Lecture 2 Flashcards
Classification of proteins by: 1) 2) 3) 4)
1) Location in an organism - intra/ extracellular.
2) By function - structural/ biological active
3) By shape - fibrous/ globular
4) By chemical composition - simple/ complex
Classification of proteins according to their 3D structure
1) Globular proteins: spheroidal shape, both secondary structures are abundant.
2) Fibrous proteins: rod-like shape, one secondary structure predominates.
Conjugated protein
3 examples
It is a protein that functions in interaction with other chemical groups, attached by covalent bond or weak interactions.
- Lipoproteins + lipids
- Glycoproteins + carbohydrates
- Phosphoproteins + phosphate groups
Peptide bond formation
- Dehydration synthesis.
- Required the input of energy.
-Carboxyl group of one amino acids, reacts with the amino group of another amino acid, releasing a water molecule.
Peptide bond characteristics (4)
-KNOW THE STRUCTURE OF A PEPTIDE BOND
- Partial double bond character.
- Trans configuration (more stable)
- Uncharged, but polar.
- Planar
Structure of a simple peptide
Amino- end: left side (usually, look where is it)
Carboxyl end: right side.
Peptide bonds (o=c-n-h) in between amino acids.
Primary structure of proteins (3)
- Order of amino acids.
- Stabilized by peptide bonds.
- Reads from N- to C- end.
Secondary structure of proteins (3)
- Spatial arrangement of the polypeptide chain by rotation of the planar peptide bonds around the alpha carbon.
- Stabilized by hydrogen bonds.
- It can be a-helix or B- helix.
α – helix structure (6)
- Backbone is formed by hydrogen bonds.
- Bond between the carbonyl oxygen and the amide hydrogen of an amino acid residue located 4 residues further down the chain.
- Right- handed helix.
- Peptide bond planes are parallel to the axis of the helix.
- Stabilized by hydrogen bonds.
- R-groups are perpendicular.
β-sheet (3)
- Hydrogen bonds occurs between regions of separate neighboring polypeptide strands aligned parallel to each other.
- It can be parallel or anti parallel.
- R- are placed above or below the plane of the sheet.
β-bend (reverse or β-turn) (5)
- Reverse the direction of the polypeptide chain.
- Helps it to form a compact, globular shape.
- Often connect successive strands of anti parallel sheets.
- Hydrogen bond stabilizes it.
- Are found on the surface of the polypeptide.
Non-repetitive secondary structure (3)
- Loop or coil formation.
- Less regular than α- or β-.
- 1/2 of a protein molecule exist in it.
Motifs (3)
- Structural characteristics.
- Super-secondary structure.
- Do not allow us to predict the biological functions.
Tertiary structure of proteins
-Spatial arrangement of the secondary structures.
-Stabilized by interaction between side chains, it can be:
1- Hydrogen bonds (polar and hydrophilic side chains).
2- Hydrophobic (predominant).
3-Disulfide bonds (oxidizing conditions).
4- Ionic (two oppositely charged side chains).
Domain
- Functional and 3- dimensional structural units.
- Different domains have different functions.
- Can be independently stable and folded.
Quaternary structure of proteins (3)
- Oligomeric structure of a protein.
- Composed of 2 OR MORE SUBUNITS.
- Stabilized by non- covalent interactions and disulfide bonds.
Folding - a stepwise process
- Interactions between AA side chains determine how long a polypeptide chain folds.
- Secondary structures form first.
- Ionic interactions play an important role.
- Process continues until complete domains form and the entire polypeptide is folded.
- Fully folded (native) form = low energy state.
Assisted folding
- Information needed for correct protein folding is contained in…
- A protein begins to fold in stages during….
- Definition of Chaperones
- the primary structure of the polypeptide.
- its synthesis.
- A specialized group of proteins required for the proper folding of many proteins.
Example of molecular chaperones
- Hsp70: present in cell with elevated temperature, it binds to regions rich in hydrophobic residues. Prevent inappropriate aggregation.
- Chaperonins: serve as a template for the folding process.
Examples of diseases caused by protein misfolding
- Alzheimer’s disease.
- Type 2 diabetes.
- Parkinson’s disease.
Systemic amyloidosis
- Primary systemic amyloidosis.
- Secondary systemic amyloidosis.
Soluble proteins that are secreted from the cell in a misfolded state and converted to amyloid fiber (insoluble)
- Misfolded immunoglobin.
- Increase in secretion of amyloid A protein.
Prion disease
- Transmissible spongiform encephalopathies.
- Fatal neurodegenerative.
- Result from the deposition of insoluble protein aggregates in neural cells.
Prion disease
- Infectious protein form.
- Non- infectious protein form.
- PrPSc - form insoluble aggregates of fibrils, greater amount of B- sheets, highly resistant to proteolytic degradation.
- PrP - normal proteins, greater amount of alpha helices.
Prion disease
-Key to becoming infectious lies in…
Changes in the 3-dimensional conformation.
