L3-5: Structure of Protein I, II & III Flashcards
What is the structure of histidine? What are the properties of this AA? What is it’s pKa?
-histidine, basic, pKa = 6.00
Describe what happens at a molecular level when oxygen binds to a heme in deoxygenated hemoglobin. How do these events contribute to allosterism? How does the oxygen-binding behavior of hemoglobin translate into an efficient oxygen carrier?
Deoxygenated Hb is in a T-form (tight) with low o2 affinity. A valine reside partially blocks the o2 binding site in the beta subunits. When o2 concentration increases (ie. in lungs), o2 is forced by mere concentration onto alpha subunits. A conformational change occurs as a result of this binding and the valine residues are rotated out of the o2 binding site in the beta subunits. The Hb molecule is now in a high o2 affinity form known as the R-form (relaxed). The importance of this is considered when looking at the physiological range when o2 is loaded / unloaded from Hb.
What are the properties of this AA?
-cysteine, polar uncharged
What are the properties of this AA?
-glutamine, polar uncharged
What is collagen?
Collagens are the most abundant family of proteins in the body. They are glycoproteins of CT. It is composed of triple helical units, ie. three polypeptide chains wrapped around each other. These are not alpha-helices as the helix turns to left and also, proline is present. The helices are held together covalently.
What are the properties of this AA?
-asparagine, polar uncharged
How do the oxygen-binding properties of HbF and HbA1 differ? Why is this important?
- HbA1 refers to the alpha2beta2 Hb tetramer, which is the most common form in adults, account for over 90% of total in blood - HbF is the predominant Hb tetramer present in the 2nd/3rd trimester of development. In contrast to adult Hb, HbF curve is shifted to the left indicating that at a specific o2 pressure, HbF is more saturated than adult Hb. Has higher affinity for o2 than adult Hb. This ensures that the fetus’ high metabolic o2 requirements are met. - This is due to the replacement of a histidine residue with a serine residue in the gamma chain of HbF. As a result, HbF has reduced affinity for 2,3-BPG and is left shifted.
Describe the 4 main groups of amino acids. What are their characteristics?
a.) non-polar, aliphatic: hydrophobic and chained/branched, found interior aspect of proteins, uncharged Gly, Ala, Val, Leu, Ile, Met, Pro • Gly – no asymmetric carbon (2 Hs) • Pro – ring structure • Met – sulfur-containing AA b.) aromatic: hydrophobic (non-polar rings), often found interior of water-soluble proteins, uncharged Phe, Tyr, Trp • Tyr – has OH group and can be phosphorylated c.) polar, uncharged: hydrogen bond, interior/exterior of proteins Ser, Thr, Cys, Asn, Gln • Ser/Thr – have OH groups that can be phosphorylated • Cys – sulfur-containing AA, forms disulfide bridges with other thiol containing molecules (ie. cystine = 2 cysteines) d.) Ionizable side chained AA – basic/acidic: Acidic: Asp, Glu (net -1 charge at physiological pH) Basic: Lys, Arg, His* (net +1 charge at physiological pH) * His can be basic/uncharged as pKa = 6.0
What is meant by the term “post-translational modification”?
Post-translational modifications refer to changes made to protein following translation from RNA to protein. This includes attachment of prosthetic groups, glycosylation, lipid attachments, phosphorylation and proteolysis.
Describe the tertiary structure of myoglobin. What is the essential prosthetic group in myoglobin and what is its function?
Myoglobin is an oxygen binding protein found in muscle tissue. It comprises eight alpha-helices. Mb has a heme prosthetic group, which is a porphyrin ring bound to iron. Binding of oxygen occurs at iron. It effectively binds oxygen at low concentrations.
Describe the structural features of an α-helix. What amino acid is disruptive to the formation of α-helices?
Alpha helices are rod shaped spirals where the polypeptide chain winds in a clockwise direction. Each peptidyl C=O is hydrogen bonded to H-N groups four amino acids down the chain. Proline residues disrupt the H-bonding of the alpha helix by putting a sharp bend in the polypeptide. Bulky R-groups of multiple like-charged R-groups can block the formation of alpha helices.
What is meant by the term “hemoglobinopathy”?
This refers to pathologies related to Hb structure.
The formation of native protein structure is said to be cooperative. What does this mean? Outline the ‘seeding and nucleation’ model for the progression of prion diseases, Parkinson disease, and Alzheimer disease. What proteins are associated with these disease states?
Cooperative native protein structure indicates that the protein folding cannot be a random process, but instead occurs through favored pathways. This involves the rapid formation of short stable segments of secondary structure, which generate structural motifs which continue to fold into a thermodynamically stable protein structure. The seeding/nucleation model is where a misshaped protein (typically beta-sheets) induces other proteins (during folding) to change confirmation, which has a trickle down/domino effect on other proteins. Parkinson’s: alpha-synuclein is implicated, affect NT release (?) Alzheimer’s: tau and amyloid-beta are implicated, affecting microtubule (?) and neuronal plasticity (?) respectively
Describe how a mutation in the amino acid sequence could affect protein structure and/or function. Give several examples.
A change in amino acid sequence will lead to different interactions and therefore different folding (see 14). Different structure will confer different function. The original purpose of the protein can no longer be served. Examples of diseases where misfolded proteins are implicated: • CJD: inherited or spontaneous • Kuru: infectious • vCJD: infectious Above diseases lead to spongiform encephalopathies (neurodegeneration, brain becomes spongy) • Parkinson’s: loss of dopaminergic neurons, formation of Lewy bodies (aggregates of alpha-synuclei protein seeds more) leads to tremor, bradykinesia, postural instability • Alzheimer’s: neurological condition leading to dementia from plaque/fibrillary structures in brain containing amyloid-beta and tau proteins that seeds more
Explain what occurs to the Hb binding curve as pH, 2,3-BPG, temp, CO2 change? Draw it.
Identify the α-carbon and an L-amino acid. Which amino acid does not have a chiral α-carbon?
The alpha-carbon is the central carbon to each amino acid. All amino acids except glycine have a chiral alpha-carbon and will have either a D or L stereoisomer. All mammalian proteins contain only L-amino acids.
What are the properties of this AA?
-phenylalanine, aromatic hydrophobic
What are the properties of this AA?
-tryptophan, aromatic hydrophobic mostly, slightly polar
What are the properties of this AA?
-tyrosine, aromatic hydrophobic (typically)
Define primary structure, secondary structure, tertiary structure, and quaternary protein structure.
a. Primary structure: the amino acid sequence of the polypeptide chain b. Secondary structure: a segment of polypeptide chain that has regular repeating structure. Results from H-bonding between the C=O and H-N groups of the polypeptide backbone. Alpha-helices and beta-pleated sheets. c. Tertiary structure: the 3D structure resulting from the interaction of various secondary structures and non-ordered regions of the polypeptide chain, results from disulfide bridges (covalent) and hydrogen bonding, ionic interactions (salt bridges) an hydrophobic forces (all non-covalent) d. Quaternary structure: protein molecules that have more than one subunit, each with tertiary structure, have overall quaternary structure. The subunits associate through same forces found in tertiary structures
What are the properties of this AA?
-Glycine, non-polar
Identify the amino acids that contain sulfur.
Met, Cys
What are the properties of this AA?
-threonine, polar uncharged
Describe the quaternary structure of hemoglobin. Compare and contrast the structure and oxygen binding properties of hemoglobin and myoglobin.
Hemoglobin is comprised of two alpha-globulin subunits and two beta-globulin subunits. Each has an iron containing heme prosthetic group. The hemoglobin forms by association of two alpha-beta-dimers which interact through H-bonds and salt bridges. Each subunit resembles that of myoglobin. Myoglobin has high affinity for o2 at low partial pressures of oxygen (hyperbolic o2 binding curve), whereas hemoglobin has a lower affinity for oxygen at lower partial pressures and its affinity increases as partial pressures increase and a conformational change takes place (sigmoid binding curve), changing affinity of each heme group that is to be “loaded.”
Explain how 2,3-BPG; CO2 and H+ influence Hb’s affinity for oxygen. Provide physiological relevance.
- Increase in 2,3-BPG decreases Hb’s affinity for o2 (binds in central cavity, stabilizing T-form through strong ionic interactions) promoting release - Increase in H+ conc (low pH) decreases Hb’s affinity as they bind His, forming positive residue which binds aspartate, stabilizing T-form and promoting o2 release - CO2 binds to N-terminal of Hb subunits forming carbamates. Carbamates carry a negative charge and participate in salt bridges that stabilize T-form, promoting o2 release Physiological relevance: In rapidly metabolizing tissue, CO2 and proton concentration is high, o2 requirement is high. Protonated His and carbamate formation stabilize the T-form of Hb resulting in offloading of o2 here. Conversely, in lungs, removal of CO2 (requiring proton with bicarb ion), causes deprotonation of Hb and conversion to R-form where conveniently o2 tension is also high. Amount of o2 carried to peripheral tissues increases as a result.
What are the properties of this AA?
-proline, non-polar
What are the properties of this AA?
-glutamate, acidic
What is meant by a prosthetic group?
Many proteins require association of metal ions and / or certain organic molecules in order for them to function. Prosthetic groups are associated organic molecules permanently bound to them.