exam 2 biochem practice questions Flashcards
what is the major themes in chapter 4
primary sequence to 3-D structure
structure = function
each protein has a unique structure (is also not static but dynamic)
non-covalent forces are very important
many structures have common patterns that are given a name (like domain and motif….I think)
what is different about protein compared to other organic polymers
what does the conformation of a protein allow the protein to do
has a specific 3-D conformation
allows the protein to function
what is a native fold
what can be said about its energy
the properly folded, functional conformation of a protein
it has the lowest free energy
what does the native fold have and are examples of it
The native fold has a large number of favorable interactions within the protein for stability
example: ”burying” hydrophobic groups and maximizing H-bonding
how is protein conformation stabilized by
what do these combat
Disulfide bonds
Weak, non-covalent interactions
THESE COMBAT ENTROPY
what are the Favorable Interactions in Protein Folding used to Maintain a Native State (fold)?
hydrophobic effect
hydrogen bonds
van der waals interactions
electrostatic interactions
what does the Hydrophobic Effect do for the native fold
Release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy
Correctly position hydrophobic side chains depending on the environment
what does hydrogen bonding do for the native fold
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.
what does van der waals do for the native fold
Weak attraction between all atoms contributes significantly to the stability in the interior of the protein
what do Electrostatic Interactions
dof ro native fold
Long-range strong interactions between permanently charged groups
Salt-bridges, especially buried in the hydrophobic environment strongly stabilize the protein
what does secondary structure start with
starts with primary structure
2 structures
describe the peptide bond
describe carbon-carbon bonds, what is another name for it
describe the carbon-nitrogen bond, what is another name for it
for psi/phi bonds, what can occur but what will be prevented
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…
what does steric hindrance effect and what is the result
steric hindrance can affect side chains and the backbone reduces possible rotations
what does a Ramachandran plot show
what does steric hindrance prevent
Shows common secondary structural elements and the acceptable range of rotation
Steric hindrance prevents all but a handful of secondarystructures
what is the structure of a peptide bond?
how many atoms does it have
is rigid and planar, constraining the protein to certain conformations
has 6 atoms
what do secondary structures consist of
alpha helix
beta-sheets
parallel beta sheets
antiparallel beta sheets
how is the helical backbone of an alpha helix held together?
what kind of direction is an alpha helix
what stabilizes the alpha helix
where are the side chains for the alpha helix
which residues align on top of each other
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
ann alpha helix is a right-handed helix
the hydrogen bond aligns roughly parallel with the helical axis and this stabilizes it
Side chains point out and are roughly perpendicular to the helical axis
residues 1 and 8 align on top of each other
describe the inner diameter of alpha helix, what can fit innside
describe the outer diameter of alpha helix, what can fit inside
what can amphipathic alpha helices form
what is the relatiionship between proline, glycines and alpha helices
does every polypeptide forrm a alpha helcies
what amino acids are strong helix formers
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 kink(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.
what is the cause of the sheet-like zig zag structure of beta sheets
what holds together the sheet-like arrangement for beta sheet
where are the side chains in beta sheets
what amino acids are found in beta sheets
what amino acids are not found in beta sheets
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
in parallel beta sheet, where do the H-Bonds run and what does it result in
where can the individual strands be in the primary structure
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
in anti-parallel beta sheet, where do the H-Bonds run and what does it result in
where can the individual strands be 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
how are most proteins shaped
what is the reason for this shape
how many A.A residues are in turns or loops
what do the arrows in strands and sometimes in helices indicate
when do beta turns occur
how is the 180* turn accomplished
how are beta turns stabilized
what amino acid is found in beta turn type 1
what amino acid is found in beta turn type 2
Most proteins are globular in shape
the globular shape is due to 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 (so whenever the beta sheets turn to change direction)
The 180° turn is accomplished over 4 amino acids
Turn stabilized by a H-bond
type 1: proline
type 2: glycine
what is the tertiary structure and what does it include
how is it stabilized
what interactions largely make it up
how else can it be stabilized
what Is also possible
what are two major of tertiary 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.)
what do tertiary structures often have and is it solute in water
what does it contain a high proportion of and what are examples of these
are the underlying structures complicated
what does it have a high proportion of
what does it have extensive of
what are examples of fibrous proteins
Often have structural rather than dynamic roles and are water insoluble
Typically contain high proportions of α-helices (keratin) or β-pleated sheets (fibroin)
High proportion of hydrophobic AAs–that is why it is water insoluble!!!!!!!!!
Extensive supramolecular complexes
Fibrous Proteins: α-keratin, collagen, silk fibroin
where can you find alpha keratin
what is alpha keratin made of and what is ti strengthened by
what is the fact from legally blonde
how isa super tight coiled coil made
how is permanent waving of hair done
Hair, nails, hooves, horns, outer skin
made of Strong, RH α-helix; LH parallel super helix; strengthened by cross-links by covalent disulfide bonds – stabilizes!
perm removes disulfide bonds
Super-twisting helices, in a left-handed fashion, wrap around each other to make a very tight coiled-coil
permanent waving of hair: reduce disulfide bonds, moist heat breaks H-bonds and causes uncoiling of alpha heckles, remove reducing again, add oxidizing agent, new SS bonds
what does collagen provide and how many different types are there
where can collagen be found
how does each protein fold
what is the structure of collagen
what amino acids are found in collagen
which amino acid provides tensile strength for collagen
how many variants are there in mammals
Provides tensile strength and structure (~30 types of collagen).
can be found in 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).
find Gly, Ala, Pro, HyLys and HyPro (essential! specific to collagen)
Lys-HyLys (Hydroxylysine) form cross-links for added strength
30+ variants in mammals
in antiparallel beta sheets, where do H-bonds run
does this make the H-Bonds linear or bent and does it make them stronger or weaker?
what kind of amino acids is silk fibroin rich in
what kind of structure is it mostly made of
does it stretch
what kind of interactions are within
what kind of cross-links does it have, does it make it rigid or flexible
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
Fully extended: no stretching
Extensive hydrogen bonding and van der Waals interactions between sheets, but no covalent cross-links for flexibility.
for silk fibroin
what is it used for today?
what are its characteristics?
what structure is it made of
what are its cross-links
used for silk
soft and flexible filaments
made of beta conformation
no cross-links
for collagen of tendons, bone matrix
how is it used today?
what are its characteristics?
what structure is it made of
what are its cross links
tendons, connective tissues, organic bone matrix
high tensile strength without stretch
made of collagen triple helix
– hydroxylysine (unique) cross-links structure = function
for alpha keratin
how is it used today?
what are its characteristics?
what structure is it made of
hair, feathers, and nails
tough, insoluble protective structures of varying hardness and flexibility
made of alpha helix, cross-linked by disulfide bonds
what are examples of globular proteins
what structures can be found in them
how are the different secondary structures arranged?
what does the folding provide
what is the general rule for globular proteins
examples: enzymes, transport proteins, molar proteins, regulatory proteins, immunoglobulins etc
alpha helices, beta sheets, beta turns can all be found
the different secondary structures are
- compact conformation
- folding provides structure diversity
general rule:
- bury nonpolar amino acid R-groups
- distant segments may come together, but not the norm
- optimize the number of weak interactions
what is an example of a globular protein?
what does this protein bind and where is it found
what is this protein related to but has a higher affinity for what
what are the rules followed for this protein?
what structures is this protein made of
how many amino acids is it made of
what kind of structure is it and what is at its center
what is its prosthetic group?
what is a prosthetic group?
what amino acid is attached to what molecule in its center
myoglobin!
binds iron and O2 and is found in muscles
related to hemoglobin but has a higher affinity for O2
general rules: the hydrophobic R groups are buried
made of alpha helices connected by loops
made of 153 amino acids
it is a porphyrin ring and has iron at its center
heme is it a prosthetic group
a prosthetic group is a nonprotein group forming part of or combined with a protein.
a proximal histidine group is attached to the iron, a distal histidine group hovers near the opposite face
what are
chymotrypsin
ribonuclease
carboxypeptidase
cytochrome C
lysosome
myoglobin
they are secondary structures!
what are the steps taken for X-ray crystallography?
Purify the protein
Crystallize the protein
Collect diffraction data (light bending)
Calculate electron density
Fit residues into density
what are the pros and cons of X-Ray crystallography
Pros:
- No size limits
- High resolution
- Well-established
Cons:
- Difficult for membrane proteins
- The crystal form may not represent the protein in solution or in the cell
- Not dynamic (cannot determine how the protein interacts with things)
what steps are taken for NMR
Steps
Grow the protein with a NMR-active isotope (usually of Carbon-13)
Purify the protein
Collect NMR data
Assign NMR signals
Calculate the structure
what are the pros and cons of NMR
Pros:
- No need to crystallize the protein
- Dynamic studies possible
- Interaction with ligands
Cons:
Difficult for insoluble proteins
Works best with small proteins
Nuclear Magnetic Resonance
what is a motif associated with
what are motifs
what are motifs composed of
what are what a motif is composed of also considered
motifs can be found as what
what are proteins made of
what are examples of secondary strcutures that can be found in motifs
Globular Proteins are associated with Motifs
Motifs are stable arrangements of several secondary structure elements
All alpha-helix
All beta-sheet
Combination
These are sometimes considered supersecondary structures
Motifs can be found as reoccurring structures in numerous proteins
Motifs can be found as reoccurring structures in numerous proteins
examples of secondary structures that can be found in motifs:
twisted beta-sheet
alpha alpha corner
beta alpha beta loop
beta barrel
what can you find in large motifs
what are the two classes that a motif can be organized into
You can find small motifs as a part of large motifs
People have determined the structure of so many proteins, so we must organize. Two classes of organization are shown here.
what are domains and where can they be found
what can a domain have
when do domains adopt the same folding pattern
what can a single protein have
can be found in globular proteins
Domains are relatively stable, independently folded regions within the tertiary structure of a globular protein
Each domain may encompass one or more motifs and have the same combination of motifs (EF-hand)
Domains having more than 30% of their amino acid sequence in common normally adopt the same folding pattern.
A single protein can have several domains with each domain performing a different function (e.g., enzymatic, docking, regulatory, pore, membrane anchoring, etc)
what cause a Quarternary (4°) Structure
how do the the polypeptide subunits associate into a larger functional cluster
What drives Quarternary Association?
Results from the association of two or more polypeptide subunits into a larger functional cluster
These polypeptide subunits associate into a larger functional cluster via side chain – side chain and side chain – polypeptide backbone interactions
what drives quaternary association:
Stability: reduction of surface to volume ratio
Genetic economy and efficiency (using quarternary structure makes our genome more efficient)
Bringing catalytic sites together
Cooperativity (biological function may be regulated by complex interactions of multiple subunits)
what do Intrinsically Disordered Proteins or Protein Segments
lack
what can this type of protein remain as or what can it also do
how many humans proteins fit this designation
what amino acids form then and
Contain protein segments that lack a definable structure. Or, the entire protein
The protein can remain in a primary structure indefinitely; or it may have a domain that can interact with other molecules, but the rest of the protein will remain disordered.
Possibly 1/3 of all human proteins fit this designation.
