Summary Foundational Concepts In Neuroscience - chapter 1-22 PDF

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Chapter 1: Origins ● 1994 - Speleologists found limestone cavern in southern France containing prehistoric art ○ Dated 30,000 years ago ● Paintings far removed from the entrances in deep darkness → Paleolithic humans carried torches & stone lamps, used small fires to illuminate cave ● Darkness → absence of compelling visual stimuli ○ Catalyst to enter inner recesses of the mind w/out distraction ● Shamans = healers of communities, access states of mind that are sources of knowledge & power → modern society considers this

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ill-informed and primitive due to modern science ○ Ancient cave paintings (prominently animals) suggest shamanic connections between ancient humans & local animals Oldest fossils of human ancestors found in eastern Africa between five and six million years old Hominins: the group of primates that includes modern humans and the ancestors of modern humans going back perhaps five million years ○ Three primary groups: ■ Ardipithecus ■ Australopithecus ■ Homo Field of hominin paleontology is dynamic and only partially discovered Substantial increase in brain size over years of hominin evolution ○ Size of brain increases w/overall size, but last two million years of evolution have brought disproportionate development: ■ Tool use, nuanced social interaction, language, mathematical skill, a capacity to construct explanatory frameworks for our world, etc. Ability to create and deploy powerful weapons → primal capacity for fear & violence → capacity to kill our fellow humans Human capacity for compassion/kindness possibly strongest and most natural tendency Mind: the collection of our subjective mental experiences, including thoughts, feelings, perceptions, mental images, and a sense of self Consciousness: the awareness of such mental experiences Potential mental experience w/out consciousness → dreaming

● Additional example: Freudian unconscious → cognitive content out of our awareness may nonetheless have substantial impact on our behavior ● From 2001: A Space Odyssey → does HAL have a mind?

○ Key feature: consciousness and mental experience are irreducibly subjective phenomena ● The fact that brain & mind are related does not mean that the mind is solely a product of the brain and nervous system physiology

Chapter 2: Nervous Systems and Brains ● William James (1842-1910) wrote in The Principles of Psychology of the nervous system’s relation to mental experiences ● Brain = central control of the nervous system, which consists of rapid communication signals throughout the body ● Complex makeup of human brain → several hundreds of billions of cells interconnected by trillions of connections ○ Neurons (cellular units of signal transmission) & glia (also involved in signaling) ● Shared basic structure of vertebrate animal brains ○ Develops in embryo when the neural tube folds in and then closes off and expands at one end → interior spaces of the tube will become ventricles: fluid-filled internal spaces ○ General similarities: embryonic forebrain, midbrain, and hindbrain regions expand in mature brain to distinct anatomical structures ■ Forebrain → cerebrum ■ Midbrain → optic tectum

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■ Hindbrain → medulla & cerebellum ○ Movement from evolutionarily older fish, amphibians and reptiles to birds and mammals shows an increase in the size of the cerebrum Specific to mammalian brains - cerebrum consists of bumps and grooves called gyri and sulci (singular: gyrus and sulcus) ○ Cerebrum = folded structure ○ Outer layer of cerebrum that is folded = cerebral cortex ■ Neural tissue around 3 mm thick ■ Four lobes of cerebral cortex: frontal, parietal, occipital, temporal ○ Central sulcus separates separates frontal and parietal lobe, while the lateral fissure separates the temporal lobe from the frontal and parietal lobes Corpus callosum: bundle of 200 million nerve fibers connecting right and left hemispheres Diencephalon: structure between base of cerebral cortex and midbrain consisting of hypothalamus and thalamus Brainstem consists of medulla, pons, and midbrain Meninges = layers of tissue that protect the brain ○ Inflammation → meningitis ○ Skin-like sheet of tissue called dura mater covers the brain below the skull ○ Below dura mater → delicate layer called arachnoid ○ Below arachnoid → third layer called pia mater

○ Cerebrospinal fluid cushions brain inside the skull between the arachnoid and pia mater layers ● Early anatomists such as Vesalius noted the brain’s fiber pathways to the entire body ● Rene Descartes (1696-1650) → pondered the human body, perception, and their relation to one another ○ Speculated connection between eye & brain ○ Eye captured light → signals transmitted to brain ● Signaling in nervous system fundamentally electrical - involving the movement of charged particles ● Italian physician Luigi Galvani (1737-1798) → electrical stimulation & animal muscles ○ Conclusion: muscles move as a result of internal electrical forces that can be triggered by external electrical stimulation ● Hermann von Helmholtz (1821-1894) measured the speed of an electrical signal moving along a nerve fiber → about 100 km per hour in frog muscle ● Nerve cells consist of basic construction: chromosomes containing genetic info, structures that synthesize and transport protein, structures that generate cellular energy. ○ Additional structures: dendrites and axons → specialized for communication of signals from one cell to another ● Nerve fibers - the threadlike structures connecting the brain to various parts of the body = bundles of axons ● Camillo Golgi (1843-1926) and Santiago Ramon y Cajal (1852-1934) illustrated the elaborate interconnectivity of nerve cells in the brain by looking at slices of brain tissue ● Golgi → the black reaction: potassium dichromate + silver nitrate + silver chromate → made neurons visible under the microscope ○ Only about 1% of neurons are stained → we think this has to do with the cell’s recent state of physiology

Chapter 3: Chemistry and Life ● Chemistry: study of the nature of matter and its transformations ○ Matter → fundamental constituents: molecules → formation of chemical elements or atoms → composed of protons, neutrons, and electrons ● Alchemists - known for “magical” essence of extracting metals from rock, preparing extracts from plants for healing, etc. ○ Also an aspect that dealt with the investigation of the psyche → psychotherapy and/or vision quest ○ Philosopher’s Stone = legendary substance to turn common metals into precious metals, in terms of the human psyche → understood as a self-transformation ■ The achievement of integrated wholeness ● Robert Boyle (1627-1691) and Isaac Newton (1642-1727) considered themselves alchemists, but made contributions to chemistry w/out references to mind or magic ● Antoine Lavoisier (1743-1794) and Joseph Priestley (1733-1804) focused on the discovery of oxygen and its roles in combustion and respiration ○ Priestley → published works on electricity, carbonated water, gases ○ Lavoisier → comprehensive list of all chemical elements he was aware of ● Dmitri Mendeleev (1834-1907) → periodic table ○ Large amount of info compacted, even predicted not-yet-discovered elements ○ Identity of element determined by # of protons (positively charged subatomic particle) in nucleus ● Carbon = primary structural atom for large molecules that make up living organisms ● Humans made primarily of water, thus elemental abundances of human body are: ○ Oxygen - 65% ○ Carbon - 18.5% ○ Hydrogen - 9.5% ○ Nitrogen - 3.2% ○ Calcium - 1.5% ● Following five elements include: phosphorus, potassium, sulfur, sodium, & chlorine ● If represented by # of atoms, hydrogen would be first ● Ions: charged atoms, formed when atoms either gain or lose electron(s) ● Element’s position on the table exposes its likelihood to ○ Give up electrons and become a positively charged ion: cation ■ Far left column → ex: sodium, potassium, calcium ○ Take on electrons and become a negatively charged ion: anion

■ Far right side (except for last column) → ex: chlorine ● Noble or inert gases: unreactive gaseous elements in rightmost column → tend to neither gain nor lose electrons → not known to be a part of life process ● Water = essential for life = H-O-H ● Covalent chemical bond: the sharing of electrons between atoms ○ In water - each hydrogen atom contributes one electron and the oxygen atom contributes two electrons for mutual sharing → a sort of glue holds them together ● Molecules usually more complex than water ○ Fluoxetine ● Molecules produced by life → organic molecules → composed largely of carbon and hydrogen & may contain dozens, or thousands of atoms ○ Hydrogen has only one electron to share, and thus can only form one bond at a time ○ Carbon has four electrons to share → thus each atom can form four bonds and be covalently joined w/up to four other atoms ○ Oxygen → two electrons to share/two bonds ○ Nitrogen → three electrons to share/three bonds ● Example: Ethyl alcohol = primary psychoactive component of alcoholic beverages ○ C - 4 bonds, H - 1 bond, O - 2 bonds ● Hydrocarbons: organic molecules built from exclusively carbon and hydrogen ○ Simplest combination = single C atom bonded to four H atoms ○ With increasing number of carbons, liquids develop oily consistency & get progressively thicker → 20+ carbons = waxy solid ○ Geologically transformed living material remnants (fossils) ○ Combustible → combination w/oxygen results in burning and releasing of energy = fossil fuels

■ Complete combustion will break all C-C and C-H bonds & convert them to a mix of carbon dioxide and water ○ Carbon (and some other atoms) can participate in bonds with atoms w/more than one electron → double bond ○ In all cases of the arrangement of carbon, it will form four covalent bonds ● Benzene molecule → six carbons in a ring structure w/six hydrogens ○ Friedrich Kekule (1829-1896) suggested that the C-C bonds are equivalent & intermediate between single and double bonds in strength ○ This structure exists for many biological molecules, such as dopamine and serotonin (two neurotransmitters) ● Shorthand language for depicting organic molecule structures ○ Dopamine ○ Serotonin ○ Covalent bonds drawn as lines - no letter → carbon atom, other letters shown ○ Hydrogen → any non-explicitly expressed bonds are assumed to be hydrogen ● Shorthand structure allows us to compare similarities in shape between molecules ○ Neurotransmitters - dopamine, norepinephrine ○ Psychoactive drugs - amphetamine, methamphetamine, ephedrine ○ All share basic similarity of shape ● Difference in shape determines different functions of molecules in living organisms ● Water effectively dissolves things due to its polarity → hydrogen atoms prone to being positively charged, oxygen prone to being negatively charged, thus electrons spend more time in the oxygen vicinity → hydrogen become slightly positive, oxygen slightly negative ○ Polar = separation, polarity → separation of charge between diff. parts of water molecule ○ Water’s polarity causes molecules to loosely stick together = hydrogen bonding ○ Hydrogen bonding is noncovalent (does not involve sharing of electrons)

■ Heated - molecules jitter and shake ■ Boiling point - jittering becomes vigorous enough to overcome hydrogen bonding and H20 molecules escape as steam ■ Cooled water - molecular vibration lessens ■ Freezing point - molecules lock into a rigid matrix interconnected by hydrogen bonds (ice) ● Polarity of water allows it to dissolve ions ○ Example: table salt (NaCl) → Na gives up electron to form Na+, Cl takes electron to form Cl-, will fall apart when exposed to even a small amount of water ○ Can dissolve any atoms w/a net electrical charge or other polar molecules ● Hydrophilic substances → like to be around water ● Hydrophobic substances → do not dissolve in water ● Cells = fundamental organizational units for all known living organisms ○ Shared features of all cells: ■ Boundary membrane, genetic material, ribosomal structures, protein receptors, pumps, and channels within the cell membrane ● Four fundamental types of biological membranes: lipids, proteins, carbohydrates, nucleic acids ○ Fats/lipids: medium-sized molecules comprised primarily of carbon and hydrogen atoms in long chains → often few oxygen atoms at one end of chain of carbons ■ Roles: energy storage, signaling within/between cells, making certain neurotransmitters and hormones, formation of membranes ■ Fatty acid: lipid molecule consisting of hydrogen carbon chain w/carboxylic acid group at one end ■ Examples of lipid molecules: palmitic acid, oleic acid ● Saturated fatty acid: carbons fully bonded with hydrogen atoms (no double bonds) → palmitic acid ● Unsaturated fatty acid: contains one or more double bonds → oleic acid ■ Fats/lipids largely hydrophobic in nature/lipophilic ■ Phospholipids: composed of two carbon-hydrogen chains joined together at one end by group of atoms containing oxygen, phosphorus, perhaps nitrogen → have highly hydrophilic portion & highly hydrophobic portion

■ Phospholipid bilayers form three-dimensional sheets that fold to form enclosed surfaces separating two aqueous environments → cell membranes for all of life on Earth ○ Proteins: large molecules built by amino acids linked into long chains by covalent chemical bonds (called peptide bonds) ■ Amino acid: molecule that contains an amine group (NH2) and a carboxylic acid group (-COOH) linked to the same carbon atom → specifically called alpha-amino acids ■ Twenty different amino acids form molecular building blocks of proteins ■ Chain of amino acids possible in an appropriate environment in living cells → polypeptide ■ Ribosomes = cell structure serves as site for protein synthesis ■ Polypeptide - any chain of amino acids, protein - more than 40 amino acids long ■ Describing proteins: ● Primary structure = linear sequence of amino acids forming the protein ● Secondary structure = interactions of nearby amino acids to produce patterns of local folding within the protein ● Tertiary structure = overall shape of the entire protein molecule, created by electrical and geometric properties of the constituent amino acids ● Quaternary structure = some proteins composed of complex of more than one polypeptide subunit, consisting of hundreds of amino acids ○ Carbohydrates: built from carbon, hydrogen, and oxygen, covalently joined to form molecules ○ Nucleic acids: DNA and RNA containing genetic or hereditary information ■ DNA double helix → composed of two very long chains of four component nucleotides = adenine, cytosine, guanine, and thymine

Chapter 4: Genes and the History of Molecular Biology ● Molecular building materials for life: lipids, carbohydrates, proteins, nucleic acids ○ Genetic information stored in nucleic acid molecules (DNA and RNA) ● Known for thousands of years that characteristics of organisms are carried from one generation to the next systematically ○ Selective breeding of animals and plants ○ Charles Darwin proposed that all life is deeply related, and diversity of living organisms can be explained by variation and selection ■ Must be an underlying source of variation ● Gregor Mendel (1822-1884) investigated inheritance in pea plants ● Connection between genes and physical properties of cells unknown at the time ● Inheritance involved fundamental units of information = gene ● Albert Einstein (1879-1955) → theories of relativity (changed physical description of space and time and notions of mass and energy) ● Quantum mechanics = new physics created by physicists in the 1920s after groundwork of Max Planck (1858-1947) and Einstein ○ New physics - human interaction/observation played critical role in defining properties of systems being measured ● Niels Bohr (1885-1962) → act of observation places limits on what we know about the universe ○ When studying living organisms at the subcellular level, probing a cell would disrupt the molecular component and kill the living aspect that scientists want to study ● Max Delbruck (1906-1981) → published biological work “On the Nature of Gene Mutation and Gene Structure” ○ Genes likely to be large molecules, atomic configurations ○ Went to U.S. to study genetics using viruses (small, simple particles that contain genes) ● Erwin Schrodinger (1887-1961) → What is life? ● People believed genetic material was composed of proteins, & not nucleic acid ● Oswald Avery (1877-1955) demonstrated that DNA carries genetic info from one cell to another, his publication was almost entirely ignored by scientific community

● Alfred Hershey (1908-1997) and Martha Chase (1927-2003) conducted experiment that convinced scientific community that DNA was carrier of genetic information ○ Bacterial virus called phage T2 grown on two diff. media: ■ Radioactive sulfur atoms → result in radioactive protein ■ Radioactive phosphorus atoms → result in radioactive DNA ○ Using centrifuge, could be seen that radioactive phosphorus transferred to bacteria during infection → ●

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thus, DNA contains genetic info Francis Crick (1916-2004) and James Watson (born 1928) proposed double helical structure of DNA molecule ○ Each strand of DNA consists of a sequence of nucleotide bases joined by covalent bonds to a large backbone of sugar molecules & phosphates ○ Strands wrap around each other, form a double helix, and are held together by hydrogen bonds between nucleotides (A-T, C-G) Each of the 20 diff. amino acids used to build proteins is represented by a triplet of nucleotides in DNA (called codons) Relationship between codons and corresponding amino acids is called genetic code Gene transcription ○ DNA double helix unwinds ○ One side of unwound strands used as a template for creating RNA molecule w/nucleotides complementary to the DNA’s sequence ○ This RNA molecule = copy of DNA molecule Gene translation ○ RNA molecule carries genetic message from DNA to the site of protein synthesis → called messenger RNA (mRNA) ○ Ribosomes: structures in which synthesis of proteins takes place ○ In ribosomes, the molecules of transfer RNA match nucleotide triplets in mRNA with their corresponding amino acids ○ Amino acids then enzymatically joined into linear chain by way of peptide bonds

Chapter 5: How Neurons Generate Signals ● Electricity = the movement of charge ○ Ions = charged particles ○ Calcium, chlorine, potassium, and sodium are among top ten abundant elements in human body, they occur as ions dissolved in fluids of the body: Ca++, Cl-. K+, and Na+ ● Diffusion: particles in a solution randomly move, tending to cause particles to distribute uniformly over whatever volume of fluid is available ● Neuronal boundary made of phospholipid bilayer membrane which are impermeable to ions ○ Highly hydrophobic environment ● Nerve cell’s membrane consist of various protein molecules, some of which contain channels that open/close to certain ions ○ Chlorine will tend to move to where it is less concentrated (“down the gradient of concentration”) ■ As long as channels are open, chlorine will move until the tendency to equalize concentration is offset by the tendency of positive charge in upper compartment to pull chlorine back to its side ● Sodium-potassium pump moves sodium ions out of neuron and potassium ions into the neuron ○ Energy to pump the Na/K pump comes from adenosine triphosphate ○ ATP consists of adenine portion, ribose sugar potion, and three phosphate groups linked by covalent phosphorus-oxygen bonds ■ Phosphate bonds primary currency for moving energy around inside cells and powering cellular processes ● Net electric charge on inside of cell differs from that on outside of cell → voltage across cell membrane ○ Voltage = measure of stored energy that can be used to do work ● Hyperpolarization → occurs when Cl- or K+ channels open, allowing the ions to cross the cell membrane, making the membrane potential more negative ○ Larger magnitude of membrane voltage ○ Inside of the cell more negative than the outside ● Depolarization → Na+ or Ca++ channel opens, making the inside of the cell more positive than the outside ○ Decrease in magnitude of charge difference