Lecture 8: Proteins II Flashcards
Proteins II
What stabilizes α and β secondary structures of proteins?
Hydrogen Bonding
What is irregular arrangement of the polypeptide chain termed?
Random Coil
What three factors affect the α-helix? Where are the R-groups located?
- Hydrogen bonds between amide and carbonyl groups of amino acids 2. Proline causes disruptions 3. Bulky or Like Charged Amino Acids in proximity R-groups are located on the exterior of the helix
L-Amino Acids result in what type of α-helix?
Right Handed Helices
D-Amino Acids result in what type of α-helix?
Left Handed Helices
What types of amino acids are strong helix formers?
Small, hydrophobic R-groups, such as Alanine and Leucine
What two Amino Acids act as helix breakers?
Proline due to bond angles, and Glycine due to small size
What are the forms of β-Pleated Sheets? Which is stronger and why?
Parallel and Antiparallel Antiparallel is stronger due to linear hydrogen bonds
What is the orientation of hydrogen bonds in α-helices and β-pleated sheets?
α-helices: parallel to the backbone β-pleated sheets: perpendicular to the backbone
Which will be longer with same amount of AA residues–α-helices or β-pleated sheets? Why?
β-pleated sheets, almost fully extended, whereas α-helices are coiled
What two AA’s play a role in β-turns? What types of turns do these cause? (answer)
Proline (Type I), Glycine (Type II)
What configuration are most peptide bonds NOT involving Pro?
Trans (>99.9%)
What is required for Proline isomerization? Why are these clinically relevant?
proline-cis, trans-isomerases Cyclophilins participate in protein folding of viral invaders
What type of folding requires NAD+-dependent Dehydrogenases?
What binding domain does this include?
Rossman Fold
Nucleotide binding domain
What is the Φ angle around the α-carbon?
What is the Ψ angle around the α-carbon?
What are these in a fully extended polypeptide?
α-carbon - amide nitrogen bond
α-carbon - carbonyl carbon bond
180o
What type of diagram can predict protein secondary structure bond angles?
Ramachandran Diagram
What interactions stabilize protein tertiary and quartenary structure?
Hydrophobic/Hydrophilic (Van der Waals)
Ionic (salt bridges)
Hydrogen Bonds
Disulfide Bonds
What are the two first important steps of X-Ray Crystallography?
What does the 2nd step lead to?
- Purify Protein (95-100%)
- Crystallize the Protein
Leads to static representation of the sample
What are pros and cons of X-Ray Crystallography?
Pros: No size limits, well established
Cons: Difficult for membrane proteins, can’t see hydrogens
What are the pros and cons of NMR for proteins?
Pros: No need to crystallize (visualize dynamic structure), can see hydrogens
Cons: Difficult for insoluble proteins, works best with small proteins
What often regulates Quaternary protein structures?
oligomers
What is difference between monomeric and dimeric proteins?
What is difference between homodimers and heterodimers?
Mono is single protein, dimeric is non-covalent forces holding two chains
Homodimers are same chain, hetero are different
What structure do proteins emerge from and begin folding?
Ribosome
What enzymes are involved in formation of β-turns upon initial folding?
Proline cis-trans isomerases
