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105 Cards in this Set

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What is the chemical equation for Free Energy? What is the idea behind this?
^G = H + T^S
System requires energy
Spontaneous reactions have negative free energy
coupling a reaction provides what?
A faster and more favorable reaction process that decreases a reaction barriar by combining a positive and negative free energy. The net reaction gives a more favorable situation.
Why is evolution the driving force behind biology?
mutations in the genetic code occur at a measurable rate over time, can last throughout the evolutionary pattern; Certain diseases are caused by these mutations, and can interfere w/ protein function; advantageous mutations propagate
mutation
What did Miller and Urey's experiment do for biochemistry?
The reaction apparatus was set up in a contained chamber w/ early earth gases which were thought to make up the atmosphere. Spark electrodes were to simulate electricity for lightning and these reactions helped to stimulate the abiotic production of basic building blocks for life.
Early Earth
The boiling point and melting point of water compared to other liquids...
is very high
What makes water special?
waters structure makes it a perfect hydrogen donar and accepter. Oxygen is very electronegative and withdraws the negative charge to set up a dipole of partial negative charge on O. H then have partial positive charges.
What is the perfect coordination state of water?
its when the water molecule is involved in a maximum of 4 bonds; two accepting H bonds and two donating H bonds.
Why is liquid water more dense than ice?
because the crystal lattice of ice collapses in liquid form and molecules form a more dense material of water molecule clusters w/ an average of 3.4 H bonds
Why is water a good solvent?
because through strong charge-dipole interactions, water molecules can isolate and protect ions from reacting with one and other; NaCl example
Coulombs law: Q1Q2/r^2 This shows that water helps to reduce the force between to molecules weakening thier attraction and thus aids in dissolution
What is the Hydrophobic effect?
When nonpolar substances interfere with the entropy of water causing it to become ordered, this is an unfavorable situation b/c it decreases the randomness in which water can react w/ itself. The hydrophobic effect causes the spontaneous clustering of lipids/other nonpolar molecules so that less water molecules are ordered and entropy increases. This is essential to the formation of biological membranes.
Why is ionization of water important?
Many reactions count on the concentration of protons [H+] to occur, therefore water has a very small fraction of molecules that ionize but it is important that it does this. Water has an equilibrium w/ itself and its components of H and OH.
What is the molarity of water?
55.5M (very high)
What does the logritmic scale help us to accomplish?
Because the H concentration is a very wide and cumbersome range, its more convienient to use this scale which gives numbers between 1-10. -log[x]=pH pure water is 7.0 which is a neutral substance.
what is acetic acid???
Vinegar
Define acids and bases
Acids are proton donars or electron pair acceptors
Bases are proton acceptors and electron donars
What is the diff. between a weak and a strong acid/base?
weak acid/bases only partially ionize in solution; strong acids have a greater tendency to release protons.
what is pKa?
this is the logritmic scale associated w/ the dissociation constant of an acid or base. [H][A-]\[HA]. The dissociation can be described by an equilibrium constat: how much product exists to the concentration of ions present. This equilibrium can be expressed in pKa = -log [Ke]
what is the Henderson Hasslebach equation?
pH = pka + log[A]/[HA]
What is the pH of 0.1M Acetic acid and 0.1M of its
conjugate base Sodium acetate?
Use of Henderson Hasselbach equation gives
pH = pKa + log [A-] / [HA]
= 4.76 + log [1]
= 4.76; this shows that right at the pka, the amount of acid and base are equal.
What happens after addition of an equal volume of
0.05M HCl? HCl is totally ionized.0.1M Acetic acid and 0.1M of its
conjugate base Sodium acetate?
[HA] = 0.15/2 [A-] = 0.05/2
(Concentrations are divided by 2 because volume doubles)
pH = 4.76 + log [0.025] / [0.075]
= 4.76 -.48 = 4.28
(Does not change much!)
What equilibrium reactions involve water?
Hydrolysis and reverse is Condensation
Why is pH carefully controlled in cells?
b/c cells have an optimum pH that they can function at and enzymes are sensative to pH
what is a buffer?
A system able to resist change in pH, where the conjugate acid-base ability to donate and accept protons is nearly the same
What are the most abundent macromolecules in the body?
Proteins
What is underlying simplicity of Proteins?
They are all polymers of amino acids

There are only 20 different amino acids defined by the genetic code
What roles to Proteins play in regard to cells?
Metabolism, replication and structure
Proteins can be understood in terms of a hierarchy of structure. Describe that structure
1. Primary
2. Secondary
3. Tertiary
4. Quaternary
Primary Structure of a Protein?
basic compilation of amino acids along the polypeptide chain. Position of disulfide bonds
Secondary structure of a Protein?
the local 3D sturcture associated w/ the amino acid in the Protein (a-helix, random coil, b-strand, b-sheet)
Tertiary structure of a Protein?
3D arrangement of secondary structural elements (Protein fold)
Quartenary Structure of a Protein?
arrangement of protein subunits in macromolecular assembly
All amino acids in Proteins are what?
L-stereoisomers, except for Glycine b/c it does not have a chiral center
What are the functional groups that make up an Amino Acid?
a Carboxyl Group and an Amino group +NH3-CHR-COO-
Isoelectric point
where charges of equation are equal and neutral
Post-translational modification
changes to the protein structure after it is assembled
Zwitterion
net charge is zero
As an amino acid ionizes, what happens to its pK?
It gets larger
What is Peptide bond breakage and makeage?
make: condensation reaction- lose water
break: gain water; Hydrolysis
What is the approximate isoelectric point?
Given that the approximate pKa's of
Glutamic acid are 2.2, 4.3 (s side chain pKa), and 9 ide 9.0 .0
Alanine are 2.3, 9.7
Lysine are 2.2, 9.0, and 10.5 (side chain pKa)
Histidine are 1.8, 9.2 a and 6. nd 6.0 (side chain pKa)
pH NH3 Glu Ala Lys His COO Net
3.0 +1 0 0 +1 +1 -1 +2
5.5 +1 -1 0 +1 +1 -1 +1
8.0 +1 -1 0 +1 0 -1 0
11.0 0 -1 0 0 0 -1 -2
The isoelectric point is going to be a around round 8.0.
To better estimate, average t the p he pKa values of all groups t Ka that a hat are re
ionizing around pH 8:
(NH3, Lys, His) = (9.0 + 10.5 + 6.0)/3 = 8.5
What is the process of Ion Exchange Chromatography?
Positively charged proteins
will stick to negatively charged
beads. Elution (removal) of protein
is achieved by changing pH or salt
conditions
GelFiltration Chromatography?
Size filtration
Affinity Chromatography?
Specific to property of affinity to a ligand which it can react with and then seperate it out.
Specific Activity? total activity units?
fraction of desired Protein; same amount of protein in different volumes
Electrophorisis?
Separating Protein using charged feild to
Isoelectric focusing?
helps determine Protein sample by seperating on basis of pH. Once Protein hits isoelectric value, it will no longer progress along the electric current.
2D Gel Electrophorisis
Uses Isoelectric focus gel and then SDS page to seperate by size
What can protein sequences tell us?
Initially protein sequences told us that proteins with the same
function from different organisms have similar but not
identical sequences. These differences arise from point mutations.
It provides a measure of the evolutionary distance between
species and can be used to develop phylogenetic trees.
Why are some Protein sequences completley conserved over time?
because some mutaions are disadvantagous and there is enormous pressure to maintain protein function.
What is the overall method for protein sequencing?
1. Separation of chains, S-S reduction
2. Amino acid composition
3. N- and C-terminal analyses
4. Cleavage of protein into fragments
5. Sequencing of fragments
6. Overlap of fragments, assembly of the complete sequence
7. Identification of the location (if any) of disulfide bonds.
Edman Degredation?
This is a refinement of the determination of the N-terminal
amino acid and amino acid composition.
In principle label and remove one amino acid residue at a
time. Key is gentle hydrolysis of the labeled N-terminal
residue.
Stepwise removal of one amino acid at a time. To sequence a Protein.
Mass Spectomotry?
Using a gas to seperate Proteins based on size and charge; Mass specs det charge/mass ratio for proteins
What does Tandom Mass Spec help accomplish?
certain portions of sequence have identifiable masses
What is the dif. between a gene and a protein?
Protein is an amino acid sequence

Gene is a DNA sequence
What is the value of knowing the protein sequence?
its very important in det. disease cause
What methods are used to denature a Protein?
Heat, organic solvents and detergents can be used b/c Proteins are only mildly stable.
What is the most accurate depiction of a Protein structure?
Space filling model
What are some characteristics of a Peptide bond?
It is planar and also exists almost always in the trans configuration. It has two kinds of bond angles capable of rotating phi and psi.
What is steric clash?
Its when the size of atoms does not allow for it to rotate.
What is the The Ramachandran plot:
it is a graphical depiction of allowed regions of protein folding
what property do a-helix have?
They are almost all right handed, which fulfills the bonding potetion of the protein.
Describe the secondary structure of beta strands
There are two types: Parallel and Antiparallel. Hydrogen bonds are formed and side chains are on opp. sides of sheet to form pleated sheet
Describe Turns, coil, etc: the rest of secondary structure:
Most of the amino acids in a Protein are not found in the sheet or helix form, but are used to form b-turns, b-bends, hairpins. These allow the protein to fold back on itself in a sterically acceptable mannar which is essential for the formation of a globular protein. usually composed of 4 amino acids
What are the classes of Proteins?
1. Fibrous: Keratin (hair, skin nails) and collagen (most abundant in humans)
What is a rare example of a left handed helix?
collagen: a major component of connective tissue.
How are protein structures solved?
Protein diffraction using x-ray, electron density map then formed, model devised and structure determined
What is known about secondary structure regarding is uniformity in different proteins?
It varies greatly
How can we measure the stability of a Protein?
The stability is the difference in free energy between the folded and unfolded states; this is not much more than a few simple H bond strengths.
What is the Primary stabalizing factor regarding Proteins?
The Hydrophobic effect: the hydrophobic side chains seek the interior of the Protein in the denatured state, away from the aqueous environment to create its folded state. This is a property of water.
Do H bonds in a protein have a thermodynamic affect?
No because they are thermodynamically equal to the H bonds formed by water, but they are important to the conformation of the Protein
How do disulfide bonds contribute to a Protein?
They can add considerable stability to the Protein; they are crosslinks to form folded states
Name the stable folding patterns of a Protein
1. b-a-b loop
2. a-a corner
2. all b-motif
What is an oligomer?
it is a motif constructed w/ smaller components/multiple subunits. Proteins are often oligomers and add to its stability and control.
There is a limit to Protein size...why?
Its more efficient to build large structures from smaller ones. ie building

Also there is an error rate in Protein syntesis of 1 mistake for about 10,000 amino acids. (nature is extremely accurate) but proteins about 10,000 amino acids would have a mistake in it and wouldnt function well. Usually less than 1000 amino acids in Proteins.
What did Anfinsen do for Protein structure?
His protein folding experiment proved that a Protein can be experimentally unfolded and it will go back to its original sequence proving that Proteins have primary sequences which encode for the 3D structure
How do myoglobin and Hemoglobin contribute to our understanding of biochemistry?
Myoglobin is the key instrument in oxygen transport. The body would not be able to get enough oxygen w/o it. Sequestering Heme (porfrin ring + Iron) inside Myoglobin and Hemoglobin allows the body to get Oxygen in muscle tissue and blood. B/c oxygen does not dissovle in solution. Good for diving animals.
How does the Protein fold influence binding?
It adds specificity for binding of certain ligands...for example in the blood, myoglobin is discriminatly favors O2 over CO gas, but CO has a stronger affinity (bond strength which is why its so dangerous)) to heme, this makes it harder to get blood poisoning of carbon monoxide
What does an oxygen binding curve show?
its shows the percentage of myoglobin bound to oxygen as a result of the partial pressure of oxygen in solution
What is the association constant?
it is the amount of bound and unbound protein which can be calculated by
Ka = [L][P]/[LP] which describes free ligand to bound protein ratio
What is the formula for fraction of a Protein bound?
theta = [PL]/[P] + [PL] = [L]/ [L] + 1/Ka

1/Ka = Dissociation Constant Kd
when [L] equals Kd...
Half the binding sites are occupied
Hemoglobin transfers oxygen...
in the blood; its quaternary structure versus myoglobins tertiary structure is the major difference.
myoglobin...
stores oxygen; it holds oxygen too tightly which makes it a lously transporter.
Partial pressure is the same thing as...
dissociation constant 1/Ka
Hemoglobin exits in two states....
T (tense) and R (relaxed) states; oxygen binds much more so w/ the R-state
Transporter...
binds oxygen in the lungs and releases oxygen in the tissues
What does the sigmoidal binding curve of Hemoglobin indicate?
it is the result of the coopertivity of the 4 subunits. This is the key difference between Hemo adn Myoglobin
What other function does Hemoglobin have other than oxygen transport?
Hemoglobin must also transport CO and H from the tissues to the lungs in order to finish the respiration cycle.
At low pH what does Hemoglobin do to oxygen
it binds with less affinity and favors release of H and CO in the lungs
Oxygen binding is regulated by what?
2,3-bisphosphoglycerate (BPG) w/o it there would be no coopertivity between the Hemoglobin subunits
What does it mean when we say Hemoglobin is allosteric?
It means that it is bound by many ligands, each which affect the binding potential at other sites; allostery is action from a distance
How does BPG work among the structure of Hemoglobin?
BPG binds to positivly charged residues between the b-subunits. This then lowers the affinity of Hemo to oxygen, the R-state then narrows and eliminates the BPG.
Without BPG
Hemoglobin would only exist in the R-state and would not be a good transporter.
What are the properties of Enzymes?
1. almost all are proteins
2. Catalysts
3. Enormously specific
4. regulate many metabolic
5. 3D structure essential
what is the difference between Holenzymes and apoenzyme/apoproteins?
Holoenzymes: complete w/ polypeptide + cofactors

Apo: protein w/o cofactors
What are the classes of Enzymes?
1. Oxidoreductases: transfer e'
2. Transerases: group trans
3. Hydrolases: Hydrolysis rxn
4. Lyases: add of groups to double bonds or formation of double bonds
5. Isomerases: Transfer of groups w/i molecules to yield isomeric forms
6. Ligases: catalyze joining together fo two molecules coupled w/ the hydrolysis of ATP
What are enzymes physically doing to a reaction when it is catalyzed?
They lower the activation barriar of a reaction so that it proceeds faster. Enzymes are complimentary to the transition state. This utilizes binding energy which reduceds the the energy of the transition state. They bind more tightly than to reactant or product.
Describe Acid Base Catalysis
Enzymes provide additional functional groups that aid in catalysis. General acids and bases are some of teh most important contributors.
Describe Covalent Catalysis
Characterized by covalent bonds. Incorporate the formation fo an acyl intermediate in their mechanisms. However also incorporate elements of acid base catalysis. Form bonds
How are metals used in catalysis?
metals stabilize charge build- up at trans state.
Enzymes change the rate of a rxn, what dont they do?
they dont change the equilibrium
The rate of a reaction is dependant on what?
the concentration fo the substrate which as it increases, the rate also increases. this can help det. how affective an enzyme is
What is the Enzyme Substrate complex?
Rpid reversible formation of ES
E + S = ES
ES = E + P rate limiting thus rxn rate is proportional to rate limiting [ES]
What is the Ka
it is the dissociation constant:
pKa = -log Ka
would pKa be higher or lower for a strong acid?
lower
Solutions of weak acids or bases will buffer w/i what of their pH
+-1 pH unit of their pKa