Download Proteins We now know about the building blocks of proteins (amino

Proteins
We now know about the building blocks of proteins (amino acids) in great detail. So now let’s see how
these building blocks are put together.
• In a protein, amino acids are linked together by a peptide bond (amide bond)
• This bond forms as a result of a condensation reaction of the carboxylate of amino acid #1, and the
amino group of amino acid #2.
• Why do we not show arrow pushing??
• This reaction is extremely unfavorable (remember Le’Chat?)
• There are lots of intermediates and enzymes (catalysts) involved.
Chemistry C483
Fall 2009
Prof Jill Paterson
7-1
• Notice that we lose the negative charge on the a carboxylate and a positive charge on an amino group.
• This loss is why the pKa of an amino acid side chain is different when part of a protein as compared to a
free amino acid.
- the COO- is no longer ___________
- the NH3+ is no longer ____________
- therefore their interactions with e- are much weaker
- if there are other side chains close by, they can exert effects on each other
• Notice that the backbone of the protein is still zwitterionic (+1 & -1)
• Thus, the overall solubility, ionic properties, rxn capabilities, basic chemistry of the protein stem
Proteins play many roles in the cell
1.
Enzymes (biological catalysts)
2.
Involved in storage and transport
3.
Structural proteins: provide support/shape
4.
Allow for movement : muscle contraction
5.
Decoders of DNA
6.
Regulators (hormones)
7.
Defense (antibodies)
reactant
(substrate)
enzyme
A
B
A
B
enzyme
enzyme
Enzyme stays same! Does not change- is not used in the reaction
substrate binds and is released from an “active site”
Chemistry C483
Fall 2009
Prof Jill Paterson
7-2
Refer to Table 3.4
How do proteins serve such distinct and various roles?
Each protein specifically (and strictly) recognizes its substrate, partner(s) protein, or DNA.
What allows for this exact recognition?
There are four levels of protein structure:
Primary (1⁰): Linear sequence of amino acids
Secondary (2 ⁰): Localized 3-D structure of the peptide backbone
Tertiary (3⁰): Arrangement of secondary structure, side chains, and prosthetic groups (metals, heme)
Quaternary (4⁰): Arrangements of multiple proteins to form complexes
• The order in which amino acids are linked together is called the primary (1⁰) structure.
• Because the chemistry of a protein is determined by its side chains, the 1⁰ structure sets the chemical
properties of the protein.
• When amino acids are linked together, it is called a peptide.
• Have a few specialized names to tell us the length of the peptide:
Name
# of aa
# of peptide bonds
Dipeptide
Tripeptide
Oligopeptide
Polypeptide
Chemistry C483
Fall 2009
Prof Jill Paterson
7-3
Proteins usually have > 20 amino acids.
When referring to the size of a protein we might state this as the number of amino acids, however it is more
common to talk in terms of molecular weight.
As we have already discussed, in biochemistry we use the unit of Dalton to represent g/mol.
1 Da =
Because proteins are quite large, you will usually discuss protein size in terms of kiloDaltons:
1 kDa =
Let’s look at a peptide:
We usually write the peptide as the 3 or 1 letter code:
Met-Tyr-Ile-Asn-Asp-Ile-Ala-Asn-Ala
or
The N-terminus is always to the left, the C-terminus is always to the right
N’-Met-Tyr-Ile-Asn-Asp-Ile-Ala-Asn-Ala-C’
or
There is a peptide bond between each amino acid.
All proteins start with the amino acid Methionine.
(although this can be removed later)
How do you calculate the pI of a peptide?
1.
First we will assume the pKas of each amino acid side chain are the same in the peptide, as
when they are free amino acids.
2.
Next, we determine the charge on the peptide at various pHs
3.
When we determine the ~pH the molecule is neutral, we then take the average of the pKa
below this, and the pKa above this.
Chemistry C483
Fall 2009
Prof Jill Paterson
7-4
So, for the peptide :
MYINDIANA
1.
What are the ionizable groups?
2.
What are the pKas for each group? (Assume the pKa in the peptide is the same for the free acid).
3.
What is the overall charge on the molecule at pH 1?
4.
What is the overall charge of the molecule at pH 2?
5.
etc….
6.
At what pH is the molecule neutral?
7.
What is the approximate pI of this peptide?
8. How close is this to the actual pI? (3.1)
http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-propertycalculator.asp
9. Is this peptide considered basic or acidic?
Chemistry C483
Fall 2009
Prof Jill Paterson
7-5
N-EAEDLQVGQV ELGGGPGAGS LQPLALEGSL Q-C
H-Tyr-Gly-Gly-Phe-Met-Thr-Ser-Glu-Lys-Ser-Gln-Thr-Pro-Leu-Val-Thr-OH
H-Tyr-Gly-Gly-Phe-Met-Thr-Ser-Glu-Lys-Ser-Gln-Thr-Pro-Leu-Val-Thr-Leu-OH,
Tyr-Gly-Gly-Phe-Met
Tyr-Gly-Gly-Phe-Leu.
(Glu-Trp-Pro-Arg-Pro-Gln-Ile-Pro-Pro)
Chemistry C483
Fall 2009
Prof Jill Paterson
7-6