tasnimjaisee's version from 2017-10-21 18:36

Lecture 4 part 1

Question Answer
smallest proteininsulin (15)
largest proteintitin
Most important forces stabilizing the specific structures of a given protein are...non-covalent
Native proteins are ___ stablemarginally
StabilityDifference in the free energies of the folded/unfolded states
Folded proteins occupy a ___-energy state that makes the native structure most stable.Low
Protein folding a ___ process (rapid/slow)rapid
Protein folding and unfolding is a ___ processcooperative
Primary Structurelinear sequence of amino acids
Secondary Structurelocalized interactions within a polypeptide
Tertiary Structurefinal folding patter of a single polypeptide
Quaternary Structurefolding pattern with multiple polypeptides
What does primary structure tell of the 3d structure?Nothing
Primary Structure can be determined by..investigation of the protein or corresponding gene
Secondary Structure important typesa-Helicies and b-Sheets
Secondary structure regularities in local conformation is maintained by Hydrogen bonds between (2) amide hydrogen and carbonyl oxygen
To represent a viable form of secondary structure the folding pattern must... (2)Optimize the hydrogen bonding potential and polypeptide chain conformation
Oxygen of the carbonyl group and the hydrogen of the amide nitrogen are ____ to each othertrans
Rotation around C-N bond is restricted due to the partial double-bond nature of the peptide bond, which is?No freedom of rotation
Most residues within biological peptides and proteins tend to be in the ____ configurationtrans
Each α-carbon is held within the _______ through single bonds, about which there is complete ______main-chain - freedom of rotation
phi and psi can range from –180 to 180
Which handed helix is A-HelixRight-Handed
Each C=O (residue ___) forms a hydrogen bond with the amide hydrogen of residue ___n and n+4
All C=O groups point toward?C-terminus
Secondary Structure: α-Helix: Entire helix is a ___ with (___) N, (___) C-terminidipole and + and -
Proline is considered a helix breaker because?Rigidity
Which AAs are are not usually found in α-helicies?Glycine - Proline
Do stretches of similarly charged residues destabilize or restabilize the helix?Destabilize
Residues separated by 3-4 positions in the primary structure are close together in helical structure3-4
positively and negatively charged residues found ___ positions away from each other3 or 4
Aromatic residues separated by 3 or 4 positions to enablehydrophibic interactions
Secondary Structure: A small electrical ___ exists in each peptide bonddipole
Residues which are four residues away from each other in the primary sequence will be on ___ side of an alpha-helixsame
Conformation of β strands (2)Polypeptide chains - Side chains above and below
Hydrogen Bonding Pattern of β strandsstabilized by hydrogen bonds between C=O and -NH on adjacent strands
Are B strands in a sheet parallel or anti-parallel?Both
Are Anti-parallel B or Parallel B strands more stable?Anti-parallel B
How can a rise to amphipathic beta sheet be done?Alternating polar & non-polar residues in primary structure
Tertiary structure describes the ___ range aspects of sequence interactions within a polypeptide chain (longer/shorter)longer
Residues separated by great distance in primary structure may be in ___ in tertiary structureClose
What actually determines tertiary structure?AAs
Proteins exhibiting quaternary structure are composed of?Multiple subunits separated by polypeptide chain
Can Quaternary structures have multiple subunits of the same type of polypeptide? or be composed of different types of polypeptidesBoth
Quaternary structures often associate by which type of interactions?Non-covalent interactions
Fibrous ProteinsKeratin - Collagen - Silk
Globular ProteinsMyoglobin - Hemoglobin

Lecture 4 part 2

Question Answer
Keratin contains a ____ where positions a and d are ____pseudo7repeat - hydrophobic
In which structure form does Keratin contain a pseudo-seven repeat?Primary Structure
In which structure form does Keratin contain a right-handed, amphipathic alpha-helicies?Secondary Structure
In Keratin secondary structure, where does "a" and "d" end up?same face of the helix; hydrophobic strip
In which structure form does Keratin have a polypeptide strand presenting an alpha-helical rod?Tertirary Structure
In which structure form does Keratin have pseudoseven repeat generates hydrophobic surfaces?Quaternary Structure
Coiled-coil are formed by ____ surfaces interactions in ____ structures of Karotenhydrophobic - quaternary
The coiled-coil of keratin involves ___ right-handed helicies wrapping around each other in a ___ fashion2 - left-handed
Keratin individual units are linked together through which types of bonds?disulfide bonds
In which structure form does Collagen contain multiple repeats of Gly-X-Y?Primary Structure
In primary structure of X is often known as?proline or hydroxyproline
In which structure form does Collagen contain formation of left-handed helicies of three residues per turn?Secondary Structure
In which structure form does Collagen have a nearly the full length helical polypeptide?Tertiary Structure
In which structure form does Collagen have 3 left-handed helicies wrapping around each other in a right-handed fashion?Quaternary Structure
In which structure form does Collagen have coiled-coils?Quaternary Structure
What are collagen's individual units are linked together through?amino acid residues that undergo post-translational modification
What are hydroxyproline and hydroxylysine related to?amino acid residues that undergo post-translational modification (collagen bonds)
In which structure form does Silk contain six residue repeat?Primary Structure
In which structure form does Silk contain beta-sheets?Secondary Structure
To appreciate how silk has both strength and flexibility one needs to consider its structure in each of the three dimensions (3)polypeptides - hydrogen bonds - VDW and hydrophobic interaction sheets

Lecture 5

Question Answer
Ligandsmall molecule that binds specifically to a larger one
Enzymes are a unique class of proteins where the ligand is called the ___ and the binding site is called an ___substrate - active site
Which element will serve as a ligand for myoglobin?Oxygen
Hemoglobin’s ligands will include...oxygen and 2,3 bisphosphoglycerate
The binding of a ligand may cause a ___ change in the proteinconformational
Myoglobin (Mb)monomeric protein - oxygen storage in peripheral tissue
Hemoglobin (Hb)tetrameric protein in erythrocytes transporting oxygen from lungs to the periphery
Cellular iron is bound in which forms?Sequester - Less reactive
What system does heme consist of?Protoporphyrin ring system bound to single Fe2+
In what way does Fe2+ bind to O2?Reversibly
Protoporphyrin ring system provides ___ coordinating interactions with the iron atom4
Which characteristic of nitrogen prevent the conversion of Fe2+ to Fe3+?The electron-donating
Myoglobin and hemoglobin both used as a ___ oxygen-binding groupHeme
Explain Fe2+ seeking six coordinating interactions (3)4: heme ineractions - 5th: proximal histidine residue imidazole group - 6th: O2 Binding
A distal ___ provides a stabilizing interaction for bound oxygenhistidine
Carbon monoxide exerts its deadly effects by competing with ___ for binding to ___Oxygen - Heme
CO binds with ___ times greater affinity than O2200
Which animal's myoglobin was the first protein structure to be determined through x-ray crystallographySperm Whale
Myoglobin is a small globular protein consisting ofSingle polypeptide of 153 residues arranged in 8 A-helicases
Myoglobin is a small globular protein consisting of153 residues arranged in 8 A-helicases polypeptide - heme prosthetic group
Oxygen saturation curve of myoglobin is ____, indicating a single O2 binding constanthyperbolic
Amount of O2 required to half saturate the MyoglobinP50
P50 is how many torrs?3
Calculation of Fraction Saturationθ= [pO2] / ([pO2] + [P50])
How many torrs are in peripheral tissues regarding the partial pressure of O2?30
How many torrs are in lungs regarding the partial pressure of O2?100
O2 is transported bound by hemoglobin contained withinerythrocytes (RBC)
Hemoglobin is an example of ___ structurequaternary α2β2
Which type of protein is hemoglobin?Allosteric
R stateActive
T stateInactive
Allosteric Effector (Modulator)bind allosteric proteins separate from functional binding site
Allosteric ProteinProtein - Multiple subunits and multiple ligands - Ligand binding at one site affects ligand binding at another
Allosteric activators stabilize which state?R
Allosteric inhibitors stabilize which state?T
HomotropicNormal ligand and modulator are the same
HeterotropicModulator is different from the normal ligand
How would a protein that binds O2 with high and constant affinity react in the body?Saturate O2 in the lungs but not release it to tissues
How would a protein with a lower O2 affinity react in the body?Release O2 to tissues - Can't saturate in the lungs
How does hemoglobin solves saturation issues?Undergoes transition from a low-affinity state to high affinity state -> More O2 molecules bound (and vis versa)
The binding and release of O2 from Hb are ___ regulatedallosterically
Positive cooperativity --> Binding O2 by hemoglobinCauses conformational change making easier to bind subsequent
O2 binding promotes and stabilizes the R state which has ___ O2 affinity than the T statehigher
Where is the iron atom locaated on T state hemoglobinoutside the plane of the heme ring
With the partial pressures of oxygen found in the lungs, Hb will ___ ___ with O2completely saturate
With the partial pressures of O2 typically found in the extremes of the body Hb will release ___ of its O2 load1/2
When an initial highly purified hemoglobin suggested an extremely high affinity for oxygen, what happens?Limits proteins releasing oxygen into periphery
What does bisphosphoglycerate decrease?hemoglobins’ affinity for oxygen
Bisphosphoglycerate is a ___ allosteric ___ of hemoglobinheterotropic - inhibitor
Shape of BPG5 negative charged units binding to +ve pockets between subunits of deoxyhemoglobin
How does a fetus "breathe" inside a womb?Stripping O2 from material blood
Which has a higher oxygen affinity? Adult Hb of Fetal HbFetal Hb
Decreased affinity for 2,3 BPG translates into ___ O2 affinity for fetal Hbhigher
Adaptation to high altitude can rapidly occur through ___ production of BPG, from ___ mM to ___ mMincreased - 5 - 8
The increased BPG ___ the O2 affinity of Hb to ensure maintained O2 delivery to the peripherydecreases
The Bohr Effectdescribes the pH dependence of hemoglobin’s affinity of O2
During moderate exercise, ___ muscle activity increases the rate of the CO2 productionincreased; eventually lowering pH
In extreme exercise, muscle may produce ___ ___ to further drop pHlactic acid
CO2 + H2O ------>H+ + HCO-3
H+ + HCO-3 ------->CO2 + H2O
carbaminohemoglobinCO2 in tissues form covalent carbamate linkage to N terminus of hemoglobin chains
carbaminohemoglobin has three important outcomesCO2 transport to lungs - Release O2; lower Hb - Proton released contribute to Bohr O2
Sickle Cell AnemiaDefective hemoglobin; recognized by the sickling of red blood cells when exposed to low oxygen levels
Phi Anglealpha carbon to the amide nitrogen
Psi Anglealpha carbon to the carbonyl carbon.
Ramachandran PlotCommon structural motifs such as elements of secondary structure.


Question Answer


Question Answer
Alaninelooks like glycine but with CH3 on top
IsoleuineBar brought down from leucine
Methionineupside down cross
TyrosineHO from hexa
PenylalaninePenta with glycine
Cystine and methanonineHas S, Cystine is smaller
SerineLike cysteine but no S
AsparaginePerson structure with 1 ch2 in middle
GlutaminePerson with 2 ch2 in middle
ThreonineLike valine but with OH ontop insetad of CH3
HistidinePenta with glycine
LysineUpside down corss with N
ArgininePerson with N
AspartatePerson with dashed O's and 1 ch2
GlutamatePerson with dashed O's and 2 ch2