Protein Structure Flashcards
Covalent bonds bind which degree of protein structure
Primary
Noncovalent interactions bind which degree(s) of protein structure
Secondary
Tertiary
Quaternity
Primary structure
The sequence of amino acid residues
Secondary structure
The localized conformation of the polypeptide backbone
Tertiary structure
The three-dimensional structure of an entire polypeptide, including all of its side chains
the packing of structural elements like the alpha helices and the beta sheets into a complicated and roughly spherical globular protein
Quaternary structure
The spatial arrangement of polypeptide chains in a protein with multiple subunits
Which factors are most important in determining the higher levels of protein structure
Protein folding and protein stabalization depends of non-covalent interactions
Intermolecular interactions
involved in interactions between molecules
intramolecular interactions
involved in interactions between different parts of the same molecule
Types of non-covalent interactions
ionic
vander waals forces (includes H bonds, diplole-dipole interactions and London dispersion forces)
Ionic interactions
involve permanently charges species
ion-ion
ion-dipole
Salt bridges
favourable ionic interactions
Van der waals interactions
noncovalent associations between neutral molecules
can involve permanent, induced, or spontaneous dipoles
London dispersion forces
type of van der waals
non-permanent dipole interactions
weak, but cumulatively are super strong
Hydrogen bonds
a special kinf of dipole-dipole interaction
an attractive interaction between the H atom of a donor group and a pair of nonbonding electrons on the acceptor group
The hydrogen donor must be strongly electronegative (N, O, F)
The hydrogen acceptor must have a free lone pair of elections and be relatively small (F, O and N)
H bonds are weak compared to covalent bonds but are stronger than normal dipole-dipole interactions
H-bond is directional and only capable of forming one H-bond
Is a linear of bent hydrogen bond stronger
linear
R-OH - - - OR
Formation of favourable noncovalent interactions
result in a negative deltaH and a favourable contribution to deltaG
Formation of unfavourable noncovalent interactions
result in a positive deltaH and and unfavourable contribution to deltaG
What are the most electronegative elements we will be dealing with
O and N
Non-covalent interactions in biomolecules
Play an important role in structure and fuction
examples include:
multi-subunit enzymes that catalyze biochemical reactions: assembly and dissaembly of protein monomers
Interactions between enzymes and substrate
What is an importanty similarity between a hydrogen bond and a dipole-dipole interactins
Both are intermolecular interactions
Transient and polar in nature and help to stabilize transition states
non-charges
What is the difference between a hydrogen bond and a dipole-dipole interaction
H-bond is btwn H-FON
Dipole-dipole not directional in nature, but h-bonding is
Is sulfur electronagative
nope, for us it will be treated similarly to carbon
How do water molecules dissolve proteins
they create a hydration shell around each ion
Water as a solvent
chemicall inert, yet can dissolve a vast number of substances
Poor solvent for non-polar substances
is responsible for the 3D structure of proteins and other biomolecules
Hydrophillic substances
soluble in water
tend to be ionic, strongly polar, and or are capable of H-bondig
“Entropy Driven”
If something is entropy driven, it is the entropy term that makes the delta G negative
So, the -T delta S is negative and delta S is positive
process is spontaneous despite positive delta H
Hydrophobic effect
The tendency of water to minimize its contact with hydrophobic molecules
Note: Hydrophobic interactions are not a separate “force” as such. Basically occurs in order to maximize the entropy of the system (ie hydrophobic compounds are excluded from water in order to prevent the unfavourable formation of the highly ordered “cage”
What is the purpose of the cager water forms around dissolved solids
to maximize the entrophy of the system????
Primary structure and the amide plane
Linking of amino acids by peptide bonds
resonace stabilization provided rigidity and means that the nitrogen cannot pick up an extra proton
also means that all amino acids are trans….. except for proline. This cis isomer is super useful for beta bends
Alpha helixes beta strands
H-bonded to stabalize the backbone
R groups influence the shape of the backbone
Lysine and proline influence the B-bends
Fibrous protiens
usually static and insoluable
ropelike
typically built upon a single type of secondary structure, this repetitive structure is usually assembled into cables or threads
ex// collagen, alpha keratin and silk fibroin
Globular protiens
complex and dynamic
contain several types of secondary structure
compact and roughly spherical
can be water soluble, and, if so characteristically have hydrophobic interior and an hydrophilic surface = unimolecular micelle
can also be water insoluble (such as when bound to a biological membrane) if so, have a hydrophilic interior
Protien misfolding in alzhiemers
missfolded protiens ex// Prp shows an increase in B-sheet formation
The overall flatness of these sheets allows the to stack and lead to protein aggregates
F198S (phe -> ser) causes this mutation
Protein folds
collections of secondary structures
are observed in protein structure and are common in multiple protein families
Alpha helix
uses the full H-bonding capacity of the polypeptide backbone
Carbonyl O of each reside forms an H-bonds with the backbone NH group four residues ahead
backbone H-bonds are parallel to the axis of the helix
R-groups protrude outward from helical backbone
Can alpha helixes be amphipathic
YESSIR
beta sheet// beta pleated sheet
uses sthe full H-bonding capacity of the polypeptide backbone
H-bonding occurs BETWEEN neighbouring peptide chains
R-groups extend above and below the plane of the sheet
peptide chain is fully extended
Turns and loops
in a globular protein, nearly 1/3 of amino acids are in turns or loops where chain reverses direction
most commonly the Beta turn
Beta turn
so named because often connects the ends of two adjacent segments of an antiparalle Beta sheet
Is a hair pin turn involving 4 amino acids
often includes gly and pro
How are proteins flexible
dymanic alterations is non-covalent interactions
allows small and large conformational changes
How are subunits associated in quaternary structures
noncovalent interactions and in some cases di-sulfide bonds
What is the most important interaction for the maintenance of the tertiary structure of a protein
hydrophobic interactions!!!
Which factor fo the gibbs free energy equation drives the nonpolar residues to reside mostly in the interior of a globular protein
Delta S
Which factor fo the gibbs free energy equation drives the charged polar residues to be located on the surface of a globular protein
favourable delta H and delta S
Which factor fo the gibbs free energy equation drives the formation of the alpha helix and beta sheets through hydrogen bonding
maximize favourable delta H
