BIOLOGY EOC TEST STUDY GUIDE Ms. DeCandia

CHARACTERISTICS OF LIVING THINGS

1. made up of one or more cells- unicellular: one cell- multicellular: > one cell up to trillions of cells

*** only non living matter that has cells was once livingEx: cork, tree bark

2. reproduce: produce organisms of same type- sexual: 2 cells from different organisms make one new organism- asexual: single organism reproduces without aid of another

3. grow and develop: through growth of size and number of cells- differentiation: process whereby cells become different to perform specialized tasks- size of cells is limited by surface area to volume ratio

- volume (inside of cell) grows faster than surface area (outside of cell)

4. obtain and use energy- anabolism: formation of complex substance from simpler ones

ex: protein synthesis photosynthesis

- catabolism: breakdown of complex substances into simpler oneEx: digestion

- metabolism: total sum of all chemical reactions in an organism

5. respond to their environment

types of stimulilight sound water odortemperature gravity pressure heat

irratibility: ability of living organism to respond to stimuli***improves organisms chances for survival

homeostasis: constant or stable conditions necessary for life- loss of homeostasis can result in life threatening conditions for an organism

ex: plantsleaves and stems: respond to light and grow upwardroots: respond to gravity and grow downward

ex: - Suppose it’s a hot day, how does your body cool off? - Suppose you are sweating for an hour, how do you feel?

- What do you do in response to feeling thirsty?

THE MICROSCOPE

Parts and Specifications 

Historians credit the invention of the compound microscope to the Dutch spectacle maker, Zacharias Janssen, around the year 1590.   The compound microscope uses lenses and light to enlarge the image and is also called an optical or light microscope (vs./ an electron microscope).  The simplest optical microscope is the magnifying glass and is good to about ten times (10X) magnification.  The compound microscope has two systems of lenses for greater magnification, 1) the ocular, or eyepiece lens that one looks into and 2) the objective lens, or the lens closest to the object.  Before purchasing or using a microscope, it is important to know the functions of each part.   

Eyepiece Lens:  the lens at the top that you look through.  They are usually 10X or 15X power. 

Tube:  Connects the eyepiece to the objective lenses

Arm:  Supports the tube and connects it to the base

Base:  The bottom of the microscope, used for support

Illuminator:  A steady light source (110 volts) used in place of a mirror.  If your microscope has a mirror, it is used to reflect light from an external light source up through the bottom of the stage.

Stage:  The flat platform where you place your slides.  Stage clips hold the slides in place.  If your microscope has a mechanical stage, you will be able to move the slide around by turning two knobs.  One moves it left and right, the other moves it up and down.

Revolving Nosepiece or Turret:  This is the part that holds two or more objective lenses and can be rotated to easily change power.

Objective Lenses:  Usually you will find 3 or 4 objective lenses on a microscope.  They almost always consist of 4X, 10X, 40X and 100X powers. When coupled with a 10X (most common) eyepiece lens, we get total magnifications of 40X (4X times 10X), 100X , 400X and 1000X .

Condenser:  The purpose of the condenser lens is to focus the light onto the specimen. 

Diaphragm or Iris:  Many microscopes have a rotating disk under the stage.  This diaphragm has different sized holes and is used to vary the intensity and size of the cone of light that is projected upward into the slide. .

How to Focus Your Microscope:  The proper way to focus a microscope is to start with the lowest power objective lens first and while looking from the side, crank the lens down as close to the specimen as possible without touching it.  Now, look through the eyepiece lens and focus upward only until the image is sharp.  If you can't get it in focus, repeat the process again.   Once the image is sharp with the low power lens, you should be able to simply click in the next power lens and do minor adjustments with the focus knob.  If your microscope has a fine focus adjustment, turning it a bit should be all that's necessary.   Continue with subsequent objective lenses and fine focus each time. 

COMPOUNDS OF LIFE

4 Biomolecules

1. Carbohydrates2. Lipids3. Proteins4. Nucleic Acids

Biochemical Reactions: Building and Breaking Organic Compounds

Dehydration synthesis/ condensation reaction: chemically joining two monomers with loss of H2Oto make a polymer

Hydrolysis: splitting of a polymer into monomers with addition of water

Carbohydrates (sugars)- composed of C : H : O

1 : 2 : 1 ratio- function: energy and structure

- types of carbohydrates

1. Monosaccharides: (C6 H12 O6) A. glucose – most important : main

energy source in cells - all di/polysaccharides broken

down into glucose

B. galactose – milk

C. fructose – fruitsIsomers: same chemical formula, different structure

2. Disaccharides: (C12 H22 O11) - two monosaccharide units

A. sucrose – table sugar B. maltose – malt sugar (beer) C. lactose – milk sugar

3. Polysaccharides : very large saccharide chains A. starch – energy storage for plants

- 100’s of glucose molecules

B. glycogen – energy storage for animals (muscles and liver)

C. cellulose – structure for plant stems - wood and bark

- cell walls of plants

Lipids (fats)- waxy or oily compounds- function: energy storage

Structure: 1 glycerol (alcohol) + 3 fatty acids

Types of lipids:Saturated: solid at RT

- max number of H bonds with C (saturated with bonds)

Unsaturated: liquid at RT- double bonds between C, not all C bonded to H

Proteins- composed of C, O, H, and N- functions: Structure, Growth , Repair

- Carrier molecules- Initiate chemical reactions

- structure: Amino acids: building blocks

Peptide bond: type of bond that joins amino acids (condensation)

Enzyme: biological catalyst (ends in “ase”), type of protein works by lowering activation energy of substance (substrate) to be broken down

Nucleic acidsDNA, RNA

THE CELL

Cell Theory ( Schleiden, Schwaan, Virchow)1. all living things are composed of cells2. cells are basic units of structure and function3. all cells come from pre existing cells

2 types cells 1. prokaryotes: no nucleus or membrane bound organelles, more primitive cells2. eukaryotes: contain nucleus and membrane bound organelles

Generalized animal cell Generalized plant cell

Functions of organelles (tiny structures within cell with specific jobs)CELL ORGANELLE FUNCTIONS FOUND IN

CELLS Cell wall Support  Plant, bacteriaCentrioles Form spindle in cell division  AnimalChloroplasts Site of photosynthesis  plant

Cilia Short hairlike structures, Cell movement Animal,plant, bacteria

Cytoplasm Gel like substance in cell, holds organelles Animal,plant, bacteria

Endoplasmic Reticulum Intracellular highway for substances/proteins Animal, plantFlagella  Long whiplike structure, movement Bacteria, protists

Golgi apparatus, Bodies Repackages substances, secretes them in sacs (vesicles)  Animal, plant

Lysosomes Sacs contain digestive enzymes, break down cell waste Animal, plant

Mitochondria Powerhouse of cell, cell respiration (makes ATP)  Animal, plant

Nucleolus Inside nucleus, makes ribosomes  Animal, plant

Nucleus  Control center, site of DNA Animal, plant

Plasma (cell) Membrane

Protects cell, controls movement of substances in and out of cell 

 Animal, plant

Ribosomes Site of protein production Animal, plant

Vacuoles Large fluid filled sacs, make up most of cell volume  plant

CELLS AND THEIR ENVIRONMENT

Types of cell transport

I. Passive transport (like swimming with the current in the ocean)Movement of molecules of a solute from areas of high to low concentration without the use of energy

3 types:1. diffusion

- movement of molecules of a solute from areas of high to low concentration (concentration gradient) until equilibrium is reached- equilibrium: steady state where equal numbers of molecule move in each direction- concentration gradient: differences in concentration of a substance across a space

2. osmosis: - movement of water from areas of high to low concentration until equilibrium is reached

- Types of solutions

Results of solutions on cells

3. facilitated diffusion

- movement of a substance from areas of high to low concentration with the aid of a carrier protein (driven by diffusion, does not use energy)

II. Active transport (like swimming against waves in ocean, needs energy)Movement of substances through a membrane against a concentration gradient requiring energy (from ATP)2 types

1. membrane pumps- channels in cell membrane that pump substances in and out 2. endocytosis/exocytosis

TYPE OF

SOLUTION

CONDITIONSINSIDE CELL

CONDITIONSOUTSIDE

CELL

DIRECTION OFWATER

MOVEMENT

HYPOTONIC LESS WATER

MORE WATER

INTOCELL

HYPERTONIC MORE WATER

LESS WATER

OUT OFCELL

ISOTONIC EQUAL WATER

EQUAL WATER

IN & OUTOF CELL

AT SAME RATE

- endocytosis: process where cells engulf substances too large to enter by passing thru membrane - exocytosis: process of removing large substances out of cell (opposite mechanism of endocytosis)

Membrane pumps Endocytosis/ Exocytosis

CELLULAR ENERGY, PHOTOSYNTHESIS, RESPIRATION

Two fundamental biological processes for cellular energy:Energy: ability to do work, needed for all biological processes

1. Photosynthesis: process by which plants convert radiant energy to chemical energy ( deposits energy)

2. Respiration: process by which glucose molecules are broken down and stored energy is released (withdraws energy)

****opposite processes*****

TYPES OF ORGANISMS BY ENERGY PRODUCTION1. Autotrophs: organisms that produce organic molecules from inorganic substances (photosynthesis)

- make own food

2. Heterotrophs: organisms that obtain energy from other organism (heterotrophs or autotrophs)- do not make own food

Photosynthesis: plants make glucose Respiration: animals break down glucose for energy

ENERGY PRODUCTION

ATP: adenosine triphosphate- molecule that stores useable energy- composed of 3 parts

- adenine (N compound)- ribose (5 C sugar)- 3 phosphate groups

ATP/ADP CYCLE - energy is stored in high energy bonds between phosphate groups- bond must be broken to use energy

ATP ADP A - (P~ P ~ P) ------------ A - ( P ~ P) + P + energyHigh energy molecule Adenosine diphospate mid energy molecule

ADP AMP A - (P ~ P) ----------- A – P + P + energyMid energy molecule Adenosine monophosphate

Low energy molecule

PHOTOSYNTHESIS

6 CO2 + 6 H2O + light energy C6H12O6 + 6 O2- occurs in chloroplast (green pigment chlorophyll absorbs suns energy)

Thylakoid discs (photosysytem:200-300 thylakoids) Harvest sunlight

Contains chlorophyll and accessory pigments Photosystem I and II are linked structurally and functionally

Grana (stacks of thylakoid discs) location of light reactions

Stroma (protein rich solution, outside grana) location of dark reactions

Pigment: substance that absorbs light

• in photosynthesis: absorbed light energy is used to make chemical bond energy• wavelengths not absorbed are reflected (color we see)• Absorption spectrum: colors (wavelengths) absorbed by a particular pigment

• chlorophyll a - primary photosynthetic pigment - directly involved in converting light into chemical energy - hides other pigments

• chlorophyll b- accessory pigment- absorbs light and transfers energy to

chlorophyll a

• all other accessory pigments transfer energy to cholorphyll a

Two Stages of Photosynthesis

1. light reactions: must take place in light, occurs in thylakoid membranes

- sun’s energy is trapped by chlorophyll- water is split and oxygen is released- purpose: ATP (energy) and NADPH (electron acceptor)

is formed

2. dark reactions (also called Calvin cycle): light independent (occur in light or dark), happen after light reactions

- carbon fixation takes place- ATP, NADPH act with CO2 to form glucose3 basic steps- carbon fixation to glucose- reduction of NADP to NADPH- regeneration of RuBP to start cycle over again

End product of dark reaction

Glucose

RESPIRATION (aerobic- uses oxygen)

Glycolysis (Glucose/breaking)Process where one molecule of GLUCOSE (6 C) is broken down into 2 molecules of PYRUVIC

ACID(PYRUVATE) (3C) - occurs in cytoplasm - occurs before respiration or fermentation - occurs in the absence of oxygen - makes 2 ATP

Two Pathways for pyruvic acid:

1. Fermentation (anaerobic respiration)- makes 0 ATP- purpose: to regenerate NAD for glycolysis- occurs in cytosol- animals produce lactic acid- plants produce ethyl alcohol

2. Aerobic Respiration

C6H12O6 + 6 O2 6 H2O + 6 CO2 + 36 ATP

- occurs in mitochondria- two major stages

1. krebs cycle- oxidation of glucose is completed

- NAD+ is reduced to NADH

2. electron transport chain- NADH is used to make ATP via

oxidative phosphorolation - most ATP produced here

DNA (deoxyribonucleic acid)

Molecule responsible for all cell activities and contains the genetic code.

Composed of nucleotides (basic unit of DNA): A. PhosphateB. Deoxyribose sugar (5 C)C. 4 Nitrogenous bases

- purines Adenine A Guanine G

- pyrimidines Thymine T Cytosine C

Complementary pairs: - 1 purine bonds with 1 pyrimidine on one rung of the ladder - connected by a weak H bond- bonding pairs: C – G, A – T

REPLICATION OF DNA - Process of duplication of DNA- before cell can divide a new copy of DNA must be made for the new cell- each strand acts as a template (pattern) for new strand to be made

There is another nucleic acid: RNA (ribonucleic acid)

DIFFERENCES BETWEEN DNA AND RNA DNA RNA1. deoxyribose sugar 1. ribose sugar2. double strand 2. single strand3. bases A, T, C, G 3. bases A, U, C, G

TRANSCRIPTION OF RNAProcess where RNA is produced from DNA

PROTEIN SYNTHESISFormation of proteins using information coded on DNA and carried out by RNA

***DNA like the president RNA like the vice president PROTEINS like the workers that carry out the jobs

Functions of proteins:- cell structure, repair , and growth- cell movement- control biochemical pathways (enzymes)- direct synthesis of lipids and carbohydrates- chemical messengers (hormones)

The genetic code from DNA is transcribed onto m RNA by Codons.

Codon ( triplet): specific group of 3 successive bases on DNA and mRNA- codes for a specific amino acid to be placed on the protein chain

- 20 biological amino acids, but more than 20 codons- Like “genetic words”

Ex: DNA triplet: ACT, GCA, TTARNA codons: CGU, ACG, AAA

BUILDING OF PROTEINSRemember………the genetic code determines which proteins will be made.

STAGES OF_PROTEIN SYNTHESIS1. transcription (nucleus)

- DNA makes mRNA

2. translation (cytoplasm at ribosome)- production of protein- mRNA directs the sequence of amino acids to be placed on the protein chain

CELL DIVISION

Why cells must divide:

If membrane is stretched too large:- cytoplasm will flow out of cells- movement of materials in and out of cell would not be controlled

(suffocation and waste poisoning)- cell would not be able to supply enough materials needed for life- not enough RNA would be able to be produced- eventually cell would die

Cell division: process whereby a mother cell divides into 2 daughter cells

TYPES CELL DIVISION1. asexual reproduction

- no exchange of genetic material, daughters identical to mother - occurs in somatic (body cells)

A. Prokaryotes (bacteria) : binary fission

B. Eukaryotes: mitosis - same result as binary fission except DNA and many organelles have to be duplicated - chromosomes: tightly coiled DNA and proteins - before mitosis: interphase occurs- DNA is replicated- so both cells have equal DNA

90% of cell cycle spent in interphase

Stages of Mitosis

End result: Two diploid (2n) daughter cells with identical genetic information to mother cell.

2. sexual reproduction - exhange of genetic material, daughter cells not genetically identical to mother cell - occurs in gametes (sex cells- egg, sperm) - crossing over occurs: chromosomes cross over each other & exchange genetic material (prophase I)

Meiosis: process whereby gametes are formed that contain half the chromosomes of mother cell

Meiosis I Meiosis IIEnd result: 2 diploid cells End result: 4 haploid cells

End result: Four haploid (n) cells with different genetics.

Mutation: any sudden chemical change in genes or chromosomes (mistake)- most mutations are recessive (important because if they were dominant, they would eventually

destroy the species)- can occur in any cell

- germ mutation: affect reproductive or germ cells (inherited in offspring)- somatic mutation: affect body cells (not inherited in offspring

Mutant: organism that has a mutation and shows a completely different trait than its parents (can also carry 1 recessive gene and not express mutation)

Mutagen: agent that causes a mutation

Mutations can occur in genes, a portion of a chromosome, or the whole chromosome.

Deletion Genetic material is removed or deleted. A few bases can be deleted (as shown on the left) or it can be complete or partial loss of a chromosome (shown on right).

FrameshiftThe insertion or deletion of a number of bases that is not a multiple of 3. This alters the reading frame of the gene and frequently results in a premature stop codon and protein shortening.

InsertionWhen genetic material is put into another region of DNA. This may be the insertion of 1 or more bases, or it can be part of one chromosome being inserted into another, non-homologous chromosome.

Duplication segment of chromosome is repeated ....TTTGGGAAACC…TTTGGGAAAGGCCCC

PointA single base change in DNA sequence. A point mutation may be silent, missense, or nonsense.

Translocation

Broken piece of one chrom. breaks off and attaches itself to another non homologous (replicated) chromosome

What causes mutations?  - external (exogenous) factors

 environmental factors such as sunlight, radiation, and smoking can cause mutations, chemicals- endogenous (native) factors

errors in the cellular machinery, errors during DNA replication can lead to genetic changes

What are the consequences of mutations?           Mutations can be advantageous and lead to an evolutionary advantage of a certain genotype. Mutations can also be deleterious, causing disease, developmental delays, structural abnormalities, or other effects.

Cancer: mutation of genes which cause abnormal uncontrolled cell growth

GENETICS AND HEREDITY

Heredity: transmission of traits from parents to offspring

Genetics: study of heredity

1851: Gregor Mendel (Austrian Monk), father of heredity, studied pea plants

P homozygous dominant X homozygous recessive

F1 100% heterozygous dominant

F2 3 dominant : 1 recessive --------------------------------------------------- homozygous: two same genes heterozygous: two different genes

phenotype: outward physical expression of trait genotype: actual genes in pair

GENOTYPE DETERMINES PHENOTYPEI. Law of Dominance and Recessiveness

- one factor (gene) in a pair may mask the other factor (gene) preventing it from having an effect dominant: stronger trait (allele codes for a protein that works) recessive: weaker trait, will only appear when dominant trait is not present (allele codes for a protein that doesn’t work)

ex: **genes occur in pairs (alleles)TT, Tt : talltt: short

II. Law of Segregation- the two factors (genes) for a trait segregate (separate) during the formation of egg and sperm and each

reproductive cell (gamete) receives only one factor for each trait (gene)ex: male would give one trait : T or t

female would give one trait: T or toffspring could have these combinations: TT, Tt, tt

III. Law of Independent Assortment- Factors (genes) for different traits are distributed to gametes independently of each other.

- Mendel also crossed plants that differed in 2 characteristics- He found that traits from dominant factors did not appear together- Factors for each trait were not connected

Genetics and Probability

Probability: possibility that an event will occur

Probability = # one kind of event # of all events

Punnett Square: chart used to predict probability in genetic crosses

Monohybrid Cross (one trait)

Guinea pigs: coat typesDominant : rough RRecessive: smooth r

A. Cross a homozygous rough with a homozygous smooth. Determine the phenol. and geno. ratios for coat types.

Cross:

Phenotype ratio:Genotype ratio:

B. Cross a homozygous smooth with a heterozygous rough. Determine the phenotype and genotype ratios

for coat types.

Cross:

Phenotype ratio:Genotype ratio:

C. Cross a heterozygous rough with a heterozygous rough. Determine the phenotype and genotype ratios for coat types.

Cross:

Phenotype ratio:Genotype ratio:

Test Cross: procedure where an individual of unknown dominant genotype is crossed with a homozygous recessive individual (determines if dominant trait parent is homozygous or heterozygous)

Problem: RR x Rr

- All the guinea pigs had a phenotype of rough coat- How would we determine which of these guinea pigs was homozygous or heterozygous? - Do a TEST CROSS (homo. dom. x recessive / homo. dom. x recessive)

RR x rr

Rr x rr

Dihybrid crosses (two traits)

Product rule: Chance of 2 or more independent events occurring together equals product of chances of each of the separate occurrences.

Yellow – dominant Round - dominantGreen – recessive Wrinkled – recessive

Ex: YyRr x YyRr

Yy x Yy Rr x Rr

What is the probability of the offspring of this cross having:

a. yellow round seeds _______________________________b. yellow wrinkled seeds _______________________________c. green round seeds _______________________________d. green wrinkled seeds _______________________________

Chromosome Theory of Heredity (Sutton) 1. Genes are located on chromosomes and each gene occupies a specific place (locus) on a chromosome 2. Genes can exist in several forms (alleles) 3. Each chromosome contains only one of the alleles for each of its genes

Gene linkage: attachment of certain genes to each other on a chromosomes (by chemical bonds that keep them together), tend to move with each other during crossing over in meiosis

Linkage groups: group or packages of genes located on one chromosome which are usually inherited together (they do not undergo independent assortment)

- groups can be independently assorted, but always go together

Sex Linked Genes (X linked) Genes generally carried on X chromosome, missing on Y chromosomeCriss cross inheritance: trait expressed in P generation, does not express in F1, ½ sons express in F2

Ex: color blindness, hemophelia

- also known as criss cross inheritance

P male express geme (hemizygous)

F1 females carry geme (heterozygous)

F2 ½ males express gene (hemizygous)

** hemizygous- Y chromosome is missing gene

Incomplete dominance Active allele does not entirely compensate for inactive allele

* this is considered non Mendelian inheritance because it does not exhibit true dominance and recessiveness.

- heterozygous phenotype is mixture or 3rd new phenotype (in the case below, pink is the 3rd phenotype)

Using example to left: RR: red RW: pink WW: white

Co-dominance Both alleles of a gene are expressed, instead of a third new phenotype

- heterozygous phenotype: both phenotypes will show

Ex: : BW- roan cow (roan is a combination of both colors, not tan) * no third new phenotype

Polygenic inheritance Two or more genes responsible for a single trait

Ex: skin, eye color

Multiple alleles Three or more alleles for same gene code for a single trait

Ex: blood types

BLOOD TYPE DETERMINATIONAllele from

Parent 1Allele from

Parent 2Genotype of

offspring Blood types of

offspring A A AA A A B AB* AB A O AO A B A AB* AB B B BB B B O BO B O O OO O

Inheritance of diseases and conditions

Blood types

For simplicity,we call these

IA AIB Bi O

- Non Disjunction Inheritance : improper segregation of chromosomes during cell division Ex: sex chromosomes: Kleinfelters (XXY), Turners syndromes (XO)Ex: autosomes: Trisomy 21 (Down syndrome), extra 21st chromosome

- Autosomal Recessive Inheritance: caused by point mutation (one codon) - sickle cell anemia- when O2 deprevation occurs, RBC become sickle shaped and clog blood vessels

- Autosomal Dominant Inheritance- Huntington’s Disease: domiant mutation in gene

- progressive destruction of nervous system starting in 30- 40’s, only single copy of gene needed

- Sex Influenced Traits: genes found on autosomes but different expression in each sex- dominant in one sex/ recesive in other sex

Ex: baldness

- Sex Limited Traits: genes located on both sex chromosomes- only expresses in one sex (usually males) due to hormones

Ex: beard growth

Methods of studying inherited traitsKARYOTYPES PEDIGREES

Methods of pre-natal testing for genetic disorders

AMNIOCENTESIS CHORIONIC VILLUS SAMPLING

GENETIC ENGINEERING (GENE SPLICING/GENE CLONING)

Process of direct gene manipulationGoal: to introduce new characteristics into organisms to increase their usefulness

GENETIC ENGINEERING TECHNIQUES

I. Recombinant DNA1. Restriction enzymes

Proteins that cut DNA into pieces - cuts specific area of DNA into fragments that can be isolated and separate

2. Production of recombinant DNARecombinant DNA: DNA composed of fragments of DNA segments from at least two different

organisms- restriction enzymes cut bacterial plasmids (extra circular DNA molecules in bacteria)- plasmids have “sticky ends” (unpaired bases)- original DNA is attached to plasmid sticky ends

3. Reintroduction of DNA into bacterial vector- recombinant DNA taken up with bacterial DNA and now produced by bacterial cell- recombinant DNA is isolated and CLONED (duplicated) to make 1000’s of copies

4. DNA sequencing: process of reading exact order of bases in a fragment of DNA- makes it possible for scientists to discover specific genes and defective proteins of diseases (need to be able to read sequences to see proteins being made from them and

determine any problems)Results of genetic engineering

Transgenic organisms/ genetically modified organisms (GMO’s) : organisms that contain foreign genesCLONES

exact copies of an organism

Applications of Genetic Engineering 1. DNA fingerprinting (used in forensics)

Process of identifying and distinguishing DNA of individuals2. Gene therapy

Replacing defective gene with copy that works3. Pollution control

Genetically altered bacteria used to decompose garbage, sewage, and petroleum products4. Medicines/vaccines

E coli (bacteria) : used to make human insulin5. Increased food yields (animal and plant)

Human Genome Project- begun in 1990: coordinated by US Dept of Energy and NIH- purpose: To identify the 20-25,000 genes in human DNA

- To determine sequences of 3 billion DNA base pairs - To license info to biotech companies to foster new medical applications for diseases - Completed in 2003 - Could possibly help in targeted gene therapy for disease states

HISTORY OF THE EARTH

Earth’s age: - about 4.6 billion years old

• Big Bang Theory: - evidence shows 15 billion years ago universe was a concentrated super dense mass - this mass exploded, hurled matter and energy into space- gravity pulled some matter together to form galaxies and stars- gravity also pulled matter into orbit around stars- sun attracted clumps of matter (planets), and planets attracted smaller clumps of matter (moons)- meteors: thought to be bits of material left over from formation of our solar system.

Models of Formation of Life

1. Primordial Soup Model 1920’s: Oparin (Russian), Haldane (British)

• Atmosphere made of H2O vapor, NH3, CH4, and CO2 (no free O2- atmosphere couldn’t sustain life )• Thunderstorm drenched earth

Oceans contained large amount of organic molecules (like soup with many vegetables and meats)• Molecules pushed together by energy of sun and lightening• Molecules split, and formed new organic molecules (a.a., nucleic acids)• Disproven by Miller and Urey in 1953- no ozone (O3) to protect molecules

2. Bubble Model (Luis Lerman)

Determining the Age of the Earth

- radioactive dating: how age of earth determined

- radioisotope: unstable isotopes of certain elements that break down (decay) and lose protons or neutrons. As they break down, they release charged particles in the form of radioactivity

- decay: changing of one element into another as particles are given off

- half life: time period in which half the initial number of atoms decay into atoms of the element they change into (non radioactive)

Origins of Life• Spontaneous generation: principle that living things could arise from non living things• Biogenesis: principle that states that all living things come from other living thingsExperiments on spontaneous generation

1. early 1700’s Francesco Redi - questioned spontaneous generation(said that flies actually came from eggs laid by flies on meat)

Redi’s meat experiment - control: open jar with raw meat in it- experimental: cheesecloth over jar with meat on it- let sit a few days

Results: open jar- maggots, cheesecloth jar- no maggotsConclusion: no spontaneous generation

II.. mid 1700’s Lazzaro Spallanzini (Italian)

Experiment: thoroughly boiled gravy in both jars, one open and one sealed- Results: open jar: microorganisms, sealed jar: no micro- Conclusion: no spontaneous generation

III. 1864 Luis Pasteur- finally disproved spontaneous generation

Experiment: boiled nutrient broth in long curve necked flask allowed air to enter, but no dust or other airborne particles - Results: after an entire year, no microorganisms - Conclusion: no spontaneous generation

Development of Organisms Prokaryotes Eukaryotes Sea life Plants and fungi Arthropods Vertebrates

EVOLUTION

Evolution is “change over time”

History of Evolutionary Theory

Jean Lamarck (French)1. theory of desire

- organisms change due to inborn desire to change to become more fit for environmentex: ant eaters develop long snouts

2. theory of use and disuse (use it or lose it)- organs that are being used get large, organs that are not used shrink and eventually disappear

ex: snakes- didn’t use legs so disappeared whales- used to be land creatures, legs disappeared and became fins

3. theory of inheritance- acquired traits were passed on to offspring

ex: snakes that lost legs passed trait weight lifters would produce muscular offspr.

*******Lamarcks theory found untrue*********

Charles Darwin (English)Theory of Natural Selection: Individuals that have physical or behavioral traits that better suit their environment are more likely to survive and will reproduce more successfully than those without traits.

Parts of Theory1. Overproduction

- organisms produce more offspring than can survive2. Struggle to survive

- all organisms face constant struggle to survive (limited resources) ex: pond ecosystem – cattails compete with duckweed for surface of lake water

3. Genetic variation- individuals in a given species vary by chance (due to gene recombination- normal).

exception: identical twins 4. Survival of the fittest

- Individuals best adapted to environment are more likely to survive and reproduce

Ex: industrial melanism

The evolution of the peppered moth over the last two hundred years has been studied in detail. Originally, the vast majority of peppered moths had light coloration, which effectively camouflaged them against the light-colored trees and lichens which they rested upon. However, due to widespread pollution during the Industrial Revolution in England thetrees which peppered moths rested on became blackened by soot, causing most of the light-colored moths to die off due to predation. At the same time, the dark-colored moth flourished because of their ability to hide on the darkened trees.

Evolution can lead to:Speciation: process whereby new species evolve from old ones over long period of time

Extinction: permanent disappearance of a species

Differences in TheoriesLamarck: organisms change in order to survive in environment in its lifetime

Darwin: environment determines which organisms survive thru natural selection over many generations

** desire is not a factor**** natural selection works same way as artificial selection but over longer periods of time without control

or direction**

Mechanisms of Evolution

1. natural selection 2. mutation3. gene flow thru migration: The movement of individuals between populations. Causes reproductive isolation of populations. Any adaptations are passes to offspring and causes speciation4. genetic drift: In each generation, some individuals may, just by chance, leave behind a few more descendents (and genes, of course!) than other individuals. The genes of the next generation will be the genes of the "lucky" individuals, not necessarily the healthier or "better" individuals. That, in a nutshell, is genetic drift. It happens to ALL populations — avoiding the vagaries of chance.

Genetic drift affects the genetic makeup of the population but, unlike natural selection, through an entirely random process. So although genetic drift is a mechanism of evolution, it doesn't work to produce adaptations.

Convergent Evolution vs Adaptive Radiation

Convergent evolution Process whereby organisms not closely related, independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. ex: flight/wings of insects, birds, and bats. All four serve serve the same function and are similar in structure, but each evolved independently.

Evidences of Evolution

1. Fossils: - Most occur in layers of rock, with the youngest usually on top, and the oldest in deeper layers

(sedimentary rock)- Some found in amber (fossilized tree sap)- Record incomplete due to soft outer coverings on organisms not leaving imprints- 99% of all species that lived on Earth are now extinct.

 2. Chemical similarities: ex- DNA similarities in different species

- amino acid similarities

 

Adaptive radiation Rapid speciation of a single or a few species to fill many ecological niches. This is an evolutionary process driven by adaptation to changed environment and/or mutation and natural selection.

Ex: Darwin's finches

Darwin's finches are an excellent example of the way in which species' gene pools have adapted in order for long term survival via their offspring. The Darwin's Finches diagram below illustrates the way the finch has adapted to take advantage of feeding in different ecological niche's.

Their beaks have evolved over time to be best suited to their function. For example, the finches who eat grubs have a thin extended beak to poke into holes in the ground and extract the grubs. Finches who eat buds and fruit would be

less successful at doing this, while their claw like beaks can grind down their food and thus give them a selective advantage in circumstances where buds are the only real food source for finches.

Species Amino AcidDifferencesfrom HumanHemoglobinProtein

Gorilla

1

Rhesus monkey

8

Mouse 27Chicken 45Frog 67Lamprey 125

3. Embryonic similarities: suggest a common ancestor

4. Analogous Structures: Structures that serve the same function in different species but they evolved independently from different ancestors.

Bat wing vs Bird wing

5. Homologous Structures: Structures that have evolved from a common ancestor but have different functions.

6. Vestigial structures:• Structures which have lost all or most of their original function in a species through

evolution. • Degenerated, atrophied, or rudimentary condition• Largely or entirely functionless, may retain lesser functions or develop new ones

Factors in Evolution

1. Genetic Equilibrium: if species is very well adapted to environment and there is no competition, no change occurs

Ex: horseshoe crabs

2. Gradualism: evolutionary change occurs slowly and gradually over time

3. Punctuated equilibrium: long stable period interrupted by brief periods of change (sometimes events occur to disturb equilibrium)

- causes rapid change in small groups of organisms - usually fills new niche

- could cause mass extinctions

Evolution Updates1. Genes are carriers of characteristics and source of random variation. (caused by mutations)

2. Variation is the raw material for natural selection.Natural selection can operate only thru phenotypic variations.(physical and behavioral characteristics produced by genotype and environment)

3. Evolutionary change involves change in frequency of alleles in the gene pool of a populationPopulation: collection of individual of same species in specific area that can successfully breed. - offspring share same gene pool

Gene pool: common group of genesRelative frequency: how often alleles show up

- Since genes come in pairs (alleles), some occur more frequently- As relative frequency changes, distribution of traits changes

4. Evolutionary fitness and adaptation depends on success of organism passing its genes (traits) to its offspring

- adaptation: genetically controlled characteristics that increase fitness

5. Formation of species- species: group of organisms that breed and produce fertile offspring

- variation within species is normal- members share a common gene pool - if beneficial gene is spread thru a population and increases fitness, members of a species

can evolve together (coevolution)

- speciation: development of a new species thru evolution - reproductive isolation: two populations of same species do not breed with each other

due to geographic separation

POPULATIONS

affected by: growth rate, available resources, predators and disease

Population Model: hypothetical population which exhibits key characteristics of a real populationTypes:1. Stage I model: birth rate vs death rate

2. Stage II model (exponential): J shaped curve, rate stays same and population size increases steadily

3. Stage III model (logistical): S shaped, exponential growth limited by a density dependant factor (food and water), most realistic model in nature

Causes of Population Genotype/Phenotype Changes

I. Natural Selection Distribution Curves1. Directional selection:

- eliminates one extreme of the phenotypes so it becomes less common- causes frequency of particular trait to move in one direction- characterizes evolution of single gene traits

2. Stabilizing selection- eliminates extremes at both ends of phenotype- intermediate phenotypes increase- results in fewer extreme phenotypes

3. Disruptive selection- individuals with either extreme variation of a trait have greater fitness- reduces or eliminates average phenotype- results in two extreme phenotypes (new species)

II. Founder EffectThe establishment of a new population by a few original founders carry only a small fraction of the total genetic variation of the parental population- reason: a small number of individuals may colonize a place previously uninhabited by their species- effect: the frequencies of the genes may differ from the parental population

III. Bottleneck effect:- an evolutionary event in which a significant percentage of a population or species is killed or prevented from reproducing (usually from catastrophic geologic event, i.e. earthquake, hurricane, temp. change)- effect: reduction of a population’s gene pool and the accompanying changes in gene frequency produced

when a few members survive the widespread elimination of a species

ECOLOGY

The study of the interactions between organisms and the living (biotic) and non living (abiotic) components of their environment (field named in 1866)

Impacts on the Environment

1. exploding human population: requires increasing amts. of energy, food, and waste disposal, space from earths resources

2. sixth mass extinction- habitat destruction, over-hunting, global warming, disease and predator introduction - last mass extinction: dinosaurs

3. thinning of ozone layer

- due to chloroflourocarbons CFCs- increases skin cancers

4. climate changes- greenhouse effect: trapping of CO2 in atmosphere which prevents Earth’s cooling - causes climate changes, rising sea levels, extinction

Levels of Organization

1. Biosphere: thin volume of Earth and its atmosphere that supports life

2. Ecosystems: all living organisms and non living

environment found in a particular place

Organisms interact to affect survival.

3. Communities, Populations, Organisms Community: all interacting organisms living an area

Ex: all fish, turtles, plants, algae, bacteria, etc. Population: all members of

species that live in one place at one time

Organism: simplest level of organization

ALL ORGANISMS IN AN ECOSYSTEM ARE INTERDEPENDENT UPON THE BIOTIC AS WELL AS ABIOTIC COMPONENTS OF SYSTEM.

Factors Affecting Organisms

A. Survival Factors

1. Biotic factors: all living components that affect organisms

2. Abiotic factors: nonliving physical and chemical characteristics O2 conc. amt. nitrogen

temperature humidity pH salinity sunlight amount of precipitation

*** temp. change one of most important factors ***

3. Biological Tolerances

Tolerance curve: graph of performance versus environmental variable- organisms can’t live outside their tolerance limits (sometimes just one or more factors)

4. Acclimation: ability of an organism to adjust their tolerance to abiotic factors

ex: ability of organisms to adapt to life at high sea levels (increase in RBC)

Difference between acclimation and adaptation - acclimation occurs within lifetime of organism

- adaptation is a genetic change in a species that occurs over many generations5. Ability to control internal conditions

Conformers: do not regulate internal conditions, they change as their external environment change ex: lizards, snakes

Regulators: use energy to control some of their internal conditions over a wide variety of environmental conditions

ex: mammals: body temperature

6. Ability to escape unsuitable conditions

Dormancy: long term state of reduced activity during unfavorable environmental conditionsex: bears hibernate

Migration: move to a more favorable habitat ex: birds

7. Availability of resources

Resources: energy and materials a species needs(varies from species to species) ex: food, energy, nesting sites, water, sunlight, etc.

Niche: “way of life”, role an organism plays in its habitat

- Fundamental niche: range of conditions that species can potentially tolerate and range of resources it can potentially use

- Realized niche: range of resources a species usesEx: We can use the resources from anywhere in the US (fundamental niche) We use the resources of NJ (realized niche)

Generalists: species with broad niches, can tolerate large range

ex: Virginia opossum- feeds on anything

Specialists: species have narrow niches ex: panda- eats only eucalyptus trees

Major Types of Symbioses Symbiosis: relationship between organisms

1. Predation: - powerful force that regulates population size, predator captures, kills, and consumes preya. Mimicry: - harmless species resembles poisonous or distasteful sp.- two poisonous or distasteful species look alike

b. Plant/herbivore interactions: - plants develop adaptations to prevent being eaten

- physical defenses: sharp thorns, tough leaves, spines, etc.- secondary compounds: poisonous, irritating, bad tasting

ex: poison ivy, oak

2. Parasitism: species interaction where one individual is harmed and one benefits - parasite feeds on host, does not immediately cause death of prey

ectoparasites: external, live on host not inside ex: fleas, lice , leeches, mosquitoes

endoparasites: internal ex: bacteria, protists, worms

3. Competition: results from niche overlap with one or more species (one species more efficient at using resources than another species)

competitive exclusion: condition where one species is eliminated due to competition for same resources

competition reduction: competition between species is reduced because they use different parts of

same resource

4. Mutualism and Commensalism Mutualism: cooperative relationship where both species benefit (sometimes one can’t live without other) ex: pollination

Commmensalism: one species benefits and other is not affected ex: sailfish on sharks

Properties of Communities- species richness: total number of different species - species diversity: number of different types of species

Succession: the gradual sequential re-growth of species in an area

Primary: development of a community in an area that has not previously supported lifeSecondary: sequential replacement of a species following disruption of an existing communityPioneer species: small fast growing and reproducing species well suited for invading and occupying a

disturbed habitatClimax community: stable end point in a community

Energy Transfer in Ecosystems

• Producers- autotrophs (bacteria, protists, plants)

• Consumers- heterotrophs: bacteria, protists, all fungi, animals

• herbivores: eat producers (plants)• carnivores: eat consumers• omnivores: eat producers and consumers• detritivores: eat “garbage” of ecosystems (recently dead organisms, fallen leaves, etc. - decomposers: class of detrivores that causes decay by breaking down dead

tissues and wastes into simpler molecules

Trophic Levels: organism’s position in the

sequence of energy transfers

1st level all producers

2nd level herbivores

3rd levelpredators of

herbivores

Food chains- single pathway of feeding relationships of an ecosystem

- less energy at higher levels, so supports fewer individuals

Food web- interrelated food chains in an ecosystem

Quantity of Energy Transfers

• About 10% of total energy consumed in one trophic level is incorporated into organisms of the next level- maintaining body temp, ability to move, and high reproductive rate require a lot of energy leaving less for higher levels- energy pyramids show the rate that each level stores energy as organic material

Ecosystem Recycling

Biogeochemical Cycle: cyclical abiotic/ biotic pathway through which water and minerals pass in an ecosystem

The Water Cycle

processes a. evaporation

b. transpiration c. precipitation

The Carbon Cycle

cyclical relationship of photosynthesis and respiration

The Nitrogen Cycle

- pathway of nitrogen through an ecosystem

- plants use nitrogen in form

of nitrates

- nitrogen fixation: process of converting nitrogen gas to

nitrate

- nitrogen fixing bacteria: convert N(g) NH3 nitrite

(NO2) nitrate (NO3)

BIOMES• the world's major communities (ecosystems)• classified according to the predominant flora (vegetation)and fauna (animals)• characterized by adaptations of organisms to that particular environment• do not have distinct boundaries, overlap each other

Basic Necessities for Plants 1. Sunlight 2. Nutrients 3. Warm temperatures 4. Water

Aquatic Biomes Freshwater Marine

Stratification of Aquatic Biomes • Zones based on light penetration:

• Vertical zones– photic zone - light sufficient for

photosynthesis – aphotic zone - light insufficient for

photosynthesis

• Temperatures vary with depth

Freshwater Biomes• only 3% of the world's water is fresh• 99% of this is either frozen in glaciers and pack ice or is buried in aquifers• remainder is found in lakes, ponds, rivers, and wetlands• low salt concentration: usually less than 1%

1. Lakes and Ponds• Inhabited by fishes, otter, muskrat, ducks, loons, turtles, snakes, salamanders, frogs

A. eutrophic lakes- rich in organic matter and vegetation- waters relatively murky- low in dissolved oxygen

B. oligotrophic lakes- little organic matter- clearer water- sandy or rocky bottom- desireable fishery of large fish

2. Rivers and Streams• Body of freshwater that flows in one direction down a gradient or slope toward its mouth• At source: cooler temp., clearer, higher O2 levels• Mouth: murky from sediments, less light, less O2 - Catfish, carp (need less O2)

3. Wetlands• covered by fresh water for part of the year• most productive freshwater ecosystems• wide variety of birds, ducks, fishes, mammals, amphibian, invertebrates, and reptiles

– marshes: woody plants such as cattails– swamps: woody plants such as trees and shrubs– bogs: dominated by mosses

MARINE BIOMES

• covers about 70% earth• approximately 3% salinity• marine organisms affected by availability of light

1. oceans 2. coral reefs 3. estuaries

1. Oceans- Largest of all ecosystems- Great diversity of species- Divided into separate zones like lakes

Ocean Zones• intertidal – where ocean meets land

- region that is covered at high tide, but exposed at low tide - organisms must withstand waves

• neritic zone - inshore, shallow, high light– most organisms and species (plankton)

• coral reefs

• oceanic zone - offshore, high to low light– less organisms that neritic– upper zone: protists, bacteria, plants – lower zone: near freezing temp.

• pelagic zone - water column; contains both photic and aphotic regions

• benthic zone - bottom surface; often rich in detritus

2. Coral Reefs - widely distributed in warm shallow waters along continents, island, and atolls - dominated by corals - contain microorganisms, invertebrates, fishes, sea urchins, octopuses, and sea stars

3. Estuaries - areas where freshwater streams or rivers merge with the ocean - brackish (fresh/salt) - contain algae, seaweeds, marsh grasses, and mangrove trees (only in the tropics) - support a diverse fauna, including a variety of worms, oysters, crabs, and waterfowl.

TERRESTIAL BIOMES

Major Land Masses 1. Tundra 2. Forest 3. Grassland 4. Desert

Characteristics of BiomesBIOME TEMP

RANGE*C

AVG. YEARLYPRECIPITATION

SOIL VEGETATION

TUNDRA -26 to 12 < 25 cm Moist, thin topsoil over permafrost, low nutrients. sl. acidic

Mosses, lichens, grasses, and dwarf woody plants

TAIGA - 10 to 14 35- 75 cm Low in nutrients, highly acidic

Coniferous evergreen trees

TEMPERATE FOREST

6 to 28 75- 125 cm Moist, moderately thick topsoils, moderate nutrients

Broad leaved deciduous trees, shrubs or evergreen coniferous trees

TROPICAL FOREST

20 TO 34 200- 400 cm Moist, thin topsoil, low in nutrients

Broad leaved evergreen trees and shrubs

TEMPERATE GRASSLAND

0 to 25 25- 75 cm Deep layer of topsoil, very rich in nutreints

Dense, tall grasses in moist areas, short grasses in drier areas

SAVANNA 16 TO 34 75 150 Dry, thin topsoil, porous, low in nutrients

Tall grasses and scattered trees

CHAPPARAL 10 TO 18 < 25 cm Rocky, thin topsoil, low in nutrients

Evergreen shrubs and small trees

DESERT 7 TO 38 < 25 cm Dry, often sandy, low in nutrients

Succulent plants and scattered evergreens

1. Tundra – Northernmost biome from northern N. America, Asia, and Europe– Cold, largely treeless– Covered by permafrost (permanently frozen layer under soil

surface)– Long cold winters– short growing season, (~ 2 months)– Small plants with shallow roots (grasses, mosses)– Caribou, oxen, snowy owls, arctic foxes, snowshoe hares– Short summer creates swamps and bogs– Insects, ducks, geese, cranes, waterfowl

2. Forests– Occupy about one third of Earth’s land area– Contain about 40% of carbon in living things– Classified by seasonality– Types

• Tropical (rain forest)• Temperate (deciduous)• Boreal (taiga)

• Tropical Forest – Near the equator– Only two seasons (rainy and dry)

– Daylight: 12 hours, little variation– Greatest diversity of species (over ½ of worlds species)– Trees compete for light- create canopy which shades

floor, so very little vegetation– Flora: tall trees, orchids, vines, ferns, mosses, palms– Fauna: monkeys, snakes, lizards, colorful birds, insects

• Temperate Forest– Occur in eastern North America, northeastern Asia, and

western/central Europe– Well defined seasons– Moderate climate – Growing season 140- 200 days – Flora: deciduous broad leaf trees (oak, maple,

hickory, etc.), coniferous trees– Fauna: squirrels, rabbits, skunks, birds, deer

mountain lion, bobcat, wolf, fox, black bears

• Boreal Forest (taiga)– Largest terrestial biome– Large areas of Eurasia, Siberia, Scandinavia, Alaska, and

Canada– Short moist warm summers– Long, cold and dry winters– Flora: cold tolerent evergreens (pine, spruce, firs)– Fauna: woodpeckers, hawks, moose, bear, lynx, fox,

wolf, deer, hares, chipmunks, bats

3. Grasslands

Dominated by grasses rather than shrubs or trees Asia: steppes North America: prairies South America: pampas Africa: veldts

Main divisions - Savannas (tropical grasslands) - Temperate grasslands - Chaparral

• Savanna– Cover almost half of Africa– Dry and rainy season, fires and thundestorms– Seasonal fires– Fauna: giraffes, zebras, buffaloes, kangaroos, mice,

snakes, worms, termites, beetles, lions, leopards, hyenas, elephants

• Temperate Grassland

– Grasses dominant vegetation, trees and shrubs absent– Less rain than savannas– Hot summers and cold winters– Seasonal draughts with fires– Flora: purple needlegrass, buffalo grass asters,

coneflowers, goldenrods, sunflowers, clovers– Fauna: gazelles, zebras, rhinos, wild horses, lions,

wolves, prarie dogs, jack rabbits, deer, coyotes, skunks, quails, sparrows, hawks, owls, snakes, insects, spiders

• Chaparral– Found in middle latitudes near coastlines– Dominated by dense spiny shrubs, scattered coniferous

trees– Mild rainy winters, hot dry summers with periodic fires– Flora: oaks, sagebrush, olive tree, torrey pine– Fauna: jack rabbits, wrens, jackals, foxes, pumas, skunk,

wild goat

4. Deserts - Cover about one fifth of Earth’s surface - Specialized vegetation - Very few large mammals - Very little shelter from sun - Types:

• Subtropical (hot)• Temperate (cold)

• Semiarid/Subtropical (hot and dry)– Great temperature swings during day and night– Very little rainfall, very hot in summer, warm throughout

year– Flora: adapted to dry conditions: spines rather than

leaves, photosynthesis in stems, thick waxy cuticles, dense coating of hairs, extensive underground root systems, ground hugging shrubs, short woody trees (yuccas, prickly pears, mesquite, agave, brittlebush)

– Fauna: very small animals: seek shade, nocturnal lifestyle, burrows, slender bodies to shed heat, waxy body coatings, long eyelashes(insects, arachnids, reptiles, birds)

• Temperate (cold)– Cold winters with snow and rain– Located in Antarctic, Greenland, Nearctic– Short moist moderately warm summers, long cold

winters– Flora: widely scattered, deciduous with spiny leaves– Fauna: widely distributed (jack rabbits, kangaroo rats,

kangaroo mice, pocket mice, grasshopper mice, squirrels)

CLASSIFICATION

Terms:• Biodiversity: variety of organisms at all levels from populations to ecosystems.

• Taxonomy: the science of classifying living organisms according to their characteristics and evolutionary history

• Taxa: categories into which the organisms are classified.

• Phylogeny: evolutionary relationships between organismsTypes of classification systems (3 major types)I. LinnaeunII. PhylogeneticsIII. Cladistics

I. Linnaeun System

Carolus von Linnaeus (Swedish biologist, 1735)

• developed classification system based only on structural feature similarities- different features= different species- same features= same species

• Widely accepted by early 19th century• Basic framework for all taxonomy today

• Binomial Nomenclature (2 word naming system)Genus: category containing similar species

(noun, capitalized)

Species: single descriptive word (always lower case)

Ex: Red oak: Quercus rubra Willow oak: Quercus phellos (common name) (scientific name)

Kingdom System (Linnaeus)

most broad category least inclusive

Taxa:

Kingdom KingPhylum PhillipClass CameOrder OverFamily For

Genus Great Species Spaghetti

Each category includes the category below

Five Kingdom System (1969)1. Kingdom Monera (monerans) - 1 cell

- no true nucleus - prokaryote(genetic material scattered and not enclosed by a membrane) - some move (flagellum); others don't - autotrophs and heterotrophs

ex: bacteria, blue-green bacteria (cyanobacteria)

2. Kingdom Protista (protists) - 1 cell- have a true nucleus – eukaryote- some move (cilia, flagella, pseudopodia); others don't- some autotrophic; others heterotrophic

ex: amoeba, diatom, euglena, paramecium, some algae (unicellular), diatoms, etc.

3. Kingdom Fungi - multicellular

- have nuclei- mainly do not move from place to place- heterotrophic (food is digested outside of fungus)

Ex: mushroom, mold, fungus, yeast, etc.

4. Kingdom Plantae - multicellular- have nuclei- do not move - autotrophic

Ex: multicellular algae, mosses, ferns, flowering plants,trees, etc

5. Kingdom Anamalia - multicellular- have nuclei- do move - heterotrophic ex: sponges, jellyfish, insects, fish, frog, bird, man

• Linnaeus classified organisms by outward structural similarities.• Modern biologists also consider similarities in embryos, chromosomes, proteins, and DNA.

Systematics Study of evolutionary relationships among organisms

II. Phylogenetics: analysis of the evolutionary relationships among taxa (categories)based on:

- visible similarities- embryological similarities- chromosome, DNA, RNA similarities - fossil record- homologous features

Phylogenetic Tree (Phylogeny)Diagram that has branching pattern that shows relationship of organisms

Reading Phylogenetic Trees• like reading a family tree• root of the tree represents the ancestral lineage• tips of the branches represent the descendents of that ancestor• as you move from the root to the tips, you are moving forward in time.

• When a lineage splits (speciation), it is represented as branching on a phylogeny• When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.

III. Cladistics: system of taxonomy based on evolutionary relationships based on shared and derived characteristics

- determines sequence that different groups of organisms evolved- focuses on nature of characters (traits) in different groups of organisms

ancestral (shared) characters/traits: - evolved from common ancestor of both groups - feature that evolved only within the group

ex: feathers in birds (evolved only in bird lineage, not inherited from ancestors) derived character/traits: - set of unique characteristics found in specific group of organisms (common in all members of group) - evolved in an ancestor of one group but not the other

ex: hair in mammals

• Cladogram: phylogenetic diagram that is compares organisms • Clade: evolutionary branch that includes common ancestor and all its descendents (living and extinct) • Outgroup: organism that is only distantly related to other organisms, starting point for comparisons with

other organisms being evaluated

• For any speciation event on a phylogeny, the choice of which lineage goes to the right and which goes to the left is arbitrary.

• The following phylogenies are equivalent:

• It is important to remember that:- Humans did not evolve from chimpanzees. - Humans and chimpanzees are evolutionary cousins and share a recent common ancestor that was neither chimpanzee nor human.

• Humans are not "higher" or "more evolved" than other living lineages. • Since our lineages split, humans and chimpanzees have each evolved traits unique to their own lineages

Three Domains/Superkingdoms (1990’s)

Three Domains (Superkingdoms) Of Living Organisms

I. Bacteria: Most of the Known ProkaryotesKingdom (s): Not Available at This Time Division (Phylum) Proteobacteria: N-Fixing BacteriaDivision (Phylum) Cyanobacteria: Blue-Green BacteriaDivision (Phylum) Eubacteria: True Gram Posive BacteriaDivision (Phylum) Spirochetes: Spiral BacteriaDivision (Phylum) Chlamydiae: Intracellular Parasites

II.  Archaea: Prokaryotes of Extreme Environments

Kingdom Crenarchaeota: Thermophiles Kingdom Euryarchaeota: Methanogens & Halophiles Kingdom Korarchaeota: Some Hot Springs Microbes

III.  Eukarya: Eukaryotic Cells

Kingdom Fungi Kingdom Plantae Kingdom Animalia

BACTERIA (PROKARYOTES)• Most numerous organisms on earth • Earliest life forms (fossils: 2.5 billion years old)

• one circular chromosome • small rings of DNA called plasmids • May have short, hairlike projections called pili on cell wall to

attach to host or another bacteria when transferring genetic material

• unicellular

• Found in most habitats • Most bacteria grow best at a pH of 6.5 to 7.0• Main decomposers of dead organisms• Some beneficial, most harmful  • Move by flagella, gliding over slime they

secrete

Classification- two main groups

1. Archaebacteria- “ancient bacteria”

- live in very extreme environment (undersea volcanic vents, acidic hot springs, very salty water) 2. Eubacteria

- most bacteria- some undergo photosynthesis- most heterotrophs- larger ribosomes, larger numbers of rRNA nucleotides

Bacterial Identification

1. Shape (morphology)cocci (spheres) bacilli (rods)spirilla/spirochetes (spirals)

2. Cell wall- made of peptidoglycans and lipids- many surrounded by a sticky, protective coating of sugars- pili: short hairlike projections that allow bacteria to attach to host or connect to each other or allow passage of genetic material between cells

3. Motility (movement)- flagella, cilia

4. Endospores- thick coated internal resistant structure- reproductive structure, contains DNA- allows DNA to survive after bacteria dies- resistant to environmental conditions- gives rise to normal bacterial cell

5. Reaction to Gram stain- diagnostic identification techniques- gram positive: purple color

- high peptidoglycan in cell wall- gram positive: pink/red color

- high fat content in cell wall

6. Method of energy acquisition - Aerobes:

undergo cellular respiration

must live in an environment with oxygen- Anaerobes:

undergo glycolysismust live in an environment without O2

Reproduction• Asexual:

- binary fission• Sexual:

- conjugation

VIRUSESViruses are not living organisms because they are incapable of carrying out all life processes.

Viruses- are not made of cells- can not reproduce on their own- do not grow or undergo division- do not transform energy- lack machinery for protein synthesis

What Are Viruses Made Of?

• Nucleic Acid DNA orRNA, But not both

• Capsid – a protein coat surrounding the nucleic acid.

• Envelope- membrane like

structure outside the capsid in some viruses

Examples: Influenza Chickenpox Herpes-simplex HIV

Viral Shapes• The shape of the virus is

determined by either its capsid or its nucleic acid.

• Polyhedral/Spherical Icosahedron has 20 trianglular faces ex: herpes simplex, chicken pox and polio

• Helix is a spiral shape (like DNA) ex: rabies, measles and tobacco mosaic virus

• Complex is a combination of two

other shapes ex: bacteriophages

Two Types of Viruses1. DNA Replicated in one of two ways

- Directly produce RNA that make new viral proteins- Join with the host cell’s DNA to produce new viral proteins

2. RNA- Viral RNA is released into the host cell’s cytoplasm and uses the ribosomes to produce new viral proteins- Known as retroviruses containing an enzyme called reverse transcriptase. - These use the RNA as a template to make DNA. This DNA is integrated into the host cell’s DNA.

Infection by viruses– viruses infect bacteria, plants, animals and other living organisms in order to reproduce– a given virus usually infects a limited number of species.

within a host organism, usually only a limited number of cell types are susceptible to infection by a given virus

How Do Viruses Reproduce

Viruses reproduce via three basic steps.1. Viruses deliver their genomes into a host cell.2. Viruses commandeer the host cell transcription and translation machineries and utilize host cell building blocks

to copy viral genomes and synthesize viral proteins.3. Viral genomes and proteins are self-assembled and exit host cells as new infectious particles.

The Lytic Cycle

The basic steps of the cycle are:1. The virus attaches to the cell and injects its DNA leaving its capsid on the outer surface of the cell.2. Phage DNA is injected into the host cell where the ends attach and form a circle.3. The phage DNA takes control of the host’s protein synthesis and copies the viral genome, replicating

the viral DNA4. The head proteins bind to the newly made genomes, bind the tails, and assemble tail fibers.5. Finally lysozyme (phage enzyme) digests the bacterial cell wall and release the newly formed viruses.

The Lysogenic Cycle• While the lytic cycle directly bursts the host cell, the lysogenic cycle is a bit more sneaky. • It will allow a virus to hide in its host cell for days, months, or years. • Viruses that replicate by the lysogenic cycle are called temperate viruses.

The basic steps of the lysogenic cycle are:1. The virus enters the bacteria the same as in virulent phages.

2. The phage DNA incorporates itself into the host cell’s chromosome and is called a prophage.3. The propahge is replicated when the host bacterium replicates its own DNA, thereby infecting many cells. During lysogenic growth, the prophage does not harm the host cell. ( no symptoms)4. The prophage then enters the lytic cycle, replicates, and its copies will be released when the host cell lyses.

HIV, the AIDS Virus

HIV is a retrovirus

Retrovirus- an RNA virus that reproduces by means of a DNA molecule

It copies its RNA into DNA using reverse transcriptase

Viroids• Smallest known particles able to replicate• Short single strand of RNA• No capsid• Disrupts plant metabolism and may damage an entire crop

Prions• Abnormal forms of proteins that clump in cells• Linked to diseases of the brain• Consist of 250 amino acids and not associated with any nucleic acid Examples:

mad cow disease in cattle: brain cells die leaving the brain of the cow to look like a sponge. It is believed to have come from similar disease in sheep called scrapie.

Remember……….

Study, study, or you’ll be cruddy!!!!!!!!!!!!