Biophysics Final Review

Multiple weak bonds and lock and key shape compatibility

What are the two design concepts necessary for successful self- assembly?

Yes there is a drag force due to the water and it must be balancing the thrust force for the bacterium to be at a constant velocity. It's magnitude is 2 pN

A bacterium is swimming in a pond at a constant velocity of 50 um/s.  It's flagella is providing 2*10^-12 N ( 2 picoNewtons or 2pN) of thrust pushing the bacterium through the water.  Are there any other forces of the bacterium? If so what force and what is it's magnitude. If not, why not?

True

At the scale of the cell, diffusive motion is remarkably fast. If you release a typical protein inside a bacterial cell, within one one-hundreth of a second, it is equally likely to be found anywhere in the cell (T/F)

True

A very small object has larger surface to volume ratio than a very large object (T/F)

It is the electric charge of a proton or + 1.6*10^-19 C

What does the symbol e mean ?

Interaction between Polar Water Molecules

Hydrogen Bond

any electrically neutral object with positive and negative charge separated

Electric Dipole

The process where an electron is removed from an atom leaving it with a net charge

Ionization

A molecule that is an electric dipole

Polar Molecule

Material in which valence electrons are tightly bound

Insulator

Material in which valence electrons are free to move

Conductor

0.045 N

What is the magnitude of the electrostatic force  that 1 μC charge applies to a  20 μC charge sitting 2 m away? (calculate)

Remember that the symbol μ or "micro" means 10^-6

The positive charge induces a separation of charge in the neutral atom or "polarizes" it. Negative charge will migrate to the side of the atom nearest the positive charge and will cause attraction

If a positive charge is brought near a neutral atom, what happens?

laminar

orderly stream-lined flow in a fluid is described with the term

turbulent

disorderly chaotic flow in a fluid is described with the term

6*pi*n*r*v

What is the equation you would use for fluid drag force for a bacterium swimming through water ?

0.5*Cd*p*A*v²

What is the equation you would use for fluid drag force for a whale swimming through water ?

p*v*L / n

What is the equation you would use to determine whether the fluid flow for a particular system will be laminar or turbulent ?

primary structure

structure of sequence of amino acids

tertiary structure

structure of globular

different regions off a polypeptide

di-sulfide bond connects…

unique part of amino acid

side-chain is a…

secondary structure

structure of alpha/beta helix

20^10

Imagine are going to make a small segment of a protein 10 amino acids long. How many different sequences can you make assuming any amino acid can be in each of the 10 spots ?

Every amino acid has an amine group and a carboxylic acid group. The part that is different for each amino acid is the "side-chain"

What parts of the amino acid are the same for all amino acids? What parts are different?

The properties of the side chains of the unique sequence of amino acids that make up the protein

What determines the 3 dimensional structure of a protein ?

3/2*Kb*T

What is the average kinetic energy of an oxygen molecule in the room right now if at temperature T ?

125 J

How much energy does it take to heat up a mole of air molecules from 20 to 30 degrees K ? (calculate)

False

Heat and Temperature are basically the same thing (T/F)

The Hemoglobin and calcium have the same average kinetic energy, but the calcium ion is moving faster on average

Imagine a hemoglobin molecule (64,500 Da) and a calcium ion (40 Da) are in water at room temp. How would you compare their average kinetic energy and speeds to each other?

410 m/s

In the air right now around you on of the gas molecules crashing around is carbon dioxide (mol. mass = 44 Da or 44 g/mol). How fast on average are the C02 molecules moving in the room you're in right now (assume T = 295 K) (calculate)

Pascals [Pa], or N/m²  Like Pressure

What are the units of stress?

It is unitless

What are the units of strain ?

0.5

Imagine you cut a rubber band so it's just one straight length. It is originally 5 cm long and you stretch it to 7.5 cm. What is the strain? (calculate)

20,000 Pa

Imagine that in a cell, a myosin motor pulls on an actin filament with 1 pN of tensile (pulling) force. The actin filament is 4nm in radius. What is the tensile stress that the motor is applying? (calculate)

stiffness

The modulus of elasticity or Young's Modulus is a measure of a material’s…

Hydrogen bonds are very direction dependent (the angle matters). They are also much stronger than a regular dipole-dipole interaction

How are hydrogen bonds different than regular dipole-dipole interactions ?

False

dipule-induced-dipole is stronger than dipole-dipole (T/F)

False

induced dipole-induced dipole is stronger than dipole-induced-dipole (T/F)

True

ion-dipole is stronger than hydrogen bond (T/F)

True

Hydrogen bons are 10 times stronger than ordinary dipole-dipole interactions (T/F)

False

Non-Polar molecules can be attracted to Polar Molecules, but Non-Polar molecules can not attract each other (T/F)