Molecules to Cells Quiz #1 Flashcards
What is the structure of an amino acid?
Each amino acid (except for proline) has a carboxyl group, an amino group, and a distinctive side chain (often called the R group) bonded to the α-carbon atom.
All amino acids (except glycine) found in proteins are in what configuration?
L-configuration
Protein secondary stucture: The process of folding typically follows a hierarchical sequence in which secondary structures involving __________ between __________ groups and __________ form first.
H-bonds, peptide bond carbonyl (C=O) groups, peptide bond amide hydrogens (>N-H)
Cystic Fibrosis
Chloride ion channel inhibited
Each amino acid (except for proline) has a ________ group, an ________ group, and ________ bonded to the ________.
carboxyl, amino, an R group, α-carbon atom
Name all of the hydrophobic aliphatic amino acids.
GAVLIMP Glycine Alanine Valine Leucine Isoleucine Methionene Proline
Name all of the hydrophobic aromatic amino acids and their characteristic UV absorbance spectra
WYF (wives smell good)
Tryptophan
Tyrosine
Phenylalanine
280 nm
Name all of the hydrophilic uncharged polar amino acids.
Why are these called uncharged?
STNQC (stinks) Serine Threonine (N) Asparagine (Q) Glutamine Cysteine
Their side chains do not ionize at physiological pH.
Note that the _______ groups of asparagine and glutamine are _______ and never carry a __ charge. Those side-chains are ______, not _______.
–NH2, not ionic, +, amides, amines
Name the hydrophilic charged amino acids. Indicate which can be positively and negatively charged.
K HERD (K) Lysine Histidine (E) Glutamic acid (glutamate) (R) Arginine (D) Aspartic acid (aspartate)
Lysine, histidine, and arginine are positively charged and glutamic and aspartic acid are negatively charged.
The ratio of protonated (HA) to unprotonated (A) forms can be calculated from the Henderson-Hasselbalch Equation: ___________________. Note that when the pH is one unit higher than the pKa, the [A]/[HA] ratio is ___; 2 pH units higher and [A]/[HA] is ___.
pH = pKa + log[A]/[HA], 10, 100
Define the isoelectric point, pI
The pH at which an amino acid, peptide or protein will have a net charge of zero
pKa = pH -> 50% prot/50% unprot \+1 pH unit -> \_\_% prot/\_\_% unprot \+2 pH units -> \_\_% prot/\_\_% unprot -1 pH unit -> \_\_% prot/\_\_% unprot -2 pH units -> \_\_% prot/\_\_% unprot
+1 pH unit -> 9% prot/91% unprot
+2 pH units -> 1% prot/99% unprot
-1 pH unit -> 91% prot/9% unprot
-2 pH units -> 99% prot/1% unprot
How do you calculate the isoelectric point (pI) from two pKa’s?
pI = (pK1 + pK2)/2
Explain the buffering effect of amino acids.
The pH of a solution is stabilized to changes from added base or acid near the pKa values of ionizable groups on amino acids.
The _________ group of __________ can spontaneously _________ to form a disulfide bond.
thiol/sulfhydryl, cysteine, oxidize
__________ bonds are important in stabilizing the circulating peptide hormone __________
Disulfide, insulin
The amino acids of proteins are joined by ________ bonds between the ________ group of one amino acid and the ________ group of the next.
peptide, carboxyl, amino
Proteins are synthesized on ribosomes from __-terminal to __-terminal and they are by convention drawn with the __-terminal to the left, __-terminal to the right.
N, C, N, C
Explain what limits the rotation around a peptide bond between amino acids.
The strong electronegativity of the carbonyl oxygen relative to the amide nitrogen within the peptide bond tends to delocalize electrons and create resonance. The C-N linkage has double bond character in 40% of structure. Since double bonds are always planar, peptide bonds exhibit this planar character with little bond rotation around the amide bond.
The preferred (i.e., low energy) orientation of adjacent R groups is \_\_\_\_\_\_\_\_\_\_\_\_\_ because \_\_\_\_\_\_\_\_\_\_\_\_\_ is minimized. This limits the number of available conformational states.
trans, steric hindrance
What are the orientations of the bonds flanking the alpha carbon in a polypeptide chain called? How do they limit conformational possibilities of protein folding?
phi (N-C) and psi (C-C) angles; the rotation around these bonds is limited, many combinations
of phi and psi angles cause the side chains of amino acids to clash and are thus unfavored. (Ramachandran plot)
The ______-handed alpha helix contains ___ residues per turn and is stabilized by ________ bonds
between the carbonyl of amino acid i and the amide proton of amino acid i+__. The H-bonds are ________ to the helix axis and the amino acid side chains (R groups) project ________________, minimizing ____________. Alpha helices on the surface of a protein are ___________, having a ___________ face projecting out into solvent and a __________ face projecting inward to the apolar core of the protein.
right, 3.6, hydrogen, 4, parallel, radially outward, steric repulsion, amphipatic, hydrophilic, hydrophobic
The beta pleated sheet is stabilized by _______ bonds running between _____________ atoms and _______ protons of non-contiguous parts of the polypeptide chain. Hydrogen bonds are ________ with the beta sheet. Side chain R groups ___________________________ the plane of the sheet. Beta sheets often form _________________ of proteins.
hydrogen, carbonyl oxygen, amide, co-planar, alternately project above and below, the hydrophobic core
Parallel beta sheets have ________ aligned in the __________. Anti-parallel beta sheets have ________ that ____________________.
peptides, same direction, peptides, alternate in direction
Which amino acid are often found in the places where α-helices or β-pleated sheets end and why?
Proline, because its ring structure prevents it from forming the H-bonds required for α-helices or β-pleated sheets.
What is a domain?
Domains are the smallest thermodynamically stable units of protein structure
What are metamorphic proteins?
Metamorphic proteins are proteins that exist in multiple distinct structures of approximately equal energy that are in equilibrium (envision a thermodynamic folding funnel with two wells of similar depth)
Where is keratin found, and explain the structure of keratin.
Keratin is the primary component of hair and nails.
It is a coiled coil protein that consists of two right-handed α-helices intertwined in a left-handed super-coil (called an α-coiled coil). Coils bond with each other via non-covalent (hydrophobic interactions, ionic bonds, H-bonds) and covalent (disulfide bonds) bonds.
A much higher number of disulfide cross-links makes nails (and horns, claws and hooves) rigid.
What is the most abundant protein in the body?
Collagen (20-25%)
What is the structure of collagen?
A typical collagen molecule is a long, rigid structure in which three left-handed helices (called α-chains) are wound around each other in a right-handed triple helix (called a coiled coil or super-helix).
What amino acids are important in collagen? Explain.
Collagen is rich in proline and glycine. The proline rings stack along the outside of the helix giving it rigidity. Glycine, having the smallest R group, is found at every third position of the polypeptide chain (repeating sequence, -Gly-X-Y-, where X is frequently proline and Y is often either hydroxyproline or hydroxylysine) so that it can fit into the restricted central space where the three strands come together.
Describe the mechanism of scurvy
The enzymes that hydroxylate the prolines and lysines of collagen to stabilize the triple-helical structure require ascorbate (vitamin C). The symptoms of scurvy (e.g., bleeding gums) are due in part to the decreased tensile strength of collagen.
“Cork screw” hair is often the earliest sign of scurvy and is thought to be due to inability to _________________________________.
rearrange the disulfide bonds of keratin
Outline the steps of type I collagen synthesis
Synthesis, post-translational modification, and triple helix assembly occur inside the cell, then the resulting procollagen molecule is secreted into the extracellular matrix where peptidases cleave N- and C-terminal propeptides. Once removed, the mature collagen triple helix (termed tropocollagen) self-assembles into fibrils, with subsequent cross-linking to form mature collagen fibers.
Where is elastin found, and describe its structure and assembly
Elastin found in the lungs, large arterial walls, and elastic ligaments.
The elastin polypeptide is comprised predominantly of small, nonpolar amino acids and is also rich in proline and lysine
Synthesis and Assembly: Elastin is synthesized from a precursor, tropoelastin, which is
secreted into the extracellular space where it interacts with specific glycoprotein microfibrils. Some of the lysyl side chains are oxidized to form allysine residues which cross-link with lysine amino groups of neighboring polypeptides to produce an extensively interconnected, rubbery network that can stretch and bend in any direction when stressed
Explain the mechanism of emphysema.
Elastase degrades elastin. Alpha1 antitrypsin (alpha1-AT) is a small protein that inhibits elastase, which is released by neutrophils. Elastase can destroy the alveolar epithelium if unregulated by alpha1-AT.
Causes:
Genetic: Inheritance of an allele with a E342K substitution that causes alpha1-AT to be retained inside the cell.
Environmental: Elements in cigarette smoke can oxidize a methionene residue in alpha1-AT that is essential for binding to elastase. This renders alpha1-AT unable to bind and inactivate elastase.
Explain the cooperative binding of oxygen to hemoglobin.
Binding of each O2 molecule to the hemoglobin tetramer increases the affinity with which the next O2 binds. Similarly, dissociation of each O2 decreases affinity for those remaining and they dissociate more easily. This cooperativity results in a sigmoidal O2 binding curve and that greatly increases the ability of Hb to release O2 in tissues.
What four things decrease hemoglobin’s affinity for oxygen?
Which of these is important in allowing hemoglobin to release oxygen in peripheral tissues?
Which is important in adapting to hypoxia?
H+ (lower pH), CO2, 2,3-DPG and increasing temperature (fever).
H+ and CO2 play an important role in allowing oxygenated hemoglobin to release O2 in tissues. 2,3-DPG allows hemoglobin to adapt to hypoxia by more easily releasing O2.
Explain the mechanism behind sickle cell disease.
Sickle cell disease is caused by an inherited homozygous mutation of the β-globin gene causing a change from glutamate (Glu) to valine (Val) at position 6 (E6V). This results in patients’ RBCs containing mainly hemoglobin S (HbS), which is comprised of two normal adult alpha-globin subunits and two sickle adult β-globin subunits. Valine is hydrophobic and its presence creates a sticky patch on deoxyHb that leads to polymerization of HbS tetramers into long chains. Those intracellular fibers cause the sickle cell shape of the RBCs that leads to problems in their passage through the microcirculation. These structural changes also lead to a shorter erythrocyte half-life and chronic hemolytic anemia.
Describe the structure of the hemoglobin genes.
Two alpha genes on chromosome 16, one beta gene on chromosome 11. The hemoglobin tetramer is comprised of 2 subunits coded by the α-globin gene family and 2 subunits coded by the β-globin gene family.
Why does oxygen need to be transported by hemoglobin in RBCs?
Because oxygen has low solubility in plasma (the non-cellular part of blood)
What happens to carbon dioxide in a RBC?
RBCs contain carbonic anhydrase which catalyzes the rapid reversible hydration of CO2 to carbonic acid (H2CO3). Carbonic acid then rapidly and spontaneously dissociates to bicarbonate (HCO3-) and a H+.
CO2 and, especially, bicarbonate are soluble in plasma and RBC cytosol and most of the CO2 made in tissues returns to the lungs as those species. About 14% of the CO2 made is carried bound to Hb (bound to α-amino groups of Hb).
Which form of iron can bind oxygen?
The ferrous form (Fe2+); Fe3+ is the ferric form of iron that cannot bind O2
What is myoglobin? How is it related to hemoglobin?
A monomeric protein abundant in muscle that is designed to store oxygen.
The alpha and beta subunits of hemoglobin are evolutionarily related to myoglobin, both proteins contain a Fe2+-protoporphyrin IX (Heme) prosthethic group that is responsible for binding O2.
Explain the differences between the oxygen binding curves of myoglobin and hemoglobin.
Myoglobin gives a normal binding curve which is hyperbolic in shape. Hemoglobin shows sigmoidal cooperative binding of oxygen. The cooperativity of hemoglobin allows it to release a much larger fraction of its O2 load at the pO2 levels found in the blood of working and even resting muscle.
For both proteins, the partial pressure of oxygen yielding 50% saturation of binding is termed the P50
What are the oxygenated and deoxygenated forms of the hemoglobin subunits called?
deoxygenated: T form (tense)
oxygenated: R form (relaxed)
What does it mean when a hemoglobin oxygen binding curve shifts to the right?
When the binding curve shifts right, hemoglobin loses its affinity for oxygen, making it more apt to release it into the surrounding tissues.
What is the difference between the oxygen binding curves for adult and fetal hemoglobin?
The fetal hemoglobin binding curve is shifted to the left, because it has a higher affinity for oxygen. This means the fetus’ circulation can draw oxygen from maternal blood at the pO2 present in placenta.
Clinical Correlation: Carbon monoxide (CO) has a much higher affinity for Hb than does O2. When bound to the heme group of one subunit, it causes all four subunits to “lock” in the R conformation. What effect would this have on O2 delivery?
Hemoglobin would be locked in the conformation that has very high affinity for oxygen (R conformation), causing it to not release oxygen into the surrounding tissues. This would also tie up binding sites preventing any more oxygen to be taken up and transported.
How does O2 binding change the conformation of a Hb subunit?
Without oxygen bound, the heme Fe2+ is pulled away from the plane of the porphyrin ring by a His residue of the hemoglobin polypeptide chain (a His ring N is bound to the Fe2+). When oxygen binds, it pulls the Fe2+ back into the plane of the ring and that moves the His residue and causes the hemoglobin subunits to shift to an arrangement that favors the R-conformation.
Describe the allosteric regulation of hemoglobin.
H+, CO2, and 2,3-DPG ALL can bind to hemoglobin and reduce its affinity for O2. Correspondingly, if oxygen is high, then the equilibrium is driven to the right and H+ and CO2 and DPG will dissociate from hemoglobin as oxygen binds.
What kind of effectors are H+ and CO2 to hemoglobin?
Heterotropic negative allosteric effectors
They are heterotropic because they are not O2; negative because they decrease affinity for O2; and allosteric because they bind to a site other than the O2 site(s) affected.
What is the Bohr effect/isohydric shift?
Hemoglobin’s oxygen binding affinity is inversely related to both acidity and concetration of carbon dioxide. Changes in H+ binding result from a shift in the pKa of specific residues (mostly histidines) due to microenvironment effects triggered by conformational changes in the hemoglobin molecule.
Where does 2,3-DPG bind to the hemoglobin tetramer?
Between the beta subunits
What is the relationship between 2,3-DPG and high altitudes?
Because there is less O2 at high altitudes, tissues tend to become somewhat hypoxic. RBCs adapt to this by increasing the concentration of 2,3-DPG, making it easier for O2 to dissociate from Hb.
Other causes of tissue hypoxia such as anemia and smoking also cause RBCs to increase 2,3-DPG.
What type of genetic disease is sickle cell?
Homozygous recessive
What causes HbS not to polymerize in sickle cell disease?
The presence of HbF (fetal hemoglobin).
What is the effect of hydroxyurea on sickle cell disease patients?
It stimulates HbF production. More HbF means less HbS in a sickle erythrocyte, which reduces sickling and the associated clinical complications.
Which amino acids have more than one chiral center?
Threonine and Isoleucine have 2 chiral centers
Name four factors that contribute to stabilizing the native structure of a protein?
Covalent (peptide, disulfide) bonds, hydrogen bonds, hydrophobic (van der Waals) interactions, ionic interactions (+ to – attraction).
Which amino acids contain sulfur?
Methionene and cysteine
Why is the R group of histidine particularly well suited to both accept and to donate a proton during enzyme catalysis?
It can either be protonated (+) or deprotonated (uncharged) at physiological pH without needing significant microenvironment effects. pKa ~ 7
What is the three letter code for aspartic acid?
Asp
What is the three letter code for asparagine?
Asn
What is the three letter code for glutamic acid?
Glu
What is the three letter code for glutamine?
Gln
What is the single letter code for asparagine?
N
What is the single letter code for glutamine?
Q
What is the single letter code for glutamic acid?
E
How does a perm work?
A thiol is used to reduce the disulfide bonds that stabilize α-keratin and then after creating the desired shape, hydrogen peroxide is used to reform new disulfides.
What hemoglobin are present during embryonic stages of development?
2 epsilon and either 2 alpha or 2 zeta chains; declining in first 10 weeks of gestation.
What would the dissociation of hemoglobin into its subunits do to the oxygen dissociation curve?
It would shift the curve substantially to the left because they would all have myoglobin-like affinities to oxygen, very high affinity.
Individual nucleotides are joined to each other at the __ and __ carbons through a ___________ bridge
3’, 5’, phosphodiester
How many angstroms are there in the major and minor grooves of B-form DNA?
12 angstroms and 6 angstroms
DNA structure: ______ are on the inside of the helix and ______ is on outside. The planes of the bases are “stacked” ______ to the helix axis. Stacking resonance helps stabilize double helix.
Bases, phosphate sugar backbone, perpendicular
DNA structure: Relaxed DNA has \_\_ bp per turn of the helix at intervals of \_\_ angstroms. Two chains of helix are held together by \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_. Spacing constant (space between bases): \_\_ angstroms.
10.5, 36, hydrogen base pairing, 2.9
The two strands of a double helix separate when _________ are disrupted by ______ or _______. The _______ composition (______ concentration) of the solution will effect denaturation and annealing rates.
hydrogen bonds, changes in pH, heating, ionic, salt
What property of DNA does a FISH assay take advantage of?
Denaturation and rehybridization. FISH uses small fluorescently labeled probes that bind to specific sequences on the denatured DNA to measure the presence of specific genes.
Define hyperchromic shift
Hyperchromic shift allows for the monitoring of DNA melting spectrophotometrically, because denatured DNA strands absorb much more UV light than double stranded DNA at 260 nm. This is because in double stranded DNA, bases are stacked on top of each other, whereas in denatured DNA the bases are exposed.
Define the melting temperature (Tm) of DNA and what two factors it is affected by.
The temperature at which 50% of the helical structure is lost. It is affected by the GC content of the DNA (higher GC content = higher Tm). It is also affected by ionic strength–high saltfavors duplex, low salt favors denatured.
In cells, DNA is usually found in a somewhat _____ supercoiled state, which means it is twisted in the _____ direction as the helix, turning it ____ward, which ______ the DNA.
negatively, opposite, left, unwinds
What is the function of a topoisomerase?
To change the topological state of circular or supercoiled DNA.
What kind of enzyme is a type I topoisomerase? What is it’s main function? How is this accomplished?
They are nicking-closing enzymes. They create transient single-stranded breaks to relax supercoiled DNA.
The enzyme acts by:
1) cleaving one strand of DNA
2) passing a segment of DNA through the break
3) resealing the break
4) DOES NOT require ATP
What residue in the active site of type I topoisomerase attacks the DNA strand to be cleaved, and what part of the DNA does it target?
Tyrosine residue, attacks the phosphodiester bond
