(Dr. Choy) (Unit A) Topic Note 3 Flashcards
What are amino acids connected to each other by?
Peptide bonds
Where is a peptide bond formed?
Between:
1. a-amino group of one amino acid
2. a-carboxyl group of another amino acid
What type of reaction forms a peptide bond?
Condensation reaction
How are peptides written conventionally?
Starting from the N-Terminus
What is the “backbone”?
NCC-NCC-NCC-NCC…
Is a peptide bond a single bond?
Peptide bonds actually have some characteristics of double bonds
* Due to resonance
* Makes bonds unrotateable
Primary Structure
The sequence of residues making up the protein
What bonds do primary structures involve?
Covalent bonds
What is the average molecular weight of a residue?
110 Daltons
Secondary Structure
Local folding pattern of the polypeptide backbone
What forces are present in secondary structure?
Hydrogen Bonds
What are the most common secondary structures?
a-Helices
b-Sheets
In an a-helix, how are the hydrogen bonds formed?
Each carbonyl is linked to a N-H located 4 residues further on in the sequence within the same chain
What are the dimensions of an alpha helix?
- 3.6 residues per turn
- 0.54 nm per turn
Where do side chains go in a alpha helix?
Project outward
What determines whether a sequence will fold into a specific secondary structure?
- Steric hindrance between nearby large side chains
- Charge repulsion between nearby similarly-charged side chains
- Presence of proline and glycine
Why will proline and glycine prevent alpha helix and beta sheet formation?
- Proline: Forms ring, creates no H-bond, cannot fit into alpha helix
- Glycine: Small, imparts flexibility and disrupt structures
Tertiary structure
How regions of secondary structure fold together to form 3D arrangement of single polypeptide chain
Tertiary structures result from interactions between what?
- Side chains
- Between side chains and polypeptide backbone (often distant)
What forces are present in tertiary structure?
All 4 “weak forces”
Do polypeptide chains contain both hydrophobic and hydrophilic residues?
Yes
When are proteins most stable?
When hydrophobic parts are buried in the core
What forces can contribute to tertiary structure?
- Hydrophobic effect
- Ionic bonds between side chains
- Hydrogen bonds
- van der Waals forces
- Disulfide bonds
Where do disulfide bonds form?
Between cysteine residues
What proteins have disulfide bonds? Why?
Only important in non-cytoplasmic proteins
* Enzymes are present in cytoplasm to remove disulfide bonds
What is a domain of a protein?
An independently folded part of a protein that folds into a stable structure
How many domains can proteins have?
- One single
- Multiple
What kind of unit are domains?
Structural units and/or Functional units
Quaternary structure
The number and arrangement of the individual polypeptide chains
In a quaternary structure, what is each polypeptide known as?
Subunit of the protein
What is native state?
A folded, biologically-active protein, generally though to be the conformation with least free energy
How can proteins be unfolded?
Treatments with solvents that disrupt weak bonds
How does high concentrations of urea or guanidine cause unfolding?
Disrupt hydrophobic effects and interfere with hydrogen bonding
Besides solvents, what else can cause protein denaturing?
Extreme pH and Heat
Renaturation
Proteins refolding and regaining activity
Is renaturing easy for proteins? What can help?
No, renaturing is hard for some proteins
“Molecular chaperones” assist in protein folding
How are chaperones thought to work?
Masking the exposed hydrohpobic regions to prevent aggregation during the multi-step folding process
Lipoproteins
Proteins that combine tightly with lipids
Metalloproteins
Proteins that combine tightly with metal ions
Glycoproteins
Proteins are modified by the attachment of carbohydrates
Why is obtaining a pure protein challenging?
There are thousands of proteins inside a cell as well as nucleic acids, lipids, and carbohydrates
