Chapter 2
The
Chemical
Level of
Organization
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The Chemistry of Life
• Matter made up of atoms (protons, neutrons, electrons)
• Elements - chemical substances consisting of one type of atom
distinguished by its atomic number (# of protons in its nucleus).
Examples of atoms: carbon, hydrogen, calcium, sodium, nitrogen
• Molecule - Two or more atoms joined by strong bonds (H2O)
• Ions are atoms or molecules that carry an electrical charge (H+
Ca2+ Na+ Cl-) - unequal number of protons and electrons; loses 1
or more electrons= cation (+); gains 1 or more electron = anion(-)
• Water- accounts for 2/3s of body mass; most prominent solvent
• Hydrophilic (hydro- = water / philos = loving- Interacts with water
• Hydrophobic (phobos = fear - Does NOT interact with water (fats
and oils)
• Inorganic Compounds - Molecules not based on carbon and
hydrogen
• Minerals, oxygen, water, and inorganic acids, bases, and salts
• Organic Compounds - Molecules based on carbon and hydrogen
• Carbohydrates, proteins, lipids, and nucleic acids
•2-2
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The most important structural feature of an atom for determining its
chemical behavior is the number of electrons in its outer shell. A
substance that has a full outer shell tends not to engage in chemical
reactions (an inert substance). Because atoms seek to reach a state
of maximum stability, an atom will try to fill its outer shell.
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Electrolytes and Chemical Reactions
• Inorganic ions that conduct electricity in solution
• Primary electrolytes: Na+, Cl-, K+
• Electrolyte imbalance seriously disturbs vital body functions
• Electrochemical gradients determine nerve, heart, and muscle
actions
• Osmotic effects (influence water movement)
• Imbalances have ranging effects from muscle cramps, brittle
bones, to coma and cardiac arrest
Types of Chemical Reactions
1. Decomposition reaction (catabolism)
• Breaks chemical bonds AB A + B
2. Synthesis reaction (anabolism)
• Forms chemical bonds A + B AB
Activation energy = amount of energy needed to get a reaction
started
o Enzymes are protein catalysts that lower the activation energy
of chemical reactions
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Figure 2-8 The Effect of Enzymes on Activation Energy
•Activation energy
required
•Energy
•Without
enzyme
•Reactants
•With enzyme
•Stable
product
•Progress of reaction
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pH and Homeostasis
pH (“power of hydrogen”) is the measurement of the concentration
of H+ ions
• Neutral pH
• Pure water = 7.0
• Acidic pH LOWER than 7.0
• High H+ concentration
• Basic (or alkaline) pH HIGHER than 7.0
• Low H+ concentration
• pH of Human Blood
• Ranges from 7.35 to 7.45 (fatal below 6.8 or above 8.0)
• The pH scale is logarithmic where each whole pH value below 7 is
10x more acidic than the next higher value. EX: pH 4 is 10x more
acidic than pH 5 and 100x (10 x 10) more acidic than pH 6. The
same is true for pH values above 7, where each is 10x more
alkaline/basic than the next lower whole value. EX: pH 10 is 10x
more alkaline than pH 9 and 100 x (10 x10) more alkaline than pH 8.
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Chemistry of Life - Compounds
• Nutrients
• Essential molecules obtained from food (carbohydrates, proteins,
and fats)
• Buffers
• Stabilize pH by adding or removing hydrogen ions
• Nuclei acids/nucleotides
• DNA
• Backbone: Sugar: Deoxyribose / Phosphate group
• Protein/nitrogen bases:
• Adenine (A) and thymine (T) Cytosine (C) and guanine (G)
• RNA (transfer [tRNA]; messenger [mRNA])
• Backbone: Sugar: Ribose / Phosphate group
• Protein/nitrogen bases:
• Uracil (U) replaces thymine (T)
• Cytosine (C) and guanine (G)
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Chemistry of Life
Free Radicals- Result of unpaired electrons
• Result from normal metabolic reactions, radiation, chemicals
• Free radicals are very unstable and react quickly with other
compounds, trying to capture the needed electron to gain stability.
• Important for biological processes
• Role in cell communication
• Required for phagocytosis (destroy intracelluar bacterial)
• Blood vessel tone- neurotransmitter: Nitric oxide
• Causes tissue damage
• Cell membranes, vital proteins
• Parkinson’s disease, aging process, schizophrenia, and
Alzheimer's
• CONTROL: Because free radicals are necessary for life, the
body has a number of mechanisms to minimize free-radicalinduced damage and to repair damage that occurs.
• Enzymes such as the superoxide dismutase
• Antioxidants such as Vitamin A, C, E,
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Chapter 3
The Cellular
Level of
Organization
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Introduction to Cells
Cell Theory- Cells are the building blocks of all plants and animals
• Cells are the smallest units that perform all vital body functions
• Approximately 200 types of cells in the human body
• Extracellular Fluid (Interstitial Fluid) -watery medium that
surrounds cell
• Plasma membrane (cell membrane) separates cytoplasm from
the extracellular fluid. Most of the important physiological events
occur on or near the membrane.
• Cytoplasm comprised of cytosol (liquid) and intracellular fluid and
organelles, proteins, salts, sugars, and other materials. Cells can
contain up to 10 billion protein molecules.
Categories of body cells:
• Sex Cells (Germ Cells) - Reproductive cells
• Male sperm
• Female oocyte (a cell that develops into an egg
• Somatic Cells - Soma = body
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Plasma Membrane
1. Physical Isolation –barrier- first part of the cell exposed to changes
2. Regulation of Exchange with the Environment –nutrients and
waste products
3. ATP production, hormone binding, nerve conduction, fertilization
4. Structural Support - Anchors cells and tissues
5. Contain vital receptors for recognition and response to specific
molecules in the external environment.
Phospholipid bilayer
• Hydrophilic heads — toward watery environment, both sides
• Hydrophobic fatty-acid tails — inside membrane
• Permeable to small, non-polar, uncharged molecules and water
• Impermeable to larger, polar, charged molecules (Na+, K+)
• Cholesterol molecules stabilize bilayer
Membrane carbohydrates proteoglycans, glycoproteins, and
glycolipids form sticky “sugary fuzz-like coat” (glycocalyx ).
• Glycocalyx contributes to cell-cell recognition and immune
response (identification tags such as blood types, MHC), provides
lubrication and protection, cellular adhesion.
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EXTRACELLULAR FLUID
Phospholipid Integral protein
bilayer
with channel
Glycolipids
of glycocalyx
Integral
glycoproteins
Hydrophobic
tails
Plasma
membrane
Cholesterol
Gated
channel
CYTOPLASM
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Peripheral
proteins
 2 nm
Hydrophilic
heads
Cytoskeleton
(Microfilaments)
Membrane Proteins
1. Integral Proteins- Within the membrane act as channels or
transporters; can influence binding capacity of other proteins by
changing the confirmation (shape) of the protein. Penetrates
through entire membrane Ex: G proteins in 2nd messenger system
2. Peripheral Proteins- Bound to inner OR outer surface of the
membrane
3. Anchoring Proteins (stabilizers) Do not pass through membrane
4. Recognition Proteins (identifiers- Ex: RBC antigens) - Label cells
as normal or abnormal
5. Enzymes - Catalyze reactions such as dipeptide breakdown into
peptides in enterocytes of intestines (disaccharide to
monosaccharide); attached to integral proteins
6. Receptor Proteins- Bind and respond to ligands (ions, hormones)
insulin, calcium; relay signals between the cell's internal and
external environments.
7. Channels - regulate water flow and solutes through membrane
8. Carrier Proteins - Transport specific solutes through membrane
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Plasma Membrane
Receptor
enzyme
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channel
gated
channel
cell –identity
cell
markers
adhesion
Organelles and the Cytoplasm
Cytoplasm- materials inside the cell/outside the nucleus
• Cytosol (intracellular fluid)
• Nutrients, ions, proteins, and waste products
• Organelles
• Non-membranous organelles: cytoskeleton, microvilli,
centrioles, cilia, ribosomes
• Membranous organelles: endoplasmic reticulum (ER), the Golgi
apparatus, lysosomes, peroxisomes, and mitochondria
The Cytoskeleton - structural proteins for shape and strength
• Microfilaments- thin filaments- Attach plasma membrane to
cytoplasm
• Intermediate filaments- mid-sized between micro and thick
• Most durable (collagen) (Ex: keratin fibers in the skin)
• Strengthen cell; maintain shape; stabilizes the position organelles
• Microtubules- large, hollow tubes
• Provide transportation of vesicles ; Involved in cell division
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Organelles
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Microvilli –never move
• Extension of membraneIncreases surface area for
absorption
Cilia - produce movement
• Small hair-like slender
extensions of membrane that
move fluids across the cell
surface
Cell Nucleus
Nuclear envelope - double
membrane around the
nucleus
Nuclear pores allows
communication between
nucleus and cytoplasmbrings 100s of molecules into
contact with nucleus
• Raw materials for DNA
and RNA, enzymes,
hormones
Nucleus contains
• Chromosomes- TIGHTLY coiled DNA
• Chromatin –LOOSELY coiled DNA
• Information stored in the nucleus
• Gene- DNA instructions for one protein
• Protein synthesis: transcription, translation
• Genetic code -The chemical language of DNA instructions
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Membranous Organelles
Ribosomes - Build polypeptides in protein synthesis
1. Free ribosomes in cytoplasm manufacture proteins for cell
2. Fixed ribosomes attached to ER manufacture proteins for
secretion
Endoplasmic reticulum (ER) –connected to nuclear envelope
Storage of synthesized molecules and materials
 Smooth - No ribosomes attached
o Synthesizes sex hormones- high amount of smooth ER in
testes and ovaries
o Synthesis and storage of glycogen in muscle cells
o Synthesis of cholesterol
o Detoxification of drugs or toxins –high volume of ER in liver
 Alcohol and drug abuse produces metabolic tolerance due
to increased proliferation of smooth ER providing the ability
to detoxify more quickly.
 Rough – attached ribosomes
• Primary synthesis of proteins and phospholipids
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Figure 3-5a The Endoplasmic Reticulum
Nucleus
Rough endoplasmic
reticulum with fixed
(attached) ribosomes
Ribosomes
The three-dimensional
relationships between the rough
and smooth endoplasmic reticula
are shown here.
Cisternae
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Smooth
endoplasmic
reticulum
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Organelles
Golgi apparatus
• Modifies and packages secretions (ex: new proteins)
• Renews or modifies the plasma membrane
• Releases through exocytosis (pages 74-75)
Lysosomes - (lyso- = dissolve; soma = body) powerful enzymecontaining vesicles produced at the Golgi apparatus. Provide
protection (attack bacteria) and “waste removal”; “recycling”;
detoxify alcohol, other drugs, and a variety of blood-borne toxins
Peroxisomes- SMALLER than lysosomes with different type
enzyme-containing vesicles; produced at the Golgi apparatus
• Break down fatty acids, organic compounds
• By- product hydrogen peroxide (H2O2) produces free
radicals
• Contains enzyme catalase to counteract free-radical
damage
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Figure 3-6a The Golgi Apparatus
Secretory
vesicles
Secretory
product
Here is a three-dimensional
view of the Golgi
with a cut edge.
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apparatus
Transport
vesicles
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Organelles
Mitochondria – energy (ATP) production for cell
• smooth outer and inner membrane with numerous folds
• Glycolysis, Kreb Cycle, Electron transport chain
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Diffusion and Osmosis
• Plasma membrane is selectively permeable
• Allows some materials to move freely; restricts
other materials
• Selective permeability restricts substances based on Size /
Electrical charge / Molecular shape / Lipid solubility
• Transport through a plasma membrane can be:
• Active (requiring energy and ATP)
• Passive (no energy required)
• Diffusion (passive) the net movement of particles FROM HIGH
CONCENTRATION TO LOW CONCENTRATION
• Lipid based substances (solutes) diffuse easily through plasma
membrane.
• Protein substances (solutes) move via facilitated passive
diffusion through protein channels (“leaky” channels) in the
membrane down its concentration gradient (high to low) or active
transport
• Osmosis - diffusion of water across the membrane
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EXTRACELLULAR FLUID
Lipid-soluble molecules
diffuse through the
plasma membrane
Plasma membrane
CYTOPLASM
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Large molecules that cannot
diffuse through lipids cannot
cross the plasma membrane
unless they are transported
by a carrier mechanism
Channel
protein
Small water-soluble
molecules and ions
diffuse through
membrane channels
Carrier-Mediated Transport
Proteins transport molecules too large to fit through channel proteins
• Passive (glucose, amino acids)
• Molecule binds to receptor site on carrier protein
• Protein changes shape, molecules pass through
• Receptor site is specific to certain molecules
• Active transport proteins
• Moves against concentration gradient
• Require energy, such as ATP
• Ion pumps move ions (Na+, K+, Ca2+, Mg2+)
• Exchange pump - countertransports - one substance moves in
while another moves out –Sodium Potassium Pump
• Ex:Sodium ions (Na+) out, potassium ions (K+) in
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menu/membranes/c8.7x17.transport.jpg
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Vesicles- Vesicular Transport
Materials move into or out
of cell in vesicles
• Endocytosis (endo= inside) is active
transport using ATP
• Receptor
mediated
• Pinocytosis“drink”
extracellular fluid
• Phagocytosis Engulfs large
objects
• Exocytosis (exo- = outside)
• Granules or droplets are released from the cell
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Osmosis and Tonicity
Osmolarity- total solute concentration
• Two fluids may have equal osmolarity, but different tonicity –
effect of the osmolarity of a solution
• Tonicity – effect of various osmotic SOLUTIONS on cells.
Movement of fluid in and out of the CELL
• Isotonic (iso- = same, tonos = tension)
• A SOLUTION that does not cause osmotic flow of water in
or out of a cell
• Hypotonic SOLUTION (hypo- = below) – fluid outside of the
cell has less solutes than the cell so water moves INTO the
cell where there is a higher solute concentration
• Swells and Ruptures (hemolysis of red blood cells)
• Hypertonic SOLUTION (hyper- = above) – fluid outside of
the cell has higher solute concentration than cell so fluid
moves OUT of the cell
• Shrinks and shrivels (crenation of red blood cells)
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HYPOTONIC
water
water
CELL
water
water
water
solids
solids
water
water
Cat = water
Mouse = solid substances
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HYPERTONIC
solids
CELL
water
solids
solids
solids
solids
water
solids
solids
Cat = water
Mouse = solid substances
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Figure 3-17 Osmotic Flow across a Plasma Membrane
Water
molecules
Solute
molecules
isotonic solution
NO flow
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hypotonic solution
Flow INTO the cellmore solutes inside cell;
Swells and burst
hypertonic solution
Flow OUT of cell – More
solutes outside the cell
Shrinks/crenation
Cellular Life Cycle
• Most of a cell’s life is spent in a non-dividing state (interphase)
• DNA replication duplicates genetic material exactly
• Mitosis divides genetic material equally producing 2 identical
cells.
• Sex cells divide by meiosis which divides the DNA material. This
enables the male and the female to each contribute ½ of the DNA
material.
• Cells specialize or differentiate to form tissues (liver cells, fat cells,
and neurons) by selecting only the area of the chromosome (genes)
that will be utilized by that cell. For example, eye cells do not need
to make digestive enzymes.
• All cells are programmed for function and termination. Cells that do
not respond to specified instructions can form cancer cells.
• Tumor (Neoplasm) Abnormal cell growth and division producing an
enlarged mass of cells
• Benign tumor Contained, not life threatening unless large
• Malignant tumor Spreads into surrounding tissues (invasion),
Starts new tumors (metastasis)
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Cell Division and Cancer
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metastasis