Sunday, August 25, 2013

Anatomy and Physiology

I am doing an anatomy course with a couple of young men this year.  Here are my notes covering the first few weeks of class and I will try to post more info about reading material, worksheets, etc. later on:


Protons, Electrons, Neutrons…

…but also Gluons, Muons, Higgs-Bosons, Fermions, Quarks, Neutrinos, Bosons, Hadrons, etc.

Elementary particles are particles with no measurable internal structure; that is, they are not composed of other particles. They are the fundamental objects of quantum field theory.   Many families and sub-families of elementary particles exist. Elementary particles are classified according to their spin.

Atoms are the smallest neutral particles into which matter can be divided by chemical reactions.  Each type of atom corresponds to a specific chemical element.

Chemical element - any of the more than 100 known substances (of which 92 occur naturally) that cannot be separated into simpler substances and that singly or in combination constitute all matter.

Molecules are the smallest particles into which a non-elemental substance can be divided while maintaining the physical properties of the substance (water). Each type of molecule corresponds to a specific chemical compound. Molecules are a composite of two or more atoms.  An electrically neutral group of two or more atoms (covalent bonds).  Covalent bonding is a common type of bonding, in which the electronegativity difference between the bonded atoms is small or nonexistent (water is polar covalent, so O end has partial neg. charge and H ends have partial pos. charge).
24 Atoms to make up human body.

95% = Oxygen, Carbon, Hydrogen, Nitrogen

(Actually, if you add in calcium and phosphorus, you have 99% of the body.)

About .85% is composed of another five elements:  potassium, sulfur, sodium, chlorine, and magnesium.  The other .15%  are trace elements.

Properties of Water

Charge – results in properties of cohesion (sticks to itself) and adhesion (sticks to other things) due to hydrogen bonds (polar covalent).

Cohesion results in surface tension, and this, in turn, results in capillary action (seen in plants, for example).

How is this important in the human body? (Osmosis)

Hydrogen bonds also result in ice floating, since water forms crystalline structures at 32 degrees and this form is lighter than liquid water.  The properties of ice are still not completely understood.

High Specific Heat – Water is held together by hydrogen bonds.  Because the molecules are being held tightly in place by these bonds, the H2O molecules don't move much when heated. It takes more and more heat to move the molecules, causing water to have a high specific heat capacity.  This concept is important on a world-wide scale. The oceans and lakes help regulate the temperature ranges that billions of people experience in their towns and cities. Water surrounding or near cities take longer to heat up and longer to cool down than do land masses, so cities near the oceans will tend to have less change and less extreme temperatures than inland cities. This property of water is one reason why states on the coast and in the center of the United States can differ so much in temperature patterns.

Water's specific heat capacity is 4.184 joules per gram, meaning that it takes 4.184 joules to raise the temperature of 1 gram of water by 1 degree Celsius. If this number sounds familiar, it's because a common unit called the calorie is based on the heat capacity of water; 1 calorie is equal to 4.184 joules.

How is this important in the human body? (Helps us maintain homeostasis.)

High Heat of Vaporization - Heat of vaporization is the amount of energy needed to vaporize a given amount of mass of a substance; water's heat of vaporization is 2,257 joules per gram, or 539.4 calories.When boiling water on the stovetop, the metal pan used to boil the water can become scalding hot while the water inside remains lukewarm. This is because the pan has a much lower specific heat than water, meaning it changes temperature much more quicklyWhen boiling water on the stovetop, the metal pan used to boil the water can become scalding hot while the water inside remains lukewarm. This is because the pan has a much lower specific heat than water, meaning it changes temperature much more quicklyWhen boiling water on the stovetop, the metal pan used to boil the water can become scalding hot while the water inside remains lukewarm. This is because the pan has a much lower specific heat than water, meaning it changes temperature much more quickly.When boiling water on the stovetop, the metal pan used to boil the water can become scalding hot while the water inside remains lukewarm. This is because the pan has a much lower specific heat than water, meaning it changes temperature much more quickly.

When boiling water on the stove, the pan may be scalding hot while the water is still lukewarm.  This is because it has a lower specific heat than water, so it changes temperature more quickly.
·The high heat of vaporization of water is important for the earth's climatens can absorb a great amount of heat generated from the sun. Also, when evaporation from the tropical waters occurs, it moves to the earth's poles, and heat is released as it condenses and rain is formed.
The high heat of vaporization of water is important to the earth’s climate.  Tropical oceans can absorb a great amount of heat generated from the sun.  Evaporation from those waters moves toward the earth’s poles, where it is released as it condenses.

Evaporative cooling is important on many levels (stabilizes temps of lakes and ponds; prevents plants from becoming too hot, etc.).  How is it important to humans?

Sweat evaporation from humans helps them dissipate heat and prevent overheating (but too much of a good thing could make us unstable)….

The above two properties can vary some with temperature (but very slightly) and pressure (so altitude can cause changes)….

Solubility – dissolves ionic molecules.  Universal Solvent. (Hydrophobic substances will not dissolve in water: oils, for instance.)

Water can pretty easily dissolve ions (electrically charged atomic molecules, such as NaCl) and polar molecules (Glucose, for example, the body’s main source of energy). 

How is this important to humans?  (Most trace elements, etc. are easily absorbed into the body and transferred around the body via H20 in blood and other bodily fluids).

The ability of water to dissolve ionic molecules is vitally important to life as salts are very important in the body. For instance, Sodium helps with absorption of Glucose; it allows some molecules to pass the cell membrane that could not otherwise pass (facilitated diffusion); and it helps with transport of molecules and communication between cells because it helps establish a negative charge on the cell membrane relative to the fluid outside the cell.  It’s essential to the sending of nerve signals, muscle contractions, fluid balance in the body, etc.

Passive Transport

Diffusion - Diffusion is the tendency of molecules to spread into an available space. This tendency is a result of the intrinsic thermal energy (heat) found in all molecules at temperatures above absolute zero. Without other outside forces at work, substances will move/diffuse from a more concentrated environment to a less concentrated environment. No work is performed for this to happen, as diffusion is a spontaneous process.


Passive transport is the diffusion of substances across a membrane. This is a spontaneous process and cellular energy is not expended. Molecules will move from where the substance is more concentrated to where it is less concentrated. (The membrane must be permeable or at least semi-permeable, of course, as most are….)  Give facilitated diffusion diagram.

Osmosis is the spontaneous net movement of solvent molecules through a partially permeable membrane into a region of higher solute concentration, in the direction that tends to equalize the solute concentrations on the two sides. It may also be used to describe a physical process in which any solvent moves, without input of energy, across a semipermeable membrane (permeable to the solvent, but not the solute) separating two solutions of different concentrations.

Osmosis is essential in biological systems. In general, cell membranes are impermeable to large and polar molecules, such as ions, proteins, etc. while being permeable to non-polar and/or hydrophobic molecules like lipids, as well as to small molecules like oxygen, carbon dioxide, nitrogen, nitric oxide, etc. Permeability depends on solubility, charge, or chemistry, as well as solute size. Water molecules travel through the plasma membrane or tonoplast membrane (the membrane surrounding a vacuole) by diffusing across the phospholipid bilayer via aquaporins (small trans membrane proteins similar to those in facilitated diffusion channels). Osmosis provides the primary means by which water is transported into and out of cells.

Give diagram regarding Osmosis in hypertonic, isotonic, and hypotonic solutions.



Carbon based life forms

Living things are carbon based.  Carbon forms the key component for all known naturally occurring life on Earth. Complex molecules are made up of carbon bonded with other elements, especially oxygen, hydrogen and nitrogen, and carbon is able to bond with all of these because of its four valence electrons. Carbon is abundant on earth. It is also light weight and the atom is relatively small in size, making it easier for enzymes to manipulate carbon molecules.

Carbon based molecules in the human body:

Carbohydrates - (C, H, O); important source of food energy; starch, sugar, cellulose; monosaccharides, disaccharides, etc.

Proteins – large molecules that consist of one or more chains of amino acids (which we will discuss shortly; key elements are C, O, H, N) and serve many, many functions in the body, as we’ll be discussing all year.  

Nucleic Acids – DNA and RNA; initially named because found in nucleus, but also in prokaryotes; DNA is largest molecule; C, O, H, N.

Lipids – fats and oils (built from fatty acids – saturated or unsaturated; C and H; yield large quantities of ATP; heart and skeletal muscles prefer as energy source); don’t dissolve in H2O; no charge: non-polar.

Phospholipids – (C, O, H, P) are major players in the construction of cell membranes.  They are composed of a hydrophilic head (polar) and a hydrophobic tail (non-polar).  They thus form into a water free double layer surrounding cells and organelles.

This is where we ended after week 1....  In addition to the couple of worksheets I gave them to take home, they are going to work on a project regarding organization of systems.  Here is that assignment:
We talked today about levels of organization in the Universe: within the atomic world, within galaxies, within biomes, within our bodies.  The assignment is to draw, label and color an example of each of the following items on a single sheet of paper.  I told them that they could elect to find pictures online to create a small poster, or instead use Lego's to create examples of the different items, use clay to create examples, or pipe cleaners, etc., etc.
Subatomic particles





Subcellular organelles


Unicellular Organisms



Organ System

Multicellular Organism

(the above are the most important to what we are doing this year)

The original list also included:






(They don't have to do these, but can if they want)

Some Cell Organelles and Structures


Cytoskeleton – microtubules (tent poles) composed of actin (a type of protein) filaments and interwoven intermediate filaments (like the warp and woof of fabric) provide structure to the cell.  All are made of proteins.

Cytoplasm – comprised of the cell’s organelles and the cytosol, a jelly like substance that fills the cell.  70-90% water.  In eukaryotes, the nuclear material is separated and is called the nucleoplasm. 

Nucleus – the “brain” of the cell.  Contains most of the cell’s genetic material: DNA, which combines with proteins to form chromosomes.  Contained on each chromosome are many genes, which are molecular units of heredity. All organisms have many genes corresponding to various biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type, increased risk for specific diseases, or the thousands of basic biochemical processes that comprise life.

DNA is carried in chromosomes – 46 in humans, which carry ~ 25,000 genes, or instruction sets for different proteins.  The building blocks of DNA are nucleotides, which are composed of a nitrogenous base, and a backbone composed of a  phosphate group and a sugar. 

Nitrogenous bases:  A, G, C, T (Adenine, Guanine, Cytosine, Thymine).  The different order in which these occur creates different proteins.

DNA forms a double stranded helix (generally).  The two strands are attached by weak hydrogen bonds.  A=T; C=G; T=A; G=C

Every nucleus contains over 6 feet of DNA.


Making copies of the DNA instructions available to other parts of the cell for the purpose of creating proteins, etc. is the job of RNA.  (RNA World Theory – RNA was first lifeform and still creates mutations via free-floating fragments, etc.)

Where do free floating RNA sequences come from?  RNA can self-replicate and there is at least one theory that it may have been the first life form on earth….

DNA uncoils and unzips a section of itself, free floating RNA attaches, enzymes edit and mRNA gets translated into proteins.  First part of the process is transcription and second part is translation.

During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement.

In translation, mRNA produced by transcription is decoded by a ribosome to produce a specific amino acid chain, or polypeptide (a polymer, or chain, or amino acids), that will later fold into an active protein.  Transfer RNA delivers a matching set of bases to the mRNA while it is in the Ribosome. Translation takes place in the cytoplasm.  Three sequences of bases are read at a time.

Ribosomes – a large and very complex molecular machine found within all living cells that synthesizes (creates – translates) proteins.  (May be made of tangled RNA.)

Most proteins are assembled in ribosomes attached to the Rough Endoplasmic Reticulum.  Membrane sacs are filled with proteins, then budded off and transported to the Golgi Apparatus.  Here the proteins are trimmed, tagged, and sorted.  Some are exported through the tubes of the Cytoskeleton and expelled through the cell membrane (digestive enzymes, for instance).

Proteins – provide a huge array of services in the human body.  They provide structural support, accelerate chemical reactions (enzymes), immobilize germs (antibodies), carry messages (hormones), regulate the body’s circadian rhythms (internal clock) – they are the most versatile of molecules.  Not organelles as not confined to the cell.  Work throughout the body.  Created in the cells.  They are constructed of 20 building blocks called amino acids (which we will look more closely at later).  Each amino acid has a common core, or backbone, with a different projecting side chain of molecules. 

Two types of proteins in the cell include:  Channel Proteins and Carrier Proteins.  A channel protein forms a pore that spans the lipid bilayer of the cell membrane and allows certain solutes to traverse the membrane.  Carrier proteins, like transporins, also transfer molecules across the membrane (see diagram of facilitated diffusion).

Cells assemble proteins according to instructions carried in DNA, our own personal library and instruction guide for life. 

So, to recap:

Endoplasmic Reticulum serves as the site for modification of proteins, manufacture of macromolecules and lipids, and the transfer of substances throughout the cell. The ER is also the site of protein translation and protein folding. It is involved in other processes as well, such as the transport of those proteins that are to become part of the cell membrane (e.g., trans membrane receptors and other integral membrane proteins) and the transport of proteins that are to be secreted from the cell.

Specifically, the rough ER (RER) manufactures and transports proteins destined for membranes and/or secretion. On the ribosomes attached to the cytoplasmic surface of the RER, proteins are assembled and released into the lumen. They then undergo modifications.

In leukocytes, a type of white blood cell, RER makes antibodies while in the pancreas, RER produces insulin.

The Smooth ER (SER) has functions in several metabolic processes, including synthesis of lipids, fatty acids, and steroids, metabolism of carbohydrates, and detoxification of drugs and poisons (in the liver and kidney). In the brain, SER produces male and female hormones.

Golgi Apparatus (body, complex) – packaging and transport of proteins (particularly those that will be excreted).  While it primarily modifies proteins delivered from the RER, it is also involved in the transport of lipids around the cell, and the creation of lysosomes.   In this respect it can be thought of as a sort of “post office.”

Lysosomes – contain enzymes that break down waste material and cellular debris, releasing atoms for re-use.  Digest excess or worn out organelles and food particles; engulf viruses and bacteria.  The “stomach” of the cell.  They will even digest themselves at times (autolysis – suicide bags).

Perixisomes – begin the process of breaking down long chains of fatty acids to help the mitochondria.  A by-product of their breakdown is hydrogen peroxide.  There are lots of these in the liver, where they break down alcohol, drugs, etc. as well as food.  One of the main enzymes in the Perixisome is Catalase, which breaks down literally millions of molecules per second into hydrogen peroxide.





Millions of controlled chemical reactions are taking place in the cell every second.  This requires energy.  Favored source:  Glucose (carbohydrate).  Fatty acids are also important.

Energy dispensing molecules called ATP (adenosine triphosphate) are readily available throughout the cells.  (Plants use ADP to make ATP during photosynthesis.)

10% of the energy locked in glucose is released in the cytoplasm.  Mitochondria in the cell deal with the other 90%.
Mitochondria – produces the energy to run the cell.  They oxidize (any chemical reaction that involves the moving of electrons) glucose through a process called cellular respiration, which makes ATP to be used as a source of energy. 

Glucose + Oxygen = Carbon Dioxide + Water + Energy (ATP)

(Four stages, which we are not going to cover: glycolysis, link reaction, Krebs cycle, electron transport chain)

Endosymbiotic Theory was advanced by Lynn Margulis in about 1964.  Attempts to explain the evolution of eukaryotic cells.  According to the theory, ancient prokaryotes developed a symbiotic relationship with small prokaryotes that lived inside them.  Some of these smaller prokaryotes could use oxygen to generate ATP.  These aerobic prokaryotes evolved into mitochondria.  Others could perform photosynthesis.  These evolved into chloroplasts. 

Prokaryotes – “before kernel” – no membrane bound nucleus.

Eukaryotes – “good kernel” – have a true nucleus.

Vacuoles – an enclosed compartment of water, containing enzymes in solution.  Larger forms of membrane vesicles.  They engulf foreign materials, contain wastes, export materials, etc.  They assist in the processes of endocytosis (absorption of molecules by engulfing them) and exocytosis (throwing stuff out of the cell). 

There are other organelles in addition to these….

Cell Cycle


Interphase - new proteins are built; organelles are duplicated; DNA is replicated; ATP is stockpiled.

Mitosis – reproductive phase of the cell.


Prophase – chromosomes appear; spindles appear.

Pro/Metaphase – nuclear envelope disintegrates; poles develop; microtubules overlap.

Metaphase – chromosomes are lined up at the equator of the cell.

Anaphase – chromosomes split into chromatids; pulled to opposite poles; elongation of the cell begins.

Telophase – chromosomes detach from spindle; nuclear envelope reforms; spindle disappears; chromosomes uncoil.

Telophase and Cytokinesis overlap.

Cytokinesis – cell is pinched in half to form two daughter cells, each with the same genetic material as the parent cell.

Cell Differentiation

Different cells look and act differently because different genes are switched on and off in them.  There are about 200 different types of human body cells. (stem cells)

Some types of cells: 

Epithelial – many types; generally a membranous tissue that occurs in a single layer (but not always).  Forms the covering of most internal surfaces and organs and well as the external covering of an animal’s body. 

So what type of cells form a human’s outer covering?

Osteocytes – star shaped cell present in mature bone; can last a lifetime; do not divide. Created from osteoblasts.

Osteoclasts – resorb bone; work with osteoblasts to control amount of bone. Created by Osteogenic cells in the periosteum, which is the tissue surrounding the bone.

Osteoblasts – responsible for bone formation; do not divide.  Created by Osteogenic cells.

Macrophage – a type of white blood cell involved in primary immune response. 

What does that mean?

Pericyte - It is a type of hybrid cell, part nerve and part vascular.  It is a nerve cell that is primarily found encasing and protecting the vascular blood vessels of the brain. One of its most important functions is as an agent of the so-called “blood-brain barrier.”

Lymphocyte – a type of white blood cell.  Three main types: T-cells, B-cells and natural killer cells (think Navy SEALS).

Neutrophil – the most abundant type of white blood cells  in mammals.

Rod – photoreceptor cells in the retina that allow us to see in low light environments (black and white vision).

Cone – photoreceptor cells in the retina that allow us to see color.

Tissues – 4 main types in the body

Epithelial – line cavities and form exterior surfaces.  (Adhesions)

Muscle – striated (skeletal or cardiac) or smooth (organs).

Nervous – found in the brain, spinal cord, and peripheral nerves.  Composed of neurons and glia.

Connective – most widespread type of tissue in the body and includes bone, cartilage, and fat.

Tissues are joined together by material they secrete and also rely on special junctions to hold them together.  Anchor proteins are locked together by linking proteins.  Tissues have an underpinning membrane of interwoven fibers (warp and woof again).  Proteins may form a quilt like pattern that binds individual cells together.

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