From Molecule to Mind – Summary
September – October 2025 | Master Biomedical Sciences
Table of Contents
Basics in Cell and Neurobiology .................................................................................................................................2
ECB chapter 4: Protein Structure and Function .......................................................................................................2
ECB chapter 5: DNA and Chromosomes .................................................................................................................4
ECB chapter 7: From DNA to Protein .......................................................................................................................4
ECB chapter 15: Intracellular Compartments and Transport ....................................................................................6
ECB Chapter 16 & Purves Chapter 7: Cell Communication ......................................................................................8
ECB Chapter 17: Cytoskeleton .............................................................................................................................13
Purves Chapter 5: Synapses & Synaptic transmission ...........................................................................................14
Purves Chapter 6: Neurotransmitters and their Receptors .....................................................................................17
Purves chapter 8: Molecular Memory and Synaptic Plasticity ................................................................................19
Methods and Models in Neuroscience .....................................................................................................................22
Model Organisms: Yeast .......................................................................................................................................22
Model Organisms: C. Elegans ...............................................................................................................................23
Model Organisms: Drosophila ..............................................................................................................................26
Model Organisms: Mouse .....................................................................................................................................27
Methods: Proteomics ...........................................................................................................................................28
Between proteins and DNA ...............................................................................................................................28
Protein – protein interactions ............................................................................................................................30
Synapse Biology ......................................................................................................................................................32
Synapse biology I: Synaptic Probability .................................................................................................................32
Synapse biology II: Postsynaptic Organization.......................................................................................................33
Synapse biology III: Ca2+-dependent Triggering & Modulation ................................................................................35
Neurophysiology......................................................................................................................................................38
Neurophysiology: Purves Chapter 2-4 – Action Potential .......................................................................................38
Neurophysiology: Resting Membrane Potential .....................................................................................................40
Neurophysiology: Active Properties ......................................................................................................................41
Neurophysiology: Action Potential Propagation .....................................................................................................42
Neurophysiology: Synaptic Plasticity ....................................................................................................................43
Neurophysiology: Nabavi paper ............................................................................................................................47
,Basics in Cell and Neurobiology
ECB chapter 4: Protein Structure and Function
Proteins
- Backbone: amino acids with C + N
o N-terminus: -NH3 (plus end)
o C-terminus: -COOH (minus end)
o Amino acids bound with peptide bond
- Side chains are different in every amino acid
Amino acids
- Negative
o Strongest in charge with positive
o Aspartic acid (ASP, D)
o Glutamic acid (Glu, E)
- Positive
o Strongest in charge with negative
o Arginine (Arg, R)
o Lysine (Lys, K)
o Histidine (His, H)
- Uncharged polar
o Have polar sides (-C=O, -NH2, -OH) but do not carry any net charge. They can bind to water, so are
hydrophilic
o Asparagine (Asn, N)
o Glutamine (Gln, Q)
o Serine (Ser, S)
o Threonine (Thr, T)
o Tyrosine (Tyr, Y)
- Non polar
o Do not have polar sides, have no unequal distribution of charges. Cannot bind to hydrogen
therefore, and are hydrophobic
o Alanine (Ala, A)
o Glycine (Gly, G)
o Valine (Val, V)
o Leucine (Leu, L)
o Isoleucine (Ile, I)
o Proline (Pro, P)
o Phenylalanine (Phe, F)
o Methionine (Met, M)
o Tryptophan (Trp, W)
o Cysteine (Cys, C)
Bonds between proteins
- Covalent bonds: is strongest bond (N-C) and cannot be broken by boiling it. Another protein/enzyme is
needed to break
- Electrostatic bond: second one in the line. For instance: negative O and positive N attract each other
- Hydrogen bonds: water atom that binds due to charge difference with other atoms (H-O)
- Van der Waals attractions: least strong bond
Polypeptide folds into conformation in aqueous environment:
- Hydrophilic side chains find each other
- Side chains attract to one another (protein number 3 can have interaction with number 140)
- Mutations in patients: after mutation, side chains can be different, due to different amino acid and therefore
have disrupted interactions with other amino acids
- Mutations in healthy individuals: not every amino acid has critical role/interaction in the protein. If there is a
mutation in such an amino acid, nothing really goes wrong
- Mutations in healthy + patient: healthy person can be resistant to mutation or this specific mutation is not
the main factor for disease occurring (Complex Trait Genetics), this is synthetic lethality
Interactions in a folded protein:
- Backbone + backbone
- Backbone + side chain
- Side chain + side chain
,Prion proteins (PrP)
- Adopt an abnormal, misfolded form. This usually is a rare conformational change
- Misfolded protein can induce formation of protein aggregates
o Normal + abnormal protein → heterodimer is misfolded by the abnormal protein → homodimer
o Converting more and more PrPs, aggregates can form
Protein structure
- All distributions of charges can make different 3D structures
- Alpha helix and beta sheets, both are rigid structures
- With many hydrophobic amino acid side chains: protein will be located (partially) in the lipid bilayer
o Some side chains do not fold into the inside of the protein, are on the side of the protein. They
attract/bind to other hydrophobic structures
▪ SNARE complex that pulls the vesicle to the side of the membrane
Polypeptides
- Secondary structures alpha helices and beta sheets bind: single polypeptide domain
- Polypeptide domains bind to each other: protein molecule
In muscles and other structures
- Elastic fibers are connected to each other and can stretch and relax
Disulfide bonds (SH-SH)
- Interchain disulfide bonds: between > one polypeptide
- Intrachain disulfide bonds: between the polypeptide (conformational change)
- Oxidation: makes the SH-SH bonds, reduction removes SH-SH bonds
Ligand binds a binding site of a protein to form a new complex. Usually the bonds are noncovalent.
- Specificity: the ligand must have the correct shape/side chains to bind
- Number of non-covalent bonds determine the affinity
- Antibody binding sites (Variable domain of light chain) can become binding sites for many different binding
sites, but must be folded correctly.
Enzymes can break covalent bonds
- Used to break down nutrients for instance
- S=protein to be broken down, E=enzyme: S+E → ES → EP → E+P (P is the protein that is broken down)
Negative regulation
- Enzymes can inhibit one of the upstream steps to inhibit production
- Metabolism uses negative feedback systems and humans are great at this
Modifications
- Enzymes can be inactivated by cofactors
- Cofactors are sometimes necessary to activate an enzyme
o ADP + cofactor: enzyme goes from 10% active towards 100% active
- Protein kinases: ATP→ ADP.
o ADP can be cofactors to inactivate or activate proteins
o Adds phosphor group to the protein, which has 2 negative charges. This can drastically change
conformation of the protein.
- Protein phosphatase: removes Pi group from the protein
o Protein can be activated or inactivated again
- GTP binding proteins: can also be inactivated/activated by binding GTP
o GTP bound → GTP hydrolysis: inactive
o GDP detaches from the inactive protein
o Inactive protein binds GTP again: active
, ECB chapter 5: DNA and Chromosomes
DNA
-Nucleotide: sugar-phosphate backbone + base (ACTG)
-Nucleotides in a double helix organized, strong hydrogen bonds pair bases
o Adenine + thymine: 2 hydrogen bonds
o Guanine + cytosine: 3 hydrogen bonds
Genome is organized in 22 pairs of chromosomes and 1 pair of sex chromosomes
- Karyotyping: observe chromosomes and find possible abnormalities
Yeast and human genome specifically are very different in the regulatory domains between genes.
Important phases in cell division
- Interphase: chromosomes are replicated
- M phase: during mitosis, mitotic spindles pull the two identical
chromosome strengths apart
o Replicated chromosome consists of two identical chromatids
- Interphase: during cell division, each cell has its own chromosome again
Chromosome structures
- Telomere: edges of chromosomes, probability prevent damage to encoding regions
o Shortened during life
- Replication origin: origin where transcription starts
- Centromere: cytoskeletal elements bind to pull them apart in cell division
- Chromatin: DNA + proteins (histones etc)
- Nucleolus: in the nucleus involved in production and assembly of proteins
- Heterochromatin: transcriptional inactive part of DNA
DNA is folded/organized by histones
- Beads-on-a-string:
o 4 x 2 proteins that form an octomer: proteins on surface interact with side chains of
DNA
▪ Each histone winds DNA two times
▪ Nucleosome: histone + DNA
o Linked with linker-DNA
These beads-on-a-string are densely packed with each other and eventually form condensed
section of chromosomes. DNA is folded 10 000 fold shorter than in extended length
Histones are polypeptides at which the side chains can bind to modifying amino acids
- Methylation: usually associated with silencing
- Acetylation: usually associated with gene expression
- Phosphorylation: context dependent if gene expression enhanced or silenced
ECB chapter 7: From DNA to Protein
DNA replication, repair and genetic recombination → transcription (RNA synthesis) → translation (protein synthesis)
- RNA contains ribonucleic acid, DNA contains deoxyribonucleic acid → there is one O atom more in RNA
- Uracil is building block in RNA, DNA had thymine → thymine has CH2 group
- RNA is single strand and its side chains interact with each other to make structure
Transcription
- DNA → RNA
- DNA template strand is read from 3’ → 5’, RNA is thus made from 5’ → 3’
o Both strands can code for genetranscription
September – October 2025 | Master Biomedical Sciences
Table of Contents
Basics in Cell and Neurobiology .................................................................................................................................2
ECB chapter 4: Protein Structure and Function .......................................................................................................2
ECB chapter 5: DNA and Chromosomes .................................................................................................................4
ECB chapter 7: From DNA to Protein .......................................................................................................................4
ECB chapter 15: Intracellular Compartments and Transport ....................................................................................6
ECB Chapter 16 & Purves Chapter 7: Cell Communication ......................................................................................8
ECB Chapter 17: Cytoskeleton .............................................................................................................................13
Purves Chapter 5: Synapses & Synaptic transmission ...........................................................................................14
Purves Chapter 6: Neurotransmitters and their Receptors .....................................................................................17
Purves chapter 8: Molecular Memory and Synaptic Plasticity ................................................................................19
Methods and Models in Neuroscience .....................................................................................................................22
Model Organisms: Yeast .......................................................................................................................................22
Model Organisms: C. Elegans ...............................................................................................................................23
Model Organisms: Drosophila ..............................................................................................................................26
Model Organisms: Mouse .....................................................................................................................................27
Methods: Proteomics ...........................................................................................................................................28
Between proteins and DNA ...............................................................................................................................28
Protein – protein interactions ............................................................................................................................30
Synapse Biology ......................................................................................................................................................32
Synapse biology I: Synaptic Probability .................................................................................................................32
Synapse biology II: Postsynaptic Organization.......................................................................................................33
Synapse biology III: Ca2+-dependent Triggering & Modulation ................................................................................35
Neurophysiology......................................................................................................................................................38
Neurophysiology: Purves Chapter 2-4 – Action Potential .......................................................................................38
Neurophysiology: Resting Membrane Potential .....................................................................................................40
Neurophysiology: Active Properties ......................................................................................................................41
Neurophysiology: Action Potential Propagation .....................................................................................................42
Neurophysiology: Synaptic Plasticity ....................................................................................................................43
Neurophysiology: Nabavi paper ............................................................................................................................47
,Basics in Cell and Neurobiology
ECB chapter 4: Protein Structure and Function
Proteins
- Backbone: amino acids with C + N
o N-terminus: -NH3 (plus end)
o C-terminus: -COOH (minus end)
o Amino acids bound with peptide bond
- Side chains are different in every amino acid
Amino acids
- Negative
o Strongest in charge with positive
o Aspartic acid (ASP, D)
o Glutamic acid (Glu, E)
- Positive
o Strongest in charge with negative
o Arginine (Arg, R)
o Lysine (Lys, K)
o Histidine (His, H)
- Uncharged polar
o Have polar sides (-C=O, -NH2, -OH) but do not carry any net charge. They can bind to water, so are
hydrophilic
o Asparagine (Asn, N)
o Glutamine (Gln, Q)
o Serine (Ser, S)
o Threonine (Thr, T)
o Tyrosine (Tyr, Y)
- Non polar
o Do not have polar sides, have no unequal distribution of charges. Cannot bind to hydrogen
therefore, and are hydrophobic
o Alanine (Ala, A)
o Glycine (Gly, G)
o Valine (Val, V)
o Leucine (Leu, L)
o Isoleucine (Ile, I)
o Proline (Pro, P)
o Phenylalanine (Phe, F)
o Methionine (Met, M)
o Tryptophan (Trp, W)
o Cysteine (Cys, C)
Bonds between proteins
- Covalent bonds: is strongest bond (N-C) and cannot be broken by boiling it. Another protein/enzyme is
needed to break
- Electrostatic bond: second one in the line. For instance: negative O and positive N attract each other
- Hydrogen bonds: water atom that binds due to charge difference with other atoms (H-O)
- Van der Waals attractions: least strong bond
Polypeptide folds into conformation in aqueous environment:
- Hydrophilic side chains find each other
- Side chains attract to one another (protein number 3 can have interaction with number 140)
- Mutations in patients: after mutation, side chains can be different, due to different amino acid and therefore
have disrupted interactions with other amino acids
- Mutations in healthy individuals: not every amino acid has critical role/interaction in the protein. If there is a
mutation in such an amino acid, nothing really goes wrong
- Mutations in healthy + patient: healthy person can be resistant to mutation or this specific mutation is not
the main factor for disease occurring (Complex Trait Genetics), this is synthetic lethality
Interactions in a folded protein:
- Backbone + backbone
- Backbone + side chain
- Side chain + side chain
,Prion proteins (PrP)
- Adopt an abnormal, misfolded form. This usually is a rare conformational change
- Misfolded protein can induce formation of protein aggregates
o Normal + abnormal protein → heterodimer is misfolded by the abnormal protein → homodimer
o Converting more and more PrPs, aggregates can form
Protein structure
- All distributions of charges can make different 3D structures
- Alpha helix and beta sheets, both are rigid structures
- With many hydrophobic amino acid side chains: protein will be located (partially) in the lipid bilayer
o Some side chains do not fold into the inside of the protein, are on the side of the protein. They
attract/bind to other hydrophobic structures
▪ SNARE complex that pulls the vesicle to the side of the membrane
Polypeptides
- Secondary structures alpha helices and beta sheets bind: single polypeptide domain
- Polypeptide domains bind to each other: protein molecule
In muscles and other structures
- Elastic fibers are connected to each other and can stretch and relax
Disulfide bonds (SH-SH)
- Interchain disulfide bonds: between > one polypeptide
- Intrachain disulfide bonds: between the polypeptide (conformational change)
- Oxidation: makes the SH-SH bonds, reduction removes SH-SH bonds
Ligand binds a binding site of a protein to form a new complex. Usually the bonds are noncovalent.
- Specificity: the ligand must have the correct shape/side chains to bind
- Number of non-covalent bonds determine the affinity
- Antibody binding sites (Variable domain of light chain) can become binding sites for many different binding
sites, but must be folded correctly.
Enzymes can break covalent bonds
- Used to break down nutrients for instance
- S=protein to be broken down, E=enzyme: S+E → ES → EP → E+P (P is the protein that is broken down)
Negative regulation
- Enzymes can inhibit one of the upstream steps to inhibit production
- Metabolism uses negative feedback systems and humans are great at this
Modifications
- Enzymes can be inactivated by cofactors
- Cofactors are sometimes necessary to activate an enzyme
o ADP + cofactor: enzyme goes from 10% active towards 100% active
- Protein kinases: ATP→ ADP.
o ADP can be cofactors to inactivate or activate proteins
o Adds phosphor group to the protein, which has 2 negative charges. This can drastically change
conformation of the protein.
- Protein phosphatase: removes Pi group from the protein
o Protein can be activated or inactivated again
- GTP binding proteins: can also be inactivated/activated by binding GTP
o GTP bound → GTP hydrolysis: inactive
o GDP detaches from the inactive protein
o Inactive protein binds GTP again: active
, ECB chapter 5: DNA and Chromosomes
DNA
-Nucleotide: sugar-phosphate backbone + base (ACTG)
-Nucleotides in a double helix organized, strong hydrogen bonds pair bases
o Adenine + thymine: 2 hydrogen bonds
o Guanine + cytosine: 3 hydrogen bonds
Genome is organized in 22 pairs of chromosomes and 1 pair of sex chromosomes
- Karyotyping: observe chromosomes and find possible abnormalities
Yeast and human genome specifically are very different in the regulatory domains between genes.
Important phases in cell division
- Interphase: chromosomes are replicated
- M phase: during mitosis, mitotic spindles pull the two identical
chromosome strengths apart
o Replicated chromosome consists of two identical chromatids
- Interphase: during cell division, each cell has its own chromosome again
Chromosome structures
- Telomere: edges of chromosomes, probability prevent damage to encoding regions
o Shortened during life
- Replication origin: origin where transcription starts
- Centromere: cytoskeletal elements bind to pull them apart in cell division
- Chromatin: DNA + proteins (histones etc)
- Nucleolus: in the nucleus involved in production and assembly of proteins
- Heterochromatin: transcriptional inactive part of DNA
DNA is folded/organized by histones
- Beads-on-a-string:
o 4 x 2 proteins that form an octomer: proteins on surface interact with side chains of
DNA
▪ Each histone winds DNA two times
▪ Nucleosome: histone + DNA
o Linked with linker-DNA
These beads-on-a-string are densely packed with each other and eventually form condensed
section of chromosomes. DNA is folded 10 000 fold shorter than in extended length
Histones are polypeptides at which the side chains can bind to modifying amino acids
- Methylation: usually associated with silencing
- Acetylation: usually associated with gene expression
- Phosphorylation: context dependent if gene expression enhanced or silenced
ECB chapter 7: From DNA to Protein
DNA replication, repair and genetic recombination → transcription (RNA synthesis) → translation (protein synthesis)
- RNA contains ribonucleic acid, DNA contains deoxyribonucleic acid → there is one O atom more in RNA
- Uracil is building block in RNA, DNA had thymine → thymine has CH2 group
- RNA is single strand and its side chains interact with each other to make structure
Transcription
- DNA → RNA
- DNA template strand is read from 3’ → 5’, RNA is thus made from 5’ → 3’
o Both strands can code for genetranscription
