Proteins

Question 1

structure of an amino acid?

Answer 1

Question 2

Which form are all amino acids in ?

Answer 2

L optical isomer

• the alpha carbon is the chiral centre and four different things bond to the central carbon
• this gives rise to optical isomers

glycine is the only nonchiral amino acid as it has no side chain

Question 3

what are the characteristics of a peptide bond?

Answer 3

• there is no free rotation
• C – O and N-H are in the same plane
• Other two bonds in the backbone of the peptide are able to rotate
• Only conformation in which the side chains do not clash with the main chain (steric hindrance) are allowed

Question 4

how are peptide formed?

what is the anatomy of a peptide?

Answer 4

• formed by condensation reactions
• functionality requires a definite 3D structure or conformation of the polypeptide chain

Question 5

Hydrophobic

Answer 5

Glycine Alanine Proline Valine Leucine Isoleucine Tryptophan Phenylalanine, Methionine

giant ants take lollipops inside picnics, maybe vinegar pringles?

giant anal prolapses vary

leucine and isoleucine may take pharmacology

Question 6

Hydrophilic

Answer 6

Serine Thereonine Tyrosine Asparagine Glutamine Cysteine

small timid tigers can grab ants

sometimes terrorizing teachers acquire giant cysts

Question 7

amino acids with positively charged side chain

Answer 7

Arginine Lysine always protonated at physiological pH

Histidine is protonated (+) under pH 6

Question 8

Negatively charged

Answer 8

Glutamate Aspartate are always negatively charged at physiological pH

Question 9

Why can proteins not tolerate a great change in pH?

Answer 9

Ionisation state of amino acids is essential for function. Changes in pH = change in ionisation state = change in property.

Amino acids can take up and release protons which gives them some buffering capacity = gives them capacity to resist some changes in pH

Question 10

what hold a protein together?

what bonds?

Answer 10

covalent bonds

hydrogen bonds

ionic interactions

van der waals forces

hydrophobic interactions

Question 11

When do disulphide bridges form?

Answer 11

Cytosine chains are oxidised

Covalent bond between 2 amino acids

Question 12

explain covalent bonds

Answer 12

• The strongest bonds within a protein and exist in the primary structure
• Covalent bonds can also exist as DISULPHIDE BRIDGES

Question 13

explain hydrogen bonds?

Answer 13

• Occur when two atoms bearing partial negative charges share a partially positively charged hydrogen
• These can occur between atoms on different side chains and the backbone of the protein OR between water molecules

Question 14

explain ionic interactions?

Answer 14

• Arise from the electrostatic attraction between CHARGED SIDE CHAINS
• Relative STRONG bonds
• Within any particular protein molecule, the majority of charged groups are at the surface of the folded protein - there they can be neutralised by counter ions such as salts

Question 15

explain van der waals forces?

Answer 15

• Transient, weak electrostatic attractions between two atoms - due to the fluctuating electron cloud surrounding each atom which has a temporary electric dipole
• the transient dipole in one atom can induce a dipole in the other atom
• The appropriate distance required for Van der Waals attractions differs based on the size of each electron cloud - referred to as the Van der Waals radius
• because there are lots of van der waals forces they can be strong all together

Question 16

explain hydrophobic interactions?

Answer 16

• They put hydrophobic side chains close together by packing them into the interior of the protein
• This creates a hydrophobic core and a hydrophilic surface to the majority of proteins

Question 17

Why does proline cause a kink in the peptide chain?

Answer 17

• When proline is added to a polypeptide chain there is a loss of NH group of the amino acid
• Side chain can’t form hydrogen bonds with C=O of another part of chain
• this distorts the helical conformation
• it puts a kink into it

Question 18

how are proteins usually folded?

Answer 18

• proteins are generally folded into the single conformation of the lowest energy
• Chaperones may be involved to make sure that folding occurs in the most energetically favourable way

Question 19

what does functionality require?

Answer 19

requires a clear 3D structure or conformation of the polypeptide chain

Question 20

What is a parallel beta strand?

Answer 20

• Beta sheets run parallel to each other

Beta sheets run in opposite directions = antiparallel beta sheet

the pleating in each case allows the best alignment of the hydrogen-bonded groups

Question 21

how are beta pleated sheets held together?

how are alpha helices held together?

Answer 21

• Hydrogen bonds between the C=O and the N-H of two or more beta strands hold the entire structure together
• they are held together by hydrogen bonds

Question 22

what is a domain?

Answer 22

compact globular structure that the secondary structure motifs are arranged into

Question 23

what is denaturing

what are common denaturants?

Answer 23

• urea breaks hydrogen bonds

• 2-mercaptoethanol (breaks disulphide bonds)

Question 24

what is the post-modification of proteins?

Answer 24

• the starting set of 20 amino acids can be modified to create novel amino

acids enhancing the capabilities fo the protein

• The formation of g-carboxyglutamate residues within several proteins of the blood clotting cascade is critical for their normal function by increasing their calcium binding capacities

Question 25

How does warfarin work?

Answer 25

Glutamate needs to be converted to gamma-carboxylglutamate This is needed for calcium binding

• Warfarin inhibits this reaction