Midterm Flashcards
Why is water essential to biological systems?
- Physiochemical properties of water help form 3D shapes of biomolecules. 3D shape are related to functions.
- Water can ionize H+ and OH-. Acts as key reactant in reactions, and can also affect pH.
What is an hydrogen bond?
Electrostatic interaction between a weakly ACIDIC DONOR group (ex. O-H, N-H) and a weakly BASIC ACCEPTOR atom (ex. O, N)
How are hydrogen bonds typically drawn (represented)?
D-H ——– A
Where D = donor & A = acceptor
What are the requirements for H-bonding?
- A donor group: An H attached to an O, N, S. (positive end)
- An acceptor: An electronegative atom (O, N, S) with a lone pair. (negative end)
How many hydrogen bonds can water form?
4
2 donors, 2 acceptors
What are van der Waals forces?
NON-COVALENT associations between molecules due to ELECTROSTATIC nteractions among permanent/induced DIPOLES.
What are London Dispersion Forces?
Attractive forces between electrically NEUTRAL molecules in close PROXIMITY.
Is formed from electrostatic interactions due to the random movement of negatively charged electrons around a positively charged nucleus.
What does it mean to be hydrophilic molecule?
The molecule is polar and soluble in water. (“Water Loving”).
Contains a lot of electronegative molecules (O, N, S)
What does it mean to be a hydrophobic molecule?
Nonpolar molecule and nonsoluble in water. (“Water Fearing”).
Contains few, if any electronegative molecules (O, N, S)
Why do salts (NaCl) dissolve in water and form a salt in a nonpolar substance?
In water: water weakens attractive forces between oppositely charged ions, and hold ions apart (dissolving). The ion is attracted the charged ends of the solvent dipoles which keeps them apart. (Solvated)
In nonpolar solvents: ions attract each other so strongly that they form a solid salt.
What does it mean when ions are solvated (or hydrated in water)?
When ions in polar substances attract the opposite charged solvent dipole which surrounds the ion (like a shell) keeping it effectively apart.
What functional groups does water form hydrogen bonds with?
Hydroxyl group
Keto group
Carboxylate ion
Ammonium ion
What occurs when you add a nonpolar substance to a polar solution?
Hydrophobic effect
What is an amphiphatic molecule?
A molecule that has a distinct hydrophobic and hydrophilic portion.
What is the hydrophobic effect?
The minimization of contact by water with hydrophobic molecules by “forming” a “cage” (Clathrate cage) around nonpolar solute.
How does a nonpolar substance intrude the hydrogen bonding of water?
It ruins the network of bonds in water because it cannot donate nor hydrogen bond.
Why is the hydrophobic effect favourable when a nonpolar substance in placed in a polar solution?
It minimizes the surface area of the nonpolar solute—> maximizes H-bond ability and entropy.
Amphilies often form Micelles and Bilayers. What are micelles and bilayers?
Micelles - GLOBULES of amphiphilic molecules arranged so that HYDROPHILIC portions are on OUTer surface and HYDROPHOBIC portions in the INner core of the globule. (spheroidal aggregate)
Bilayer - A SHEET where the HYDROPHOBIC portions make up the OUTside sheet and the HYDROPHILIC in the INside. (Extended planar aggregate)
What are the three types of noncovalent interactioins that can form between water and hydrophilic biomolecules? (in decreasing strength?)
- Ionic bonds
- Hydrogen bonds
- Dipole-dipole Interactions
What type of interaction form between hydrophobic biomolecules?
London Dispersion forces.
What are ionic bonds?
An electrostatic interaction between groups of OPPOSITE charge.
What are dipole-dipole interactions?
A van der Waal reaction where an interaction occurs between an atom that has a partial positive charge and an atom that has a partial negative charge.
What do you call the condition where the pH of blood is too acidic (<7.4)?
Acidosis
What are some symptoms of acidosis?
Coma, diabetes.
What do you call the condition where the pH of blood is too basic (>7.4)?
Alkalosis
What are some symptoms of alkalosis?
Tetany
Vomiting, hyperventilation, convulsing, muscle spasms etc.
Give examples of biochemical processes that are deeply affected by pH changes.
- Transport of oxygen in the blood
- Enzymatic catalysis
- Generation of enegery in metabolic pathways
- Proteins, cells and tissues need to maintain specific pH for proper function and survival.
What is the ideal buffer range?
+-1 when pH=pKa
Why are weak acids good buffers?
It has two components:
1: Conjucate base, which absorbs H+ and buffers against acids
2. Acid, releases H+ which buffers against bases
How are bicarbonate and carbonic acid carried in blood between tissues and lungs?
O2 in lungs —> hemoglobin absorbs O2—> Releases O2 and binds H+ in muscle cell—> comes back to the lungs, releases CO2 and H20
What does the 3D structure of proteins depend on?
- presence of water
- pH
- Building blocks (amino acids)
In what configuration are amino acids in proteins?
L configuration (clockwise)
What are the three classifications of amino acids?
- Hydrophobic
- Polar (Hydrophilic)
- Charged (Hydrophilic and Charged)
List the hydrophobic amino acids
Alanine Valine Methionine Leucine Phenylalaline Glycine Tyrosine Tryptophan Isoleucine Proline
List the polar amino acids (Hydrophilic)
Serine Histidine Gluatamine Threonine Cysteine Asparagine
List the charged amino acids (Hydrophilic and Charged)
Aspartate
Glutamate
Lysine
Arginine
How can amino acids allow proteins to act as buffers?
Amino acids are weak polyprotic acids. (They contain more than one acidic proton)
Amino acids can be diprotic or triprotic
What is the difference between diprotic and triprotic amino acids?
Diprotic have neutral side chains and triprotic have an side chain that has an acidic proton
How do amino acids form chains?
Condensation reaction.
The two H’s of Amine and one O from the carboylate form H20 which gets released form a CO-NH bond (peptide bond)
What is the bond that links amino acids together called?
Peptide bond
Each polypeptide is polarized. What does this mean?
One end has a free amino group (N terminus) and the other end has a free carboxyl group (C terminus)
What do the electrostatic properties of a polypeptide primarily depend on?
The identities of the side chains
How do the 4 subunits hold on to one another in Hemoglobin?
- Hydrogen bonds
- Hydrophobic effect
- Vander Waal Interaction
- Salt bridges (Ionic bonds)
- Dipole-Dipole
What determines the protein’s ability to act as a buffer?
The number of acidic proteins the protein has.
What ae the two major oxygen transport proteins and what are their functions?
- hemoglobin (Hb) = transports oxygen in the blood
2. myoglobin (Mb) = transports oxygen within heart and skeletal muscles.
Specifically, which part of hemoglobin does O2 bind to?
Heme group
The O2 binding curve with Hb is sigmoidal. What does that indicate about Hb’s affinity for oxygen?
The different subunits of Hb bind to O2 with different affinities.
At different pressures, you get a different ratio of HbO2.
Varying affinitiy for O2 at specific tissues or organs due to a difference in pressure.
What is deoxy-Hb and what is its affinity with oxygen and the strength of binidng?
Hb not bound to O2.
Has the lowest affinity for O2 and the weakest binding (because the first O2 is the hardest to bind.)
What is oxy-Hb and what is its affinity with oxygen and the strength of binding?
Hb fully bound to O2.
Has the highest affinity for oxyen and the strongest binding.
What are the two types of conformations of Hb?
- T state = tense = weak binding conformation = deoxy-Hb
2. R state = relaxed = tight binding conformation = oxy-Hb
After the first conformational change due to the first binding of O2, what occurs next?
The conformation triggers the conformation of other subunits which in tern increases their binding affinities for O2.
When is the T state desirable and when is the R state desirable?
T state: at the tissue (O2 exchange can occur)
R state: at the lungs (O2 can be absorbed)
What is the heme group and what is it’s function?
The heme group is part of the hemoglobin that contains an Fe2+ group that is vital for the conformational change of hemoglobin.
How does the hemoglobin change it’s conformation from T—> R?
- O2 binds to the Fe2+ of the heme, which shortens the Fe - N (poryphorin) bonds into the heme plane. (1 Angstrom)
- Fe2+ drags the bonded His F8 0.6Angstroms towards the heme lane. This causes the F helix to tilt by 1Angstrom across the heme plane.
- Conformational shift of one subunit causes the conformational shift of all subunits which increases the O2 affinity of the unoccupied subunits.
How does affinity for O2 change as pressure changes?
At a higher pressure, there is a higher affinity for O2.
What are allosteric effectors?
A small molecule whose binding to a protein affects the function of another site on the protein. Bind to Hb and affect the binding/release of O2.
What are examples of allosteric effectors?
H+ and CO2 and 2,3-BPG
How does pH alter the affinity of hemoglobin for oxygen?
H+ and CO2 stabilize the T state by binding to deoxy-Hb. This leads to the Bohr effect.
What is the Bohr Effect?
Hb has a lower affinity for O2 at a low pH. (Lower the pH, the more stable the T state)
How does the Bohr Effect explain why Hb is at a T state at the muscles?
pH of tissues decrease when tissues lack O2. A decrease in pH stabilizes the T state causing the release of O2 to the tissues.
What is 2,3-BPG and what function does it serve?
It is another allosteric effector that is found in the Red blood cells at a 1:1 ratio with Hb. It stabilizes the T state. (reduces amount of HbO2)
How does BPG stabilize the T state?
Binds to positively charged regions rich in Lys, HIs and Arg residues near the Hb tetramer.
Only binds to the T state of Hb when the central cavity is big enough.
How does the central cavity differ in the T state and the R state
T state: big
R state: small
At a pH of 8 will you have more or less HbO2 than at a pH of 7?
More HbO2
An increased concentration of BPG will result in more HbO2 or less HbO2?
Less HbO2
Peptide bonds are PLANAR and cannot rotate. Why?
Peptide bonds are polar and have a partil double-bond charactionter. Therefore, they cannot rotate.
If peptide bonds cannot rotate, what account for the polypeptide chain twist?
phi bond: rotation angle about N-Ca bond
psi bond: rotation angle about Ca-C bond
As displayed by the Ramachandran plot, why are some combination of phi and psi forbidden?
Due to steric hindrance.
Why are peptide bonds usually trans? What is the exception?
Less steric hindrance in trans formation.
Exception: proline found in cis.
What is the difference between myoglobin and hemoglobin?
Myoglobin: monomeric, one heme, higher affinity for O2 at all pO2
Hemoglobin: heterotramer, 4 hemes, increasing infinity for O2 as pO2 increases.
Which structure of the protein determines all other levels of protein structure?
Primary
What are secondary structure?
Regular, LOCAL CONFORMATIONS stabilized by H-BONDS between peptide carbonyl O and amide hydrogens (H-bond networks)
What is the difference between antiparallel and parallel beta-sheets?
Antiparallel: both beta sheet strands move in opposite directions: N—> C and C—> N
Parallel: both beta sheet strands are moving in the same directions: both N—> C or both C—> N
What are the portions of the protein that don’t have secondary structures called? What is the function of these portions?
Loops or coils.
They are important in the activity of enzymes and allow the polypeptide to turn.
What is the pitch/rise of an alpha helix?
0.54 nm = 1.5 A for 3.6 amino acid residues
How long is each amino acid in an alpha helix?
1.5 A
Why are amino acids in beta sheets said to be extended? What is the rise of a beta sheet?
Because they are longer than alpha helix
2 amino acids = 7 A
1 amino acid = 3.5 A
What two characteristics of the peptide bond contribute to it’s role in allowing different secondary structures?
- Polar
2. partial double bond character (resonance)
Why are peptide bonds planar and unable to rotate around the peptide bond?
Due to the partial double bond character, there is resonance of the peptide bond which prevents rotation
What is the highest level of structure for a monomeric protein?
Tertiary
Why are teritary structures layered?
The outside layer contains hydrophilic and charged amino acids and the inside layer contains hydrophobic.
How are alpha helices packed? Why are they packed like this?
In an antiparallel orientation.
Peptide bonds are polar, so having them antiparallel with align S+ with S-
How are beta sheets packed?
polar with polar and non polar with non polar
How do secondary structures stick together?
- H-Bonds
- dipole-dipole
- Van der Waals
- Ionic
- Hydrophobic effect
What is are additional factors (besides non-covalent) that can stabilize tertiary structure?
- disulfide bridges (covalent)
2. cofactors (help the folding of the protein
How come the secondary structures are located in the inside of the protein, yet loops are on the outside?
Loops do not have fully satisfied H-bonding, thus they interact with water on the outside of the protein
What physiochemical properties can be used in protein purification?
- size
- solubility / pH / temp.
- charge
- polarity
What is salting out?
Ammonium sulphate precipitation, or fractionation with (NH4)2SO4
precipitation of the protein of interest when the salt outcompetes the amino acids for the out layer interactions with water.
In column chromatography, how does interaction affect elution rates?
High interaction = slow elution
Low interaction = fast elution
How does size exclusion chromatography work?
Smaller proteins = slower elution
Larger proteins = faster elution
How does ion exchange chromatography work?
More charged = slower elution
Less charged = faster elution
What are the two different types of resin used in ion exchange chromatography?
- Anion exchanger (positively charged beads)
2. Cation exchanger (negatively charged beads)
What is pI?
The pH at which the GREATEST amount of the form of the protein with a NET CHARGE OF 0 will be found.
How can proteins be denatured physically?
1) heating
(disrupts disulfide bridges and noncovalent interactions)
2) stirring or creating air bubbles
(Air is nonpolar—> disrupts hydrophobic interactions—> protein flips inside out—> irreversible denaturation)
How can proteins be denatured chemically?
1) Using buffer at wrong pH or no buffer at all
(pH increase and decrease will cause repulsion and protein will expand—> reversible as long as it’s between 4-10)
2) Adding organic solvent
(Same effect as water, except polyols)
3) Adding urea or guanidinium HCl
(dentaure, but reversible. Urea disrupts H-bonds and hydrophobic interactions. Guanidinium HCl disrupts H-bonds, hydrophobic interactions and ionic interactions)
4) Adding a detergent
(Detergents, ex. SDS—> irreversibly denature same way as air.)
How does SDS fix the problem with PAGE?
- SDS binds to proteins—> denatures—> loss of shape
- SDS adds 2 negative charges—> proteins constant charge to length —> takes away charge
Therefore proteins can be separated only be SIZE
