produce the amino acid.
This is less of a problem with very simple very small proteins

Question 9

Are the two ends of a polypeptide chain same

Answer 9

No they are different there is an amino terminus NH2/NH3+ and a carboxyl terminus COOH / COO-
Conventionally N to C terminus direction

Question 10

What are some examples of things that influence the way proteins fold

Answer 10

Proteins tend to fold with non polar (hydrophobic) chains buried inside to avoid contact with water.
Proteins fold with polar hydrophillic chains on the outside –> these form hydrogen bonds with water
Polar groups tend to hydrogen bond with other polar groups

Fold into a conformation of lowest energy
- Free energy is minimised

Question 11

Small proteins are often

Answer 11

Soluble
Diffusible 
In the blood stream 
Most proteins in the body are small
Tend to be globular

Question 12

Large proteins are often

Answer 12

Structural
e.g. actin and myosin
Tend to be fibrous

Question 13

What do hydrogen bonds do for the protein

Answer 13

Stabilise the molecule in 3D

Question 14

The primary structure is

Answer 14

The sequence of the polypeptide chain
Understanding what the amino acids are
This influences the secondary structure

Question 15

Secondary

Answer 15

either alpha helix
- H bond every 4th amino acid
-Abundant in membrane proteins (e.g. Receptors)
- If 2 of these have non polar side chains on one side they form a coiled coil.
- Found in rod like elongated proteins
or
Beta sheet
- Parallel and antiparallel–> dependent on the directions of the proteins

Question 16

Tertiary

Answer 16

3D Conformation

- Often fibres

Question 17

Quaternary structure

Answer 17

Complete structure if more than 1 polypeptide chain

- Might have non proteinous structures that sit within the protein itself

Question 18

What is a protein domain

Answer 18

Any part of a protein that can fold independently into a compact stable structure

Domains are 50-350 amino acids

These are the modular units from which larger proteins are constructed
Different domains have different functions

Proteins are so precisely built that a single amino acid change –> catastrophic loss of function

Question 19

Proteins have binding sites which are

Answer 19

Complemetory
-they fit together depending on structure– the binding sites will decide what attaches and how many
A chain or helix can be formed if the binding site on a protein is complementary to another region on the same molecule

Question 20

Disulphide bond

Answer 20

The only covalent bond you would see in a protein
Can’t denature these
Only happen if you have a certain amino acid in the sequence (quite rare)– Cystine
Usually present in larger proteins
These only ever form between oxidation and reduction
Cystine amino acid SH2SH
Cystine’s have sulphur and you need this present for the disulphide bridge
These happen after the protein has been built
These stabilise extracellular proteins by covalent cross links
Can tie two amino acids in the same proteins of link subunits in a multi subunit protein

Very stable
Wherever you have a cystene it is almost certain you’ll have a disulphide bridge.

Question 21

Protein function: How

Answer 21

Proteins function by binding to other molecules
This interaction is always very specific
Ions, small molecules and macro molecules can bind
This binding involves non covalent bonds and a binding site.

Question 22

Binding site

Answer 22

Usually cavities formed by certain amino acid arrangements

Binding sites of antibodies of antibodies are extremely versatile –> meaning they can bind to almost any other molecule

Question 23

Enzymes

Answer 23

Are themselves proteins
Powerful and highly specific catalysts
All end in -se
Enzyme substrate complex involves multiple non-covalent bonds

Question 24

Lysozyme

Answer 24

• Is a model enzyme
• Hydrolyses bacterial polysaccharide
• Easy to work on experimentally
• Cheap, easy and quick to purify
• Stable to work on
• Stresses substrate by bending critical bonds that participate in reaction

There are two key amino acids in the active site of the lysozyme that matter.

• Aspartic acid 52 - Stabalises positively charged transition state
• Glutamic acid 35 - accurately positioned high concentration of acidifying H+ ions

Question 25

Active sites can

Answer 25

Bring two substrates together
Can rearrange electrons
Physically force a transition state

Question 26

Kinetic rates of enzymes

Answer 26

• Vary considerably
• Can be measured using purified enzymes, substrates and defined conditions
• Some enzymes have more of an affinity to a substrate–> means ‘tighter’ bonds
• Concentration of enzyme - There reaches a plateau where an increase in concentration will not help as all the active sites are occupied.

Question 27

How is enzyme catalytic activity regulated

Answer 27

• Negative inhibition
• Positive inhibition
• The product at an end point acts as an inhibitor for an enzyme further up

Question 28

Allosteric inhibitors

Answer 28

These are enzymes that have 2 binding sites that interact

• Active Site - substrate attaches
• Regulatory site - ‘switches’ it on and off

Binding of a regulatory molecule causes a conformational change in the enzyme –> This alters the enzymes activity

Conformational change

• can alter enzyme activity
• can be driven by protein phosphorylation

Question 29

What does phosphorylation do to a protein

Answer 29

Changes its function

Whether it turns it on or off you need to know more about the proteins

Question 30

What do protein kinases do

Answer 30

Catalyse phosphate transfer to Ser Tye of Thr side chains