- 2 -

Using a Compound Microscope ...................................................................................... - 5 - Cell Structure ................................................................................................................... - 5 - Mitosis ............................................................................................................................. - 6 - Cytokinesis ....................................................................................................................... - 9 - Differentiation ................................................................................................................. - 9 - Meiosis ............................................................................................................................ - 9 - Mistakes in Meiosis ....................................................................................................... - 11 -

Abnormal Chromosome Number ............................................................................ - 11 - Abnormal Chromosome Structure ........................................................................... - 11 -

The Origin of Genetics ................................................................................................... - 12 - Punnett Squares ............................................................................................................ - 13 - Genetics after Mendel................................................................................................... - 14 -

Incomplete Dominance ............................................................................................ - 14 - Co-Dominance .......................................................................................................... - 14 - Multiple Alleles ........................................................................................................ - 14 -

Sex Linkage .................................................................................................................... - 15 - Applications of Genetics in Society ............................................................................... - 15 -

Recombinant DNA Technology ................................................................................ - 15 - Plasmids in Genetic Engineering .............................................................................. - 16 - DNA Fingerprinting .................................................................................................. - 16 - Cloning a Gene in a Bacterial Plasmid...................................................................... - 17 -

Nucleic Acids ................................................................................................................. - 18 - Protein Synthesis ........................................................................................................... - 19 -

Transcription ............................................................................................................ - 19 - Translation ............................................................................................................... - 20 -

Adaptation and Variation .............................................................................................. - 21 - Selective Advantage ...................................................................................................... - 22 - Natural Selection ........................................................................................................... - 22 - Artificial Selection ......................................................................................................... - 24 - Evolution ....................................................................................................................... - 24 - Developing the Idea of Natural Selection ..................................................................... - 26 - Evidence for Evolution .................................................................................................. - 27 - Mechanisms of Evolution .............................................................................................. - 28 -

Genetic Drift ............................................................................................................. - 28 - Gene Flow ................................................................................................................ - 29 - Non-Random Mating ............................................................................................... - 29 - Mutation .................................................................................................................. - 29 - Natural Selection ...................................................................................................... - 29 -

Stabilizing Selection ............................................................................................... - 29 - Directional Selection ............................................................................................. - 30 - Disruptive Selection .............................................................................................. - 30 -

Pre-Zygotic Isolating Mechanisms ........................................................................... - 31 -

- 3 -

Post-Zygotic Isolating Mechanisms .......................................................................... - 31 - Types of Speciation ....................................................................................................... - 32 -

Sympatric Speciation ............................................................................................... - 32 - Allopatric Speciation ................................................................................................ - 32 -

Adaptive Radiation ........................................................................................................ - 33 - Models of Evolution ...................................................................................................... - 33 -

Gradualism ............................................................................................................... - 33 - Punctuated Equilibrium ........................................................................................... - 33 -

Classification of Living Things ........................................................................................ - 33 - Classification of Living Things ........................................................................................ - 34 - The Linnaean System of Classification .......................................................................... - 34 - The Six Kingdoms ........................................................................................................... - 35 -

Archaebacteria ......................................................................................................... - 35 - Eubacteria ................................................................................................................ - 35 - Protista ..................................................................................................................... - 35 - Fungi ......................................................................................................................... - 35 - Plantae ..................................................................................................................... - 35 - Animalia ................................................................................................................... - 35 -

Kingdom Protista ........................................................................................................... - 36 - Animal-Like Protists ................................................................................................. - 36 - Fungus-Like Protists ................................................................................................. - 36 - Plant-Like Protists .................................................................................................... - 36 - Reproduction ........................................................................................................... - 37 -

Kingdom Bacteria - Archaebacteria and Eubacteria ..................................................... - 38 - Classifying Bacteria by Shape ................................................................................... - 38 - Classifying Bacteria by Gram Stain ........................................................................... - 38 - Reproduction in Bacteria ......................................................................................... - 39 - Binary Fission ........................................................................................................... - 39 - Conjugation .............................................................................................................. - 39 - Endospore Formation .............................................................................................. - 39 - Nutrition ................................................................................................................... - 40 - Respiration ............................................................................................................... - 40 -

Viruses ........................................................................................................................... - 40 - Life Cycles ................................................................................................................. - 40 - Lytic Cycle ................................................................................................................. - 41 - Lysogenic Cycle ........................................................................................................ - 41 -

Kingdom Fungi ............................................................................................................... - 42 - Reproduction ........................................................................................................... - 42 - Division Zygomycota ................................................................................................ - 42 - Division Ascomycota ................................................................................................ - 43 - Division Basidiomycota ............................................................................................ - 43 - Imperfect Fungi ........................................................................................................ - 43 - Fungal Associations .................................................................................................. - 44 -

Kingdom Plantae ........................................................................................................... - 44 -

- 4 -

Classifying Plants ...................................................................................................... - 44 - Non-Vascular Plants (Bryophytes) ........................................................................... - 45 - Vascular Plants (Tracheophytes) .............................................................................. - 45 - Spore Producing Plants ............................................................................................ - 45 - Seed Producing Plants.............................................................................................. - 45 - Gymnosperms .......................................................................................................... - 46 - Angiosperms ............................................................................................................ - 46 -

Kingdom Animalia ......................................................................................................... - 48 - Phylum Porifera ....................................................................................................... - 48 - Phylum Cnidaria ....................................................................................................... - 49 - Phylum Platyhelminthes .......................................................................................... - 49 - Phylum Nematoda ................................................................................................... - 50 - Phylum Annelids ...................................................................................................... - 50 - Phylum Chordata ..................................................................................................... - 51 - Class Vertebrate ....................................................................................................... - 51 - Superclass Agnatha .................................................................................................. - 51 - Class Chondrichthyes ............................................................................................... - 51 - Class Osteichthyes ................................................................................................... - 51 - Class Amphibia ......................................................................................................... - 51 - Class Reptilia ............................................................................................................ - 51 - Class Aves ................................................................................................................. - 52 - Class Mammalia ....................................................................................................... - 52 - Phylum Mollusca ...................................................................................................... - 52 - Class Bivalva ............................................................................................................. - 53 - Class Gastropoda ..................................................................................................... - 53 - Phylum Cephalopoda ............................................................................................... - 53 - Phylum Echinodermata ............................................................................................ - 53 - Phylum Arthropoda.................................................................................................. - 53 - Class Arachnida ........................................................................................................ - 53 - Class Crustacea ........................................................................................................ - 53 - Class Insecta ............................................................................................................. - 54 - Class Diplopoda and Class Chilopoda ...................................................................... - 54 -

Glossary ......................................................................................................................... - 55 -

- 5 -

Using a Compound Microscope

Structure Function

Eye Piece To look through at the specimen, has 10x

magnification

Body Tube Contains the optical components of the

upper microscope Revolving Nosepiece Rotate to change magnification lenses

Objective Lens Primary optical lenses: low is 4x, medium

is 10x, and high is 40x magnification Stage The specimen is placed here

Diaphragm / Condenser Adjusts the amount of light Illuminator / Mirror Provides illumination

Base Supports the microscope, used to carry

Fine Adjustment Knob Precise adjustment, used on medium and

high power Coarse Adjustment Knob Imprecise adjustment, used on low power

Arm Connects the eyepiece to the base, used to

carry Stage Clips Hold the specimen in place

Cell Structure

Typical Animal Cell Typical Plant Cell

- 6 -

O2

O2

Although there is a tremendous variety among cells, all cells share some common structures: a cell membrane to protect and regulate what enters and leaves the cell, as well as hereditary material in the form of DNA. In addition, all cells must make food for energy and rid themselves of waste products. While no such thing as a typical cell exists, all cells can be classified as prokaryotic or eukaryotic.

Type of Cell DNA Size Organization Metabolism Organelles

Prokaryotic

in nucleoid region

usually smaller

usually single-celled

may not need oxygen

no organelles

Eukaryotic

within membrane-

bound nucleolus

usually larger usually multi-cellular

usually needs oxygen

membrane-bound

organelles

Mitosis

DNA in our cells takes the form of chromatin. Chromatin is the form that DNA takes during interphase. It is an irregular network of strands and granules. During mitosis, chromatin condenses into chromosomes. When a chromosome replicates, it is called a double-stranded chromosome. Each strand is called a sister chromatid, and chromatids attach to one another at the centromere. However, a double-stranded chromosome is still considered to be one chromosome.

Chromatin

- 7 -

In humans, somatic cells (all cells on our bodies, excluding gametes) have 46 chromosomes. These chromosomes form 23 pairs called homologous pairs. Our cells have two of each kind of chromosome: one paternal (from the father) and one maternal (from the mother). Homologous pars are double-stranded too. For human somatic cells, 46 is known as the diploid number, and 23 is the haploid number. The cell theory, as proposed by Rudolph Virchow, states that all cells are derived from pre-existing cells.

Centromere

Sister Chromatid

Double-Stranded

Chromosome

Homologous Pair

Sister Chromatids

Single-Stranded

Chromosome

The Cell Cycle

- 8 -

Interphase:

• DNA duplicates during the S phase • centrioles double

Prophase: • DNA condenses into chromosomes and becomes visible • nuclear envelope breaks down • nucleolus disappears • centrioles begin to migrate to opposite poles of the cell, sprouting microtubules

Metaphase: • mitotic spindle attaches to the sister chromatids at the centromere • double-stranded chromosomes line up "single-file" at the equator (Metaphase

plate) of the cell Anaphase:

• sister chromatids detach from one another and move to opposite poles of the cells as the protein fibres in the mitotic spindle shorten

Telophase: • DNA reforms chromatin • nuclear envelope reforms • nucleoli reappear and spindle and aster disappear • two nuclei are visible • cleavage furrow begins

Pair of Centrioles

Nucleus

Replicated, Uncondensed DNA

Metaphase Plate

Mitotic Spindle

Spindle Fibres Shortening

Separating Chromosomes

Nuclear Envelope Forming Cleavage Furrow

- 9 -

Cytokinesis

Differentiation

Differentiation is the process by which cells in a multi-cellular organism change so they can take on specific functions. After mitosis and Cytokinesis, daughter cells are identical to the mother cell. During the development of a multi-cellular organism, each cell has exactly the same number and kinds of chromosomes as those in every other cell. Cells must undergo differentiation so that the cells within one organism have different functions.

Meiosis

The purpose of meiosis is to ensure that sex cells have a haploid number of chromosomes. This ensures that, upon fertilization of an egg cell by a sperm cell, the resulting zygote receives the correct number of chromosomes. Meiosis only occurs in reproductive tissues. In humans, spermatogonia are sperm-producing cells, and oogonia are egg-producing cells. Meiosis is characterized by two major divisions called meiosis I and meiosis II. A gamete is a specialized sex cell. The female gamete is the egg, and the male is the sperm. Gametes are formed by meiosis because if they were produced by mitosis, the number of chromosomes in the cell would double each time, producing new organisms. The haploid number for human cell is n, and the diploid number is 2n, 23 and 46 respectively. Chromosomes are referred to in pairs called homologous chromosomes. One chromosome in each pair is inherited from the mother (maternal chromosome), and the other is inherited from the father (paternal).

Animal Cell Plant Cell

• Begins in late Anaphase • Membrane-lined vesicles

accumulate near the Metaphase plate

• Vesicles fuse together, forming a cell plate that grows toward the parent cell wall

• Cellulose is added to the cell plate to form a new cell wall

• Begins in late telophase • Cell membrane pinches in at

the equator, producing a furrow

• Furrow deepens until two separate daughter cells form

• Parent cell's organelles are distributed among the daughter cells

- 10 -

Prophase I of meiosis is similar to Prophase of mitosis in that the chromosomes condense, shorten and become visible. However, in Prophase I, chromosomes undergo a process called synapsis, such that the double-stranded pairs lie side-by-side along their entire length. The unit formed by each homologous pair of chromosomes now consists of four chromatids and is called a tetrad. In this configuration, the maternal and paternal homologous pairs can break and exchange sections of the chromosome in a process called crossing over. This process allows for greater genetic variation. In Metaphase I, the homologous pairs are moved by the spindle fibres to the Metaphase plate of the cell (similar to mitosis). However, in Metaphase I, the homologous pairs do not line up "single file", because having formed a tetrad, they line up side-by-side with their homolog. In Anaphase I, the sister chromatids do not separate from one another as they do in mitosis. Instead, the tetrads separate and are pulled to opposite poles of the cell. Depending on how the chromosomes arrive at the equator, maternal and paternal chromosomes can assort randomly. In Telophase I, the chromosomes condense slightly and a nuclear membrane may or may not form. At the end of meiosis I, the two daughter cells that form each have half the number of chromosomes as the parent cell. This is why meiosis I is often called the reduction division. In meiosis II, there is no duplication of chromosomes in the interphase between meiotic divisions. The second meiotic division is similar to mitosis, but it begins with half the genetic material. At the end of meiosis II, there are four haploid cells.

Sister Chromatids

Tetrad

or

- 11 -

Mistakes in Meiosis

There are two common errors in meiosis: abnormal chromosome number and abnormal chromosome structure.

Abnormal Chromosome Number

This happens during Anaphase I or Anaphase II, when one pole gets too many or too few chromosomes. Aneuploidy: a condition in which there are too many or too few chromosomes. Trisomy and polysomy are conditions when there are too many chromosomes, and monosomy is a condition when one chromosome is missing. Non-Disjunction: the failure of chromosomes to separate and move apart Polyploidy: the possession of more than two complete sets of chromosomes

Abnormal Chromosome Structure

This happens when errors occur during crossing over. Duplication: the chromosome piece is attached to the wrong chromosome Deletion: the chromosome piece is lost and does not re-attach Inversion: the chromosome piece is re-attached backwards Translocation: the chromosome piece attaches at the wrong location, but to the right chromosome If non-disjunction occurs during meiosis I, as a result, all four gametes produced will have an abnormal number of chromosomes: either one too many or one too few. On the other hand, if non-disjunction occurs during meiosis II, only two of the four gametes produced are impacted.

- 12 -

The Origin of Genetics

Gregor Mendel is considered to be the "father" of genetics. Through his many experiments, he established the basis for the modern study of genetics. He established purebred plants for seven different traits in the common pea plant, Pisum satiuum. He then conducted controlled experiments where he crossed purebred plants that were different for only one contrasting pair of traits. He called these plants the P (Parental) Generation. He called the hybrid offspring the F1 (First Filial) Generation. The trait that was seen in this generation was termed dominant, while the trait that was not expressed was termed recessive. Mendel then crossed plants from the F1 Generation to yield the F2 (Second Filial) Generation. Having done this, he identified the genotypic and phenotypic ratios for all three generations.

Mendel suggested that an organism's phenotype was determined by a pair of alleles that could be identical or different. Mendel's Law of Segregation states that members of a pair of alleles for a given trait are segregated (separated) during gamete formation. Mendel's Law of Independent Assortment states that when two or more pairs of traits are considered simultaneously, each pair shows dominance, recession and segregation independently of each other. A monohybrid cross is the reproduction of two heterozygous individuals for one trait. The expected phenotypic ratio is 3:1 (T:t), while the genotypic ratio will be 1:2:1 (TT:Tt:tt). A dihybrid cross is the reproduction of two heterozygous individuals for two traits. The expected phenotypic ratio for this cross is 9:3:3:1 (Ab:ab:AB:aB). The genotypic ratio is the same. A testcross is the mating of an individual of unknown genotype with an individual that is homozygous recessive for a certain trait.

P Generation: Tall - 50% Short - 50% F1 Generation: Tall - 100% Short - 0% F2 Generation: Tall - 75% Short - 25%

P Generation: Tall : Short = 1 : 1 F1 Generation: Tall : Short = 1 : 0 F2 Generation: Tall : Short = 3 : 1

Homozygous Dominant : TT Heterozygous : Tt

Homozygous Recessive : tt

- 13 -

Punnett Squares

Punnett squares illustrate the possible outcomes (offspring) of a particular cross. For example, a homozygous dominant individual is crossed with a homozygous recessive individual. P Generation (parental genotypes): AA x aa F1 Generation (offspring genotypes): Aa Each gamete can only contain one of the alleles for a gene for any given trait, because each gamete contains only one of each homologous pair of chromosomes. This is Mendel's Law of Segregation and is a result of the separation of homologous pairs during Meiosis I.

A A

a Aa Aa

a Aa Aa

Gamete Genotype (haploid)

Offspring Genotype (diploid)

By separating the alleles, we are applying Mendel's Law of Segregation.

Parent cell Prophase I Anaphase I

Metaphase II

Gametes

= T = t

- 14 -

Genetics after Mendel

Incomplete Dominance

Neither gene is completely dominant over the other. The F1 hybrids have an appearance somewhere in between the phenotypes of the two parental varieties. A snapdragon flower is an example of incomplete dominance.

Co-Dominance Both alleles are separately manifested in the heterozygous phenotypes. For example, in cattle, the red coat colour (R) and the white coat colour (r) behave as co-dominants. In its heterozygous state, the colour of the cattle's coat is roan (Rr): it has both the red and the white hair pigments.

Multiple Alleles

When there are more than two allelic forms for a gene, the organism has what is known as multiple alleles for that particular trait. The ABO blood types are an example of multiple alleles.

Blood Type

Genotype Antibodies

in Blood Serum

The blood reacts (clumps) when red blood cells from the groups below are added to the serum

from the groups are the left.

O A B AB

O ii anti-A anti-B

No Yes Yes Yes

A IAIA or IAi anti-B No No Yes Yes B IBIB or IBi anti-A No Yes No Yes

AB IAIB N/A No No No No A and B are carbohydrates on the surface of the blood cells that act as blood markers ("nametags"). Type A blood has A markers, type B blood has B markers, type AB blood has AB markers, and type O blood doesn't have markers. Blood type O is the universal donor, and blood type AB is the universal receptor.

P Generation RR x rr

(red x white)

F1 Generation Rr

(pink)

F2 Generation RR, Rr, rr

(red, pink, white)

The intermediate variation is not a blending of colours since the F1 cross results in the

reappearance of the red and white individuals.

- 15 -

Sex Linkage

The sex of an individual is determined by the sex chromosomes, X and Y. XX is ♀ (female), and XY is ♂ (male). Thomas Hunt Morgan, in his work with the common fruit fly, Drosophila melanogaster, noticed that the inheritance of certain traits seemed to be linked to the sex of the fly. Traits that are controlled by genes on the X chromosome are called "sex-linked", since the chromosome is also involved in determining the gender of the individual.

Applications of Genetics in Society

Recombinant DNA is a technique in which gene segments from different sources are combined in vitro (in glass) and transferred into cells where the DNA may be expressed. Restriction enzymes are enzymes that recognize and cut up DNA. These enzymes are very specific, recognizing short nucleotide sequences in DNA and cutting at specific points within these sequences.

Recombinant DNA Technology The DNA fragment is attached to a different source of DNA. The two fragments stick together by complimentary base pairing. The strand is then sealed with DNA ligase - an enzyme that allows the DNA backbone to form covalent bonds.

X Y

Since the X-chromosome is larger, it carries more genes than the smaller Y-chromosome. A gene on the X-chromosome for a male has no matching allele on the Y-chromosome. Therefore, any gene on the X-chromosome, whether it is dominant or recessive, will be expressed in males.

G A A T T C C T T A A G

A A T T C :::::::::: G

G :::::::::: C T T A A

The restriction enzyme cuts the DNA into pieces at a certain point.

Stic

ky E

nds

:::::::::::

:::::::::::

Different source of DNA

Same sticky ends

G C T T A A

A A T T C G

Recombinant DNA molecule

- 16 -

Plasmids in Genetic Engineering

Once the altered plasmid has been returned to the bacterium, that bacterium is cloned. Once there are many copies of this bacterium, its' protein can be injected into animals (human growth hormone, heart attack therapy), or copies of the gene can be inserted into plants and other bacteria (pest resistance for crops, bacteria can be used to clean up toxic waste).

DNA Fingerprinting

1. Isolation of DNA. DNA must be recovered from the cells or tissues of the body. Only a small amount of tissue, like blood, hair, or skin, is needed. For example, the amount of DNA found at the root of one hair is usually sufficient.

2. Cutting, sizing and sorting. Special enzymes called restriction enzymes are used to cut the DNA at specific places. For example, an enzyme called EcoR1, found in bacteria, will cut DNA only when the sequence GAATTC occurs. The DNA pieces are sorted according to size by a sieving technique called electrophoresis. The DNA pieces are passed through a gel made from seaweed agarose (a jelly-like product made from seaweed). This technique is the DNA equivalent of screening sand through progressively finer mesh screens to determine the particle sizes.

3. Transfer of DNA to nylon. The distribution of DNA pieces if transferred to a nylon sheet by placing the sheet on the gel and soaking it overnight.

4. Probing. Adding radioactive or colored probes to the nylon sheet produces a pattern called the DNA fingerprint. Each probe typically sticks in only one or two specific places on the nylon sheet.

5. DNA fingerprint. The final DNA fingerprint is built by using several probes simultaneously. It resembles the bar codes used by grocery store scanners.

Bacterium

Plasmid: a small ring of DNA that carries accessory genes separate from the chromosome

Chromosome

DNA

1) The plasmid is isolated

Cell containing the gene of interest

2) The DNA is purified

3) The gene is inserted into the plasmid

4) The plasmid is returned to the bacterium

- 17 -

There are many applications of DNA fingerprinting: • Diagnosis of inherited disorders • Developing cures for inherited disorders • Forensic or criminal • Personal identification

Cloning a Gene in a Bacterial Plasmid

Tetracycline Resistance

Ampicillin Resistance

1) Isolate DNA from two sources

Human cell

2) Cut both DNAs with the same

restriction enzyme

Human DNA containing gene of interest

3) The human gene is inserted into the plasmid

4) Return the plasmid into the bacterium by

transformation

5) The cells containing the recombinant plasmid can be identified by their ability to grow in the presence of Ampicillin but

not Tetracycline.

- 18 -

Nucleic Acids

Nucleic acids are polymers made from nucleotide monomers. A polymer is a long chain of repeating units; a monomer is the basic unit of a polymer. DNA and RNA are nucleic acids. Nucleotide monomers themselves are made of three sub-units: 1. Nitrogenous Base:

• Adenine (A) • Guanine (G) • Cytosine (C) • Thymine (T)

2. Five-Carbon Sugar (Pentose):

• Deoxyribose 3. Phosphate Group In DNA, the sugar and phosphate groups form the "backbone" and the bases point toward the interior. Bases on one strand form hydrogen bonds to bases on the other strand. Complimentary strands (A pairs only with T, and C pairs only with G) and the two chains form a double helix. Therefore, if one strand of DNA has a given sequence of bases, it is possible to predict the sequence of bases on the complimentary strand.

G A T T C C G A T A A C C T A A G G C T A T T G

Monomer Polymer

Two Rings

One Ring

P

O

O

Sugar Nitrogenous Base

sugar |

phosphate |

sugar |

phosphate

ɹɹɹns |

ɹɹɹɹdsoɹd |

ɹɹɹns |

ɹɹɹɹdsoɹd

- a ∙∙∙∙ ɹ -

- g ∙∙∙∙ ɹ -

- 19 -

Protein Synthesis

Protein synthesis is the process of assembling amino acids into polypeptides based on "instructions" encoded on a DNA molecule. It occurs in two steps: transcription and translation.

Transcription

Transcription is the production of an mRNA molecule from a DNA strand.

Transcription

Double-stranded DNA

One strand of DNA is copied ("transcribed") into "messenger RNA" (mRNA) by

complimentary base pairing*

mRNA passes through nuclear pores into the cytoplasm, where it is carried to the ribosomes

on the rough endoplasmic reticulum

DNA mRNA C G G C A T → U (Uracil) T A

*

- 20 -

Translation

Translation is the formation of a protein from the instructions encoded on an mRNA molecule at the ribosome. tRNA molecules bring the required amino acids, one at a time, to build the "primary structure" of protein, according to the instructions on the mRNA. Each amino acid links to the next by a peptide bond. After protein synthesis:

1. Polypeptides enter the rough endoplasmic reticulum. 2. The protein assumes 2º, 3º and 4º structures by folding itself repeatedly. 3. The protein is sent to the Golgi Apparatus in the vesicle. 4. The protein is modified in the Golgi Apparatus. 5. The protein is packaged in a vesicle, ready for export.

Protein synthesis begins when a strand of DNA unravels. The code for producing a protein is carried in the sequence of the nucleotides in the DNA. Each group of three nucleotides forms a codon, which represents a particular amino acid. One of the unwound strands of DNA forms a complimentary strand called mRNA. This process is called transcription. It takes place in the nucleus of the cells. Afterwards, the mRNA moves into the cytoplasm, where it attaches to a ribosome. A phase of protein synthesis called translation then begins. A cloverleaf-shaped molecule of tRNA approaches the ribosome. At one end of this molecule are three bases (nucleotides), known as an anticodon. At the ribosome, each anticodon aligns with its complimentary codon on the mRNA. This occurs according to complimentary base pairing. At the other end of the tRNA, an amino acid is attached. As the ribosome moves along the strand of mRNA, new tRNAs are attached. This brings the amino acids close to each other. The amino acids are joined by peptide bonds, and the resulting strand is a polypeptide.

Amino Acid

tRNA (transfer RNA) transfers specific amino acids to the ribosome to

build a protein

The complimentary bases to codons on the mRNA strand triplet

Every tRNA carries a specific amino acid

Anticodon

mRNA U A U C G C C A U A A U Nucleotide triplets make a

codon - the code to a specific amino acid

- 21 -

Adaptation and Variation

Adaptations are structures, behaviours or physiological processes that help an organism survive and reproduce in a particular environment. Structural Adaptations:

• mimicry • camouflage • skunk scent • rose thorns • porcupine quills • different bird beaks • different teeth • claws for digging • webbed feet • hooves • feathers

Behavioural Adaptations:

• mating rituals • hissing snakes • locating safe places for building nests • turtles hiding in shells • opossums play dead • migration

Physiological Adaptations:

• hibernation Variations are differences between individuals, which may be structural, functional or physiological. Variations arise in populations because of continuously occurring mutations - permanent changes in the genetic material of an organism. Mutations come about because of errors that occur during DNA synthesis. They can be harmful, beneficial, or neutral. Mutations that occur during gamete formation are passed on to subsequent generations and can become established in entire populations. Environmental conditions determine whether a variation in an individual has a positive, negative, or no effect on the individual's ability to survive and reproduce. A particular variation may have no impact on survival at one time, but due to environmental changes in the future, this variation might become beneficial to survival.

Protection from Predators

Obtaining Food

Locomotion

Reproduction

Availability of Food

Protection from Predators

Variation (already exists in a population)

New Variation

(mutation)

Adaptation (environmental conditions)

- 22 -

Selective Advantage The offspring of sexually reproducing organisms inherit a combination of genetic material (genes) from both biological parents. The number of possible combinations of genes that offspring inherit from their parents results in genetic variation among individuals within a population. A change in the content of the genetic message - the base sequence of one or more genes - is referred to as a mutation. Some mutations alter the identity of a particular nucleotide, while others remove or add nucleotides to a gene. Mutations that occur in somatic tissue can have significant effects on an individual, but will not be passed on to offspring. Some mutations have negative effects, some have neutral effects, and some have positive effects for the individual. Mutations that occur in gametes can have significant effects on offspring and on the entire species. Mutations result in new alleles and therefore underlie all other mechanisms that produce variation, the raw material for evolutionary change. Selective advantage is the genetic advantage of one organism over its competitors that causes it to be favoured in survival and reproduction rates over time. For example, some flies have a mutation that makes them immune to the effects of the insecticide DDT. This mutation, however, reduces the flies' growth rate. Before the introduction of DDT to their environment, this mutation was a disadvantage to the flies. When DDT was introduced, this mutation enabled the individuals that possessed it to survive. These flies had a selective advantage in the population. They were more likely to survive and reproduce, potentially passing on this now-helpful mutation to their offspring. Adaptations are the result of gradual, accumulative changes that help an organism survive and reproduce. Mutations like the one that allows some flies to survive DDT exposure come about completely by chance. Organisms do not alter their genetic information so they can exist in new environments. When an environment changes, some individuals in a population have mutations that allow them to take advantage of the chance. If so, they may survive and pass their beneficial genes on to their offspring. Organisms that do not have this mutation may not survive or may not be healthy enough to reproduce. The rate at which resistance develops in a population is influenced by genetics and also by other biological properties, such as the organisms' rate of reproduction.

Natural Selection

Natural selection is a process whereby the characteristics of a population change because individuals with certain heritable traits survive specific local environmental conditions and pass on their traits to their offspring. In order for this to occur, diversity within a species or variability within a population must already exist. The environment exerts a selective pressure on a population as it selects for certain characteristics, and against others. Organisms with a high degree of fitness have high reproductive success. This is because they are well-suited to the environment. Their advantageous genes can be passed on to their offspring.

- 23 -

Evolution: 1. Genes mutate 2. Individuals are selected 3. Populations evolve

There exists phenotypic variation within a population. Some phenotypic variation is heritable. Within populations there is differential reproductive success. The differential reproductive success is influenced by the phenotypic differences between individuals. Reproductive success leads to a decline in undesirable genotypes. It also increases the frequency of desirable genes, which are more fit to the environment. "Survival of the fittest" is commonly associated with natural selection. Natural selection is the differential success in reproduction. It occurs between the environment and the species. The product of natural selection is the adaptation of populations of organisms to their environment. Once organism can survive a change in its environment, it can pass on its successful genes to its offspring. For natural selection to occur, there must be pre-existing diversity within a species. This is what allows changes in the population's proportions. Natural selection has no will, purpose or direction. Rather, it is situational. A trait that at one time seemed irrelevant may be the trait that allows a population to survive in a different situation.

Abiotic Factors: • air • wind • light • temperature • gases • water • soil

Biotic Factors: • predators • humans • disease

DNA

Mutations

Change in Genotype

Change in Phenotype

Variability in Populations (adaptation)

Change in allele frequency in the gene pool

New Species EVOLUTION EXTINCTION

- 24 -

Artificial Selection People artificially select organisms for particular traits. Selective breeding is an example of artificial selection. Most grains, fruits, vegetables, meats and milks are obtained through artificial selection. The environment plays no role in artificial selection; rather, humans do.

Positive Negative Breeding animals for certain

characteristics Health problems

Breeding plants to express their most desirable qualities

Lack of genetic diversity

Most of the food we eat today is artificially selected

Monocultures are susceptible to disease

A gene bank contains a population of early ancestors of modern plants. Their genetic combination allowed them to thrive for thousands of years. If the need ever arose, their genetic diversity could be reintroduced into modern plants.

Evolution

Evolution is the process in which significant changes in the inheritable traits (genetic material) of a species over time. Fossil evidence and geological processes are some of the scientific evidence. The fossils and their geographic distribution provided important scientific insights into the past.

Name Theory

Cuvier

"Catastrophism" and "Creationism": local catastrophes caused widespread extinctions. Extinct species are replaced by newly created species, or by

repopulating from nearby areas.

Lyell

"Uniformitarianism": the Earth's surface has always changed and continues to change through similar, uniform and very gradual (not "catastrophic")

processes. Therefore, the Earth must be very old. Dramatic change could result over extremely long periods of time through slow, seemingly slight

processes. This was an important stepping stone for other theories.

newer fossils

older fossils

(supports theory)

more complex

less complex (does not support

theory)

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Buffon

Species change over time, leading to new organisms (similar organisms may have a common ancestor)

Lamarck

He was the first to recognize that the environment plays a role in the evolution of a species, since species need to adapt to environmental

conditions. "Theory of Inheritance of Acquired Traits": each species gradually becomes more complex and new species are formed by spontaneous generation (arising from non-living matter). However, this theory is

incorrect.

Common Ancestor

New Organisms

The origins of life are strongly influenced by religion and philosophy. These ideas suggest that all forms of life have existed

unchanged since their creation. A system of empirical studies

(observations and experiments) is used to explain the natural world.

The idea that life forms are unchanging was challenged. The similarities

between humans and apes suggest a possible common ancestor; therefore

species do change over time.

Catastrophic events periodically destroyed species (caused extinction).

Subtle, slow geological processes could happen over a long period of time and

result in substantial change. Characteristics that are acquired over a lifetime can be passed on to offspring.

The theory of evolution by natural selection is developed.

The development of palaeontology - the study of fossils

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Developing the Idea of Natural Selection

Darwin's journey on the Beagle provided him with important evidence which he then used to develop his ideas about natural selection. 1. Plants and animals observed in the temperate regions of South America were more similar to plants and animals in the South American tropics than to plants and animals in other temperate regions in the world (the rodents in South America were structurally similar to one another, but were quite different from the rodents Darwin had observed on other continents). Q: If all organisms originated in their present forms during a single event ("creation"), why was there a distinctive clustering of similar organisms in different parts of the world? A: Organisms living relatively close together more likely evolved from a common ancestor. 2. Darwin found fossils of extinct animals (such as the glyptodont) that looked very similar to animals presently living in the same region (for example, the armadillo). Q: Why would living and fossilized organisms that looked similar be found in the same region? A: Extinct animals are recent ancestors. Changing environmental conditions selected for certain traits over others. 3. Plants and animals living in the Galapagos Islands closely resemble plants and animals living on the nearest continental coast (the west coast of South America). Q: Why are these plants and animals similar to one another? A: Once, they were the same species, but at one point in time, the island broke off from the continent. 4. Species of animals (such as tortoises and finches) that at first looked identical actually varied slightly from island to island. Q: Why are these animals different from one another? A: Different variations were selected for because of different environmental conditions on the different islands (such as different predators and food sources). 5. Through his experience with artificial selection (such as breeding pigeons), Darwin knew that traits could be passed on from parent to offspring, and that sexual reproduction resulted in many variations within a species. Q: Could the same thing happen in nature? Could the environment "select" the desirable traits? 6. After reading Lyell's work, Darwin understood that geological processes are slow and subtle - over time, they can result in substantial changes.

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Evidence for Evolution

The Fossil Record: • Most fossils are very different from species we see today • More recent fossils are more similar to species alive today, since they have had

relatively little time to change • Fossils appear in a chronological order • Organisms do not all appear in the fossil record simultaneously: gradual change

is seen (ancestral fish → ancestral amphibian → ancestral reptile) • Transitional fossils show links between different organisms since they share

characteristics common to two separate groups (Archaeopteryx had reptilian teeth, claws and a bony tail, but it also had bird-like feathers)

Geographic Distribution of Species:

• Geographically proximal environments are more likely to be populated by related species than are locations that are geographically separate but environmentally similar

Anatomy:

• Homologous structures are anatomical structures that have the same evolutionary origin and may or may not have the same structure and function (a human arm and a bat wing). They point to a common ancestor both species shared

• Analogous structures are body parts of organisms that do not have a common evolutionary origin but perform similar functions (a bat wing and a butterfly wing)

• Vestigial structures are structures that were functional in the organism's ancestors, but are no longer functional because they have lost their use (pelvic bone in baleen whales)

Embryology:

• When embryos are examined, similar stages of embryonic development are evident (early stages of development in fish, bird, reptile and mammal embryos all have a tail and gill pouches, revealing a common ancestral origin)

Genetics and Molecular Biology:

• Species with similar patterns in their DNA indicate that they have a common ancestor from which this DNA was inherited (T-Rex and chicken)

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Mechanisms of Evolution

Individuals do not evolve - populations do. Therefore, to study evolution, we focus on changes within populations. Macroevolution refers to large-scale changes in organisms, which are significant enough that over time, the newer organisms would be considered an entirely new species. Microevolution refers to changes in the gene pools or changes in allele frequencies within populations that can lead to the formation of a new species. A gene pool is all of the alleles of all the genes of all the individuals in a population. Allele frequencies are the number of copies of an allele compared to the total number of alleles in a population (expressed as a percentage). There are five factors that cause microevolution:

• Genetic Drift • Gene Flow • Non-Random Mating • Mutation • Natural Selection

Genetic Drift

Genetic drift is the change in allele frequency in a population as a result of random chance. This typically occurs in small populations. This can be caused by either the bottleneck effect or the founder effect. The bottleneck effect is a change in the gene pool that occurs after a rapid decrease in population size. Populations can be driven to near extinction because of natural disasters (floods, fires, earthquakes, etc...) or due to humans (over-hunting, loss of habitat, etc...). The surviving population (random individuals who survived the calamity by chance) does not have the same allele frequency as the original "parent population". The genetic drift then follows, and the surviving population has less diversity/variation. The northern elephant seals and the whooping cranes are such examples; both were hunted until there were only 20 and 12 individuals left in each species, respectively. All of the individuals of these species that exists today have arisen from these few ancestors - there is very little diversity within the species. The founder effect is a change in the gene pool that occurs when a few individuals start a new, isolated population. The founders may not carry all of the alleles of the original population (alternatively, they may carry a rare, recessive allele). In the new environment, the founding population has less diversity/variation. Many cases of polydactoly in an Amish population of Philadelphia and many cases of Huntington's disease in a Venezuelan village can all be traced back to a single individual, who acted as a founder of that particular colony.

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Gene Flow

Gene flow is the movement of genes into and out of gene pools due to migration of individuals from one population to another. Gene flow can decrease the genetic differences between populations. If the gene flow is extensive, neighbouring populations can become a single population with a common genetic structure.

Non-Random Mating

Non-random mating is the mating of individuals on the basis of mate selection or inbreeding. Only certain individuals contribute to the gene pool of the next generation. Inbreeding is the mating between closely related partners. This results in a population with many homozygous individuals. Therefore, harmful recessive alleles are more likely to be expressed. An example of inbreeding are self-fertilizing plants. Mate selection occurs when individuals choose a partner that has a similar of desirable phenotype, such as size. An example of this is the competition for mates among caribou.

Mutation

If a mutation alters DNA in a gamete, it can be passed on to subsequent generations. Mutations can have effects that are favourable, unfavourable or neutral. Favourable mutations that provide a selective advantage will eventually appear with increased frequency in a population. Neutral or negative mutations may ultimately provide a selective advantage in a rapidly changing environment; otherwise, they will disappear.

Natural Selection

Selective forces work on populations, therefore some individuals are more likely to survive and reproduce than others. Selection causes changes in a population's allele frequencies in three ways:

• Stabilizing Selection • Direction Selection • Disruptive Selection

Stabilizing Selection

The intermediate phenotype is favoured and the phenotypes at both extremes are unfavoured, reducing genetic variation. This type of selection improves a population's adaptations to constant aspects in the environment. An example of this type of selection is the birth weight of babies: too light is unhealthy, and it is difficult to give birth to a heavy baby.

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Directional Selection

An extreme phenotype is favoured, and so the distribution curve shifts in that direction. Some examples of this type of selection include the peppered moth and antibiotic-resistant bacteria.

Disruptive Selection

The extremes of a phenotype range are favoured, and so the intermediate phenotypes are eliminated or extremely decreased. An example of this is the Coho Salmon: there are large and small male salmon, but no intermediately-sized ones.

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Isolating Mechanisms There are two isolating mechanisms that ensure that different species cannot interbreed: pre-zygotic and post-zygotic isolating mechanisms. Pre-zygotic isolating mechanisms either impede mating between species or prevent the fertilization of eggs. Post-zygotic isolating mechanisms prevent hybrid zygotes from developing into viable, fertile individuals.

Pre-Zygotic Isolating Mechanisms

There are five pre-zygotic isolating mechanisms:

• Behavioural Isolation: Any special signals or behaviours that are species-specific that prevent interbreeding of closely-related species, such as bird calls or courtship rituals

• Temporal Isolation: Species reproduce at different times of the day or during different seasons, such as tropical orchid species, which reproduce at different times of the month

• Habitat Isolation: Two species may live in the same general area but in different habitats, thus rarely encountering each other, such as the common garter snake and the northwest garter snake, which are found near water and in open areas, respectively

• Mechanical Isolation: Species may attempt to mate but will fail because they are anatomically incompatible, such as different insect species

• Gamete Isolation: The gametes will not fuse to form a zygote because the sperm may not survive in the female, or may be unable to germinate the female, such as sperm dying in a hostile female environment

Post-Zygotic Isolating Mechanisms

There are three post-zygotic isolating mechanisms:

• Hybrid Breakdown: First-generation hybrids are viable and fertile, but after mating with another hybrid or either of the parent species, the resulting offspring are either sterile or weak, such as the hybrids of cotton plants

• Hybrid Inviability: The interbred species are genetically incompatible, and the development of a hybrid zygote stops, because mitosis is prevented, such as the hybrids of sheep and goat

• Hybrid Sterility: Although two species mate and produce a viable offspring, that offspring is sterile due to a failure of meiosis to occur, because the chromosomes differ in number or structure, such as the mule, the cross between a horse and a donkey

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Types of Speciation

A biological species is a population or a group of populations in nature where individual members can interbreed to produce viable, fertile offspring that can also interbreed. Speciation is the formation of a new species from a pre-existing one (also called macro-evolution). When a population is reproductively isolated, it means that there is little or no gene flow between the populations. Phyletic speciation is the result of sequential changes, through which one species become another. Converging speciation is the result of similar traits arising because different species have independently adapted to the same or similar environmental conditions.

Diverging speciation is when species that were once similar to an ancestral species diverge to become increasingly distinct.

There are two types of divergent speciation: sympatric and allopatric speciation.

Sympatric Speciation

Sympatric speciation is a form of divergent speciation in which populations within the same geographical area diverge and become reproductively isolated. This form of speciation is more common in plants than in animals. There are two forms of sympatric speciation: polyploidism and hybridization. In polyploidism, parent plants can produce offspring that are polyploidy (generally tetraploidy, 4n), given that mistakes occur during meiosis. These individuals are reproductively incompatible with the parent population, and are therefore considered as a new species. These organisms can reproduce with other tetraploidy organisms, or can self-fertilize themselves (if they are plants). In hybridization, two different species can interbreed to produce a sterile offspring. Asexual reproduction by the offspring results in the formation of a separate population. Through mistakes in meiosis, namely non-disjunction, sterile hybrids can become fertile polyploids, this forming a new, fertile species.

Allopatric Speciation

Allopatric speciation is a form of divergent speciation in which a population and its gene pool are split into two or more isolated groups by a geographical barrier. If enough time passes, the two populations become so distinct over time that they are unable to interbreed if they are ever reunited.

A B

A B

C

A B

C

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Adaptive Radiation

Adaptive radiation is the relatively fast evolution of many species from a single ancestral species. This often happens when an organism is presented with many new, unprecedented opportunities:

• Organisms enter a new ecological area (Darwin's Finches) • Mass extinction (mammals after the death of dinosaurs) • A new trait evolves (plant flowers attract pollinators)

Models of Evolution

There are two models that attempt to explain the speed of evolutionary change: gradualism and punctuated equilibrium. Currently, both models are accepted: while many species have evolved rapidly during periods of Earth's history, the fossil record also shows very gradual change for some species over extended periods of time.

Gradualism

Evolutionary change is slow and steady, occurring before and after divergence. Big changes are the result of the accumulation of small changes. However, the fossil record does not support this model, as species are found to appear and disappear suddenly in the record.

Punctuated Equilibrium

Evolution consists of long periods of stasis - equilibrium - that are punctuated by periods of divergence. Most species undergo much of their morphological change when they first diverge from the parent species. After that, they change relatively little, even as they give rise to new species.

Gradualism Punctuated Equilibrium

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Classification of Living Things

The biosphere is the part of the Earth inhabited by living organisms. This area is only about 1/10,000,000,000 of the Earth's mass. Nevertheless, as many as 100 million different organisms live here. Aristotle identified about 1,000 different organisms approximately 2,300 years ago. Today, biologists estimate that there are approximately 30-100 million different organisms that exist. Many scientists tried to classify these organisms according to specific categories: land, air or water dwellers, useful or harmful organisms, consumer or producer, etc... As our knowledge of the number of organisms increases, a better system was created. John Roy, an English clergyman, tried to classify all organisms in the world in the 17th century. He was the first to use the word "species". To be a member of the same species, three criteria must be met:

1. the organisms must be similar in nature 2. the organisms must be able to interbreed under normal conditions 3. the offspring must be fertile

The Linnaean System of Classification

This system was developed by Carolus Linnaeus. He is considered the "Father of Modern Taxonomy". In this system, organisms are organized according to their structural similarities. His classification system is known as binomial nomenclature. It is very useful because a species may be known by several different common names in different parts of the world (cougar, panther, and mountain lion). There are two parts to an organism's scientific name. The first part of each name is the organism's genus, and the second word is its species. Each species must be classified into seven main classification groups. Each group is called a taxon (plural: taxa). They are: kingdom, phylum, class, order, family, genus and species. They go from the broadest to the most specific. For instance, if a human were being classified, he would be put in the: Kingdom: Animalia Phylum: Chordata Class: Mammalia Order: Primates Family: Hominidae Genus: Homo Species: Sapiens Therefore, if you are a human, your scientific name is Homo Sapiens.

(animals with a notochord - the axis around which the spinal chord develops) (animals that have hair and nurse their young)

(monkeys, baboons, etc...) (no other living species in this family)

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The Six Kingdoms

To classify an organism, biologists first place them in the correct kingdom. There are six: animalia, plantae, fungi, protista, archaebacteria and eubacteria.

Archaebacteria

These bacteria are unicellular prokaryotes. The have neither nuclei nor organelles. They are known for living in harsh habitats (low oxygen, extreme temperatures, acid). They are ancient bacteria, believed to be the first forms of life.

Eubacteria

Like archaebacteria, the eubacteria are also unicellular prokaryotes, lacking both nuclei and organelles. They can be found living almost anywhere. As many as 4 million of these "true bacteria" may exist.

Protista

Unicellular for the most part, these eukaryotes have nuclei, organelles, and several contain chloroplasts. They are found everywhere (land or water). They are the evolved descendants of prokaryotic bacteria. This kingdom includes all eukaryotes that are not plantae, fungi or animalia.

Fungi

Organisms in this kingdom are multicellular eukaryotes. They have nuclei, organelles, no chlorophyll, and no cellulose in their cell walls. They inhabit a variety of environments. They are unable to photosynthesize, do not need sunlight, and live of dead organic material (decomposers). There are over 100,000 types of these organisms.

Plantae

The organisms in the plantae kingdom are multicellular eukaryotes. They have nuclei, organelles, but unlike fungi, they have both chlorophyll and their cell walls contain cellulose. These autotrophs can also inhabit a vast variety of environments. They are for the most part land dwellers, but there are also plants that live on water.

Animalia

The organisms of this kingdom are multicellular eukaryotes. They have nuclei, organelles, but not chlorophyll and cell walls. They live in many different environments. These organisms are heterotrophic, and can be either vertebrates or invertebrates.

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Kingdom Protista

The organisms of this kingdom have existed for about 1.5 billion years; they are the first eukaryotes. It is a very diverse group, containing about 115,000 different species. Because of the diversity of this group, there is no single correct way to categorize its members. Since the species differ in many different categories, such as cell structure, nutrition, metabolic needs, reproduction and habitat, they can be classified by any of these diverse characteristics. Here, they will be classified by their nutrition patterns: whether they are animal, plant, or fungi-like protists in their diet.

Animal-Like Protists

While some parasites are harmful to their hosts, others are beneficial. For example, Giardia cause digestive problems in humans and Trypanosoma Gambiensis cause sleeping sickness, but Trichonympha live in the termite's gut and help it digest wood. Amoeba and other animal-like protists use endocytosis to obtain their food, a process in which they use their pseudopodia ("false feet") to capture and take in particles to be internally digested.

Fungus-Like Protists

Some examples of these protists is the acellular slime mould - a single-celled organism with many nuclei, cellular slime mould, which live in fresh water, damp soil and in decaying matter, and the water mould, which lives in water.

Plant-Like Protists

These plant-like protists contain chlorophyll and can undergo photosynthesis. For example, a Euglena is autotrophic in sunlight, but turns heterotrophic in the dark. Algae such as diatoms (very abundant, glass-like shells, are a key marine food source) and dinoflagellates (have two flagella that cause a spinning motion, are luminescent, can have toxic effects on humans if they are concentrated in shellfish) are also autotrophic protista. Protists have developed many different methods to move. Some use flagella: long, thin, tail-like structures composed of microtubules. They have a whip-like action that propels the protist forward, such as Euglena. Others have pseudopodia: "false feet" that are temporary projections of the cytoplasm that allow the organism to move in an oozing, creeping motion, like Amoeba. Others yet have cilia: short, thin, hair-like structures composed of microtubules. They have a wave-like action that propels the protist forward. However, some protists are non-motile, meaning they have no means of locomotion, such as the Plasmodium.

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Euglena

Reproduction

Protists can reproduce in four different ways. During asexual reproduction, protists like Paramecium undergo binary fission, similar to bacteria. During sexual reproduction, they undergo a form of conjugation, exchanging micronuclei during meiosis. Some protists are able to form fruiting bodies: for example, in acellular slime moulds when food is abundant, the slime moulds exist as a mass of cytoplasm with many nuclei. However, when food becomes scarce, they form fruiting bodies, which produce spores that are dispersed and germinate elsewhere. Finally, some protists produce spores without making fruiting bodies, such as Plasmodium.

pellicle

Paramecium

Life Cycle of Plasmodium

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Kingdom Bacteria - Archaebacteria and Eubacteria

Bacteria are the oldest and most diverse group of organisms on the planet. They are unicellular prokaryotes, and lack a nucleus and organelles. Bacteria live and thrive in extreme habitats (heat and acidity). They can be harmful, but the majority are helpful.

There are two ways to classify bacteria: by shape and by gram stain.

Classifying Bacteria by Shape

Shape Diagram Name Single Cells

Pairs Linear Chains

Clusters

Sphere Coccus (Cocci)

Mono- Diplo- Strepto- Staphy-

Rod Bacillus (Bacilli)

Mono- Diplo- Strepto-

Spiral Spirillum (Spirilli)

Mono-

Classifying Bacteria by Gram Stain

Adding crystal violet stain and iodine to bacteria on a slide is another form of classifying bacteria. Gram-positive bacteria will retain the purple because of their thick cell walls, but gram-negative bacteria lose the purple colour and appear pink; these tend to be pathogenic.

DNA

Plasmid

Flagellum

Cell Wall Cell Membrane

Cell Wall

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Reproduction in Bacteria

Bacteria reproduce very quickly: most divide every 15-20 minutes. However, their reproduction is limited by factors such as space, food and temperature. Because of this speed of reproduction, there is a high mutation rate during DNA replication, which often results in antibiotic immunity. Bacteria can reproduce both sexually and asexually, but are also able to form endospores.

Binary Fission

This is the bacteria's form of asexual reproduction. The parent cell divides into two identical offspring, provided there is no genetic mutation.

Conjugation

Conjugation is a form of sexual reproduction that occurs between bacteria when conditions are not ideal. Two bacteria connect by a protein bridge and a plasmid from one bacterium is transferred to the other, altering its genetic makeup. This might give the bacteria antibiotic resistance, since those genes are found on the plasmid. The plasmid transfer is a one-way process, not an exchange.

Endospore Formation

Under extremely unfavourable conditions, some bacteria form resistant structures called endospores. The original bacterium replicates its DNA, and one copy becomes surrounded by a durable wall which allows it to survive harsh conditions (drought, malnutrition, extreme heat and cold, poison, etc...).

DNA

Cytoplasm

Cell Wall

DNA has been replicated

Cleavage furrow forms

The two daughter cells formed are identical to the parent cells

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Nutrition

Bacteria have a source of energy and carbon to produce the organic compounds needed for cellular metabolism.

Mode of Nutrition Energy Source Carbon Source Photoautotroph Light CO2

Chemoautotroph Inorganic Chemicals CO2 Photheterotroph Light Organic Compounds

Chemoheterotroph Organic Compounds Organic Compounds

Respiration

All living things must carry out cellular respiration to receive a supply of energy to function. Bacteria vary on whether or not the process of cellular respiration requires oxygen. Bacteria are classified in one of five categories based on these criteria:

1. Aerobes: cellular respiration involves oxygen to produce energy from food 2. Obligate Aerobes: oxygen is absolutely necessary for the bacteria's survival 3. Anaerobes: cellular respiration is carried out in an oxygen-free environment 4. Obligate Anaerobes: the presence of oxygen kills these bacteria 5. Facultative Aerobes: can survive with or without oxygen

Viruses

A virus is a submicroscopic pathogen. A virus is composed of genetic information surrounded by a protein coat. When they are not invading a host, they take on a crystalline form. Biologists agree that viruses are not alive, as they cannot move, grow or carry out respiration, and need a living host to reproduce. There are many kinds of viruses, such as the common cold, the flu, West Nile Virus, AIDS and SARS. Viruses have very geometric shapes, such as spheres and spindles. They have molecules on their shell that are used to attach the virus to its host. A virus that attacks bacteria is called a bacteriophage. Viruses are very specific - they can only attack certain kinds of cells.

Life Cycles

Viruses have two distinct cycles: the lytic cycle and the lysogenic cycle. In the lytic cycle, the host cell is taken over and the viruses are released after one generation, and symptoms appear immediately. In the lysogenic cycle, the DNA of the virus is integrated with that of the host, and the viruses are released only after several generations, resulting in delayed symptoms.

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Lytic Cycle

The lytic cycle is the "life cycle" of the virus. A. The virus attaches itself to a cell. B. DNA from the virus enters the cell. C. The cell's original DNA is destroyed. The cell makes new viral DNA and proteins. D. New viruses are made from the protein and DNA. E. The cell breaks open in a process called lysis and the viruses are released.

Lysogenic Cycle

In the lysogenic cycle, the virus does not destroy the host cell immediately. Instead, it integrates its DNA with that of the host, and then becomes inactive. As the bacteria reproduces, it copies the DNA of the virus along with its own. At some later point in time (several generations later), the DNA of the virus is activated by an environmental stimulus, and enters the lytic cycle.

Virus

Viral DNA

Cell DNA Host Cell

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Kingdom Fungi

All fungi are saprobes: they release enzymes on dead organic matter and then absorb the nutrients through the cell well, in contrast to slime moulds, which use endocytosis. Although fungi can vary significantly in appearance, they have the following structures in common:

• Hyphae: thread-like filaments that make up the body of the fungus • Mycelium: tangled mass of hyphae used for absorbing nutrients • Cell Wall: made from chitin rather than cellulose

Reproduction

Most fungi reproduce both sexually and asexually. Their reproduction involves the use of spores (haploid reproductive cells). Their reproduction patterns are used to subdivide the 100,000 species into divisions (the equivalent of phyla). There are four main divisions:

1. Division Zygomycota (case-like fungi) 2. Division Ascomycota (sac-like fungi) 3. Division Basidiomycota (club-like fungi) 4. Imperfect Fungi

Division Zygomycota

The spores of these fungi are in caselike structures, such as bread mould. These fungi reproduce asexually by spreading out threadlike hyphae called stolons over the food surface. Root-like hyphae called rhizoids extend into the food and absorb nutrients and water. Reproductive hyphae form black case-like structures called sporangia, each containing thousands of spores. After the spores are released, they germinate and begin to grow on a new food source.

During sexual reproduction, two genetically different types of reproductive hyphae (+ and -) make contact. The nuclei join to make a zygospore. Zygospores remain dormant until growing conditions are good. They then germinate and form new mycelial masses.

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Division Ascomycota

The fungi in this division, such as mildews, moulds, yeasts and truffles, have spores in a case-like structure. Spores produced sexually in an ascus (sac) are called acospores. Spores produced asexually are called conida. Yeasts divide asexually by budding when conditions are good. When conditions are bad, they form acospores by sexual reproduction and remain in a dormant phase until conditions improve. Yeasts carry out anaerobic respiration (fermentation) in order to break down sugar molecules and release energy for the cells. Carbon dioxide and alcohol are by-products of this respiration. Therefore, yeasts are used extensively in baking (carbon dioxide makes dough rise) and in wine-making. However, yeasts also cause infection and disease in plants and animals.

Division Basidiomycota

The spores of the fungi in this division are in a club-like structure called a sporangium. Mushrooms, rusts, smuts, puffballs and bracket fungi are all examples of fungi from this division. Many are saprobes, but some can be parasitic. They have complex reproductive cycles. They can cause extensive damage to crops.

Imperfect Fungi

The fungi in this division have no known sexual phases, so they cannot be classified in any of the other three divisions. Many of these fungi are responsible for diseases in plants and animals. One notable fungus in this division is Penicillium, the source of penicillin. Another is Trichophyton rubrum, the fungus responsible for athlete's foot.

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Fungal Associations

Fungi have many symbiotic relationships with other organisms: • Lichens provide water, minerals and protection for algae, who in turn provide

nourishment through photosynthesis • The fungal mycelium of Micorrhizae absorbs water and minerals from the soil for

plant roots, who provide the fungus with amino acids and sugar • Certain fungi in the Amazon rainforests provide food for leaf-cutting ants, while

the ants leaves food for the fungus and removes competing fungi

Kingdom Plantae

All plants are eukaryotic multicellular organisms that can carry out photosynthesis. They have cell walls made of cellulose, are for the most part land-dwellers, and develop from embryos that are protected by the parent's plant tissue. One characteristic common to plant life cycles is the alternation of generations. One generation is haploid (n, gametophyte), and the other is diploid (2n, sporophyte).

Classifying Plants

There are two broad divisions of plants: non-vascular plants (bryophytes) and vascular plants (tracheophytes). Vascular plants are further categorized into spore producers and seed producers. Lastly, the seed-producing plants are grouped into cone producers (gymnosperms) or flower producers (angiosperms).

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Non-Vascular Plants (Bryophytes) These plants appeared on Earth 400 million years ago. They have no true stems, leaves or transport tissues, and they grow in moist environments. This category of plants includes mosses, liverworts and hornworts. Bryophytes reproduce both sexually and asexually. Their asexual reproduction is vegetative propagation, where a small segment of the parent plant breaks off and grows into an identical new plant. Water is critical for the sexual reproduction of the bryophytes, because the sperm have to swim from the male reproductive organ to the female reproductive organ through it. Peat moss grows in open, wet environments. As the moss begins to decay, it accumulates and the lower layers are compressed by their own weight and by gravity, Because of the moisture and the lack of oxygen, moss layers only partially decay, and can grow up to 10m in height. Peat moss has many uses, such as fuel, soil additive, heat and electricity.

Vascular Plants (Tracheophytes)

These plants appeared 40 million years after their predecessors, the bryophytes, approximately 360 million years ago. Unlike the non-vascular plants, these plants have transport tissues called xylem and phloem. It is because of these newly developed tissues that these plants are able to grow taller. They are all land-dwellers. Vascular plants are classified into spore-producing and seed-producing plants.

Spore Producing Plants

Club mosses, horsetails, ferns and other plants in this category produce spores during their reproduction. They grow in marshes and on the edges of streams and rivers. Ferns grow in a broad range of environments.

Seed Producing Plants

This is by far the most successful group of plants due to their highly specialized organs, namely leaves, stems and roots that allow them to adapt to almost any environment. They can reproduce sexually by means of pollination: the transfer of pollen from the place it was formed to a receptive surface. They are subdivided into two groups: cone producers, like the ginkgo, cycads and conifers, and seed producers, such as roses and tulips. Cone producers are called gymnosperms, literally meaning "naked seed", and flowering plants are called angiosperms.

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Gymnosperms

Gymnosperms reproduce using cones. The male cone is called a pollen cone, and the female equivalent is the seed cone. Gymnosperms are used extensively for softwood, which is used for a variety of purposes, such as in construction, for pulp, furniture, shingles, doors, fencing, decks, plywood and lumber.

Angiosperms

During self-pollination, pollen from a plant fertilizes the same plant's egg cells. In cross-pollination, the plant's pollen is transferred from one plant to another of the same species by vectors such as air, water or animals. During fertilization, the pollen grain germinates when it lands on a stigma. A pollen tube grows down into the ovary. One of the two nuclei in the pollen grain divides into two sperm nuclei. One sperm nucleus fuses with the ovum to produce a zygote. The other sperm fuses with the two polar nuclei of the ovum to become endosperm tissue (3n). The endosperm stores nutrients for the developing seed. After fertilization, the ovum develops into a seed and the ovary into a fruit. The ovary enlarges, and the other flower parts die. Similar to self-pollination, seed dispersal is done by mean of air, water or animal.

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Kingdom Animalia

All animals are eukaryotic, multicellular, heterotrophic organisms. They lack cell walls, but are the only kingdom whose organisms have muscle and nerve tissue. Most animals reproduce sexually. Animals are thought to have evolved from colonial, flagellated protists. Some colonies had cells that became specialized for things like movement or feeding, which gave them an advantage over other colonies whose cells did not specialize. Animals are often described and classified by the way their internal structures are organized (their body plan):

• body symmetry (bilateral, radial, asymmetric) • extent of cellular organisation (independent cells vs. tissues, organs and systems) • presence of coelom and other structural and physiological modifications

Phylum Porifera

This phylum consists for the most part of sponges. They live in warm, quiet waters, where they are sessile (stay fixed in one place). The sponge's body plan is asymmetric, lacks a mouth, a digestive cavity, and has no muscle or nerve tissues.

Sponges reproduce both sexually and asexually. They are hermaphrodites, and water currents carry sperm cells to other individuals. Their form of asexual reproduction is budding.

Osculum: opening that allows water to be expelled from the sponge Epithelial Cells: cover inner and outer surface; some surround pores and control pore size to regulate water flow Collar Cells: flagella beat to maintain water flow and filter micro-organisms for ingestion Amoeboid Cells: move between epithelial cells and collar cells; they are used for digestion, the distribution of nutrients, the production of reproductive cells and the development of the internal skeleton

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Phylum Cnidaria

Jellyfish, coral, sea anemone, hydrozoans and sea fans are all part of this phylum, which includes animals with a radial symmetry and two layers of cells. The outer layer is called the ectoderm, and the inner later can be called either the endoderm or the gastrodermis. In between these layers is a jelly-like layer called the mesoglea.

Part Function Muscle Fibres contract to move the animal

Nerve Net allows the organism to respond to environmental stimuli Nematocysts stinging structure in specialized ectodermic cells (cnidocytes)

Tentacles arm-like structures that release toxic substances through the nematocysts to paralyze prey

Gastrovascular Cavity sac with a role in digestion, circulation and gas exchange

Phylum Platyhelminthes

This phylum contains flatworms, all of which exhibit bilateral body symmetry. An important advantage to their flat body plan is that more of the organism's surface area can absorb nutrients, release waste and participate in gas exchange than in another body plan.

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Planarians are 2cm-long flatworms that live in fresh water. They have a pharynx, an organ that connects the mouth and the gastrovascular cavity which the planarian uses for feeding. They have simple nerve cells at their anterior for sensory: eye spots are able to sense light, and the sides of their head are sensitive to touch. Flukes are parasitic flatworms, which spend part of their life in a mammal host. They have an outer cuticle which protects them from being digested by the acids in the mammal, and a sucker which they use to attach themselves to their host. Tapeworms are very flat and slender parasites, equipped with a sucker and a cuticle. However, they lack external body extensions for locomotion. They absorb their food directly through their body wall (they do not have a mouth or a digestive sac).

Phylum Nematoda

This phylum is that of the roundworms. Most roundworms are scavengers which inhabit soil and the bottom of lakes, but several are parasites, which infest plants and animals. Roundworms have a more efficient digestive system that the flatworms, as they have a separate exit for the waste (an anus), allowing food to move in one direction, like all complex animals. They do not require a respiratory and a circulatory system because their thin body wall and round shape minimizes energy consumption.

Phylum Annelids

The segmented can are found in terrestrial, marine and freshwater environments. They have repeating, mostly identical body segments with the same structure. Because of this segmentation, they have an improved locomotion compared to other worms, and can grow to a greater size without losing the capacity to transport molecules and relay messages. Annelids have a coelom: a fluid-filled body cavity surrounded by mesoderm. It separates the body wall from the digestive track, protects internal organs and acts like a hydrostatic skeleton. Annelids need a circulatory system because they are much bigger than worms of other phyla. Since they have thin body walls, the gas exchange occurs on the surface of the body, but only in a moist environment. The body wall of sandworms extends outwards to serve as parapodia, improving gas exchange and locomotion. They have bristles on the end of each parapodium called setae, which improve the grip. They have a distinct male and female gender. Earthworms are hermaphrodites; during copulation, they exchange sperm to fertilize each other's eggs. The worms are born into cocoons. Leeches are external parasites that feed on blood. They secrete an anti-clotting agent that keeps blood flowing. They were used by doctors for a long time to let blood, and are used today to reduce swelling and to remove pools of blood.

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Phylum Chordata

The members of this phylum have nerve chords, notochords and gill slits at one point in their life. Their body symmetry is bilateral, they have a ventral heart, and the body extends past the anus into a tail. They are believed to be evolved from marine animals. This phylum is separated into seven classes.

Class Vertebrate

This is the largest class in phylum Chordate. The notochord of these organisms develops into a backbone; they have two pairs of appendages, a skull with a large brain, and a skin-covered body. In aquatic animals, the gas exchange takes place in the gills; for terrestrial organisms, in occurs in the lungs.

Superclass Agnatha

This is the class of jawless fishes, such as the lamprey and the hagfish; they also do not have paired fins.

Class Chondrichthyes

This is the class of cartilaginous fish, such as sharks, rays and skates. They are marine animals with paired fins. They undergo internal fertilization, and are ovoviviparous.

Class Osteichthyes

This is the class of bony fish. They have scales and undergo external fertilization.

Class Amphibia

This is the class of amphibians, such as frogs, toads and salamanders. Most live in fresh water at some point in their life. They undergo metamorphosis, the abrupt change in body structure (tadpole → frog), are able to breath through their skin, and have three-chambered hearts.

Class Reptilia

This is the class of reptiles, such as crocodiles, alligators, lizards and snakes. They do not need water to reproduce; instead, they undergo internal fertilization, and then lay eggs. The gas exchange takes place in the lungs.

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Class Aves

This is the class of birds. They have horny scales on their legs, lay eggs, are endotherms (warm-blooded), have feathers and have hollow bones.

Class Mammalia

This is the class of mammals. They have hair, a four-chambered heart, glands to produce link, specialized teeth, are endotherms, and undergo internal fertilization. There are three main types of mammals: monotremes, marsupials and placentals. Humans fall under the last category.

Phylum Mollusca

The animals of this phylum are mostly marine, although a few are terrestrial. They vary greatly in size, ranging from 1mm to 18m. They are the descendants of annelids. Their moist, muscular body lacks a skeleton. Their body plan consists of three main components:

Structure Function Foot locomotion, feeding

Mantel thin tissue that covers gills and secretes the shell in shelled species Visceral Mass contains internal organs

Foot

Mantel

Visceral Mass

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Class Bivalva

This class includes organisms such as clams, oysters, scallops, mussels, and other shelled fish. They have a two-part shell connected by a hinge, are sessile, and have no head. Clams use their foot to burrow into the sand or mud; mussels use the foot to hold themselves in place; scallops do not have a foot. Organisms in this class use gills to capture food from water and for gas exchange.

Class Gastropoda

This class includes organisms such as snails and slugs. They use their foot for locomotion, and feed using a radula. The gas exchange happens through gills and moist skin.

Phylum Cephalopoda

This class includes squids, octopuses and the nautilus. They are ocean predators who can see prey at a great distance; they have a well-developed brain.

Phylum Echinodermata

This phylum includes starfish, sea urchins, sand dollars and sea cucumbers. All these organisms have a radial symmetry. The adults and larvae look very different - adults have a radial symmetry while larvae are bilateral.

Phylum Arthropoda

The organisms in this phylum are animals with an exoskeleton made of chitin and jointed legs. They have a segmented body which they can moult (shed). They have a hemocoel (body cavity), and open circulatory system and circulatory system, eyes and antennae.

Class Arachnida

This class includes scorpions, spiders, mites and ticks. Their body plan consists of two main parts: the cephalothorax (the head and body fused) and the abdomen. Most have six pairs of appendages; their offspring hatch from eggs, and several have silk glands, such as spiders.

Class Crustacea

This class includes shrimp, lobsters, crayfish and crabs. They have three main parts in their body plan: the head, the thorax and the abdomen. Each body segment has paired appendages attached to it.

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Class Insecta

Like the class Crustacea, the animals in this class have a head, thorax and abdomen. The head has one pair of antennae, and the thorax has three pairs of legs. Flying insects have two pairs of wings attached to the thorax (flies only have one pair of wings). Like amphibians, they can go through metamorphosis.

Class Diplopoda and Class Chilopoda

Organisms from class Diplopoda are millipedes; while they do not have 1,000 legs, each body segment has two legs attached to it. Organisms from class Chilopoda are centipedes; they have one pair of legs attached to each body segment.

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Glossary

Gamete: a specialized sex cell (sperm and egg) Gene: a segment of DNA that carries the code for a specific protein Locus: specific location of a gene on a chromosome Allele: one form of a gene for a specific trait Cancer: a group of diseases characterized by abnormal cell division. Tumour: an abnormal lump of cells produced by uninhibited cell division Benign: a tumour that shows no sign of spreading Malignant: a tumour capable of spreading Metastasis: a life-threatening malignant tumour capable of moving through the body and infecting new tissues Radiation Therapy: a cancer treatment that disrupts the mitotic process, and as a result, daughter cancerous cells are flawed, and die off Chemotherapy: a cancer treatment involving the use of a wide range of drugs, which affect all the cells of the body, not just cancerous cells; as a result, chemotherapy patients can often be seen without hair Immunotherapy: a cancer treatment that uses the body's own immune defences and naturally occurring chemicals Blending Theory of Inheritance: a 19th century hypothesis that "seeds" control hereditary traits and blend with other seeds when they pass to the next generation Pangenesis: an outdated theory that suggests that traits could be modified during a person's lifetime and these modifications could be passed on to his or her offspring Heredity: the transmission of genetic characteristics from parent to offspring Gene: a distinct packet of hereditary information passed from generation to generation Allele: one form of a gene for a specific trait Dominant: the allele that is expressed in a heterozygous individual (TT) Recessive: the allele that is only expressed in the homozygous recessive condition (tt) Genotype: the genetic make-up of an organism Phenotype: the physical characteristic of an organism Homozygous: describes an organism with two identical alleles of a certain gene Heterozygous: describes an organism with two different alleles of a certain gene Incomplete Dominance: neither gene is completely dominant over the other; in a heterozygous individual, there is an intermediate phenotype that is expressed, instead of the dominant one Co-Dominance: neither allele dominates or hinders another; the two are expressed at the same time Multifactorial Trait: traits whose phenotypic expression is controlled by genes found at many loci (polygenic); multifactorial traits are further grouped into continuous and discontinuous distribution Gene Linkage: when genes are found in the same chromosome do not undergo independent assortment, they are not separated during meiosis; instead, a small fraction of the genes are exchanged during the process of crossing over

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Evolution: The process in which significant changes in the inheritable traits (genetic makeup) of a species occur over time Immutable: Unchanged and unchanging, believed (before the evolutionary theory became accepted) to be characteristic of life forms Fossil: Any preserved remains or traces of organism or its activity; many fossils are such of hardened body parts, such as shells and bones Permineralized Fossil: A fossil formed when dissolved minerals precipitate form a solution in the space occupied by the organism's remains Fossilization: The process by which traces of past organisms become part of sedimentary rock layers or, more rarely, hard tar pits, volcanic ash, peat bogs or amber Microfossils: Microscopic remains of tiny organisms or structures that have hard and resistant outer coverings Palaeontology: The scientific study of fossil remains Catastrophism: Cuvier's theory that numerous global catastrophes in the past had repeatedly caused the extinction of species that were then replaced by newly created forms Relative Age: An estimate of the age of a rock of fossil specimen in relation to another specimen Absolute Age: An estimate of the actual age of a rock or fossil specimen Radioactive Decay: The release of subatomic particles from the nucleus of an atom, which results in the change of a radioactive parent isotope into a daughter isotope; when the numbers of protons is altered, a different element is formed Radioisotopes: atoms with an unstable nuclear arrangement that undergo radioactive decay Parent Isotope: changes into a daughter isotope as radioactive decay occurs Daughter Isotope: what a parent isotope changes into during radioactive decay; may be stable or radioactive and capable of further decay Half-Life: the time required for half of a radioactive material to undergo decay; the half-time for any given isotope is constant Radiometric Dating: calculation of the age of rock - and of embedded fossils and other objects - through the measurement of the decay of radioisotopes in the rock Sexual Selection: the perpetuation of alleles in a population for characteristics that give males the advantage of being selected by females as a mate Virus: non-cellular particle of DNA or RNA surrounded by a protein coat, which lives as a parasite within a host cell Provirus: virus whose DNA has been inserted into the host cell Recombinant DNA: DNA molecule formed when a biologist splices two different and combines portions of DNA from two different sources Restriction Enzyme: bacterial enzyme that cuts up foreign DNA; used in genetic engineering to create recombinant DNA Lysis: bursting of a host cell infected by a replicating virus RNA: nucleic acid made of a single strand of nucleotides, involved in protein synthesis Binary Fission: division of an organism into two identical individuals through a type of asexual reproduction

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Gram Stain: dye made of crystal violet and iodine that biologists use to classify bacteria based on the organism's reaction to the stain Plasmid: Small ring of DNA in a bacterium, often used in genetic recombination Prokaryote: single-celled organism that lacks a membrane-enclosed nucleus and membrane-enclosed organelles Eukaryote: organism made of one or more cells that have both a membrane-enclosed nucleus and membrane-enclosed organelles Bacterium: single-celled prokaryote that belongs to the kingdom Archaebacteria or the kingdom Eubacteria Conjugation: transfer of DNA between two bacterial or protist cells that unite in a type of sexual reproduction Endospore: tick wall produced in some bacteria in unfavourable conditions to enclose its DNA and cytoplasm DNA: nucleic acid encoded with instructions to produce proteins that stores and transmits genetic information Saprobe: living organism that feeds on dead organisms and organic waste Bacteriophage: virus that infects specifically bacteria Retrovirus: virus with a complex reproductive cycle