Biochemistry Lecture 3 -
By the end of today you will:
1. Be able to calculate net charge of an amino acid with an uncharged side chain.
2. Describe the characteristics of a beta sheet.
3. Define and describe tertiary and quaternary structure.
4. Be able to describe a protein domain’s characteris9cs.
5. Understand the molecular structure of disulfide bonds.
6. Learn how proteins fold and how they become unfolded.
7. Understand the concept of protein families.
Amino acid charge problem: alanine
Q. What is the net charge of alanine(only has amino and carboxyl group) at pH 5?
Given: pKa of α-amino group = 10.0
pKa of α-carboxyl group = 2.0
*We will work this out in class together.
Do it separately then combine
Alpha- Amino group
NH3+: NH2 is 10^5 :1
Assume 100% NH3+
Therefore, a charge on a alpha-amino group is +1(1)=1
Alpha- Carboxyl Group
COOH:COO- is 1:10^3
Assume 100% COO-
Therefore, charge on alpha-carboxyl group is -1(1)=-1
Therefore, charge net charge on amino acid is (+1) + (-1)=0
2° structure: Beta sheets
Hydrogen bonds occur between the backbone of two or more polypeptide chains arranged
adjacently and in parallel
Side chains project alternately up and down
1 “pleated sheet”
2 Beta sheet (movie)
Anti-parallel form (C-terminus lined up with N-terminus, N with C )
Parallel Beta pleated sheet C-terminus lined up with C, N lines up with N
Hydrogen bonding between these makes the folds in the beta sheet
2 structure, Summary
Silk fibroin (extremely strong material) consists mostly of β-sheets.
Most proteins have both α-helices and β-sheets, plus turns and other less regular structure.
Primary sequence determines type of structure formed.
Human cystatin C Biomarker of kidney function
3 Tertiary Structure
Concerns the 3D arrangement of the polypeptode chain
Stabilized by bonds between side chains or side chains to
Interactions between residues distant
Gives overall shape of protein
“Birds of a feather flock together...”
_Hydrophobic interactions most important
“The tendency of hydrocarbons to form intermolecular aggregates in an aqueous medium”
o Something hydrophobic in aqueous medium have tendency to flock together
Hydrophobic side chains 'hidden' from water - Cluster together; exclude water from
This causes Charged side chains (which are hydrophilic) are mainly exterior
Long extended polypeptide sequence (filled balls are hydrophobic residues) all these
aggregate together (form in the center) hydrophilic(not filled balls) stay on the outside
Hydrophobic interactions continued
4 Cannabinoid Receptors
There is a couple of these receptors and any cannabis plant has many of them
The receptor is made primarily of alpha helices and what binds to this receptor (ligand) is
Primary sequence of receptor
Plasma membrane interior is hydrophobic and thus in this AA sequence, hydrophobic
residues stick to hydrophobic regions which is the plasma membrane
Hydrophilic residues go to hydrophilic region
Hydrophillicity and hydrophobicity This therefore has impact on function and structure of
3 structure is stabilized by multiple weak bonds and a very important covalent bond!
5 Weak forces (other than hydrophobic interactions):
- Hydrogen bonds
- Van der Waals forces
- Ionic bonds
However, one type of covalent bond
- Disulfide bond
o Between cysteine residues in distant parts of the protein
o Only form in oxidizing environments
“weak” bonds -- Panel 2-7
Hydrogen bonds can form in many different places!
Disulfide bonds formation depends on state of oxidation and also on the fact they these bonds can
Formed between two separate polypeptides or within one polypeptide
Forms intrachain disulfide bond in oxidized state which holds tertiary structure together
3 structure: Domains
Domain is distinct region of protein that can fold independently of other regions
- A critical concept for larger proteins
- Definition: distinct region of a protein
o Domain often can fold independently
o Domains provide structure and/or function
- Many proteins made up of connected domains
- Related domains of