Module 1 - Amino Acids and Peptides Flashcards
Describe three ways an ‘unfavorable’ reaction can be made favorable.
KEEP CONCENTRATION OF PRODUCTS MUCH LOWER THAN REACTANTS
- Remove one or more of the products at a rate much faster than it is produced
- Replenish one or more of the reactants at a rate much faster than it is consumed
- Couple unfavorable reactions with highly favorable reaction.
Why is ATP considered as an ‘energy rich’ molecule?
- ATP has a higher negative charge density than ADP (ATP less stable)
- Pi is very stable: multiple resonance states exist
- ATP phosphoanhydride bonds are relatively weak, while ADP phosphoanhydridebonds and Pi bonds are relatively strong.
Hence, more energy is released to reform the bonds of ADP compared those absorbed to break ATP bonds.
Proteins are ____________ of alpha amino acids.
linear heteropolymers
Characteristics of alpha amino acids are:
- The alpha carbon has four substituents and is tetrahedral
- All (except proline) have: a carboxyl group, amino group, and a hydrogen connected to the alpha carbon
- the fourth substituent (R) is unique to each amino acid
The only achiral amino acid is ____.
Glycine (it has 2 hydrogen connected to the alpha carbon)
Protein is only made up of ______.
L-amino acids.
D-amino acids do not all rotate light clockwise, while L-amino acids do not all rotate anti clockwise. Why is it named so then?
D- and L- amino acids are made by starting synthesis from D- and L-glyceraldehyde, which do rotate clockwise and anti-clockwise respectively.
Explain how are the omega, phi, and psi backbone dihedral angles are defined.
Omega: rotation angle about the C-N bond (between the C-alpha (i-1) - C bond and N-C-alpha(i) bond)
Phi: rotation angle about the N-C-alpha bond (between the C-N and C-alpha - C bond)
Psi: rotation angle about the C-alpha - C bond (between the N-C-alpha and C-N bond) Note: LEFT-MOST acts as reference
Which isomeric state is favoured for peptide linkages? Explain.
The trans- form is favored sue to the severe steric hindrance (van der Waals repulsion) caused by the interfering side chains in cis- formation.
Usually, trans- formation of amino acids is favored over cis- by over 1000:1. Mention an exception to this and explain.
The trans- formation of proline is only favored 4:1 due to similar steric hindrance for the two conformations. But trans- is still slightly favored for steric reasons.
Why is there only limited rotation about the C-N single bond (peptide bond)?
The double bond within the carbonyl group is interchangeable with the C-N bond (resonance) causing a partial double bond character in the C-N bond (hence, peptide bond is planar).
Mention the amino acids with non-polar, aliphatic groups (with their three letter and one letter code).
- Glycine (Gly, G)
- Alanine (Ala, A)
- Valine (Val, V)
- Leucine (Leu, L)
- Isoleucine (Ile, I)
- Proline (Pro, P)
- Methionine (Met, M)
Mention the amino acids with aromatic groups (with their three letter and one letter code).
- Phenylalanine (Phe, F)
- Tyrosine (Tyr, Y)
- Tryptophan (Trp, W)
Mention the amino acids with alcohol groups (with their three letter and one letter code).
- Serine (Ser, S) - Threonine (Thr, T)
How does a peptide bond form?
A dehydration reaction between the carboxyl and amino group of adjacent amino acids.
