UNIT 2-BIOCHEM
What are micelles?
clusters of lipid molecules
hydrogen bonding in water is?
cooperative
What are strong bonds found in biomolecules? ______ bonds are weak but contribute to structure, stability, and function
covalent bonds, non-covalent bonds
When the hydrogen bond is a straight line you get? when the hydrogen bond is bent you get?
strong H-bond, Weaker H-bond
The attraction between the partial electric charges is ______ when O, H and O atoms are aligned in a _________
stronger, straight line
The equilibrium of the ionization of water is?
strongly to the left
In the ionization of water which direction is the equilibrium shifted toward?
strongly to the left, hydrogen bonds form quickly, water is more stable
Lipid molecuels disperse in the solution- nonpolar tails of each lipid molecues is?
surrounded by ordered water molecules which decrease the entropy of the system
What does the hydrophobic effect refer to?
the association or folding of nonpolar molecules in the aqueous solution.
The elecronegativity of the oxygen atom induces?
a net dipole moment
What are the hydrogen acceptors in biomolecules? What are the hydrogen donors in biomolecules?
acceptor-oxygen or nitrogen donor- electronegative atom
When is the buffering capacity of a buffer at its maximum?
acid/anion system is greates at pH=pKa
What is the relative [H+] in an acidic, neutral, and basic solution?
acidic-proton is high neutral-proton is equal to OH- basic-proton is low
What does pKa measure?
acidity pKa= -log Ka
phosphatidylcholine is an example of __________ molecue as it has both _____ and _____ regions in its structure
amphipathic, polar (hydrophilic) and non-polar (hydrophobic)
What are van der waals interactions?
Attractive forces that depend on the polarity. Repulsive forces depend on the size of the atom. There are weak interactions between the molecules and asymmetric distribution.
What is a micelle?
Clusters of hydrophobic groups are sequestered from water, hydrophilic ends associated with water, phospholipid bilayer.
What is the role of water as a reactant?
-Hydrolysis of ATP and ADP and Pi.- releases energy § Exergonic -Carbonic anhydrase CO2 + H2O <-> HCO3- + H+ § Endergonic
What is the importance of van der waals interactions?
-determines steric complementarity -stabilizes biological macromolecules -facilitates binding of polarizable ligands
Effect of extracellular osmolarity: -If the cell is in isotonic solution then? -if the cell is in hypertonic solution then? -if the cell is in hypotonic solution then?
-no net water movement -water moves out and cell shrinks -water moves in, creating outward pressure; cell swells, may eventually burst
the attractive force (london dispersion) depends on? the repulsive force (steric repulsion) depends on? Which dominates at longer distances?
-polarizability -size of atoms -attractive dominates at longer distances
The hydrophobic effect is one of the main factors behind?
-protein folding -protein-protein association -formation of lipid micelles -binding of steroid hormones to their receptors
In what chemical form does a proton exist in solution? why can protons hop? what is the effect of this in terms of speed of proton movement in an aqueous solution?
-proton exists in a hydronium ion -they are able to hop bc they ahve the ability to form hydrogen bonds -the speed of proton movement is extremely fast becasue of the presence of protons
Why can some biomolecues act as buffers?
-they can give/accept protons -ionizable groups -amino acids examples: phosphate, histidine, bicarbonate
the pH and pOH must always add up to?
14
in neutral solution, [H+]=[OH-] and the pH is?
7
What are hydrophobic interactions?
A force that brings the nonpolar groups together. Clustering of non-polar groups drives entropy
What is an amphipathic molecule?
Has a polar and non-polar part like membranes
what is a hydrophobic group?
Hates water, nonpolar, does not dissolve in water
The relationship between pH and the concentration of conjugate acid and conjugate base is described by?
Henderson and hasselbach equation
What is a hydrogen bond?
Hydrogen bonds are weak. It is a bond between hydrogen and oxygen or hydrogen and nitrogen. Hydrogen is the donor. It is an electronegative atom.
if [H+] is 2 X 10^-3 mol/L in an aqueous solution, calculate [OH-] of the solution.
Kw= [H+][OH-] 1 X 10^-14 M^2 = 2 X 10^-3 M [OH-] 1 X 10^-14 M^2 / 2 X 10^-3 M = [OH-] 0.5 X 10^-14 X 10^3 = [OH-] 5 X 10^-12 M = [OH-]
What is the ionic product of water?
Kw=Keq (H2O)= [H+][HO-]= 1 X 10^-14 M^2 pH
What is a hydrophilic group?
Loves water, polar or charged, dissolved in water
What is an isotonic solution?
There is no net movement, equilibrium is reached.
What is alkalosis?
Too much base in the blood, pH above 7.4
What is proton hoping?
Transfer of protons from hydronium ions. It happens in the hydronium ions. Interchangeable covalent and hydrogen bonds which allows for fast mobility of protons.
What are weak interactions between all atoms, regardless of polarity?
Van Der Waals interactions
_________ interactions involve weak interatomic attraction between two uncharged atoms resulting from transient asymmetry in the electron clouds around interacting atoms. Such interactions have two compounds _______ and _________
Van Der Waals, attration and repulsion
What is a hypotonic solution?
Water moves into the cell, osmolarity of the cell is lower than outside the cell, cell will burst
What is a hypertonic solution?
Water moves out of the cell, osmolarity of cell is much higher than outside the cell. Cell will shrink.
What are buffers?
Weak acids with a conjugate base. Acetic acid-acetate, phosphate-histidine, bicarbonate-carbonate
High _______ of water reduces attraction between oppositely charged ions allowing strong electrostatic interactions between ______ of ______ ions and water molecules. This in turn _______ the entropy and weakens the crystal lattice.
dielectric concentration, solulated or ionized, increases
What is an electrostatic interaction between uncharged, but polar molecules?
dipole interactions
Entropy of water increases as ordered crystal lattic is?
dissolved
concentrations of participating species in an equilibrium process are not independent but are related via the?
equilibrium contant
nonpolar portions of the amphipathic molecule aggregate so that?
fewer water molecules are ordered
Water is a _________ solvent for charged and polar substances
good solvent -examples: amino acids & peptides, small alcohols, and carbs
up to 4 H-bonds per water molecule give it?
high boiling point, high melting point, large surface tension
Why are non-polar molecues poorly soluble in water?
highly ordered which means entropy is low, thermodynamically unfavorable
unique properties of water such as high melting and boiling point are due to?
hydrogen bonds
Water can serve as both a? due to?
hydrogen donor and acceptor, due to dipole nature
Water can serve as both ____ and ________ due to its ____ nature?
hydrogen donor, hydrogen acceptor, dipole nature
________ bonds stabilize Watson and Crick base pairing while ________ bonds stabilize stacking of purine and pyrimidine bases.
hydrogen, van der waals
protons do not exist free in solution. They are immediately hydrated to form ___________. This is a water molecule with a proton associated with one of the non-bonding pairs. they are _______ by nearby water molecules. The colvalent and hydrogen bonds are interchangeable. This allows for a ________ of protons in water via "proton hopping"
hydronium ions, solvated, extremely fast mobility
binding sites in enzymes and receptors are often _______.
hydrophobic
Aggregation of non-polar groups in aqueous solution is called the ________. It is driving force of protein folding, protein-protein interactions, formation of micelles and hormone receptor interactions
hydrophobic effect
What is a complex phenomenon associated with teh ordering of water molecules around nonpolar molecules
hydrophobic effect
ligand binding sites can bind __________ and ligands such as steroid hormones
hydrophobic substrates
all hydrophobic groups are sequestered fsrom water;ordered shell of H2O molecules is minimized, and entropy is _______
increased
What is an electorstatic interaction between permanently charged species, or between the ion and a permanent dipole?
ionic interactions
hydrophobic effect favors?
ligand binding
Why are nonpolar molecuels poorly soluble in water?
low entropy is thermodynamically unfavorable, thus hydrophobic solutes have low solubility
In these structures called _______ the hydrophobib groups are sequestered from water and hydrophilic groups are oriented outwards to interact with the aqueous medium. This results in ____ entropy
micelles, high
what are buffers?
mixtures of weak acids and their conjugate base
what is the polarity of the following? Nitrogen, Oxygen, carbon dioxide, ammonia, hydrogen sulfide
nitrogen- non polar oxygen-non polar carbon dioxide-non polar ammonia- polar hydrogen sulfide- polar
Water is a poor solvent for _______ molecules such as ______
non-polar, aliphatic chains
buffer resist change in?
pH
What is the Henderson and Hasselback equation?
pH = pKa + log [A-]/[HA]
buffering capacity of acid/anion system is greatest at?
pH=pKa
Water is a ______ molecule?
polar
Water is a good solvent for _____ molecules such as _____ and ________
polar, glycose and carbohydrates
What is a ____ molecule in which oxygen atom carries a _____ charge and hydrogen atoms have a ____ charge
polar/dipole, negative, positive
Water is a ________ solvent for non polar substances?
poor solvent
Water is a critical determinant of the structure and function of?
proteins, nucleic acids, and membranes
What are the products of ionization of water?
proton (H+) and a hydroxide ion (OH-)
dissociation of water is a?
rapid reversible process
Protons generated from the ionization of water are ___________ and ________ with other molecules
rapidly hydrated via proton hopping and hydrogen bonding
stronger the acid, ________ its pKa value stronger the base, _________ its pKa value
smaller, larger
If pH of diet soda is 3.0, then it's [H+] relative to blood (pH: 7.4) is approximately
solution A pH=3 soultion B pH=7 10^-3 X 10^7 = 10^4 the first solution has 10,000 times more H+ than solution B
What is pH?
the negative lagarithm of the hydrogen ion concentration pH= -log[H+]
Water bound to proteins is essential for?
the proteins functions
Water acts as a powerful reactant in hydrolytic reactions and drives _________ and __________
thermodynamically unfavorable processes, and CO2/HCO3 buffering system
What is acidosis?
too much acid in the blood, pH below 7.4
hydrogen bonding of water imparts its _______
unique properties
What has an attactive (dispersion) and repulsive (steric) component?
van der waals interactions
hydrogen bonds between neighboring molecules are?
weak (easily broken)
Hydrogen bonds are often shown as 3 lines and are _______ and ________ than covalent bonds (length and strength)
weaker and longer
