Molecules of Biology

Nitrogen- proteins, nucleic acids

Phosphorus- nucleic acid, ATP, membrane
Sulfur- sulfide bridges in protein

1. Protein(polypeptide)
Protein has an amine group (NH2) and carboxyl group (COOH)
Peptide bonds (dehydration synthesis)- broken in hydrolysis process
A. Primary structure- results from the sequence of amino acids
B. Secondary structure- results from hydrogen bonding. Helical nature (circles)
C. Tertiary structure- conformation (intricate, 3-D shape), most directly determines the
way it functions and its specificity. Enzymes denature (lose their original chain)
D. Quaternary structure- consist of more than one polypeptide chain (hemoglobin)

2. Carbohydrates
Glucose+Glucose= maltose (dehydration synthesis)
Glucose+fructose= sucrose (dehydration synthesis)
Polysaccharides (glycogen, starch, cellulose)

3. Lipids
1. Triglycerides (3 fatty acids (hydrocarbons with carboxyl group) and glycerol)
2. Phospholipids- one of fatty acids replaced by phosphate group (polar head and
Nonpolar tail)- forms lipid bilayer
3. Cholesterol- rings and forms steroid hormones (estrogen, testosterone, etc)
HDL- good cholesterol LDL- Bad cholesterol

4. Nucleic Acid (polynucleotides)

DNA-deoxyribonucleic acid RNA-ribonucleic acid
Nucleotide- sugar (5 carbon), phosphate, and a base
Adenine, guanine, cytosine, thymine for DNA
Adenine, guanine, cytosine, uracil for RNA
Hydrogen bonds between bases
Purines- larger- adenine, guanine
Pyrimidines- smaller- thymine, cytosine

Cell Structure

Cell walls
1. Plants- cellulose
2. Bacteria-peptidoglycan
3. Fungi-chitin

Cell membrane
1. Lipids (phospholipids)

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 2. Proteins (passages)

Going across cell membrane

1. Simple diffusion (high to low, Nonpolar) (oxygen, cholesterol, carbon dioxide)
2. Facilitated diffusion- proteins form channels (high to low, polar) (ions)
3. Active transport (low to high, energy) (Nonpolar or polar)
4. Osmosis- movement of water across cell membrane (waters concentration gradient is
opposite to solutes concentration gradient), (facilitated diffusion)
Hypertonic- concentrated (shrinks, plasmolysis)
Hypotonic- dilute (swell, turgid)
Isotonic- same concentration (0.9% sodium chloride solution)
5. Bulk transport- endocytosis, exocytosis
Endocytosis- into the cell (phagocytosis, pinocytosis) (vesicles) (receptor-mediated
endocytosis- large quantities of very specific substances)

Cytoplasm- cyclosis (cycles that carry organelles around the cell)

Vacuole-storage or pumping out water (contractile vacuoles) (paramecium and amoeba)
Ribosome-protein synthesis, no membrane; in the cytoplasm, or in the rough ER
Smooth endoplasmic reticulum- connects rough ER to the Golgi apparatus, makes steroid
hormones and lipids, detoxifies the cell
Rough endoplasmic reticulum- ribosomes bound to it (membrane proteins or secreted proteins)
Golgi apparatus- receives vesicles from the rough ER and modify, store, and packages stuff
Mitochondria- cellular respiration, ATP, double membrane, contains DNA and ribosomes.
Cristae, folded inner membrane.
Lysosomes- Digest foreign substances and worn-out organelles (intracellular digestion)
Programmed cell death (apoptosis) happens here. Plant cells usually do not have lysosomes.
Centrioles- help to form the spindle during mitosis (not in plants, 2 makes one centrosomes)
Plastids- double membrane, found only in plants and algae
1. Chloroplasts- own DNA and ribosomes; grana, stroma
2. Leucoplasts- colorless and store starch. (roots, tubers)
3. Chromoplatsts- carotenoid pigments and are responsible for the red-orange-yellow
coloring of carrots.
Nucleus- control center, double membrane
Nucleolus- ribosome synthesis
Cell membrane- regulates what comes in and out
Cytoskeleton- microtubules, microfilaments
Microtubules- rods made of polymerized tubulin protein
Makes cilia (short), flagella (long), spindle fibers
Microfilaments- actin, support the shape of the cell. Enable animal cells to form a cleavage
furrow, amoeba to use pseudopods; enables the cell to move
Cell wall- fungi (chitin), plants and algae (cellulose). Thin gluey layer is formed between the two
cell walls (cell plate, then middle lamella)

Cytoplasm- chemical reaction and enzymes

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Enzymes- catalysts, reusable, active sites, lock and key theory or induced-fit model,
particular enzyme, substrates. Ends in -ase
Denatured- lose their shape Proteins Coenzymes- Vitamins Cofactors- minerals
Prions- infectious proteins that cause brain diseas. Misfolded version of a protein.

Compound microscope

Ocular lens (eyepiece), objective lens

1. Phase-contrast microscope- enhances contrasts; living, unstained cells
2. Transmission electron microscope- interior of cells (dead)
3. Scanning electron microscope- surface of cells (dead)
Ultracentrifuge- tool that enables cell fractionation (isolate specific components of cells in large
quantities)
Freeze fracture- study details of membrane structure
Tissue culture- cells that grow in the laboratory

Cellular Respiration

Adenosine triphosphate (bond between third and second phosphate molecule-energy)

ATP= ADP+1phosphate molecule+energy
Electron Carriers- NAD+ and FAD (accept 2 electrons)
Oxidation reaction

1. Glycolysis (glucose+ 2ATP+ 2NADplus= 2 pyruvate+ 4 ATP+ 2 NADH)

Anaerobic, occurs in cytoplasm
2. PDC (pyruvate dehydrogenase complex)
2 pyruvate+ coenzyme A+ 2 NADplus= 2Co2+ 2NADH+ 2 Acetyl CO-A
3. Krebs Cycle (citric acid cycle) (matrix)
Oxaloacetic acid generated (or citric acid)
6 NADH, 2 FADH2, 2ATP, and 4 CO2 (per glucose)
4. Electron transport (cristae membrane) and oxidative phosphorylation
ETC- use energy of electrons to pump H+ between membranes.
Collection of carrier molecules (including cytochromes) that uses redox reactions
Goals- oxidize the carriers, use energy to make ATP
Oxidize the carriers- O2 becomes H20 and oxidizes the carriers
Oxygen- final electron acceptor
Oxidative phosphorylation (chemiosmosis)- ATP synthase allows H+ into the membrane
by facilitated diffusion.
Total of 36 ATP molecule is produced (2 in glycolysis, 2 in Krebs cycle)
NAD- 3 ATP, FAD- 2 ATP

Oxygen not available? Fermentation- emptying electron carriers in absence of oxygen

In glycolysis NADH gives electrons to pyruvates
In alcoholic fermentation, products are 2 ethanol and CO2 (yeasts)

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In lactic acid fermentation, products are 2 lactic acid (muscle)
Products are only 2 per glucose

Transcription and translation

DNA replication (nucleus)

DNA unwinds and separate. DNA polymerase pairs it up. Hydrogen bonds form, and bonds form
between sugar and phosphate. It twists.
Parent DNA, Daughter Stands, origin of replication (both directions), entire thing replicated and
checked.
Two sets- diploid (46 chromosomes)

Chromosomes
Genes- portion of DNA that carry instructions for protein synthesis

RNA transcription (nucleus)

DNA unwinds and separate. RNA polymerase pairs it up. New RNA molecule is released, and
DNA rejoins with its partner. (ONLY a portion of DNA molecule is used) not checked
Operon- regulates transcription (promoter, operator)
Promoter- binding site of RNA polymerase (on switch)
Operator- binding site for repressor (off switch)

RNAs
1. mRNA- carries information for protein synthesis from nucleus to ribosomes
2. rRna- makes ribosomes functional (ribosomes made up of rRNA and protein)
3. tRna- transfer RNA carries amino acids from cytoplasm to the ribosomes.

Splicing- removal of mRNA parts that do not encode for a protein

Exon- codes for a protein
Intron- do not code for a protein (cut out when transcripted to RNA)

Translation (cytoplasm)
Codon- three nucleotides to one amino acid (64 possible codons) (mRNA)
AUG (methionine)- start codon
UAA, UGA, and UAG- three stop codons

1. tRNA- amino acid attachment site, anticodon (base pair with codons on mRNA)
2. ribosomes- P-site and A-site
mRNA binds to the ribosome, and tRNA base pairs and forms peptide bond

Mitosis and Meiosis

Internal regulators- cyclins, external regulators- growth factors

Plants do not have centrioles or centrosomes

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Interphase- normal activities, chromosomes replicate (longest phase)
G1- cell double in size,
S- synthesis of DNA takes place
G2- prepares for mitosis, organelles are replicated

Prophase
Chromosomes becomes visible
Centrioles begins to move away and form mitotic spindle
Nucleoli disappear
Nuclear membranes begins to break up

Metaphase
Centrioles go to opposite poles
Replicated chromosomes line up at metaphase plate
Spindle fibers attach to the centromeres

Anaphase (swiftest)
Centromere splits in two and moves to opposite poles
Pinches inwards which is called cleavage furrow

Telophase
Nuclear membrane forms
Chromosomes begins to unravel

Telomeres- ends of the chromosomes- nonsense sequence to protect against possible loss
Cytokinesis- split, animal cells- cleavage furrow. Plant cells- cell plate (middle lamella cements)

Meiosis (reduction division)

Prophase I (longest phase of meiosis not cell cycle)

Chromosomes condense
Centrioles starts to move to opposite poles and spindle is formed
Nuclear membrane disintegrates
Synapsis- homologous chromosomes pair up line up (tetrad)
Crossing over- chiasmata (exchange genetic info)

Metaphase I
Centrioles go to opposite poles
Spindle fibers attach to the homologous pair
Chromosomes line up at the equator
Independent Assortment of Chromosomes happened here- how the chromosomes line up is
random (we got one of the homologous pairs from our dad and one from mom)

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Anaphase I
Disjunction- Homologous pairs separate

Telophase I (haploid)
Divides their cytoplasm
Nuclear membranes form

Only difference between mitosis and meiosis II is the interphase II where chromosomes do not
replicate, and in metaphase I, chromosomes line up in double file, while in metaphase II, they
are lined up in single file.

Spermatogenesis: new sperm cells, continuous (LH makes testes to produce testosterone)
Spermatogonium (2n)- initial cell (lives in seminiferous tubules)- divides by mitosis to produce
primary spermatocytes (2n) - which undergoes meiosis I to produce secondary spermatocytes
(n) which undergoes meiosis II to produce spermatids (n).
Spermatids- not motile, but go to epididymis and make sperm
4 functional sperm (spermatozoa)
Germ cell- cell that is committed to the production of gametes

Oogenesis: formation of ova, discontinuous

Primary oocyte- initial cell (found in ovaries), within the embryo, oogonium divides by mitosis
to become primary oocyte which becomes dormant. Thats all she has
At puberty, hormone activate primary ooctye to become secondary oocyte at ovulation.
Meiosis II does not occur until sperm penetrates the secondary oocyte.
Ovum- final cell
Single ovum (2 polar bodies)
Monthly basis, beginning at puberty and ending at menopause (46-54)

Three causes of variation among offspring

1. Independent assortment of chromosomes during metaphase I of meiosis
2. Crossing over during synapsis in Prophase I of meiosis
3. Random fertilization

Genetics

Phenotype- actual appearance

Genotype- actual genes
Alleles- version of the gene
Homozygous, heterozygous, codominance (both expressed), incomplete dominance (blending)
Sex chromosomes- one pair of 23 pairs that determine sex
Autosomes- not sex chromosomes
mtDNA- we all get from our mom
gene mutations (not visible under the microscope)
Point mutations- changes in single nucleotide bases in the DNA sequence

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Frame-shift mutations- insertion or deletion of nucleotides
Chromosome mutation- can be observed under microscope
Aneuploidy- Abnormal number of chromosomes (polyploidy, nondisjunction)
Deletion- a fragment lacking a centromere is lost during cell division
Inversion- A chromosomal fragment reattaches to its original chromosome but in the reverse
orientation
Translocation- piece of chromosome breaks off and rejoins a different chromosome (break link)
Nondisjunction- failure of homologous pairs to separate following meiotic synapsis, it results in
trisomy (Down syndrome (21)) 2n+1 or 2n-1
Polyploidy- failure of meiosis during formation of the gametes. 3n or 4n. Lethal in humans,
common in plants
Cystic fibrosis (autosomal recessive)- most common lethal genetic disease. Buildup of
extracellular fluid in the lungs.
Phenylketonuria (PKU) (autosomal recessive)- inability to break down amino acid phenylalanine,
elimination of phenylalanine from diet or serious mental retardation
Tay-Sachs disease (autosomal recessive)- early in life and caused by lack of enzyme needed to
break down lipids. Results in seizures, blindness, and early death. Jews
Huntingtons disease (autosomal dominant)- degenerate disease of the nervous system
resulting in early death. Middle age
Klinefelters syndrome- XXY 47 chromosomes= male with an extra X chromosomes- Have male
genitals, but testes are abnormally small and sterile.

Karyotype- laboratory procedure that analyzes the size, shape, and number of chromosomes

Mendellian Genetics
Monohybrid cross- one trait being studied
Dihybrid cross- two traits being studied
Test Cross- to determine the genotype, cross it with recessive plant

1. Law of Dominance- one trait masks the effect of the other

2. Law of segregation- alleles separate and recombine
Ratio of phenotype (3:1)
Ratio of genotypes (1:2:1)
3. Law of Independent Assortment (In Dihybrid cross)- traits segregate randomly
Ratio (9:3:3:1) significant variation indicates linkage

Sex-Linked Traits gene carried on sex chromosomes

Always X-linked in this test
Hemophilia, color blindness
Carriers- females who are heterozygous for a disease
An x linked recessive trait cannot go from father to son
All daughters of males affected by an X-linked recessive condition are carriers
Sex-influence traits- influenced by the sex

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male pattern baldness (Females express the genes for pattern baldness differently)

Pedigree analysis
Individuals who marry into the family are completely normal
Males-square females-circles
1. Dominant or recessive? Recessive skip generations (The afflicted children must have
afflicted parent if it is dominant)
2. Sex linked or autosomal? More male with disease, sex linked (look at the afflicted
female, and if sex-linked, the father must be afflicted)

Polygenic inheritance- results from a blending of several separate genes that vary along a
continuum. (Skin color, hair color, and height) (results in bell-shaped curve)

Evolution- the origin of life

Todays atmosphere- nitrogen, oxygen. Todays primary organisms- aerobic

Early atmosphere- Hydrogen, ammonia, methane, and water (heterotroph hypothesis)
Heterotrophs were formed first, and then autotrophs (anaerobic)
Theory of endosymbiosis- mitochondria, nucleus, and chloroplasts were individual cells

Comparative Embryology- the earlier that embryonic development diverges, the more
dissimilar the mature organisms are
Archaeopteryx- dinosaurs to birds
Hyracotherium (Eohippus)- ancient horse
Gene pool- all the genes of all the people in the whole population
Genetic variability- each person has distance set of genes
Cause of genetic variability- random mutation of DNA (other sources as well)
Natural selection- driving force of evolution
Species- able to interbreed in nature and produce viable, fertile offspring
Evolution- change of population over time or population undergoes a change in the frequency
of alleles in its gene pool
Evolution is defined in terms of population but occurs in terms of individuals.
Fitness- ability to contribute to the next generations gene pool producing surviving offspring .
Darwins points
1. Each species produces more offspring than can survive
2. These offspring compete with one another for the limited resources
3. Organism in every population vary which makes some more fit than others. The
offspring with the most favorable traits are most likely to survive and will pass their
traits to their offspring.
Random mutation of DNA- slow Competition-Rapid
Evolution happens because
1. Genetic variability allows some individuals to be better competitors than others.
2. The winners survive, reproduce, and pass their genes on to their offspring

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 3. The offspring have genes like their parents, hence the gene pool changes. With each
generation, it has more and more of the alleles that come from the better competitors.

Hardy-Weinberg principle- allele frequency remain constant

1. Random mating so that no particular trait is favored. No assortative mating (no
organism may select partners that resemble themselves)
2. No immigration or emigration
3. No mutation
4. Large population
5. No natural selection
6. P= dominant q= recessive. p+q=1, p2+2pq+q2=1
Genetic drift- changes in the gene pool caused by random events in a small population
Population bottleneck- reduced population due to disasters (genetic drift)
Founder effect- colonization of new habitat (genetic drift)
Genetic drift, mutation, and migration are random but natural selection is not
Stabilizing selection- does not change the average but values of population lie closer to average.
It weeds out the extreme values.
Disruptive selection- either extreme in the trait (two peaks)
Directional selection- alters the average value for a trait
Kin selection- altruistic behavior, sacrifice itself so that its kin might survive
Six types of isolation that causes speciation
1. Geographic isolation- new species may form when a group of individuals are isolated
2. Polyploidy (plants)
3. Habitat isolation- two organism that live in the same area but encounter each other
rarely (water snake and terrestrial snake)
4. Behavioral isolation- some change in behavior of one member (blinking in fireflies)
5. Temporal isolation- mature in different seasons (Flowers)
6. Reproductive isolation- anatomical incompatibility (large dog and a small dog)
Lamarcks theory- theory of use and disuse and inheritance of acquired characteristics (giraffe)
Comparative anatomy- convergent and divergent evolution, vestigial organs
Patterns of evolution
1. Divergent evolution- two population of the same species end up having different traits
Homologous structures- common in species that share a common ancestor
2. Convergent evolution- production of similar traits between two separate population or
species.
Analogous structures- similar adaptation resulting from convergent evolution (wings)
Convergent evolution never results different species becoming a same specie.
3. Parallel Evolution- two related species that made similar evolutionary adaptations after
their divergence from a common ancestor (grey wolf, placental; Tasmanian wolf,
marsupial)
4. Coevolution- adaptation between two interacting species (prey-predator; pollinator-
plant)
5. Adaptive radiation- production of different species from a single ancestral species; once
was same niche but occupied different niches

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Speciation- formation of new species (extreme form of divergent evolution)
1. Allopatric speciation- speciation due to physical barrier
2. Adaptive radiation- production of different species from a a single ancestral species;
once was same niche but occupied different niches

Theories about evolution

1. Gradualism- descend from common ancestor gradually (abandoned)
2. Punctuated equilibrium (Gould and Eldridge)- new species appear suddenly after long
periods of no change
3. Spontaneous generation- (disapproved by Redi and Pasteur)

Two mass extinctions- Permian mass extinction (enormous volcanic eruption in Siberia),
Cretaceous mass extinction- 10-km wide asteroid crashed in Yucatan peninsula. (dinasours)

Industrial melanism- darkening due to industrialization (frequency of alleles changed).

Broad categories- heterotrophic aerobes (amoebae, earthworms, humans), heterotrophic
anaerobes (yeasts), autotrophic aerobes (green plants), autotrophic anaerobes
(chemosynthesis bacteria)
Phylogeny-classifying based on evolutionary relationships
Taxonomy- science of classification and naming
Binomial system- both italics, genus capitalized
Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
Dumb King Philip Came Over From GermanySo?

Domain Bacteria- bacteria most people are familiar with (E. Coli)
Eubacteria- one kingdom
Cyanobacteria (blue-green algae)- contain chlorophyll and can photosynthesize
They lack a nucleus, or any membrane-bound organelles (except ribosomes), cytoskeleton,
circular DNA.

Domain Archaea- extremophiles- lack nuclei and organelles and have circular DNA but some
features are common with eukaryotes.
Halophiles- live in extremely salty condition
Thermophiles- live in extremely hot conditions
Methanogens- methane gas as waste products

Domain Eukarya
Contains nuclei, membrane-bound organelles, and linear DNA
4 kingdoms

Kingdom Protista
Some are unicellular and some are multicellular. Most diverse kingdom
1. Phylum Rhizopoda (Amoebas)- Unicellular, pseudopods, contractile vacuole

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 2. Phylum Apicomplexa (Sporozoans)- Animal parasites, cause malaria (plasamodium), life
cycle of sexual and asexual stages that often require two or more different hosts species.
3. Phylum Ciliophora (Ciliates) unicellullar, ciliates, contractile vacuole, paramecium
4. Slime Molds- many nuclei
5. Phylum Euglenophyta (Euglena)- unicellular, photosynthetic algae, move with flagellum
6. Phylum Bacilariophyta (Diatoms)- unicellular, glass-like walls, form diatomaceous earths,
most important producers in phytoplankton
7. Phylum Phaeophyta (Brown Algae)- seaweeds, most complex, multicellular

Kingdom Plantae
Alternation of generation
Multicellular, eukaryotic, photosynthetic, and cell walls made of cellulose
Nonvascular and Vascular. Within Vascular, seed or non-seed, Within seed, angiosperms or
gymnosperms.
Tracheophytes- plants with vascular tissue, bryophytes- nonvascular plants
1. Division Bryophyta (nonvascular plants)
Lacks vascular tissues, live in places where water is abundant, do not have true stems,
leaves and roots. Mosses, Liverworts, and hornworts.
2. Division Pterophyta (Ferns)
Have xylem and phloem, as well as true stems, leaves, and roots. Reproduce by spores.
3. Division Coniferophyta (nonflowering plants- gymnosperms)
Vascular plants, produces seeds, but dont produce flowers
4. Division Anthophyta (flowering plants- angiosperms)
Produce flowers and pollen
A. Monocots- single cotyledons, parallel veins, flower petal in multiple of threes,
scattered arrangement of vascular tissue, and fibrous root system
B. Dicots- two cotyledons, netlike veins, flower petal in multiple of four or five, ringed
arrangement of vascular tissue, and a taproot system

Kingdom Fungi
Eukaryotic, multicellular (except yeasts), cell wall made out of chitin. Lack chloroplasts and
therefore heterotrophic. Lack digestive system and therefore absorptive feeder (extracellular
digestion). Saprobes- obtain food from decaying organic matter. They are decomposers.
1. Division Zygomycota
Reproduces sexually and includes common molds
2. Division Basidiomycota (club fungi)- mushrooms, shelf fungi, and puffballs

Kingdom Animalia
1. Phylum Porifera (sponges)
Sessile, no symmetry, reproduce asexually by fragmentation, are hermaphrodites,
perforated body wall made of two layers of cells (mesoglea), no nervous or muscle
system, small amount of specialization
2. Phylum Cnidaria (coelenterates)

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 Two layers of cells (mesoglea) and a gastrovascular cavity (extracellular digestion), also
intracellular digestion in lysosomes. Radial symmetry. No circulatory or respiratory
system, simple nerve net, cnidocytes, nematocysts (Hydra, jellyfish, sea anemones)
Polyps- mouth upward, asexual, sessile
Medusa- mouth pointing downward, sexual, motile
3. Phylum Platyhelminthes (Flatworms)
Three layers of cell, lack circulatory system, single opening digestive system, lack coelom
Bilateral symmetry, moderate cephalization, exchange oxygen and nutrients through
skin. Planaria (nonparasitic), flukes, and tapeworms (both parasitic).
4. Phylum Nematoda (roundworms)- three layers, digestive system with two openings,
pseudocoelom- muscle lining in the interior body wall but not around the gut. No
respiratory or circulatory system, exchanging gases directly with the environment.
5. Phylum Mollusca (Mollusks)
Soft-bodied animals with hard external shells (snails, oysters) except octopus and squids
(internal shells). Mollusks have three major body regions(foot, visceral mass, mantle)
open circulatory system with hemocoels or sinuses. radula- rasping tongue
6. Phylum Annelida (Segmented Worms)
Closed circulation with five pairs of aortic arches, blood contains hemoglobin, two-
opening digestive tract (mouth, anus), crop and gizzard, excrete waste through
nephridia. Coelom, nervous system, exchange gases through their skin (Earthworms and
leeches)
7. Phylum Arthropoda (Arthropods)
Most diverse phylum in animal kingdom. Jointed appendages, hard exoskeleton contain
chitin, and a segmented body with head, thorax, and abdomen. Crop and gizzard.
Respiratory system, Open circulation through open spaces called sinuses (hemocoels),
eliminate wastes through Malpighian tubules (digestive tract). Direct exchange- no
oxygen carriers needed (blood is needed to exchange food) Insects- spiracles and
tracheal tubes. Arachnids- book lungs. Largest and most diverse phylum (Crustacean,
insects, and arachnids).
8. Phylum Echinodermata (Echinoderms)
Radial symmetry, spiny exoskeletons. Water vascular system with tube feet that
functions in feeding, gas exchange, and movement; deuterostomes (Sea stars, sea
urchins, and sand dollars)
9. Phylum Chordata (Chordates)
Notochord, ventral heart, a dorsal nerve cord, pharyngeal gill slits, and a tail. (Notochord
and gill slits- embryonic)
A. Class Chondrichthyes (cartilaginous fishes)
Skeletons made out of cartilage, they breathe through gills, oil-producing livers.
B. Class Osteichthyes (Bony Fishes)
Bone skeletons, lay eggs without shells, swim bladder, 2-chambered heart
C. Class Amphibian (Amphibians)
Adapted to both land and water. Breath through lungs and/or skin. Lay eggs without
shells in water. Frogs and Salamanders. 3-chambered heart
D. Class Reptilia (Reptiles)

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 Terrestrial with thick, scaly skin adapted to resist waterless. Eggs have shells, breath
through lungs. Crocodiles, lizards, and snakes. 3-chambered heart
E. Class Aves (Birds)
Tetrapods, breath through lungs and lay shelled eggs, endothermic. 4-chambered
heart
F. Class Mammalian (Mammals)
Endothermic, have hair, sweat glands, nourish their young from mammary glands,
breathe through lungs.
Dorsal- backbone. Ventral- opposite side
Protostomes- embryo divide in spiral pattern (Annelida, Arthropods, Mollusks)
Deuterostome- embryo divide in radial pattern (Echinoderms, Chordates)
Coelom- cavity between the gut and external wall, muscle lining gut and interior wall
FARBM
Cladograms (phylogenetic tree)- shared and derived traits
Microorganisms

Fungi
Multicellular eukaryotes, chitin, some are multinucleate, absorptive feeders, digest their food
outside their bodies, decomposers.
Reproduction
1. Asexual spores- like seeds that form new fungus
2. Sexual spores- It combines to form new fungus
3. Vegetative growth- portion of fungus breaks off to form new fungus
4. Budding- new fungus grows off a side the old fungus (yeasts)

Bacteria
Reproduce by binary fission, only prokaryotes, DNA found in cytoplasm, circular DNA,
peptidoglycan cell wall.
Binary fission (algae and bacteria) - equal cytoplasm
Budding (yeast and hydra)- unequal cytoplasm
Genetic recombination-mixing up DNA-of bacteria.
1. Transformation- new DNA from the environment
2. Conjugation- replicates its DNA and donates it to another bacteria through pilus
3. Transduction- virus carries DNA from one bacterium to another during infection.
How bacteria get its nutrition
1. Photosynthesis- Cyanobacteria (autotrophs)
2. Obligate aerobes- needs oxygen
3. Obligate anaerobes- poisoned by oxygen
4. Facultative anaerobes- survive with and without oxygen
Auxotrophs- organism that requires supplementary nutrition
Wild type- doesnt need supplementary nutrition
Nitrogen-fixing bacteria- lives in nodules of legumes, mutualism.

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Viruses
Capsid- coat made of protein, Genome- nucleic acid (RNA or DNA)
Viral life cycle starts with 1. Attachment- can attach to a particular host 2. Infection- the virus
injects its genome.

2 possible life cycle of a virus

1. Lytic cycle- the viral genome is first transcribed and translated to make protein, host
DNA polymerase so replicate the viral genome, and host cell breaks apart (Lysed)
2. Lysogenic cycle- not transcribed or translated immediately but inserted (integrated) into
hosts genome and replicated with the host cell. If the host cell experiences hardships, it
begins the lytic cycle. (Cold sores)
Animal viruses does not have to kill the host cell because they dont have cell walls. It can
simply bud out and coated in plasma membrane (envelope).
Viruses with RNA genomes has to use RNA-dependent RNA polymerase
Retroviruses are RNA viruses that go through lysogenic life cycle. To insert its DNA, it has to
make one in the first place. They make it by RNA-dependent DNA polymerase also called
reverse transcriptase. (HIV)

Recombinant DNA Technology- DNA from two sources and combining them in one cell
Restriction enzymes- recognize a particular short DNA sequence and cut the DNA strand.
Restriction fragments- pieces of DNA that are resulted from the cuts
Palindrome (it reads the same from both direction)
Staggered cut- stick ends are left (can combine with any other DNA cut with same restriction
enzyme).
Blunt cut- blunt ends (can be litigated to any other piece of DNA cut with any other enzyme)
Gel electrophoresis- separates DNA on the basis of the rate of movement through a gel in an
electric field. Smaller the molecule, the faster it runs through the gel.
Polymerase Chain Reaction (PCR)- cell free technique in which a piece of DNA can be rapidly
copied or amplified.
Plasmid- circular piece of DNA found in bacteria and yeasts. Used in recombinant DNA
DNA ligase permanently joins the base-paired regions
Vector- shuttle used to move DNA between species
Restriction enzymes gives us ability to cut and paste DNA

Control: the Nervous and Endocrine Systems

Nervous system
Process-dendrites and axons
Polarized- resting neurons
Resting membrane potential (RMP)- -70mV
Two membranes that maintain RMP- NA+/K+ ATPase and the K+ leak channel
Sodium-potassium pump pumps out sodium and pumps in potassium
Potassium Leak channel will allow potassium to leak out of the cell
Voltage-gated Channels- open when cell reaches certain voltage

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Threshold potential- potential at which the voltage-gated channels open.
Sodium voltage-gated channels and potassium voltage-gated channels.
Action potential (in axon)
1. Depolarize slightly to -50 mV and voltage-gated channels will open
2. Sodium voltage-gated channel will open first, depolarizing it to +35mV
3. Then, voltage-gated sodium channel close and voltage-gated potassium channels open.
4. Leaving potassium repolarizes the cell to -90mV and potassium voltage-gated channels
close.
5. Na+/K+ ATPase and potassium leak channel bring the cell to its polarized state.
Wrapping of Schwann cells is called Myelin sheath
Nodes of Ranvier- spaces between Schwann cells, only part that fires action potential
Saltatory conduction- jumping type of conduction
Refractory period- short period of time that cannot fire action potential
Larger the neuron, the faster. Size of the action potential is the same but frequency is not
Multiple sclerosis- body mounts a reaction against myelin sheath
Synapses- point where impulse gets transferred
Neurotransmitters- chemicals in synapses
Acetylcholine- most common neurotransmitter (in vesicles; calcium causes vesicle to fuse)
Synaptic cleft- small gap between axon and the dendrite
Summation- sum of all the information
Neuromuscular junction- synapse of neurons and the muscle
Stimulated- depolarize toward threshold
Inhibited- move away from threshold
Turning off a synaptic neurotransmitter
1. Diffusion
2. Enzymatic inactivation
3. Reuptake into cells by transporter

CNS- Interneurons (brain and spinal cord)

Cerebrum- controls voluntary motor activity. Outer portion- gray matter (cell bodies), inner
portion- white matter (axons)
Olfactory bulb- smell
Thalamus- relays signals to and from cerebrum
Hypothalamus- controls the endocrine system through pituitary gland and regulates
homeostatic function such as hunger, thirst, and water balance. Bridge between endocrine and
nervous system.
Cerebellum- muscle activity is coordinated here

Brainstem- midbrain, pons, medulla oblongata reticular formation

Pons- links cerebrum with cerebellum
Medulla oblongata- breathing, heart rate, and gastrointestinal activity (swallowing)
Reticular formation- switch of the cerebrum, alertness and attentiveness

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Reflex arc (knee jerk reaction)- simplest nerve response; consist of only sensory and a motor
neuron. Spinal cord not involved.
More complex arc (hands from a hot iron)- sensory neuron to interneuron in spinal cord to
motor neuron and brain
Dorsal horn- entrance point for sensory nerve fibers
Ventral horn- contains cell bodies of motor neurons connected with cerebrum
PNS- sensory neurons, motor neurons.
PNS- Somatic (voluntary, acetylcholine), Automatic (involuntary)
Automatic- sympathetic (norepinephrine)- lowers the digestive rate, causes pupil dilation,
glycogen into glucose, increased heart/breathing rate
parasympathetic (acetylcholine)- increases digestive rate, do not cause pupil dilation, lowered
heart/breathing rate

Eyes- optic nerves, cornea, lens, iris, pupil

Retina- contains photoreceptors, converts light into nerve impulses
Humor- fluid that maintains the shape of the eyeball
Cone- color
Rods- black and white

Ears- outer ear, inner ear

Outer ear- auricle (pinna), auditory canal
Middle ear- tympanic membrane, ossicles (malleus, incus, and stapes) (hammer, anvil, stirrup)
Inner ear- cochlea-fluid filled, send nerve impulses; semicircular canal- balance

Endocrine system- slow, hormones, target organs

Tropic hormone- stimulate other glands to release hormones
Peptide hormones-amino acid-base, rapid effects, extracellular (insulin, glucagon, prolactin,
ADH). Act through intracellular secondary messengers (signal transduction cascade)(amplify)
Steroid hormones- steroid base, slow effects, intracellular (estrogen, cortisol, progesterone
testosterone, aldosterone). Primary messenger
Positive feedback- enhances an already existing response (makes it stronger) (baby being born)
Negative feedback- common mechanism in endocrine system to maintain homeostasis, keeps
hormones check on each other
Endocrine Glands
Pituitary gland- controlled by the hypothalamus
Anterior pituitary gland (Flat Pig)
1. Growth Hormone (GH)- target all tissues and organs, growth, older cell are replaced
with newer cells (cell-turnover rate)
2. Thyroid stimulating hormone- target organ thyroid
3. Adrenocorticotropic hormone- target organ adrenal cortex to secrete corticoids
4. Follicle stimulating hormone- target organ gonads, maturation of ova, estrogen, sperm,
maturation of seminiferous tubules and follicles
5. Luteinizing hormone- target organ gonads, corpus luteum, testosterone, surge of it
stimulates ovulation

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 6. Prolactin- after childbirth, target organ mammary glands to make milk
Posterior pituitary gland-hypothalamus makes hormones
1. Oxytocin- causes uterus to contract during childbirth, causes mammary glands to
release milk.
2. Antidiuretic hormone (vasopressin)- kidneys to retain water

Thyroid gland
Thyroxine- increase rate of metabolism
Calcitonin- remove calcium from blood to make new bone
Goiter- not enough iodine and thyroxine

Parathyroid glands- parathyroid hormone (parathormone) dissolve bone to release calcium.

Adrenal Glands- Adrenal medulla (middle) adrenal cortex (outer)

Adrenal medulla- epinephrine and norepinephrine (lot longer than neurotransmitters)
Adrenal cortex- steroid hormones (corticosteroids) - glucocorticoids, mineralocorticoids, and
sex hormones.
Glucocorticoid- target organ liver, gluconeogenesis- produce glucose from fats and protein, also
target other body cells to use fats for fuel. Also strong anti-inflammatory agents (cortisol).
Cortisol deals with stress but represses immune system.
Mineralocorticoids- target organ kidneys, aldosterone- retain sodium and water
Sex steroid- not comparable with that of gonads

Pancreas- secrete hormones and digestive enzymes(endocrine and exocrine)islet of Langerhans

Insulin- targets all cells, decrease blood glucose level by storing it as glycogen
Glucagon- targets liver, increase blood glucose level by breaking glycogen (glycogenlysis)

Thymus- thymosin- stimulates T lymphocytes

Pineal- melatonin- biorhythms

Gonads- testes, ovaries (all steroid)

Androgens- male sex hormone (testosterone)
Estrogen-estradiol-stimulates growth of the uterine lining in the first half of the cycle
Progesterone- maintains the lining in the second half of the cycle.

Transport and Ventilation: The circulatory and respiratory systems

Circulatory system
Pump, tubing, and fluid
Blood-erythrocyte
Plasma water, 50% of blood, glucose, etc (carries carbon dioxide)
Red blood cell (erythrocytes)- 45% of blood volume, do not have a nucleus and mitochondria
Contains hemoglobin which becomes oxyhemoglobin

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Immune system
Passive immunity- antibodies are borrowed; temporary
Histamine- causes vasodilation (enlargement of blood vessels) and causes inflammation and
responsible for symptoms of the common cold
Interferons- chemicals released by immune system to block against viral infection
Active immunity- permanent, one makes antibodies for oneself
White blood cells- phagocytes and lymphocytes
Phagocyte- engulf bacteria (macrophages)
Neutrophils- phagocytic cell that are first cells to arrive at a site of inflammation
Lymphocyte- B cell, helper T and killer T cells (specific antigen- triggers immune response)
B-cells- make antibodies, produce memory cells (humoral response)
Helper T-cells- help B-cells and T-cells divide and proliferate.
Killer T-cells- kill the cell that is infected (cell-mediated response- hand to hand combat)
Once lymphocytes recognize an antigen, it becomes active and proliferates into (plasma cells-
primary immune response- do not live long) (memory cells- immunological memory- lifetime)
Carbon dioxide-bicarbonate buffer (pH of 7.4)
HIV- kills helper T-cells, retrovirus
Bone marrow produces blood cells
Allergies- responds to allergens, produce histamine, can cause anaphylactic shock
Antibiotics- cure vaccines- prevent autoimmune disease- MS, rheumatoid arthritis

Blood types- determined by membrane protein that sit on the surface of red blood cells
Agglutination- clumping of red blood cell; happens when the body doesnt recognize the
proteins on the newly received blood.
Blood AB- universal recipient. Blood O- universal donor
Platelets release enzyme thromboplastin, and that with aid of calcium and vitamin K activates
prothrombin into thrombin which converts fibrinogen into fibrin.
Serum- plasma minus clotting factors

Arteries-Arterioles-capillaries-venules-veins
Arteries- thick, muscular walls, high pressure, regulate diameter to regulate blood flow, pulse
Veins- lower pressure, no muscle, no pulse, do have valves(passive-muscles help them)
Intracellular fluid- net loss of fluid to the tissue

Lymphatic System- network of vessels that begins at the tissues and ends at the veins.
Thoracic duct- largest lymph vessel
Filters the intracellular fluid through lymph nodes
Edema- swelling of a body due to trapped tissue fluid
Lymphatic vessels- similar to veins- low pressure, no muscle, have valves
Right side- pulmonary circuit. Left side- systemic circuit
Anterior vena cava, posterior vena cava- two largest veins
Vena cava- right atrium- right AV valve (tricuspid) right ventricle- pulmonary semilunar valve-
pulmonary artery- lungs- pulmonary veins- left atrium- left AV valve (bicuspid valve) left
ventricle- aortic semilunar valve- aorta

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Atrioventricular valves- valves between the atria and the ventricles
Semilunar valves- valves between ventricles and arteries
AV valves close first then semilunar valves close second
Sinoatrial node- tissues in right atrium that start the beat
Systole- contraction of the ventricles (systolic pressure)
Diastole- relaxation of the ventricles (diastolic pressure) (120/80)
Fish- two chambered heart- single circuit
Amphibians, turtles, snakes, and lizards- three chambered heart- two circuit. Amphibians (skin)
Crocodiles, alligators, and birds- four chambered hearts- two circuits
Arthropods- open circulatory system. Water (gills) terrestrial (tracheae)

Ventilation and Gas Exchange- The respiratory system

Ventilation- move air into and out of the lungs
Gas exchange- exchange oxygen and carbon dioxide
Also regulates pH of the body

Conduction Zone- no gas exchange

Nose- pharynx (throat)- Larynx (voicebox)- trachea (windpipe)- right and left primary bronchi-
bronchioles- alveoli (Not in conduction zone). Trachea and bronchi have mucus and cilia.
Respiratory Zone- Gas exchange
Alveoli- passive diffusion because gases are hydrophobic

PH regulation is by respiratory system and renal system but respiratory system is better
Blood pH- 7.35-7.45
Carbon dioxide makes an acid. If body gets too acidic then you breathe faster, and if it is too
alkaline, you breathe slower.
Diaphragm- curves up while relaxing, and flattens out when it contracts
Inspiration, expiration

Processing, Support, and Reproduction: The Digestive, Urinary, Skeletal, Muscular, and
Developmental Systems

Digestive system
Mechanical (cutting and grinding), chemical (enzymatic hydrolysis)
Alimentary Canal, Accessory organs two major groups
Peristalsis- rhythmic contraction (all alimentary canal organs)
Alimentary Canal- Mouth-Esophagus-Stomach-Small Intestine- Large Intestine- Rectum- Anus
Accessory Organs- teeth, tongue, salivary glands, liver, gallbladder, and pancreas (plays part in
the digestion but not part of the alimentary canal)
Endocrine secretion-secretion of hormones into the blood
Exocrine secretion- secretion of hormones into the body cavities or onto the body surface (skin)

Alimentary Canal
Ingestion, bolus, salivary glands, esophagus, epiglottis, epithelial

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Salivary amylase- digestive enzyme, in saliva, digest starch into maltose
Stomach- acidic, contains pepsin (breaks protein), chyme
H.pylori- causes ulcers
Small intestine- most digestion and absorption, duodenum (digestion), middle (absorption)
pyloric sphincter (bottom), cardiac sphincter (top), contains villi. Basic (8)
Villi- contain capillaries and lacteals (projection of the lymphatic system). Capillaries absorb
amino acids, glucose while fats are transported in lacteal in lymphatic system..
Bile- produced by the liver and concentrated in the gallbladder (emulsifies fat) (pH 11)
Livers function- stores glycogen, produces glucose, metabolizes fats (Beta-oxidation of fatty
acids to ketones), interconversion of carbohydrates, fats, and amino acids, destruction of old
erythrocytes, produces blood proteins, stores vitamin B12 and iron, and detoxifies the blood.
Pancreas- secretes nucleases, amylase, lipases (fats), peptidases (protein)(trypsin,
chymotrypsin), bicarbonate (base to neutralize acids)
Hepatic portal system- deliver nutrients from the intestines to the liver (portal veins)
Large Intestine- reabsorbing water, keeps E. Coli (Vitamin K, B vitamins)

Urinary System- Carbon dioxide and water are eliminated by respiratory system but other
wastes go through kidneys and eliminated as urine.
Three waste products- Urea (mammals, earthworms; amino acids; liver), Uric acid (insects, birds,
reptiles; minimum water loss), Ammonia (toxic, soluble in water; fish, hydra), creatinine
(muscle metabolism)
Nephron- functional unit of the kidney
1. Glomerulus- tiny knot of capillaries at the beginning. Blood pressure forces through
the pores of Bowmans capsule.

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 2. Bowmans capsule- receives only plasma (filtrate not lymph) (cells are too big)
3. Proximal convoluted tubule- most reabsorption and secretion
4. Loop of Henle- lot of water reabsorbed, salt transported out of filtrate into the kidney.
Longer the loop, the greater the concentration gradient, more water absorbed. Medulla
is saltier than the cortex.
5. Distal convoluted tubule- Fine tuning of reabsorption and secretion. Aldosterone has its
effect (increases sodium reabsorption therefore increasing blood volume)
6. Collecting Duct- water absorption is regulated. Antidiuretic hormone has its effect. It
causes the walls of collecting duct more permeable to water. ADH (vasopressin) levels
are high when body is dehydrated.
Antidiuretic hormone (ADH, vasopressin)
Produced by hypothalamus and secreted by posterior pituitary, makes collecting duct
more permeable to water, leads to rise in blood volume and pressure
Aldosterone- produced by adrenal cortex; reabsorbed sodium and secrete K, leads to
rise in blood volume and pressure.
Three process in the nephron
1. Filtration- forcing plasma out of the capillaries into Bowmans capsule
2. Reabsorption- taking substances out of the filtrate and returning them to the blood
(glucose and amino acids are always absorbed. Ions and water depends.)
3. Secretion- Taking substances out of the blood and adding them to the filtrate.
(Creatinine, some ions, drugs, and toxins are always secreted)
Filtration is depended on blood pressure. Kidneys play a role in maintaining blood pressure.
Renin- Enzyme that kidney releases when blood pressure is low.
Angiotensin II- constricts blood vessels and produced by renin and causes secretion of
aldosterone
Ureter- connects kidney and bladder
Urethra- outermost part of the kidney
Metanephridia- worms kidney like structure
Malpighian tubules- insects kidney like structure

Skeleton system- shape and support

Vertebrates- skull and backbone with vertebrae
Hydrostatic skeleton- muscle of flatworms and annelids- incompressible fluid
Endoskeleton- bone- calcium and protein collagen
Osteoclasts- destroys osteoblasts- creates
Dermal bone- bone made from direct ossification (bones of the skull) (dont grow)
Replacement bone- osteoblast replace the cartilage (long bones of legs and arms) (grows)
Bone marrow- create blood cells
Spongy bone- central portion of bone, marrow-filled spaces, low density, lateral stress
Compact bone- located on the outer surfaces, hardness of the bond, longitudinal stress
Haversian system- cylindrical unit which makes up compact bone
Axial skeleton- skull, vertebral column, rib cage
Appendicular skeleton- bones of the appendages, pectoral and pelvic girdles

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Muscular system
Cardiac muscle- heart, single nucleus, striated, dont require synapses
Smooth muscle- walls of hollow organs, walls of vein and arteries, single nucleus
Skeletal muscle- multinucleate, striated, sarcomeres, neuromuscular synapses
Muscle proteins- actin (thin chains) and myosin. (Thick fibers)
Actin and myosin- sarcomere- myofibrils- muscle cell- fascicle- whole muscle
Sarcomere- first component that actually contracts
Z-lines- ends of the sarcomere; where actin attaches
Sliding filament theory, striated, muscle contraction requires calcium.
Motor end plates (neuromuscular junctions)- special synapses to muscle (acetylcholine)
Flexor- bends to an acute angle
Extensor-straightens the bones

Skin- largest organ

Job- protect the body from abrasion, heat and water loss, infection, and UV radiation, vitamin D
production, sensation, and thermoregulation. Osmoregulation- water and salt
Cold-blooded (ectothermic, poikilothermic) Warm blooded (endothermic)

Reproduction and Development- Male system

Testosterone- normal sperm development, puberty, produced in response to luteinizing
hormones.
Scrotum- sac contains testes
Prostate gland- secretes semen
Seminiferous tubules- tubes inside testes that produces sperm in response to follicle-
stimulating hormones.
Vas deferens (sperm duct)- connects with urethra to carry sperm out of the body

Reproduction and Development- Female System

Two main organs- ovaries (gametes), uterus (pregnancy)
Ovaries controlled by pituitary gland (FSH and LH). Uterus controlled by estrogen and
progesterone. Two cycles (ovarian and uterine cycle)

Uterine cycle- menstruation, proliferative phase, and secretory phase.

Menstruation- shedding of the old uterine lining (endometrium), Day 1 of the cycle, hormone
levels are low, last for 5 days
Proliferative phase- endometrium is built under the control of estrogen. Last from Day 6 to
about day 13.
Secretory phase- endometrium is maintained and enhanced, new blood vessels are added,
under the control of progesterone. When level of progesterone fall, it ends in day 28.

Ovarian cycle- Follicular phase, ovulation, luteal phase

Follicle phase- Day 1 to Day 13. FSH causes development of a follicle in the ovary. Follicle is a
maturing oocyte and its surrounding cells which divide and secrete estrogen.

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Ovulation- release of the oocyte from the follicle into the Fallopian tube (oviduct). Cause by
large surge of LH. Some follicle stay behind and form corpus luteum under the control of LH
which marks the onset of the luteal phase.
Luteal phase- corpus luteum secretes mostly progesterone, and after two weeks, degenerates

Or

Gonadotropin-releasing hormone (GnRH)- from hypothalamus produce FSH and LH

FSH, LH- from pituitary gland produce estrogen and progesterone
Estrogen and progesterone inhibits the production of FSH and LH except in ovulation

1. Follicular stage (day 4-14)

FSH stimulates follicles to mature and produce estrogen (thickens uterine lining)
2. Ovulation (day 13 or 14)
Release of ovum from ovary. LH surge is key factor. Constant high level of estrogen
block the LH surge; therefore estrogen is low, and LH is high.
3. Corpus Luteum Stage (luteal stage)- (day 15-28)
Remains of the follicle create corpus luteum. LH stimulates corpus luteum to produce
progesterone and estrogen, which stimulates vascularization. If no fertilization occurred
the increase estrogen and progesterone block LH production and corpus luteum shrinks.
4. Menstruation- if fertilization did not occur, bleeding happens (4 days)
If fertilization did occur, placenta produces human chorionic gonadotropic hormone
(hCG) which maintains corpus luteum and produce progesterone and estrogen.

If ovum becomes fertilizes and implants, the embryo secretes hormone called human chorionic
gonadotropin which prolongs the life of corpus luteum which secretes more progesterone.
Fraternal (dizygotic) twins- two separate sperm fertilize two eggs
Identical (monozygotic) twins- separation of identical cell, identical genomes
Ovary- where meiosis occurs
Uterus- where blastula will implant
Cervix- mouth of the uterus
Endometrium- lining of the uterus

Reproduction and Development- Fertilization, embryology, and fetal development

1. Gametes are formed
2. Egg (ovum) is fertilized- Egg is in Fallopian tube when fertilized. Top of the sperm is a
region called acrosome which helps penetrate the barriers.
3. Zygote is formed
4. Cleavage- rapid mitosis with no accompanying growth. It becomes solid ball of cells
called morula. It travels down the uterine tube toward uterus.
5. Implantation in the uterus. Morula continues to divide and hollow out to become
blastula. The fluid-filled cavity is called blastocoel and individual cells are called
blastomeres. It further developed and becomes blastocysts Inner cell mass becomes

23
 embryo and all embryonic structures and membranes (umbilical cord, amniotic sacs)
and outer ring of cell becomes placenta.
6. Embryonic Stage- last till eight weeks of development, gastrulation and neurulation

Gastrulation- inner cell divides into three layers called primary germ layers.
(Differentiation)
Endoderm- inner linings of respiratory system, digestive system, reproductive system,
and the urinary system. Forms glandular organs (digestive) (bladder, liver, pancreas, and
salivary glands)
Mesoderm- middle structures such as bones, blood vessels, muscles, heart, and non-
glandular organs (kidneys, ureters, gonads).Primitive animals such. As sponges and
cnidarians develop mesoglea instead of mesoderm.
Ectoderm- forms external structures (skin, teeth, hair, nails, etc) linings of the mouth
and anus, and all nervous system structures (brain, cord, nerves, eyes, etc)

Neurulation- All organs are formed (organogenesis)

7. Fetal stage- baby simply grows and matures

Gametes- fertilization- zygote- cleavage- morula- blastocyst- implantation in the uterus-

gastrulation- neurulation- fetus- Birth
Fish and amphibians- external fertilization, non-water proof egg, little parental care
Turtle, snakes, lizards- internal fertilization, waterproof egg, little parental care
Crocodiles, alligators, and birds- internal fertilization, hard waterproof eggs, some parental care
Mammals- prolonged period of parental are.

Extraembryonic membranes- outside the embryo; yolk sac, amnion, allantois, and chorion.
Yolk sac- surrounds the yolk of an egg (food). Placental mammals have little yolk because we
get nutrition from placenta. Human yolk is source of the first blood cells.
Amnion- clear membrane that surrounds the developing embryo filled with amniotic fluid.
Allantois- In humans, it becomes umbilical cord (all embryonic). In birds and reptiles, becomes
disposal site for solid wastes. It does respiration and excretion, particularly gas exchange.
Chorion- outermost membrane, in humans it forms embryos part of the placenta, it encloses
all membranes. In birds and reptiles, it lines the inside of the eggshell. Permits, not do, gas
exchange.

Plants

Apical meristem- roots and stem

Roots- zone of cell division, zone of elongation, zone of differentiation
Zone of cell division- meristemic, cells dividing
Zone of elongation- cells are elongating
Zone of differentiation- undergo specialization: epidermis, ground tissue, xylem and phloem

Roots- epidermis, cortex, stele (vascular cylinder), endoderm (part of stele that lines the stele)

24
Epidermis- modified for absorption
Cortex- storage, and consist of parenchyma cells that contains plastids for storage
Stele (vascular cylinder)- transports (xylem and phloem)
Endodermis- surrounds the vascular cylinder. Each cell is wrapped with Casparian strip, which is
impervious to water and dissolved minerals. Function is to select which minerals enter the
vascular cylinder and the rest of the plant.

Absorption of nutrients and water (lateral movement)

Apoplast and symplast. Symplast- continuous system of cytoplasm of cells interconnected by
plasmodesmata. Apoplast- network of cell walls and intercellular spaces.
Mycorrhizae- symbiotic structure consisting of plants roots mingled with hyphae of a fungus.
Rhizobium- type of nitrogen-fixing bacteria that lives in the nodules of legumes

Adventitious roots- roots that rise above ground

Aerial roots- plants that are in swamps or salt marshes. Serves to aerate root cells.
Prop roots- it helps to support the plant

Types of Plant tissue: dermal, vascular, ground tissue, and meristem tissue
Dermal- outer protective layer, some are covered in cuticle, some are covered in trichomes
(tiny spikelike projection that protects the leaf)
Vascular tissue- xylem- tracheids and vessel elements. Phloem- sieve tube, companion cells
Ground tissue- makes up everything except dermal, vascular, and meristematic tissue.
Parenchyma- traditional, primary cell well, all parts of the plant
Collenchyma- unevenly thicken primary cell walls but lack secondary cell walls (strings of celery)
Sclerenchyma-very thick primary and secondary cell walls that contain lignin. purely for support

Transport within the plant

Xylem (dead)- carries water up (tracheids, vessel elements) (lignin)- requires no energy
Heartwood- dead sapwood- living
Upward pull is caused by transpiration pull, capillary action, and root pressure
Phloem- carries food down (sieve, companion cells)- alive
Translocation (phloem)- circulation in plants transporting carbohydrates (requires energy)
Cambium- located between the xylem and phloem
Pith- storage cortex- strength, structure, storage epidermis- protects tissues

Root cap- protects the root tip

Lateral meristem- cambium
Gene expression- when gene creates a protein
Diploid- two sets, haploid- one set

Epidermis- outer layer of both the top and the bottom

Cuticle- waxy layer to protect the leaf from fungi attacks and to keep water from escaping.
Palisade layer- where most photosynthesis takes place
Spongy cells- gas exchange

25
Stomates- bottom surface of the leaf and opened and closed by guard cells when turgid
(modified epidermal cells that that contain chloroplasts)
Chloroplasts- photosynthesis, double-membraned
Stroma- inner fluid
Thylakoids- flattened membrane
Grana- consisting of layers of membrane called thylakoids
Chlorophyll- green pigment
Gametangia- prevents gametes and zygotes from drying out
Sporopollenin- found in walls of spores and pollen

Photosynthetic pigments
Chlorophyll a- participate directly in the light-dependent reaction
Antennae or accessory pigments (other pigments)- chlorophyll b, carotenoids, phycobilins
Phycobilins- red and found in red algae

Photosynthesis- reduction reaction because carbon dioxide is gaining electron from water
Light-dependent and light-independent reaction both occur during the day.
Light-dependent reactions-Makes ATP, NADPH (not NADH in cellular respiration), protons for
Calvin cycle
Happens in the membranes of the thylakoids (photosystems- light absorbing complexes)
Water is split- not hydrolysis but photolysis because using photons
1. Electrons replace those lost by chlorophyll to electron transport chains
2. Protons- get carried by NADP to the stroma for light-independent reaction
3. Oxygen-released into the atmosphere
Light-chlorophyll-energized electron-ETC-photon gradient-ATP synthetase- ATP

Light-independent reaction (Calvin cycle, carbon fixation)

Takes plast in the stroma
Ribulose bisphosphate (5-carbon enzyme) is regenerated each time like Krebs cycle, and
produces PGAL (3 carbon sugar; later combines to form glucose)

Flowers and Reproduction

Stamen- male part (anther, filament); anther produces pollen, grain divides into 2 cells.
Pistil- female component (stigma, style, ovule, and ovary)
Pollen falls on stigma- pollen germinates- pollen tube grows- Two sperm enter ovule- Egg is
fertilized and becomes embryo- Polar bodies are fertilized and become endosperm (3n)
endosperm is absorbed by cotyledons in dicots- The entire ovule becomes a seed and the ovary
becomes a fruit.
Epicotyl- develops into leaves and upper part of the stem
Hypocotyl- lower stem and root
Radical- first organ to emerge from the germinating seed

Turning Behavior in Plants: Tropisms

Phototropism- growth of a plant toward light

26
Geotropism- growth of the roots downward, toward the earth
Negative geotropism- growth of the plant stem upward, away from the earth.
Thigmotropism- growth of the plant along a surface
Circadian rhythm- biological clock on daily basis. Instinctive.
Symbiosis- mutualism, parasitism, commensalism,
ectoparasites, endoparasites

Hormones in plants
Auxin- hormone that cause tropism and rapid growth, apical stem to remain dominant
(opposite roots), used in weed killer and rooting powder.
Gibberellins- rapid stem and leaf elongation, germination of dormant seeds
Abscisic acid- inhibits growth and promotes seed dormancy
Cytokinins- promotes cell division, growth, delay aging (in flowers)
Ethylene- ripening of fruit
Antiauxins- regulate activity of auxins

Asexual reproduction
Bulbs- part of the stem that split to form several new bulbs (tulip)
Tubers- modified underground stems have buds (eye of a potato)
Runners- stems that run above and along the ground (lawn grasses)
Rhizomes (stolons)- woody, underground stems (iris)
Vegetative propagation
Cutting, layering (stem into ground) grafting (scion, stock)

Sexual reproduction in plants

Alternation of generations- diploid (sporophyte, asexual), haploid (gametophyte, sexual)
In sporophyte (2n) generation, diploid divide by meiosis to form haploid spores and those
spores germinate to form haploid or gametophyte generation. Gametophyte (n) generation
produces male and female gametes by mitosis and the reunion of those gametes produce
sporophyte generation.
Antheridium- produces sperm in gametophyte
Archegonium- produces eggs in gametophyte
Megaspores- produced by large female cones and will develop into female gametophyte
Microspores- produced by small male cones and will develop into male gametophyte.
Protonema- branching, one-cell-thick filaments produced by germinating moss spores, becomes
the gametophyte in moss
Sporangia- located on the tip of a sporophyte, where meiosis occurs to produce haploid spores
Sori- clusters of sporangia
Moss- gametophyte is dominant, Ferns- sporophyte is dominant.
Evolutionary trend- reduction of gametophyte generation and increasing importance of the
sporophyte generation.

Behaviors

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Instinctive Behavior- Fixed-action patterns
Fixed-action patterns- stereotypical behaviors that are triggered by specific stimuli (sign stimuli;
same species: releasers) (mating rituals, when baby bird opens its mouth, mother bird will put
food in it)

Learned behaviors- require interaction (imprinting, habituation, conditioning, insight learning)

Imprinting (Lorenz)- recognition of some object as mother, critical period
Habituation- simplest form of learning, non-harmful stimulus is repeated and learn to ignore it.
Conditioning (associative learning)- particular stimuli is associated with particular behavior
Classical conditioning (Pavlov)- neutral signal (tapping) leads to an action (preparing to eat)
Operant conditioning (Skinner)- learning that occurs because of a reward and punishment
Insight learning (reasoning)- approach new situation and figure out how to deal with them.
Extinction- gradual elimination of conditional responses in the absence of reinforcement
Spontaneous recovery- recovery of such a conditioned response after extinction
Frisch-bee waggle dance

Intraspecific interaction- communicate with its species

Pheromones- Communicate with other members of their species
Behavioral Display- innate behavior that has evolved as a signal for communication. (Dog
wagging its tail, bear raising its body onto its hind leg)
Pecking order-social hierarchy like caste system
Territoriality, cooperation, agonistic behavior, altruism (kin selection)

Ecology

Cell- tissue- organ- organism- population- community- ecosystem- biome- biosphere

Population- group of a specie that interbreed and therefore have the same gene pool.
Evolution happens in terms of population (defined by size, density, and dispersion)
Dispersion- clumped (common), uniform pattern, random spacing
Rate of growth depends on -population size, birth rate, death rate, immigration and emigration

Biotic potential- maximum rate at which a population could increase under ideal conditions.
1. Age at which reproduction begins
2. Lifespan during which the organisms are capable of reproducing
3. Number of reproductive periods in the lifetime
4. Number of offspring the organism is capable of having at one time

Limiting factors- density-dependent (food, buildup of waste), density-independent (earthquake)

Sexual reproduction- slower but more diversity
Asexual reproduction-reduced cost but less diversity (fission- amoeba, bacteria; budding- yeast,
hydra; fragmentation- sponges, planaria, sea stars; parthenogenesis- honeybees, some lizards)
Hermaphrodites- functional male and female gonads (hydra and earthworms)
Parthenogenesis- egg divides in the absence of fertilization by male (bees)
Regeneration- regrow a missing body parts

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K-selected species- slow maturation, few large young, parental care, reproduce many times
R-selected species- many small young, rapid maturation, reproduce once
Solving overlap in niches 1. Competition (drive out) 2. Resource partitioning (exploit different
resources) 3. Character displacement (different beak sizes)
Exponential growth (recently introduced), limited growth, carrying capacity, niche, predation.
Passive defenses against predation- aposematic coloration, batesian mimicry, mullerian
mimicry
1. Aposematic coloration- very bright colors which contain poison
2. Batesian mimicry- copycat coloration (viceroy butterfly mimics monarch butterfly)
3. Mullerian mimicry- two or more poisonous specious resemble each other and gain
advantage from their combined numbers
Population and evolution
1. Populations occupy different niches within their environment
2. If two populations have similar niches, they will compete for sole ownership of the
niche.
3. Winning population retains the niche, and the losing population must evolve to survive.
4. Evolution results in populations that occupy different niches, thereby reducing
competition and promotion a more stable community.

Community
Primary producers- primary consumers- secondary consumers- tertiary consumers
Decomposers- bacteria, fungi. Scavengers. Detritivores
Producers- diatoms, phytoplankton Primary consumers- zooplankton
Tertiary consumers- least stable and most sensitive to fluctuations in populations
Productivity- rate at which organic matter is created by producers. Gross primary productivity-
amount of energy made by producers. Net primary productivity- GPP minus respiration
10% rule, trophic levels
Primary ecological succession- soil removed secondary succession- soil intact.
Rock- lichen- mosses and herbs- grasses and shrubs- pine trees- deciduous trees (sere- stages)
Lichen- pioneer organism
Deciduous trees- climax community (stable)

Ecosystem- community + environment (abiotic factors)

Water cycle, carbon cycle, nitrogen cycle
Water cycle- water to the clouds by evaporation and transpiration, and returns by precipitation.
Soil returns water to the ocean through runoff

Carbon cycle
Carbon dioxide used by plants for photosynthesis, and returned to the atmosphere by
respiration. Animal eats plants and returns the carbon dioxide by respiration and waste
products. Soil returns carbon dioxide by soil respiration.

Nitrogen Cycle- nitrogen-fixing bacteria converts nitrogen into ammonia

Nitrifying bacteria converts ammonia into nitrates

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Denitrifying bacteria converts nitrates into nitrogen

Biomes (climax vegetation)

1. Tundra- permafrost, short shrubs, grasses, lichen.
2. Taiga- largest land biome, coniferous forest (spruce), larger mammals,
3. Deciduous forest- lots of rain, distinct hot and cold seasons, hibernation
4. Grasslands- low growing plants, bison, pronghorn antelope, prairie dogs
5. Tropical Rain Forests- highest rainfall, greatest diversity in flora and fauna. Covered in
epiphyte- photosynthetic plants that grow on other trees
6. Desert- less than 10 inches of rainfall every year.
Aquatic biomes
1. Intertidal zone- land and water meet
2. Neurotic zone- intertidal zone to edge of continental shelf; wide variety
3. Oceanic zone- open ocean; little nutrient concentration except for phytoplankton. Can
be divided into pelagic (open water) and benthic (ocean bottom) (abyssal)
4. Littoral zone- shore of a lake
5. Limnetic zone- farther from the shore and extends downward as far as light will
penetrate.
6. Profundal Zone- aphotic region of a lake
Photic zone- light penetrates
Aphotic zone- light doesnt penetrate

Biological control (vs.pesticide)- crop rotation, natural enemies, birth control

Chlorofluorocarbons- depletion of ozone layer
Eutrophication of a lake- lake disappearing
Pollution- DDT (pesticide) biomagnification- more concentrated

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