Ch. 4 Protein Structure Flashcards
What is protein primary structure?
The sequence of amino acids.
How are amino acids grouped?
Amino acids are grouped by chemical properties.
What are nonpolar amino acids involved in?
Nonpolar amino acids are involved in hydrophobic interactions.
What are polar and charged amino acids involved in?
Polar and charged amino acids are involved in forming hydrogen and ionic bonds.
How are amino acids linked?
peptide bonds
What do the C-C-N-C peptide bonds of the backbone lead to?
These connections lead to these atoms and bonds being on the same plane (trans isomer) instead of being on different planes (cis isomer).
What does the trans orientation and size of R groups lead to?
They generally restrict bond rotation and can affect polypeptide conformations because larger R groups have more steric hinderance.
How do primary structure and evolution connect?
Amino acids important for protein function will be conserved over time, but those that are less important can change.
How can ancestry be determined by primary structure?
By comparing protein sequences to each other, a relative ancestry can be determined based on the number of amino acid changes in common proteins.
Why is the analysis of protein primary structure for evolution more reliable than analysis of DNA?
Proteins have 20 amino acids while DNA has 4 nucleotides.
What is protein secondary structure?
The common formations of polypeptides that mostly result from H-bonds in the backbone. ⍺ helices and β sheets.
Is the portion of a polypeptide that forms helices and sheets constant among all polypeptides?
No. The portion of a polypeptide that forms helices and sheets varies between peptides. Some only have helices, some only have sheets, and some have a mixture.
What is a loop/turn?
The portion of a polypeptide NOT involve in a helix or sheet conformation.
What is protein tertiary structure?
The 3D structure of a polypeptide including ALL secondary structures.
What is protein quaternary structure?
The structure achieved when multiple polypeptides interact.
What is supersecondary structure?
Complex combinations of secondary structures; “2.5 structure”.
What are a few examples of supersecondary structure?
helix-turn-helix
beta barrel (aquaporins)
coiled-coil motif
What are the categories of quaternary structure (4)?
There are simple and complex quaternary structures.
Homooligomers are two+ identical subunits.
Heterooligomers are two+ non-identical subunits.
What are intrinsically unstructured proteins?
Polypeptides that don’t have tertiary structure; lots of structural flexibility of one gene product (one gene, multiple functions).
What are intrinsically unstructured proteins capable of doing?
They can bind several sites and patterns, and they can be used in different pathways.
What are the two models for protein folding?
The Hierarchal Model and the Molten Globule Model.
Is it one or the other when it comes to protein folding models?
No. Both can occur for a single protein.
What is the hierarchal model?
Regions of secondary structure form first, followed by interactions between secondary structures unitl the entire peptide is folded.
What is the molten globule model?
Hydrophobic residues group together and achieve a partially ordered state while H-bonds form between polar residues until a native shape is achieved.
