Chapter 4: The 3D structure of proteins Flashcards
The most important forces stabilizing the specific structure maintained by a given protein are _________________
noncovalent & hydrophobic effect
Conformation
is the spatial arrangement of atoms in a protein
Native protein
Proteins in any of their functional folded conformations
A protein’s conformation is stabilized by ____________
Weak interactions
The term stability in context to protein structure can be defined as the ________
Tendency to maintain a native conformation
The chemical interactions that stabilizes the native conformation are ________
Disulfide (covalent) bonds & weak (noncovalent) interactions & forces such as hydrogen bonds, the hydrophobic effect & ionic interactions
Protein biological function depends on _______
Its 3D structure & are dynamic & marginally stable
The ________ has the lowest energy with the maximum number of weak interactions
Native 3D Structure
The proteins conformation that is most stable (lowest free energy) is the one with the maximum number of ____________
Weak interactions
The ________ predominates in weak interactions stabilizing a protein
hydrophobic effect
Hydrophobic effect(predominant stabilizing force)
Cluster nonpolar groups from a hydrophobic core reducing highly ordered water shells
What are the forces in proteins?
- Hydrophobic effect (predominates stabilizing force)
- Hydrogen bonds between protein hydrogen bond donor & acceptors
- London dispersion weak interactions between atoms
- Electrostatic interactions (between charged groups)
Hydrophobic residues are largely buried in the protein’s ____________
Interior
The peptide bond is _____ & ______
Rigid & Polar
Protein structure are partially dictated by _____ properties
Peptide bond
Peptide group
Contains 6 atoms that occupy the same plane due to the peptide bond double bond characteristic
Partial double bond characteristic restricts conformation in either the ____ or ____ configurations
Trans or cis
Phi angle (circle with line across)
Is between the amino group & alpha carbon
Psi angle (look like a y)
Is between the carbonyl group & alpha carbon
Steric hinderance from backbone & R group size/shape limit a peptide conformation which is why ____ conformation is favored
Trans
Ramachandran plots
Shows the distribution of phi & psi angle
Peptide bond ___________ allows for an observed range of angle in proteins structure
flexibility (Gly- less restricted & pro more restricted)
Secondary structure
Refers to any chosen segment of a polypeptide chain & describes the local spatial arrangement off its main chain atoms
What are the two regular secondary arrangement common in most proteins structures?
- Alpha helix- hydrogen bonding between nearby residues
- Beta sheets-hydrogen bonds between adjacent peptide segments that may not be nearby
Irregular arrangement of the polypeptide chain is called
Random coil
________ alpha helix is the common form in most proteins
Right handed
A right handed twist has _____ residues per turn (5.4A) & hydrogen bonds roughly parallel to the helix & optimal distance between N & O is 0.28nm
36
10A = how many nm?
1nm
The C=O groups point towards the _______
C -terminal
Negatively charged residues are positioned near _____ helix dipole
positive
Side chains spiral outward from heli axis where the helix are diameter is ______(when no side chains) & _____ (with side chains) & fits into major grooves of dsDNA
4-5A, 10-12A
The average length of an alpha helix is ____ amino acids per helix
12
The most form an alpha helix consisting of a D-amino acid is ________
Left hand alpha helix
Interaction between ______ side chains can stabilize & destabilize the alpha helical structure
Amino acid
Amino acids usually stabilize an alpha helix if it has the prefer helical ____ & _____ angles
Phi & psi (small & hydrophobic (ala, leu))
Amino acids are usually disrupted if they are too _____ or inflexible (gly,pro) or highly charged (arg, lys)
flexible
A constraint on the formation of the alpha helix is the presence of ____ or _____ since they have the least prodivity to form alpha helices
Pro or Gly
________ destabilize an alpha helix because in proline the nitrogen atom is part of the rigid ring & rotation about the N-Calpha bond is not possible & the nitrogen atom of a pro residue in a peptide linkage has no substituent hydrogen to participate in hydrogen bonds with other residues
Proline
______ & ____ aren’t found in alpha helix
Gly & pro
_______aren’t in alpha helix because its two flexible & polymers of glycine tend to form a coiled structure different from alpha helix
Glycine
The other factor that affects the stability of an alpha helix is the identity of the amino acid near the end of the alpha helix where negative charged amino are found near the _________ & positive charge amino acids found near __________
Amino terminus, Carboxyl terminus
What are the five constraints that affect the stability of an alpha helix?
- The intrinsic propensity of an amino acid to form an alpha helix
- The interactions between R groups (ones spaced 3-4 residues apart)
- The bulkiness of the adjacent R group
- The occurrence of Pro & Gly
- Interactions between amino acid residues at the ends of the helical segment & electric dipole inherent to the alpha helix
The beta conformation organizes polypeptides chains into _______
Sheets
___________ diagram shows how amino acids sequences influence helix properties
Helical wheel
________ alpha helix are from sperm whales myoglobin
Amphipathic
___________ are extended peptide chains & have hydrogen bonding between backbone
Beta sheets
A _________ is an arrangement of several beta segments side by side
beta sheet
What are the two possible beta sheet arrangement?
- Antiparallel beta sheet
- Parallel beta sheet
In the anti-parallel beta sheet the strands are in the _______ directions & have straight H bonds (0.35nm (3.5A) per residue))
Opposite
In parallel beta sheets the strands are in the _______ directions distorted hydrogen bonds & lower stability (0.33nm (3.3A) per residue)
Same
