BIOL 201 Lecture Notes - Lecture 3: Reynolds Number, Petroleum Jelly, Mass Diffusivity
Very far from equilibrium, constant burning of energy to
supply cellular processes
•
“Watery interior” of a cell, “Material” in which
organelles are embedded
•
What is it like? Salty water, petroleum jelly, jello?
Depends who you ask!
•
What is cytoplasm?
This stuff
Properties of Cytoplasm
Contains… ions (~0.1 nm), sugars and amino acids, small molecules; proteins, DNA, RNA (10-100nm), organelles (1 um) that
are membrane bound or free protein assemblies, massive compared to amino acids and ions
a.
Contains protein in ordered crystalline array
▪
RBCs are about 35% protein by weight
▪
A "dilute" solution of protein is about 0.1% protein by weight
▪
More similar to glass than salty water, resembles solid structure
▪
About as crowded as protein crystals (20-60% protein by weight!)
b.
Cytoplasm is crowded
1.
Explores a lot of space, but with an average 0 net displacement
▪
Molecules move continuously due to Brownian motion
a.
diffuse with characteristic diffusion coefficient (D), where smaller molecules undergo faster diffusion, have larger D
b.
Constant collisions with water, ions and other cytoplasmic components
▪
Also distorts active site of an enzyme: allows for energy to be pushed above activation energy to catalyze metabolism
▪
Protein crystal structure is only one of large number of conformations that a protein can adapt
▪
The structure of individual proteins is distorted by collisions
c.
Large molecules essentially trapped by dense surrounding proteins
▪
Crowding can actually accelerate biochemical reactions, as large components exclude volume, raises concentrations of
other amino acids, sugars etc.
▪
Use polyethylglycol in the lab to simulate these conditions
□
You can make any reaction go faster by crowding volume around an enzyme to reduce effective volume in which
reactants are dissolved
▪
The bacterial cytoplasm can be simulated in a computer, with all proteins at physiological concentrations
d.
Cytoplasm is a rough-and-tumble place
2.
Ex. Swimming through cytoplasm…will you glide like in water?
i.
Inertia: resistance of an object to any change in its state of motion, something that is moving wants to stay moving
a.
Viscosity: a measure of a fluid's resistance to flow
b.
High value means inertia dominates, tendency to maintain state of motion
i.
Reynold's number is ratio of inertia to viscosity
c.
Cytoplasm is viscous
3.
Reynold's Number Re =
Cells, organelles and proteins are in a low Reynold's number environment: inertia is negligible!
c.
In water Re = 104, in cytoplasm Re = 10-4
▪
Smaller things have lower Re, thus swimming through water for them is more like swimming through honey
▪
Anything that is moving must actively maintain its motion with ENERGY, no ballistic motion
d.
Elasticity: the tendency of an object to return to its original shape after deformation
a.
Cytoplasm will deform and resume original shape
b.
Cytoplasm is elastic
4.
Organelles, polymers, and other structures define "pore size"
a.
Cytoskeletal components like actin filaments create filamentous "net"
b.
If you are larger than said pore size, you are effectively trapped by the medium unless it is reconfigures to allow motion
c.
Cytoplasm is a meshwork
5.
Continuous burning of energy to drive cellular processes
a.
Ceases motion of protein within the cell
▪
Carbon starvation of bacteria turns cytoplasm into glass
b.
If bacteria are in a carbon depleted environment, their cytoplasm becomes glass and they go into dormant "pill" state:
survival mechanism to control physical properties of cytoplasm?
▪
Diffusion in a cell is ACTIVE, not thermal, requires constant enzymatic activity of cytoplasm that is forcibly
disturbing it!
▪
Rapid ATP depletion also freezes cytoplasm of E. coli
c.
Cytoplasm is an active material
6.
Lecture 3: The Nature of Cytoplasm
January 12, 2018
7:15 AM
Section 1 Page 1
Document Summary
Very far from equilibrium, constant burning of energy to supply cellular processes (cid:862)water(cid:455) i(cid:374)terior(cid:863) of a cell, (cid:862)material(cid:863) i(cid:374) which organelles are embedded. Co(cid:374)tai(cid:374)s io(cid:374)s (cid:894)~(cid:1004). (cid:1005) (cid:374)(cid:373)(cid:895), sugars a(cid:374)d a(cid:373)i(cid:374)o acids, s(cid:373)all (cid:373)olecules; protei(cid:374)s, dna, rna (cid:894)(cid:1005)(cid:1004)-100nm), organelles (1 um) that are membrane bound or free protein assemblies, massive compared to amino acids and ions. About as crowded as protein crystals (20-60% protein by weight!) A dilute solution of protein is about 0. 1% protein by weight. More similar to glass than salty water, resembles solid structure. Explores a lot of space, but with an average 0 net displacement b. c. diffuse with characteristic diffusion coefficient (d), where smaller molecules undergo faster diffusion, have larger d. The structure of individual proteins is distorted by collisions. Constant collisions with water, ions and other cytoplasmic components. Also distorts active site of an enzyme: allows for energy to be pushed above activation energy to catalyze metabolism.
