Introduction to neurobiology

Teacher: Neta Zach(netazach@pob.huji.ac.il, 03-5610921,052-2574626)

Course site (my alice account)- alice.nc.huji.ac.il/~netazach(includes tutorials, assignments and the articles mentioned in class/tutorial)

Course requirements and grade:• 8 exercises, which should be submitted on the following week

either via e-mail (deadline Monday 23:59) or printed. 5% of final grade

• 3 assignments (reading an article and answering questions about it). 15% each

• Final (home test) assignment –reading of a second article. 50%

Introduction to cellular function I- Genetics

Why study physiology?

All are capable of:•Metabolism•Reproduction•Growth•Respiration

Animal’s specialty- being able: •To Move•To respond to stimuli

Meaning:

Functionally, Central nervous system = animal

Mechanically, however, animal is a group of cells

1. Like unicellular organisms, animal cells can look after themselves.

2. The shift from eukaryota to animalia is in union and specialization- they also care for one another.

• Before we ignore statement #1 completely, two lessons need to pass…

What a cell needs for us to ignore it

• Osmotic balance• Electrical balance• Ionic concentration balance

This is how we will usually treat a cell- a black box with input and output

What a cell actually needs

• Maintenance• Reproduction• Metabolism• Growth• Garbage disposal

And the functions that would make a body (the black box from the outside)

Cell- a general scheme

Mitochondria(respiration,nutrition)

Nucleulos (in nucleus) (maintenance, reproduction)Lysosome (disposal)

Memebrane,cytosol

Endoplasmatic reticulum (transport),Dotted by ribosome(maintenance)

Cellular information's elementary unit is DNA

Griffith 1922• S stain is lethal

• R stain isn’t

• Dead S stain isn’t lethal

• Dead S stain+R stain is

=> Lethality trait is in the DNA

Cellular information's elementary unit is DNA

All the information necessary to replicate all cells of a particular organism is coded in its genes (meaning- later).

Genes are chains of nucleic acids(DNA), which include phosphate + sugar (pentose, 5 carbon structure) + base.

bases can be one of 4: adenine (A)

guanine (G)

cytosine (C)

thymine (T)

Hydrogen bond

The double helix model (watson & crick)

• a sugar+phosphate+sugar+ phosphate chain holds bases (attached to sugar) together

• Bases face each other to form hydrogen bonds A=T, G=C to create a coil made of intervening helixes .

Gene packaging

DNA is wrapped around regulatory proteins called histones to form nucleosome

Nucleosomes are arranged in a sphere- coiled coil. A group of nucleosomes is called a Chromatin.The entire length of the chromatin = chromosomes

chromatin

nucleosome

Coiled coil

helix

histones

nucleosome

Chromatin I

Chromatin II

chromosome

Why do we call it genetic information

The genius of Watson and Crick: the double helix structure allows replication, i.e

heredity. But it will be proven informative only if can direct protein synthesis:

Unlike glucose or fatty acids,the variety of amino acids types(20 n combinations of different side chains) allows… well, every known bodily function

unique side chain

amine group

- Carbon

proton

Protein synthesis-transcription

• RNA polymerase I/II/III attaches to DNA=>double helix opens• RNA bases (AUGC) match the helix, forming a complementary

RNA helix.• RNA helix’s unnecessary parts

(introns) are removed by splicing out,

leaving only exons

=> messenger RNA(mRNA)

Protein synthesis-translation

mRNA leaves the nucleus through pores to:

1. Endoplasmatic reticulum (ER) or 2. cytosol

Either way to ribosome:• 3 RNA molecule form a codon. • Starting codon- AUG • tRNA attaches specifically to codon,

carring an amino acid.• Peptidyl transferase

connects amino acids• Ribosome jumps a codon • Termination-stop codon

Structure of proteins

From ribosome- primary structure

Naturally fold to secondary structure.

a-helix and b-sheets are common motifs.

• Tertiary structure is full 3D folding, sometime

requires assistive proteins- chaperons, occurs at Golgy apparatus or cytosol

• Quaternary structure is formed by several polypeptide subunits

quaternary structuretertiary structure

Structure of proteins II

Protein structure summary

From ribosome,(ER/cytosol), natural folding

Advanced folding and modification,(Golgy apparatus)

Golgy

ER

Protein synthesis - summary

Splicing out

folding

Functions of proteins- enzymes chemical reactions (intro)

Laws of thermodynamics:

1. The total energy of a system and its surroundings is constant

2. The total entropy of a system and its surroundings always increases in a spontaneous process

=>If a reaction seems to reduce entropy, then energy is released as heat (increasing surrounding disorder).

Measurement: Gibbs free energy: spontaneous reaction

equilibrium state

requires energy input

0G0G0G

Functions of proteins- enzymes (how)

E + S ES EP E + P

Binds specific substrates and accelerates specific reactions through conformational change, (Sometimes using coenzymes)

Lock-and-key Induced fit

Specificity is due to enzyme’s elaborated 3D structure

Functions of proteins- enzymes (what)

Reaction types:

1. Isomerization, A->B - structural rearrangement without any change in its net atomic composition

2. Synthesis, A+B->C - combination of two or more elements (RNA polymerase, for example)

3. Analysis( Decomposition), A->B+C – decomposition to smaller compounds

4. Substitution (single displacement), A+BC->AC+B –shifting of one element between compounds.

5. Substitution (double displacement), AC+BD-> AB+CD exchange of single elements between compounds.

Functions of proteins- beyond enzymes

• The one gene one enzyme idea (Beadle & Tatum) :

Advantages: Solved a lot of diseases (genetic therapy).

Disadvantages: unrealistic.

• Two mistakes:

1. Not one gene-polygenetic trait (from personality to cancer … all that is not clearly hereditary)

2. Not an enzyme- most of what the body needs is not reactions, it’s regulation-signaling, markering, protein networks…

Rhys evans was a bobble boy (had

SIDS). Now he’s not

Reproduction (cellular)- Mitosis

Stage I- replication:•Helicase breaks helix, •Primase transcribes matching RNA•DNA Polimerase transcribes back to DNA- Okazaki fragments.

•Occurs simultaneously at multiple sites, unidirectional

At the end:• DNA ligase attaches fragments• Holoanzyme attaches the identical (not complementary!) helixes- sister chromatids

Stage II-Mitosis

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

Nuclear envelope breaks, chromosomes align in cytosol

Microtubules (cytoskeleton), attach to centromer, align at two poles and start shortening, thereby pulling chromosomes until rapture.

Cell pinches inward to create two cells

Reproduction (cellular) –when

Formally, mitosis is part of the cell cycle, thus the tissue lives forever. However, animal cells acquire their very specific functions through differentiation and cell cycle ceases (why?). (exceptions- the liver)

Solution- a stock of undifferentiated stem cells. Requires:

• control of the fate of a tissue• ability to guide differentiation by external signals

alone. Green

marks neuronal stem cells

Neuro-genesis in the human brain

• Erikson 1998- new cells in the Hippocampus. 2000-also olfactory bulb. Cortex-unclear.

• What does it mean?

arrows mark new neurons

Green marks new cells

Brain transplant? (someone else's stem cells)

Sexual reproduction- meiosis

One diploid cell divides to 4 haploid cells(gametas):• Replication-like mitosis(46 pairs of sister cromatids)• Division I - 23 pairs on each daughter cell.• Division II-pair separation (like mitosis)

=> 4 cells, half the information

Where genetic variability kicks in-Mutations

Source: Structural change in the replicated DNA strand (radiation, oxidative damage...mutagen) or replication error.

Types: 1)Attaching the wrong base or deletion/insertion of one base- point mutation. Can be neutral, silent, missense or nonsense.

2)Changes of many bases: deletion/insertion or Defects in Okazaki fragment attachment- translocation, deletion, inversion (fragile X, Down syndrome…)

Where genetic variability kicks in-effects of mutations

Point mutation can eliminate /create /increase /decrease /reverse a certain function.

Occurs in transcription>mitosis>meiosis (better control)

Importance: Recombination, chromosomal translocation occurring in meiosis between mother’s chromatid and father’s cromatid (“crossing over”)- breaking the linkage between genes to create new combinations of traits.

•From recombination frequency, distance between genes can be calculated•Poorly understood- unity of traits, silent X…

Examples of induced “natural” selection

20 generations

Agent orange, atomic bomb…

Expression

For all but X and Y we have 2 homologies chromosomes=>two alleles. Same is called Homozygote, different-Heterozygote.

Heterozygote-We are interested in what will the trait be Phenotype vs. Genotype) :

One gene is dominant over the other- Dominant expresses-examples-normal enzyme vs defected, pigment vs. albino.

(mechanism- one gene is quite enough or stronger (pigment) or mechanically favorable

Both are evidenced in phenotype-”blend”/mixed (Incomplete dominance)-

Mechanisms-1.both expressed (examples-carnation, snapdragon and roses, when pink, are “daughters” of red and white parents.

2. Only one expressed in each cell completely randomly (examples-grey pets have black and white hair cells). Mechanism-mechanically favoring one allele.

3. If expression is in patches- selection of one allele but done early in development.

Note: not always one allele is favorable!

Genetic expression

dominant- always expressed in trait

mixed patches

mixed-dots

recessive-expressed if second copy is same

Introduction to cellular function II-

cellular processes

What a cell actually needs

• Maintenance• Reproduction• Metabolism• Growth• Garbage disposal

And the functions that would make a body (the black box from the outside)

Cell- a general scheme

Mitochondria(respiration,nutrition)

Nucleulos (in nucleus) (maintenance, reproduction)Lysosome (disposal)

Memebrane,cytosol

Endoplasmatic reticulum (transport),Dotted by ribosome(maintenance)

Nutrition-general

Requirements: substrates, energy.

Substrate, how: polymers (food) ->monomer->polymer

Catabolism- break down, energy released.

Anabolism-building up, energy required,

• Substrate, what: Protein (amino acids)-mostly muscles, energy

Fat (fatty acids)-membranes, energy

Carbohydrate (glucose)-energy only.

Few-minerals and vitamins for co-enzymes

Nutrition-energy

• Cell receives glucose and through glycolysis (in cytosol) produces pyrovate + ATP

ATP

Glycolysis

If oxygen isn’t present- free protons are moved to lactate and out as disposal (fermentation) -anaerobic respiration

The tie between nutrition and respiration- mitochondria

Organelle of endosomic origin and maternal heredity, double membrane with invaginations that form a membranal matrix.

If oxygen is available, Pyrovate is transferred to (using Porins(co-anzyme A =>Krebs cycleProducts 3 NADH+, FADH+

2.

Electron transfer chain:Passes proton(+) and usesEnergy for ADP+P=ATP(4 times)

Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O →

CoA-SH + 3 NADH + H+ + FADH2 + GTP + 2 CO + 2 3H+

FADH and NADH are electron carriers

Respiration is good for you

• Improvement from(2 ATP):

Glucose 2 ATP, 2 lactate (useless)

To(30 ATP)

Glucose +6O2 6CO2+6H2O+~30ATP

ATP production and breakdown is the common currency of cellular energy

Cleaning up after the meal-lysosomes

Organelles containing enzymes to digest macromolecules (lipase, Carbohydrase, protease, nuclease… ).

Purpose: Garbage, bacteria, necrosis

Mechanism-hydrolysis. PH 4.8 (cytosol 7)- Leakage less harmful (proton pump in (single) membrane)

Importance: Tay-Sachs causes blindness,

deafness, paralysis and death (due to ganglioside GMS accumulation)

Cleaning up after the meal-peroxisomes

Oxidative stress (free radicals) is the main cause of

mutation and cell death (in apoptosis):

To eliminate oxidative stress-(single-membrane) organelles:

2H2O2 (catalase)→ 2H2O + O2. • No peroxisomes- Zellweger syndrome (mental retardation and

death). But also in cytosol-no superoxide mismutase-ALS

Anyway, oxidative stress still accumulates:” Apples brown. Butter turns rancid. Iron rusts. brain degenerates.”

• Solutions?

Transport-protein transport

The way of the protein: Nucleus-rER-(golgi), transport from rER to golgi- vesicles (created-with other lipids- in sER).

In golgi(cis-> lumen-> trans ): protein modification- folding, attaching glucose, phosphate…and out in new vesicles

Secretion in vesicles:

ER

Golgi

ER

Golgi

trans

cis

folds=cisternea

Golgi

vesiculeout

Transport-cellular transport-cytoskeleton

3 types:

1.Microtubuli 23-25nm across neuron structure. Circle of 13 subunits (unequal length), each made of a pair of a+b tubulin. binds GTP->GDP->instability, breakdown-a cycle ->microtubuli constantly changes length

+

-

Transport-cellular transport-cytoskeleton II

2.neurofilaments-10nm most common. cytokratins

alzhaimer-neurofilmentary tangles

(senile plaques). stable

3.Microfilaments- 3-5 nm made of actin. Cell periphery/membrane, for secretion (and muscle contraction). Changes dynamically.

Looks like a neuron but in fact it’s neuro-filaments

Cell boundaries- membranes (briefly)

Membranes are lipid bilayers(phospholipids form close shapes naturally in aqueous solutions), hydrophobic and therefore impermeable to all polar substances.

Membranes are crossed by proteins, some act as transporters of polar or large substances: channels (open/close), pores (“holes”), active pumps (ATP), transporters (gradient dependent).

Other proteins do not transport materials but transmit their presence-receptors To be continued…

Cell boundaries-neuron shape

• Cell body-soma• Dendrite (generally many)• Axon

Cell boundaries- shape divergences

• The most diverse human tissue

Cell boundaries - Glia

• Non - neuronal cells, 50:1 more prevalent in the

brain than neurons. Do not possess neurons’ electrical signaling ability but do respond to/secrete neurotransmitters.

• Believed to provide: structural support, nutrition but mostly electrical isolation by wrapping neurons with myelin.

• Myelin-fatty acid coating that improves electrical conductance

Glia in CNS- oligodendrocytes

• Myelin coating, only in higher vertebrates each “Arm” wraps about 1mm of axons

Glia in CNS-astrocytes

• The most common glial cell, surround neurons and blood vessels and form scar tissue

• Can control neurotransmitter levels• ”a second neural network" -slower, electrically

coupled and communicates through calcium waves.

Microglia-similar to macrophagues, for immunity in the CNS, and mostly clearing dying cells from a site of injury

Glia in PNS-schwann cells

• Wrap myelin by spiraling around the axon, sometimes with as many as 100 revolutions. A well-developed Schwann cell is shaped like a rolled-up sheet of paper of 1mm diameter.

Quantum theory of mind

First assumption- the mind is a quantum object. Therefore, it should be comprised of quantal mechanisms

Rational: In Quantum Mechanics a particle can take up several states at once and then “collapse“ to one state.

The mind has normally several states at once (subconsciously) and collapses to one-This is the threshold of consciousness.

Evidence : none. Not for the mind description, nor for the mechanisms.

Problems: numerous. One of them: If metaphors were always to be followed, we wouldn’t need the word “like” in our dictionaries.

(”minimization of mystery-both are mystery, therefore related”-David Chalmers)

Second assumption: microtubuli are a good candidate to be the quantal elements

Rational- 1.unlike neurons, they are small enough.

2. They are constantly being constructed and deconstructed (the stability point is the consciousness)

3. They, like consciousness, are effected by anesthetics.

Evidence: the above is all correct. The rest is un-researchable.

Problems: 1.in 37 degrees, quantal process should take 10-20

sec. Neuron changes in milliseconds.

2. microtubulis of different cells aren’t connected.

3. Many microtubuli problems are known, none are related to consciousness.

4. All microtubule effects are well described by regular mechanics,.

5. Many other things are related to anesthetics.

6. If they had any evidence, maybe we could argue about it, but they have NONE.