Chapter 4 Flashcards
What are the 7 psychological roles of proteins?
- Enzymes
- Storage and transport
- Physical cell support and shape
- Mechanical movement
- Deciding cell information
- Hormones and/or hormone receptors
- Other specialized functions
Roughly how many proteins do humans have?
~25 000 unique proteins
What is the smallest and largest proteins in length?
What’s the formula for finding the number of amino acids in a formula?
Insulin- 51 amino acids
Titin- 34 350 amino acids
An approximation by dividing the proteins molecular weight by 110
What are the most important forces stabilizing the specific structures of proteins?
Non-covalent forces
What does a protein conformation with a low free energy mean?
Means it has a bigger number of weak interactions
How is the stability of a protein determined?
It is the difference in the free energies of the folded and unfolded states
Folded proteins occupy a low energy state
What is denaturation?
Disruption of native conformation with loss of activity
(Reversible process)
Renaturation
Fast process (sigmoidal curve)
What is the primary structure, secondary structure, tertiary structure and quaternary structure summed up?
Primary structure- linear sequence of amino acids
Secondary structure- localized interactions within a polypeptide
Tertiary structure- final folding pattern of a single polypeptide
Quaternary structure- folding patter with multiple polypeptides
How is the primary structure of proteins written out?
The one letter code of amino acids
Ex: NCCNCC
What are the two types of secondary structure?
α-helicies- loops (like handwritten l)
β-sheets- rolled over each other (like a drifty mountain road)
What are the two things the folding pattern must do to represent a viable form of secondary structure?
- Optimize the hydrogen bonding potential of main chain carbonyl and anode groups (anything that can must form hydrogen bond)
- Represent a favoured conformation of the polypeptide chain
What are the hydrogen bond donors and acceptors on a polypeptide main chain?
O-C acceptor
N-H donor
The carbon of oxygen and the hydrogen of nitrogen are in opposite sides of each other
(Therefor the side chain of amino acids will rotate sides of the main polypeptide chain)
What is native conformation?
The biologically active form of a protein
Can there be rotation around the C-N bond in polypeptides?
No it is restricted due to partial double bond nature of the peptide bond
What does cis and trans mean?
Cis- the carbon of oxygen and the hydrogen of nitrogen are on the same side so the side chains would be on the same side
Trans- the carbon of oxygen and the hydrogen of nitrogen are on opposite sides so the side chains rotate sides every connection
What is a α-carbon?
What are he two types of bonds?
Means a carbon held within the main chain by single bonds (means freedom of rotation)
Phi (Φ) Cα-N
Psi (Ψ) Cα-C
Both can range from -180 to 180 rotation but interference prevents it
What is a ramachadran plot?
Illustrates all possible combinations of phi and psi and highlights combinations that are observed in actual proteins
Areas that are white are known as the disallowed region
What is a α-helix? (Direction, etc)
Right handed helix (right hand fingers curl around thumb direction) 🔄
3.6 residues per turn (residues separates by 3-4 positions in primary structure are close in helical structure)
Each C=O (residue n) forms hydrogen bond with snide hydrogen of residue n+4 (bends around)
Diagram on α-helix slide
What are the rules/trends with the helicies of proline and glycine?
Proline- because of its rigidity it is a helix breaker and is not usually found in α-helicies
Glycine- because of its flexibility it is uncommon in α-helicies
What is the helix dipole?
A small electrical dipole that exists in each peptide bond that is communicated through the helix by hydrogen bonding
An uneven distribution of charge that results in the helix having a net dipole (N terminus has partial positive charge while C terminus has partial negative charge)
What are β-sheets?
They involve multiple β strands arranged side by side
The strands can be parallel (strands run in same direction) or anti-parallel (strands run in opposite direction)
Anti parallel are more stable (better geometry of hydrogen bonding)
Look at diagram on parallel and anti parallel slide
What does amphipathic β sheets mean?
Alternate polar, non polar, polar, non polar, etc
The side chains are in trans alternating above and below the polypeptide chain
What ultimately determines tertiary structure?
The amino acids sequence creates the final folding pattern which results in unique functions
What are quaternary structures composed of?
Multiple subunits in which each subunit is a separate polypeptide chain (can be multiple units of the same polypeptide or different ones)
What are the biological advantages associated with quaternary structure?
- may help stabilize subunits and prolong life of protein
- helps facilitate unique and dynamic combos of structure function
What is keratin?
Principle component of hair that contains a pseudo-seven repeat
(Diagram on keratin slide)
Keratin forms right handed amphipathic α-helicies (results in hydrophobic strip running across length
What is the quaternary structure of keratin?
Hydrophobic surfaces and each two helicies interact and form a coiled coil where right handed helicies wrap around each other in a left handed fashion
(Very strong because of this)
Disulfide bonds like individual units
What is collagen?
Major part of vertebrates that are multiple repeats of Gly-X-Y which forms left handed helix ↩️ of 3 residues per turn
The quaternary structure has left handed helicies wrapping in a right- handed fashion
What diseases related to collagen and lack of vitamin C?
Scurvy
Why is silk so strong and flexible?
It has fully extended polypeptide chains for strength, has an association of strands by hydrogen bonding, and has an association of sheets by van der waals and hydrophobic interactions
What are disease specific prion vaccines?
Diseases caused when a protein unfolds and new regions are exposed for antibody binding
Also called disease-specific epitopes (DSEs)
