protein structure and function

Question 1

describe the functions of prteins

Answer 1

They are functional products of the genome providing

→ CARRIER FUNCTIONS: trafficking oxygen

→METABOLIC FUNCTIONS: enzymes producing and utilising energy

→FORM PARTS OF THE CELLULAR MACHINERY: spliceosomes, ribosomes

→ MAKE UP STRUCTURAL SCAFFOLD: microtubules, nucleosomes

→SENSING MOLECULES: receptors and their ligands

Question 2

How do we differentiate between L (levo) and D (dextro) forms of amino acids?

Answer 2

An L isomer reads Co-R-N CLOCKWISE, while a D isomer reads Co-R-N ANTICLOCKWISE.

Question 3

why do all amino acids have D and L isomers and what is the exception?

Answer 3

All amino acids except for Glycine have the two isomers due to them being tetrahedral in arrangement and due to the α carbon being chiral.

Question 4

describe how secondary structures are formed

Answer 4

• Formed from the folding of the polypeptide chain, eg, beta pleated sheet is formed by the polypeptide chain folding back on itself. The hydrogen bonds stabilise the overall sheet

Question 5

what are tertiary structures stabilised by?

Answer 5

• Tertiary structures are stabilised by non-covalent bonds and sometimes INTRA-CHAIN covalent bonds

Question 6

what are quaternary structures stabilised by

Answer 6

• Quaternary structures – stabilised by non-covalent bonds and sometimes INTER-CHAIN covalent bonds.

Question 7

what are intrachain covalent bonds ?

Answer 7

• INTRA-CHAIN bonds mean bonding between different parts of the same chain.

Question 8

briefly describe how beta sheets and beta turns are formed

Answer 8

→They are formed by H bonds between the β strands.

→ In sheets, the H bonds are between the strands.
→In turns, there are loops or turns linking the β sheets.

Question 9

describe the 3 secondary structures

Answer 9

Beta pleated sheets.
- Formed from the polypeptide chain folding back upon itself. Beta strands with hydrogen bonds to form cross-links and are connected by loops or short turns in either parallel or anti parallel arrangement.
- The orientation of the strands determines the relative positioning of the groups forming the hydrogen bonds, affecting the strength and stability of the strands ,
- Anti-parallel produces a beta sheet with greater stability as the hydrogens are linear.
Beta turns :
contains four amino acid residues. Allow for abrupt 1800 turns. These are common in Proline, CIS conformation R group, and Glycine, small R group/flexible.

Alpha helix :

• Right-handed helix
• Stabilised by hydrogen bonds.
• each turn contains 3.6 amino acid residues or 0.54 nm per turn. Stabilised by h bond between 1 and 5 residues so h-bonds are 4 residues apart.

Question 10

why is The orientation of amino acid side chains is structurally and functionally important and give proteins their properties? and give examples

Answer 10

This is because the side chains form the specific contacts within and between the proteins, cofactors and enzyme substrate or ligands.
 Side chains in alpha helix and beta sheet protrude outwards from the structures, providing the properties of the alpha helix and sheet.
 Trans arrangement allows for beta sheet.

Question 11

how are tertiary structures formed ?

Answer 11

Tertiary

• Formed from folding into densely packed generally globular structures.
• Formation depends on:
  1) Interaction between outward facing side chains
  2) Many weak chemical bonds
  3) But may be stabilised by covalent bonds

Question 12

describe the relationship between secondary and tertiary structures

Answer 12

• Combining secondary structures such as alpha helices, beta sheets and beta turns gives rise to tertiary structures, e.g. bundles of alpha helices that spans the membrane and anchor the structure in membranes, or the seven helices of the transmembrane domain of the CXCR4 chemokine receptor.

Question 13

how are quaternary structures formed

Answer 13

• two or more folded polypeptides that combine to form the mature protein.

Question 14

what is a key difference between quaternary and tertiary structures

Answer 14

The key difference is the bonds and forces are acting between different polypeptide chains in quaternary structures, and the same chain in tertiary structures. ( ie the difference between interchain and intrachain bonding )

Question 15

what do some proteins require for their function and others for their folding. give examples.

Answer 15

Some proteins require cofactors for their function, others for their folding.
Eg. Heme of haemoglobin, NAD, FAD, NADH.
- Organic cofactors are sometimes called coenzymes.
- Other proteins might include other ions like zinc, magnesium, calcium
- Eg, insulin requires zinc for its structure and function.

Question 16

describe water soluble proteins

Answer 16

Water-soluble proteins often have globular shapes as it means that the hydrophobic amino acids can be buried and folded internally, contributing to the overall structure and stability. and are often found in aqueous environments. Hydrophilic residues external ( allowing their charged sidechains to interact with the surrounding) and hydrophobic buried within. Can be filaments ( e.g actin) or coiled coils ( cortexillin) or tubes ( e.g tubulin) instead.

Question 17

describe membrane spanning proteins

Answer 17

• it is the opposite in membrane spanning proteins , the Membrane spanning proteins have external hydrophobic residues for lipid interaction and hydrophilic central channels.
• Eg CXCR4 receptor. In the membrane spanning section, externally the hydrophobic residues are predominant and the external and internal portion is predominantly hydrophilic.

Question 18

what are secondary structures stabilised by?

Answer 18

hydrogen bonds