Lecture notes Flashcards
Concept side of notes
1
Q
(From intro slides) Mechanics/Physics are Mechanics + what?
A
Biology
2
Q
(From intro slides) what are the 3 kingdoms and give examples?
A
Human-made kingdom: planes, shoes, cars
Animal kingdom: cats, polar bears, dogs
Plant kingdom: trees, flowers, vegetables
3
Q
(From intro slides) True or False: One example of Failure is when DNA damage leads to mutations and cancer progression.
A
True
4
Q
(From intro slides) True or False: Physical laws are universal.
A
True
5
Q
How much does the Brian weigh?
A
3 lbs
6
Q
How much percentage of the brain is made of fat?
A
60%
7
Q
(Gentle) walking (exercise) has what effect on the brain?
A
Positive effect, it makes the brain sharper
8
Q
What differentiates a living thing from a non-living thing?
A
Living things: reproduction, harness energy, memory-genetic code, self-organize, replicate. Ex: Bacteria, whale
Nonliving things: does NOT generate energy by themselves. Ex: Virus is nonliving
9
Q
What are the fundamental units?
A
For Matter it is Atom.
For Life it is Cell.
10
Q
What are the core ingredients of living things? (Also macromolecules perform specific functions)
A
Proteins, lipids, carbohydrates, and nucleic acids.
11
Q
What function does the macromolecule proteins perform?
A
Form structural elements within cells, catalyze chemical reactions.
12
Q
What function does the macromolecule lipids perform?
A
Membrane barriers house proteins, transport.
13
Q
What function does the macromolecule carbohydrates perform?
A
Energy storage, rigid structural units
14
Q
What function does the macromolecule nucleic acids perform?
A
Memory and operational instructions for fabrication of macromolecules
15
Q
True or False: Biology is driven by experiments.
A
True. (Experiments to Quantitative data to Quantitative model to Experiments again. It’s a cycle.)
16
Q
True or False: Fundamental proposition: Biological entities can NOT violate laws of physics and chemistry.
A
True
17
Q
Model building: Ex. Using Google maps
A
You can have a different focus:
- Look at traffic of Houston
- Look at network of Houston
- Look at geographical/typography of Houston
18
Q
Europe has a “pitch” that is so viscous that a drop falling takes 5-7 years. So is it solid or liquid?
A
Due to time relative scale:
- treat it as a solid if considering for a few minutes
- treat it as a liquid if considering for a 100 years etc.
19
Q
Cartoons and models: Do cartoons suffice?
A
Most animations do NOT follow physics (things don’t work like that).
20
Q
True or False: Joel E. Cohen said this quote, “ Mathematics is Biology’s Next Microscope, Only Better; Biology is Mathematics’ next Physics, Only Better”
A
True
21
Q
Example of applications and Healthcare
A
Better drugs and better technology (such as electroporation device is used for drug discovery)
22
Q
What is the spring energy/ harmonic oscillator equation?
A
E = (1/2)k(x^2)
23
Q
What is the restoring force equation?
A
F = -k*x
24
Q
Roles of estimates: how to make an estimate and what is it’s formula?
A
Here’s an example, guess Agrawal’s weight. First set lower bound (100 lbs) and upper bound (200 lbs). Then do the formula sqrt(lower boundupper bound). So sqrt(100200) = 141 lbs as the estimate. Agrawal actual weight is 170 lbs.
25
"If, in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words?" - Feynman Lecture Series on Physics
All things are made of atoms
26
Humans owe a lot to?
1. Bacteria (E. Coli), 2. Fruit flies,
3. Squids (for neuroscience due to their big neurons),
4. Mice,
5. and C. Elegan (since they are clear worm-like organism 0.75 mm size)
27
How does Fluorescence Microscopy operate?
It shoots laser at a certain frequency, receives a different frequency back at an object
28
How does Atomic-Force Microscopy operate?
A laser hits a cantilever beam and moves beam to poke AFM tip
29
How does Electron Microscopy operate?
An electron wave hits object, reflects to deflector
30
Assuming this but what are two types of electron microscopy?
Cryo-electron microscopy and image reconstruction
31
What are the 3 main branches of the tree of life?
Bacteria, Archaea, and Eukaryotes (ex. Animals, plants, fungi etc)
32
Why do we use Escherichia coli (E. Coli)?
Biological standard ruler. Has a size of 1 micrometer width and 2 micrometer length. (So about 50 E. Coli is the thickness of a strand of human hair)
It is also: FEET
1. Fast application
2. Easy to isolate
3. Easy to produce mutants
4. Tolerates oxygen
33
What are HH Discoveries/Contributions?
- Devised voltage clamp
- Separated Na+ and K+ currents => Na+ and K+ conductance
- Postulated gating (showed the binary nature of channel opening from instantaneous current measurements)
- Obtained time and voltage dependence of conductance
- Discovered inactivation of Na+ channel
- Constructed the mathematical model
34
Dry mass is what percentage and protein mass is what?
Dry mass = 30% = 0.3 pg
Total Protein mass = 50% dry mass = 0.15 pg or 0.15x10^-12 g
35
1 protein has how many amino acids?
300
36
Mass of 1 protein?
300x100 Da = 5x10^-20 g
37
Total protein equation
(1/3) in membranes + (2/3) in cytoplasm
38
1 micron equals
10^-6 m = 1000 nm
39
1 mL equals
10^-6 m^3
40
1 pg equals
1x10^-12 g
41
Mass of amino acid equals
100 Da
42
1 Da equals
1.6x10^-24 g
43
Avogadro's number equals
6x10^23 molecules/mol
44
What percentage of surface area of membranes is covered by lipids?
50%
45
Area of a lipid is approximately?
0.5 nm^2
46
What drives diffusion?
Entropy
47
Number of proteins equals
3x10^6
48
Assume lifespan of E. Coli equals
30 minutes or 2x10^3 sec
49
Number of lipids
2x10^7
50
Number of water molecules (water uptake)
2x10^10
51
Average protein has a diffusion constant equal to?
100 micrometers^2 per sec
52
Length of E. Coli for the time diffusion equation
1 micron
53
What is kinesin?
Kinesin is a motor protein that helps cells to develop/divide cells
- it has two legs and "walks" along a microtubule, and other end hooks to a "cargo"
- more efficient than a car
- its the transportation within cells
54
What is kinesin speed?
1 micron/sec
55
What is the rate of ions moving across a membrane?
Transport rate across ion channel:
D = 2000 micrometers^2 per sec [Na+K+]
Concentration gradient:
Delta C = 100 mM = 6x10^-2 molecules/nm^3
Note: when the gate opens, the ions flow
56
True or False: higher the diffusion constant, higher the flux
True.
Also note:
dNion/ dt = Ac (cross sectional area) * Jion
Jion = D * delta C/ delta X
57
What are the electrical properties of the neurons?
- Dendrites: passive signal
- Axons: Active signal
58
What two things does a passive signal have that a membrane also has?
Resistance and capacitance
59
Ohm's Law eqn
V = I * R
V = volts
I = Amperes
R = Ohms
60
True or False: Electrons go from negative to positive
True
61
True or False: Current goes from positive to negative
True
62
In cells, current across cell membrane is caused by?
- Cations (Na+, K+, Ca2+, Mg2+)
- and Anions (Cl-, HCO3-)
63
Current is constant in a BLANK circuit.
Series circuit
64
True or False: Current is different in parallel circuit.
True
65
Is series arrangement or parallel arrangement more applicable to cell membranes?
Parallel arrangement
66
Conductance equation
g = 1/R [Siemens (S)]
So it's the inverse of resistance
Parallel: gt = sum of i * gi
67
Conductance in membranes is mostly determined by what?
Proteins
68
What is the Boltzmann constant?
1.38x10^-23 J/K
69
Voltage is constant in a BLANK circuit.
Parallel circuit
70
What is capacitance?
Capacitance is the ability of a circuit element to store charge
71
Capacitance eqn
C = a / V
C [Farads]
a [coulombs]
V [volts]
72
What is specific conductance?
Conductance per unit area (we can measure current through membranes)
Neuronal membranes about 10^-4 to 10^-5 Siemens/cm^2
73
Specific conductance eqn
gm = gt / 4* pi * a^2
Note:
gt = gm(4* pi * a^2) with a = 10 microns
Rt = 1 / gt = 1 / gm(4* pi * a^2) which equals 10^9 to 10^10 ohms or 1-10 GigaOhms
74
1 GigaOhm equals
1x10^9 ohms
75
Specific resistance eqn
Rm = 1 / gm = 10^4 to 10^5 Ohms*cm&2
Note:
(Rt/ 4*pi*a&2) = ohm/cm^2 is NOT specific. Normalizing by area inverse messes things up! So do NOT normalize specific resistance
76
Specific capacitance of neuronal membranes
Cm = 0.7 to 1x10^-6 F/cm&2
CT = Cm*(4*pi*a^2) = 10 picoFarads (pF)
77
3 cells example where cells increase in size
conductance: g1 < g2 < g3
Specific conductance:
gm1 = gm2 = gm3
- Experience same Vin and Vout (patches all connected in parallel)
- Same membrane
- potential across membrane is uniform
- cell 3 has largest conductance (most protein)
78
How to rank specific conductance?
- Conductance increasing with area
- if made out of same thing, will have same specific conductance
79
For isopotential, small cells, open circuit example
- Electrode is inserted into the cell
- Current is passed from inside to the outside (t = 0)
- Current flows outside through the parallel combination of the cell's resistance (R) and its capacitance (C)
80
How can ions flow through an insulator like a lipid bilayer?
- Ions do NOT flow across an bilayer, since the bilayer is very resistive
- instead, there's a CHANGE in the CHARGE on the two sides of the bilayer (called displacement current)
81
On the V/V initial vs. Time graph, which is higher? Cable equation or isopotential?
Cable equation
82
What is voltage rise determined by?
Voltage rise is determined by how fast the capacitance of the membrane can be charged
83
For small spherical cell, whole plasma membrane must be charged BLANK.
Uniformly
84
For cable, charging occurs BLANK and is the fastest at the BLANK of the current.
Non - uniformly; point of application
85
On the V/V initial vs. Time graph, as the X value increases, the graph does what?
The graph gets smaller and further away from V/V initial = 1
Note: increasing X is applicable for dendrites
86
What is neuroscience?
Neuroscience is the multidisciplinary sciences that analyze the nervous system to understand the biological basis for behavior
87
Modern studies of the nervous system have been ongoing since when?
The middle of the nineteenth century
87
Earliest study of the nervous system dates when?
Ancient Egypt when they did trepanation
88
What was the Egyptian view?
The heart was the seat of intelligence
89
What was Hippocrates view?
Brain was the seat of intelligence
90
What was Plato view?
Brain was rational part of the soul
91
What was Aristotle view?
Heart was the center of intelligence and that the brain regulated the amount of heat from the heart
92
The brain is sometimes referred to as what?
The last frontier of biology
93
What do neuroanatomists study?
The brain's shape, its cellular structure, and its circuitry
94
What do neurophysiologists study?
The brain's bioelectric properties
95
What do neurochemists study?
The brain's chemical composition, its lipids and proteins
96
What do psychologists and neuropsychologists do?
Investigate the organization and neural substrates of behavior and cognition
97
Who is the founder of modern neuroscience? What are his two major conceptual achievements?
Santiago Ramón y Cajal
Neuron doctrine: neurons interact by way of contact and contiguity and thus are structural independent units (electron microscope proved this)
Functional polarity: dendrites and cell bodies receive information, whereas the single axon with its collaterals transmits information to the other cells. This rule allows prediction of information flow direction through neural circuits...
98
The BLANK are the interconnected, highly differentiated, bioelectrically driven, cellular units of the nervous system; and their more numerous support cells are called the BLANK.
Neurons; glia
(Both are cellular building blocks of the nervous system)
99
Glia outnumber neurons by BLANK.
At least a factor of 10
100
At the molecular level of operations
The emphasis is on the interaction of molecules typically proteins that regulate transcription of genes, their translation into proteins, and their posttranslational processing
101
At the cellular level of neuroscience
The emphasis is on interactions between neurons through their synaptic transactions and between neurons and glia
102
At the systems level
Emphasis is on the spatially distributed sensors and effectors that integrate the body’s response to environmental challenges. There are sensory systems, which include specialized senses for hearing, seeing, feeling, tasting, and balancing the body.
103
At the behavioral level of neuroscience research
emphasis is on the interactions between individuals and their collective environment. Behavioral research includes the operations of higher mental activity, such as memory, learning, speech, abstract reasoning, and consciousness.
104
How many neurons does the human brain have? Axonal connections?
100 billion neurons; 100 trillion axonal connections
105
True or False: Neurons are highly polarized cells.
True
106
What are the two major domains of the cell that receive inputs?
Cell body and dendrites
107
What are the typical ions in the central nervous system (CNS)?
Na+, K+, Cl-
108
Equilibrium requires BLANK for the solute on both the sides of the membrane to be the same (NOT the concentrations)
Chemical potential
109
The potential from the nernst equation would be the BLANK if the membrane were permeable to a single ion species.
Resting potential.
Note: that is NOT the case, we have MULTIPLE species
110
What are the driving forces that act on the ions?
Electrophoresis and Diffusion
110
What is electrophoresis?
Force on a CHARGED particle in response to a difference in POTENTIAL across the membrane
111
What is diffusion?
Force on particles in response to a difference in CONCENTRATION across the membrane
112
What is the resting potential?
-70 mV
113
Goldman - Hodgkin - Katz (GHK eqn) uses what equation? Also what is it's key assumption?
- Uses nernst eqn
- Key assumption: E is constant through the thickness of the membrane
114
Based on the graph, which equation (GHK or nernst) is linear while the other is similar to exponential?
- GHK similar to exponential
- Nernst is linear
115
What is the mass of water in 1 E.coli?
0.7 pg or 0.7x10^-12
116
Gas constant equals
8.31 J/ K * mole
117
True or False: V = J/C
True
118
True or False: In nernst equation, concentration of ions outside/ inside
True
119
Faraday's constant equals
96,487 Coulombs/mole
