Week 1: Primary Level of Protein Structure Flashcards
What are the pKas of COOH and amino groups?
2 and 10
What is a zwitterion?
At neutral pH the carboxylic acid will be deprotonated and amino group will be protonated
What hybridization is the alpha carbon for all amino acids? What geometry?
sp3, tetrahedral geometry
Which form do all amino acids exist in body? What are the 2 consequences of this?
L. 1) surface of any protein is asymmetric - basis for highly specific molecular recognition of binding targets. 2)promotes formation of secondary structures.
Which two amino acids have an additional stereocenter at the beta carbon?
Isoleucine and threonine
What is a peptide bond?
Amino acids link together via amide bonds between the alpha carboxylic acid group on one and alpha-amino group on another - peptide bond and products are peptides.
Which end are amino acids added to?
C-terminal
What is a portion of an amino acid without water? What suffix do they get?
Amino acid residue, gets suffix -yl.
What does the partial double bond character of peptide bonds mean? (see images)
Peptide bonds have partial double bond character: there is no free rotation about the peptide bond (w), the two alpha carbons are usually trans and the six backbone atoms (C, C, C, O, N, H are coplanar). Rotations around the phi and psi are possible but may be sterically hindered by side chain steric clash.
Most possible angles of phi and psi are impossible due to the clashes.
How do you find what combinations of psi and phi are allowed? (see images)
- Hold psi at fixed angle. 2. rotate phi through given angle. If steric clash occurs, this combination is not allowed. 3. Rotate phi a bit more, repeat step 2. 4. Change the angle of psi and repeat 2-4.
What is a Ramachandran plot? See images
map of all theoretically possible combinations of phi and psi angles on which are in yellow - those combinations that are sterically permitted and green, those actually found in proteins.
Where are psi and phi found?
Psi - between alpha carbon and carboxyl carbon
Phi - between alpha carbon and amide.
What two conformations can peptide bonds be? Which is favoured? When is the other favoured instead?
Can be trans or cis. Trans is favored because R groups on adjacent alpha carbons can interfere in cis. Except in sequence X-Pro where cis is sometimes favoured.
Describe the resonance hybrids of peptide bonds. (see images)
Double bond on oxygen, or double bond with nitrogen.
What is an oligopeptide?
Chains with only a few amino acid residues
What is a polypeptide?
Chains with 15-20 residues
What is a protein?
Chain greater than 50 residues
Are the amino and carboxylic acid ends reactive in oligopeptides and polypeps?
Most are unreacted with exception of rings.
How do you write polypeptide sequences?
N-terminus -> C-terminus
What is a conservative mutation to a protein? Non-conservative?
Conservative - conserve chemical properties and/or size of chain or nonconservative.
What did Pauling and Corey discover?
Linus Pauling and R.B Corey, understanding of hydrogen bond and knowledge of amino acid structures led to their prediction as the alpha helix and beta sheet as underlying structural elements of proteins.
What is an alpha helix? How many residues per turn? What is translation per residue? What is the helix pitch?
H-bonds are co-linear with chain direction, they form between residue n and n+4. Residue n provides backbone (C=O - h bond acceptor) and residue n+4 provides backbone N-H (h-bond donor).
Are 3.6 residues per turn. The translation is 1.5 amperes per residue. Helix pitch = 5.4 amperes per turn
What is beta sheet? Describe parallel vs. antiparallel
Each strand is nearly flat, each residue is flipped by 180 degrees relative to neighbour. Backbone H-bonds are at nearly right angles to chain direction. Always has 2+ strands.
Parallel strands have flatter extended sheets and antiparallel have a slight twist and can form barrel-like structures.
What polypeptide starts translation?
N-formylmethionine (prokaryotes and eukaryotic organelles) and methionine (in eukaryotes) at N-terminal position.
What are the stop codons?
UGA, UAA, UAG
What is the start codon?
AUG
What is sequence identity and similarity?
distinguish sequence identity from sequence similarity - match amino acids. Sequence similarity is based on finding best alignment of sequences compared. Can score high, medium or low.
What does it mean if two aligned protein sequence share at least 25% amino acid sequence?
They will have similar structure and likely function.
What does it mean if protein sequences are homologous?
Protein sequences are homologous were any sequence similarity is though to be result of common evolutionary ancestry. Greater degree of protein sequence similarity = closer evolutionary relationship.
What can be determined when several homologous protein sequences are aligned?
Consensus sequence, can be represented by sequence logo to show degree of amino acid conservation.
