3D Structure Of Proteins

Question 1

Folding of polypeptide chain is determined by:

Answer 1

Amino acid sequence 
Molecular structure + properties of its amino acids 
Molecular environment (solvents + salts)

Question 2

Amino acids fall into categories defined by …… and …… properties

Answer 2

Structural

Chemical

Question 3

Properties of amino acids are determined by their structure

Answer 3

Properties of individual amino acids are determined by variable side chain
Charged amino acids may be subdivided into acidic(-ve) and basic (+ve)
Charged amino acids are polar in nature

Question 4

Carboxyl groups COO- are …… or ….

Answer 4

Charged or acidic

Question 5

Amine groups NH3^+ are ……. or……..

Answer 5

Charged or basic

Question 6

2^o amine groups NH + carbonyl group C=O are …….

Answer 6

Polar

Question 7

Hydroxyl group OH^- are …….

Answer 7

Polar

Question 8

Hydrocarbon is. ……..

Answer 8

Non-polar hydrophobic

Question 9

Describe the structure of peptide bond?

Answer 9

Is flat planar structure with rotational freedom within molecule found around alpha carbon

Question 10

What role does non covalent bonding play in determining folding?

Answer 10

Weak

Determine most of structure

Question 11

What role of electrostatic attraction in determining folding?

Answer 11

Falls off exponentially as distance increases, affected by electrostatic environment
Typically occurs in aqueous environment

Question 12

What are Van Der Waals attraction?

Answer 12

Weak forces occur between 2 atoms in non covalent attractions
Determined by their fluctuating change
Attraction at close distance is balanced by repulsion due to proximity that is determined by VDW radius of an atom
VDW forces are induced by proximity of molecules

Question 13

What are hydrophobic interactions?

Answer 13

H2O is polar molecule
Hydrophobic interactions minimise disruption of H2O network
4th weak force

Question 14

What are forces determining protein structure?

Answer 14

Electrostatic interaction= attraction of oppositely charged groups such as carboxyl and amine groups of aspartic acid and lysine
Hydrogen bonds
Hydrophobic effect
VDW interaction

Question 15

What are disulphide bonds?

Answer 15

Covalent bonds
Form between side chains of 2 cysteine molecules
Bonds form in oxidative reaction
SH group from each cysteine cross link
Can form on same (intra-chain) or different (inter-chain) polypeptide chains

Question 16

What is primary structure?

Answer 16

Covalent bonds forming polypeptide chain

Order of amino acid residues joined by peptide bonds

Question 17

What is secondary structure?

Answer 17

Regular folded forms stabilised H bonds

Question 18

What is tertiary structure?

Answer 18

Overall 3D structure stabilised by H bonds, hydrophobic, ionic + VDW’s forces + sometimes by intra-chain covalent (disulphide) bonds

Question 19

What is quaternary structure?

Answer 19

Organisation of polypeptide into assemblies, stabilised by non-covalent + covalent bonds + sometimes by inter-chain covalent (disulphide) bonds

Question 20

Give examples of secondary structure

Answer 20

Beta sheets
Beta turns
Alpha helices

Question 21

How are alpha helices formed?

Answer 21

Formed from intra-chain H bonding

Usually H bond between every 4th residue

Question 22

How are beta sheets formed?

Answer 22

Formed from intra-chain H bonding which is formed between adjacent beta strands to stabilise the sheets

Question 23

How are beta sheets arranged?

Answer 23

Can have 2 different arrangements where strands are either parallel or anti-parallel

Question 24

How are beta turns arranged?

Answer 24

Very specific arrangement of peptide chain forming U-shaped structure stabilised by H bonds
Beta often contain glycine or proline

Question 25

Tertiary structure involves combining…

Answer 25

Secondary structures of single polypeptide

Question 26

Quaternary structure involves combining …..

Answer 26

Multiple chains

Which constitutes functional molecule

Question 27

What happens to function of mis-folded protein?

Answer 27

Is almost always lost +reduced

Question 28

What do misfolded proteins often have tendency to do?

Answer 28

Have tendency to self associate + form aggregates
E.g. Huntington’s, Alzheimer’s, Parkinson’s disease, type 2 diabetes etc
Other misfolded proteins result in cellular processing that lead to their degradation e.g. cystic fibrosis

Question 29

What are the reasons why misfolding occurs?

Answer 29

Somatic mutations in gene sequence
Errors in transcription or translation
Failure of folding machinery
Mistakes of post-translational modifications or in trafficking of proteins
Structural modifications produced by environmental changes
Induction protein mis folding by seeding and cross seeding by other proteins