CHAPTER 1 MOLECULAR BIOLOGY; CELLULAR RESPIRATION

1.2 Water
Hydrolysis: Addition of H2O to a bond to break it apart. Most macromolecules use this process to
dissemble.
Dehydration: Removal of H2O to a bond to form it. Most macromolecules use this process to
assemble.
1.3 Lipids
Any biological molecules that is hydrophobic.
E.G.:
Fatty acids: building blocks for most complex lipids. CH3(CH2)nCOOH
Triglycerides: 3 fatty acid + glycerol. Energy storage.
Phospholipids: Triglyceride with one fatty acid replaced by phosphate group. Cell membrane
Glycolipids: Same as phospholipids except phosphate group replaced by one or more
carbohydrate. Found in membranes of myelinated cells of the nervous system
Steroids: 4 ringed structure. Hormones, vitamin D, cholesterol
Terpenes: Vitamin A for vision.
Transported via lipoproteins. E.G. Chylomicrons, VLDL, LDL, HDL.
1.4 Proteins
Chains of AA linked by peptide bonds. AKA polypeptides
10 Essential AA body cannot synthesize them
20 Total AA
4 types:
Non-polar: Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan,
Methionine, Proline
Polar: Serine, Threonine, Cystein, Tyrosine, Asparagine, Gluamine
Acidic: Glutamic Acid, Aspartic Acid
Basic: Histidine, Arginine, Lysine
Structure:
Primary: AA acid sequence
Secondary: Alpha helix or Beta pleated sheets. Reinforced by H-bond
Tertiary: 3D shape. Disulfide bonds (btwn cysteine residues), ionic btwn acidic and basic side
chains, H-bond, hydrophobic/hydrophilic interaction with H2O
Quaternary: Multiple subunits.
Denaturing agents:
Urea disrupts H-bond
Salt or change in PH electrostatic bonds
Mercaptoethanol disulfide bonds
Organic solvents hydrophobic forces
Heat all forces
Basic structure of one AA: NH2-CH-R COOH
How to tell L vs D AA: Use CORN rule. Put H in back, look at direction of COOH, then, R, then, NH2
group. L-left D-clockwise
1.5 Carbohydrates
Empirical formula: C(H2O)
Glucose: 80% of carbs absorbed by body is glucose
Anomers: Alpha: OH on C1 is on opposite side of methoxy group of C6. Beta: opposite of
alpha
Humans absorb alpha bonded glycogen.
Glycogen: polymerized polysaccharide used by humans
Storage: stored in liver as glycogen. Reforms sugar from glycogen and vice versa.

Starch: composed of amylose and amylopectin.

Cellulose: beta linked. Animals cannot digest it.
1.6 Nucleotides
3 components: 5 carbon sugar, Nitrogenous base, phosphate group
Base attach to C1, phosphate attach to C5, C3 used to attach to another sugar
DNA is missing OH on C2
1.7 Minerals
1.8 Enzymes
Lowers activation energy, do not alter equilibrium
Cofactor: used by many enzymes for optimal activity
Two types: Coenzymes: vitamins, ATP, etc. Minerals: Ca++, Na+
1.9 Enzyme inhibition
Irreversible: tend to be highly toxic, cannot be unbound.
Competitive: competes with substrate. Vmax unaffected, Km decreased
Non-competitive: do not compete with substrate. Vmax lowered, Km unaffected
1.10 Enzyme Regulation
4 types:
Proteolytic cleavage: Zymogen transformed into active enzyme
Reversible covalent modification: E.G. phosphorylation
Control proteins: protein subunits that associate with enzyme to activate or inhibit activity. E.G.
G-protein
Allosteric interaction: binding of activator or inhibitor
Feedback: Negative shut down upstream activity to inhibit further production of product. Positive:
opposite.
1.11 Enzyme Classification
1. Oxidoreductase
2. Transferase
3. hydrolase
4. Lysase
5. Isomerase
6. Ligase
Note: Compounds that have ase ending most likely enzyme. They are prone to denaturing.
Kinase: phosphorylates something
Phosphatase: de-phosphorylates something
1.12 Cellular Metabolism
Metabolism: Are all cellular chemical reactions
1.13 Glycolysis
Type of anaerobic respiration. Oxygen is not required
1st stage of respiration. Glucose turns into 2 pyruvate, 2 ATP, 2 NADH. Occurs in the cytosol.
1.14 Fermentation
Anerobic respiration.
Turns Pyruvate into ethanol or lactic acid.
Turns NADH back to NAD+
Expends 2 ATP, forms 4 ATP. Net: gains 2 ATP per glucose molecule
1.15 Aerobic Respiration

Requires oxygen
Occurs in the mitochondria
Pyruvate facilitate diffused into mito.
Convert Pyruvate into acetyl CoA. Forms CO2 and NADH
1.16 Krebs Cycle
Acetyl CoA is a coenzyme that transfers two carbons from pyruvate to oxaloacetic acid to start the
cycle
Uses substrate-level phosphorylation to produce ATP
1.17 Electron transport chain
Series of proteins in the inner membrane of mito.
NADH oxidized in the first protein
Electrons passed down chain of proteins
Protons are pumped into the intermembrane space (low pH)
High concentration protons propels through ATP synthase to synthesize ATP
Oxidative phosphorylation: synthesis of ATP by using proton-motive force.
CHAPTER 2 GENES
2.1 The Gene
Central Dogma: DNA -> RNA -> protein
2.2 DNA
Polymer of nucleotides
C&T Pyrimidine
A&G Purines
C&G Three H-bonds
A&T Two H-bonds
5 to 3 directionality
2.3 Replication
Semiconservative replication
Bidirectional
Reads 3 to 5, but synthesizes the complimentary strand 5 to 3
Steps:
1. Helicase unzips the double helix;
2. RNA Polymerase builds a primer;
3. DNA Polymerase assembles the leading and lagging strands;
4. the primers are removed;
5. Okazaki fragments are joined.
Telomerase: repeated 6 nucleotide units that protects chromosomes from being eroded through
multiple replication.
2.4 RNA VS DNA:
U instead of T
C2 has OH instead of H only
Single stranded
Can move through nuclear pores
3 Types:
mRNA: delivers DNA code to be translated
rRNA: combines with proteins to form ribosomes
tRNA: transfers AA to ribosome for translation
2.5 Transcription

Requires a promoter: short piece of DNA tells RNA pol where to begin transcription
The template strand or (-) antisense strand is transcribed
The coding strand or (+) sense strand protects its partner from degradation
Moves in 3 to 5 direction, but synthesizes 5 to 3
Terminates at the termination sequence
Most regulation occurs at transcription. Activators or repressors bind close to promoter for regulation.
Prokaryotic gene: The genetic unit including the operator, promoter, and genes is called the operon.
2.6 Post-transcriptional Processing
Initial mRNA sequence: primary transcript
5 cap added
3 poly A tail added
Introns excised out
2.7 DNA Technology
Restriction Enzyme: cuts nucleotide at a specific palindromic sequence
cDNA Library: complimentary library made from reverse transcribed mRNA
PCR: denature, anneal, amplify cycles
Southern blot: DNA restricted, resolve using electrophoresis, probe using radioactive DNA or RNA
compliment, visualize
Northern blot: RNA
Western blot: Protein via primary and secondary antibodies
RFLP: analyze individuals by different restriction site digestion
2.8 The Genetic Code
AUG: start codon. Methionine
UAA, UAG, UGA: stop codon
2.9 Translation
Ribosome is the machinery used to translate mRNA to protein
Ribosome requires nucleolus to be manufactured
3 sites: E (exit), P (peptidyl) , and A (amino); physically located the same sequence
Translation steps:
Initiation: Methionine settles at the P site. Both subunits join together.
Elongation: Next AA with its corresponding tRNA settles in the A site. Peptide bond forms.
mRNA shifts 3 peptide down.
Termination: Stop codon reaches A site. Peptide is freed from tRNA and ribosome.
Post translational processing may occur. Sugars, lipids or phosphate groups may be added
Protein destination:
Rough ER: 20 AA signal peptide sequence near the front of the polypeptide routes the
ribosome onto the rough ER. Proteins made at the rough ER is to be excreted or membrane bound.
Cytosol free floating ribosome synthesizes proteins to be used in the cell.
2.10 Mutations
Gene mutation: alteration in the DNA sequence in a single gene
Chromosomal mutation: structure of chromosome is changed
Point mutation: change in a single base pair
Base-pair mutation: one base-pair is replaced by another
Missense mutation: base-pair mutation that occurs in the amino acid coding sequence
of a gene. May or may not alter AA sequence of a protein
Insertion or deletion: may result in frame shift mutation if deletion or insertion of peptides other
than 3n.
Nonsense mutation: stop codon created from a mutation. Protein is truncated.
Translocation: one chromosome inserted into another

Inversion: orientation of a section of DNA is reversed on a chromosome

Transposition: a segement of DNA called transposable element may move from one location to
another on a chromosome
Forward/backward mutate: mutation that leads away/towards the wild type
2.11 Cancer
Unrestrained and uncontrolled growth of cells.
Proto-oncogenes: genes that stimulate normal growth in human cells
Oncogenes: converted from proto-oncogenes that causes cancer.
2.12 Chromosomes
Histones: proteins that wraps DNA around itself to compact its size
Nucleosome: 8 histones
In nucleus, we have 46 double stranded DNA molecules or 23 homologues
2.13 Cell Life Cycle
G1, S, G2, M
Interphase: G2, S, G2
G1: cell has just split. Growth in size and synthesize organelles and proteins
G0: nongrowing phase distinct from interphase. Enteres from the end of G1 phase
S: synthesize of DNA.
G2: cell prepares to divide.
2.14 Mitosis
Prophase: condensation of chromatin into chromosomes
Centrioles move to opposite of cell
Nucleolus then nucleus disappear
Spindle apparatus forms consisting of aster, centromeres, and spindle microtubules.
(kinetichore is locatged at the contromere of the joined chromatids)
Metaphase: chromosomes line up
Anaphase: sister chromatids split at centromeres and move apart.
Cytokinesis (separation of cellular cytoplasm due to controction of microfilaments about he
cnetger of the cell) may commense towards the end of the phase
Telophase: nuclear membrane reform, then nucleolus. Cytokinesis continue.
2.15 Meiosis
Only spermatogonium and oogonium undergo meiosis
Prophase I: homologous chromosomes line up along side each other. Cross over occur. The X shape
formed is called a tetrad
Crossing over forms an x shape calleld chiasma
Metaphase I: homologues remain attached and move to metaphase plate
Anaphase I: Separate homologues from their partners. 2n -> n
Telophase I: nuclear membrane reform and cytokinesis occur. New cells are haploid with 23
replicated chromosomes called secondary permatocytes or oocytes. In female, one of the oocytes is called
polar body with much smaller cytoplasm.
Prophase, metaphase, anaphase II: appears much like normal mitosis, except results in 4 haploid
cells with 23 chromosomes.
CHAPTER 3 MICROBIOLOGY
3.1 Viruses
Size comparable to large protein
Composition:
Capsid: protein coat surrounding genetic material

Genetic material: either single or double stranded DNA or RNA, but not both (can be sense or
anti-sense)
Envelope: outer protective covering borrowed from host cell or manufactured. Present in most
animal, some plant, and few bacterial viruses.
Bacteriophages: tail, base plate, tail fibers
Not considered living because virus requires host cell for ATP and machinery to replicate. Can be
crystallized and retain virulence.
Infection steps:
Virus binds to specific chemical receptor (often a glycoprotein). Virus cannot infect if receptor
is not present.
Nucleic acid penetrates the cell.
For bacteriophages: Chemicals digest cell wall and nucleic acid injected through the tail
of the virus
For eukaryotic viruses: Most enter cell via endocytosis.
Latent period: period between infection and first fully formed virus appear.
Two pathways:
Lytic: virus begins to replicate. Virus called virulent virus.
Lysogenic: DNA incorporated into host genome. Becomes virulent when host cell is under
stress.
Temperate virus: virus in the lysogenic cycle.
Provirus: Virus in the lysogenic cycle if the host is bacterium
Types:
Plus-strand RNA: Protein can be directly produced from RNA
Retrovirus: virus with RNA and reverse transcriptase to produce DNA from RNA
Minus-strand RNA: compliment of mRNA. Must be transcribed into plus-RNA before being
translated.
Other: double stranded RNA, single and double stranded DNA
3.2 Defense Against Viral Infection
Antibodies bind to virus and cytotoxic T cells destroy the tagged virus.
Antibodies recognize the spike proteins present in the outer membrane that gives viruses their ability
to recognize new host cells
Carrier population: one or more animals that acts as a carrier to a virus. Virus coexist in them while
infecting other animals.
Broad classification according to energy and carbon source:
Energy source:
Phototrophs: Uses light for energy
Chemotrophs: uses chemicals
Carbon source:
Autotrophs: uses
CO2
Heterotrophs: uses pre-formed organic material
Electrons or hydrogen source:
Lithotrophs: inorganic matter
Organotrophs: organic matter
3.3 Prokaryotes
No membrane bound nucleus
Split into two domains:
Archaea: typically found in extreme environments such as salty lakes and boiling hot springs.
Have more similarities with eukaryotes than bacteria. Cell walls are not made from peptidoglycan.
Bacteria:
3.4 Structure of Prokaryotes

Usually single double stranded circular DNA. Associated with histones in Archaea and similar protein
in Bacteria.
No nucleus. Instead, DNA, RNA, and protein form nucleoid. Not bound by membrane.
No complex, membrane bound organells. But they do have organells such as ribosomes,
mesosomes, etc, but not membrane bound and complex.
Bacterial shape: bacterial naming usually contain shape information. E.G. staphylococcus,
spiroplasma.
Cocci: round
Bacilli: rod shaped
Spirilla: spiral, ridgid
Spirochetes: spiral, non-ridgid
3.5 Membranes
Plasma membrane: Cytosol of bacteria is surrounded by a phospholipid bi-layer called plasma
membrane.
Proteins found on plasma membrane:
Integral (intrinsic) proteins: Proteins that traverse the plasma membrane
Extrinsic (peripheral) proteins: Proteins that is found on the surface of the plasma membrane.
Do not easily flip orientation on the plasma membrane.
Fluid mosaic model: everything on the plasma membrane, including the membrane itself, is fluid-like.
Everything moves laterally in a random fashion. Cholesterol moderates fluidity.
3.6 Membrane Transport
Passive diffusion: No energy is used. Molecules diffuse down concentration gradient. Depends upon
lipid solubility
Facilitated diffusion: Transport protein assist in the diffusion of molecules down the concentration
gradient. E.G. glucose into cell
Active transport: Energy used to transport molecules against electro-chemical gradient
3.7 Bacterial Envelope
Envelope surrounding bacterial plasma membrane.
Function: Prevent hypertonic bacteria plasma from bursting.
Composition: Peptidoglycan. More flexible than cellulose. Porous.
Gram staining:
Gram positive: thick bacterial envelope. Purple.
Gram negative: think bacterial envelope. Pink. Outside of envelope, another phospholipids
bilayer exist. This membrane posses polysaccharides to resist antibiotics.
Flagella:
Long, rotates for movement, made from flagellin.
3.8 Bacterial Reproduction
Major reproduction method: Binary fission. 1 cell -> 2 identical cells
Genetic recombination methods:
Conjugation: One bacteria contain a plasmid called sex pilus. Sex pilus is a hollow tube that
connects two bacterium for exchanging DNA material. Once two bacterium connects, they exchange
plasmid DNA.
Important plasmids:
F plasmid: fertility plasmid
R plasmid: Resistance plasmid. Plasmid that codes for antibiotic resistance.
Transformation: bacteria incorporates DNA from external environment.
Transduction: virus assisted DNA transfer into bacterium
3.9 Endospores
Bacteria in a highly resistant dormant stage that can survive for hundreds of years.

3.10 Fungi
Eukaryotic heterotrophs
Absorb nutrient by secreting digestive enzymes and absorb digested nutrient from the external
environment.
Life cycle mostly in haploid form
Most fungi are saprophytic
Septa: fungi cell wall made of chitin (same stuff as exoskeletons)
Reproduce sexually and asexually
Multicellular except for yeast
3.11 Fungal Reproduction and Life Cycle
Asexual: spores carried by air, water, or host, or budding in yeast
Sexual: Hyphae from two mycelia of different mating types (+ and ) touch, forming a conjugation
bridge. Two gametes form at the bridge and they fuse into a diploid zygote. The zygote differentiate into
haploid spore forming cell.
CHAPTER 4 THE EUKARYOTIC CELL; THE NERVOUS SYSTEM
4.1 The nucleus
Contains all genetic material (except a small amount from mito)
Double phospholipids bilayer (nuclear envelope)
Nuclear pores enable RNA to escape
Nucleolus reside within nucleus to transcribe rRNA and assemble ribosome
4.2 The membrane
Phagocytosis: (greek: to eat)
engulfing large particles
few specialized cells
Pinocytosis: (greek: to drink)
small invagination, random, non selective, performed by most cells
Exocitosis: opposite of endocytosis
ER: Maze of cell walls,
contiguous in many places with cell membrane and space between double bilayer of nucleus
Smooth ER:
tubular in shape.
Produce proteins destined for cytosol, glucose from glycogen, triglycerides, cholesterol,
conversion of cholesterol to various steroids, neutralizing toxic chemicals, and oxidize forein
substances.
Rough ER:
Shape like flattened sacks.
Synthesize virtually all proteins not used in cytosol.
Golgi apparatus:
Series of flattened membrane bound sacks.
Proteins with correct signal sequence move from rough ER to Golgi, shuttled across using
transport vesicles, organize, concentrate, modify proteins.
End product is a vesicle full of proteins
End product: secretory vesicles, lysosome
Secretory vesicles: growth factors, enzymes, cell wall components destined for exocitosis
Lysosomes:
acid hydrolases in low PH environment capable of digesting all major cell components.
Fuse with endocytotic vesicles to digest content.
Undigested content ejected from cell using exocytosis.
May autolysis and kill cell under certain conditions.

Tay-Sachs disease autosomal recessive for missing protein in lysosome, accumulation of

lipids in brain.
Peroxisomes:
self-replicate. Produce and break down of hydrogen peroxide.
Inactivate toxic chemicals such as alcohol.
Play role of synthesis and breakdown of lipids.
Metabolism of nitrogenous bases and carbohydrates.
4.3 Cellular Filaments
Cytoskeleton:
responsible for structure and mobility of cell.
Anchor some proteins and cell components.
Move cell components and cell itself. Two major types:
Microfilaments:
Actin polymerized
contractile force in microvilli and muscles
responsible for squeezing membrane together in phagocytosis and cytokinesis.
Microtubule:
Larger than microfilaments.
Hollow tubes made from alpha and beta tubulin.
Mitotic spindle, Flagilla, cilia.
- end attach to microtubule organizing centers (centrosome) + grows outwards
4.4 Cellular Junctions
Tight Junctions:
Watertight seal blocks water, ions, and other molecules from moving past cell. Complete fluid
barrier
Epithelial tissue such as bladder, intestine, skin
Desmosomes:
Spot welds btwn cells
Found in tissues that experience stress such as skin and intestinal epithelium
Gap junctions:
Small tunnels connecting cells. Allow small molecules and ions to flow between cells. Action
potential propogation.
Plasmodesma:
Narrow channels between plant cells. Contains narrow tube of ER surrounded by cytoplasm.
4.5 Mitochondria
Endosymbiont theory: symbiotic relationship between ancient eukaryot and prokaryot.
Own circular DNA
Independent replication, from mothers side only
Own mitochondria
Structure:
Double phospholipids layers.
Inner layer forms invaginations called cristae
Intermembrane space: space between outer and inner membrane where electron transport
chain takes place
4.6 The Extracellular matrix
Definition: elastin and collagen excreted by fibroblasts that forms a molecular network that holds
tissue cells in place.
Different tissue forms drastically different matrix. E.G. liquid in blood or solid in bone
Function:
May provide support

May help determine cell shape and mobility

May affect cell growth
4.7 Organization in Multicellular Eukaryotes
4 Types of tissues:
Epithelial: Separates free body surfaces from their surroundings. E.G. endothelium linings
Connective Tissue: Extensive matrix. E.G. Bone, blood, lymph, cartilage, tendon, ligaments
Muscle:
Nervous:
4.8 Intercellular Communication
3 types:
Neurotransmitters: nervous system
Local mediators: paracrine system
Hormones: endocrine system
Differences between neurotransmitters and hormones: Neurotransmitters are fast, direct, specific.
Hormones are slow, affect many cells in different ways, affects globally.
4.9 Paracrine system
Local mediators released in interstitial fluid
Acts on neighboring cells a few mm away
4.10 Nervous system
Transmission path: Dendrites -> axon hillock -> axon -> axon terminal
4.11 Action potential
Resting potential:
Negative inside due to Na/K pump.
Pumps out 3 Na and 2 K per cycle.
Always on and in equilibrium of Na/K diffusion
1st: Na voltage gated channels open, Na flows in, polarizing the cell. Potential spikes to positive
2nd: Na channels close, K channels open, K flows out, hyperpolarizating the cell. Potential spikes to
more negative than resting because K channels are slow
All or nothing
Must match threshold potential in order to start potential propogation
4.12 The synapse
Slowest part of neural cellular communication
Two Types: electrical and chemical synapse
Electrical: uncommon. Bidirectional. Fast. E.G. Cardiac muscles, visceral smooth muscle, and very
few neuron in brain
Chemical: unidirectional
Ca++ channels open upon action potential reaching synapse.
Ca++ flows into cell
Neurotransmitter vesicles release content into synaptic cleft
Neurotransmitter diffuse across cleft and attach to receptor proteins
Ions flow into post synaptic neuron, transferring the action potential
Receptor proteins:
Ion channels: action potential directly transferred.
G-protein coupled: neurotransmitter binds, alpha subunit detaches from cytosol side and
perform one of the following:
1. activate separate specific ion chaIu1els;
2. activate a second messenger (i.e. cyclic AMP or cyclic GMP);
3. activate intracellular enzymes;

4. activate gene transcription.

4.13 Support Cells
6 types: microglia; ependymal cells; satellite cells; astrocytes; oligodendrocytes; and
neurolemmocytes or Schwann cells
Schwann cells: cells that wrap around axon to form myelin in the PNS.
Oligodendrocytes: cells that wrap around axon to form myelin in the CNS.
4.14 Structure of Nervous System
Three functions:
1. Sensory (afferent) neurons: (mnemonic: Arrive) Located dorsally (towards the back)
2. Interneurons: Transfer signal from neuron to neuron. 90% of all neurons
3. Motor (efferent) neurons: (mnemonic: Exit) Located ventrally (towards the front)
CNS: Interneurons. Integrate signals between the sensory and motor neurons. Brain and spinal cord
PNS: everything not in CNS. Divided into:
Somatic nervous system:
Voluntary.
Primarily respond to external environment.
Contains sensory and motor neurons.
Motor neurons enervate only skeletal muscles.
Cell bodies of somatic motor neurons located in ventral horn of spinal cord.
Uses acetylcholine and synapse directly on effectors.
Sensory neuron cell bodies are located in dorsal root ganglion
Autonomic nervous system:
Sensory neurons receive signals from viscera (organs inside ventral body cavity).
Motor neurons effects smooth muscle, cardiac muscle, and glands.
Involuntary.
Divided into two systems: Most organs are innervated by both.
Sympathetic: fight or flight
Cell bodies located in spinal cord
Sympathetic post ganglion bodies are located in paravertebral ganglion
Preganglion uses Acetylcholine
Postganglion uses epinepherin or norepinepherine (aka adrenalin or
noradrenalin)
Parasympathetic: rest or digest
Cell bodies located in both spinal cord and brain
Parasympathetic post ganglion bodies are located near their effectors
Preganglion AND postganglion uses Acetylcholine
4.15 The Central Nervous System
Hindbrain:
Pons - relay between cerebrum and cerebellum
Cerebellum coordination, timing, balance
Medulla breathing, heart rate, GI activity
Midbrain:
Joins forebrain with spinal cord
Motivation, motor control, visual/auditory impulses
Forebrain:
Cerebrum (cerebral cortex) thought, conciousness, memory
Olfactory bulb
Hypothalamus water balance, blood pressure, and temp regulation
Thalamus - relay for cerebral cortex / spinal cord
4.16 Sensory Receptors: not important to learn for DAT

4.17 The Eye

Light path: cornea -> lense -> retina
Lense: attached by ciliary muscles. Contraction\relaxation cause the lense to thicken\flatten which
cause the focal point to shorten\lengthen. Age cause elasticity to decrease, causing difficulty to focus on
nearby objects
Retina: Rods = light/dark. Cones = 3 types, red, blue, green.
Iris: Increase/decrease pupil size by sympathetic/parasympathetic nervous system.
4.18 The Ear
Outer ear: auditory canal, timpanic membrane
Middle ear: stapes, malleus, incus
Inner ear: coclea, semicircular canals
4.19 The nose and mouth
4 taste sensations: bitter, sour, salty, sweet
CHAPTER 5 THE ENDOCRINE SYSTEM
5.1 Hormone Chemistry
Exocrine glands: glands that release hormones through ducts
Endocrine glands: glands that release hormones directly to the blood stream
Role of hormones: alter metabolic activities, regulate growth, guide reproduction
Peptide hormones:
Derived from peptides.
Rough ER
Water soluble
Membrane bound receptor
May activate ion channels or activate intracellular second messenger system such as cAMP,
cGMP, calmodulin
Anterior pituitary: ACTH, LH, FSH, prolactin, TSH, hGH
Posterior pituitary: oxytocin, ADH
Parathyroid: PTH
Pancrease: glucagons, insulin
Steroid hormones:
Smooth ER
Lipid soluble
Pass through membrane, bind to cytosol receptor, and act on transcription
Ovaries: estrogen, progesterone
Testies: testosterone
Adrenal cortex: cortisol, aldosterone
Tyrosine derivatives:
Lipid or water soluble
Thyroid: T3 (triiodothyroxine), T4 (thyroxine). Lipid soluble
Adrenal medulla (catecolamines): epinephrine, norepinepherine. Water soluble
5.2 Negative feedback
Control point of the feedback is the conduct of the effector.
In other words, glad lags behind the effector.
In yet other words, hormone responds to the condition.
E.G. High glucose levels cause high insulin levels.
5.4 Anterior Pituitary: Peptide hormones
hGH: (somatotropin) human growth hormone stimulates growth in almost all cells of body

ACTH: adrenocorticotropic hormone stimulates adrenal cortex to release glucocorticoids (e.g.

cortisol)
TSH: thyroid stimulating hormone stimulates thyroid to increase in size and release T3 & T4. T3&T4
negative feedback on TSH
FSH & LH: see reproduction
Prolactin: increase milk production.
5.5 Posterior Pituitary: peptide hormones. Produced in hypothalamus and released here.
Oxytocin: Milk let-down
ADH: (mnemonic: always digging holes in collecting duct). Increase water reabsorbtion, blood
pressure, urine concentration
5.6 Adrenal Cortex: Steroid hormone
Aldosterone: (mineral corticoid) increase ion reabsorption in distal tubule. Na+, Cl- reabsorption, K+ &
H+ secretion.
Eventually leads to increase water retention and higher blood pressure due to net ion increase
in blood.
Cortisol: (glucocorticoid, stress hormone) Increase blood glucose concentration. Stimulate
gluconeogenesis creation of glucose from lactic acid, amino acid, or glycerol. Degrade adipose tissue to
fatty acids.
5.6.b Adrenal Medulla: Catecholamines (tyrosine derivative)
Epinephrine & norepinephrine: Long lasting vasoconstrictors of skin and organs. Vasodialators of
muscles. Stress hormones.
5.7 Thyroid
T3 & T4: 3 vs 4 iodine. Lipid soluble tyrosine derivative. Increase basal metabolic rate.
Calcitonin: peptide hormone. Decrease blood calcium level.
5.8 Pancrease: peptide hormone
Insulin: Produced by beta islet cells. Decrease blood glucose level by increasing cell glucose
permeability and increase cell metabolism.
Glucagon: Produced by alpha islet cells. Stimulate glycogenolysis (glycogen -> glucose) and
gluconeogenesis in the liver. Net effect is to raise blood glucose level.
5.9 Parathyroid
PTH: Increase blood calcium. Increase osteoclast activity, renal Ca++ reabsorption.
5.10 Reproduction
5.11 Male Reproduction
Sperm production:
Occurs in the seminiferous tubules in the testes
Epithelia tissue differentiate into Spermatogonia cells -> spermatocytes -> spermatids ->
spermatozoa
FSH stimulates sertoli cells which surround and nurture spermatocytes
Leydig cells release testosterone when stimulated with LH
Testosterone stimulate maturation into sperm
Androgen: hormone that stimulate masculine characteristics. Testosterone is the primary one
Sperm composition:
3 areas:
Head: Nucleus and Acrosome (tip of the sperm. Contains hyaluronidase, an enzme to dissolve
cell membrane.)
Midpiece: mitochondria dense region that provides energy

Tail:
Semen composition:
Spermatozoa, fluids from seminal vesicles, prostate, bulbourethral glands (aka cowpers gland)
Capacitation: process in which spermatozoa becomes activated for fertilization in the vagina
5.12 Female Reproductive System
All eggs arrested at primary oocyte at birth
Ovulation stages
Follicular:
FSH rise
Several follicles are stimulated, but one ultimately matures
Maturing follicle secretes estradiol (a type of estrogen), which stimulate buildup of
endometrium
Ovulation:
Immediately before ovulation, estradiol peaks, causes luteal surge (rapid rise in LH)
Follicle walls weaken, releases secondary oocyte
Luteal:
FSH and LH cause follicle to transform into corpus luteum
Corpus luteum secretes estrogen and progesterone (which maintains endometrium
wall)
If implantation occurs, hCG is released, maintaining the corpus luteum
If not, corpus luteum degrades, causing menstruation
5.13 Fertilization and Embryology
Takes place in the fallopian tube
Enzyme in acrosome dissolve cell membrane
Cell membrane of sperm and oocyte fuse
Oocyte undergo cortical reaction to prevent additional sperm entering
Oocyte undergo second meitotic stage and release second polar body
Fertilization occurs when genetic materials fuse, forming zygote
When repeated cleavage forms 8 or more cells, it is now called morula
blastocyst forms and implants in the uterus at day 5-7.
Upon implantation hCG is secreted by the egg
Gastrulation occurs and forms gastrula in second week. Forms the following:
Ectoderm: skin, nail, tooth enamel, nervous system, sense organs
Mesoderm: digestive tract, liver, pancrease
Endoderm: muscle, bone
Nurulation occurs and forms nurula in third week.
Notochord (from mesoderm) cause ectoderm to form neural plate -> neural tube -> nervous
system
A placenta is formed and takes over hormone secretion of estrogen and progesterone by the end of
first trimester
Apoptosis: death of cells. E.G. btwn toes and fingers. Absense of apoptosis occurs in cancer.
CHAPTER 6 DIGESTION
6.1 Anatomy
Mouth, esophagus, stomach, small intestine (duodenum, ileum jejunum), large intestine (ascending,
transverse, descending, sigmoid), rectum, and anus.
6.2 Mouth and Esophagus
Digestion begins in mouth with alpha amylase digesting starch into polysaccarides.
Chewing increase surface area of food

Swallowing along with peristaltic action move food into stomach.

6.3 Stomach
Begin protein digestion via pepsin
Stores food for gradual digestion
Low PH kills bacteria and denature protein for digestion
4 cell types:
Mucus cells: produce mucus
Chief (peptic) cells: Pepsinogen
G-Cells: produce gastrin which stimulate parietal cells to produce HCl
Parietal cells: Produce HCl into stomach and bicarbonate into blood.
6.4 Small intestine
90% absorption takes place
Duodenum: most digestion takes place
Ilium & Jejunum: most absorption takes place
Walls of small intestine:
Villi: finger-like projections that increase surface area.
Microvilli: smaller finger-like projections on villi. Fuzzy under light microscope called brush
border. Contain digestive enzymes.
Goblet cells: produce mucus for protection
Nutrient pass into capillary network and lacteal (lymph vessels) inside villi.
6.5 The Pancrease
Bicarbonate ion: Produced by pancrease to increase PH of chyme to 6.
Digestive enzymes: trypson, chymotrypson, pancreatic amylase, lipase, ribonuclease,
deoxyribonuclease
Trypson & chymotrypson: degrade proteins into small polypeptides. Brush border reduce polypeptide
into mono, di & tri peptides
Pancreatic amylase: hydrolyze polysaccharides into di and trisaccarides. Brush border hydrolyze
polysaccarides into monosaccarides
Lipase: Degrades triglycerides into monoglycerides and fatty acids. Crossed brush border.
Bile: Produced by liver and stored in gall bladder. Emulsifies fat. Do NOT digest fat.
6.6 The Large Intestine
Major functions: water resorption & electrolyte absorption.
Symbiotic relationship with bacteria E.G. E-coli produce vitamin.
6.7 GI hormones
Cholecytoskinin: Increase bile release & slows down digestion due to large amount of fat present.
6.9 Carbohydrate Absorption and storage
95% monosaccaride in blood is glucose
Glucose absorbed by secondary active transport down Na gradient.
All carbohydrates absorbed and carried by portal vein to the liver.
Liver converts galactose and fructose into glucose then into glycogen for storage
When glycogen storage is full, liver convert glucose into fat, a long term storage.
6.10 Proteins Absorption and storage
Polypeptide -> mono, di, & tri peptides during digestion
Converted into monpeptide inside enterocyte and absorbed into the blood stream directly
All cells absorb amino acids especially liver.
When AA storage reach their peak, AA can be converted into fat or burned for energy.

Urea: Ammonia is produced as a by-product of gluconeogenesis from amino acids which is converted
into Urea by liver.
6.11 Fats Absorption and storage
Most energy dense nutrient
Triglycerides digested into monoglycerides and fatty acids. Shuttled via bile micelles into enterocyte.
Smooth ER converts back into triglycerides
Golgi package triglycerides along with other proteins into globules called chylomicrons
Exocytosis occurs and transport them into lacteals which empties into the large veins at the neck.
Majority absorbed by liver, and some by adiposites.
6.12 Liver
Hepatic portal vein receives blood directly from intestines, spleen, stomach, and pancrease and
processed.
Hepatic artery supplies second blood supply
Hepatic vein collects all processed blood and pass into vena cava
Functions:
Blood storage
Blood filtration: Phagocytize bacteria
Carbohydrate metabolism: gluconeogenesis (synthesize glucose and glycogen from non
glucose source)
Fat metabolism: Bile production. Convert carb and protein into fat. Oxidize fatty acid for energy
Protein metabolism: Convert AA into fat, produces ammonia->urea. Synthesize plasma
proteins.
Detoxification:
Erythrocyte destruction: Minor role compared to spleen
Vitamin storage:
When metabolizing fat or protein for energy, keytone bodies increase, decreasing blood PH.
6.13 Kidney
Functions:
Excrete waste such as urea, ammonia, uric acid, phosphate
Maintain homeostasis of body fluid volume and solute composistion
Help control PH
Functional unit: nephron
Nephron path: Renal corpuscle, proximal tubule, descending loop of henle, ascending loop of henle,
distal tubule, collecting duct, collecting tubule.
Renal corpuscle:
composed of capillary bed (glomerulus) and bowmans capsule (surrounding capsule).
Hydrostatic pressure forces small ions, water, molecules, proteins from glomerulus into
bowmans capsule
Proximal tubule:
Majority of resorption takes place. Active resorption of proteins and glucose.
Drugs and other toxins secreted into tubule.
Change solute composition but does not change osmolarity
Loop of Henle
Descending: Permeable to water. Water flows out, concentrating urine
Ascending: Permeable to ions. Ions actively flow out, diluting urine
Distal tubule:
Reabsorbs Na & Ca. Secrete K, H, HCO3
Aldosterone increase Na & K transport proteins. Net effect is to decrease filtrate osmolarity.
Collecting duct:
ADH increase water reabsorption, concentrating urine.
Juxtaglomuerular apparatus:

Sense filtrate pressure in distal tubule.

CHAPTER 7 CARDIOVASCULAR SYSTEM & RESPIRATORY SYSTEM
7.1 cardiovascular anatomy
Path: L Atrium, L ventricle, aorta, arteries, arterioles, capillaries, venuoles, veins, superior and inferior
vena cava, R atrium, R ventricle, Pulmonary artery, Pulmonary vein
Heart electrical path:
SA node -> atriums -> AV node -> Bundle of his -> purkinje fibers -> ventricles
SA node: Autorythmic. located in R atrium. Vagus nerve innervates SA node, SLOWING it
down
AV node: Located in the walls between the aortas. Slower, creates a timed delay.
Bundle of his: bundle of fibers located between the ventricles
Purkinje fibers: fibers branching out of the bundle of his. Propogates action potential more
simultaneously to all cells of the ventricle, allows for more unified and stronger contraction.
Arteries: elastic. Wrapped in smooth muscle that is typically enervated by sympathetic nervous
system. Large, so vasodialation do not affect much.
Arterioles: Very small, so vasodialation may be used to reroute blood.
Capillaries: microscopic. Single RBC pass through. One cell thick walls. Nutrient exchange occurs
here only.
Arteriole side: hydrostatic pressure dominate, fluid flows out
Venule side: osmotic pressure dominate, fluid flows in
Net: 10% fluid loss into interstitium
7.2 Respiratory System
Path: Nose, Pharynx, Larynx, Trachea, Bronchi, Bronchiole, Alveoli
Larynx: voice box
Epiglottis: cartilaginous member that prevent food from entering the trachea when swallowing
Trachea: lies in front of the esophagus
7.3 Chemistry of Gas Exchange
98% O2 binds to hemoglobin.
Hemoglobin is composed of 4 subunits with one heme cofactor and one iron in the middle. Exhibit
cooperativity when binding AND releasing O2.
Oxygen dissociation curve: %O2 saturation vs O2 tension (mm Hg). Inc [H+], temp, PCO2 -> shift
right (decrease O2 affinity)
CO2: By far carried in blood as bicarbonate. Other: physical solution, carbamino (combined with
hemoglobin and other proteins)
Carbonic anhydrase: enzyme to convert CO2 to bicarbonate ion
Breathing and PH in blood: Low PH cause increase breathing in order to expel bicarbonate which
increase PH
7.4 Lymphatic System
Returns excess interstitial fluid to the blood for most all tissue, except for the nervous system
Monitor blood for infection
Open system
One way valves
7.5 The Blood
Type of tissue: Connective. Composed of cells and matrix (plasma)
Centrifuged blood separates into:
Plasma: water, albumin (transport fatty acids, regulate osmotic pressure), immunoglobulins,
clotting factors,
Buffy coat: white blood cells (leukocytes).

Red blood cells (erythrocytes): transport O2 and CO2. Live 120 days.
Serum: plasma with fibrinogen removed
Platelets: membrane bound cytoplasm split from magakaryocytes. Stick to injured endothelium then
swell and activate other platelets
Clotting: Platelets aggregate, making a loose plug. Prothrombin convert to thrombin. Thrombin
convert fibrinogen to fibrin attaches to platelet to form tight plug.
7.6 Immune system
Two types:
Innate: skin, stomach acid, phagocytic cells, chemicals in blood
Acquired: Two types:
Humoral (B-cell immunity):
Macrophage present antigen to B lymphocytes.
If recognized, T-helper cell helps B lymphocytes to differentiate into memory (to
retain memory) and plasma cells (to produce immunoglobulin).
Effective with bacterial, fungi, protozoans, virus, blood toxins.
Cell-mediated (T-cell immunity):
T-lymphocytes mature in thymus and have antibody-like protein on surface.
Produce no free antibodies.
Effective against infected cells
Steps of bacterial infection:
Inflammation
Macrophages then neutrophils engulf bacteria
Interstitial fluid flushed into lymph where macrophage present antigen to B lymphocytes.
T-helper cells assist activated B lymphocyte differentiate into plasma and memory cells
Plasma cell produce antibody
Single antibody is specific against single antigen
Single B lymphocyte produce single antibody type
7.7 Blood types
Easy
CHAPTER 8 MUSCLE, BONE, AND SKIN
8.1 Muscle
Types: skeletal, smooth, cardiac
8.2 Skeletal Muscle
Voluntary, connected by tendon to bone
Work in groups. Agonist contract while antagonist lengthen
Synergistic muscles assist by stabilizing the joint
Squeeze blood and lymph while contracting to aid in circulation
Shivering from muscles is used as one mechanism to warm the body
8.3 Physiology of Skeletal Muscle Contraction
What part of the sarcomere change length during contractions? H zone and I band
All or none contraction.
Composition:
Sarcomere: functional unit of skeletal muscles with many strands of myosin and actin
Myofibril: sarcomeres positioned end to end
Sarcoplastic reticulum: surrounds myofibril. Contains Ca++ ions
Sarcolemma: membrane that wraps several myofibrils together to form a muscle
Multinucleated
Contraction:

Ca++ released from SR.

Troponin pulls tropomyosin back, exposing binding site on actin
Myosin binds to actin
ADP release, myosin head moves, contracting muscle
ATP binds to myosin, releasing grip on actin
Troponin moves back to cover binding site
ATP -> ADP. Myosin head cocked and ready to go
Action potential that leads to contraction:
Acetylcholine released into the neuromuscular synapse
Ion channels open, propagating action potential along the transverse tubule that carries the
action potential deep within the tissue and allows for even contraction
Action potential propagates into SR, releasing Ca++ ions
8.4 A Motor Unit
Unit of muscle fibers innervated by one nerve. Can be 2 to 2000 fibers in one motor unit.
Force of contraction for a muscle group depends on number and size of motor unit recruited
8.5 Skeletal Muscle Type
Myoglobin: stores O2 in muscles. Only 1 subunit instead of 4 like hemoglobin
Type I slow oxidative: Red from large amount of myoglobin, lots of mitochondria, slow to fatigue, low
contractile force
Posterior muscles
Type IIa fast oxidative: Red, fast contraction, intermediate resistance to fatigue
Upper legs
Type IIa fast glycolytic: White (low myoglobin), fast contraction, quick to fatigue, large amount of
glycogen
Upper arms
Note: most muscles are mixture of above 3 types
8.6 Cardiac Muscle
Striated: composed of sarcomeres
Mononucleated
Intercalated disks between muscle cells
Large amount of mitochondria
Slow voltage gated Ca++ channels create a positive potential plateau after depolarization to lengthen
contraction
8.7 Smooth Muscle
Involuntary
Innervated by autonomic nervous system
Not organized into sarcomeres
Intermediate filaments connects on dense bodies forming a web on each cell that enables the cell to
contract length wise
8.8 Bone
Function: Support, protection, mineral storage, blood cell production, energy storage
Cells that make up the bone:
Osteoblasts: secrete collagen and other compounds to make bone. Once trapped within bone,
it becomes osteocytes
Osteocytes: exchange nutrients and waste material with blood
Osteoclasts: resorb bone matrix
Long bone composition:
Spongy bone at ends of the bone. Contains red bone marrow for RBC production
Hollow compact bone in the middle. Contains yellow bone marrow for fat storage

8.9 Bone Function in Mineral Homeostasis

Ca++ stored as hydroxyapatite
Hydroxyapatite crystals lie alongside collagen fibers to give bone high compression strength
Stores and releases Ca++ and HPO4 -8.11 Cartilage
Flexible resilient connective tissure
Composed primarily of collagen
8.12 Joints
Fibrous joint: close and tightly held together with little or no movement. E.G skull
Cartilaginous joint: allows for little movement. E.G. Ribs, sternum
Synovial joint: joint with synovial fluid in between. Allows for wide range of movement
8.13 Skin
Functions of skin:
Thermoregulation: Heat dissipation
Protection: physical barrier to the outside world
Environmental sensory input: Pressure, pain, touch
Excretion: water and salt loss
Immunity: Specialized cell of epidermis are components of the immune system
Blood reservoir:
Vitamin D synthesis: Requires UV light to synthesize precursor.
Composition:
Epidermis: avascular (no blood vessels) tissue.
Keratinocytes: produce keratin for water proofing
Melanocytes: skin pigment
Langerhans cells: interact with helper T-cells
Merkel cells: one component of touch sensation
Dermis: derived From mesodermal cells
Embedded with blood vessels, nerves, glands, and hair follicles
CHAPTER 9 POPULATIONS
9.1 Mendelian Concepts
Fn designation: nth filial generation. E.G. F1 is the generation after the first crossing
Phenotype: expression of a trait
Genotype: genetic makeup in a particular locus. E.G. blood type 6 genotypes: AA, AO, BO, OO, BB
AB
Complete dominance: dominant allele override recessive allele completely
Locus: a region on a chromosome that codes for a particular gene
Allele: alternative DNA sequence at a locus which may or may not result in different phenotypic trait.
E.G. blood type has 3 alleles.
Mendels 1st law: law of segregation: alleles segregate independently from each other when forming
gametes
Mendels 2nd law: law of independent assortment: genes on different chromosomes assort
independently from each other
Dihibrid cross: crossing of two heterozygous genes for the phenotypic ratio of 9(both dominant):3(one
recessive):3(other recessive):1(both recessive). If found, then the two genes obey Mendels laws: 1 & 2.
How to perform two genotype cross: Write out 4x4 punnet square. For each side, write out possible
gamete genotype (1 allele from each gene 4 possible combinations). Perform cross.
Karyotype: map of chromosomes. 46 total chromosomes or 23 homologous chromosomes

Sex-linked trait: Carried on the X chromosome; therefore, expressed in males whether or not it is
dominant. Therefore, a carrier female crossed with normal male will produce 50% expressed males. On
females, normal dominance occur because of two X chromosomes.
9.2 Evolution
Gene pool: total of all alleles in a population. E.G. 70% B & 30% b
King Philip came over for good soup
Species: subset of all organisms that can produce fertile offspring
Niche: the way in which a species exploit the environment
Survival of the fittest: the most successful will mate the most time, therefore, be more successful at
propagating its genes
R-selection: many offspring, little or no care. Exponential growth. Do well in density independent
factors. E.G. flood, temp fluctuation, etc.
K-selection: few offspring, high energy spent on offspring. Sigmoidal curve that peaks at carrying
capacity. Do well in density dependent factors
Speciation: process which new specie is formed
Adaptive radiation: several species arise from single ancestral species
Divergent evolution: process in which a common structure diverges into different forms. E.G. leg of
human and flippers of whales
Convergent evolution: different species evolve similar structures. E.G. wings of bat and bird
Polymorphism: Phenotypes in which distinct forms are present as opposed to continual change. E.G.
white and red flower color vs height.
9.3 Symbiosis
Mutualism: Both organisms benefit.
Commensalism: One organism benefit while the other is neither harmed nor benefit.
Parasitism: One organism benefit while the other is harmed
9.4 Hardy-Weinberg Equilibrium
Hardy-Weinberg equilibrium: no change in alliel frequency if the following 5 conditions hold
1. large population
2. mutational equilibrium
3. immigration or emigration must not change gene pool
4. random mating
5. no selection of the fittest
Genetic drift: Occurs in small population where death of one subset of population having bias against
one alliel causes disturbance of the gene pool. Random event.
Binomial theorem: p^2 + 2pq + q^2 = 1 & p+q=1 Frequencies of alliels sums to one.
9.5 Origin of Life
Urley-Miller experiment: autosynthesis of basic molecules from primordial soup of methane,
ammonia, sulfur, etc..
First photosynthetic organism is probably photosynthetic bacteria. Ancestors of cyanobacteria.
9.6 Chordate Features
Chordata not equal to backbone
Bilateral symmetry
They are deuterostomes (anus develops from or near blastopore)
During development, they posses a notochord (embryonic axial support, derived from mesoderm not
back bone), pharyngeal slits, a dorsal hollow nerve cord, and a tail
Most chordates are vertebrata (notochord replaced with bone structure with distinct brain structure
enclosed in a skull)