1 - Size, Energy, and Time Flashcards
What are the three basic ideas of biochemistry?
Size, energy, and time
What is size?
How big or small an item is
What are some examples of size?
Length of bonds, diameters of molecules, volumes of complexes, etc.
How big is 1 angstrom?
0.1 nm
What is the length of a C-C bond?
1.5 angstroms
What item is 1.5 angstroms?
C-C bond
What is the length of a C-H bond?
1.1 angstroms
What item is 1.1 angstroms?
C-H bond
What is the length of a C-O bond?
1.0 angstroms
What item is 1.0 angstroms?
C-O bond
What is the diameter of an alpha helix (backbone to backbone plus side chains)?
10 angstroms (1 nm)
What item is 1 nm?
Diameter of an alpha helix
What is the diameter of a large protein?
100 angstroms (10 nm)
What item is 10 nm?
Diameter of a very large protein
What is the size (diameter) of an average protein?
30-40 angstroms (3-4 alpha helixes stacked together)
What is the diameter of a ribosome?
200 angstroms (20 nm)
What is the diameter of a clathrin coated vesicle?
1000 angstroms (100 nm)
What item is 100 nm?
Diameter of a clathrin coated vesicle
What is the length of an E. coli cell?
1000 nm (1 um)
What is the diameter of a cell nucleus?
5-6 microns
What is the diameter of an “average” cell?
15 microns
How many proteins can be fit inside a ribosome?
About 100
What math is done to calculate how many proteins can fit inside a ribosome?
- V = 4/3 * pi * r^3
- Radius of protein ~20 A (diameter ~40 A)
- Radius of ribosome ~100 A (diameter ~200 A)
- (100 A / 20 A)^3 ~ 100 proteins
True or false: there is a lot of free water in the cell
False: there is very little free water in the cell (tightly packed)
What is the distance of a synapse?
~200 A
What is the size of a receptor in a synapse?
~100 A
If drawn to scale, what can be said about vesicles being released into a synapse?
Vesicles are released directly on synapse (synapse ~ 200A, receptor ~100 A)
What did the study with trafficking organelles look at?
The size and copy number of various proteins
What did the study with trafficking organelles find?
Lots of proteins stuck to the surface, membrane packed with proteins, extend to different heights
Where is energy seen in biochemistry?
Reaction rates, binding mechanisms, and thermodynamics
What are some examples of energy considerations?
Thermal energy (RT), free energy, enthalpy and entropy, electrostatics
What quantity represents thermal energy?
RT (gas constant * temperature)
What is the significance of PV=nRT?
It describes how chemists could easily manipulate the environment (PV) to alter energy (nRT)
What is thermal energy?
Available energy to catalyze a reaction (jiggling molecules)
What does HEW stand for?
Hen egg white (lysozyme)
What does HEW lysozyme do?
Catalyzes breakdown of sugar
What does the cavity of HEW lysozyme have?
Strong negative charge
What is the significance of clefts and grooves in a protein?
This is where enzymes catalyze reactions
True or false: most enzymes catalyze reactions at the surface
False: most enzymes catalyze reactions in clefts and grooves
Why do enzymes catalyze reactions in the clefts and grooves?
They can bring reaction groups out of the solution and make them more reactive
Why does bringing reaction groups out of solution make them more reactive?
They are stripped from water
What is a typical value of RT at room temperature?
~600 cal/mol (~1 kcal)
What is the conversion rate between kcal and J?
1 kcal/mol = 4.2 J/mol
What is the difference between RT and kT?
RT is the thermal energy in one mole, while kT is the thermal energy in one molecule
What is the typical strength of an H-bond?
~5 kcal/mol
What is the typical energy released from hydrolysis of ATP?
~10 kcal/mol
What is the energy of a photon (500 nm)?
~50 kcal/mol
What is the typical energy of a covalent bond?
~50-100 kcal/bond
How much does energy “span” in biochemistry?
~2 orders of magnitude
Where is time seen in biochemistry?
Rates, reaction mechanisms (how enzymes change conformation over time)
What are some examples of time?
Neuronal signaling, water molecules vibrating, kinesin transport via ATP hydrolysis
How do proteins that hydrolyze ATP usually work?
They usually bend proteins (similar to Pacman) (clamping)
How do kinesin “feet” work?
They open and close through ATP hydrolysis clamps
How long is the vibrational period of a C-C stretch?
~30 fs
How long does it take to break a bond?
One period
How long does rotation of a side chain take?
~1 ns
How long does rotation of a protein domain take?
~1 us
How long does it take a small protein to diffuse 100 nm?
~1 ms
How long does it take a small protein to diffuse 10 nm?
~1 us
How fast does unmyelinated neuronal conduction take?
~2 mph
How fast does myelinated neuronal conduction take?
~200 mph
How long does it take a signal to travel from the brain to the arm?
~20 ms
What is the speed of a kinesin molecule?
~1.6 um/s (160 um per step)
How many steps does a kinesin molecule take per second?
100 steps per second (1 step in 10 ms)
True or false: one sec is a short time in a biochemical scale
False: one sec is a long time for a cell time scale
What are some examples of organic reactions catalyzed by enzymes?
Group transfer reactions, oxidation-reduction reactions, isomerization and rearrangement, breaking and making bonds
What are some group transfer reactions?
Methyl, hydroxyl, carboxyl, formyl, acyl, glycosyl transferases, transfer of N-containing, S-containing, P-containing groups
What are some oxidation-reduction reactions?
Involves OH, C=O, CH-CH, SH, metal ions
What are some isomerization and rearrangement reactions?
Racemases, epimerases
What are some bond forming and breaking reactions?
Ligases forming C-O, C-S, C-N, and C-C bonds, hydrolases, carboxylases
What are the three basic types of reaction mechanisms?
Nucleophilic catalysis, electrophilic catalysis, and acid-base
What is a nucleophilic attack?
An electron rich reagent attacks an electron poor site in a reaction
What is an example of a nucleophilic attack?
Catalytic triad in serine proteases
How do serine proteases work?
- His serves as a base to take up proton from Ser -PH
2. Ser serves as a nucleophile to attack carbonyl carbon on protein backbone
How can the reaction rate of a serine protease be increases?
By placing a positive charge near the oxygen of the carbonyl group
How does placing a positive charge near the oxygen of a carbonyl group increase the rate of a serine protease reaction?
Electron density is pulled towards the oxygen, making the carbon more partial positive (more electron poor). This makes it more reactive to a nucleophilic attack
Which is more common in biochemistry and why: nucleophiles, or electrophiles?
Nucleophiles, because proteins are electron rich
What is electrophile catalysis?
An electron “sink” to catalyze the reaction
What are good electrophiles in biochemistry?
Coenzymes, vitamins, and minerals (metal ions)
How do electrophiles catalyze reactions?
They guide reaction mechanisms of proteins, and pull electrons to catalyze cleavage
What is an example of a electrophile catalysis reaction?
Decarboxylation (through vitamin B6)
How does a groove interact with a substrate?
The groove is complementary to the substrate based on shape and electrostatics
How does excluding water increase reactivity?
By strengthening the effect of charge and other polar groups
What amino acids are found in the groove of HEW lysozyme?
Glu and Asp
Why are Glu and Asp found in the groove of HEW lysozyme?
The reactivate intermediate is a positively charged oxycarbenium substrate, so the negatively charged amino acids help stabilize this structure
What is pKa?
The disassociation constant for an acid
What is the formula for Kd for an enzyme and substrate?
Kd = [ES] / [E][S]
What reactions are needed to calculate Kd for an enzyme and substrate?
Association: E + S -> ES
Disassociation: ES -> E + S
What formulas involve delta G?
delta G = delta H - T delta S = -RTln(Kd)
What is enthalpy?
Energetics
What is entropy?
Order/disorder
What is a positive delta G?
Unfavorable reaction
What is a negative delta G?
Favorable reaction
When is free energy most negative in an enzyme/substrate reaction?
In the association (ES)
How come the delta G becomes more positive if E and S get too close together?
There are steric conflicts
What is the energy of two interacting charges in a vaccuum?
500 kJ/mol
What is the energy of two interacting charges in water?
6 kJ/mol
How does water decrease interaction energy?
By shielding charges, reducing reactivity (higher dielectric constant)
How can enzymes increase the rate through oritentation?
By constraining the reactants and reactive groups
How can enzymes constrain reactive groups?
Bonds, rings, etc. (less rotation)
What coenzymes are used in DHFR?
NADP+ and tetrahydrofolate
How do the two coenzymes in DHFR interact?
The reactive end of one is next to the reactive end of another (through tight groove binding)
What is chymotrypsin and what does it do?
A member of the serine proteases that cleaves aromatic amino acids
What is the role of the specificity pocket?
To determine the type of amino acid to be cleaved
What is the specificity pocket in chymotrypsin?
Hydrophobic (aromatic)
What is the catalytic triad in serine proteases?
Asp, His, and Ser
True or false: Asp changes protonation state during serine protease catalysis
False: it does not change protonation
What is the purpose of the NH in chymotrypsin?
It orients the carbonyl with the positive charge, and polarizes it (better attack from Ser nucleophile)
What does the Asp do in the catalytic triad?
It orients His properly (so His can act as a base to charge Ser)
What is the specificity pocket in trypsin?
Negatively charged (cleave positive residues)
What does trypsin do?
Cleaves positive amino acids
What do 30% of most proteins have?
Bound metal ions
What are most metal ions in biochemistry?
Cations
What is the significance of metal ions in biochemistry?
They have huge electrostatic components, making them reactive when water is excluded
What are some examples of metal ions seen in biochemistry?
Fe2+, Fe3+, Cu2+, Zn2+, Mn2+, Co3+, Mo3+, Mo6+
What are some examples of iron-containing proteins?
Hemoglobin and mitochondrial electron transport, heme proteins (porphyrin ring complex to carry O2), cytochromes, and iron-sulfur proteins
What are some examples of copper containing proteins?
One electron transfer agents (Cu+ -> Cu2+)
What are some examples of zinc containing proteins?
Carbonic anhydrase, and alcohol dehydrogenase
What are some examples of manganese containing proteins?
Arginase
What are some examples of molybdenum containing proteins?
Nitrate reductase
What does carbonic anhydrase do?
It uses water to hydrate CO2 and form bicarbonate
How does carbonic anhydrase work?
- It uses 3 His to coordinate Zn2+
- Zn2+ is used to pull H from H2O
- OH- attacks CO2 to form HCO3 (bicarbonate)
What is the purpose of zinc in carbonic anhydrase?
It pulls H from H2O to make a strong nucleophile (polarized)
What is the rate limiting step for carbonic anhydrase?
Diffusion of CO2 into the binding site (fast reaction rate)
What is the HEW lysozyme mechanism?
- Acid catalysis by Glu to form intermediate (electrostatic stabilization)
- Nucleophilic attack by water (Glu mediated)
True or false: pKa can be changed by burying groups?
True: burying groups can lead to more direct reactions, changing pKa
How do aspartic acid proteases work?
Two Asp polarize water, which is used as a nucleophile
What is an example of an aspartic acid protease?
HIV protease
How does enolase work?
- An unprot Lys attacks H, Mg2+ stabilizes charge
2. Prot Glu acts as an acid to drive the reaction
What is the significance of Mg2+ in enolase?
It stabilizes the highly negative intermediate
What is significant about Lys and Glu in enolase?
Lys is unprot, and Glu is prot, which would not occur in solution. This is needed for the reaction to occur
What would happen if there was free water in enolase?
The amino acids would have different charges, and the Mg2+ would not be as effective
How do ribonucleases work?
One His acts as a base (unprot), and another His acts as an acid (prot)
How does the pyruvate dehydrogenase complex work?
It uses many subunits, coenzymes, and reactive groups to sequester reactive intermediates
How does carbamoyl phosphate synthetase II work?
It has an internal tunnel to sequester reactive intermediates
What is the Arrhenius equation?
k = Aexp(-Ea/RT)
What is the diffusion equation?
x^2 = 2Dt
What is the equation for the diffusion coefficient?
D = kT/f (f = frictional coefficient)
What does the diffusion equation relate?
Relates the time for diffusion to the temperature and shape of the molecule
What is the HH equation?
pH = pKa + log(A-/HA)
