Midterm #1 Flashcards
how many amino acids are found in the genetic code
20
how many amino acids have ionizable chains
7
what is the structure of an amino acid
H
|
+NH3-Ca-COOH
|
R
which amino acids are exceptions to amino acid structure
glycine (R-group is an H)
proline (R group is bound to alpha amino group)
how do you name the carbon atoms on amino acids
alpha, beta, gamma, delta, episilon
how are amino acids grouped
non polar, polar, electrically charged side chains
how does the symmetry of polar vs. non polar molecules differ
polar compounds –> asymmetrical
non polar compounds –> symmetrical
which amino acids have non polar side chains
- glycine (Gly)
- alamine (Ala)
- valine (Val)
- leucine (Leu)
- isoleucine (Ile)
- methionine (Met)
- phenylalanine (Phe)
- tryptophan (Trp)
- proline (Pro)
what do all amino acids with non polar side chains have in common
possess hydrocarbons –> CH4
what does aliphatic mean
compounds that have open chains (ex. -CH2CH2CH3) that are acyclic
which amino acids have polar side chains
- serine (Ser)
- threonine (Thr)
- cystine (Cys)
- tyrosine (Tyr)
- asparagine (Asn)
- glutamine (Gln)
which amino acids have electrically charged side chains
- aspartate (Asp)
- glutamate (Glu)
- lysine (Lys)
- arginine (Arg)
- histidine (His)
whats the protonated form of aspartate
aspartic acid
whats the protonated form of glutamate
glutamic acid
what is the structure of amino acid in a vacuum
H
|
H2N-C-COOH
|
R
what is the structure of amino acid in biological conditions (water)
H
|
H3N-C-COO
|
R
rank the solubility of side chains
non polar are least soluble, then polar, and electrically charged are the most soluble
what is a delineation for typical solubility rules
molecule factors (ex. size)
why might one molecule be more soluble in water than another
polar molecules make favorable interactions with water - ex. ion dipole and hydrogen bonds
explain an ion-dipole
- ions make ion-dipole interactions in water
- ion dipole occurs between charged atom / molecule and a polar molecule
what is a hydration shell
water that surrounds a charged atom
describe a hydrogen bond
- H atom covalently bonded to N, O, or F (hydrogen donor) attracted to another EN atom (hydrogen acceptor)
what is the hydrophobic effect
occurs when non-polar molecules are excluded by water in order to maximize the number of hydrogen bonds it can make with itself
what is a diprotic amino acid
an amino acid with two places that can donate a proton
do notes on other slides
what is a triprotic amino acid
an amino acid with ionizable side chains
three places on the structure where protons can dissociate
where does alpha carboxylic group deprotonate
pKa1 (more acidic)
where does alpha amino group deprotonate
pKa2 (more basic)
where does the R-group deprotonate
pKa3
why do acidic residues want to deprotonate
to donate -OH proton so they exist primarily in their conjugate base form in biological conditions
why do basic residues want to deprotonate
to accept protons so they exist primarily in their conjugate acid form in biological conditions
conjugate acid form of amine
|
–N+–
|
conjugate base form of amine
–N–
|
what is a polypeptide
- a chain (polymer) of amino acid residues
- they are the primary structures of proteins
- they fold on themselves to make the 3-D shape
- polypeptides are synthesized during translation, when the ribosome catalyzes the reaction (between two amino acids and synthesizes a new peptide bond). the rxn that takes place is a condensation rxn
what does a peptide bond form between
carbonyl (left) and amide (right)
what is the isoelectric points of polypeptides
pH at which there is no net charge in the molecule
- protein solubility is at its least when its at its pI
how is pI calculated
(pka2+pka1)/2
what does it mean for pH if the pI increases
increasing pI means you have a more basic solution
what is the bond angle between an amino acid (tetrahedral stereochemistry)
109.5 degrees
define chirality
non superimposable mirror images
define a stereoisomer
a molecule with the same chemical bonds, but different arrangements of them in space
what form are amino acids naturally found in
L form
what is the only achiral amino acid
glycine because one of its R-groups is another hydrogen
how do you discern L vs. D amino acid isomers
if H faces you and spells CORN clockwise then it is in the L form
which amino acid is most commonly found in the cis formation (despite favoring trans)
proline
psi bond
SEA TO SEA
alpha carbon to carboxyl
trident
phi bond
amine to alpha carbon
what is conformational flexibility
the ability of the side chains and fragments of the polypeptide backbone to adopt different conformations –> facilitated by phi / psi movement
which bond in an AA is rigid (planar) and why
polypeptide due to its partial double bond character (resonance - stabilizes)
how do secondary structures form
as a result of a polypeptide maximizing the number of H-bonds it can make between its carbonyls and amides from its backbone
what are the most common types of secondary structures found in proteins
alpha helices and beta sheets
alpha helix
coiling pattern resulting from the carbonyl of an EARLIER residue hydrogen bonding with an amide of a LATER residue 4 (3.6) residues away. They are right handed and positioned 100 degrees apart
what secondary structure is myoglobin entirely composed of
alpha helices
beta sheets
results when hydrogen bonding is maximized and two or more strands of a polypeptide make hydrogen bonds with each other. H-bonds stabilize the sheet. pleats are a result of the polypeptide between the alpha carbons being fully extended.
what is porin
an example of a protein almost entirely composed of beta sheets
what effects protein function
protein structure
why dont alpha helices have prolines
its amide cannot hydrogen bond (no hydrogen) and its presence creates a destabilizing KINK
what are the three factors (overall) that contribute to alpha helix stability
- they don’t contain prolines
- opposite charges are found 3-4 residues away
- bulky R-groups enhances steric hinderence
how far away are the charges on amino acid residues
3-4 residues away to stabilize (favorable electrostatic interactions. amino acids with the same charge found 3-4 residues away can be destabilizing due to unfavorable electrostatic repulsion
how do bulky r-groups affect AA stability
AA residues with bulky r-groups found 3-4 residues away can be destabilizing due to steric hinderance
how to determine if something is parallel vs. antiparallel
identify c-term and n-term of each strand. if both go from c-n in the same direction = parallel
based on the bumps on a beta sheet, which r-groups would have the same polarity
r-groups facing up are the same polarity; r-groups facing down are the same polarity
what are beta turns
connect two antiparallel strands together (180 degrees) (tight turns ~4 AAs). proline and glycine are often found here (ex. the amino nitrogen of proline can take on the cis form which makes for a right turn)
tertiary structure
refers to the 3-D arrangement of all atoms in the folded polypeptide. the tertiary structure may be the final protein (monomers) or it may be a subunit of the complete final protein.
- results from folding
- unfolded or “denature” state (no activity nor function)
- folded or “native conformation” (functional form)
what is anfinsens dogma
3-D structure determined by the sequence of amino acids
found that denaturation is when a protein can unfold / lose its native conformation when…
- temperature is raised
- pH is increased / decreased
- salt concentration changes
- solvent changes
** denaturation is not when the covalent bonds break, instead the IMFs are interfered with
is protein folding spontaneous or non-sponatenous
spontaneous - protein folding is energetically favored
what is the gibbs free energy equation
dekta G = delta H * T * delta S
delta G
gibbs free energy - whether the reaction is spontaneous (exergonic) or non-spontaneous (endergonic)
- delta G = exergonic
+ delta G = endergonic
delta H
enthalpy - total kinetic and potential energy of the system –> energy transferred in or out of the system
- delta H = exothermic
+ delta H = endothermic
T
temperature
delta S
entropy
- delta S = lost entropy (ordered)
+ delta S = gained entropy (disordered)
what factors allow protein folding to be endergonic
- the hydrophobic effect (MOST EFFECTIVE)
- formation of IMFs
what is the hydrophobic effect - in reference to protein folding
UNFOLDED
- entropically favorable for polypeptide
- allows R-groups to be very ordered (polar sides vs. non polar R-group facing sides)
- creates a very ordered structure
- enthropically unfavorable for H2O surrounding it
- on non-polar groups, a cathrate forms (water H-bonds occur with itself to make a cage-like structure)
FOLDED
- hydrophobic side groups are excluded to a hydrophobic core
- allows water to be disordered and make favorable interaction with polar and electrically charged R-groups on the exterior of the protein
**THIS IS THE MAIN FORCE THAT DRIVES PROTEIN FOLDING
IMFs - in reference to protein folding
- IMFs (van der waals, ionic attractions, H-bonds)
- between two groups and can occur at the c or n terminus
- disulfide bonds between cysteins (covalent bonds between R-groups of two cysteins)
quaternary structure
the final protein composed of 2 or more subunits
- each subunit is its own polypeptide that folds onto its own tertiary structure
- subunits may be identical or may be different
- hydrophobic effect and IMFs keep the subunits together
primary vs. secondary vs. tertiary vs. quaternary
primary = amino acid
secondary = alpha helices and beta sheets
tertiary = folded
quaternary = two identical subunits - each subunit had tertiary structure
function of hemoglobin
- delivers oxygen to the tissues
what type of solvent is blood
its an aqueous solvent that the polar oxygen is non-soluble in
what is a heterotetramer
- TETRA = 4 subunits
- HETERO = not all subunits are identical
ex. hemoglobin
what is the structure of hemoglobin
has two alpha subunits and two beta subunits
- less than half of AA sequence is identical yet overall tertiary structure is similar between the two subunits
- subunits are almost entirely comprised alpha helices
what subunits compose hemoglobin
- alpha subunit –> 7 helices labeled A-H (missing D)
- beta subunit –> 8 helices (A-H)
what is a heme
a heme is a prosthetic group (non-protenatious part of the protein)
- responsible for binding oxygen since hemoglobin has four hemes, it can bind oxygen in four places
myoglobin
- 8 helices (A-H)
- does not have quaternary structure in the same way that hemoglobin has
- suitable for oxygen storage
- stored in muscles, has high affinity for oxygen
- important when the body is starved for oxygen
- as O2 decreases in muscles (ex. during anaerobic exercise), myoglobin releases its oxygen, which diffuses through muscle cells so the mitochondrion can pick it up to be used in generating ATP
explain the bonding affinity between protein and ligand
protein (ex. hemoglobin or myoglobin) needs a ligand (ex. oxygen)
ligand
any sort of small molecule that binds to a binding site of a protein
- must be complimentary in shape, size, and hydrophobicity for the protein to discriminate the molecule amongst thousands of others
explain the fraction of proteins bound to a ligand vs. concentration of a ligand
binding sites become occupied as the concentration of the ligand increases –> initially, the jump is rapid because there are many proteins with a free binding site
hyperbolic curve
one high line
- one ligand binding site
- or multiple negatively cooperative binding sites
ex. myoglobin
sigmoidal curve
protein has both high and low affinity forms
- multiple binding sites
- cooperative (binding sites work together)
ex. hemoglobin
what are the p50s for myoglobin and hemoglobin
myoglobin: p50 = 3 torr (mmHg)
hemoglobin: p50 = 28 torr (mmHg)
why does hemoglobin adopt a sigmoidal shape, but myoglobin does not?
hemoglobin regularly binds and drops off O2, so it has to have properties with high O2 and low O2 affinity (its ligand)
what is pO2 like in the lungs vs. the tissues
lungs –> pO2 is high
tissues –> pO2 is low
explain how hemoglobin behaves cooperatively
- binding one ligand affects the remaining sites
- initially difficult to bind ligand, but once bound then more can bind (one binding increases the propensity for more to bind)
describe the two conformations that hemoglobin adopts
a low and a high affinity for oxygen
- T state (Tense) –> deoxyhemoglobin –> low O2 binding affinity (low pO2 –> tense formed)
- R state (Relaxed) –> oxyhemoglobin –> high O2 binding affinity
(high pO2 –> relaxed formed)d
describe a porphyrin ring (heme)
Fe in the center engages in coordinate covalent bonding –> a type of covalent bond where one atom donates both electrons; these are bonds that occur between metal ions and ligands
- EWD that helps helps keep Fe in its ferrous state (Fe2+) –> Fe2+ helps oxygen bind reversibly
- when oxygenated, iron (ii) in heme participates in 6 different bonds (oxygen binds to heme at an angle which places oxygen next to another histadine called the distal His)
describe the oxygenation change of hemoglobin
oxygenation induces a conformational change of hemoglobin
- F alpha helix is flat and heme is planar
describe the deoxygenation change of hemoglobin
deoxygenation induces a conformational change of hemoglobin
- F alpha helix is angled (changes positions) and its heme is domed (non planar) which expels oxygen toward the proximal histadine
what is a dimer in terms of hemoglobin
a dimer refers to a complex formed by two subunits of hemoglobin coming together. Each hemoglobin molecule consists of four subunits: two alpha globin chains and two beta globin chains
describe the alpha an beta subunits from dimers with each other
horizontally, the subunits of the dimer are held together by 30+ residues. these subunits have stronger interactions than the ones that hold these subunits together
vertically, the subunits are held together by 19 residues
how does the central channel change from the T deoxy state to the R oxy state
narrowing of central channel in the R (oxy) state – narrows upon oxygenation
where is iron in the t state
outside of the dome (domed shape)
what drives the F alpha helix to stand straight for oxygenation
steric hinderence
what happens to the histidine as it transitions from T to R state
small movement of the proximal histadine upon oxygen binding relays a conformational shift to the rest of the subunit
which states are most energetically favored at different O2 concentrations
at a low concentration of O2, the T-state is favored. The t-state is stabilized by a larger number of ion pairs when oxygen is absent, which can be found connecting the two diners
at a high concentration of O2, the R-state is favored. not as much energy is necessary to get to this conformation
define allostery
the binding of a ligand at one site affects the binding of a ligand at another
what is positive allostery
stabilizes ligand-binding conformation
ex. O2 is positive homortrophic
(positive homotrophic affectors
what is negative allostery
destabilizes ligand-binding conformation (destabilizes the R-state)
ex. CO2, H+, BPG
(negative heterotrophic affectors) - molecules are different from the ligands
how is CO2 transferred back
- 7%-10% of CO2 can dissolve in plasma of blood (this is so low because CO2 is nonpolar and has low solubility in blood)
- 70% of CO2 dissolves in the blood as HCO3- (this rxn generates negative allosteric effector protons)
- 20% of CO2 is carried away by hemoglobin –> this formof hemoglobin is called carbaminohemoglobin (another negative allosteric effector)
describe H+ as a negative allosteric affector
- red blood cells contain carbonic anhydrase enzyme that catalyzes the folowing rxn:
CO2 + H2O <–> H+ + HCO3-
protons generated are negative allosteric effectors –> hemoglobin transports ~40% of the protons produced when CO2 is hydrated
- when pCO2 increases, the rxn is driven right increasing protons released
if an increase in protons decrease hemoglobin’s affinity for O2, how will that affect its hemoglobin’s p50?
it raises its p50
describe the Bohr effect
effects the pH on the oxygen binding curve
- protons are a negative allosteric effector
- as pH descreases, p50 increases
explain how bohr protons help facilitate electrostatic attractions
- R-groups on histidine can only interact if protonated
- when proton concentration is high in the capillaries we can see its more likely that histadine acquired a proton and is able to make these salt bridges that stabilize the t-state
does myoglobin exhibit the bohr effect
- myoglobin lacks allostery (hyperbolic curve that exists in high affinity state exclusively)
describe the negative allosteric effector CO2
what percent of histidine is in its protonated form at a pKa of 6 vs. 7
pKa of 6 –> ~10% is in its protonated form
pKa of 7 –> ~50% is in its protonated form
describe the negative allosteric effector BPG
2,3-BPG is a negative allosteric effector that stabilizes the T-state
BPG allows the significant release of O2 (without BPG not much oxygen is iven up so BPG plays a big role in giving up oxygen)
- takes on a negative five charge to bind in the central cavity
- since BPG has a negative charge, the residues in the cavity would have a positive charge (conjugate acid forms of the basic side chains and n terminal amino groups)
describe fetal hemoglobin and BPG
alpha and gamma hemoglobin subunits (not beta)
- p50 for fetal hemoglobin has a lower p50 than adult hemoglobin. this is critical to the transport of oxygen to the fetus. fetal hemoglobin needs to have lower p50 (stronger affinity for oxygen) for it to steal oxygen from adult hemoglobin)
- instead of histadine, fetal hemoglobin has a serine
what is the difference in the number of charges to stabilize BPG for adult vs. fetal
8+ charges to stabilize BPG for adult
6+ charges to stabilize fetal –> so BPG cant bind as tightly (lower p50)
what is a zwitterion
a molecule / ion having separate positive and negative charged groups
conjugate acid of H2O
H3O+
conjugate base of C6H5COOH
C6H5COO-
which compound in the forward direction is the B-L acid: H2O + C6H5COOH <–> C6H5COO- + H3O+
C6H5COOH
where is the equivalence point on a graph
where pH = pKa
for a polypeptide as it moves from an unfolded to folded state, what is the change in entropy
negative delta S
for water as it moves from an unfolded to folded state, what is the change in entropy
negative delta S
for a lysine side group as it moves from an unfolded to folded state, what is the change in enthalpy? what interaction is it participating in?
negative delta H; electrostatic interaction
for a valine side group as it moves from an unfolded to folded state, what is the change in enthalpy? what interaction is it participating in?
negative delta H; van der waals
for an amide backbone as it moves from an unfolded to folded state, what is the change in enthalpy? what interaction is it participating in?
negative delta H; hydrogen bond
describe the properties of myoglobin (p50, bonding curve, heme?, role, and cooperative bonding?
- p50 = 0.2 pKa
- bonding curve is hyperbolic
- has one heme prosthetic group
- best suited for oxygen storage
- does not cooperate in cooperative binding
describe the properties of hemoglobin (p50, bonding curve, heme?, role, and cooperative bonding?
- p50 = 4 pKa
- bonding curve is sigmoidal
- has four heme prosthetic groups
- best suited for oxygen transport
- does cooperate in cooperative binding
what are the characteristics at a high O2…
- what is the conformational state?
- is hemoglobin in a high or low oxygen affinity state?
- what is the shape of the heme prosthetic group?
- each subunit’s heme is more likely to be oxygenated or deoxygenated?
- the proximal histidine is or is not perpendicular in this state?
- this state is favored in the lungs or tissues?
- R state favored
- high oxygen affinity state
- heme prosthetic group is planar
- each subunit is more likely to by oxygenated
- proximal histidine is perpendicular
- this state is favored in the lungs
what are the characteristics at a low O2…
- what is the conformational state?
- is hemoglobin in a high or low oxygen affinity state?
- what is the shape of the heme prosthetic group?
- each subunit’s heme is more likely to be oxygenated or deoxygenated?
- the proximal histidine is or is not perpendicular in this state?
- this state is favored in the lungs or tissues?
- T state favored
- low oxygen affinity state
- heme prosthetic group is domed
- each subunit is more likely to by deoxygenated
- proximal histidine is not perpendicular
- this state is favored in the tissues
how does CO2 INDIRECTLY act as a negative heterotrophic allosteric effector of hemogrobin
by reacting to generate protons with another allosteric effector that stabilizes the T state
how does CO2 DIRECTLY act as a negative heterotrophic allosteric effector of hemogrobin
by reacting with the N termini of the hemoglobin’s subunits to form a negatively charged carbamate that participates in salt bridges that stabilize the T state
effect of BPG on oxygen affinity
higher BPG = lower afinity for oxygen
how do protons (pH) affect oxygen affinity
less protons (higher pHs - more basic) = higher oxygen affinity
how does CO2 effect oxygen affinity
higher CO2 = lower oxygen affinity
what happens to the curve when the hemoglobin is denatured
its curve and binding affinity looks more like myoglobin - lower p50
glycine R-group and is it polar / non-polar / electrically charged?
-H
nonpolar
alanine R-group and is it polar / non-polar / electrically charged?
-CH3
nonpolar
valine R-group and is it polar / non-polar / electrically charged?
-CH(CH3)2
nonpolar
leucine R-group and is it polar / non-polar / electrically charged?
-CH2-CH(CH3)2
nonpolar
isoleucine R-group and is it polar / non-polar / electrically charged?
-CH(CH3)-CH2-CH3
nonpolar
methionine R-group and is it polar / non-polar / electrically charged?
-CH2-CH2-S-CH3
nonpolar
phenylalanine R-group and is it polar / non-polar / electrically charged?
-CH2-benzene
nonpolar
tryptophan R-group and is it polar / non-polar / electrically charged?
-CH2-pyrrole-benzene
nonpolar
proline R-group and is it polar / non-polar / electrically charged?
-CH2-CH2-CH3-attached back to amine
nonpolar
serine R-group and is it polar / non-polar / electrically charged?
-CH2-OH
polar
threonine R-group and is it polar / non-polar / electrically charged?
-CH-CH3
|
OH
polar
cysteine R-group and is it polar / non-polar / electrically charged?
-CH2-SH
polar
tyrosine R-group and is it polar / non-polar / electrically charged?
-CH2-benzene-OH
polar
asparagine R-group and is it polar / non-polar / electrically charged?
-CH2=O
|
NH2
polar
glutamine R-group and is it polar / non-polar / electrically charged?
-CH2-CH2-C=O
|
NH2
polar
aspartate R-group and is it polar / non-polar / electrically charged?
-CH2-C=O
|
O-
ACIDIC electrically charged
glutamate R-group and is it polar / non-polar / electrically charged?
-CH2-CH2-C=O
|
O-
ACIDIC electrically charged
lysine R-group and is it polar / non-polar / electrically charged?
-CH2-CH2-CH2-CH2-NH3+
BASIC electrically charged
arginine R-group and is it polar / non-polar / electrically charged?
-CH2-CH2-CH2-NH-C=NH2+
|
NH2
BASIC electrically charged
histadine R-group and is it polar / non-polar / electrically charged?
-CH2-imidazole
on histidine, where does the imidazole protonate
the amine attached to the double bond
which amino acids are non polar
- glycine
- alanine
- valine
- leucine
- isoleucine
- methionine
- phenylalanine
- tryptophan
- proline
which amino acids are polar
- serine
- threonine
- cysteine
- tyrosine
- asparagine
- glutamine
which amino acids are electrically charged (BASIC)
- lysine
- arginine
- histidine
which amino acids are non polar (ACIDIC)
- aspartate
- glutamate
abbreviation for glycine
G, Gly
abbreviation for alanine
A, Ala
abbreviation for valine
V, Val
abbreviation for leucine
L, Leu
abbreviation for isoleucine
I, Ile
abbreviation for methionine
M, Met
abbreviation for phenylalanine
F, Phe
abbreviation for tryptophan
W, Trp
abbreviation for proline
P, Pro
abbreviation for serine
S, Ser
abbreviation for threonine
T, Thr
abbreviation for cysteine
C, Cys
abbreviation for tyrosine
Y, Tyr
abbreviation for asparagine
N, Asn
abbreviation for glutamine
Q, Gln
abbreviation for aspartate
D, Asp
abbreviation for glutamate
E, Glu
abbreviation for lysine
K, Lys
abbreviation for arginine
R, Arg
abbreviation for histidine
H, His
define amphipathic
a protein having both hydrophilic and hydrophobic parts.
