From the Exam 1 Study Guide:
Protein 3-D Structure, cont.
Globular Proteins, cont. :
- Hierarchy of Protein Folding Description, cont.
- Tertiary: Steric relations of residues distant in the primary structure (interactions largely due to side-chain interactions).
- Super secondary structures (motifs and folds)
- list common motifs we've looked at/are in your text
- list common folds we've looked at/are in your text
- Hinges and domains.
- Domain types: all alpha, alpha/beta, alpha+ beta, random. Note that domain types are sometimes named on the basis of the core fold.
- Split active sites
- What are the characteristics of each level
- Steric relations of residues
- Charecteristic bonding types.
- Protein 3-D Structure is largely determined and maintained by Weak "bonds"
- hydrophobic forces
- hydrogen bonds
- ion pairs = salt linkages
- why are these bonds weak?
- van der Waal's bonds
- Which are the most important at each level?
- Cooperativity effects in bonding.
- The effect of the aqueous environment on bond strength.
Secondary Protein Structure
- Based on Steric relations of residues nearby in Primary structure
- "Recognized" stuctural elements are periodic and H-bond stabilized
- Periodic peptide structures:
- alpha & beta (be able to describe these structures).
- What are some propertiesof alpha & beta structures?
- How are they stabilized?
- Why are they so common? (ease of nucleation).
- What aa's or strings of aa's may disrupt them?
- Remember there are two beta structures. beta-turn.
- Note that periodic secondary structures are stabilized, and in part specified, by H-bonding.
- Are these the only periodic structures found in proteins?
- The only extensive ones?
- The only extensive ones in globular proteins?
Disulfide bonds - when are they formed, what are they
good for, do they help in folding (as process - no), extra - vs.
Supersecondary Structure/ Motifs.
- What is the difference between a fold and a motif?
- What are some common motifs we've looked at/are in your text?
- What are some common folds we've looked at/are in your text?
Domains. Give examples to illustrate
- Hinges and domains.
- Binding site/active sites are often split between domains.
- Domain types (e.g. all alpha, alpha/beta, alpha+ beta, random)
- What's the difference between a domain type and a motif?
Or is there one? Do the definitions overlap?
- Domains, split active sites, genes and adaptation
- example of antibodies:
- What is IgG
- How many chains does it have?
- Does it represent a tertiary or quaternary structure? Defend
- How many domains ?
- How are the domains related?
- How do we believe the domains arose?
- Where are the active sites?
- Assume your genome codes for 100 light chains and 100 heavy
chains. How many different IgG molecules can you make?
- IgG has been touted as a model for the evolution of advanced
proteins in eukaryotes. Explain.
Be able to discuss a protein's structure in terms of hierachical
levels and functional units/segments.
Structural Proteins: What's special about collagen:
- The collagen triple helix
- Sequence (periodicity of primary structure)
- Why so many gly?
- Why pro?
Supramolecular Structures: Why quaternary structure?
List and explain advantages.
- How does it occur?
- why do proteins often agregate/precipitate with heat?
- Chemical agents
- Be able to discuss urea as a denaturant. Why does it work
- When is a disulfide reducing reagent needed? Why only for
- Generally the lowest global G
is not attained in folding proteins.
- What is argument for this statement?
© R. A. Paselk 2010;
Last modified 23 February 2011