Biochemistry Exam 1
What is the principle of the dissociation of weak electrolytes?
-weak electrolytes dissociate only partially in water -extent of dissociation determined by acid dissociation constant (Ka)
What are van deer waals interactions?
-weak interactions between all atoms, regardless of polarity -attractive (dispersion) and repulsive (steric) component
What is a hydronium ion?
H3O+ -water molecule with a proton associated with one of the non-bonding electron pairs -solvated by nearby water molecules
Most common form of crystal form of water
Hexagonal ice -forms a regular lattice -has low entropy -has more hydrogen bonds than water molecule so its less dense (why it floats)
Cytoplasm of cells are highly concentrated solutions and have _____________________
High osmotic pressure
The amino acid with the side chain pea near neutrality and which therefore plays an important role as proton donor and acceptor in many enzyme catalyze reactions is:
Histidine
Positively charged R groups
Histidine Arginine Lysine -basic R groups
Ionic product of water
Kw = [H+][OH−] 1 x 10^-14 In pure water: [H+] = [OH-] = 10^-7 M
Proteins only contain what type of amino acids
L amino acids
What is the attractive interaction between any pair of molecules including non polar atoms arising from the interactions of instantaneous multipoles?
London Dispersion Forces
Water surrounding nonpolar solutes has ____ entropy
Lower
Strong electrostatic interactions between the solvated ions and water molecules do what?
Lower the energy of the system
amphipathic biomolecules
Phenylalanine Phosphatidylcholine
What is a buffer?
mixture of a weak acid and its conjugate base -resist change in pH -at pH=pKa there is a 50:50 mixture of acid and anion forms of the compound
peptides
small condensation products of amino acids -they are small compared to proteins -numbering and naming starts from the amino terminus
Cell in hypotonic solution
water moves in, creating outward pressure; cell swells, may eventually burst
What happens as ordered crystal lattice is dissolved
Entropy increases
Who has optimal pH
Enzyme catalyzed reactions
Equilibrium constant of water:
Keq = [H+][OH-]/[H2O] 1.8 x 10^-16
The only amino acid that is not chiral
Glycine
Negatively charged R groups
aspartate, glutamate
Proteins are
linear heteropolymers of alpha-amino acids
Amino acids can act as buffers
-amino acids with uncharged side chains, such as glycine, have 2 pKa values -the pKa of the alpha carboxyl group is 2.34 -the pKa of the alpha amino group is 9.6 -can act as a buffer in 2 pH regimes
2 components of van der waals interactions :
-Attractive force (London dispersion) depends on the polarizability, dominates at longer distances (0.4-0.7 nm ) -Repulsive force (Steric repulsion) depends on the size of atoms, dominates at very short distances
Weak forces are important for biochemical interactions because they are...
-Crucial to macromolecule structure and function -Have significant influence on 3-D structures of proteins, nucleus acids, membrane lipids, and polysaccharides -The formation of these weak forces contributes to a net decrease in the free energy of a system -The binding of an antigen to a specific antibody depends on the cumulative effects of many weak interactions -The binding of a hormone to a neurotransmitter or to its cellular receptor protein is a result of many weak interactions
Polar biomolecules
-Glucose -Glycine -Aspartate -Lactate -Glycerol (LAGGG)
How to calculate the pI when the side chain is ionizable
-Identify species that carries a net zero charge -Identify pKa value that defines the acid strength of this zwitterion (pKa 2) -Identify pKa value that defines the base strength of this zwitterion: (pKa 1) Take the average of these two pKa values
Importance of hydrogen bonds
-Source of unique properties of water -Structure and function of proteins -Structure and function of DNA -Structure and function of polysaccharides -Binding of substrates to enzymes -Binding of hormones to receptors -Matching of mRNA and tRNA
Peptides: protection
-amanitin (mushrooms) -conotoxin (cone snails) -chlorotoxin (scorpions)
Technique to purify proteins on the basis of charge
-anion or cation exchange chromatography -isoelectric focusing
Affects of Solutes on properties of water (Colligative properties)
-boiling point -melting point -osmolarity (Do not depend on the azure of the solute just the concentration)
Structure in proteins
-collagen (connective tissue) -keratin (hair, nails, feathers, horns)
Biochemical Significance of van der Waals Interactions
-easily broken,reversible -occur between any two atoms that are near each other -determines steric complementarity -stabilizes biological macromolecules (stacking in DNA) -fascilitates binding of polarizable ligands
What are ionic (Coulombic) interactions ?
-electrostatic interactions between permanently charged species or between the ion and a permanent dipole
Catalysis in proteins
-enolase (in the glycolytic pathway) -DNA polymerase (in DNA replication)
Transport in proteins
-hemoglobin (transports O2 in the blood) -lactose permease (transports lactose across the cell membrane)
Functions of peptides
-hormones and pheromones -neuropeptides -antibiotics -protection, toxins
What are the 4 types of noncovalent "weak" interactions
-hydrogen bonds between neural and peptide groups -ionic interactions (attraction/repulsion) -hydrophobic interactions Van der waals interactions
Peptides: hormones and pheromones
-insulin (think sugar) -oxytocin (think child birth) -sex-peptide (mating fruit fly)
Motion in proteins
-myosin (muscle tissue) -actin (muscle tissue, cell motility)
Uncommon amino acids found in proteins
-not incorporated by ribosomes except for selenocysteine and pyrolysine -arise by post translational modifications of proteins -reversible modifications especially phosphorylation are important in regulation and signaling
Buffer systems in vivo are mainly based on what?
-phosphate, concentration in minimolar range -bicarbonate, important for blood plasma -histidine, efficient buffer at neutral pH
Peptides: antibiotics
-polymyxin B (for gram negative bacteria) -bacitracin (for gram positive bacteria)
Technique to purify proteins on the basis of solubility, size
-size exclusion chromatography -gel electrophoresis
What is a Micelle and what drives its formation in water
-stable structures of amphipathic (has polar and no polar regions) compounds in water -The hydrophobic effect is the driving force for the formation of micelles in water -The forces that hold the non polar regions of the molecule together are called hydrophobic interactions
Structure of amino acids
-the alpha carbon always has 4 substituents and is tetrahedral -all (except proline) have an acidic carbonyl group, a basic amino group, an alpha hydrogen attached to the alpha carbon -the 4th substituent (R) is unique -in glycine the 4th substituent is also hydrogen
The overall net charge on the peptide lys-lys-ser-glu at a pH of 7.0
0
PKa values are discernable if
2 pKa values are more than 2 pH units apart
The number of hydrogen bonds a water molecule can participate in at one time
4 Hydrogen bonds -4 electron pairs around an oxygen atom in water (4 sp3 orbitals)
Which of the following is true of hydrogen bonds? A)The attraction between the oxygen atom of a water molecule and the hydrogen atom of another constitutes a hydrogen bond B) Hydrogen bonds form as covalent bonds between positively and negatively charged ions C) Hydrogen bonds form between nonpolar portions of biomoleculles D) A and B are true E) A, B, and C are true
A) The attraction between the oxygen atom of a water molecule and the hydrogen atom of another constitutes a hydrogen bond.
Technique to purify proteins on the basis of shape or binding characteristics
Affinity chromatography
the functional differences as well as differences in 3-dimensional structures between 2 different enzymes from E coli. result directly from their different
Amino acid sequences
What other functional groups of biomolecules can form hydrogen bonds?
Any groups where the H is bonded to O, N or F. So, some examples would be carboxyl groups (COOH), amines (NH2), phenols (benzene with an OH), etc.
The purpose of SDS and beta mercaptoethanol for a PAGE is to
Break disulfide bonds
How can low solubility of hydrophobic solutes be explained by entropy ?
Bulk water has little order -high entropy Water near a hydrophobic solute is highly ordered -low entropy Low entropy is thermodynamically unfavorable, thus hydrophobic solutes have low solubility (Will always want to go to a higher entropy system)
In a typical eukaryotic cell the pH is usually around 7.4. What is the [H+] in a typical eukaryotic cell? A) 0.00000074 M B) 6.6 uM C) 4 x 10^-8 D) 2.3 nM E) 7.4 x 10^-5M
C) 4 x 10^-8
Which of the following accurately describes the effect of lowering the [CO2]dissolved on blood pH? (like climbing a mountain with thinner air) A) It will result in an increase in the dissociation of H2CO3-> H+ + HCO3- and a drop in pH B) It will result in an increase in the dissociation of H2CO3 -> H2O +CO2 and a drop in pH C) It will result in an increase in the association of H+ + HCO3- -> H2CO3 and an increase in pH D) It will result in a decrease in the association of H+ +HCO3- -> H2CO3 and a decrease in pH. E)Lowering [CO2}dissolved has no effect on blood pH
C) It will result in an increase in the association of H+ + HCO3- -> H2CO3 and an increase in pH.
The pKa values for 3 ionizable groups on tyrosine are pKa (-COOH) =2.2, pKa(-NH3+)=9.11, and pKa(-R)=10.07. In which pH ranges will this amino acid have the greatest buffering capacity? A) at all pHs between 2.2 and 10.07 B) At pHs near 7.1 C) at pHs between 9 and 10 D) At pHs near 5.7 E) Amino acids cannot act as buffers
C) at pHs between 9 and 10
Proteins: Main Agents of Biological Function
Catalysis Transport Structure Motion
What is the hydrophobic effect?
Complex phenomenon associated with the ordering of water molecules around non-polar substances
You mix 100 mL of solution of pH 1 with 100 ml of a solution of pH 3. The pH of the new 200 mL solution will be: A) 1.0 B) 2.0 C) 3.0 D) between pH 1.0 and pH 2.0 E) Between pH 2.0 and pH 3.0
D) Between pH 1.0 and pH 2.0
Water derives all of its special properties from its: A) cohesiveness and adhesiveness B) high boiling point and melting point C) small degree of ionization D)Polarity and hydrogen-bonding capacity E) high dielectric constant
D) Polarity and hydrogen-bonding capacity
Polypeptides are
Covalently linked alpha amino acids
Consider a weak acid in a solution with a pH of 5.0. Which of the following statements is true? A) The weak acid is a proton acceptor. B) The weak acid has a lower affinity for its proton than does a strong acid C) At its pKa the weak acid will be totally dissociated D) the [H+] is 10^-5 M E) All of the above are true
D) The [H+] is 10^-5 M
Which of the following is true of pH? A) pH is the negative log of [OH] B) Lemon juice, which has a pH of 2.0, os 60 times more acidic than ammonia, which has a pH of 12.0 C) varying the pH of a solution will alter the pKa of an ionizable group in that solution D) Varying the pH of a solution will alter the degree of ionization of an ionizable group in that solution E) all of the above are true
D) Varying the pH of a solution will alter the degree of ionization of an ionizable group in that solution
The pH of a sample of blood is 7.4; the pH of a sample of gastric juice is 1.4. The blood sample has an [H+]: A) 5.29 times lower than that of the gastric juice B) a million times higher than that of the gastric juice C) 6,000 times lower than that of the gastric juice D) a million times lower than that of the gastric juice E) 0.189 times that of the gastric juice
D) a million times lower than that of the gastric juice
Carbonic acid has a Ka 1.70 x 10^-4 and acetic acid has a Ka of 1.74 x 10^-5. Which of the following is true? A) Carbonic acid has the higher Ka of the two and would therefore be the best buffer at pH 6. B) The acid with the larger Ka is a better proton acceptor. C) Carbonic acid is the stronger acid and has a lesser tendency to lose its proton compared to acetic acid. D) Neither carbonic acid nor acetic acid can be effective buffers at any pH. E) Acetic acid is a weaker acid and has a lesser tendency to lose its proton compared to carbonic acid.
E) Acetic acid is a weaker acid and has a lesser tendency to lose its proton compared to carbonic acid
Why is severe dehydration potentially life threatening? A) Water is a solvent for many biomolecules B) Water is a chemical participant in may biological reactions C) Water is necessary for buffering action in the body D) Waters attraction to itself drives hydrophobic interactions E) All of the above are true
E) all of the above are true
Van deer waals interactions are a weak transient subcategory of which type of non covalent interaction
Electrostatic interactions
What are dipole interactions ?
Electrostatic interactions between uncharged, but polar molecules
What is proton hopping?
Extremely fast mobility of protons in water because of the fact that covalent and hydrogen bonds are interchangeable in proton hydration -protons do not exist free in solution 1) Hydronium ion gives up a proton 2) water accepts proton and becomes a hydronium ion
True or false: the oxygen atom in water has a partial positive charge
False. The oxygen atom has a partially negative charge
True or false: hydrogen atoms can only form between water molecules
False; they can form between any electronegative atom (usually oxygen or nitrogen) and a hydrogen atom covalently bonded to another electronegative atom in the same or another molecule
When is water a good solvent?
For charged and polar substances -amino acids and peptides -small alcohols -carbohydrates CAPS
When is water a bad solvent?
For non polar substances -nonpolar gases -aromatic moieties -aliphatic chains
Formic acid has a pKa of 3.75; acetic acid has a pKa of 4.76. Which is the stronger acid? Does the stronger acid have a greater or lesser tendency to lose its proton than the weaker acid?
Formic acid i the stronger acid. It has a greater tendency to lose its proton than does acetic acid
At physiological pH these amino acids carry a net negative charge
Glutamate Aspartate
Polar uncharged R groups
Glutamine Cysteine Asparagine Threonine Serine -these amino acid side chains can form hydrogen bonds -cysteine can form disulfide bonds
Nonpolar, aliphatic R groups (hydrophobic)
Glycine Alanine Proline Valine Leucine Isoleucine Methionine
How do hydrogen bonds contribute to high melting and boiling points of water?
Hydrogen bonds are relatively strong intermolecular forces, and thus it takes a lot of energy to break these bonds. This is why the boiling point of water is high, because a lot of heat (energy) is needed to break the intermolecular bonds holding the water molecules together.
Protons are immediately hydrated to form what?
Hydronium (oxonium) ions
This technique separates proteins based on differences in their pI
Isoelectric focusing
2 dimensional electrophoresis combines these 2 techniques
Isoelectric focusing and SDS PAGE
Henderson Hasselbach equation
Ka = [H+][A-]/[HA] —————> [H+]=Ka([HA]/[A]) —————> -log[H+]=-logKa-log([HA]/[A-]) —————> PH=pKa+ log([A-]/[HA])
When pH>pI, protein is
Net negative
when pH<pI, protein is
Net positive
ionization of water
O-H bonds are polar and dissociate heterolytically -products are a proton (H+ ) and a hydroxide ion (OH-) The equilibrium is strongly to the left -extent of dissociation depends on temperature
PH scale is logarithmic 1 unit = ?
One 10-fold
pH
PH=-log[H+] PH+pOH=14 -log[H]-log[OH]=14
Buffering capacity of acid/anion system is greatest when
PH=pKa
This amino acid is technically not an amino acid at all
Proline
The hydrophobic effect
Refers to the association of folding of nonpolar molecules in the aqueous solution One of the main factors behind: -protein folding -protein-protein association -the formation of lipid micelles -binding of steroid hormones to their receptors -does NOT arise because of some attractive direct force between 2 nonpolar molecules
Ion-exchange Chromatography
Separation using differences in sign and magnitude of the net electrical charge of proteins at a given pH
Neuropeptides
Substance P, (pain mediator)
Buffer systems in vitro of mainly based on what?
Sulfonic acids of cyclic amines -HEPES -PIPES -CHES
The overall 3-D folding of a single polypeptide is called its
Tertiary structure
Ionization of amino acids at alkaline pH
The amino group is neutral- NH2 and the amino acid is in the anionic form
Ionization of amino acids at neutral pH
The carbonyl group is deprotonated but the amino group is protonated. -the net charge is zero. -such ions are called zwitterions
Ionization of Amino Acids at acidic pH
The carbonyl group is protonated and the amino acid is in the cationic form
At the isoelectric point
The net charge is 0 -AA is least soluble in water -AA does not migrate in electric field
In a conjugated protein, the prosthetic group is
The non-amino part of the conjugated protein
Amin acids carry a net charge of zero at a specific pH
The pI -for amino acids without ionizable side chains, the isoelectric point (equivalence point, pI) is equal to: PI = (pKa 1 + pKa 2) / 2
True or false: Each hydrogen atom of water bears a partial positive charge
True; because the oxygen atom is more electronegative than the 2 hydrogen atoms, the electrons are often more in the vicinity of the oxygen, giving each of the hydrogen atoms a partial positive charge
True or false: H bonds are relatively weak compared to covalent bonds
True; hydrogen bonds have a bond dissociation energy of 23 kJ/mol, whereas covalent single bonds have a stabilization energy of approximately 200-460 kJ/mol
Nonpolar biomolecules
Typical wax
Water is... (shape & role)
Water is a distorted tetrahedron Because of dipole moment can serve as hydrogen bond donor and acceptor
Describe what happens when a crystalline salt such as NaCl dissolves in water in terms of the enthalpy and entropy of the system.
Water molecules get between the Na+ and Cl- of the NaCl. The entropy increases because the solution is much less ordered than the crystalline solid. Enthalpy also increases during the dissolution process, and energy is needed to break apart the Na and Cl ions.
Cell in hypertonic solution
Water moves out and cell shrinks
Affects of Solutes on the properties of water (Noncolligative properties)
_viscosity -surface tension -taste -color (Depends on chemical nature of the solute)
Micelles are what on the outside and what on the inside?
amphipathic outside hydrophobic core
Amino acids
building blocks of proteins have properties that are well suited to carry out a variety of biological functions: -capacity to polymerize -useful acid-base properties -varied physical properties -varied chemical functionality -forming amid bonds Differ only at R substitutent
Binding sites in enzymes and receptors are often
hydrophobic (helps bind complementary ligands) -hydrophobic effect favors ligand binding
Cell in isotonic solution
no net movement of water
Buffering capacity is lost when
pH differs from pKa by more than 1 pH unit
Henderson Hasselbalch equation
pH=pKa + log(base/acid) (Base/acid)= (proton acceptor/proton donor)
PKa
pKa= -log Ka Strong acid = large Ka = small pKa
Aromatic R groups
phenylalanine, tyrosine, tryptophan -these amino acid side chains absorb UV light
