Lecture #1 - Introduction to proteins, aa', peptides and peptide bonds

Question 1

Proteins form non-branching polymers that form macromolecules about how much in size?

Answer 1

50 - 100 Å (1Å = 10^-10m)

Question 2

All amino acids are chiral - what form used in nature?

Answer 2

L form (also has D form)

Question 3

What part of the protein does the chemistry?

Answer 3

Side chain

Question 4

Non polar aa’

1. How many? Name them
2. Found where in the protein?
3. Which ones have aromatic side chains?
4. What about glycine?
5. What about proline?
6. What about cysteine?

Answer 4

1. 10 of them (GALVIMPPTC)
   - Alanine, Ala, A
   - Valine, Val, V
   - Leucine, Leu, L
   - Isoleucine, Ile, I
   - Glycine, Gly, G
   - Cysteine, Cys, C
   - Phenylalanine, Phe, F
   - Tryptophan, Trp, W
   - Methionine, Met, M
   - Proline, Pro, P
2. Inside because hydrophobic
3. Phe and Trp (remember Trp has tWo rings)
4. Its R = H so non-chiral, flexible, almost in a group itsled
5. Proline inflexible bc R group binds to its own aa’ so different to rest of aa’ = IMINO ACID
6. A little bit of polar character (like alanine but + SH group)

Question 5

Negative charged (acidic), polar aa’:

1. How many? Names?
2. What’s their most common form?

Answer 5

1. Two of them (AG):
   - Aspartic acid, Asp, D (asparDate)
   - Glutamic acid, Glu, E (glutamatE)
2. Proton donors and usually found in conj base form

Question 6

Positively charged (basic) polar aa’:

1. How many and name?
2. Most common form?

Answer 6

1. Three of them (LAH):
   - Lysine, Lys, K (WEIRD #1)
   - Arginine, Arg, R
   - Histidine, His, H
2. Most common conj acid - mostly accept p+

Question 7

Uncharged polar amino acids

1. How many are there and names?
2. What is like F?
3. Which ones are alcohol and which ones are amide?

Answer 7

1. Five of them (STTAG):
   - Serine, Ser, S
   - Threonine, Thr, T
   - Tyrosine, Tyr, Y
   - Asparagine, Asn, N
   - Glutamine, Gln, Q
2. Tyrosine (F = Phenalyanine because has a ring)
3. First three alcohol (S, T, Y) and last two amide (N and Q). Amides are like D and E.

Question 8

Which aa’ have ionisable side chains?

Answer 8

1. A and G - acidic
2. H, L and R - basic
3. Also C and Y

Question 9

pKa and pI:

1. What is pKa?
2. What is pI?

Answer 9

1. The pKa value for an ionizable group on an amino acid or protein is the pH at which the group is 50% ionized.
2. The pI, or isoelectric point is the pH at which the net charge on an amino acid (or protein) is 0 (so zwitterion form)

Question 10

Look at slides for PTM examples

Answer 10

Yeah - important

Question 11

What does “E6V” mean?

Answer 11

First letter = wild type or native aa’

Number = location of mutation

Second letter = mutated residue

So here, glutamate becomes valine at positin 6

Question 12

Diff between peptide, protein and residue

Answer 12

A short stretch of amino acids joined together is a peptide.

A longer chain of amino acids joined together, usually with a defined biological function, is a protein.

(In biochemistry and molecular biology, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid. One might say, “This protein consists of 118 amino acid residues” or “The histidine residue is considered to be basic because it contains an imidazole ring.”)

When an amino acid is added to a protein, the remaining part is often called an amino acid residue or residue for short.

Question 13

Peptide bond:

1. Who discovered it and how?
2. What percent double character lead to planarity?
3. Planar conformation maximises what bondings overlap?
4. Rotation barrier of ~____kJ/mol
5. Is there a dipole?
6. Predominantly cis-trans?

Answer 13

1. Linus Pauling Corey and determined structure by X-ray crystallography
2. 40%
3. Pi
4. 80 (so protein stuff and holds 3D shape)
5. Yeah
6. Predominantly trans

Question 14

The amide bond or peptide bond C-N bond is ___ shorter than C-N bond. C=O is ____ longer then those for ______ and aldehydes

For a trans peptide bond, the dihedral angle is ___ by definition.
In a cis peptide bond, the dihedral angle is ___ by definition.
Most peptide bonds are trans, ~10% that precede proline may be cis

Answer 14

The amide bond or peptide bond C-N bond is 0.13Å shorter than C-N bond. C=O is .02 Å longer then those for ketones and aldehydes

For a trans peptide bond, the dihedral angle is 180° by definition.
In a cis peptide bond, the dihedral angle is 0° by definition.
Most peptide bonds are trans, ~10% that precede proline may be cis