Week 3: Protein Structures & Examples Flashcards
In free amino acid, carboxyl (-) and amino group (+)
______ at neutral pH
charged
Amino acids without _______ groups on side chains
exist as _______ (“twin ions”)
charged
zwitterions
Zwiterrions are _______ in solutions
electrically neutral
Isoelectric pH (pI) is pH at which molecule has _____
_____ of (+) and (-) charges
no net charge
same number
for most amino acids, pI =
pKa1 (a-carboxyl) + pKa2 (a-amino)/2
amino acids are usually more soluble at ________ than they are at _______ because they have _______ at ______, and the molecules tend to ________. When the molecular charge is zero, the amino acids can _________.
pH extremes
neutral pH
a net charge
repel each other
aggregate more easily.
four levels of protein structure:
primary, secondary, tertiary, and quaternary.
Not all proteins have ______. For example, only proteins with ______ have quaternary structure.
all four levels
multiple polypeptide chains
Amino acids linked by ______
covalent peptide bonds
Primary protein structure (1°) is the ____ in which amino acids are _____
order
covalently linked together
Both ______ and ______ important in primary structure
amino acid content
order
Primary structure helps determine _____, which determines _____
3D conformation
properties
The three-dimensional arrangement of all atoms
Tertiary structure
Sickle cell anemia results from change in ________
_____ mutation
primary structure
Glu -> Val mutation
The order of amino acid residues in the polypeptide chain
Primary structure
The interaction between subunits in proteins that consist of more than one polypeptide chain
Quaternary structure
The hydrogen-bonded arrangement of the polypeptide backbone.
Secondary structure
When a protein is denatured, the interactions that determine _________ are overcome by the presence of the denaturing agent. Only the ______ remains intact.
secondary, tertiary, and any quaternary structures
primary structure
What is the nature of “random” structure in proteins?
three-dimensional features of these parts of the protein are repeated from one molecule to another
Replacement of tryptophan causes the greatest effect on protein structure and function because Tryptophan has the _____ of any of the common amino acids, and it tends to require _____.
largest side chain
a nonpolar environment
Replacements such as Lys -> Arg usually have very little effect on protein structure and function because
Lysine and arginine are both basic amino acids; exchanging one for the other would not affect the side-chain pKa in a significant way.
Glycine is frequently a ________ because its side chain is…
conserved residue
so small that it can fit into spaces that will not accommodate larger ones.
An amino acid is usually more soluble in aqueous solvent at pH extremes than it is at a pH near the isolelectric point of the amino acid. (Note that this does not mean that the amino acid is insoluble at a pH near its pI.) Why?
At pH extremes, the amino acid molecules mostly carry a net charge, thus increasing their solubility in polar solvent.
Based on the pKa values for the 20 amino acids commonly found in proteins, is there any amino acid that could serve as a buffer at pH 6?
Yes, histidine is the amino acid that can act as a buffer at pH 6 because its side chain pKa is very close to 6, meaning it can readily accept or donate protons over the pH range 5-7.
How do the resonance structures of the peptide group contribute to the planar arrangement of this group of atoms?
The two resonance structures give the C-N bond partial double bond character while leaving the C=O bond with partial double bond character.
The pKa values for the α-COOH and α-NH3+ ionizations ________ with changing side group functionality.
vary relatively little
Globular proteins tend to be ______ in the cytosol or extracellular medium, while fibrous proteins tend to _____.
soluble
form insoluble aggregates
Globular proteins often participate in _____, while fibrous proteins are often employed ____.
biochemical reactions,
employed as structural elements regulating cell shape
Globular proteins are _______ in shape, while fibrous proteins ________.
roughly spherical
usually have extended shapes
On average, the relative composition of globular and fibrous protein types are _____
similar.
Globular and fibrous proteins are different in this respect:
Globular and fibrous proteins are similar in this respect:
Differ in: aqueous solubility, biological function, and molecular shape
Similar in: amino acid composition
Proline is often found at places in proteins that are not alpha-helical because…
unlike other amino acids, proline has a fixed angle of rotation around its C(alpha)-N bond. Proline fits well into beta-turns.
Five possible features limit possible protein configurations and conformations:
- Only one of the 20 available amino acids is used at each position along the primary sequence.
- D- or L-amino acids could be used in proteins. Biology chooses to use only the L-steroisomers.
- The partial double bond character of the C=O and C-N bonds in the peptide group restricts the conformations of the amide plane to the cis and trans forms.
- Steric clashes between atoms restrict the possible Ramachandran angles (or conformations) between amide planes.
- The primary structure of a protein determines the protein’s optimum tertiary structure due to the intrinsic restrictions on possible molecular geometries inherent to each amino acid residue.
There are two critical amino acid residues near the heme group in both myoglobin and hemoglobin. These residues are…
His and His
Two histidine residues on either side of the heme group plane play an important role in the binding of O2 to the heme iron atom. One His forms part of the coordination system for the iron. The other His is near the O2-Fe binding site and modulates ligand interactions with the iron atom.
________ is primarily an O2 storage protein. It has a hyperbolic O2 saturation vs. PO2 curve that allows it to bind O2 readily at the low PO2 values found in peripheral tissues.
Myoglobin
______ is primarily an O2 transport protein. It has a sigmoidal O2 saturation vs. PO2 curve that allows it to bind O2 readily at the high PO2 values found in the lungs and to release O2 readily at the low PO2 values found in peripheral tissues.
Hemoglobin
Both myoglobin and hemoglobin are dominated by ________ and both contain ______ with a central iron atom that forms the ________ of the proteins.
α-helical secondary structure
heme groups
O2 binding site(s)
2,3-BPG promotes ____ among the _____.
2,3-BPG causes movements in the _______ to be coordinated.
The amino terminal nitrogens of the two α subunits of hemoglobin interact with the _____ on 2,3-BPG.
cooperativity, subunits of hemoglobin
four subunits of hemoglobin
negative charges
In oxygenated hemoglobin, pKa = 6.6 for the histidine residues at position 146 on the β-chain. In deoxygenated hemoglobin, the pKa of these residues is 8.2. This data indicates that deoxygenated hemoglobin is a _____ acid than oxygenated hemoglobin. This change in the pKa of the histidine residues underlies the Bohr effect in which _____ in the hydrogen ion concentration reduces the affinity of hemoglobin for O2. The binding of H+ to these His residues _____ their interactions with
___ residues via ______.
weaker
an increase
increases
Asp
salt bridges
How does the difference between the β-chain and the γ-chain of hemoglobin explain the differences in oxygen binding between Hb A and Hb F?
The loss of a histidine residue _____ the interaction of fetal hemoglobin with 2,3-bisphosphoglycerate.
The replacement of ____ in fetal hemoglobin reduces the cooperative interactions of fetal hemoglobin subunits as compared to adult hemoglobin subunits.
reduces
His with Ser
Fetal hemoglobin is essential for the survival of placental animals because Hb F has a _____ affinity for O2 at oxygen partial pressures found in the placenta as compared to the oxygen affinity of Hb A. This difference in affinity for O2 allows O2 from the hemoglobin in the _____ to transfer to the hemoglobin in the ____
higher
mother
fetus
Compared to Hb A, Hb F has a higher affinity for oxygen at the PO2 values found in the placenta. Thus, fetal hemoglobin will “steal” O2 from the mother’s hemoglobin, providing the fetus with oxygen.
A prion is a potentially infectious ______ found in multiple forms in _______. It tends to form plaques that destroy the
______ . Prions ____ species
protein
mammals
nervous tissue
are transmissible across
A series of encephalopathies have been found to be caused by prions. In ____, the disease caused by prions is called bovine spongiform encephalopathy, or more commonly mad-cow disease. In _____, the disease is called scrapie. In ____, it is called Creutzfeldt-Jakob disease.
cows
sheep
humans
Several side chains can be coordinated to a _____ ion.
metal
Hydrogen bonding occurs between the _______
side chains of amino acids.
In secondary structure, each amino acid residue has two bonds with _______ designated by _______
Types - ______ arrangements
free rotation, Ramachandran angles
α-helix and β-pleated sheet
Ramachandran Angles:
____ around these bonds
- phi (Φ): bond between the α-carbon and amino nitrogen
- psi (Ψ): bond between α-carbon and carbonyl carbon
Free rotation around these bonds!
α-Helix:
Helical conformation allows for _______ of _______
* _______ bond strength
* ______ conformation
linear alignment, hydrogen bonds
Maximum
Stable
α-Helix:
Each peptide bond is ______
* Coil of helix is _______
trans and planar
clockwise or right-handed
α-Helix
* ____ of each peptide bond H-bonded to ______
C═O
N-H of fourth amino acid residue
α-Helix:
* C═O≡H—N H bonds ______ to helical axis
* All R groups _______ from the helix
parallel
point outward
Factors That Disrupt the α-Helix:
Proline bends the backbone and restricts rotation due to cyclic structure. Results in absence of N—H for H-bonding in α-
amino group.
Strong electrostatic repulsion caused by proximity of
like charges
Steric repulsion caused by proximity of bulky
side chains
Examples of electrostatic repulsion due to like charges in alpha helix:
Adjacent Lys and Arg or Glu and Asp
Examples of steric repulsion due to bulky groups in alpha helix:
Val, Ile, and Thr
________ in alpha helical structures _______ regular nature of helix
Irregularities
break up
The alpha helix is stabilized by _________ to the helix axis within the ______ of a _________.
hydrogen bonds parallel
backbone
single polypeptide chain
The peptide backbone in the ______ is almost completely extended.
beta sheet
β-Pleated Sheet:
* Backbone _______
* Hydrogen bonds between peptide chains can be _____
Polypeptide chains lie ______ to one another
mostly extended
interchain or intrachain
adjacent
In β-Pleated Sheet:
If polypeptide chains ________, the sheet will be parallel
If polypeptide chains _______, sheet will be antiparallel
run in the same direction
run in opposite direction
In β-Pleated Sheet, _______ -> more linear alignment of H bonds
Antiparallel strands
β-Pleated Sheet:
* Gives rise to _______
* H bonds ________ to protein chain (not parallel)
* R groups _____
* Each peptide bond is ______
zigzag structure
perpendicular (not parallel as seen in alpha helix)
alternate above and below the plane
trans and planar
Irregularities in Regular β-Pleated Structures:
Beta bulge
Reverse turns
β-bulge: Common nonrepetitive irregular secondary
motif in ________
antiparallel β-sheets
Reverse Turns
* Where polypeptide chain _______
* Due to presence of _______
* Polypeptide chain ______
folds back on itself
glycine and/or proline
changes direction
Ramachandran angles are the angles of the ______ as they rotate about the ______. The angles are both defined as zero when the two planes would be overlapping such that the _______ of one contacts the _______ of the other.
amide planes
a-carbon
carbonyl group
N—H
A β-bulge is a common ______ found in _______. A misalignment occurs between strands of the β-sheet, causing _______.
nonrepetitive irregularity
antiparallel β-sheets
one side to bow outward.
A reverse turn is a region of a polypeptide where the _______. There are two kinds—those that contain _____ and those that do not.
direction changes by about 180°
proline
Proline is frequently encountered at the places in the myoglobin and hemoglobin molecules where the polypeptide chain ______ because the geometry of the proline residue is such that it does not fit into the _____, but it does fit exactly ________.
turns a corner
a-helix
for a reverse turn
_______ is the only residue small enough to fit at crucial points in the collagen triple helix.
Glycine
Supersecondary structures - Result from combination of _________
α-helices and β-strands
βαβ unit -
Two parallel strands of β-sheet connected by α-helix
αα unit -
Also called ________
Contains two antiparallel α-helices
helix-turn-helix
β-meander -
Antiparallel sheet with series of tight reverse turns
Greek key is formed when _______ on itself
polypeptide chain doubles back
Motifs are ______ structures
repetitive supersecondary
β-barrel -
Created when β-sheets extensive enough to fold back on themselves
Significance of Motifs:
Provide information about _______
* Don’t predict _______
Relates to function of _________
protein folding
biological function of protein
conformational domains
The experimental technique used to determine the tertiary structure of a protein is _________.
X-ray crystallography
_______ relates to way secondary structures fold back on each other
tertiary structure
General characteristics of fibrous proteins:
Extended backbone, rod-like shape
In long fibers or large sheets
Insoluble in water
Fibrous proteins tend to be _______ and therefore…
mechanically strong
often make up structural components of cells and tissues
Collagen can be found in connective tissue, including…
cartilage, bones, teeth, skin, and blood vessels
Collagen Triple Helix:
* Each chain has repeating sequence of ______
X—Pro—Gly or X—Hyp—Gly
three amino acid residues
In collagen triple helix: Gly is every ______
3rd residue
Hydrogen bonds between __________ form to strengthen structure of collagen
hydroxyproline and hydroxylysine residues
General characteristics of globular proteins:
______ critical for _____
Backbone _____ to give ______
_______ tend to be buried in core
_______ tend to be on surface
- __________ with H2O
Interactions of side chains, folding
folds back on itself, spherical shape
Hydrophobic (nonpolar) residues tend to be buried in core
Hydrophilic (polar) residues tend to be on surface
H bonds and ion-dipole interactions
Solubility of globular proteins?
Soluble in water and salt solutions due to hydrophilic surfaces
Process of protein denaturation and renaturation:
Folding instructions in the ______ of amino acids
sequence
Forces involved in tertiary structures:
H bonds
Electrostatic
Hydrophobic
Metal ion coordination
Disulfide bonds
The final conformation of a protein is the result of the…
interplay of all the stabilizing forces
Configuration refers to the position of groups due to _______. Examples include…
Conformation refers to the positioning of groups in space due to _______. An example is…
covalent bonding
cis and trans isomers and optical isomers
rotation around single bonds
the difference between the eclipsed and staggered conformations of ethane
Methods for determining protein tertiary structure:
X-ray crystallography
NMR spectoscopy
Primary method of determining protein tertiary structure
X-ray crystallography
NMR spectroscopy:
Analyzed at _____
Protein samples in _____
Computer interprets data and converts ____
distinct frequencies
aqueous solution
to 3D shape
X-ray crystallography:
Need _____ in which molecules have _____
Subjected to _____
Electrons in atoms scatter _____
Produces ____
Computer interprets data and converts _____
perfect crystal, same 3D structure and orientation
X-ray beam
beams
diffraction pattern
to 3D shape
What is the similarity between X-ray crystallography and NMR spectroscopy?
Computer interprets data and converts to 3D shape
Myoglobin does NOT exhibit ____
quaternary structure
Myoglobin consists of _____ polypeptide chain of _______ + ______
single
153 amino acid residues
heme prosthetic group (added after like prosthetic limb)
General structure of myoglobin (Mb):
______ in ______ pocket
100% _______
Heme (Fe). hydrophobic
a-helical (8 helices), No β-strands
Heme:
Iron-containing cyclic compound
Like other _____ proteins, myoglobin has ______ on exterior and _______ on interior
globular
polar side chains
nonpolar side chains
6 coordination links to heme iron (Fe2+) in myoglobin:
* Four _____ of four ______
* 5th coordination one of ______
* ______ at 6th coordination site
N atoms, pyrrole-type rings
N atoms of His F8
O2 bound
Significance of His E7 and His F8?
In absence of His E7, CO bound in linear alignment
His E7 forces angled binding
Denaturation: _______ caused by breakdown of ______
Unraveling of 3-D structure
noncovalent interactions
Denaturation is accomplished by:
Heat (overcomes intramolecular forces)
Large changes in pH
Detergents
Detergents in denaturation:
SDS
Urea and guanidine hydrochloride
β-mercaptoethanol
Detergents
* Sodium dodecyl sulfate (SDS): disrupts ______
* Urea and guanidine hydrochloride: disrupt _____
* β-mercaptoethanol: reducing agent that disrupts ______
hydrophobic interactions
H bonding
disulfide bonds
Denaturation and Refolding in Ribonuclease:
* _____ used to reduce disulfide bridges
* Urea added to:
* Native conformation recovered by _____
β-mercaptoethanol
Urea added to facilitate unfolding and Increase accessibility of disulfides to reducing agent
removing mercaptoethanol and urea
The function of hemoglobin is ______, and it must be able both to ______, depending on conditions.
oxygen transport
bind strongly to oxygen and to release oxygen easily
Hemoglobin has a ________ structure
quaternary
Quaternary Structure of Proteins:
* Pertains to proteins with _______ polypeptide chain
* Each chain ____
> 1
is a subunit
Oligomers: Molecules of ________
* Include dimers, trimers, and tetramers
number of smaller subunits
Hetero oligomers have…
different polypeptide chains
Example of heterotetramer:
Example of homotrimer:
hemoglobin
collagen
Quaternary Structure of Proteins:
* Chains interact with one another _________
* May be _______ between subunits
* ________
noncovalently
Electrostatic attractions, H bonds, hydrophobic interactions
disulfide bonds
Covalent bond
Allosteric: Property of _______
* “Allos” = “other”
* _________ in one subunit induces ______ in another subunit
multisubunit proteins
Conformational change, change
Hemoglobin is a ______ with an overall structure of ______
tetramer
α2β2 (two a-chains, two β-chains)
One molecule of myoglobin binds _____ O2
* Hemoglobin can bind _____ O2
one
up to four molecules of O2 because it has 4 heme groups
between hemoglobin and myoglobin:
Similarities: both contain _____; both are _____; secondary structure is ______.
Differences: hemoglobin is a ______, while myoglobin is a _____; oxygen binding to hemoglobin is _____, but _______ to myoglobin.
a heme group
oxygen binding
primarily a-helix
tetramer, monomer
cooperative, noncooperative
Myoglobin’s highest level of organization is ______.
Hemoglobin’s is ________.
tertiary
quaternary
Binding of O2 to Hemoglobin (Hb) exhibits ________
* When one O2 bound, _________
* Sigmoidal shape indicates _________
positive cooperativity
becomes easier for next O2 to bind
2 possible conformations
Structure of __________ (different from
__________
oxygenated hemoglobin - R (relaxed) state
deoxygenated hemoglobin - T (tense) state
Myoglobin
* Function - Oxygen _______
* Requirement - Bind O2 strongly ______
Saturation - 50% at ______ partial pressure of O2 (pO2)
storage
very low pressures
1 torr (p50)
Hemoglobin
* Function - Oxygen ______
* Requirement - Bind ______
transport
strongly to O2 and release O2 easily (need 2 conformations)
The function of hemoglobin is oxygen _____; its sigmoidal binding curve reflects the fact that it can ______ at comparatively high pressures and _______ at lower pressures. The function of myoglobin is oxygen _______; as a result, it is easily saturated with oxygen at _______, as shown by its _______ curve.
transport, bind easily to oxygen, release oxygen
storage, low pressures, hyperbolic binding
Bohr effect: In the presence of _____ and _____ , both of which bind to hemoglobin, the oxygen-binding capacity of hemoglobin _______.
H+, CO2
decreases
In the absence of 2,3-bisphosphoglycerate, the binding of oxygen by hemoglobin resembles that of myoglobin, characterized by _______. 2,3-Bisphosphoglycerate binds at the center of the hemoglobin molecule, increases _______, stabilizes the deoxy conformation of hemoglobin, and modulates the binding of oxygen so that it can easily be released in the capillaries.
lack of cooperativity
cooperativity
Fetal hemoglobin binds oxygen _______ than adult hemoglobin
more strongly
Hb conformation altered at ______
Promotes ______ and ______ in tissues
_______ a stronger acid
high [H+]
O2 release, CO2 binding
Oxygenated Hb
Myoglobin _______ by pH
unaffected
Hb also bound to __________
* Binding is _______
2,3-bisphosphoglycerate (BPG)
electrostatic
Binding of BPG ______ oxygen affinity
lowers
Bioinformatics in predicting ______
Search for regions of ______
_______ methods used
protein structure
sequence homology (similarity of monomer sequences)
Different methods used
Protein folds to _______ surface
minimize hydrophobic
_______ form from aggregation of lipids
_______ in contact with water
______ away from water
Liposomes
Polar head groups
Nonpolar tails
Hydrophobic interactions are _______ processes
* Result in _______ in entropy of Universe
spontaneous
increase
Molecular chaperones and their basic function:
Promote correct folding
Prevent aggregation
Consequences of protein misfolding: _____ can result
Disease states such as prion disease
The normal form of the prion protein has a ______ content compared to the beta-sheet content. The abnormal one has an ________.
higher a-helix.
increased beta-sheet content
Which two amino acids are usually found at reverse turns? Why?
Proline: Cyclic structure allows for unusual contortion of the polypeptide chain
Glycine: Lacks steric strain so chain is more flexible.
Bohr effect relates what two factors?
Partial pressure of CO2 and pH (hydrogen ion concentration) are both related to oxygen affinity. Some students took this to mean how carbon dioxide and pH were related:
* As P CO2 increases, H+ also increases. (pH will decrease)
* When considering LeChatlier’s principle, the equilibrium of
* H+ + HCO3 - H2 CO3 CO2 + H2 O
* As pH decreases, H+ increases, and equilibrium is pushed to the right, increasing carbon dioxide.
* As carbon dioxide partial pressure decreases, it pulls the equilibrium to the right, also decreasing the
hydronium ion concentration and increasing pH.
What we were really going for was the connection to oxygenation of hemoglobin:
HbO + CO2 + H+ O2 + Hb(CO)H+
Changes in pH (and, related, CO2 ) affect the equilibrium between oxygenated and deoxygenated hemoglobin.
Higher CO2 / H+ will decrease oxygen affinity (so there will be more oxygen release) whereas low CO2 and H+
will increase oxygen affinity.
Disulfide bridges are a form of _________.
Tertiary structures are formed by interactions between ______ and result in _________-.
tertiary structure
R-groups
3D configurations
When studying sickle cell anemia, you learn about the substitution that replaces a glutamic acid
residue with a valine residue. You happen to come across a case where a patient has a mutated β-
hemoglobin allele but miraculously has no symptoms. How is this possible?
Their mutation involves the substituting aspartate in place of glutamic acid, not valine.
(both with negatively charged side chains)
Despite the fact that the body operates at a pH of 7.4, the carbonate buffer system HCO3-/H2CO3 (pK
6.1) still works rather well. How can this be?
It is also influenced by CO2 content in the body, which can shift the equilibrium to a more favorable pH.
We usually assume a buffer system to have an ideal operating range of within 1 of its pKa value. However, this is
not the case for our bodies. This is because CO2 has an influence on acid-base equilibrium in the body, so we do
not assume that our buffer system is closed; there are external factors that allow it to still be effective at our higher
operating pH.
a protein denatures when its _______ are deactivated, but _______ will remain intact.
IMFs
covalent bonds
