1-39 Protein Sequence, Structure, and Function Relationships Flashcards
alpha carbon (Ca)
carbon bound to the carboxyl group, amino group, R group, and hydrogen
the phi bond?
N-Ca bond
the psi bond?
Ca-C bond
why are the phi and psi angles restricted?
some angles would lead to steric interference in the protein - allows us to deduce the types of secondary structures that are possible for a given aa squence.
What does the ramachandran map show us?
easy way to visualize the distribution of the dihedral angles of a protein structure
What are four non-covalent forces that operate on proteins and all other biomolecules in aqueous solution
Electrostatic forces
hydrogen bonding
van der waals forces
hydrophobic effect
electrostatic forces
attractive/repulsive interactions between charged species. Calculated via coulombs law
hydrogen bonding
interactions between highly EN atoms (S, O, N) and hydrogen atoms bound to (S, O, N).
hydrogen takes a slightly + character, and is noncovalently attracted to the non-bound EN atom.
(the atom bound to it steals some e- density)
linearity of hydrogen bonds?
The more linear the hydrogen bond is with respect to the covalent bonds of the hydrogen and the electronegative atom, the stronger the interaction will be.
van der waals forces
atoms close together, charge distribution of electron cloud becomes uneven, creating transient dipoles.
when an atom takes a temporary dipole state, can influence neighbor to do the same.
weak and temporary
hydrophobic effect
certain molecules (uncharged, non polar) tend to interact more with themselves than with water in aqueous environment.
water also will more favorably interact with itself
electrostatics and protein secondary structures
proteins fold to maximize favorable charge-charge and charge-water interactions
determines which aa are on inside or outside of protein structure. charged tend to be on exterior
hydrogen bonding and protein secondary structure
most common occurance?
hydrogen bonds always satisfied in proteins.
every hydrogen bond donor is paired with a receiver
most commonly occurs from interactions between peptide bonds - this is why alpha helices and beta sheets are so common
why are beta sheets and alpha helices so common?
hydrogen bonding frequently occurs between peptide bonds
van der walls and protein secondary structure
proteins fold to MAXIMIZE van der waals energy.
do this by packing atoms close together - as a result, proteins are incredibly dense organic molecules
why are proteins so dense?
they fold to maximize their van der waals energy in a way that packs their atoms closely together
hydrophobic effect and secondary structure
hydrophobic residues will remain away fom the exterior of the protein structure, will want to stay buried
what is a dipole?
two charges separated by a distance. No formal charge needed to be dipolar, area withdrawing electrons from another portion
hydrogen bonding is a special case of…
electrostatic interactions, 2 EN atoms compete for same H+
what makes a strong hydrogen bond?
peptide-charged carboxylate = strong
peptide-peptide = weak
peptide -noncharged carboxylate = weakest
linear = strong
bent=weak
the most important bond/force in terms of protein structure
hydrophobic effect
rise vs exended rise, turn of alpha helix
rise 1.5, extended fully is 4.5
1 turn = 3.6 residues
why a 3.6 residue repeat?
favorable backbone dihedral angles
near optimal h bond geometry
good van der waals contacts between backbone atoms
what is a giveaway that section of aa is an alpha helix?
lots of alanines, no prolines
pKa of a protein?
pH at which 50% of the molecules are ionized and deionized
peptide bond forms between the
carboxyl of one amino acid and the NH of another
c alpha? c beta? c gamma? c delta? c epsilon?
c-alpha, the central alpha that the R group hangs off of
c beta - first carbon of r group
c gamma - second carbon of r goup
c delta - …..
two words that describe the peptide bone
how many rotatable bonds per residue?
planar and trans (side groups alternate)
2
what does planarity do?
reduces bond rotations
not planar - 3 rotations per bond residue
planar - 2
ramachandran map
maps allows phi and psy angles
dark gray - allowed
dashed area - tolerated
individuality of proteins is provided by
side chains
hydrophobic (non polar)
hydrophilic (polar) (charged or polar but uncharged)
unique (pro, gly, cys)
aliphatic AA
what are they?
aliphatic are most hydrophobic
ala, val, leu, ile, pro
aromatic and sulfur containing are…
less hydrophobic
Phe, Tyr, Trp, Met
pKa is the
pHpKa
pH at whcih half of the ionizing groups are pronated
pHpKa = lower H+ concentration, H+ drawn off
pKa of terminal amine and carboxylic acid?
terminal amine, pKa of 8
carboxylic acid pKa = 4
unique side chains
Gly - lack of side chain makes it flexible
Pro - cis peptide bond favors kinks, turns, no h-bond donor
cys - thiol group can oxidize s-s, way crosslinks are introduced
what determines the individual functions of proteins
- polymer length
- amino acid composition
These factors specify the unique 3D structure that dictates function
proteome
content of proteins within the cell at any given time
TF
the proteome is more complex than the genome
T. Genome stays constant, proteome changes.
proteins are less relavent than genes in respect to disease
F - the defective gene is not what makes you sick, it is the abherent function of the corresponding protein that makes you sick
the alpha helix bonds are between..
between the peptide NH of residue i and the peptide CO of residue i+4,
helix forming residue
Ala - lack of sidechain
strong helix breakers
proline - lacks NH to hydrogen bond
glycine- is too flexible
medium helix breakers
Val, Thr, Trp, Phe - lose too much rotation freedom (entropy) when in a helix
entropy -
rotational freedom
helix indifferent aa’s
long-straght chains (Arg, Lys, glu)
lose less rotational freedom
planarity _____ bond rotations
reduces
phi, psy angles are limited by…
steric clashes
