APHY 101, Lecture 1
Terminology
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Anatomy
Ana = up, Tome = to cut
Physiology
Physis = nature, Logia = to study
Iris – rainbow
Autopsy
Auto = self, opsis = to view
Form of organism
Function
Homeostasis
 Homeo = same, Stasis = Still
1. Maintain a stable internal environment
 e.g. Body temperature (98.6°), Heart rate (72beats/min), pH balance
 Consumes most metabolic energy of all processes

Requirements for homeostatic mechanism
1. Receptors – Provide information about environment
 Thermoreceptors –detect temperature
2. Control Center with Set point
 Control Center = sets the range at which the value is maintained
 Hypothalamus = Control Center
 Set point = range of values
 98.6°F = set point
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3. Effectors
 Muscles or glands
 Responds to input from control center
 Alters conditions
 e.g. Sweat glands secrete sweat to cool body
Example of Homeostatic Mechanism
1. Stimulus = hot environment → Body temperature increases →
Detected by thermoreceptors (receptors) → info into hypothalamus (control center) → Hypothalamus
detects deviation from body temp (set point) →
output signal to sweat glands (effectors) → Sweat glands secrete sweat →
response = body temp cools → Stimulus decreases
Negative Feedback = response to decrease the deviation from a set point
o Most homeostatic mechanisms rely on negative feedback
Positive Feedback = response to increase deviation from set point
o Short lived and uncommon
o e.g. Child birth
Characteristics of Life
 Organized system
 1 or more cells, humans have 50-100 Trillion cells
 Reproduction
 Consumes energy, usually ATP
 Maintains homeostasis
 Growth
Requirements to maintain life
 Water (H2O) – Transportation & required for metabolic processes
 Food – energy & building blocks
 Oxygen – required to release energy from metabolic processes
 Heat – energy, regulates metabolic reactions
 Pressure – force, for breathing & circulation
Organization
Subatomic Particles
↓
Atom
↓
Molecules
↓
Macromolecules
↓
Organelles
↓
Cell
↓
Tissue
↓
Organ
↓
Organ System
↓
Organism
Protons, Neutrons, Electrons
Hydrogen, Oxygen, Carbon
H2O (water), C6H12O6 (Glucose)
Proteins, Nucleic Acids, Polysaccharides
Mitochondria, Golgi Apparatus
Neuron, Muscle Cell, Osteocyte
Neural tissue, Epithelial Tissue, Bone tissue
Liver, Stomach, Brain
Digestive, Skeletal, Cardiovascular
Human
Chemistry
Common Terms
 Biochemistry = chemistry of living things
 Matter = Anything that has mass and takes up space
Solids, Liquids, Gas
 Element = Fundamental substance of matter
Groups of atoms of 1 type, e.g. Carbon, Oxygen, Hydrogen
 Compund = Combination of 2 or more atoms, e.g. H2O, C6H12O6
 Molecule = 2 or more atoms chemically bonded together
o May either be an element or may be a compound
Bulk Elements-99.9% of elements in human body
 Carbon (C)
Oxygen (O)
 Nitrogen (N)
Magnesium (Mg)
 Sodium (Na)
Potassium (K)
 Chlorine (Cl)
Phosphorus (P)
Hydrogen (H)
Sulfur (S)
Calcium (Ca)
Trace Elements <0.1% of elements, but have important functions
 Cobalt (Co)
Zinc (Zn)
Copper (Cu)
 Iron (Fe)
Fluorine (F)
Mangenese (Mn)
 Iodine (I)
Atomic Structure
 Nucleus
1. Protons
2. Neutrons
 Electrons – Orbit nucleus
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Subatomic Particle
Proton
Neutron
Electron
o
o
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Atomic Weight (Daltons)
1
1
0
For most atoms, number of protons = number of electrons, and therefore are neutral
Number of neutrons may vary
Atomic Number (AN) = Number of protons in an atom
o Defines the identity of an atom
o Changing the atomic number changes the atom
Atomic Weight (AW) = Number of protons + number of neutrons
Examples:
1. Hydrogen = 1proton, 1 electron, 0 neutrons
o Atomic Number = 1, Atomic Weight = 1
2. Helium = 2 protons, 2 electrons, 2 neutrons
o Atomic Number = 2, Atomic Weight = 4
3. Lithium = 3 Protons, 4 Neutrons, 3 Electrons
o Atomic Number = 3, Atomic Weight = 7

Isotopes
o Same atomic number, but different atomic mass
o Number of neutrons may vary
Example:
Isotope 1:
Oxygen (O)
8 protons
8 electrons
8 neutrons
Atomic Number: 8
Atomic Weight: 16
Isotope 2
Oxygen (O)
8 protons
8 electrons
9 neutrons
8
17
Atomic Weight is the average of all isotopes

Charge
+1
0
-1
Molecular Formula
o Shorthand of molecules
 Water = H2O……2 Hydrogen + 1 Oxygen Molecule
 Glucose = C6H12O6……6 Carbon + 12 Hydrogen + 6 Oxygen
Bonding Atoms
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Ions

Electron Orbit (Shell)
o Electrons orbit the nucleus in discrete orbits
 Inner orbit = holds 2 electrons
 2nd orbit = holds 8 electrons
 3rd orbit = holds 8 electrons
o Octet Rule
 Except for the 1st electron orbit, which holds 2 electrons, each additional orbit holds 8 electrons
o Examples
 Helium = 2 protons, 2 neutrons, 2 electrons
(both electrons in 1st orbit)
 Lithium = 3 protons, 4 neutrons, 3 electrons
(2 electrons in 1st orbit, 1 electron in 2nd orbit)

Ion = atom that gains or looses electrons
o Cation – Positively charged ion
o Anion – Negatively charged ion
o Example:
 Sodium (Na) = 11 protons, 12 neutrons, 11 electrons
 1 electron in outer orbit
 Outer lone electron is easily lost
 Na + = cation
 Chlorine (Cl) = 17 protons, 18 neutrons, 17 electrons
 7 electrons in outer orbit, which can hold 8 electrons
 1 electron is easily gained
 Cl- = anion
Bonds
1. Ionic Bond
 Oppositely charged ions attract and form a bond
 Ionic bonds form arrays such as crystals, but do not form molecules
2. Covalent Bond
 Atoms share electrons
o Hydrogen forms single bonds, H-H
o Carbon forms four bonds, Oxygen forms 2 bonds, O=C=O
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NonPolar Covalent Bond
 Equal sharing of electrons, e.g. H2 (H-H)
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Polar Covalent Bond
 Unequal sharing of electrons, e.g. H2O (H-O-H)
o Oxygen has stronger attraction to electrons & is slightly – charged
o Hydrogen partially gives electrons to Oxygen & is + charged
3. Hydrogen Bond
 Attraction of + hydrogen end to – Oxygen end
 Weak bonds at body temperature
 Forms crystals at lower temperatures, e.g. ice

APHY 101, Lecture 2
Chemical Bonds
4. Ionic Bond
 Oppositely charged ions attract and form a bond
 Ionic bonds form arrays such as crystals, but do not form molecules
5. Covalent Bond
 Atoms share electrons
o Hydrogen forms single bonds, H-H
o Carbon forms four bonds, Oxygen forms 2 bonds, O=C=O
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Structural Formulas on top row
Molecular Formulas on bottom row:
A. NonPolar Covalent Bond
 Equal sharing of electrons, e.g. H2 (H-H)
B. Polar Covalent Bond
o Unequal sharing of electrons, e.g. H2O (H-O-H)
 Oxygen has stronger attraction to electrons & is slightly – charged
 Hydrogen partially gives electrons to Oxygen & is + charged
6. Hydrogen Bond
 Attraction of ⁺ hydrogen end to ⁻ Oxygen end
 Weak bonds at body temperature
 Forms crystals at lower temperatures, e.g. ice
 Stabilize large molecules
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Chemical Reactions
Reactants (start) →Products (end)
1.
Synthesis
A + B → AB
2.
Decomposition
AB → A + B
3.
Exchange
AB + CD → AD + BC
4.
Reversible
A + B ↔ AB
Catalysts = speeds up reactions, but are not consumed by reaction.
Electrolytes
1.
Electrolytes = release ions in water
e.g. NaCl → Na⁺ + Cl⁻
(ions dissociate in water)
2.
Acids – electrolytes that release H⁺ (protons) in water
e.g. HCl → H⁺ + Cl⁻
3.
Base – electrolytes that release OH⁻(hydroxide ions) in water
e.g. NaOH → Na⁺ + OH⁻
4.
Acid + Base → Salt + Water
e.g. HCl + NaOH → NaCl + H2O
5.
pH = Concentration of H⁺
Logarithmic scale (change in 1 pH = change in 1 decimal place)
e.g.
pH
H⁺ Concentration (grams/Liter)
5
0.00001
4
0.0001
3
0.001
2
0.01
1
0.1
0
1
6.
pH decreases as H⁺ increases
a. Neutral, pH = 7.0
 number of protons = number of hydroxide ions (H⁺ = OH⁻)
 e.g. Water H2O → H⁺ + OH⁻
b. Acids, pH < 7.0
 Number of protons is greater than number of hydroxides (H⁺ > OH⁻)
c. Bases, pH> 7.0
 Number of protons is less than number of hydroxides (H⁺ < OH⁻)
1.
pH of Blood
a. average pH is 7.35-7.45
b. Acidosis = pH < 7.3
c. Alkalosis = pH > 7.5
d. Buffers = chemicals that resist changes in pH, stabilizes blood plasma pH levels
Chemicals of Cells
Organic = compounds with both Carbon and Hydrogen
Inorganic = molecules that lack either carbon, hydrogen, or both
Inorganic Molecules
1.
Water (H2O)
 2/3 of weight in person
 Most metabolic reactions occur in water
 Transports gasses, nutrients, wastes, heat
2.
Oxygen (O2)
 Used to release energy from nutrients
3.
Carbon Dioxide (CO2)
 waste byproduct of metabolic reactions in animals
Inorganic Salts
 Na⁺, Cl⁻, K⁺, Ca2⁺, HCO3⁻ (bicarbonate), PO42⁻ (Phosphate), ect.
 Role in metabolism, pH, bone development, muscle contractions, clot formation
4.
Organic Molecules
Building blocks (monomers) form larger macromolecules (polymers)
1. Carbohydrates – provides energy for cells
A. Twice as many Hydrogen as Oxygen (C6H12O6)
B. Monomers:
 Monosaccharides (simple sugars)
 Disaccharides
 Example: Glucose (C6H12O6)
 Straight Chain
Ring Formation
1. Polymers (Complex Carbohydrates)
 Cellulose = dietary fiber
 Starch = digested by
 Glycogen = storage form of energy, synthesized by liver from glucose
2.
Lipids (insoluble in water)
A. Fats = Triglycerides = energy for cellular activities
(1 glycerol + 3 Fatty Acids)
1. Glycerol
2. Fatty Acids (many types)
 Saturated = all carbons linked by single bonds
 Unsaturated = one or more double bonds
B. Phospholipids
1. Building Blocks
A. Glycerol
B. 2 Fatty Acid chains
 Creates a nonpolar “tail”- water insoluble
C. 1 Phosphate group
 Polar “head” – water soluble
C. Steroid
i. Rings of carbon molecules
ii. Examples include: Cholesterol, testosterone, estrogen, ect.
3.
Proteins
A. Overview
1. Many functions: structure, messengers, receptors, enzymes, ect.
2. Enzymes = biological catalysts – speeds up reactions, but are not consumed
3. Monmers = Amino Acids
B. Amino Acids
1. Amino Group (-NH2)
2. Carboxyl Group (-COOH)
3. Central Carbon (-C-)
4. R group (varies, rest of molecule)
5. Examples:
C. Peptide Bonds
1. Joint Amino Acids between carboxyl group of 1st amino acid and amino group of second amino
acid
2. 2 amino acids joined by peptide bond = dipeptide
3. Polypeptide = many peptide bonds
 Forms complex 3 dimensional shape called conformation
D. Protein Structures
1. Primary Structure
 Amino Acid sequence (anywhere from 100-5000 amino acids)
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2. Secondary Structure
 Shapes within small regions of polypeptides
 Result from hydrogen bonds
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Alpha helix & Pleated sheets
3. Tertiary Structure
 3 dimensional (conformation) shape of a polypeptide
4. Quaternary Structure
 Multiple polypeptides connected together
 Only proteins with more than one polypeptides have a quaternary structure
4.
Nucleic Acids
A. Overview
 DNA & RNA
 Monomers = Nucleotides
B. Nucleotides:
 5-Carbon sugar (S)
 Nitrogenous Base (B)
 Phosphate Group (P)
C. Polynucleotides
i. RNA
1. Ribose = sugar
2. Single Stranded
3. Information for protein synthesis
ii. DNA
1. Deoxyribos = sugar
2. Double stranded helix
3. Information for RNA synthesis (transcription)
RNA
DNA
APHY 101, Lecture 3
Proteins
Denature = To change shape of protein so it is nonfunctional
5.
Nucleic Acids
A. Overview
 DNA & RNA
 Monomers = Nucleotides
B. Nucleotides:
 5-Carbon sugar (S)
 Nitrogenous Base (B)
 Phosphate Group (P)
C. Polynucleotides
i. RNA
1. Ribose = sugar
2. Single Stranded
3. Information for protein synthesis
ii. DNA
1. Deoxyribose = sugar
2. Double stranded helix
3. Information for RNA synthesis (transcription)
RNA
DNA
CELLS
I.
Overview
1. Basic unit of life
2. 50-100 Trillion cells in human body
3. Size and shape vary
 Size
 measured in micrometers (µm)
 1 µm = 1/1000mm
 Red Blood Cell = 7.5 µm
 Varieties
 260 types of cells in body, all from 1 fertilized egg
 Differentiation = forming specialized cells from unspecialized cells
 Cells include neurons, skeletal muscle, osteocytes (bones), red blood cells, ect.
Structure of Cells
2. 3 major components
1. Cell membrane
2. Cytoplasm
 Cytosol = liquid
 Organelles = provides specific functions
3. Nucleus
Cell Membrane
I.
Overview
1. Maintains integrity of cell
2. Fluid membrane
 Flexible & elastic
3. Selectively Permeable
 Allows only selective substances into and out of cell
4. Permits communication between cell and environment
 Signal Transduction = cell interprets incoming messages
II.
Structure
1. Bilayer of phospholipids
 Phosphate “Head”
1. Polar group
2. Hydrophilic “water loving” = water soluble
 Fatty Acid Chains “tail”
1. Nonpolar groups
2. Hydrophobic “water fearing” = insoluble in water
3. Oily
2. Cholesterol
3. Membrane Proteins
III.
IV.
Formation of Cell membrane
1. Phospholipids align in water
 Expose polar heads to water = polar outside
 Hide nonpolar tails from water = oily inside
2. Nonpolar interior
 Allows nonpolar molecules to cross into and out of cell
e.g. O2,CO2, steroid hormones
 Polar molecules cannot cross cell membrane
e.g. H2O, sugars, amino acids
3. Cholesterol
 Rigid steroid rings that add support to cell membrane
4. Membrane Proteins = Many types embedded in cell membrane
Membrane Proteins
1. Integral Proteins
i. Spans across membrane
ii. Forms channels and pores
1. e.g. aquaporins, Na+ channels
2. Peripheral Proteins
i. Project from outer surface
ii. May be glycoprotein (protein + sugar)
iii. Does not penetrate hydrophobic portion of membrane
iv. Usually attach to integral proteins
3. Transmembrane Protein
i. Spans from outside cell to inside cell
ii. Example 1 : Cellular Adhesion Molecules (CAM)
1. CAMs bind cells to other cells, or to proteins
a. May anchor cell, or communicate with other cells
iii. Example 2: Many receptors
1. Transmits signals from extracellular environment into cell
I.
Nucleus
1. Nuclear Envelope
 Double layered membrane
 Nuclear Pores
a. Channel proteins that allow specific molecules into and out of nucleus
o Messenger RNA leaves nucleus through pores
o Ribosomes leave nucleus through pores
2. Nucleolus “little nucleus”
 Dense body of RNA & Proteins
 Produces ribosomes
3. Chromatin “colored substance”
 DNA wrapped around proteins, called histones
 Tightly coil and condense during mitosis to form chromosomes “colored body”
Movements into and out of cell
Passive = requires no energy from cell
Active = requires energy from cell in form of ATP
I.
Passive Movements
1. Diffusion
a. Random movement of molecules from higher to lower concentration
b. Molecules tend to diffuse = become evenly distributed
c. Requirements:
 Cell membrane must be permeable to substance (small & nonpolar)
o e.g. CO2, O2, Steroids
 A concentration gradient must exist across membrane
o One side of cell membrane must have a greater concentration than the other
2.
Facilitated Diffusion
a.
Diffusion with the aid of a carrier protein
b.
Allows selective molecules to cross membrane
 e.g. ions, sugars, proteins, amino acids
c.
Carrier protein changes conformation
d.
Substances move down concentration gradient
e.
Limited by number of carrier protein
3.
Osmosis
a.
b.
4.
Diffusion of water across selectively permeable membrane

Water passes through channels, called aquaporins

Large solutes (salts) cannot cross membrane

Water follows salts
Osmotic pressure exerted on cell

Isotonic = same solute concentration inside and outside cell

Hypertonic = Greater solute concentration outside cell than inside cell
o Water leaves cell & cell shrinks

Hypotonic = Greater solute concentration inside cell than outside
o Water enters cell and cell swells
o Cell may lyse “burst”
Filtration
a.
Fluid is pushed across a membrane that larger molecules cannot cross
 Separates solids from liquids
b.
Force = hydrostatic pressure – derived from blood pressure
II.
Active Transport
1. Movement against a concentration gradient
2. Requires ATP for energy (up to 40% of cell’s ATP)
3. Includes carrier proteins

e.g. Na+/K+ pumps can pump sodium out of cell and potassium into cell

Establishes a concentration gradient
III.
Endocytosis
1. Cell membrane surrounds and engulfs particle
2. Types include
a.
Pinocytosis
 Cell takes up a fluid
b.
Phagocytosis
 Cell takes up a solid
 Example: white blood cell engulfing a bacteria
c.
Receptor mediated endocytosis
 Selective endocytosis
 Receptors on cell membrane bind to substance and trigger endocytosis
 Provides specificity
 Removes substances in low concentrations
IV.
Exocytosis
1. Reverse of endocytosis
a.
Transport substances out of cell
b.
Vesicle merges with cell membrane and releases content
 Example- neuron releasing neurotransmitters
V.
Transcytosis
1. Endocytosis & Exocytosis
2. Allows passage through a cell
a.
e.g. HIV enters body by transcytosis through epithelium of anus, mouth, or reproductive
tract.
Cell Cycle
1. Interphase
2. Mitosis
3. Cytokinesis = division of cytoplasm
4. Differentiation
Interphase
1. G1 (Gap) Phase
a. Cell is active and grows
b. Growth followed by a checkpoint that determines cell’s fate.
c. Cell May:
1.
Continue to grow, then divide
2.
Remain active, but not divide
3.
Die
2. S phase (S = synthesis)
a. DNA replicates
3. G2 phase
a. Cell prepares for cell division
Mitosis
1. Overview
a. Mitosis occurs in somatic (non-sex) cells
b. Sex cells divide by meiosis
c. 46 chromosomes –paired

23 paternal & 23 maternal
d. Chromatin condenses to become chromosome

Each replicated chromosome consists of 2 sister chromatids

Chromatids held in place by centromeres
2. Phases of mitosis (PMAT)
a. Prophase

Chromatin condenses into chromosomes

Centrosomes (paired centrioles) move towards opposite poles of cell

Nuclear envelope breaks down

Spindle fibers arise from centrioles
b.
Metaphase

Spindle fibers attach to centromeres

Chromosomes align along equatorial plate
c.
Anaphase

Sister chromatids separate

Individual chromosomes move towards opposite poles

Cytokinesis begins – forms small furrow
d.
Telophase




Chromosomes complete migration towards opposite poles
Nuclear envelope reforms
Chromosomes unwind
Cytokinesis completes
3. Cytokinesis
a. Begins in anaphase and lasts through telephase
b. Division of cytoplasm
c. Cell membrane constricts around middle
Control of Cell Division
1. Mitotic Clock
a. Cell seems to “Know” when to divide

Some cells divide continually (skin, lining of small intestines, ect.)

Some divide only a few times than cease (neurons)
2. Influences of Cell division
a. Telomeres

Hundreds of repeated short nucleotide sequence

Located on tips of chromosomes

Up to 1200 nucleotides removed with each mitotic cycle

Cell stops dividing after so many nucleotides are removed
b. Growth Factors & Hormones

Chemicals secreted from other cells

Influence cell division
3. Tumors
a. Uncontrolled cell division results in tumor formation
b. Benign tumor =
1. solid lump that remains in place in body
2. May interfere with nearby tissue
c. Malignant tumor “Cancerous”
1. Invasive = spreads to nearby tissue
2. Metastasize = spreads throughout body
Stem Cells
260 Specialized types of cells from 1 fertilized egg cell
Differentiation = process of specialization
I.
Stem cells divide into
1. New stem cells = self renewal
a. Stem cells can give rise to any cell type
2. Progenitor cells
a. Committed but not yet specialized
b. Can give rise to any one of a limited number of cells

II.
III.
IV.
e.g. Muscle progenitor cells can give rise only to smooth muscle, skeletal muscle, cardiac
muscle
Descriptions of stem cells
1. Totipotent

Stem cells that can give rise to every cell type

Exists primarily in very early embryos
2. Pluripotent

Stem cells & progenitor cells that can follow any one of several pathways, but not all
Naming Cells
1. Blast = budding
Fledgling of a cell
2. Cyte = cell
Specialized adult cell
Examples
1. Ostoblasts specialize to form osteocytes (bone cell)
2. Erythroblasts specialize to form erythrocytes (red blood cell)
Apoptosis
1. Programmed cell death

Removes damaged cells = protection

Sculpts body = fingers & toes
2. Process

Cell receives signal on a “death receptors”

Cell activates enzymes, called capsases

Capsases cut up cell components