Chapter 4.2 Starting at Helices
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In an alpha helix, the N-H is hydrogen bonded to C=O how many amino acids down?
How are alpha helices formed?
A complete righ-handed turn is every how many amino acids?
Beta sheets are arranged antiparallel with hydrogen bonding where and in adjacent what?
Four amino acids away.
By having similar subunits next to one another about the same repeated relationship.
Between peptide bonds in adjacent strands (antiparallel).
Short regions of alpha helix are especially abundant in proteins that are embedded in what? What is an example?
Membrane proteins cross the lipid bilayer usually form what?
Is the polypeptide backbone hydrophilic or phobic?
Properties of polypeptide backbone in the alpha helix. How does the backbone hide itself from the lipids?
Sometimes two alpha helices will wrap around one another to form a particularly stable structure known as a _________.
Cell membrane, transport proteins and receptors.
Alpha helix that is composed of amino acids with nonpolar side chains.
The polypeptide backbone hydrogen-bonded to itself shielding itself from the lipid environment also by having the nonpolar amino acids protruding.
How do coiled-coils form?
Are they the ones that form the structures for long elongated proteins such as intracellular fibers such as myosin, motor protein in muscle contraction?
The alpha helices have most of their nonpolar side chains on one side, so they twist around each other with the side chains facing inward avoiding cytosol.
What is the protein that contains many Beta pleated sheets?
What is the bond type between the peptide bonds?
What kind of structure do they produce?
Where in the protein do they form?
What do the beta pleated sheets permit the formation of? What are they and why are they so strong?
Hydrogen bond between the neighboring segments.
A rigid, pleated structure.
- In the core.
- Amyloid fibers, protein aggregates that are in neurodegenerative diseases, the stabilized beta sheets stack together tightly like zipper teeth.
The full, three-dimensional conformation formed by an entire polypeptide chain- including the sheets, coils, and helices between the n and c-termini-is sometimes referred to as the __________ structure. If the protein molecule is formed as a complex of more than one polypeptide chain, then the complete structure is a _____________ structure.
_____________ is defined as any segment of a polypeptide chain that can fold independently into a compact and stable structure.
What do they serve as from which many larger proteins are constructed from?
How many amino acids are they between?
Tertiary structure, quatrinary structure.
40-350 amino acids long.
___________ are often found as short (unstructured) stretches linking domains in otherwise highly ordered proteins.
Intrinsically disordered sequences.
- 1. Unstructured lengths.
- 2. Lack any definite structure allowing for bending and flexing due to thermal buffeting.
- 3. Link domains in otherwise highly ordered proteins.
- 4. Able to wrap like a scarf around other protein with high specificity and low affinity (binding)
- 5. Tethers between the compact domains in a protein (provide flexibility)
- 6. Help scaffold proteins bring together other proteins in an intracellular signaling pathway.
- 7. Give elastin the ability to form rubberlike fibers, allowing tendons to stretch back.
What are the constraints to the size of polypeptide chain?
1. Biological functions depend on proteins with stable, well-defined 3d conformations.
2. Functional groups need to be "well-behaved" not associating with other insoluble proteins aggregates.
We know that evolved stable conformations occurred quite often during evolution, because many present-day proteins can be grouped into ____________________ familes, in which each family member has an amino acid sequence and three-dimensional conformation that closely resemble those of the other family members.
Give an example of two proteases, serine family.
- 1. Chymotripsin.
- 2. Elastase.
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