Atoms
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 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 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.
DO DIFFUSION EXPERIMENTS USING BALLOONS WITH FLAVORING INSIDE AND HOT/COLD WATER WITH FOOD COLORING.
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.
DO OSMOSIS EXPERIMENT WITH POTATO PIECES.
GIVE OSMOSIS WORKSHEET and CELLULAR TRANSPORT AND THE CELL CYCLE.
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.
GIVE DIAGRAM OF CELL MEMBRANE
DO PHOSPHOLIPID EXPERIMENT USING EGG YOLK
Atom
Molecule
Compound
Macromolecule
Subcellular organelles
Cell
Unicellular Organisms
Tissues
Organs
Organ System
Multicellular Organism
(the above are the most important to what we are doing this year)
The original list also included:
Population
Community
Ecosystem
Biome
Biosphere
(They don't have to do these, but can if they want)
Some Cell Organelles and Structures
GIVE CELL DIAGRAM WORKSHEETS.
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.
GIVE DNA AND PROTEIN SYNTHESIS DIAGRAMS/WORKSHEETS.
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.
DO LIVER ENZYME EXPERIMENT.
GIVE DNA/RNA/AA SEQUENCING WORKSHEET.
GIVE CELLULAR
TRANSPORT AND THE CELL CYCLE WORKSHEET.
Metabolism
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
GIVE CELL CYCLE DIAGRAM AND INFO SHEET.
Interphase - new
proteins are built; organelles are duplicated; DNA is replicated; ATP is
stockpiled.
Mitosis – reproductive
phase of the cell.
Stages:
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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