Assignments 9/25/07

Explain the relationship between the following sets of terms

1. monomer, polymer

2. amino acid, peptide bond, protein

3. monosaccharide, disaccharide, polysaccharide

4. hydophobic, hydropohilic

5. nucleotide, nucleic acid, RNA

Answer the following questions

1. How does the polarity of water give it unique properties that make it essential to life

2. What factor determines the shape of a protein

3. How do lipids store energy efficiently

4. How does the carboxyl end of the fatty acid molecule differ from the hydrocarbon end of the molecule

http://www.biology.arizona.edu/biochemistry/biochemistry.html Do the large molecules problem set

Resources, readings, and videos

http://ocw.mit.edu/OcwWeb/Biology/7-012Fall-2004/VideoLectures/, biochemistry lectures

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

http://webcast.berkeley.edu/stream.php?type=real&webcastid=14260, Biopolymers: Carbohydrates, Lipids, Nucleic Acids

http://www.biologymad.com/, go to the sitemap, biochemistry section

http://en.wikipedia.org/wiki/Biochemistry

Class Notes 9/25/07

Go over homework, discuss labs

Modern Biology p. 3C, 43

Cabbage indicator

Today

Water

As we discussed last time, waster is a polar compound. What kind of bond does water have? (polar covalent) Which atom is postively charged? Which is negatively charged? This means that the electrons are not shared equally between the oxygen and hydrogen atoms. (Draw water on the board). Water has several properties that make it essential to life. One is the previously mentioned polarity. Water's polarity makes it an excellent solvent. Water is sometimes referred to at the "universal solvent" becuause of its ability to solubilize a wide variety of compounds. A second property of water is that of the attraction between water and solid surfaces known as adhesion. This adhesion allows water to actually defy gravity on a small scale. Water can actually travel upward through a narrow tube against the force of gravity. As mentioned last class, water's ability to form hydrogen bonds is also important. One effect of hydrogen bonding in water means that water cools down and heats up slowly. When water is heated up, the energy must first overcome the hydrogen bonds before the temperature of the water can increase. Conversly heat is release when water cools and hydrogen bonds are formed. In organism, this means that cells can maintain even temperatures even in the face of changing environmental conditions. Coastal areas, ocean temperature.

Macromolecules

Macromolecule literally means large molecule. Most of lifes macromolecules are polymers. Can anyone give me an example of a polymer? A polymer is a large molecule made up of repeating small molecules linked together. The subuints that serve as the builiding blocks of polymers are known as monomers. Monmers are linked together by a process known as condensation synthesis (draw on board). Polymers are broken down by the reverse process known as hydrolysis (to break with water)

Four classes of bio-macromolecues

Carbohydrate

The most common carbohydrates are sugars and starches. The simplest sugars are know as monosaccharides or simples sugars (glucose, galactose, fructose). Generally have structure CH2O. Glucose is the sugar that is probably the most important for living organism at least in terms of abundance. Table sugar (sucrose) is a disaccharide of glucose and fructose. One form of long chain polysaccharides are called starches. Glycogen (a polymer of glucose) is the storage form of sugar in animals. Plants also store sugar as starch. Bonds in starch are alpha linkages.

Cellulose is also a polymer of glucose and is found in plant cells. Both are made from glucose, but the difference is the carbons between which bonds are fomed. bonds on cellulose are beta likages. Beta linkages require different enzymes. Only a few organisms have enzymes that are able to hydrolyze cellulose.

Another important polysaccharide is chitin. Chitin is the material that makes up the exoskeletons of insects. The monomer is chitin is a glucose molecule with a nitrogen containing group bonded to one of the carbons. Chitin also makes up the bodies of some fungi.

Lipids

Lipids are what are known as hydrophobic compounds, that is they do not dissolve in water, (what happens when you mix water and oil). Three categories of lipids are fats, phospholipids and steriods.

Fats

Fats are large moleculs constructed from glycerol and fatty acids, draw on board. Acid end, hydrocarbon tail.

Saturated, unsaturated, trans fat. Most animal fats are saturated (lard, butter), solidify at room tempurature.

The major function of fats is energy storage. Food labels are based on a 2000 calorie diet. Most people have 600-800 calories stored in glycogen. Even the skinniest person has >50,000 calories stored in body fat. Fats also serve as insulation and cushioning for vital organs. Two fatty acids are essential for the human diet as they cannot be synthesized. The C-H bond has more energy than C-O bond which is why fats have more energy than carbohydrates.

Phospholipids.

Phopholipids have two fatty acids instead of three. The third carbon of glycerol is joined to a phophate group. Further small molcules can be joined to the phophate group. Draw on board. Phopholipid bilayer (biological membranes). Hydrophobic and hydrophilic properties.

Steroids

Steroids have a ring structure (4 interconnected rings). Different steroids have different groups attached to the rings. Cholesterol is a steroids. Many hormones, including the sex hormones (estrogens and testosterones) are steroids.

Other

Fats include waxes and some pigments.

Protein

Poteins account for more than 50% of the dry weight of cells and are instrumental to nearly all cell functions. Proteins perform a wide variety of functions from structural support, storage, to transport of other molecules. A human has tens of thousands of different proteins each with a unique function.

Amino acids

Amino acids are the building blocks of proteins. Draw basic amino acid structure (Carbon, hydrogen, NH2, COOH, R group). There are 20 amino acids that are the alphabet of protein structure. Amino acids are linked by peptide bonds formed between the acid group of one amino acid and the amino group of another amino acid. Chains of amino acids are called polypeptides. Proteins can be made of one or more polypeptides.

Protein Structure

Proteins can have up to four levels of structure. The primary structure of a protein is its amino acid sequence. The secondary structure of protein consists of regular coiling or layering as a result of hydrogn bonds along the polypeptide backbone (acid and amino groups). Alpha helix and beta sheet. The tertiary structure is a result of interactions between the amino acid side chains. Can be hydrogen bonding as well as covalent bonds. A protein has quaternary structure if it contains more than one peptide subuint. A proteins stucture is determined by its amino acid sequence.

Nucleic acids

nucleic acid structure-sugar (ribose or deoxyribose), phosphate, nitrogenous base (purine A,G-double ring, pyrimidine C,T,U-single ring)

A-T(U), G-C

There are two types of nucleic acids, DNA, RNA. These are the molecules that allow living organism to reproduce. DNA is the genetic material that organism inherit from their parents. Double helix structure (Campbell p.88)

RNA's function is to translate DNA into protein synthesis.

http://www.biology.arizona.edu/biochemistry/biochemistry.html Do the large molecules problem set

http://www.biologymad.com/

http://ocw.mit.edu/OcwWeb/Biology/7-012Fall-2004/VideoLectures/

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

http://webcast.berkeley.edu/course_details.php?seriesid=1906978265 lecture 2

Example Lab Report

Introduction
A major theme across all areas of biology is that of classification. Organisms are grouped according to shared characteristics at many different levels. The biolocal classification systems consists of seven traditional levels. These levels are Kingdom, Phylum, Class, Order, Family, Genus, and Species. A nemonic device to help remeber the classification system is: King Phillip Came Over for Good Soup. Athough there are seven traditional levels to the classification system, many of the levels are broken down into super and sub levels for further differentiation.

Experimental Plan
This lab will examine the classification of a single organism in order to gain a better understanding the biological classification system. The organism will be identified at all seven levels and the some of the distinguishing characteristics of each of the levels will be explored.

Observations and Data

The organism I chose for this lab was the sugar maple. The classification is shown below

Common Name: Sugar Maple

Kingdom: Plantae

Sub Kingdom Tracheobionta (Vascular plants)

Phylum/Division Magnoliophyta (flowering plants)

Class: Magnoliopsida (dicotyledons)

Order: Sapindales

Family: Aceraceae

Genus: Acer

Species: Acer Saccharum (2 varieties)

The Kingdom Plantae is made up of multicelluar organisms that produce food through photosynthesis.
The Sub Kingdom Tracheobionta contains all vascular plants. A vascular plant is any plant containing food-conducting tissues (the phloem) and water-conducting tissues (the xylem). These include ferns and seed-bearing plants but not mosses or algae.
The Phylum Magnoliophyta contains all flowering plants also known as angiosperms.
The Order Sapindales is an order of mostly woody dicotyledonous plants in the subclass Rosidae with compound or lobed leaves and polypetalous, hypogynous to perigynous flowers with one or two sets of stamens.
The Family Aceraceae is a family of flowering plants also called the Maple Family. It contains two to four genera, depending upon the circumscription, of some 120 species of trees and shrubs. A common character is that the leaves are opposite, and the fruit a schizocarp.^[1]
The Genus Acer is a group of trees and shrubs commonly referred to as maple. Plants in this genus have opposite, palmately lobed and veined leaves (Acer negundo has compound leaves ). Fruits are winged schizocarps (samaras) .
The Species Acer saccharum refers the the common sugar maple of which there are two recognized varieties.

Discussion and Conclusion
This lab helped me to learn more about a tree that I see on a daily basis. I also learned about some of the characteristics used to differentiate the maple tree from other trees and plants.

Bibliography/References
List here any websites or publications used.

Class Notes 9/11/07

Hello, My name is Jamie Collins and will be your instructor for this biology course

First a little background about myself. I graduated from the College of Wooster in 1998 with a Bachelor's Degree in chemsitry with a minor in biology.

After graduation I worked for Procter & Gamble in Cincinnati, OH for three years as an analytical chemist in the Skin Beauty Care Division.

After three years at P&G I decided to go back to to school. I enrolled in the Sports Studies program at Miami University in Oxford, OH where I studied sport behavior and performance including sport psychology and sport nutrition.

Following grad school I was a professional triathlete and lifeguard for two years

Currently I am working for Dow Chemical in Marietta testing the physical properties of polyurethane systems.

So, that is how got here. Now I need to know your names, so if we could just go around the room and give me your names, that would be great.

logistics

I am still finalizing the syllabus and will have that for you next week. I just received my copy of Top Shelf yestersday so I will need a little time to look that over to finish the syllabus. From glancing through Top Shelf in the time that I have had I can say that the book is covers most of the major concepts that we will be covering in class, but is very light on the details. As such there will be a lot of material and activites that are not from Top Shelf. For a more detailed text, Biology by Campbell is a very good one. I have the 3rd edition from my college biology class. I believe the 8th edition is being released in november. You can pick up the 5th and 6th editions at a big discount on Ebay. Another option that is less expensive and somewhere inbetween Top Shelf and Campbell in terms of detail is the SATII prep guide. There are several different ones out there. I got the Barron's guide on Ebay for 2.00. I would highly recommend picking this up if you are planning on taking the SATII, and even if you are not, it will fill a lot of the gaps that Top Shelf leaves out. If you are planning on taking science classes in college, Campbell will be a resource you can used for years, if you are just taking this for your science requirement then SATII would be enough.

I sent an email out saying that I would have copies of Top Shelf available so if anyone was planning on purchasing that book today, raise your hand and I can give you a copy. The book is 12.00 and there is also the monthly fee of 40.00 that I would like to get after class today or at next weeks class.

Today

Originally I had planned on trying not to do much lecturing and spending most of class time on labs and experiential exercises, but Top Shelf skips over most of the introductory information that would be included in a high school biology class so we are going to spend some time today talking about that.

First we need to talk about what biology is. Can anyone answer that question for me, What is Biology? Take student answers

In is broadest sense, biology is the study of life. Biologists study all aspects of living organisms. Within biology there are several (5) major themes or frameworks that are essential to understand.

One is the cellular basis of life. The cell is the smallest unit that can carry out all of the activities of life. All living things are made up of cells. Some organisms are a single celled such as bacteria and yeast and some like us human are made of of many different kinds of specialized cells. See p.43 in barrons, p.6 in campbell, p.11 in modern biology. Lets go over some of the basic characteristics of living things. Get ideas from class, see note below.

Organization

Energy Use response to the environment

reproduction

growth and development

homeostasis

evolutionary adaptation

Compare how nonliving things do not exhibit these characteristics

A second major theme is the relationship between structure and function. If you had to nail two pieces of wood together, what tools would you use? If you had to remove a swithplate from a light switch on the wall, what sort of tools would you use. Why would you not use a fork to eat soup? how a device works is correlated with its structure, form fits funciton. p. 9 in campbell. Just as will the tools, the same holds true in biology. For example, the stucture of a birds wing is such that is makes flight possible. This concept of form and funciton holds true all the way from the sub cellular level all the way up to the shape of the entire organism. Birds beaks, different beaks for different foods.

A third major theme in biology is Ecology. Ecologists study living things and how they ineract with one another and their environment. How are you interacting with your environment right now? (Five senses)

Sight

Sound

Touch

Smell

Taste

breathing

At the core of the ecosystem model of biology is the concept of energy transfer. Who has heard the term energy transfer before? p.10 campbell. Can anyone tell me the first law of thermodynamics? Energy can neigher be created nor destroyed, it can only be converted from one form to another. Also known as the law of conservation of energy. campbell p. 93

What is the primay source of all energy on earth? The sun

Which organisms are the primary capturers of this energy and what is that process called? Plants, Photosynthesis, make sugar and other complex molecues. Organism that harvest energy are call producers.

organisms like us that eat the producers are called consumers

The 4th major theme in biology is classification.

All organisms in biology are classified by grouping organism together that are similar. Biologists have identified and named over 1.5million speices and thousands more are identified each year. Originally this system was based on shared physical characteristics that biologist observed. However, once more details about life's processes became apparent, it was realized that shared physical characteristics could cause problems when grouping organism. Whale, fish. How are they similar? How are they different? All are more closely related to other organisms than to each other.

Whale: K-Anamalia, P-Chordata, subP-vertebrata, C-mamalia, O-cetacea

Fish:K-Anamalia, P-Shordata, subP-vertebrata, C-Agnatha,Chrondrichthyes, Osteichthyes

Human K-anamalia, P-Chordata, subP-vertabrata, C-mamalia, O-Primate

Now the tendency is to also use DNA in classification which shows relationships based similarity of gene sequesces.

There are five major Kingdoms

Anamalia-contains all animals

Plantae-all plants, mostly made up of photosynthetic organism

Fungi-mostly decomposers that break down dead organisms and waste

Monera-bacteria

Protista,Protoctista-leftover, mostly unicelluar eukaryotes

Will go into more deatail in each Kingdom as study it.

King Phillip Came Over For Good Soup

Finally Evolution. If there is anysingle unifying theme in biology it is evolution. At its core, evolution is based on the genetic code contained in DNA.

Chemistry

Scientific Method p.29 modern biology, p. 15 campbell, p14 in barrons

Microscope, p.39 in barrons, hair, lab books.

Assignments 9/11/07

Assignments for Indroductory Biology 9/11/07

1. Read through page 15 in Top Shelf.

2. Do the online microscope exercise including all example slides.

http://www.udel.edu/biology/ketcham/microscope/

3. Go outside and observe three organisms. Based on the information in Top Shelf, create a food chain for each organism. Be sure to include producers, consumers, scavengers and decomposers in each food chain. Try to choose organisms from differerent kingdoms.

4. Pick one organism of your choice and classify it in terms of Kingdom, Phylum, Class, Order, Family, Genus and Species. Be prepared to discuss the unique characteriestics of the of each level of classification the organism belongs to. For example, humans are classified as Anamalia, Chordata, Mammalia, Primate, Hominidae, Homo, Homo Sapiens. You would be expected to identify some of the distinguisihing characteristics of the Kingdom Anamalia, Phylum Chordata, Class Mammalia, Order Primate, Family Hominidae, Genus Homo, Species Homo Sapiens. Record a lab in your lab book. You cannot use humans as your organism.

Common Name: Common Tru Kadydid

Kingdom: Anamalia (Animals)

Phylum: Arthropoda (Athropods)

Super Class Hexopoda (Six Legs)

Class: Insecta (Insects)

Sub Calss Ptergota (winged inscts)

Order: Orthoptera (Grasshoppers, Katydids, Crickets)

Sub Order Ensifera (long horned orthoptera)

Family: Tettigoniidae (katydids)

Subfamily Pseudophyllinae (tru Kadydids)

Genus: Pterophylla

Species: Pterophylla camellifolia

Common Name: Sugar Maple

Kingdom: Plante

Sub Kingdom Tracheobionta (Vascular plants)

Phylum/Division Magnoiophyta (flowering plants)

Class: Magnoliopsida (dicotyledons)

Order: Sapindales

Family: Aceraceae

Genus: Acer

Species: Acer Saccharum (2 varieties)

5. Bring a lichen sample for next week’s lab. Lichens can usually be found growing on trees and rocks. Bring the lichen in a Ziploc baggie and try to collect the specimen as close to class time as possible. Read over the lichen lab in Top Shelf and familiarize yourself with it.

Syllabus

Week 1 September 11, 2007

Introduction to Themes in Biology

Scientific Method exercise: predicting changes in heart rate

Homework assignment #1: Classification and food chains

Unit I: Chemistry

Week 2 September 18, 2007

Lichen Lab, Hands on microscope exercise

Chemistry I: Atoms and Molecules

Homework Assignment #2: Acids and bases lab, chemistry reading

Week 3 September 25, 2007

Chemistry II: Biological Molecules

Unit II: The Cell

Week 4 October 2, 2007

Cells: Homeostasis and Transport

Lab: Testing for macromolecules

Week 5 October 9, 2007

Cell: Respiration and Photosynthesis

Week 6 October 16, 2007

Cells: Nucleic Acids and Protein Synthesis

Week 7 October 23, 2007

Cells: Chromosomes, Mitosis, and Meiosis

Exam: Cells

Unit II: Molecular Basis for Heredity

Week 8 October 30, 2007

Mendelian Genetics

Week 9 November 6, 2007

Modern Genetics I: DNA and Molecular Genetics

Week 10 November 13, 2007

Modern Genetics II: Protein Synthesis

Week 11 November 20, 2007

Modern Genetics III: Control of Gene Expression

November 27, 2007 Thanksgiving Break

Week 12 December 4, 2007

Week 13 December 11, 2007

December 18, 2007 Begin Winter Break

Week 14 January 8, 2008

Week 15 January 15, 2008 Last Day of First Semester

Semester 2 14 weeks

Week 1 January 22, 2008

Week 2 January 29, 2008

Week 3 February 5, 2008

Week 4 February 12, 2008

Week 5 February 19, 2008

Week 6 February 26, 2008

Week 7 March 4, 2008

Week 8 March 11, 2008

Week 9 March 18, 2008

Week 10 March 25, 2008

Week 11 April 1, 2008

April 8, 2008 Spring Break

Week 12 April 15, 2008

Week 13 April 22, 2008

Week 14 April 29, 2008

Week 15 May 6, 2008 Last Day of Class

Homework 9/18/2007

1. Readings

How do we know atoms exist?, and How do we know here are electrons and protons? http://dev.nsta.org/ssc/pdf/v4-0962s.pdf

Carbon Three Ways: http://www.nyu.edu/pages/mathmol/txtbk2/topic5.htm

Carbon Compounds: http://www.nyu.edu/pages/mathmol/txtbk2/topic6.htm

Water and Ice: http://www.nyu.edu/pages/mathmol/txtbk2/topic7.htm

Water and Ice II: http://www.nyu.edu/pages/mathmol/txtbk2/topic8.htm

2. Online Activities

Go to http://www.biology.arizona.edu/biochemistry/biochemistry.html

Complete the sections labeled "Chemistry" and "Acids and Bases"

3. Create your own pH indicator

Materials

Red cabbage

Isopropy alcohol (rubbing alcohol)

Disposable food storage container

Procedure

Shred 1/4 to 1/2 of cabbage as you would for cole slaw

Place the cabbage in a disposabe food storage container and cover the cabbage with the rubbing alcohol (caution, alcohol is flammable)

Cover and allow to stand overnight

Romove the cabbage from the mixture and keep the liquid. The alcohol should now be a deep red color. Dispose of the cabbage in the trash.

Save the liquid for the next lab exericse. The liquid can be used as a pH indicator and should turn a deeper red when an acid is added and green when a base is added.

When finished with the cabbage solution you can dispose of it down the drain. Dispose of the container or pass through a dishwasher before using again

4. Acid/Base lab

See handout

All materials are available at School Box (or other school supply store)

Household items may be substitued for some items

Small glasses (aoubt the size of a shot glass) may be substitued for the 30-ml beakers.

Plastic ware may be used instead stirring rods

Record exact materials used in your lab book

In addition to using the pH paper, try using the cabbage solution prepared earlier. Record observations when using the cabbage solution. Two suggestions for using the cabbage solution are 1. Place a drop of the solution on a paper towel and place a drop of the substance to be tested on the same spot. Note if there is any color change. 2. Place a few drops of liquid in a small glass or test tube, add a substace to be tested on drop at a time and note any color change.

5. Just for your information, here is link to a periodic table that gives informatin about each element

http://www.chemicool.com/

Here is an on-line biology book that contains a great deal of information, I highly recommend reading the section corresponding to each weeks classroom topic

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html

Class Notes 9/182007

15 min discuss homework

15-20 min lichen lab, microscope use

30 min chemistry lecuture

Chemistry Overview (Campbell Chapter 2)

Last week

Elements

All matter is made up of basic elements. An element is the simplest form of a substance that cannont be broken down any further by ordinary chemical means (analagous to cell). Elements are groups according to their properties. This grouping is represented by the periodic table. 92 elements occur naturally and other have been synthesized in the lab. Examples include carbon, hydrogen and oxygen. About 25 of 92 elements are known to be essential to life, but 4 C, O, N, H make up 96% of living matter. More on biological molecules next week.

Compounds

Elements combine to form coumpounds in specific proportions and has different properities than the elements that combined for form is. H, O, H2O. Na, Cl, NaCL.

Molecules

The smallest part of a substance that still has the properties of that substance is a molecule.

Atoms, basic units of matter, building blocks of everything

protons, positively charged particle located in the nucleus

electrons, negatively charged particle that orbits around the nucleus

neutrons netral partcle loacted in the nucles

subatomic particles, what you get with particle accelerator, not important for now

nucleus, center of atom, where protons and neutrons are located

Atoms are the building blocks of all matter.

Atomic number (number of protons, defines and element)

Atomic mass (number of proton + number of neutrons)

energy levels

Isotopes elements that have the same atomic number but different atomic masses due to different number of neutrons

Carbon usually has 6 neutrons for an atomic mass of 12, but sometimes has 8 neutrons for an atomic mass of 14. Carbon 14 used to carbon dating. Carbon 14 decays to carbon 12. Ration of C12 to C14 can tell age. Atomic mass of carbon is a weighted average of isotopes 12.011. Carbon 12 much more common. There is also C13. C12 and C13 are stable. C14 has a half life of 5600 years.

Chemical Reactions

Energy Levels

Chemical Bonds

interations between electrons

The chemical behavior of an atom is determined by its electron configuration, specifically the electrons in its outermost shell. Atoms with the same number of electrons in their outer shell exhibit similar properties. Noble gasses-unreactive, halides

onic bonds: electron transfer, salts

covalent bonds: sharing of electrons, polar vs. non polar

hydrogen bionds: intramolecular, weaker, water, uniqueness of water

Chemical reactions take place when chemical bonds are formed and broken

activation energy

spontaneous reaction

endothermic net absorb energy

exothermic, net give off energy

pH Scale

A measure of the hydrogen ion H+ concentration.

Biological functions usually take place in a very narrow pH range.

Logrithmic scale

0 to 14