Chapter 4: The 3D Structure of Proteins Flashcards
What is a protein’s specific three-dimensional conformation?
its native fold
Why are native folds important for proteins?
allow for a large number of favorable interactions
What is the cost associated with folding a protein into its native fold?
cost in conformational entropy
What is generally true about the Gibbs free energy of proteins?
they have the lowest Gibbs free energy
What allows a protein’s native fold to fulfill biological function?
its structure
What does water make the best hydrogen bonds with?
itself
Where are van der Waals forces the most important in a protein?
in its interior
Types of favorable interactions in proteins? (5)
hydrophobic effect, van der Waals, hydrogen bonds, ionic interactions, disulfide bridges
What type of interaction leads to a-helices and b-sheets?
hydrogen bonds
Why are hydrogen bonds maximized in a protein structures?
allows polar molecules to easily traverse the interior of proteins
Describe ionic interactions.
long-range strong interactions between permanently charged groups
What type of interaction are salt-bridges?
ionic interactions
Where are salt-bridges most used for stabalization?
in hydrophobic environments
In what types of proteins are disulfide bridges generally found in?
secreted proteins; they don’t like the reducing environment of the cell
What drives the hydrophobic effect?
entropy!
What type of standard chemical interaction are disulfide bridges?
covalent bonding
Why does entropy drive the hydrophobic effect?
when hydrophobic molecules group up, water molecules are displaced –> increasing entropy
Does there exist an attractive force between two nonpolar molecules?
no! water pushes them together
Since water pushes nonpolar molecules together, what type of bond influences the hydrophobic effect?
hydrogen bonds
What creates the hydrophobic core of most proteins?
the burial of hydrophobic side chains in the interior of the protein; polar side chains remain exposed to water
Where are ionic interactions strongest?
in hydrophobic environments with a low dielectric constant
Where are ionic interactions weakest?
in aqueous or solvent exposed locations
A low dielectric constant is associated with what type of environment?
a hydrophobic environment
What is the weakest interaction in proteins?
van der Waals forces
What is the strength of van der Waals forces (kj/mol)
2-4 kj/mol
What types of atoms are van der Waals forces present?
in all atoms!
What are the two types of van der Waals forces?
london dispersion and steric repulsion
Is london dispersion an attractive or repulsive force?
attractive
What type of van der Waals force dominates at longer distances?
london dispersion
What type of van der Waals force dominates are shorter distances?
steric repulsion
What does steric repulsion depend upon?
the size of the atoms
What are london dispersion forces caused by?
instantaneous polarization due to fluctuating charge disributions
What is the van der Waals radius?
the specific distance where attractive and repulsive forces balance
What does the van der Waals radius depend the most on?
an atom’s size
On a graph of the van der Waals radius, what are the x and y components?
x: distance between two atoms y: energy
Where, on a graph of van der Waals radius, is there the strongest attraction?
at the lowest point aka the van der Waals contact distance
Why is the reversibility of weak bonds essential in cellular biochemistry?
binding of substrates
Describe the two conditions of weak bonds that make them so effective.
reversibility and complementary
Why is it important for binding surfaces to be complementary?
allows for multiple binding interactions
What are the basics of a proteins primary structure?
amino acid residues
What are the four levels of protein structure?
primary, secondary, tertiary, quaternary
What are the basics of a protein’s secondary structure?
a-helix or b-sheet
What are the basics of a protein’s tertiary structure?
polypeptide chains; interactions of R groups
What are the basics of a protein’s quaternary structure?
assembled subunits
What is the most important bond in influence the structure of a protein?
peptide bonds
Peptide bonds are what type of bond?
partial double bonds
Describe characteristics of a peptide bond. (3)
rigid, nearly planar, and mostly in trans conformations due to steric hinderance
What conformation (cis/trans) is favored in peptide bonds?
trans (>99.95%)
What amino acid is the one exception to the trans conformation rule?
proline; found ~6% in cis conformation via proline isomerases
Can a there be rotation around the peptide bond? What about the other bonds connected to the alpha carbon?
peptide bonds CANNOT rotate, the other bonds connected to the alpha carbon are permitted to rotate
What is the phi bond angle?
the rotation of the bond from the alpha carbon to nitrogen
What is the psi bond angle?
the rotation of the bond from the alpha carbon to the carbonyl
Why are some phi and psi bond combinations very unfavorable?
steric crowding
Why are some phi and psi bond combinations favorable?
favorable hydrogen bonding interactions along the backbone
What is a Ramachandran plot?
a plot of phi and psi bond angles calculated based upon known atomic radii and bond lengths
What is the purpose of a Ramachandran plot?
used to show “allowed” phi and psi conformations
What is the term for the local spatial arrangement of the polypeptide backbone?
secondary structures
What are the two most common secondary structures?
a-helix and b-sheet
What are irregular arrangements of the polypeptide chain called?
random coil
What stabilizes an a-helix? What residues are involved?
hydrogen bonds between nearby residues
What percentage of amino acids are in the a-helix conformation?
25%
What stabalizes a b-sheet? What residues are involved?
hydrogen bonds between adjacent residues that may be far away
Are a-helixes and b-sheets the only type of secondary structures?
No, but they are the most prevelent
What is the helical backbone held together by?
hydrogen bonds
What amino acids make up the helical backbone?
n and n+4 amino acids
Are a-helixes right or left handed?
right-handed
How many residues per turn of the alpha helix?
3.6
Are peptide bonds perpendicular or parallel to the helical axis?
parallel
Are side chains perpendicular or parallel to the helical axis?
perpendicular, to reduce steric hinderance
What is the size of the inner diameter of the a-helix? Why is this significant?
4-5 angstroms; its too small for anything to fit inside of
What is the size of the outer diameter of the a-helix? Why is this significant?
10-12 angstroms; it fits well into the major groove of dsDNA (the perfect size!)
What residues align on top of each other when looking down an a-helix?
residues 1 and 8
Can all polypeptide sequences adopt a-helical structures?
Nope
What amino acids are strong helix formers?
small hydrophobic residues like Alanine and Leucine
What amino acids are strong helix breakers?
Proline and Glycine
Why is proline a helix breaker?
rotation around the N-C bond is impossible
Why is glycine a helix breaker?
the tiny R-group is too flexible, supports other conformations
In addition to specific amino acids, what else can affect the formation of an a-helix?
the attractive or repulsive interactions between side chains that are 3-4 amino acids apart
What type of side chains that are 3-4 amino acids apart will cause helical instability?
negative-negative, positive-positive, bulky residues
Why might negatively charged residues occur often at one end of the helix?
peptide bonds have strong dipole moments that can create a partial positive amino terminus and a partial negative carboxyl terminus
Describe the structure of b-sheets?
pleated sheet-like structure with side chains protruding up and down from the sheet
What is a parallel b-sheet?
a sheet where the H-bonded strands run in the same direction
What is an antiparallel b-sheet?
a sheet where the H-bonded strands run in opposite directions
Do antiparallel or parallel b-sheets have stronger H-bonds?
antiparallel, the H-bonds are linear rather than bent
How many amino acids does it take to complete a 180° turn?
four amino acids
What stabilizes a beta turn?
a hydrogen bond from the carbonyl oxygen to the amide proton of a residue three down
What amino acids are common in beta turns?
proline (cis) and glycine
What type of analysis is used in the lab to investigate the secondary structure of proteins?
CD spectroscopy
Can proteins be 100% a-helix or 100% b-sheet?
yes! but most are some combination of the two
What is the overall spatial arrangment of atoms in a protein called?
tertiary structure
What are the two major classes of tertiary structures?
fibrous and globular
What are motifs/folds?
small combinations that are associated with a specific function; rely on their environment for stability and cannot fold by themselves
What is a protein domain?
a part of a polypeptide chain that is independently stable and can fold by itself
How many domains do small proteins usually have?
one domain
What two characteristics do domains optimize?
burial of hydrophobic residues and satisfaction of aa sequence constraints
What is the purpose of having more than one domain in a single protein?
can act as a point of regulation, can be important in catalysis (open/close)
Are domains are motifs larger?
domains
Can motifs exist outside of domains?
no
Can domains exist outside of motifs?
yes
Fibrous vs Globular: shape
long and narrow versus round and spherical
Fibrous vs Globular: role
structural vs functional
Fibrous vs Globular: solubility
insoluble vs soluble
Fibrous vs Globular: sequence
repetitive sequence vs irregular sequence
Fibrous vs Globular: stability
less sensitive vs more senstivie
What are some common examples of fibrous proteins?
collagen and keratin
What are some common examples of globular proteins?
catalase and insulin
Scurvy is caused due to a deficiency in vitamin C that impacts collagen productive. Explain.
The hydroxylation of proline is required for collagen structure. This process converts Fe2+ –> Fe3+. Ascorbate (vitamin c) is required to convert Fe3+ —> Fe2+ to be used again.
What are the causes of brittle bone disease and loose joints?
amino acid substitutions of a single glycine for larger amino acids; prevents proteins from being as tightly packed together
What are the functions of globular proteins (6)?
catalysis, transport, storage, structure/movement, transmission of messages, defense
What is a common type of transport protein?
hemoglobin
What is a common type of storage protein?
myoglobin
What is a common type of structure/movement proteins?
myosin
What is a common type of transmission proteins?
insulin
What is a common type of defense proteins?
antibodies and cytokines
What is a common type of catalyst protein?
chymotrypsin and lysozyme
What is the function of myoglobin? What is its structure?
stores oxygen and allows for consistent diffusion by contracting muscles, made up of 70% a-helix with a packed hydrophobic core
What are intrinsically disorder proteins?
proteins that lack definable structure
Why are intrinsically disordered proteins important?
they can conform to many different proteins, facilitating interactions with many different partners and pathways
What are two of the well-known intrinsically disordered proteins? What are their functions?
p27 and p53; p27 inhibits protein kinases to stop the cell cycle
How is the quaternary structure formed? What is another word for quaternary structure (2)?
by the assembly of individual polypeptides (subunits) into a larger functional cluster; multimer or oligomer
What are the advantages of proteins having a quaternary structure (4)?
use the same gene and same transcription factors thus conserving space, reduces the change of mutation, speeds up translation, ensures proper folding
How does a quaternary structure reduce mistakes and mutations?
can easily discard faulty subunits, no sunk cost falacy
How does a quaternary structure make folding easier?
it’s easier to build up proteins, especially complex structures, from subunits
Roughly, what is the typical speed of translation?
1000 amino acids in one minute
What is it called when the use of quaternary structures increases the rate of translation?
parallel processing
What is cooperativity?
characteristic of quaternary structures; allows the binding of one ligand to a protein to increase the affinity for future binding
What is allostery?
characteristic of quaternary structures; allows the binding of one ligand to influence the binding site or function of the protein
How does quaternary structures impact kinetics?
the interactions between units can change protein activity and kinetics
What is substrate channeling?
characteristic of quaternary structures; when two or more enzymes interact to transfer a metabolite from one active site to another without diffusion
What is the function of the protein albumin?
carries many molecules in the blood
What is the function of the protein ferratin?
stores ~4500 iron (III) molecules in its core
What is the term for the coordination of many different pathways in order to regulate protein activity?
proteostasis
What two elements are required for a protein to be considered denatured?
the loss of its tertiary structure and accompanying loss of activity
How can proteins be denatured (4)?
heat/cold, pH extremes, organic solvents, chaotropic agents that break H bonds
Can denaturation be reversible?
yes! (but most used in lab are irreversible)
What is a Tm value?
the point where 50% of proteins are denatured
What is the significance of the 1972 Nobel Prize in Chemistry?
awarded to Christian B Anfinsen for his work concerning the connection between amino acid sequence and the functional conformation
Describe Christian B Anfinsen’s ribonuclease refolding experiment?
- ribonuclease is a small protein with four disulfide bonds
- only one of its formations (out of 105) are functional
- urea denatures ribonuclease
- when urea is removed, the protein spontaneously refolds even with the correct disulfide bonds
What did Christian B Anfinsen conclude from his experiment?
that the amino acid sequence ALONE determines the native conformation
What is Levinthal’s paradox?
it is mathematically impossible for protein folding occur by randomly trying ever conformation until the lowest-energy one is found
How can protein folding NOT be random?
direction toward the native (lowest energy) structure is always thermodynamically most favorable
Describe the idea of a folding funnel.
folding properties are related to free energy and the possible conformations of a protein are reduced as it approaches native-like structure
What is the term used to describe proteins that facilitate the folding of other proteins?
chaperonins
Describe the significance of the GroEL/s chaperonin?
10-15% of E. coli proteins require its hydrophobic pocket to fold
What is amyloidosis?
the deposition of fibrils throughout the body
How does the cholera toxin lead to disease?
unfolds in the ER, is transported to the cytoplasm for degradation
What are three disease like things caused by protein misfolding?
amyloidosis, cholera, and prions
What are the three principles that determine protein conformation?
1) like dissolves like (nonpolar buried in nonpolar)
2) folded must be happier than unfolded (solvent entropy)
3) two atoms cannot be in the same place at once (steric hinderance
