BIOLOGY
Fossils
 
Formation:  Fossils usually form in moist sediments, or rock particles, such as sand, where the object can be buried quickly, or in moist minerals, where it prevents weathering, oxygen, and bacteria, and that will prevent decay.  Fossils typically form in sedimentary rock.
 
Dating:  Scientists use absolute and relative dating to determine the age of fossils.  Absolute dating utilizes radioactive elements and relative dating utilizes estimation in relation to the age of the layer of rock in which it was formed.
 
        Absolute Dating:  Radiometric-dating measures radioactive isotopes of elements found in        
        rocks, that decay (break down) at a constant rate over time.  By knowing how much of the
        rock or fossil is left, scientists calculate a ratio to relate how much of the element there
        was originally and how much of it is left.  Because it decays at a constant rate, they can
        determine how old the fossil is.
 
        Relative Dating:  A fossil is approximately the same age as the rock layer it is found in, and    
        younger fossils/rock layers are located closer to the top of the layers (older fossils/rocks
        are found near the bottom)
 
Types of Fossils:
 
        Molds are the space left behind by a decayed organism that mirrors the outward shape of        
        the original organism.  There are also casts, which are formed by filling the filling in of the  
        mold with rock particles that harden in the shape of the original remain.
 
        Imprints are impressions of outer surfaces of organisms of sediments, like the imprint of        
        dinosaur skin on sediment surface.  
 
        Actual Remains are when the fossil consists of the actual organism that is completely    
        preserved.  An example of this is a woolly mammoth, that is found frozen in a glacier.
 
        Changed Hard Parts are fossils that used to be actual remains, that have chemically
        changed when water & minerals leaked into them, causing a chemical reaction.  An
        example of this is petrified wood (wood that has “changed” into rock).
 
 
 
Erosion and metamorphic processes destroy fossils before they are discovered.  Fossils undergoing metamorphic processes experience intense heat and pressure.
 
Fossil evidence clearly shows that life is old and has changed over time. Transitional Forms are fossils or organisms that show the intermediate states between an ancestral form and that of its descendants.
 
EvoLuTiOn
 
Evolution is the process by which all living things have developed from primitive organisms through changes occurring over billions of years, a progression that includes the most advanced animals and plants.  
 
Natural selection is a theory based on the premise that “the strong survive”, or when a change in the environment occurs organisms best suited to the change will thrive while those who aren’t will have a harder time surviving, and competing, and will most likely start to die out.  Natural selection is related to evolution because if a mutation in DNA leads to a favorable trait then the mutation will become more popular (it will be positive).  Mutations can be positive and, or negative.  Natural selection drives evolution-if the species trait is favorable, then the species will survive, if it isn’t, then it will lead to the extinction of the organism.
 
 
Some of the causes of evolution are natural selection, genetic drift, mutation, gene flow, nonrandom mating and homologies. Genetic drift is the random changes in the frequency of traits due to chance factors. Mutations are changes in an organisms DNA. Gene Flow is a change due to movement from one place to another, then having offspring at the new place. Nonrandom mating is when organisms with particular traits are chosen as mates. Homologies predict that related organisms will share similarities that are derived from common ancestors.
 
Evidence for evolution includes the fossil record, homologous structures (similar body parts or behaviors in seemingly different organisms), embryological evidence (similar structural features in developing embryos of very different animals), DNA homology (similar DNA codes between organisms).
 
Reproduction

Sexual reproduction requires 2 parents, and sex cells (sperm & egg).  Offspring look different from the parents because they are a combination of their genes (parental DNA mixes).  Organisms that reproduce sexually include:
    Animals- utilizing internal (inside the female) or external (outside the female) fertilization
    Flowering Plants- (see info. below)
    Fungus- utilizing spores

In asexual reproduction, only one parent is required, no sex cells and the resulting offspring are clones of the parent (look identical and have the same DNA).  Methods of asexual reproduction include:
    Binary Fission:  Parent cell divides in half to produce two identical daughter cells
        -Occurs in bacteria

    Budding:  Parent cell grows a small bud that eventually breaks off and grows on its own
        -Occurs in Hydra and Yeast

    Regeneration:  The ability of some organisms to re-grow lost body parts
        -Occurs in some crayfish, starfish & lizards
    
Vegetative Propagation:  non-flowering plants (see below for more information)
Reproduction in Plants

Sexual Reproduction in Plants: 
            1.  Begins with the stamen and the pistil (sexual organs).  The pistil is the female part         
            and the stamen, male. 
            2.  Pollen (male sperm) is transferred from the stamen to the stigma, located at the top of         
            the pistil in the flowers of the plant, (usually by an outside source).  Pollination can     
            occur by:
                -Movement by animals, wind or insects
                -Self-fertilization (gravity pulls the pollen off a stamen onto the pistil)
            3.  Two pollen cells then travels down the stigma to the plant’s ovary and fertilizes the             
            “egg”, creating an embryo and food for the embryo (cotyledon).
            4.  The egg develops into a seed containing a coat (protective covering), an embryo         
            (baby plant) and cotyledon (food for the embryo).

Asexual Reproduction in Plants:   Vegetative propagation is the ability of plants to reproduce without sexual reproduction, by producing new plants from existing vegetative structures. It is a process by which new plant  "individuals" arise or are obtained without production of seeds or spores.   Methods include:

            1.  Runners- also known as “Stolons” which are horizontal stems that grow along the     
            ground.  The stolons form new plants at the ends, or nodes.
                    Example:  ivy

            2.  Cuttings- One piece of the stem plant, is placed in a good medium, like soil or rocks.      
            Then the cutting produces roots or stems, or both.
                    Example:  spider plants

            3.  Grafting- a method of vegetative propagation where tissues are encouraged to fuse             
            with another.  This is used mostly in gardening.
                    Example:  apple tree

            4.  Bulbs & Tubers- fleshy, enlarged roots or stems that can be planted to grow new             
            plants year after year
                    Example:  potatoes & onions

Genetics

Traits are passed down through generations during sexual reproduction, from parents to offspring.  The information for traits are stored in the DNA /genes/chromosomes of all cells in the body.  Humans have 23 pairs of homologous chromosomes (46 total) in their body cells and half as many (23) in their sex cells.  

Genes are inherited in pairs. so there are 2 alleles for each trait.  One copy comes from your mother and one copy comes from your father.  Punnett squares are diagrams that help us understand inheritance and predict the various combinations of genes that will show up in future generations. In each gene pair there are two different alleles that can exist, either recessive or dominant.  

Dominant genes/traits are represented by a capital letter and recessive genes/traits are represented by a lowercase letter.  Because you inherit 2 alleles for each trait, possible combinations include  AA, Aa, or aa.  The rule of inheritance with these alleles states that when a dominant allele is present it usually masks the recessive trait.  For example:

If A = Brown hair and a= Blond hair then..........
AA = Brown hair  (This is an example of a purebred or true breeder for the dominant trait)
Aa= Brown hair (This is an example of a hybrid)
aa= Blond hair (This is an example of  a purebred or true breeder for the recessive trait

Punnett Squares help us to understand inheritance by helping us predict which traits the offspring is going to have.  It uses a combination of the alleles from the mother and the father, for each trait, and it gives the percentage of chance of which trait the child will have.  There can be a Punnett square for every trait, and they can be very complex, but simple ones have four different combinations of trait possibilities. 

When an individual has two dominant alleles (AA) for a trait they are said to be Homozygous Dominant for that trait.

When an individual has one dominant and one recessive allele (Aa) for a trait they are set to be Heterozgyous for that trait.

When an individual has two recessive alleles (aa) for a trait they are said to be Homozygous Recessive for that trait.


How to Create a Punnett Square:

                                                            

1.  Draw a square similar to the picture above
2.  Above the top two squares, put the allele of the father, or mother.  Then along the left    
side put the allele of the mother of father, the one you didn’t put for the top one.  
3.  Next, cross the one allele for each box, and making a gene pair with two letters in     
each box.  
4.  The alleles in the box are the possible number of outcomes that could possibly result in 
the offspring.  The 4 boxes represent the possibility of each type of offspring resulting.
5.  Calculate the genotype (the percentage of each possible gene combination) and the 
phenotype (the percentage or chance of each trait that could show up.)

EXAMPLE:  A mother and a father are considering having a child.  They want to know if he 
will have freckles or not.  Having freckles is recessive. The mother is homozygous 
dominant, and the father is heterozygous.  What is the chance that their child will have 
freckles?


A= Non-freckled        a= Freckled

Mother = AA        Father = Aa        

AA x Aa


                                                                        A        A
        
                                                            A        AA        AA

                                                            a        Aa        Aa


                                       
                                        Genotypes:          50% AA  Homozygous Dominant
                                                                      50% Aa  Heterozygous

                                        Phenotypes:         50%  AA  Non-Freckled
                                                                       50% Aa   Non-Feckled
Genetic Disorders
 
A common genetic disorder is sickle cell anemia, which is where some of your cells have an unusual crescent shape.  This makes arteries clog easier, but carrying the gene for it gives a person a natural resistance to malaria.  
 
Carriers are heterozygous individuals who carry a recessive gene, but do not show the trait or phenotype.  This means that they are heterozygous for the condition, trait or disease.  Sickle cell anemia can be an example of a carrier condition because a person can carry the gene and pass it onto offspring, but not actually have the disease.  A benefit of being a sickle cell anemia carrier is a resistance to malaria.
 
DNA and Cloning
 
 
Inside the cell you can find the Chromosomes, that store hereditary information.  Chromosomes are made up of DNA double helix (twisted staircase shaped) coiled codes of information acting as the “blueprint of life”.  Genes are specific pieces of DNA.  Each person has two genes for each trait, one from each parent.  
 
Reproductive cloning refers to the process where an animal is created with the same nuclear DNA as a previously existing animal.  This happens by removing the DNA from the nucleus of an egg and replacing it with the DNA from another cell.  The egg is then stimulated to divide and following a number of divisions it can be transferred into the uterus of a female host until its birth.  Cloned animals are not exact twins of the offspring.  More than 90% of the cloning attempts die in the process.  The most current focus in cloning is whether or not we will be able to clone humans.  South Koreans have successfully cloned a cat, which is leading us to believe that it can be done with humans also, but with much more research and observations.
Karyotypes
 
A karyotype is a picture of an individual’s chromosomes, where they are arranged by homologous pairs in order of size from chromosome 1-23.  A karyotype can be used to determine gender or to identify abnormalities in chromosome numbers.
 
A pedigree is a diagram that shows the family history of a trait, by showing the inheritance of a particular trait through a family tree.  Pedigrees are typically used when couples visit a genetic counselor to determine the chance that a future child may inherit a particular trait or genetic disorder.
 
The Five Kingdoms of Life


The five kingdoms of life include Moneran, Protist, Fungi, Plants & Animals. 

Monerans:  prokaryotic, single celled bacteria with freely floating DNA (no nucleus).  
They tend to be organisms of disease and decay although many create helpful 
relationships with other organisms.

Protists:  are mostly eukaryotic,  one-celled, pond dwelling organisms that contain nuclear 
bound DNA, move by using, flagella or cilia and reproduce sexually or  asexually by 
fission. 

Fungi:  some are one-celled, some multi-celled, eukaryotes, that live on hosts, are 
consumers and reproduce asexually through spores and budding. 

Plants: are multi-celled, eukaryotes, that carry out photosynthesis, possess chloroplasts 
and act as producers. 

Animals:  are multi-celled eukaryotes that carry out cellular respiration, and do muscular 
movements in water, air or soil. They are consumers (herbivores, carnivores and 
omnivores) and they primarily reproduce sexually.
Animal Kingdom Subgroups
 
 
 
Sponges:  obtain food by filter feeding (strain particles of food matter in the water through
small pores in the body, because they don’t have mouths), are multi-cellular, sea bottom-
dwelling creatures that attach themselves to something solid where they can receive
enough food to survive. Sponges lack nerves and the ability to do locomotion. Sponges
mostly live in salt water but they can sometimes live in fresh water environments.
Sponges that reproduce sexually are usually hermaphrodites, but they can also reproduce
asexually.
 
                                                        
 
 
 
Cnidarians:  Some examples of cnidarians are jellyfish, corals and sea anemones.
Cnidarians feed on whatever comes in contact with their tentacles including large protists,    
various worms, crabs, other cnidarians and even fish. They can range in size from
microscopic to 7 feet in diameter and 100 feet long tentacles, which is the jellyfish. Also
jellyfish have stinging cells found in their tentacles. Cnidarians don’t have a digestive,
circulatory or respiratory system; therefore they discard waste matter from their mouth
opening. Their bodies are primarily made up of tissue. Cnidarians are found in marine
environments. They reproduce sexually and asexually. They reproduce asexually by
budding.
 
                                                    
 
 
Flat & Round Worms:  They feed mainly on plankton. They have soft bodies, which allow
them to expand and contract allowing them to virtually change their body shape. They live
in fresh water, marine and terrestrial environments. They usually reproduce sexually. Also
flatworms are mostly hermaphrodites.
 
                                                    
 
 
Mollusks:  Water dwelling mollusks are clams, oysters, mussels, octopuses, and squid.  
Land living mollusks are snails and slugs. Land living mollusks move around slowly by a
sole called a foot, and ocean living mollusks swim by jet propulsion. But sometimes ocean
living mollusks attack themselves to rock or other hard surfaces. There are about 150,000
species of mollusks known. Mollusks can range in size from a 60-foot giant squid to
almost microscopic species. If a mollusk lives in the ocean then it filters feeds (filters out
particles of food matter out of the water). Mollusks have three main body parts: a foot, a
mantle, and a fleshy body. Land living mollusks move slowly around by a sole called a
foot.  Some Ocean living mollusks swim but jet propulsion, but others attach themselves
to rock or other hard surfaces. They have a very simple heart that pumps blood into open
cavities, or sinuses (the blood simply washes over the organs). Mollusks reproduce
sexually and some mollusks are hermaphrodites.
 
                                                              
 
 
 
Annelids:  Annelids are leeches and earthworms. Different species of annelids have
different diets including, active and passive hunters, scavengers, filter feeders, direct
deposit feeders, and bloodsuckers. Annelids are most commonly referred to as
segmented worms. Distinctive features of annelids are structures called chaetae. Chaetae
are bundles of chitinous, thin-walled cylinders held together by proteins. Annelids are like
segmented worms that can be as short as under a millimeter and as long as 3 meters.
They live in wet environments including terrestrial, freshwater and mostly marine.
Depending on the species annelids reproduce sexually or asexually.
 
                                          
 
 
 
Arthropods:  Most soil-dwelling arthropods eat fungi, worms, or other arthropods. Root-    
feeders and dead-plant shredders are less abundant. As they feed, arthropods aerate and
mix the soil, regulate the population size of other soil organisms, and shred organic
material. Arthropods are the most successful animals on earth and there are 4-6 million
species of them on earth. Arthropods have segmented bodies and because of their jointed
legs they have more mobility than land mollusks and worms. They shed there outside
exoskeleton then grow a new one. They live in crustacean, terrestrial or aquatic habitats.
Some arthropods are hermaphrodites and fertilization in most arthropods is internal but
not in all. They live in crustacean, terrestrial or aquatic habitats. Some arthropods are
hermaphrodites and fertilization in most arthropods is internal but not in all.
 
 
                                                        
 
 
Echinoderms:  Some echinoderms are sea stars, brittle stars, and sea urchins. Some
echinoderms are carnivores (starfish) some are detritus foragers (some sea cucumbers)
and some are plankton feeders (basket stars). They are free swimming organisms.
Echinoderms have tentacle-like structures called tube feet resulting in them moving very
slow. Also echinoderms have several arms, usually five (2 left-1 center-2 right) and a
center body. Echinoderms lack and head and a brain. Echinoderms have remarkable
powers of regeneration. Also in most of echinoderms species, skin gills preform
respiration and waste removal. Echinoderms live in marine environments of all depths.
Echinoderms reproduce sexually.
 
                                                  
 
 
Fish:  Fish include sharks, carps and seahorses. Fish are aquatic vertebrates that are
typically cold-blooded. They have a streamlined body that allows them to swim rapidly.
Fish are of great importance to humans as a source of food. Fish have limbs in the shape
of fins and gills their whole life. Fish live in all water environments except the Dead Sea
because it is too salty. Fish reproduce sexually through eggs.
 
                                                  
 
 
Amphibians:  Frogs, toads and salamanders are some examples of amphibians.
Amphibians are very vulnerable to pollutants because water and air flow easily into their
skin.  Amphibians spend most of their time on land.  There are no true salt-water
amphibians. Amphibians are cold-blooded vertebrates. There are around 6,000 species of
amphibians.  We have found fossils of amphibians from 400 million years ago. They can
live in fresh water environments and also on land (but not far from water). They reproduce
sexually they must return to water to reproduce. The eggs hatch into legless tadpoles,
they also have a tail, and then eventually the tadpole loses its tail and grows legs.
 
                                                  
 
 
Reptiles:  Crocodiles, alligators, turtles and snakes are all reptiles. They are cold-blooded
and thick skinned. They have fairly waterproof scales, and breathe using lungs. Reptiles
have advanced visual depth perception when compared to lower animals even though
they lack color vision.  They can survive with very little food. Reptiles evolved from
amphibians about 70 million years ago. Reptiles live on every continent except Antarctica.
Reptiles reproduce sexually.  Some reptiles lay eggs but there are also some that are
capable of live birth.
 
                                                            
 
Birds:  Hummingbirds and ostriches are some types of birds. Birds can be carnivores,
omnivores or herbivores (so they eat a variety of food- bugs, small animals, fish, fruit,
grain or nectar). Birds are warm-blooded, and have wings, feathers and a beak. Not all
animals that fly are birds and not all birds can fly, some swim and some run. Many birds
migrate to a cooler climate for reproducing and summer feeding, then they return to the
warmer climate in the winter. Modern day birds don’t have teeth but ancient birds did have
teeth. Birds live virtually everywhere on the earth. Birds reproduce sexually.  They lay
hard-shelled eggs that hatch and grow in time into adult birds.
 
                                                    
 
Mammals:  Some mammals are mice, bats, and monkeys. All Mammals bodies are covered
with hair and are warm-blooded which mean that they can maintain a constant body
temperature.  However the only true distinguishing feature of mammals is that they have
mammary glands. Mammal’s teeth come in a variety of shapes and sizes (incisors,
canines, premolars and molars) and they all have different jobs (stabbing, cutting, tearing
or grinding food).  Mammals live anywhere in the world. Mammals reproduce sexually;
most mammals give birth to live young.
 
                                                        
 
 
Plant Kingdom Subgroups
 
 
Vascular plants include ferns, club mosses, flowering plants, and conifer trees.  Vascular means that the plant has tube-like structures that transport water from the roots to the stem to leaves.  Having vascular tissues allows the plant to evolve in size.  
 
Non-vascular plants are relatively small because they lack particular tissues.  They usually don’t have roots, stems or leaves.  They absorb water through thin surfaces.  Green algae and liverwort are some non-vascular plants.  
 
Seeded plants have vascular tissue, and they reproduce with seeds.  Seeded plants have thick cell walls in the vascular tissue.  These plants do not need water to reproduce.  Flowers are a type of seeded plant.  
 
Seedless plants are algae, mosses, and ferns.  Algae are non-vascular, have no seeds, lives near water, and are the oldest type of plant in the world.  Mosses are generally small plants that live in moist places.  They are carpet-like, and non-vascular.  Ferns are just basically stems, leaves, and roots.  They are vascular, and popular houseplants. Ferns reproduce with spores, so they are seedless.  
 
Gymnosperms are seed-bearing plants such as pines, cedars, and spores.  Their seeds are not enclosed in an ovule, so they are known as the “naked seed”.  Trees that are gymnosperms stay green all year long.  
 
Angiosperms are trees that usually change color and die every autumn.  These have seeds, and the seeds are incased in the ovule.  Examples are plants like rhododendron, live oak, and maples.
 
Protist Kingdom Subgroups
 
 
Characteristics of protists- they can be uni-celled, or multi-cellular without highly specialized tissues.  There are one-celled protozoa, which are animal like.  There are protophyta, which are plant like, and mostly algae. There are lime molds, and slime molds, which are fungus-like.  
 
Sarcodines, include ameba, and have pseudopods (“fake feet” for feeding and locomotion) and streaming cytoplasm.  They are “animal-like”.
 
Ciliates, include paramecium, which are found almost anywhere with water, and soil, and have cilia (small hair like structures for feeding and locomotion).  They are “animal-like”.
 
Euglenas, include euglena, and have chloroplasts, and contractile vacuoles (for regulating water).  They are “plant-like”.
 
Dinoflagellates are mostly marine plankton, and some fresh water inhabitants too, are colorless, and predators on other protozoa.  They are “plant-like”.
 
Slime molds are eukaryotes found in forests and other locations throughout the world, and have very complex life cycles.   They are “fungus-like”.
 
 
Fungi Kingdom
 
 
Mushrooms are an umbrella shaped form of fungi produced above ground on soil or on its food source.  Mushrooms have spore bearing fruit bodies and play a major role in breaking down dead and decaying matter.  
 
There are approximately 1,500 species of yeast in existence. They reproduce asexually, usually by budding, but it also does binary fission as well.  Yeast is used in fermenting alcoholic beverages.  
 
The last sub-group of the fungi kingdom is molds.  Some molds cause disease or food spoilage.  Molds reproduce through small spores and get their energy from organic matter it lives on.  Mold spores can be sexual or asexual.
 
 
Moneran Kingdom
 
 
Cocci are a sub-group of monerans, and are always spherical or nearly spherical.  These bacteria can be human pathogens.  Cocci are microorganisms, and bacterium.
 
Another sub-group is bacillus, spore bearing, and rod shaped bacteria.  They feed on dead organic material, and are responsible for food spoilage.  
 
There are also the spirillums, which are bacterium shaped like a bent rod or corkscrew.  There are two types of spirilla; short rods that are slightly bent and rigid spirals.  Solitary bacteria are rarely found in chains or clusters.  
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