Protein structure and function

Question 1

What elements do proteins provide?

Answer 1

Structural and functional

Question 2

What do the functional products of the genome provide?

Answer 2

§ Carrier functions
§ Metabolic functions
§ Form parts such as ribosomes
§ Make up structural scaffolds such as microtubules
§ Sensing molecules like receptors

Question 3

What is the polypeptide backbone?

Answer 3

a repeating sequence of atoms along the core of the polypeptide chain

Question 4

What arrangement do amino acids have?

Answer 4

Tetrahedral

Question 5

What do amino acids act as at a low pH?

Answer 5

A base and accepts H+

Question 6

What do amino acids act as at a high pH?

Answer 6

An acid and donates H+

Question 7

What do amino acids act as at a neutral pH?

Answer 7

Amino acid act as zwitterion

Question 8

When an amino acid acts as an acid or base, what does this ensure??

Answer 8

Dynamic equilibrium

Question 9

What do the side chains do??

Answer 9

confer the specific physiochemical properties

Question 10

How do D and L isomers arise?

Answer 10

Due to the arrangement of atoms

Question 11

What is the arrangement around the alpha carbon?

Answer 11

Chiral

Question 12

What is exempted from D and L isomerism and why?

Answer 12

Glycine as it has 2 hydrogens attached to the alpha carbon therefore not a chiral centre

Question 13

Where are D amino acid residues found and often used for?

Answer 13

Compromise cell walls in bacteria and often used in therapeutics

Question 14

In what direction are D amino acids read?

Answer 14

Anticlockwise

Question 15

In what direction are L amino acids read?

Answer 15

Clockwise

Question 16

What is a peptide residue?

Answer 16

repeating unit of the polypeptide chain

Question 17

In what arrangement are peptide residues usually organised in?

Answer 17

Trans conformation where R groups are in opposite direction

Question 18

What percentage of peptide residues are in CIS conformation and why so less and what is the arrangement of there R groups?

Answer 18

• There are less than 0.1% with the Cis conformation because its less energetically favourable
○ where R groups are on the same side

Question 19

How are Beta sheets formed and stabilized?

Answer 19

formed by continuous folding and there are intra molecular hydrogen bonds between beta strands

Question 20

What is more stable, parallel or anti parallel beta sheets? Why?

Answer 20

• Anti parallel beta sheets are more stable than parallel beta sheets
• Loops connecting beta sheets, longer in parallel sheets compared to antiparallel

Question 21

How are alpha helix formed and what is its structure?

Answer 21

• Stabilised by H-bonds between two amino acid 4 residues apart.
• Side chains give the proteins its structure
• Side chains in both alpha helix and beta sheet protrude outwards from the structure

Question 22

How many residues per turn does an alpha helix have?

Answer 22

3.6

Question 23

How many residues is a beta turn composed of and what shape does it give?

Answer 23

Composed of 4 residues and gives a U shape

Question 24

Where are beta turns located and what does it do to the direction of the polypeptide?

Answer 24

• Located on surface of protein, reversing bends that reverse the direction of polypeptide backbone

Question 25

What do beta turns do to large protein structures?

Answer 25

• Help large protein structures to bend into compact structures

Question 26

What amino acids are commonly used in beta tuns and why?

Answer 26

• Glycine and proline commonly used in turns:
○ Glycine: lack in large side chain
Proline: built in bend

Question 27

When folded into tertiary structures, what does formation depend on?

Answer 27

weak chemical bonds between side chains like disulfide bonds

Question 28

What is the tertiary structure a combination of?

Answer 28

A combination of seondary structures

Question 29

How is it folded into the quaternery structure?

Answer 29

• Two or more polypeptide chain combine to form the mature protein
  
  • Eg, Haemoglobin have 2 alpha and beta polypeptide chains.

Question 30

What structure is required for normal function?

Answer 30

• Water soluble proteins are globular in shape
• Hydrophilic residues are mostly on the external surface
• Hydrophobic residues are usually buried inside the protein
+• Membrane spamming regions like on receptors have externally located hydrophobic residues which interact with the membrane lipids