Download Kaplan Blue Book DAT Biology Notes by bangity

KAPLAN BLUE BOOK
Bangity 2012
I. Origin of Life
- Stanley L. Miller (in 1953) set up apparatus in which 4 gases (CH4, H2, NH3, H2O) continuously circulated past electrical
discharges from tungsten electrodes => formation of organic compounds (1 week): urea, hydrogen cyanide, acetic acid, and
lactic acid.
- Coacervate droplets: a cluster of colloidal molecules surrounded by a shell of water; they tend of absorb and incorporate
substances from the surrounding environment. They were not living but possessed some living properties.
- Autotrophic anaerobes: chemosynthetic bacteria.
- Autotrophic aerobes: green plants, phytoplankton.
- Heterotrophic anaerobes: yeast.
- Heterotrophic aerobes: amoebas, earthworms, and humans.
- Compound Light Microscope: uses lens systems to magnify an object.
(Total magnification = magnification of eyepiece x magnification of objective)
- Diaphragm: controls the amount of light passing through the specimen.
- Used to observe non-living specimen due to staining (cell death).
- Phase Contrast Microscope: study living cells (differences in refractive index => produce contrast between cell structures)
- Electron Microscopy: tissues must be fixed and sections and stained with heavy metals (cell death).
- Cell Membrane: permeable to both small, nonpolar molecules, such as O2, and small polar molecules such as H2O.
- Nucleolus: a dense structure within the nucleus where rRNA synthesis occurs.
- Golgi apparatus: receives vesicles and their contents from smooth ER, modifies them (glycosylation), repackages them
into vesicles, and distributes them to the cell surface by exocytosis.
- Cyclosis: streaming movement within the cell; transport within the cytoplasm.
- Centrioles: microtubules; spindle organizing center during cell division; animal cells usually have a pair of centrioles that
are oriented at right angles to each other and lie in a region called the centrosome. Plant cells do not contain centrioles.
- Centromere: a region on a chromosome that joins two sister chromatids.
- Lysosome: contains hydrolytic enzymes involved in intracellular digestion; an injured/dying cell may "commit suicide" by
rupturing the lysosome membrane and releasing its hydrolytic enzyme => autolysis.
- Cytoskeleton: composed of microtubules and microfilaments, gives cell mechanical support, maintains its shape, and
functions in cell motility.
* Types of Transport:
- Passive diffusion: down gradient, no carrier, no energy required.
- Facilitated diffusion: down gradient, carrier, no energy required.
- Active transport: against gradient, carrier, energy required.
- Brownian Movement: the movement of particles due to kinetic energy spreads small, suspended particles throughout the
cytoplasm of the cell.
- Plasmolysis: shriveled (hypertonic solution)
- Lyse: burst (hypotonic solution).
* Enzymes:
- Lower activation energy of a reaction.
- Do not affect the overall ∆G of the reaction.
- Increase the rate of the reaction.
- Are not changed/consumed after reaction.
- Enzyme's reaction rate depends on temperature, pH, [enzyme], [substrate].
- Pancreatic enzymes work optimally in alkaline solution condition of small intestine (pH=8.5).
- Prosthetic group: cofactors that bind to the enzyme by strong covalent bonds (most coenzymes cannot be synthesized by
the body and are obtained from diet).
- Induced Fit Theory: substrate comes in contact with active site, the conformation of active site changes to fit substrate.
Lock and Key Theory no longer work where enzyme's active site is exactly complementary to substrate.
* Glucose Catabolism:
1. Glycolysis: requires input of 2ATP (occurs in cytoplasm)
NET: 2ATP, 2NADH, 2 pyruvate.
- Anaerobic condition: pyruvate undergoes fermentation (regenerate NAD+ from NADH for glycolysis to repeat).
Mg2+ (cofactor)
produces 2ATP/glucose in the absence of O2 (fermentation produces no ATP).
- Alcohol fermentation: pyruvate -> acetaldehyde (CO2 + 1 acetaldehyde per pyruvate). Energy in NADH is used to
convert acetaldehyde into ethanol to regenerate NAD+ for glycolysis to re-proceed for next glucose.
- Lactic acid fermentation: lactic acid (human muscles). Most lactate is transported to the liver where it is converted
back to glycose when surplus ATP is available.
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2. Cellular Respiration (mitochondrion): aerobic process; three stages
a. Pyruvate decarboxylation: pyruvate => acetyl CoA
NET: 2NADH, 2CO2
b. Citric acid cycle: accept acetyl CoA, and there are 2 acetyl CoA per glucose.
NET: 6NADH (2 x 3NADH), 2FADH2 (2 x FADH2), 2GTP (2 x 1GTP), 4CO2
c. Electron transport chain: uses cytochromes (electron carriers resemble hemoglobin in structure of their active site).
- 8NADH and 2FADH2 will undergoes oxidative phosphorylation. They pass their high-energy e- to an electron
transport chain in the inner mitochondrial membrane. NADH (3ATP) and FADH2 (2ATP).
- Uses energy of e- to pump H+ into the mitochondrion inter-membrane space to create H+ gradient. The gradient is
used to pump ATP synthase to produce ATP from ADP + Pi.
- Final e- acceptor of the transport chain is O2. The 1/2O2 accepts 2e- with 2H+ to produce water.
- Inner membrane: has cristae where oxidative phosphorylation occurs.
- Matrix: citric acid cycle and conversion of pyruvate to acetyl CoA. NADH and FADH2 get their e- removed and H+
pumped out into inter-membrane space.
* Chemiosmosis in Mitochondria: mechanism of ATP generation that occurs when energy is stored in the form of [H+]
gradient across a membrane.
* Fat Catabolism: requires 2ATP to activates in the cytoplasm (fatty acid); once activated, taken into mitochondrion.
* Proteins: when not enough carbohydrate and fat; amino acids undergo transamination reaction (lose an amino group to
form an alpha-keto acid) and remaining proceed through citric acid cycle.
- Oxidative deamination: removes an NH3 from amino acid; NH3 is a toxic substance in vertebrates.
----------------------------------------------------------------------------------------------------------------------------------------------------II. Reproduction:
* Mitosis:
- Chromosome: can be a single chromosome or a pair of sister chromatids joined at centromere (each case is considered one
chromosomes). At anaphase and telophase, when being pulled out, there is 4 separate chromosomes.
1. Interphase: longest, chromosome replication with centromere in middle, not condensed (chromatin).
2. Prophase: chromosome condense; centriole (animal only) separates and starting to move to poles, nuclear membrane
dissolve, spindle apparatus forms.
3. Metaphase: metaphase plate, centriole pairs at opposite poles, spindles align chromosomes at center.
4. Anaphase: centromere splits, pulling chromosome to each pole.
5. Telophase: spindle apparatus disappears, formation of new nuclear membrane, chromosomes uncoil (2N as parent).
6. Cytokinesis: cytoplasm divides into two daughter cells (cleavage furrow in animal cells = indentation of cell membrane).
7. Plant cells: lacks centrioles; cannot form cleavage furrow (cell plate, expanding partition that grows outward from the
interior of cell until it reaches the plasma membrane).
- Centromere: links sister chromatids.
- Kinetochore: spindle fibers attach to chromosomes (chromatids).
* Meiosis:
1. Interphase: chromosomes duplication resulting in 2N number of
sister chromatids (46 chromosomes - 2 chromatids each). It
originally has 23 pair of chromosomes (46 chromatids).
2. 1st Meiotic Division: separates homologous chromosomes,
producing two haploid cells (N chromosomes, 23 in humans), so
meiosis I is referred to as a reductional division. A regular diploid
human cell contains 46 chromosomes and is considered 2N
because it contains 23 pairs of homologous chromosomes.
However, after meiosis I, although the cell contains 46 chromatids, it is only considered as being N, with 23 chromosomes
(2 chromatids/chromosome)
a. Prophase I: DNA is exchanged between homologous chromosomes in a process called homologous recombination. This
often results in chromosomal crossover. The paired and replicated chromosomes are called bivalents or tetrads, which have
two chromosomes and four chromatids, with one chromosome coming from each parent. The process of pairing the
homologous chromosomes is called synapsis. At this stage, non-sister chromatids may cross-over at points called chiasmata.
b. Metaphase I: tetrads align at equatorial plane, attaches to spindle by kinetochore.
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c. Anaphase I: homologous pair separates and pulled to opposite poles (disjunction); 2 chromosomes with 2 sister
chromatids each (4 chromatids with two middle crossed over); pulling one chromosome (2 chromatids) to each pole.
d. Telophase I: two chromosomes, each with two sister chromatids joined at centromere.
Diploid (1 chromosomes-2 sister chromatids each) => duplication (2 chromosomes - 2 sister chromatids each)
=> meiosis I (1 chromosomes - 2 sister chromatids each) = 2 cells
=> meiosis II (1 chromosomes - 1 sister chromatid each) = 4 cells
-------------------------------------------------------------------------------------------------------------------------------------Diploid (23 chromosomes-2 sister chromatids each) => duplication (46 chromosomes - 2 sister chromatids each)
=> meiosis I (23 chromosomes - 2 sister chromatids each) = 2 cells
=> meiosis II (23 chromosomes - 1 sister chromatid each) = 4 cells
3. 2nd Meiotic Division: no duplication, just like mitosis.
* Human Reproduction:
- Estrogen: 2nd sexual characteristics and sex drive; thickening endometrium, secreted by ovarian follicles and corpus
luteum (after follicle ovulated secondary oocyte).
- Progesterone: secreted by corpus luteum during the luteal phase of the menstrual cycle, development and maintenance of
the endomertial walls for implantation.
* Menstrual Cycle:
a. Follicular phase: FSH from anterior pituitary promotes the development of follicle which then secrete estrogen
b. Ovulation: day 14 (ovarian follicle bursts and releases 2nd oocyte) caused by a surge in LH due to peak in estrogen.
c. Luteal: LH induces the rupture of follicle to develop into corpus luteum, which secretes estrogen and progesterone
(causes glands of endometrium to mature and produce secretions that prepare for implantation).
d. Menstruation: if not fertilized, corpus luteum atrophies becoming corpus albicans (scar) resulting in drop of estrogen
and progesterone causes the endometrium to slough off (days 1-5).
* Asexual Reproductive Mechanism:
- Fission: seen in prokaryotic organisms (new plasma membrane grows in between, invagination, and complete separation.
- Budding: replication of the nucleus followed by unequal cytokinesis (hydra and yeast).
- Regeneration: can regenerate new limbs or even an entire body as long as it contains central disk.
- Parthenogenesis: development of an unfertilized egg into an adult organism.
* Sexual Reproduction in Plants: (gametophyte = sexually, sporophyte, asexually)
- Life cycle of plants are characterized by an alternation of the diploid sporophyte and haploid gametophyte generations.
- Haploid gametophyte generation produces gametes by mitosis, union of male and female gametes at fertilization restores
the diploid sporophyte generation.
----------------------------------------------------------------------------------------------------------------------------------------------------III. Genetics
* Mendelian Genetics:
- Allele: when a gene exists in more than one form, this is the alternative forms (Yy, YY, yy).
- Test cross: A_ + aa (with recessive to determine the unknown)
- Incomplete dominance: color blending (red + white = pink)
- Codominance: multiple alleles exist for a given gene and more than one of them is dominant. IAi = A, IBi = B, IAIB = AB,
IAi = A, IBi = B, ii = O.
- Autosomes: the 22 pairs of homologous chromosomes in human, the remaining pair (XX or XY) is called sex
chromosomes. Gender is determined by male gamete (50% chance female and 50% chance male).
- Sex linked: genes that are located on the X or Y chromosome, most sex-linked genes are located on the X chromosomes in
humans.
- Sex-linked recessive: most in male offspring, recessive genes that are carried on X will produce recessive phenotype
whenever they occur in male because the other is Y and cannot mask it.
- Affected males will pass the gene to all daughters but unless the mother also passes that genes, the daughter is a
phenotypically normal carrier of the trait and will not be expressed.
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Environmental factors can often affect expression of a gene (Drosophila have crooked wings at low temp but
straight wings at higher temp).
- Nondisjunction: three copies of chromosome (trisomy = n + 1), single copy (monosomy = n - 1), Down syndrome is a
trisomy of chromosome 21. Nondisjunction can occur at meiosis I or meiosis II. Somatic cells are 2N +1 or 2N - 1.
- Mutagenic Agents: cosmic rays, X-rays, UV, radioactivity, or chemical compounds such as colchicine (inhibits spindle
formation, causing polyploidy) or mustard gas. They are generally carcinogenic.
In gene mutation, nitrogen bases are added, deleted, or substituted. Phenylketonuria (PKU) is the inability to
produce proper enzyme for metabolism of phenylalanine.
* Molecular Genetics:
- Transcription: mRNA is complementary to the template strand with T replaced by U or the same as the complementary
strain with T replaced by U.
- Codon: a series of triplets translated from mRNA (which is monicistronic that one mRNA codes for one polypeptide). An
anticodon of tRNA which matches with the codon of mRNA, it carries one amino acid into the P site of the ribosomes
(methionine-tRNA).
- Translation:
1. tRNA brings aa to ribosomes; it recognizes both aa and mRNA codon. Each aa has its own aminoacyl-tRNA.
2. One large and one small subunits only bind together during protein synthesis. It has 3 binding sites: one for
mRNA and two for tRNA (P and A sites).
3. Polypeptide synthesis: 3 stages.
a. Initiation: ribosome binds at 5' end, scan for start codon (AUG), methionine-tRNA (3'-UAC-5') comes.
b. Elongation: H-bond forms between mRNA codon and tRNA complex, peptide bond formation.
c. Translocation: ribosome advances 3 nucleotide along mRNA in 5' to 3' for next, tRNA at P site is expelled and
tRNA from A site is moved to P site and cycle repeats.
d. Termination: when ribosome reads mRNA termination codons (UAA, UAG, or UGA).
- Polyribosomes: when multiple ribosomes translate one mRNA strain.
* Bacterial Genetics:
1. Bacterial genome: consists of single circular chromosome located in nucleoid region; also contain plasmid (contain
accessory genes); episomes are plasmids that are capable of integration into the bacterial genome.
2. Genetic variance: binary fission is an asexual process, bacteria have 3 mechanism for genetic variations.
a. Transformation: a foreign chromosome (plasmid) is incorporated into bacterial chromosome by recombination.
b. Conjugation: sexual mating in bacteria, a conjugation bridge is formed between 2 bacteria and genetic material is
transferred from donor male (+) to recipient female (-).
- Only bacteria containing plasmids called sex-factor are capable of conjugating (also called F factor in E. coli)
- F+ cell make F- cell becomes F+. The plasmids may contain antibody resistance and such.
High frequency of recombination (Hfr): sex-factor get integrated into bacterial genome, entire genome duplicates
and transfer but conjugation bridge breaks before process is completed and it recombines with recipient genome.
c. Transduction: fragments of chromosome accidentally become packaged into viral progeny produced during a viral
infection; the closer two genes on chromosome => more like to be transduced together.
d. Recombination: linked genes are separated by breakage and rearrangements of adjacent regions of DNA when
organisms carrying different alleles for the same traits are crossed.
(produce repressor) (RNA pol) (repressor)
*Gene regulation: transcription is the regulation of gene expression. || regulator || promoter || operator || structural ||
- Operon: consists of structural, promoter, and operator genes.
- Operator gene: nontranscribable DNA, repressor binding site.
- Promoter: noncoding sequence of DNA that serves as initial binding site for RNA polymerase.
- Regulator: codes for synthesis of repressor that binds to operator and blocks RNA polymerase.
A. Inducible system: repressor binds to operator, formation of barrier that block RNA polymerase. An inducer must
bind repressor so that inducer-repressor complex cannot bind to operator => enable transcription.
B. Repressible system: repressor is inactive until corepressor-repressor complex which can then bind operator.
- Constitutive: operons containing mutation => defective repressor (cannot turn off) => always synthesize.
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* Bacteriophage: a virus that infects its host bacterium by attaching, make hole, and inject its DNA while protein coat
remain attached to cell wall.
1. Lytic cycle: phage DNA takes control and produce lots of viral progeny, burst the cell and release virions.
2. Lysogenic cycle: does not lyse its host, may become dormant in form on prophage which can re-emerge and enter lytic
cycle due to factors; bacteria containing prophage are prevented by further infection by same virus.
- Southern blots: detection of specific DNA in specific DNA sample. DNA is cleaved by restriction endonucleases into
restriction fragments at specific restriction sites; fragments are separated by gel electrophoresis; wash with radioactive
probe.
- Polymerase chain reaction (PCR): amplification of genes (denaturation, primer annealing, and primer extension).
----------------------------------------------------------------------------------------------------------------------------------------------------IV. Vertebrate Embryology
1. Fertilization: an egg can be fertilized within 12-24 hours following ovulation, fraternal twins may be conceived if more
than one egg is fertilized.
2. Cleavage: an increase in cell number without growth in cell protoplasm (total volume of cytoplasm remains constant).
Indeterminate cleavage is one that results in cells that maintain the ability to develop into complete organism (identical
twins). Determinate cleavage results in cells whose pathway are determined at an early developmental stage
(differentiation).
- Blastulation: begins when morula (solid ball of embryonic cells=16 cells) develops a fluid-filled cavity called
blastocoel and by 4th day, becomes hollow sphere of cells called blastula.
3. Gastrulation: once implanted in uterus, single-celled layer of blastula transform into 3-layered gastrula.
- Ectoderm: integument (including epidermis) and nervous system.
- Mesoderm: muscle system, circulatory system, excretory system, gonads, connective tissue such as bone; organs.
- Endoderm: epithelial lining.
4. Development: three types.
a. External development: such as birds, reptiles, fish, and amphibians.
- Eggs contain the following embryonic membranes.
1. Chorion: lines inside of shells (moist membrane for gas exchange).
2. Allantois: saclike structure involved in respiration and excretion and blood vessels to transport O2, CO2,
H2O, salt, and wastes.
3. Amnion: encloses the amniotic fluid, protect embryo from shock.
4. Yolk sac: encloses the yolk, has blood vessels that transfer food from yolk to embryo.
b. Nonplacental internal development: marsupials, develop in mother without a placenta.
c. Placental internal development: human (with placenta and umbilical cord) Both structures arise from the 4
structures above.
- Placenta: where gas exchange, nutrient uptake, waste elimination occur in fetus, connect fetus to uterine wall.
- Umbilical cord: connecting cord from fetus to the placenta, umbilical vein contain nutrient-rich blood from
placenta to fetus and arteries transport back deoxygenated blood.
1. Chorion: where placenta formation begins, it surround the amnion.
2. Allantois: out-pocket of gut, blood vessel enlarge and become umbilical vessels.
3. Yolk sac: site of early development of blood vessels, associated with umbilical vessels.
5. Birth and Maturation: labor, a series of strong uterine contraction (3 stages).
a. Cervix thins and dilates, amniotic sac ruptures, releasing its fluids.
b. Rapid contractions, resulting in birth of baby, cutting of umbilical cord.
c. Uterus contracts, expelling placenta and umbilical cord.
----------------------------------------------------------------------------------------------------------------------------------------------------V. Vascular Systems in Animals
A. Protozoans: gases and nutrients is exchanged through simple diffusion.
B. Cnidarians: body walls that are two cells thick (touch internal & external environment), no need for circulatory system.
C. Arthropods: open circulatory system, blood is in contact with body tissues, circulated by body movements, flows
through a dorsal vessel (near back, upper surface) and into spaces (sinuses) where exchange occurs.
D. Annelids: earthworm uses closed circulatory system to deliver materials to cells that are not in contact with external
environment, blood is confined to blood vessels and move toward head in dorsal vessel (function as main heart by
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contractions). Five pairs of vessels called aortic loops connect dorsal vessel to the ventral vessel (near abdomen, bottom
surface) and function as additional pumps; lack blood cells but have hemoglobin-like pigment.
E. Humans: exchange of gases, nutrients, and cellular waste products occurs via diffusion across capillary walls.
Capillaries have thin walls (one layer of endothelial cells) for exchange by diffusion (smallest diameter).
a. Lymph vessels: transport excess interstitial fluid (lymph), to the cardiovascular system, thereby keeping fluid levels in
body constant. Lymph nodes are swelling along lymph vessels containing phagocytic cells (leukocytes) that filter lymph.
b. Blood: plasma is the liquid portion (55%), aq mixture of nutrients, salts, gases, wastes, hormones, and blood protein
(IgG, albumin, fibrinogen). Cellular components of blood are erythrocytes, leukocytes, and platelets.
1. Erythrocytes: red blood cells, each contains 250 mil molecules of hemoglobin (4 Fe2+ each); formed from stem
cells in bone marrow, where they lose nuclei, mitochondria, and membranous organelles (120 days => spleen).
2. Leukocytes: larger, protective functions, macrophages (phagocytic - stationary cells). Lymphocytes are involved
in immune response and the production of antibodies (B cells) or cytolysis of infected cells (T cells).
3. Platelets: cell fragments that lack nuclei and involved in clot formation.
c. Clotting:
- Platelets come in contact with exposed collagen of damaged vessel, release chemical => more platelets come to
form platelet plug; both platelets and damaged tissues release thromboplastin + cofactor (Ca2+ + K) activates
prothrombin into thrombin which converts fibrinogen to fibrin (coat damaged are and trap blood cells to form clot).
- Serum is the fluid left after blood clotting.
d. Immunological reactions: two defense mechanisms: lymphocytes responsible for both.
1. Humoral immunity: production of antibodies (IgG), recognize and bind to specific antigens and trigger immune
system to remove them; cause others to come (phagocytic leukocytes) or agglutinate (form large, insoluble complexes of
antigen) => remove easier by phagocytes.
a. Active immunity: production of antibodies due to an immune response, vaccination (weaken antigens),
require weeks to build up.
b. Passive immunity: transfer of antibodies, short-lived and last only as long as they circulates in blood.
c. Gamma globulin: fraction blood contain variety of IgG, used to confer temp protection against hepatitis.
2. Cell-mediated immunity: involves cells combat fungal and viral infections.
3. Nonspecific Defense Mechanism:
a. Skin: sweat attacks bacterial cell walls.
b. Inflammatory response: injured cell release histamine (vassal dilation, more blood flow). Granulocytes
attracted to injured site and phagocytize antigenic material; often accompanied by fever.
c. Interferons: proteins; produced by cells under viral attack; diffuse to other cells, help prevent spread (1st die).
4. ABO Blood Types:
a. Type A has A antigen (anti-B antibodies)
c. Type AB has A & B antigen (no antibodies)
b. Type B has B antigen (anti-A antibodies)
d. Type O has no antigen (anti-A, anti-B antibodies)
- Rh factor: another antigen, Rh+ (has antigen) and Rh- (no antigen). If Rh- mother born Rh+ babies, she will
produce anti-Rh antibodies. At 2nd pregnancy, when meet Rh+ child, it will destroy child red blood cells.
----------------------------------------------------------------------------------------------------------------------------------------------------VI. Endocrinology: ("=>" = stimulates)
- Endocrine glands: synthesize and secrete hormones into circulatory system.
- Exocrine glands: such as gall bladder, secrete substances transported by ducts.
A. Adrenal glands: on top of kidney.
1. Adrenal cortex: if stress, ACTH (anterior pituitary) => corticosteroids.
a. Glucocorticoid: cortisol and cortisone (glucose regulation + protein metabolism); raise blood glucose level by
protein breakdown + gluconeogenesis (generate glucose from others) and decrease protein synthesis (opposite to insulin).
b. Mineralcorticoids: aldosterone, regulates plasma Na+ and K+ (total extracellular water volume), causes
reabsorption of water in nephron => rise in blood pressure and volume (hypertension).
c. Cortical sex hormone: androgens (testes) for males 2nd characteristics.
2. Adrenal medulla: produces epinephrine (adrenaline) and norepinephrine (non-adrenaline), derived class of
amino acid catecholamines. Both are neurotransmitters.
- Epinephrine increases conversion of glycogen to glucose. Both increases blood flow in sympathetic ways.
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B. Pituitary glands:
1. Anterior pituitary: both direct hormones and tropic hormones (stimulates other endocrine organs).
a. Direct hormones: GH (growth-somatotropin); overproduction in adult (acromegaly-overgrowth of bone).
Prolactin (milk production).
b. Tropic hormones: ACTH (adrenocorticotropic hormone) => adrenal cortex (corticosteroid); regulate by CRF.
TSH (thyroid) => thyroid glands (thyroxin)
LH (ovulation and formation of corpus luteum); LH (leydig => testosterone) in male.
FSH (maturation of ovarian follicles); Male (maturation of seminiferous tubules + sperm pro)
MSH (Melanocyte-stimulating): intermediate lobe; darken frog skin melanophore cells.
2. Posterior pituitary: neurohypophysis, does not synthesize hormones; stores and release:
Oxytocin: increases strength and frequency of uterine contractions, milk let down.
ADH: water reabsorption at collecting duct (aquaporins); stimulated by an increase in plasma osmolarity.
C. Hypothalamus: via negative feedback.
1. Interaction with Ant-pituitary: GnRH => FSH + LH (portal vein - hypothalamic-hypophyseal portal system).
2. Interaction with Pos-pituitary: neurosecretory synthesizes both oxytocin + ADH and for storage.
D. Thyroid:
1. Thyroid hormones (ThyroxineT4 + thiiodothyronineT3): derived from iodination of glycine, rate of metabolism.
- Hypothyroidism: thyroid hormones are under secreted or not at all; slowed heart rate + respiratory rate; weight
gain. Cretinism is in newborn, mental retardation and short stature.
2. Calcitonin (Ca2+): decreases Ca2+ plasma concentration by inhibit osteoclast (opposite to parathyroid).
E. Pancreas: both exocrine (digestive enzymes into duodenum) and endocrine (islets of Langerhans).
1. Glucagon (α-cells): protein and fat degradation, glycogen to glucose, gluconeogenesis; increase blood glucose.
2. Insulin (β-cells): in response to high blood glucose; opposite to glucagon; lower blood [glucose].
- Diabetes mellitus: high blood glucose when low insulin or insensitivity to insulin.
F. Parathyroid glands: synthesize and secretes PTH, regulate Ca2+ in blood, increase its concentration (osteoclast activity).
In response to low blood Ca2+, calcitonin responses to high blood Ca2+.
G. Kidneys: produces renin => => angiotensin II => aldosterone (increase blood volume by water retention)
H. Gastrointestinal hormones: gastrin (HCl), secretin is secreted by pancreas when acidic food enter stomach to
neutralize chyme. CCK => gallbladder contraction => bile => absorption of fats.
I. Pineal gland: melatonin (circadian rhythms), lighten skin (against MSH).
* Mechanism of Actions:
1. Peptide hormones: surface receptor, via cAMP.
2. Steroid hormones: estrogen, aldosterone, intra receptors => DNA transcriptions. (LIPID SOLUBLE)
----------------------------------------------------------------------------------------------------------------------------------------------------VII. Nervous System:
A. Neuron:
1. Structure: an elongated cell consisting of several dendrites, a cell body, and a single axon.
- Dendrite: cytoplasmic extensions that receive information and transmit it toward the cell body.
- Cell body: contains nucleus and controls the metabolic activity of the neuron.
- Axon: a long cellular process that transmits impulses away from the cell.
- Myelin: insulator which allows axons to conduct impulses faster; produced by glial cells (oligodendrocytes
produce myelin in the CNS, and Schwann cells produce myelin in the PNS).
- Nodes of Ranvier: the gaps between segments of myelin.
- Synaptic terminals: axons end as swelling; release neurotransmitters into synaptic clef and into dendrites of another
2. Functions:
- Resting potential: when neuron at rest, the potential difference between extracellular space and intracellular space.
- Neuron is still polarized (-70mV) by active transport of Na+/K+ ATPase. (K+ high inside, Na+ high outside).
- Neuron is selectively permeable to K+ (move out passively) while impermeable to Na+ and with the addition of
(-) proteins => resting potential is created. (3Na+ for every 2K+).
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- Action potential: impulses that travel the length of axon and invade nerve terminals => release neurotransmitters.
- Minimum threshold membrane potential is around -50mV where AP is initiated. Voltage-gated ion channels
open and Na+ rushes in (due to electrical and chemical gradient) in response to depolarization => further depolarized. The
Na+ voltage-gated channel then close, and open K+ voltage-gated channel to repolarize and to hyperpolarize as refractory
period (all or none response).
- Impulse propagation: proceed only in one direction; greater diameter and myelination => faster speed.
B. Synapse:
- Neuron can also synapse with other muscles/glands called effector cells.
- Neurotransmitter can lead to depolarization of the postsynaptic cell and firing its AP. The neurotransmitter in the synapse
is then degraded/reused/reabsorbed or acetylcholinesterase will degrade acetylcholine.
- Effects of Drugs:
1. Curare: blocks postsynaptic acetylcholine receptors => paralysis by blocking nerve impulses to muscles.
2. Botulism toxin: prevents release of acetylcholine from presynaptic membranes => paralysis.
3. Anticholinesterases: used as nerve gases and insecticide parathion; inhibit activity of acetylcholinesterases enzyme,
acetylcholine is then not degraded in synaptic clef and continue to effect postsynaptic membrane => no coordinated
muscular contraction can take place.
C. Vertebrate Nervous System:
- Afferent neurons: sensory back to the back.
- Efferent neurons: motor to effector organs.
- Nerve: bundles of axons covered with connective tissue.
- Plexus: a network of nerve fibers.
- Ganglia: neuronal cell bodies cluster in PNS
- Nuclei: neuronal cell bodies cluster in CNS.
1. Central Nervous System (CNS): brain and spinal cord.
- Forebrain: telencephalon (cerebral cortex-gray matter-memory + creative thought) and diencephalon(thalamus and
hypothalamus). Thalamus is a relay/integration center for spinal cord and cerebral cortex. Hypothalamus controls pituitary.
- Midbrain (Mesencephalon): relay center for visual and auditory impulses.
- Hindbrain: includes pons (cortex communicate with cerebellum), cerebellum (balance, coordination), and medulla
(breathing, hr, gastrointestinal activity). Brainstem is midbrain, pons, and medulla.
- Spinal cord: dorsal horn (sensory enter) in dorsal root ganglion, ventral horn (motor exits). For simple reflexes,
sensory fibers synapse directly on ventral horn motor fibers.
2. Peripheral Nervous System (PNS): consist of nerves and ganglia, sensory nerves (enter CNS) and motor (leaves CNS).
- Somatic nervous system: innervates skeletal muscles => voluntary movements.
- Autonomic nervous system: involuntary, cardiac + smooth muscles.
1. Sympathetic: fight-or-flight; increases blood pressure, heart rate, exercise, dilation of bronchioles (gas); uses
norepinephrine as primary neurotransmitter.
2. Parasympathetic: conserve energy and digestion; lower heart rate, increase gut motility; Vagus nerve; uses
acetylcholine as primary neurotransmitter.
D. Special Senses:
1. The Eye:
- Retina: innermost layer, contain photoreceptors (rods => low-intensity and night vision).
- Cones: absorb red, green, and blue wavelengths => high-intensity and color.
- Rods: single wavelength by rhodopsin. [ rod/cone => bipolar => ganglion => forms optic nerve ]
- Blind spot: where the optic nerve exits.
- Fovea: high concentration of cones => high-acuity vision.
- Choroid: beneath sclera, helps supply retina with blood, dark, reduces reflection in the eye.
- Sclera: covert eyeball, thick and opaque layer (white of the eye).
- Vitreous humor: helps maintain shape and optical properties.
- Aqueous humor: formed by eye, and exists through ducts to join venous blood.
- Disorder of the eye: myopia (nearsightedness), hyperopia (farsightedness), astigmatism (irregular shape of
cornea), cataracts (lens => opaque => blindness), glaucoma (increase in pressure in eye due to blocking of outflow of
aqueous humor, behind cornea).
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2. The Ear: ossicles (malleus, incus, stapes); cochlea and vestibule for balance.
E. Invertebrate Nervous Systems:
1. Protozoa: unicellular => no organized nervous system; may response to touch, heat, light, chemical.
2. Cnidaria: simple nervous system (nerve net).
3. Annelida: possess primitive CNS (defined ventral nerve cord, and anterior "brain" fused ganglia); definite nerve
pathways lead from receptors to effectors.
4. Arthropoda: similar to annelids but more specialized sense organs (compound/simple eyes, tympanum for sound).
----------------------------------------------------------------------------------------------------------------------------------------------------VIII. Respiration
- Respiration: utilization of O2 by an organism.
A. Respiration in Invertebrates:
1. Unicellular and Simple Multicellular Organisms:
a. Protozoa and Hydra (Phylum: Cnidaria): every cell is in contact with external environment (water) => simple diffusion.
2. Annelids: mucus secreted by cells on external surface => moist for gas exchange by diffusion.
3. Arthropod Phylum: tracheae (series of respiratory tubules in grasshopper); whose branches reach almost every cell;
spiracles are where tracheae access the surface in openings => gas exchange by diffusion (open circulatory system).
B. Respiration in Humans:
1. Ventilation: breathing (inhale and exhale); take in oxygen and exhale CO2. Exhalation is generally passive.
2. Control of ventilation: regulated by neuron in medulla (respiratory centers); when partial pressure of CO2 rises, it
stimulates faster rate of ventilation.
3. Gas Exchange: pulmonary capillaries surrounds the alveoli; gas moves from region of high partial pressure to lower
partial pressure.
----------------------------------------------------------------------------------------------------------------------------------------------------IV. Muscles and Locomotion:
A. Unicellular Locomotion:
- Protozoans and primitive algae moves by beating cilia or flagella (11 microtubules - 9 paired arranged in circle and 2
single in the middle). Flagella movement is by power stroke (sliding action); return is called recovery stroke. Amoeba
extend pseudopodia for locomotion (extend membrane).
B. Invertebrate Locomotion:
1. Hydrostatic Skeletons:
a. Flatworms (planaria): longitudinal/circular antagonistic layers of muscles; contract against incompressible fluid
(hydrostatic skeleton). Contraction of circular => flow longitudinally => lengthen animal. Contraction of longitudinal
muscle shorten the animal. Similar in annelids (each segment is independent).
b. Segmented Worms (annelids): setae (bristles in lower part of each segment anchor earthworm temporarily in
earth while muscles push by hydrostatic skeleton.
2 Exoskeleton: hard skeleton covers all muscles/organs; found in arthropods (chitin) secreted by epidermis
(noncellular); limit growth => molting and deposit new skeleton.
C. Vertebrate Skeleton: endoskeleton (muscles + bones).
1. Structure of Skeleton:
a. Cartilage: connective tissue that is softer/flexible than bone; nose, ear, nose, skeletal joints.
b. Bone: mineralized connective tissue; body support. Compact bone dense bone (osteons-Haversian systems).
Each osteon consists of a central channel (Haversian canal) surround by concentric circles of matrix (CaHPO4) lamellae.
Spongy bone is less dense consists of interconnecting lattice of bony spicules (trabeculae).
c. Osteocytes: osteoblast synthesize and secrete organic constituents of bone matrix => mature into osteocytes once
osteoblast is surrounded by its matrix. Osteoclasts (multinucleated) => bone reabsorption.
d. Bone Formation: endochondral ossification (cartilage replaced by bone => bone length) and intramembranous
ossification (embryonic/undifferentiated) CT replaced by bone (head) and heal bone fractures (no cartilage involved).
D. Muscular System:
1. Skeletal muscle: voluntary (SNS), each fiber is multinucleated; has striation of light and dark band => striated.
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- Myofibrils: are filaments embedded in the fibers; are further divided into contractile unit called sarcomeres; is
covered by ER called sarcoplasmic reticulum (stores Ca2+); abundant mitochondria;
- Sarcolemma: cell membrane of muscle fiber; propagate AP and connected by transverse (T tubules) which
provides ion channels. Sarcoplasm (cytoplasm of a muscle fiber).
2. The Sarcomere:
a. Structure: composed of thin (actin) and thick (myosin) filaments. Z lines define boundaries of single sarcomere
and anchor thin filament. M line runs down center. I band is region containing thin filament only. H zone region
containing thick filament only. A band spans entire length of thick filaments and overlapping portion of thin filament.
During contraction, I band and H zone are reduced in size while A band is not (stay the length of thick filament).
b. Contraction: neuromuscular junction (link between nerve terminal (synaptic bouton) and Sarcolemma of muscle
fiber. Motor neuron releases acetylcholine from depolarization => bind receptor on Sarcolemma. AP reaches throughout
fiber and fiber releases Ca2+ initiate contraction (actin and myosin slide past each other).
c. Stimulus and Muscle Response: all-or-none response, strength based on # of muscle fibers.
- Simple twitch: response of single muscle fiber to a brief stimulus at/above threshold. Latent period 
Contraction period  Relaxation period (absolute refractory period: unresponsive to stimulus).
- Summation and Tetanus: summation (frequent stimuli and cannot fully relax – vibrating); tetanus (contractions
is continuous and cannot relax => fatigue (carrying weight)).
- Tonus: partial contraction; muscles are never completely relaxed and maintain partially contracted at all time.
3. Smooth Muscle: ANS, one centrally located nuclei, lacks striation of skeletal muscle.
4. Cardiac Muscle: characteristics of both skeletal/smooth muscles, striated, only one/two centrally located nuclei; actin
and myosin arranged in sarcomeres.
E. Energy Reserves: ATP is required for contraction but little is stored in muscle.
1. Creatine Phosphate and Arginine Phosphate: vertebrates/some invertebrates (echinoderms), energy is stored here.
2. Myoglobin: storage of O2 (high O2 affinity), maintain O2 supply for muscles.
----------------------------------------------------------------------------------------------------------------------------------------------------X. Digestion
A. Digestion in Unicellular Organisms:
- Food capture is phagocytosis. Amoeba pseudopods surround and engulf food and enclose in food vacuoles. Lysosomes
then fuse with food vacuole.
- Paramecium: cilia sweep food into oral groove and cytopharynx (food vacuole forms around food at end of cytopharynx
which go towards anterior end of cell). Enzymes then secreted into vacuole => product diffuse into cytoplasm. Solid wastes
go through anal pore.
B. Digestion in Invertebrates:
1. Cnidarians: hydra uses tentacles to bring food to mouth (ingestion) and release particle inside gastrovascular cavity
which secrete enzymes.
2. Annelids: earthworms have one-way digestive tract with both mouth and anus (crop store food, gizzard grind food);
soluble food passes by diffusion through wall of small intestine into blood (one straight pathway mouth  anus).
3. Arthropods: similar to earthworms, have jaws for chewing and salivary glands.
C. Digestion in Humans:
1. Oral cavity: mechanical and chemical digestion (amylase => hydrolyses starch to maltose disaccharide).
2. Esophagus: by peristalsis passes cardiac physiological sphincter.
3. Stomach: pepsin + HCl (kill bacteria) => chyme enter duodenum through pyloric anatomical sphincter.
4. Small Intestine: contain villi (capillaries and lacteals). Large fatty acids and glycerols => lacteal and reconverted into
fat (fatty acid + glycerol). Most digestion occur in duodenum; enzymes from liver, gallbladder, pancreas enter here.
5. Liver: produces bile and store in gallbladder (emulsifies fat: large into small droplets).
6. Pancreas: produces amylase, trypsin, lipase and
to neutralizes acidic chyme.
7. Large Intestine: absorptions of salts and any remaining water.
D. Digestion in Plants and Fungi:
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1. Intracellular Digestion: storage polymers such as starch break down when nutrients are required into glucose, fatty
acids, glycerol, amino acids monomers by hydrolysis.
2. Extracellular Digestion: fungi must obtain preformed organic molecules (nutrients) from environment. Enzymes are
secreted to hydrolyze these molecules before absorption.
- Rhizoids: of bread mold (saprophyte) lives on dead organic material such as bread, secretes enzyme onto break and
then absorbed by diffusion.
- Venus flytrap: digest fly to get nitrate because they grows in nitrogen-poor soils; still an autotroph (photosynthesis)
----------------------------------------------------------------------------------------------------------------------------------------------------XI. Excretion
- Deamination: of amino acids in liver leads to production of nitrogenous wastes like urea and ammonia. All metabolic
processes lead to production of mineral salts (excreted by kidneys).
A. Excretion in Invertebrates
1. Excretion in Protozoans and Cnidarians: all cells are in contact with external environment. Water soluble wastes (NH3
and CO2) exit cells by simple diffusion (passive). Freshwater protozoa (paramecium), possess a contractile vacuole—water
excretion by active transport.
2. Excretion in Annelids: earthworms, CO2 excretion occurs directly through moist skin. Two pairs of nephridia in each
body segment excrete water, mineral salts, and nitrogenous waste in form of urea.
3. Excretion in Arthropods: CO2 is release from tissues into adjacent tubelike tracheae which are continuous with
external air through spiracles (opening). Nitrogenous wastes => uric acid crystal (water conservation); mineral salts + uric
acid accumulate in Malphigian tubules and then transported to intestine to be expelled with solid wastes of digestion.
B. Excretion in Humans:
1. Kidneys: each kidney is composed of ~1 million nephrons.
a. Structure: three regions (outer cortex, inner medulla, and renal pelvis). A nephron consists of Bowman’s capsule
embraces capillary bed called glomerulus (filtration). Bowman’s capsule leads to proximal convoluted tubule, loop of
Henle, distal convoluted tubule, and collecting duct. Loop of Henle runs through medulla and the others run in cortex.
Concentrated urine => collecting duct => renal pelvis => ureter => urinary bladder => urethra
- Peritubular capillary: network to facilitate reabsorption of aa, glucose, salts, and water.
b. Urine Formation:
1. Filtration: blood pressure forces 20% of blood plasma entering glomerulus through capillary walls into
Bowman’s capsule. Filtrates are fluid and small solutes entering nephron which is isotonic with blood plasma. Larger
particles (blood cells, albumin) remain in circulatory system; passive by hydrostatic pressure.
2. Secretion: acids, bases, and ions like K+ and phosphate by both active/passive transports.
3. Reabsorption: glucose, salts, amino acids and water are reabsorbed from filter and returned to blood. Occur
primarily in proximal convoluted tubule and is an active process => movement of water also => concentration urine
which is hypertonic to blood.
c. Nephron Function:
1. Osmolarity gradient: selective permeability => osmolarity gradient (increasing from cortex to inner medulla);
solutes that contribute to maintenance of gradient (urea and salt, Na+ and Cl-). Osmolarity of urine is established in
collecting duct by countercurrent-multiplier system (expense energy to create concentration gradient).
2. Concentration of urine: countercurrent system causes medium in medulla to be hyperosmolar with respect to
dilute filtrate. As urine flows through this region => water moves out of collecting duct by osmosis (reabsorbed by
capillaries flowing in medulla); regulated by ADH (vasopressin) which increases permeability of collecting duct to water by
aquaporins
- Countercurrent-exchange: gradients are maintained but not established.
----------------------------------------------------------------------------------------------------------------------------------------------------XII. Animal Behavior
A. Patterns of Animal Behavior:
1. Simple Reflexes: controlled at spinal cord, sensory at afferent and response at efferent to motor muscle; important in
behavioral response of lower animals but not vertebrates.
2. Complex Reflexes: neural integration in brainstem or even cerebrum; Startle response involves reticular activating
system (keeping us alert).
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3. Fixed-Action Patterns: complex, coordinated, innate behavioral responses to specific patterns of stimulation in
environment; releaser (elicits behavior); unlikely to be modified by learning; such as swimming action of fish.
4. Behavior Cycles: daily cycles of behavior (Circadian rhythms); lose their exact 24hr periodicity if they are isolated
from natural phases of light and dark but continue with approximation day to day. Daily cycle of eating are part of cycles
with both internal (natural body rhythm) and external (dinner bell or clocks) control.
5. Environmental Rhythms: patterns are established/maintained by periodic environmental stimuli; response of traffic
light signals.
B. Learning
- Involves adaptive responses to the environment; capacity of learning is correlated with neurologic development.
1. Habituation: one of simplest learning patterns, repeated stimulation decreases responsiveness to that stimulus;
suppression of normal startle responses to stimuli; if no stimulus => responses tends to recover (spontaneous recovery).
2. Classical Conditioning: Pavlovian conditioning involves association of autonomic or visceral response with
environment stimulus; also called conditioned reflex; innate stimulus for a reflex is replaced.
a. Pavlov's Experiments: bell is arbitrary
stimulus.
b. Pseudoconditioning: test conditioning
whether the conditioning process is actually
necessary for production of a response by a
previously ”neutral stimulus" which is able to elicit
response even before conditioning and thus, not
really a neutral stimulus. Pseudoconditioning can be
avoided by carefully evaluating all prospective
stimuli before conditioning.
3. Operant or Instrumental Conditioning: involves
conditioning responses to stimuli with use of reward
or reinforcement; can also condition visceral
responses (heartbeat).
a. B. F. Skinner: skinner-box (depression of lever was operant response under study); positive reinforcement
(reward includes providing food, light, or electrical stimulation of the animal's brain pleasure centers; animal => more
likely to repeat).
b. Negative reinforcement: stimulating brain's pleasure centers; links the lack of certain behavior with a reward such
as (a bird receive food pellet if it does not peck on yellow circle in its cage) => animal develops positive connection
between lack of action and reward.
c. Punishment: stop exhibiting a given behavior pattern; less likely to repeat after punishment.
d. Habit family hierarchy: stimulus is associated with several possible responses, each response having different
probability of occurrence; reward strengthen and raises its order in hierarchy.
4. Modification of Conditioned Behavior
a. Extinction: gradual elimination of conditioned responses in absence of reinforcement (unlearning). Instrumental
and operant conditioning (response is diminished and eliminated in absence of reinforcement) and is not unlearned; will
comeback if reinforcement is returned.
- Classical conditioning: extinction occurs when unconditioned stimulus is removed/never paired with conditioned
stimulus. For maintenance of conditioned response, conditioned stimulus must pair with unconditioned stimulus.
Spontaneous recovery is recovery of conditioned response after extinction.
b. Generalization and Discrimination: stimulus generalization is the ability of a conditioned organism to respond to
stimuli that are similar but not identical to the original conditioned stimulus; the less similar => less response. Stimulus
discrimination involves the ability of learning organism to respond differentially to slightly different stimuli (if rewards are
in narrow range, will not response if outside this range). Stimulus generalization gradient is established after organism
has been conditioned, whereby stimuli further away from original => stimulus with less magnitude.
C. Limits of Behavioral Change
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1. Imprinting: environmental patterns/objects presented to a developing organism during a brief "critical period" in early
life become accepted permanently.
2. Critical Period: specific time periods during an animal's early development when it is physiologically able to develop
specific behavioral patterns; if no pattern is presented properly during this period => behavioral pattern will not develop
properly. Some animals have visual critical period (if light is not present => visual effectors will not develop properly).
D. Intraspecific Interactions
1. Behavioral Displays: innate behavior that has evolved as single for communication such as a song, call, or intentional
change in animal's physical characteristics.
a. Reproductive display: specific behaviors found in all animals, including humans.
b. Agonistic displays: dog's display of appeasement when it wags its tail or dog's antagonistic behavior when it
directs its face straight and raises its body.
2. Pecking Order: minimizes violent intra specific aggressions by defining stable relationships among members of group.
When food, mates, or territory are disputed; dominant member of species will prevail over a subordinate one.
3. Territoriality: defend, distributing members of species so that environmental resources are not depleted in small region;
Intraspecific competition is reduced.
4. Response to Chemicals: olfactory sense through pheromones (influence behavior of other members of same species).
a. Releaser pheromones: trigger reversible behavioral change in recipient. Sex-attractant pheromones are secreted
by many animals; releaser pheromones are secreted as alarm and toxic defensive substances.
b. Primer pheromones: produces long-term behavioral and physiological alterations in recipient animals.
----------------------------------------------------------------------------------------------------------------------------------------------------XIII. Ecology
A. Levels of Biological Organization
1. Organism: composed of smaller unit; is the individual unit of an ecological system.
2. Population: group of organisms of same species living together in a given location; species is any group of similar
organisms that are capable of reproducing fertile offspring.
3. Communities: populations of different plants/animals. Biotic community includes only population; ecosystem includes
both community and its environment.
4. Ecosystem: includes interaction between biotic communities and abiotic environment.
5. Biosphere: include atmosphere, lithosphere (rock and soil surface), and hydrosphere (ocean).
B. The Environment
1. Physical Environment: water, temperature, oxygen supply.
a. Sunlight: photic zone (photosynthetic activity takes place, light can penetrate); aphotic zone is for animal life and
other heterotrophic.
b. Substratum (soil/rock): affected by pH, texture (determine water holding capacity; most plants grow in loams
which contain high % of each type of soil), minerals (nitrates and phosphate), and humus (amount of decaying plant and
animal life in the soil).
C. Interactions within the Ecosystem
1. Niche: defines functional role of organism in its ecosystem; distinct from habitat (physical place where an organism
lives). Niche describes what organism eats, where and how it obtains its food, what climatic factors it can tolerate, nature of
its parasites and predators and how it produces. No Two species can ever occupy the same niche (compete).
2. Nutritional Interactions within the Ecosystem
a. Autotrophs: manufacture their own food; chemosynthetic bacteria obtain energy from oxidation of inorganic
sulfur, iron, and nitrogen compounds.
b. Heterotrophs: cannot synthesize their own food and must depend on autotrophs or other heterotrophs.
c. Herbivores: consume only plants and plant; long digestive tract (symbiotic bacteria breaks cellulose).
d. Carnivores: eat only other animals (pointed and fanglike teeth; shorten digestive tract).
e. Omnivores: eat both plants and animals.
3. Interspecific Interactions
a. Symbiosis: live together in an intimate, often permanent association which may/may not be beneficial. Some are
obligatory (one or both organisms cannot live without the other).
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1. Commensalism(+/0): remora and shark (underside of shark for food, protection). Barnacle and whale.
2. Mutualism(+/+): both organisms derive some benefits; protozoa and termites (protozoa digest cellulose).
3. Parasitism(+/-): competition for food is most intense (bacteria, fungi, and animals). Ectoparasite (cling to
exterior surface of host). Endoparasite lives within the host.
- Virus and host cell: all viruses are parasites; nonfunctional outside host; DNA surrounded by protein coat.
- Disease bacteria and animals: most are chemosynthetic or saprophytic (decay).
- Disease fungi and animals: fungi are saprophytic (most). Ringworm is parasitic on man.
- Worms and animals: tapeworm and man; successful parasites do not kill host; the more dangerous the
parasite (host dead) => the less chance it will survive.
b. Predation: free living organisms that feed on other living organisms (carnivores and herbivores).
c. Saprophytism: protists and fungi that decompose (digest) dead organic matter externally and absorb nutrients;
mold, mushrooms, bacteria of decay, and slime molds.
d. Scavengers: consume dead animals; require no adaptation for hunting and killing; hyena.
4. Interactions Between Organisms and Their Environment
a. Osmoregulation: saltwater fish (Hyperosmotic environment => lose water and take in salt => gills constant
drinking of water and active excretion of salt).
b. Thermoregulation: cellular respiration only transfer a fraction of energy derived from oxidation of carb into ATP
(60% is given off as heat). Poikilothermic (cold-blooded) => most heat energy loss to environment (when temp rises =>
organisms become more active, when temp is low => sluggish and lethargic). Homeothermic (warm-blood => adaptation
such as fat, hair, and feathers retard heat loss; maintain constant body temp).
D. Relationships within the Ecosystem
1. Energy Flow
a. Food chain: energy is transferred from original sources in green plants through a series of organisms with repeated
stages of consumption and finally decomposition.
1. Producers: autotrophic green plants and chemosynthetic bacteria.
2. Primary consumers: animals that consume green plants (herbivores).
3. Secondary consumers: animals that consume primary consumers (carnivores).
4. Tertiary consumers: animals that feed on secondary consumers.
5. Decomposers: saprophytic organisms and organisms of decay (bacteria and fungi) decompose organic waste
and dead tissues to simpler compounds such as nitrates and phosphates.
d. Food Pyramids: according to 2nd law of thermodynamics (every energy transfer involves a loss of energy). In
addition to the lost in transfer, each level of food chain utilizes some energy for metabolism and loses more as heat.
1. Pyramid of mass: less mass and less mass is supported at higher level from the base (largest mass).
3. Pyramid of numbers: greatest of organisms at base (producer level) and smallest at top (final consumer).
2. Material Cycles
a. Nitrogen Cycle: essential component of amino acids and nucleic acids. Nitrogen-fixing bacteria convert N2 to a
usable form NO3-. Nitrates are absorbed by plants to synthesize plant proteins and nucleic acids. Animal eats plants => both
die (wastes) => converted to NH3 by saprophytes. (1) NH3 (chemosynthetic bacteria ) => NO2- (nitrifying bacteria) => NO3and the cycles repeat.
b. Carbon Cycle: CO2 (plants) => starch, proteins, and fats (CO2 => glucose) => Animals eat plants (produced CO2
released to air). Rest is released to air until organism decompose.
c. Other Cycles: include water, oxygen, phosphorus.
E. Stability In The Ecosystem
1. Conditions for Stability in an Ecosystem: require constant input of energy source and living system incorporate it.
2. The Climax Community: biotic part of ecosystem (population exist in balance); depends on abiotic factors.
3. Ecological Succession: one biotic community replaces or succeeds another until a climax community is established
(equilibrium unless major biotic change-disease, mutation).
F. World Biomes (Major Communities)
1. Terrestrial Biomes: each geographic region is inhabited by a distinct community (biome) existing in major climate
areas. Climax vegetation is vegetation that becomes dominant and stable after years of evolutionary development (plants as
producers) => determine climax animal population. According to temperature and rainfall.
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a. Desert Biome: receive fewer than 10in of rain each year (Sahara in Africa, Gobi in Asia).
b. Grassland Biome: low rainfall (10-30in/year), no shelter for herbivorous animals (long legs).
c. Tropical Rain Forest Biome: jungles (high temperature and torrential rain), dense growth of vegetation that does
not shed its leaves. Floor is inhabited by saprophytes; there are vines and epiphytes (plants growing on other plants).
d. Temperate Deciduous Forest Biome: cold winters, warm summers, and moderate rainfall (beech, maple, oaks,
and willows) shed their leaves during cold winter months (northeast, central-eastern US and central Europe).
e. Temperate Coniferous Forest Biome: cold, dry, inhabited by pine (water conservation-southern Canada).
f. Taiga Biome: less rainfall than temperate forest; long, cold winters, and are inhabited by single coniferous tree
(spruce). Floor contains moss and lichens; Northern part of Canada and Russia.
g. Tundra Biome: treeless, frozen plain found between taiga lands and northern ice sheet; very short summer and
short growing season when ground becomes wet (lichens, moss, polar bears).
h. Polar Region: frozen area with no vegetation or terrestrial animals; if there is, live near polar oceans.
2. Terrestrial Biome and Altitude: base of mountain to top of mountain would follow: coniferous-like biome => taiga like
=> tundra like => polar like biome.
3. Aquatic Biome: 90% of earth food and O2 production (photosynthesis) takes place in water.
a. Marine Biome: controls earth's temp by absorbing solar heat; constant amount of nutrient and dissolved salts.
1. Intertidal zone: exposed to low tides that undergoes variations in temp and period of dryness (algae, sponges,
clams, snails, sea urchins, starfish, and crabs).
2. Littoral zone: region on continental shelf that contains ocean area with depth up to 600ft and extends several
hundred miles from shores.
3. Pelagic zone: typical of open seas.
- Photic zone: sunlit layer (plankton-passive drifting masses of microscopic photosynthetic and heterotrophic
organism and nekton-active swimmers, chief autotroph is diatom-algae).
- Aphotic zone: beneath photic zone that receives no sunlight; only heterotrophs; contains nekton and
benthos (crawling and sessile).
b. Freshwater biome: links between oceans and the land; factors affecting life includes temp, transparency
(illumination due to suspended mud particles), depth, available CO2 and O2, and [salt].
- Hypotonic: water into cell, remove excess water such as contractile vacuole of protozoa and excretory system of
fish. (dilute urine).
----------------------------------------------------------------------------------------------------------------------------------------------------XIV. Classification
A. Taxonomic Classification
1. Taxonomy: the science of classification and nomenclature (groups based on evolutionary relationships).
2. Classification and Subdivisions: five kingdoms => Phyla (in animal kingdom) or Divisions (other kingdoms) =>
subphyla/subdivision => Classes => Orders => Family => Genus => Species. The full classification of human is:
Kingdom: Animal, Phylum: Chordata, Subphylum: Vertebrate, Class: Mammalia, Order: Primates, Family:
Hominidae, Genus: Homo, Species: sapiens.
3. Assignment of Scientific Names: Homo sapiens, the housecat is Felis domestica.
B. Classification Into Kingdoms
- Two modern systems: 1st uses five kingdoms (Monera, Protista, Plantae, Fungi, and Animalia). 2nd uses three kingdoms
(Monera, Plantae (including Fungi), Animalia (including Protista)).
1. Viruses: outside of 5 kingdoms, not considered living organism by itself.
2. Monera: prokaryotes; single-celled organisms that reproduce asexually.
3. Protista: primitive eukaryotic organisms with both plant-like and animal-like characteristics; such as Euglena
demonstrates both motility of animal and photosynthetic capabilities of plants.
4. Fungi: not photosynthetic, resemble plants that they are multicellular, differentiated, nonmotile. They are either
saprophytic or parasitic (athlete's foot fungus). Chitin cell wall instead of cellulose.
5. Plantae: multicellular organisms that exhibits differentiation of tissues, nonmotile, and photosynthetic.
6. Animalia: multicellular, motile, heterotrophic with differentiated tissues (organs in higher forms).
C. Viruses: parasites, lytic and lysogenic cycles, DNA or RNA and protein coat; such as bacteriophage.
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D. Kingdom Monera
1. Cyanobacteria: blue-green algae, live primarily in fresh water and also marine environments; Cell wall with
photosynthetic pigments, but no flagella, true nucleus, chloroplasts, or mitochondria; extreme temp.
2. Other Bacteria: single-celled prokaryotes with single double-stranded circular DNA; Classified by their morphological
appearances: cocci (round), bacilli (rods), Spirilla (spiral). Some forms are duplexes (diplococcic), clusters
(staphylococci), and chains (streptococci).
E. Kingdom Protista: unicellular w/ exception (eukaryotes)
1. Protozoa: single-celled (heterotrophic). Rhizopods (including amoebas), move with cellular extensions called
pseudopods. Ciliophors have cilia that are used for feeding and locomotion.
2. Algae: photosynthetic (phytoplankton).
3. Protists Resembling Fungi: slime molds, arranged in a coenocytic (many nuclei) mass of protoplasm; alternation of
life cycle of animal-like and plant-like; reproduce asexually by sporulation.
F. Kingdom Fungi
- Eukaryotes and multicellular; heterotrophs; absorb food from environment; reproduce by asexual sporulation. Examples
are mushrooms, yeast, and lichens.
G. Kingdom Animalia
1. General Characteristics of All Animals (Metazoa)
a. Differentiation of Tissues, Organs, and Organ Systems
e. Nervous System
b. Alimentation: ingest bulk foods (holotrophic), digest, and eliminate the remains.
c. Locomotion: some are sessile (stationary) and create currents to trap food, others are not.
d. Bilateral Symmetry: right and left sides that are mirror images.
f. Chemical-Coordinating System: secrete hormones that operate with nervous system to maintain homeostasis.
2. Porifera (Sponges): two layers of cells, have pores, sessile, low cellular specialization.
3. Cnidarians: coelenterates (contains digestive sac that is sealed at one end-gastrovascular cavity); two layers of cell—
the ectoderm, and endoderm; tentacles, stinging cells, and net nerves (hydra, jellyfish, coral).
4. Platyhelminthes (Flatworms): bilaterally symmetrical, 3 layers of cell (including mesoderm), no circulatory system,
nervous system includes eyes, anterior brain ganglion, pair of longitudinal nerve cords.
5. Nematoda (Round worms): long digestive tubes and anus (3 layers of cell); lack circulatory systems; nerve cords and
anterior nerve ring.
6. Annelida (Segmented Worms): possess Coelom (true body cavity) contained in mesoderm; well-defined systems
including nervous, circulatory, and excretory system (earthworms, leeches).
7. Mollusca: soft bodies and mantles that often secrete calcareous (calcium carbonate) exoskeletons; breathe by gills and
contain chambered hearts, blood sinuses, pair of ventral nerve cords (clams, snails, squid).
8. Arthropoda: jointed appendages, chitin exoskeleton, open circulatory systems (sinuses).
- Insects: three pairs of legs, spiracles, and tracheal tubes designed for breathing outside aquatic environment.
- Arachnids: four pairs of legs and book lungs (scorpion, spider).
- Crustaceans: segmented body with variable number of appendages and gills (lobster, crayfish, shrimp).
9. Echinoderms: spiny, radially symmetrical, water-vascular system, capacity for regeneration of parts (starfish, sea
urchin) and evolutionary linkage between echinoderms and chordates.
10. Chordates: stiff dorsal rod (notochord) present at some stage of embryonic development; paired gill slits and tail
(sometime in embryonic). Lancelets and tunicates (Amphioxus) are chordates but not vertebrates (no back bone).
a. Fish: two-chambered heart and gills; external fertilization.
- Jawless fish: eel-like; retain notochord; cartilaginous internal skeleton, no jaws, sucking mouth (hagfish).
- Cartilaginous fish: possess jaw, teeth; reduced notochord as segments between cartilaginous vertebrate (shark).
- Bony fish: scales and lack notochord in adult form; cartilage is replaced by bone (tuna).
b. Amphibian: tadpole (larval stage) is found in water, possesses gills and no tail, two pairs of legs, threechambered heart, no scales, external fertilization.
c. Reptiles: terrestrial animal; breathe air by lungs, lay eggs, internal fertilization; poikilothermic; scales and 3chambered heart (turtle, lizard, snake, crocodile).
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d. Birds: 4-chambered heart; warm-blooded (homeothermic) and eggs are surrounded by shells.
e. Mammals: warm-blooded feed their offspring with milk produced in mammary glands.
- Monetremes: lay leathery eggs, have horny bills, milk glands with numerous openings but no nipples.
- Marsupials: pouched; embryo begins development in uterus and completes development while attached to
nipples in abdominal pouch (kangaroo).
- Placental: embryos develop in uterus; placenta attaches embryo to uterine wall, provides exchange of materials.
----------------------------------------------------------------------------------------------------------------------------------------------------XV. Evolution
A. Evidence of Evolution
1. Fossil Records: found in sedimentary rocks. Petrification (minerals replace cells of an organism); Imprints are
impressions left by organisms (footprint); Molds form in hollow spaces of rocks; Casts (minerals deposited in molds).
2. Comparative Anatomy: Homologous structure (same anatomical features and evolutionary origins). Analogous
structures includes similar function but not from the same evolutionary origins; different pattern of development.
3. Comparative Embryology: two-layer gastrula is similar to hydra (cnidarian); three-layer gastrula is similar to
flatworms; and gill slits is with fish; suggest common ancestry.
4. Vestigial Structures: appear to be useless but had some ancestral function. Appendix is small and useless but in
herbivores (assists in digestion of cellulose).
5. Geographic Barriers: migration => lessen Intraspecific competition. After long period of time, reproductive isolation
would be maintained even if barrier is removed.
B. Theories of Evolution:
1. Darwin's Theory of Natural Selection:
a. Overpopulation: more offspring than resources.
b. Variations: mutations.
c. Competition:
d. Natural Selection: survival for the fittest.
e. Inheritance of Variations: better genes get inherited.
f. Evolution of New Species: selected for by environment
C. Forces of Evolution
1. Population Genetics: Hardy-Weinberg (look at Cliff)-ideal population
2. Microevolution: real population have unstable gene pool and migrating populations.
a. Natural Selection: genotypes with favorable variations are selected for.
b. Mutation: changes allele frequencies in population.
c. Assortive Mating: mates are not randomly chosen.
d. Genetic drift: changes in composition of gene pool by chance (more pronounced in small population).
e. Gene flow: migration of individuals in/out of population => loss/gain of gene pool.
3. Speciation: evolution of new species (interbreeding is possible).
a. Demes: small local population (all beavers along specific portion of a river form a deme); many deme may
belong to specific species.
b. Development of New Species: gene flow is impossible between two species; Factors that lead to specification
includes: variation, environment, migration, adaptation, natural selection, isolation.
c. Adaptive Radiation: emergence of number of lineages from a single ancestral species; single species diverge into
number of distinct life style (niche) even in the same island such as Galapagos finches.
d. Evolutionary History: phylogeny (evolutionary history). Convergent evolution (such as analogous structurefrom two different species coming closer due to environment). Parallel evolution (from single ancestor but evolved to have
similar characteristics even after diverge).
e. Isolation: geographic isolation of population into two groups => no gene flows between them. Mutation/new gene
combination => mating is impossible over time => new species.
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