Protein structure and function

Question 1

What elements do proteins provide to cells?

Answer 1

Proteins provide structural and functional elements that underline the dymanic processes of the cell.

Question 2

What are the functional products that proteins provide?

Answer 2

Proteins are functional products of the genome providing:-

1. Carrier functions - trafficking oxygen.
2. Metabolic functions - Enzymes producing and utilising energy.
3. Form parts of the cellular machinery - splicosomes, ribosomes.
4. Make up structural scaffold - microtubules, nucleosomes.
5. Sensing molecules - receptors and their ligands (to sense and respond)

Question 3

What is the general structure of an amino acid?

Answer 3

Question 4

What arrangement do amino acids have in space (structure wise)?

Answer 4

Thay have a tetrahedral arrangement.

Question 5

What is a zwitterion?

Answer 5

• It is a molecule or ion that has a seperate positively and negatively charged groups.
• They have no overall charge because the positive and negative charges cancel out.
• Amino acids can act as a zwitterion even in the solid state.

Question 6

What do amino acids act as at a low pH?

Answer 6

The amino acid acts as a base and accepts a H+ ion.

Question 7

What do amino acids act as at a high pH?

Answer 7

The amino acids act as an acid and donates an H+ ion.

Question 8

What is the isoelectric point of a zwitterion?

Answer 8

• The isoelectric point means pH at which a particular molecule or surface carries no net electrical charge.
• It is also the point at which a zwitterion is formed, each amino acid has its own unique isoelectric point.

Question 9

What do amino acids act as at a neutral pH?

Answer 9

They act as a zwitterion.

Question 10

What does the R chain deteremine in an amino acid?

Answer 10

It decides the physiochemcial properties of the amino acid.

Question 11

What are the two isomers amino acids and other molecules can form?

Answer 11

L(Levo) and D(Dextro) isomers.

Question 12

How to identify if the amino acid shows D or L isomerism?

Answer 12

Question 13

Which amino acid does not form L and D isomers?

Answer 13

Glycine does not form isomers as the R group is hydrogen so it does not have a chiral centre.

Question 14

In what direction does the L form read CORN?

Answer 14

In the clockwise direction.

Question 15

In what direction does the D form read CORN?

Answer 15

In the anti-clockwise direction.

Question 16

Where are L form amino acids found?

Answer 16

All amino acids incorporated into proteins by living organisms are in the L form.

(Not a protein but just know that glucose is in D form)

Question 17

Where are D form amino acids found?

Answer 17

D-amino acid residues comprise cell walls in bacteria, and are oftern used as therupatics.

Question 18

What bond is formed between two amino acids and what type of reaction is it?

Answer 18

A peptide bond is formed and by a condensation reaction releasing H20.

Question 19

What is a peptide residue?

Answer 19

Each repeating unit of the polypeptide chain is a residue. (Basically each monomer of amino acid is a residue)

Question 20

What is the favourable arrangement for peptide bonds? (Cis or Trans)

Answer 20

• The variable side chain R is usualy arranged in a trans conformation.
• 0.1% of peptide bonds have a less energetically favourable cis arrangement.

Question 21

How are beta pleated sheets in the secodary structure of proteins formed?

Answer 21

• The beta pleated sheet is formed from the hydrogen bonding between the adjacent beta strands connected by loops either in parallel or in anti-parallel arrangement.
• The way in which the strands are arranged (parallel or anti-parallel) affects the stability.

Question 22

Which is more stable (parallel or anti-parallel beta sheets)? Why?

Answer 22

• The anti-parallel strands are more stable as the hydrogen bonds are aligned directly opposite each other (between the strands) so they are more closer.
• Also the longer loops in the parallel strands cause decreased stability.

Question 23

How is the alpha helix fomed and what is its structure?

Answer 23

The alpha helix is a right handed helix and is stabilised by H-bonds between two amino acids 4 residues apart.

i.e. residue 1 and 5

There are 3.6 residues per turn or 0.54nm per turn.

Question 24

What are cofactors?

Answer 24

• Cofactors are inorganic molecules that increase the rate of reaction or are required for enzyme function.
• Cofactors are not proteins but rather help proteins, such as enzymes, although they can also help non-enzyme proteins as well.
• Examples of cofactors include metal ions like iron and zinc.
• They bind tightly to the enzymes.

Question 25

What are coenzymes?

Answer 25

* Coenzymes, are **organic** molecules that bind to enzymes and help them function. * Organic molecules are simply molecules that contain carbon. * Many coenzymes are derived from vitamins. * Coenzymes bind loosely to enzymes, while another group of cofactors do not.

Question 26

What are prosthetic groups?

Answer 26

* Prosthetic groups are cofactors that **bind tightly** to proteins or enzymes. * They can be organic or metal ions and are often attached to proteins by a **covalent bond**.