Chapter 4 Lecture Videos Flashcards
What are the four most common types of secondary structure?
alpha helices, beta conformation, beta turns, random coil
Random coils
don’t have repeating bond angles, but are not necessarily “unstructured”
Secondary Structure
describes the spatial arrangement of backbone atoms (everything but side chains) in a specific segment of a polypeptide chain (adjacent to each other)
Stability of alpha helices conformation?
most stable conformation for a polypeptide chain
What hold together alpha helices?
-held together by hydrogen bonds between carbonyl oxygen and amino hydrogen
- successive h-bonds between n and n+4 residues stabilize the alpha helix
Structure of alpha helices?
- one turn of helix = 3.6 residues
- condensed structure (tightly packed)
- no space down center, side chains project outwards
How do side chains affect the stability of an alpha helix?
They can stabilize or destabilize the helix
- alanine is ideal for alpha helices
- proline (too restricted) and glycine (too flexible) are bad for alpha helices
How can we stabilize the ends of helices where there are fewer hydrogen bonds?
- helices have overall polarity bc n-term is positive and c-term is negative
- negative charges are found @ n-term and positive charged residues are found @ c-term
Structure of beta conformation?
more extended and takes on a zigzag shape
- side chains project above and below the plane of the backbone
What contains all the “information” necessary to dictate the protein’s final structure?
the polypeptide sequence
What does protein stability refer to?
the ability of a protein to maintain its native conformation
- native conformation has the lowest free energy
What is a beta strand?
a polypeptide chain in the beta conformation
What forms a beta sheet?
a beta strand interacting with other beta strands
- can be made out of parallel (out-of line h-bonds) or antiparallel (in-line h-bonds) strands
Beta Turns
- provide a tight 180 degree turn that is ideal for connecting adjacent strands
- 4 amino acids, first and fourth amino acids h-bond to each other
Type 1 beta turn
uses proline for a tight turn
Type 2 beta turn
uses glycine at position 3
Tertiary structure
refers to the entire three dimensional arrangement of all atoms in a natively folded protein
- includes backbone atoms and side chains
What are the four major classes of tertiary structure?
- fibrous proteins
- globular proteins
- membrane proteins
- intrinsically disordered proteins
Structure of fibrous proteins
- contain repeating helical structure
-classified by having a highly repetitive 2 prime structural elements
Role of fibrous proteins?
- often serving structural roles, providing strength, and/or flexibility
- frequently insoluble (enriched in hydrophobic residues)(contain repeating helical structure)
- Example: Alpha-keratin and collagen
Alpha-Keratin Protein
- strong, super twisted coiled-coils
- bundles held together by disulfide bonds (the more disulfide the stronger)
- only found in mammals (provides strong tissue for a variety of functions)
What is the most abundant protein in mammals?
collagen
Collagen
- part of connective tissue, provides strength and flexibility
- unique left-handed helix, packed into a triple coil
- repeating sequence of Gly-Pro-Hyp (Hydroxyproline)
Globular Proteins
- have more variety in residues and structure
- constitute most cellular proteins
- ex. myoglobin
- may contain a combination of various 2 prime structural elements
Myoglobin
- O2 binding protein
- first protein crystallized
- 8 alpha helices connected via loops or beta turns
- protein core is filled with hydrophobic groups
Protein motifs or folds
folding patters involving two or more 2 prime structural elements
Protein Domain
-implies an independently stable part of the protein
- often have a specialized function
- can be “clipped off” and still maintain function
Intrinsically Disordered Proteins
- some proteins are entirely or partially intrinsically disordered
- intrinsically disordered regions lack a hydrohphobic core and contain no recognizable 2 prime structural elements
What do intrinsically disordered proteins do?
often involved in facilitating protein-protein interactions, act as scaffolds
Quaternary Structure
-encompasses the three-dimensional structure of proteins containing more than one polypeptide chain
- aka: a protein complex, multi-subunit protein, oligomer, multiuser
Subunit
- a single chain within the protein complex
- often abbreviated with greek letters
Protein folding
proteins can unfold then spontaneously refold
Stepwise protein folding
- local secondary structure folds first
- long-range connections happen second
- driven by thermodynamics to the lowest free energy conformation
Conformation
the arrangement in space of its constituent atoms which determine the overall shape of the molecule
Native conformation
-a proteins functional/ normal/ stable conformation
-has the lowest free energy
Phi Angle (circle w/ vertical line)
torsion angle between the nitrogen and the alpha carbon
Psi Angle (pitchfork lookin thang)
torsion angle between the alpha carbon and the carbonyl carbon
Multimer/ Oligomer
a protein with a quaternary structure
Denaturation
the unfolding or breaking up of a protein, modifying its standard three-dimensional structure
Renaturation
the reconstruction of a protein to its original form especially after denaturation
What forces drive protein folding?
- entropy: hydrophobic forces
- enthalpy: h-bonds, van der waals, disulfide, peptide bonds
steady-state
intermediate concentrations are equal
