biochem exam 2 Flashcards
what consists of 3;D protein structure
secondary
tertiary
quaternary
conformation of protein
what specific thing do proteins adopt?
what are the conformation of proteins able to accomplish
what is the native fold, what can we say about its energy?
what are two interactions within a protein that can provide stability?
what is protein conformation stabilized by
what do they combat
Unlike most organic polymers, protein molecules generally adopt a specific three-dimensional conformation
Those structures are able to fulfill a specific biological function
This structure is called the native fold (properly folded, functional conformation – lowest free energy (G)
The native fold has a large number of favorable interactions within the protein for stability –”burying” hydrophobic groups andmaximizing H-bonding
Protein conformation stabilized by:
Disulfide bonds
Weak, noncovalent interactions
THESE COMBAT ENTROPY
Favorable Interactions in Protein Folding and Maintaining a Native State
Hydrophobic Effect
Release of water molecules from the structured solvation layer around the molecule as protein folds increase the net entropy
Correctly position hydrophobic side chains depending on environment
Hydrogen Bonds
- Interaction of N-H and C=O of the peptide bond leads to local regular structures such as α-helices and β-sheets
- Side chain – side chain interactions. H-bonding between R-groups, H-bonding between backbone and R-groups.
Van der Waals Interactions
Weak attraction between all atoms contributes significantly to the stability in the interior of the protein
Electrostatic Interactions
Long-range strong interactions between permanently charged groups
Salt-bridges, especially buried in the hydrophobic environment strongly stabilize the protein
Secondary (2°) Structure
Secondary structure starts with primary structure…
The peptide bond is rigid and planar, constraining the protein to certain, allowed conformations
Carbon-carbon (psi - Ψ) bonds can rotate
Carbon-nitrogen (peptide) bond (phi - Φ) cannot rotate
In theory, + / - 180° rotation for phi/psi bonds can occur,but…
Steric Hinderance will prevent some angles from occurring…
Steric Hindrance of Side Chains and Backbone Reduces Possible Rotation
The peptide bond is rigid and planar, constraining the protein to certain, allowed conformations
In theory, + / - 180° rotation for phi/psi bonds can occur,but…
Steric hindrance will prevent some angles from occurring…
Ramachandran Plot
Shows common secondary structural elements and the acceptable range of rotation
Steric hindrance prevents all but a handful of secondarystructures
alpha helix
The helical backbone is held together by hydrogen bonds between the backbone amide of an “n” and carbonyl group of the “n + 4” amino acid
Right-handed helix with 3.6 residues (R groups – 5.4 Å per turn)
Hydrogen bonds are aligned roughly parallel with the helical axis. Stabilizes.
Side chains point out and are roughly perpendicular with the helical axis
Residues 1 and 8 align and are on top of each other.
more on alpha helices
how long is the inner diameter of the helix and what is it too small to fit into
how long is the outer diameter of the helix and where can it fit into
some amphipathic alpha helices can form what
what amino acids are helix breakers, and what will it cause?
what amino acids are helix forces
The inner diameter of the helix is about 4-5ÅToo small for anything to bind inside
The outer diameter of the helix (with side chains)is 10-12 Å. Fits into the major groove of dsDNA
Some amphipathic α-helices can form coiled-coildimers (stay tuned – keratin)
α-helices cannot be formed with Pro which will cause a kink that disrupts the helix. Gly is a helix breaker too.
Not all polypeptide sequences adopt α-helical structures
Small hydrophobic residues such as Ala and Leu are stronghelix formers.
beta pleated sheets
what creates it
what holds it together
what causes the up and down directions
what amino acids are found in them
what amino acids are not found in them
The planarity of the peptide bond and tetrahedral geometry of the α-carbon create a pleated sheet-like structure (zigzag)
Sheet-like arrangement of the backbone is held together by hydrogen bonds between the backbone amides and carbonyl groups in different strands
Side chains protrude from the sheet alternating in up and down directions
Found in β-Sheets:
Large, aromatic (Y, F, W)
Branched (T, V, I)
NOT Found in β-Sheets:
G, P
Parallel β-Sheets
In parallel β-sheets, the H-bonded strands run in the same direction
Resulting in bent H-bonds (weaker)
Individual strands can be close, or distant, in the primary structure
Antiparallel β-Sheets
where do the H-bonded double strands run
what does it result in
what is the proximity of the individual strands in the primary structure
In antiparallel β-sheets, the H-bonded strands run in opposite directions
Resulting in linear H-bonds (stronger)
Individual strands can be close, or distant, in the primary structure
Diagrams and Organization of Secondary (2°) Structure
Most proteins are globular in shape as a result of frequent turns or loops in the polypeptide chain that connects beta strands and alpha-helices. 1/3 of AA residues are in turns or loops
Strands, and sometimes helices, will have arrows to indicate N- and C- termini of the 2° structural element
β turns occur frequently whenever strands in β sheets change direction
The 180° turn is accomplished over 4 amino acids
Turn stabilized by a H-bond
Type 1:
Proline
Type 2:
Glycine
Tertiary (3°) Structure
Tertiary Structure – overall 3D arrangement of all atoms in a protein
Includes long-range contacts between AA’s in a single polypeptide chain
Stabilized by numerous weak interactions between amino acid side chains
Largely hydrophobic and polar interactions
Can be stabilized by disulfide bonds
Side chain with backbone interactions are also possible
Two Major Groups
- Fibrous (elongated; structural)
- Globular (enzymes, etc.)
tertiary structure
Often have structural rather than dynamic roles and are water insoluble
Typically contain high proportions of α-helices (keratin) or β-pleated sheets (fibroin)
Underlying structures are relatively simplistic
High proportion of hydrophobic AAs
Extensive supramolecular complexes
Fibrous Proteins
We will look at 3: α-keratin, collagen, silk fibroin
α-Keratin
where is it found in the body?
what structures make it up
what shape are they
how is the coiled-coil made
how is it stablized
Hair, nails, hooves, horns, outer skin
Strong, RH α-helix; LH parallel superhelix; strengthened by cross-links
Typical right-handed α-helices
Super twisting helices, in a left-handed fashion, wrap around each other to make a very tight coiled-coil
Cross-linked by covalent disulfide bonds – stabilizes!
Collagen
what does it provide
what are examples of it in the body?
each protein of collagen folds into what direction called what and not what
how is collagen ultimately arranged and in what direction does it face?
what 3 amino acids and 2 hydroxy amino acids are essential for collagen
which amino acid and hydroxy amino acids form a cross-link and what does it provide how many variants are there in mammals
Provides tensile strength and structure (~30 types of collagen).
Connective tissue (tendons, cartilage, organic matrix of bone, cornea)
Each protein folds into a left-handed helix (α-chains; NOT α-helix)
Coiled-coil of three separate α-chains supertwisted around each other in a right-handed manner to provide strength (like a rope).
Gly, Ala, Pro, HyLys, and HyPro (essential! specific to collagen)
Lys-HyLys (Hydroxylysine) form cross-links for added strength
30+ variants in mammals
vitamin C and collagen
what is an essential component of collagen?
what enzyme converts Pro to HyPro
in the absence of what causes that enzyme to be inactivated
what does the inactivation of that enzyme cause and what famous disease is this – who is it most observed in
HyPro is an essential component of collagen
the enzyme prolyl 4-hydroxylase is required to convert pro to HyPro
in the absence of vitamin C (ascorbic acid) this enzyme is inactivated, leading to collagen instability and connective tissue problems. this is the cause of scurvy – still observed today in people who don’t consume enough fruit
Silk Fibroin
In antiparallel β-sheets, the H-bonded strands run in opposite directions
Resulting in linear H-bonds (stronger)
Individual strands can be close, or distant, in the primary structure
Rich in Ala and Gly; antiparallel β-sheets
Resulting in linear H-bonds (stronger)
Fully extended: no stretching
Extensive hydrogen bonding and van der Waals interactions between sheets, but no covalent cross-links flexibility.
Globular Proteins
what are examples of these
what can be found in them?
what is the arrangement of different secondary structural elements?
what is the general rule for protein folding
what is not the norm
what do you want to optimize
globular proteins = enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins, etc
alpha helices and B turns, etc can all be found
arrangement of different secondary structural elements:
–compact conformation
– Folding provides structural diversity
General Rules:
Bury nonpolar amino acidR-groups
Distant segments may cometogether, but not the norm
Optimize the number of weakinteractions
Myoglobin
what are they; what elements are bound to them and where do it exist in the body
what is it distantly related to and how does it differ
what is the general rule?
from the sperm whale:
- what is the shape of the protein
- how many alpha helices
- how many amino acids
- what kind of ring is it
- what is directly attached to the iron
- what hovers near the histidine face
Myoglobin:
Iron- and oxygen-binding proteins found in the muscle of vertebrates
Distantly related to hemoglobin, but has a higher affinity (stay tuned)
Rules are followed: hydrophobic R groups are buried
from sperm whale
Myoglobin:
Globulin protein
Eight α-helices connected by loops.
153 amino acids.
Porphyrin ring with iron in the center (heme – prosthetic group). A proximal histidine group (His-93) is directly attached to the iron, and a distal histidine group (His-64) hovers near the opposite face.
