BIOLOGY.1.LAB.MANUAL.WD



Laboratory Manual for General Biology BI 101

(25th Edition – Fall 2020)

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AN INTRODUCTION TO

SCIENTIFIC DISCOVERY

Dr. Jay Pitocchelli

Biology Department, Saint Anselm College

TABLE OF CONTENTS

INTRODUCTION p. 3

Chapter 1 THE MICROSCOPE p. 4

Chapter 2 PLANTS AND ENERGY p. 7

Chapter 3 DIFFUSION AND OSMOSIS p. 9

Chapter 4 CELL DIVISION AND MITOSIS p. 12

Chapter 5 GENETIC ARCHITECTURE p. 14

Chapter 6 BIODIVERSITY p. 25

Chapter 7 BIOLOGICAL CHEMICALS, NUTRITION AND HEALTH p. 39

Chapter 8 SEMINARS p. 48

Chapter 9 TRANSCRIPTION AND TRANSLATION p. 50

Chapter 10 SETTING UP YOUR BLOG AND LAB SAFETY p. 55

APPENDIX - THE BALANCE p. 59

Appendix - DNA Fingerprinting Simulation p. 62

Appendix on Student Seminar Evaluations p. 64

Appendix on A Student’s Quick Guide to Hazardous Waste Disposal p. 68

Appendix on Transcription and Translation p. 70

INTRODUCTION

How to Use This Manual

This year will be a special, abbreviated lab experience because of the COVID 19 pandemic. This manual will contain an overview of each laboratory exercise for this semester. It will include background information about each lab, the exercises and experiments, the materials and equipment for the lab.

Read the appropriate chapter before every lab!! Preparation is critical for several reasons. You will know the important facts about biological phenomenon you are investigating that day. Knowledge of background material is essential to experimentation. These materials will also be on the post-lab quiz for each lab. By reading the lab manual chapter for each lab, you will not only be prepared but the lab will be a safer place to work in when you know what you are doing.

Safety

The laboratory is a safe place to work as long as you keep it safe. In some of the labs you will be handling potentially harmful chemicals, hot plates, glassware and power units for gel electrophoresis. Handle these carefully and ask your instructor when you have questions about handling these items. The best way to avoid accidents is to maintain a clean workspace. Clean up after yourself in the laboratory at your lab bench and the lab in general. There will be a protocol for emergencies posted in each laboratory. Make yourself aware of these procedures. The lab should be a safe and a fun place to work.

THE MICROSCOPE

Introduction

This lab will introduce you to light microscopes and how to use them. You will first go over the different parts of the compound light microscope and their functions. Then you will do the same for the stereomicroscope (also referred to as the dissecting scope). It is very important that you learn how to use the microscope in this lab for several reasons. The microscope is perhaps the most commonly used tool in Biology. Every Biologist uses it at one point in their career. Therefore, in order to understand Biology you should understand how to use one of its most fundamental tools. The second reason is that you will be using microscopes often during the semester for different labs and you will have to be proficient in its use to successfully complete those labs.

You will practice using the compound and stereomicroscope with some sample slides and materials. These microscopes have different applications. The stereomicroscope is used to examine materials too small for a magnifying glass but too large for fine detail. The compound microscope is used for small specimens such as details of tissues or cells. Examine and compare the magnification power of both microscope and develop a sense of when to use one versus the other (see Appendix-Microscopy and the web page in your lab syllabus for parts of the microscope). Each microscope uses light, which bounces off the object and illuminates the specimen in contrast to the electron microscope, which uses electrons that bounce off the specimen to produce an image.

Exercises

Part I. Become familiar with the parts of the microscope. Identify and learn how to use the following parts of the compound light microscope.

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|Microscope Parts |Notes/function |

|Ocular |Magnification = |

|Nosepiece | |

|Objectives | |

|Stage | |

|Specimen clips | |

|Diaphragm | |

|Light source and on/off switch | |

|Arm | |

|Coarse focus | |

|Fine focus | |

Begin using the compound light microscope by examining a series of slides of inanimate materials.

1) The letter e

2) Threads

Continue by examining some examples of live organisms. Make a wet mount of each specimen by placing a drop of water on a slide. Then carefully place a coverslip over the drop of water taking care to avoid water bubbles under the coverslip.

1) Paramecium

2) Volvox

Part II. Study the parts of the dissecting microscope. Notice the similarities and differences between the dissecting versus the compound light microscopes. Examine various specimens under the dissecting microscope.

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Various materials – live and preserved

PLANTS AND ENERGY

Introduction

Rainforests are being disturbed at an alarming rate all over the world. Trees are used for lumber and the cleared land is used for farming or grazing. Why are we so alarmed over this process? One of the reasons is that the oxygen supply for all living, breathing organisms comes from plants when they undergo photosynthesis. Oxygen is a byproduct of this complex chemical reaction. Continued destruction of the tropical and temperate rainforest ecosystems will deplete the source and production of oxygen. In order to fully appreciate this problem you must gain an understanding of the process of photosynthesis and the production of oxygen. By examining the process you will better understand some of the consequences of human encroachment and destruction of our biological resources.

Photosynthesis is a chemical reaction in the leaves of plants where CO2 molecules are converted into a chemical energy in the form of a simple sugar (glucose). The O2, which we breathe, is also released as a product of photosynthesis (Figure 2.1). During the process, H2O, which enters the plant through the underground roots, is split using energy from sunlight in the form of photons that the plant is able to harness. O2 is released from the H2O molecule. The products of the photosynthesis reaction are O2, H2O and C6H12O6. C6H12O6 is a simple sugar called glucose that is stored in the plant as an energy reserve. Most plants build complex sugars called starches using glucose as building blocks. These starches are often stored in underground organs called tubers. Organisms that are able to synthesize their own energy in this manner are called autotrophs. Animals feed on glucose from plants for energy to fuel chemical reactions in their bodies. Animals are called heterotrophs because they are unable to synthesize their own energy. They must obtain it by eating autotrophs.

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Figure 2.1. Unbalanced equation for photosynthesis: reactants are on the left, products are on the right.

In this lab you will investigate different aspects of the photosynthesis reaction. In Part I you will perform an experiment on how energy from the sun is trapped by plants.

In Part II you will observe how glucose or chemical energy is stored in plants. Your work will address the following question:

1. Where is the chemical energy from photosynthesis stored in plants?

Exercises

Part I Chromatography

This experiment involves the separation of different plant pigments from the leaves of plants. Follow the instructions on the handout to set up this preparation. Add about 20 drops to the chromatography paper instead of the suggested 4 drops in the instructions. Observe the different pigments (red – carotenoids, yellow – xanthophylls, blues and greens – chlorophyll a and b).

Part II Energy Storage in Plants

Plants use the chemical energy in glucose that is produced by photosynthesis. Some plants store extra glucose by synthesizing starches and storing them in special underground tubers. The potato is an example of an underground tuber that is full of starches that provide energy for the potato plant during the winter months when there is no photosynthesis. You will prepare a slide of potato cells. Then stain the cells with Lugol’s Iodine or IKI. The starch granules will turn purple to black in reaction to the stain.

DIFFUSION AND OSMOSIS

Introduction

The normal day-to-day activities of the body involve billions of chemical reactions inside cells. But in order for these reactions to take place chemicals must move in and out of cells. How do chemicals enter or leave cells? Most chemicals move in and out of cells through the process of diffusion. Diffusion is a simple property whereby chemicals move from an area of high concentration to an area of low concentration. When a cell does not have to use energy to move chemicals across the membrane, diffusion is a passive form of transfer of chemicals from one side of the membrane to the other. O2 and CO2 exchange between blood and alveoli in the lungs occurs by diffusion. Most hormones enter cells from the blood through diffusion. These exchanges take place because of simple diffusion gradients located at strategic points throughout the body. Osmosis is the special case of the diffusion of water. Water, like other chemicals, will also move from an area of high concentration to an area of low concentration until an equilibrium has been achieved.

There are some interesting questions about different aspects of diffusion. Chemicals must get their energy from somewhere to move during diffusion. Chemicals also come in different forms such as gas, liquid and solids. Chemists and Biologists are interested in whether chemicals in each of these different forms obey the laws of diffusion. In Part I of the lab you will address the following question:

1. Where does the energy come from for movement of molecules in diffusion?

In Part II of the lab you will address the following questions on osmosis and tonicity:

1. What is tonicity – hypotonic, isotonic, hypertonic and how does it affect osmosis?

Tonicity refers to the concentration of salts outside of the cell compared to inside the cell. It will influence the passive diffusion of water in and out of the cell. What happens to a living cell exposed to different tonicities?

Hypertonic – higher concentration of salts outside of the cell, lower concentration of water outside of the cell, water moves out of the cell, cells shrivel up and eventually die

Isotonic - same concentration of salts outside and inside of the cell, same concentration of water outside and inside of the cell, water moves in and out of the cell in an equilibrium

Hypotonic - lower concentration of salts outside of the cell, higher concentration of water outside of the cell, water moves into the cell and could burst the cell

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Figure 3.1. Impermeable (A) and semipermeable (B) membranes. Note that the semipermeable membrane allows the small black molecules through

but not the larger striped molecules.

BRAINSTORMING SCRATCH SPACE

Exercises

Part I Brownian Movement (ink or charcoal)

Observe Brownian Movement in a charcoal solution. Watch for random movement of the smallest particles caused by heat absorption from the environment.

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Part II Osmosis and Elodea and osmotic stress experiment

Observe a normal living cell of Elodea. Add some NaCl solution to the slide. Note how the cell reacts by shriveling up and losing water. You have created a hypertonic solution. There is a higher concentration of salts outside the cell compared to inside the cell. The opposite is true of water. There is a lower concentration of water outside the cell compared to inside the cell. Water moves out of the cell and it shrivels up.

CELL DIVISION AND MITOSIS

Introduction

How do organisms grow from a single-celled zygote to an adult with several billion cells? How does a tree over 100' tall grow from a sapling emerging at ground level? How do salamanders regenerate lost limbs or tails? How does your body repair itself after being injured? The simple answer is duplication of cells through the process of mitosis. Mitosis results in precise duplication of parent cells resulting in daughter cells. Salamander cells duplicate themselves to make more salamander cells. Mitosis occurs in trees, humans, fish and millions of other species.

Exact duplication is critical since errors in duplication can be fatal. Cancer is an example of when errors occur in mitosis. Duplication runs rampant and out of control, producing many non-functional cells that result in tumors. Since cancer is one of the leading causes of death it would be important to understand mitosis and its role in production of cancerous cells. In this lab you will investigate and observe the complex process of cellular reproduction, which results in precise duplication of daughter cells based on the original blueprint of the parent cell. In this lab you will become familiar with the different stages of cell division by examining prepared slides of cell division.

Cell division and mitosis occur during a small part of the cell’s life cycle, if it occurs at all. The cell cycle and the stages of mitosis are displayed below in Figure 4.1.

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Figure 4.1. The cell cycle and Mitosis.

The important activities that occur during each phase are listed below.

Phase Prominent Activities

Interphase growth and DNA duplication (during the S phase)

Prophase appearance of chromosomes

Metaphase chromosome line up along equator

Anaphase centromeres break and chromatids splits apart

Telophase formation of cell plate in plants, segregation of chromosomes

Cytokinesis split of cytoplasm and formation of two cells

Exercises

Part I Prepared slides (whole mounts)

Examine the whole mount slide(s) of mitosis and find the different phases. If you find all the phases above (except for Cytokinesis) you will earn an automatic quiz grade of 10 and you will not have to take the quiz.

GENETIC ARCHITECTURE

Introduction

The field of Genetics is one of the most rapidly developing disciplines in Biology. Geneticists are currently trying to map the human genome, locate genes responsible for genetic disease (e.g., Huntington's, Parkinson's, etc.) and provide gene therapy for victims of genetic disease. Industry has also teamed up with geneticists to find disease resistant crops or develop strains of bacteria to fight oil spills. Genetics has not advanced without some controversy. Jurassic Park is an excellent fictional example of a genetic engineering disaster. Although we are nowhere near the technology needed to recreate dinosaurs, releasing genetically engineered organisms such as bacteria or viruses into the environment could be extremely dangerous if they are not carefully tested in the laboratory and monitored in the wild. The role of genetic engineering in human genetics has been fraught with controversy since the eugenics programs of the United States in the early 1900's to Hitler's heinous experimentation during World War II. Since you will be confronted with some of these issues in your graduate life, it will be important to develop an understanding of some of the basic principles of genetics.

The DNA located on your chromosomes contains the genetic blueprint for your body's design. It is like a library of information on how to build your body. Part of that information came from your father and part of it came from your mother. The exact relationship between the genotype and your outward appearance or phenotype is the subject of intensive investigation in the field genetics. Mendel discovered some fundamental laws of genetics while studying genotypes and phenotypes of peas back in the late 1800's. Some genotype - phenotype relationships, like the one's studied by Mendel are straightforward while others are much more complex.

Mendel studied external characters of pea plants such as seed color, seed texture, stem length, flower color, etc. He studied the inheritance patterns of these characters over several generations in controlled breeding experiments. These external characters are now referred to as the phenotype. He learned that most characters came in two different forms. Seeds were yellow or green. Their texture was smooth or wrinkled. The stems were long or short. Through an analysis of the inheritance patterns of these characters he concluded that there were unseen particles in the plants responsible for the expression of the phenotype. These particles are now referred to as genes and they are found within cells of organisms. The genotype is the combination of two alleles, which are alternative forms of each gene. There is an allele for smooth (S) and one for wrinkled (s). For instance, SS or Ss or ss are three different genotypes, each having two alleles. Mendel also found that there are specific relationships between alleles. When two different alleles are combined in some individuals one of the alleles usually masks the phenotype of the other allele. In the texture example, S is dominant over s and smooth seed phenotype may be caused by SS or Ss genotypes. S is the dominant allele while s is the recessive allele. Individuals with SS or ss are called homozygous dominant and homozygous recessive genotypes respectively. Individuals with two different alleles are called heterozygous.

Where are the alleles located and why are there two alleles? Alleles are located on chromosomes. The reason there are two alleles is that there are two versions of each chromosome (called homologous pairs) and each chromosome contains one allele. For example, there are 46 total chromosomes in humans but they are arranged into 23 homologous pairs. The most famous pair of homologous chromosomes is the sex chromosomes: XX (female in humans, males in birds), XY (males in humans, females in birds). In the pea example above, S is located on one chromosome and s is located on another chromosome (both chromosomes form the homologous pair). There are some genes that are located on the sex chromosomes. These are called sex-linked alleles. Some genetic disorders such as hemophilia (blood clotting disease) are caused by sex-linked alleles.

In this lab you will study the relationship between genotype and phenotype by building fictional organisms called "Rebops" based on genes selected randomly from a gene pool. The goal of the exercise is to understand how genes contain information on the body's architecture and how the relationship between genes influences expression in the phenotype.

Exercises

Part I Building Rebops

Part II Finding your Rebop's parents

EXPERIMENTATION

Part I. For each of the Rebop characters there are two alleles located on each chromosome. Use the pairs of alleles on the chromosomes that were mailed to you by your instructor. There is a dominant/recessive relationship between most alleles of these characters.

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Build the Rebop based on your set of genes and their corresponding phenotypes. The possible genotypes and their phenotypes are listed in Table 5.1. Use this table to find the appropriate body parts that match your selection of genes. Figure 5.1 shows a completed Rebop and the body parts.

Table 5.1. Genotypes and phenotypes of Rebops.

|Phenotype |Relationship - Alleles |Genotypes |Phenotypes |

|Tail color |A>a |AA, Aa |green tail (pipe cleaners) |

|  |  |aa |brown tail |

|Tail shape |Q>q |QQ, Qq |curly tail (pipe cleaners) |

|  |  |qq |straight tail |

|Eye color |E, e codominance |EE |red eyes (thumb tacks) |

|  |  |Ee |one red eye, one blue eye |

|  |  |ee |blue eyes |

|Leg color |D>d |DD, Dd |Yellow legs (push pins) |

|  |  |dd |green legs |

|Mouth color |M>m |MM, Mm |green mouth (thumb tacks) |

|  |  |mm |white mouth |

|Ear color |T>t |TT, Tt |yellow ears (short pins) |

|  |  |tt |blue ears |

|Antennace color |L>l on X chromosome |XLXL, XLXl, XLY |white antennae (long pins) |

|  |  |Xl Xl, XlY |purple antennae (sex-linked genetic |

| | | |disorder) |

|Sexual dimorphism |  |XX |female (without hump) |

|  |  |XY |male (with hump - geometric shaped |

| | | |pins) |

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Figure 5.1. Rebop and body parts.

DATA COLLECTION

Fill in the Table 5.2 below for your Rebop. Figure out the probable phenotypes of the parents of your Rebop..

Table 5.2 Your Reebop’s Genotype and Phenotype

Your Your Possible Possible

Phenotypic Rebop's Rebop's Mother's Father's

Character Genotype Phenotype Phenotype Phenotype

Tail color

Tail shape

Eyes

Legs

Mouth

Ears

Antennae

Sex

Workspace for determining parents

Example – Tail color, A – Green tails (AA, Aa), a – brown tails (aa)

Your Rebop Aa

|Gametes |a |a |

|A |AA |Aa |

|a |Aa |aa |

|Parents Genotype |Aa, Aa | |

| | | |

|Parents Phenotype |Green, Green | |

Tail color

Your Rebop ____

|Gametes | | |

|Gametes | | |

| | | |

| | | |

|Parents Genotype | | |

| | | |

|Parents Phenotype | | |

Tail Shape

Your Rebop ____

|Gametes | | |

|Gametes | | |

| | | |

| | | |

|Parents Genotype | | |

| | | |

|Parents Phenotype | | |

Eyes

Your Rebop ____

|Gametes | | |

|Gametes | | |

| | | |

| | | |

|Parents Genotype | | |

| | | |

|Parents Phenotype | | |

Legs

Your Rebop ____

|Gametes | | |

|Gametes | | |

| | | |

| | | |

|Parents Genotype | | |

| | | |

|Parents Phenotype | | |

Ears

Your Rebop ____

|Gametes | | |

|Gametes | | |

| | | |

| | | |

|Parents Genotype | | |

| | | |

|Parents Phenotype | | |

Antennae

Your Rebop ____

|Gametes | | |

|Gametes | | |

| | | |

| | | |

|Parents Genotype | | |

| | | |

|Parents Phenotype | | |

BIODIVERSITY

Introduction

Life evolved approximately 4 billion years ago in the form of simple microbes. The first organisms resembled our present day bacteria. Since these early days, billions of new species have evolved creating an amazing diversity of life. Biologists have catalogued these organisms in a system of classification called the Linnean Hierarchy. Organisms are arranged in categories based on their similarities and inferred evolutionary relationships. You will spend the next four weeks studying representatives of each of the major taxonomic categories of organisms. The primary learning outcome for these two labs is for you to learn the following for each group of organisms:

1) Primary morphological characteristics of each group

2) Ecological niches these species have exploited

3) Name of the taxonomic group that these species belong to

During Week 1 you will be studying microorganisms and the Fungi. The second week will be spent learning the diversity of terrestrial plants. The lower invertebrates will be the subject of study for week 3. You will finish with the higher invertebrates and the Chordates that includes the most recently evolved vertebrates.

Outline of the lab

Survey of the major groups of organisms

Major Groups for Diversity Lab Week 1

Bacteria

Representative of Eubacteria (3 types)

Representatives of the Blue-green Algae

Protista

Various representatives

Fungi

Basidiomycetes

Zygomycetes

Major Groups for Diversity Lab Week 2

Plants

Representatives of the lower plants

Representatives of the higher plants

Major Groups for Diversity Lab Week 3 – Lower Invertebrates

Porifera – Sponges

Cnidaria

Corals, Hydroids, Jellyfish

Platyhelminthes

Various representatives of the flatworms

Annelida

Various representatives of the segmented worms

Arthropoda

Various representatives

Major Groups for Diversity Lab Week 4

Echinoderms

Various representatives

Chordata

Invertebrate Chordates

Vertebrate Chordates – fish, amphibian, reptiles, birds, mammals

Student outcomes for each lab

Recognize representatives of the major groups

Know the major morphological features of each group

Know very basic ecology of each group

Diversity Lab 1

The major taxonomic groups that will be covered in this lab include the Domain - Bacteria, Domain Eukarya and the Protista, Domain Eukarya and the Kingdom Plantae and Domain Eukarya and the Kingdom Fungi. You will be studying representatives of each group by examining whole mount slides, living and or preserved specimens. Your goals are to be able to recognize each organism, know the major taxonomic group that it belongs to, some basic characteristics of the organism that is shares with other species in its taxonomic group and its ecology.

Taxonomic Group and their Representatives

Domain Bacteria

These organisms are closely related to the earliest forms of life on earth that evolved over 3.5 billion years ago. They are simple, small, prokaryotic cells with the features listed below. These organisms are found everywhere on earth and are ecologically diverse. Some species are autotrophic and capable of producing their own energy. Most species are heterotrophs and must obtain their own energy from other organisms. A summary of their ecology is listed below.

Features

Small size, lack membrane bound organelles or nucleus, simple DNA

Ecology

Mostly heterotrophic (decomposers, parasites, mutualists living inside gut of higher animals), some autotrophs – blue-green algae, chemoautotrophs

You will examine whole mount slides and living cultures listed here in Table 6-1. The bacteria are heterotrophs while the Blue-green Algae (Nostoc and Oscillatoria) are photoautotrophs.

Table 6-1. Representatives of the Bacteria.

|Representatives – slides |Representatives –living materials |Representatives - preserved materials |

|Bacteria - slides of 3 shapes – Cocci, |Bacterial colonies - E. coli |  |

|Bacilli, Spirilli | | |

|  | Bacterial colonies - B. megabacterium |  |

|  |  |  |

|Blue-green Algae - Nostoc |  |  |

|Blue-green Algae - Oscillatoria |  |  |

Domain Eukarya – Protista

These organisms had the first and more modern, eukaryotic cells. The earliest fossil evidence of eukaryotes dates back 1.2 billion years ago. This group contains the ancestors of the remaining Kingdoms: Fungi, Plantae, Animalia. This group is ecologically diverse. There are unicellular free-living forms and multi-cellular species. Some species, like the multi-cellular algae (seaweed) are autotrophic. The remaining heterotrophic species feed on algae or on themselves in aquatic environments. There are also some harmful, parasitic forms. The animal-like representative species for this lab were chosen to illustrate the different forms of locomotion used by some unicellular forms: pseudopod of the Amoeba, cilia of the Paramecium. The preserved plant-like algae are examples of multicellular forms.

Features

Large size, membrane bound organelles, complex DNA and nucleus

Ecology

Mix of autotrophs, heterotrophs, parasites, primarily aquatic (marine and freshwater)

Table 6-2 Representatives of the Protista

|Representatives – slides |Representatives –living materials |Representatives - preserved materials |

|Amoeba |  |Fucus |

|Paramecium |  |Ulva |

| |  |Red Algae |

Domain Eukarya - Fungi

The oldest known fungi date back about 460 MYA. They are a diverse group of detritivores that differ from each other, primarily in their mode of reproduction.

Features

Almost all fungi have hyphae that merge together into mycelia

Zygomycetes – sexually reproduce using zygospores

Basidiomycetes – sexually reproduce using basidia and basidiospores

Ecology

These species are collectively known as detritivores. They are the decomposers that feed on dead or dying detritus, primarily on the floor of wet forests. The decomposition results in recycling important chemicals back into the forest ecosystem.

Table 6-3. Representatives of the Fungi

|Eukarya |Fungi |  |Hyphae, mycelium |Detritivores - decomposers |

|  |Zygomycetes |Live culture of bread mold |  |  |

|  |  |Slide of mycelia, hyphae, |  |  |

| | |sporangia, zygospores | | |

|  |Basidiomycetes |Mushroom specimens |  |  |

Diversity Lab 2

Domain Eukarya – Bryophyta

The Bryophytes belong to the Kingdom Plantae and are probably most similar to the first plants that colonized land about 475 MYA (million years ago).

Features

No vascular tissue, no seeds, sexual reproduction by motile, swimming sperm or asexual reproduction, photosynthetic pigments, gametophyte is dominant generation, antheridium produces sperm on the male plant, archegonium produces eggs on the female plant

Ecology

All species are autotrophs that typically inhabit wet forests, streamsides and or are never found far from water because they require water for swimming sperm and fertilization.

Domain Eukarya - Pterophyta

The ancestors of this group appeared about 425 MYA and were the dominant plants on earth for the next 50 million years.

Features

Seedless vascular plants (with xylem and phloem), motile swimming sperm, sori on underside of leaf release spores for reproduction

Ecology

Similar to Bryophytes in that all species are autotrophs that typically inhabit wet forests, streamsides and or are never found far from water because they require water for swimming sperm and fertilization.

Table 6-4. Representatives of the Primitive Plants

|Domain |Group |Representatives – slides |Representatives –living or |Ecology |

| | | |preserved materials | |

|Eukarya |Plantae - Primitive Plants |Seedless plants |Photosynthetic pigments, |Autotrophs, supply oxygen and |

| | | |alternation of generations - |sugar to terrestrial ecosystems |

| | | |gametophyte (1N) and sporophyte | |

| | | |(2N) | |

|  |Bryophyta - live mosses |Live mosses |Reproductive structures |  |

|  |Bryophyta slides |Moss - male gametophyte |Antheridium and sperm (1N) |  |

|  |  |Moss - female gametophyte |Archegonium and eggs (1N) |  |

|  |  |Moss - sporophyte |Stalk and sporangium (2N) |  |

|  |Pterophyta |Live ferns |  |  |

|  |  |Fern leaf with sori - |Sori on underside of leaf |  |

| | |reproductive structure | | |

Domain Eukarya – Higher Plants

The Gymnosperms were the first of the two groups of higher plants to evolve about 360 MYA. The second group was the Angiosperms that appeared about 140 MYA. The primary adaptation of these two groups was the evolution of wind-borne pollen or sperm that freed them from being dependent on a constant water source. These plants went on to colonize all terrestrial ecosystems because they could reproduce through wind action or pollination by insects, birds and mammals.

Features

Gymnosperms

Root system, needle-leaves, reproductive cones in most species, pollen, sporophyte is the dominant generation

Angiosperms

Root system, flowers for reproductive structures, pollen, fruit, sporophyte is the dominant generation

Ecology

These plants are the primary producers of almost all terrestrial ecosystems. They play a critical role in taking CO2 out of the atmosphere. They simultaneously supply O2 that goes back into the atmosphere for all air-breathing organisms. Gymnosperms make up most of the boreal forests at higher latitudes and altitudes. Angiosperms are the dominant plants of the tropics but are also found in substantial numbers throughout the temperate and higher latitudes.

Table 6-5. Representatives of the Higher Plants

|  |Plantae - advanced plants |Seed Plants |  |  |

|  |Gymnosperms |Needle leaves and cones |Root system, pollen, needle |Primary producer in most |

| | | |leaves and cones for reproduction|terrestrial ecosystems |

|  |  |Pollen slide |  |  |

|  |Angiosperms |Live flower |Root system, flowers, pollen and |Primary producer in most |

| | | |fruit |terrestrial ecosystems |

|  |  |Fruit examples |  |  |

|  |  |Tap root from carrot |  |  |

Diversity Lab 3

The major taxonomic groups that will be covered are members of the Animalia or animal kingdom.

Domain Eukarya - Porifera

The sponges are representatives of the Porifera. The fossil record for this group dates back about 630 MYA.

Features

Sponges are simple organisms that lack a nervous system or circulatory system. There is typically a single opening to a digestive cavity. They have flagellated cells called choanocytes that circulate fluids through the body cavity. Many species also have spicules that provide a skeletal support system.

Ecology

Most of the 9000 species are marine organisms but there are a few freshwater species. These organisms are sedentary, filter feeders.

Domain Eukarya – Cnidaria

There are three groups that form the Cnidaria or Coelenterata – Jellyfish, Hydroids and the Corals. The fossil record contains evidence of some coral-like organisms about 580 MYA.

Features

These organisms typically have a sedentary hydroid form and a mobile medusa form. The dominant stage of the life cycle of the hydroids is a sedentary hydra stage while the dominant form of the jellyfish is a mobile medusa form. The corals are sedentary and have lost the medusa stage. These species have a cnidocyte or stinging cell which is where the group gets its name.

Ecology

Most species of Cnidarians are living in shallow marine environments. The Anthozoa form the ocean’s large coral reefs. There are some freshwater hydroids. Most species are predators feeding on small plankton. Many coral reef species live in symbiotic relationships with algae.

Table 6-6. Representatives of the Primitive Animalia

|Domain |Group |Representatives |Features |Ecology |

|Eukarya |Animalia |  |  |  |

|  |Porifera |Preserved sponges |Single opening, choanocytes - |Sedentary filter feeders, marine |

| | | |flagellated cells and spicules - |and freshwater |

| | | |for support and protection | |

|  |  |Slide - spicules |  |  |

|  |Cnidaria |Preserved jellyfish - medusa|Cnidocyte - stinging cells, |Carnivorous feeding on |

| | |stage |polyp-sedentary and asexual and |zooplankton, marine and freshwater|

| | | |medusa-mobile and sexual life | |

| | | |cycle stages | |

|  |  |Coral - polyp stage only |  |  |

|  |  |Live hydra demo under |  |  |

| | |dissecting scope | | |

|  |  |Slide - hydra colony (polyp |  |  |

| | |stage) | | |

Domain Eukarya - Mollusca

This group contains 85,000 species of clams, snails octopus and their allies. Some of the earliest fossil forms date back around 270 MYA.

Features

Most species contain an inner lining or mantle that houses the internal organs and an internal radula that is used in the physical breakdown of food (cutting and scraping). Clams and their relatives have a hard shell for an outer covering. Many terrestrial and bottom-dwelling aquatic species also contain a fleshy, muscular foot for locomotion (snails, clams). Fossils date back about 500 MYA.

Ecology

Most species are grazers feeding on algae in marine environments. There are also many marine species which are carnivores, feeding on plankton, other molluscs. Clams are sedentary filter-feeders with a diet of plankton while squid and octopi are active, swimming predators. Terrestrial snails are primarily herbivores.

Domain Eukarya - Platyhelminthes

This group is also known as the flatworms for the flat appearance of these species. Some of the earliest fossil forms date back around 270 MYA.

Features

These species are known for lacking a body cavity, circulatory and respiratory organs. The Planaria have eye-spots that are only capable of detecting light. The parasitic tapeworms are made up of proglottids which form a long chain inside the host intestine. The head or scolex of the tapeworm has a series of hooks that embed into the intestinal wall of the host.

Ecology

There are both free-living forms like the Planaria and parasitic forms like the tapeworm. The Planaria are nocturnal scavengers and predators of freshwater ponds or moist forest floors. They are also capable of self-regeneration. The tapeworms are entirely parasitic. Many species use an intermediate herbivore host before infecting humans or other carnivores.

Domain Eukarya - Annelida

These segmented worms represent an important stage in the evolution of higher animals. The division of the body into segments is considered an important step in the evolution and differentiation of other body parts (forelimbs, hindlimbs, wings, etc.) by higher animals. This group dates back about 550 MYA in the fossil record.

Features

The most important feature is segmentation of the body. They have parapodia, similar to feet for locomotion. Earthworms have one large segment called a clitellum which is used in sexual reproduction. Each earthworm is hermaphroditic, containing male and female gonads that exchange sperm and eggs at the clitellum during copulation.

Ecology

There are free-living and parasitic members of this group. You are examining a representative of the free-living forms. The earthworm plays an important role in soil aeration and fertilizing the soil with its waste. It is also prey for many species and used as fish bait. Leeches are the distant cousins of the earthworms and are blood-sucking parasites.

Table 6-7. Representatives of the Animalia: Worms

|Domain |Group |Representatives |Features |Ecology |

|  |Platyhelminthes |  |Flatworms, single opening to |Free-living carnivores and |

| | | |digestive system, un-segmented, |parasitic forms |

| | | |lack internal body cavity, | |

| | | |respiration through the skin | |

|  |  |Planaria - live culture |Eye-spots for detecting light |  |

|  |  |Tapeworm slide |Scolex head and proglottids |  |

|  |  |  |  |  |

|  |Annelida |Preserved earthworm |Segmented worms, clitellum for |  |

| | | |reproduction | |

Domain Eukarya - Arthropoda

The Arthropoda is one of the most diverse phyla on earth. It is composed of the largest number of species and individuals with over 1.7 million described species that make up about 80% of all living species. This group dates back about 550 MYA. Segmentation is more complex and highly evolved in the Arthropods with such new adaptations as wings, claws, legs, tails, etc.

Features

The name Arthropoda means jointed foot or limb that all members of this Phylum share. These organisms all possess an exoskeleton made of chitin and a cuticle or waxy covering to inhibit desication or water loss.

Ecology

The Arthropods have exploited every environment on the planet including aerial (flying forms), terrestrial, marine and freshwater ecosystems. Most species are predators feeding on other invertebrates and or small vertebrates. There are also many parasitic forms (e.g., mosquitoes and other blood-sucking insects, blowflies, ticks, lice and their relatives). The large numbers of some species are important food resources in some ecosystems. The large insect blooms in higher latitudes are primary sources of protein for birds while krill are the main source of food for whales in marine ecosystems.

Table 6-8. Representatives of the Arthropoda

|Domain |Group |Representatives |Features |Ecology |

|  |Arthropoda |  |Chitinous exoskeleton, jointed |Heterotrophs, carnivores, |

| | | |appendages, exoskeleton |parasites, freshwater, marine, |

| | | | |terrestrial and aerial forms, most|

| | | | |numerous group of organisms |

|  |  |Horseshoe crab shell |  |  |

|  |  |Preserved Spiders and ticks |  |  |

|  |  |Crab shells |  |  |

|  |  |Insect metamorphosis |  |  |

|  |  |  |  |  |

Diversity Lab 4

Domain Eukarya - Echinodermata

This group is often considered a close relative of the vertebrates. They lack a bony skeleton like invertebrates but share a very similar plan of tissue development early after fertilization with vertebrates. There are about 7000 species and this group dates back over 500 MYA in the fossil record.

Features

The group is named after a characteristic of spiny skin shared by some but not all species. The group is diverse containing the starfish, sea stars, sand dollars, sea urchins and sea cucumbers.

Ecology

Most species are found in either of two marine environments. They occupy benthic or deep water ecosystems (bottom-feeders) or shallow oceans and coral reefs (filter-feeders). Starfish are voracious predators feeding on clams and or sea stars while most other species are passive filter-feeders. Sea urchins are a favorite at sushi restaurants and boiled sea cucumbers are also an Asian delicacy.

Table 6-9. Representatives of the Animalia: Higher Invertebrates

|  |Echinoderms |  |Water vascular system, tube feet,|Benthic (bottom-dwelling) grazers |

| | | |pentaradial symmetry (5 sided), |and carnivores |

| | | |skeleton made of calcareous | |

| | | |(calcite-based) plates | |

|  |  |Starfish |  |  |

|  |  |Sea urchin |  |  |

|  |  |Sand dollar |  |  |

Domain Eukarya – Chordata (invertebrates)

Amphioxus is an invertebrate member of the Chordates. It is a member of the lancelets (Cephalochordata) who are named after their knife-shape body form. They share a basic body and developmental plan with vertebrates. They date back about 520 MYA in the fossil record.

Features

The body plan is considered to be the archetype for the vertebrates. It includes 3 features shared with the vertebrates – notochord, nerve cord and gill slits. The notochord is not made of bone but performs a similar function to the vertebrate vertebral column or backbone that protects the spinal cord.

Ecology

They are marine filter-feeders of shallow temperate and tropical seas.

Domain Eukarya – Chordata (fish)

The fish refers to a large group of cartilaginous and bony species that have fins. The evolution of the group is poorly understood but the traditional classification contains the parasitic lamprey and hagfishes, cartilaginous sharks and rays, lungfish, lobe-finned fishes and the bony fishes. Fish first appear in the fossil record about 540 MYA. The great diversification of fishes began in the Devonian period about 420 MYA.

Features

Fish have fins, lack digits and breathe through a gill system.

Ecology

They are found in all aquatic marine and fresh water environments. Most species are predators feeding on a diverse array of prey, ranging from zooplankton to small whales and seals. The lampreys and hagfishes are parasitic, attaching to and sucking blood from other fish. Commercial extinction of many species by humans is an important problem for marine ecosystems.

Domain Eukarya - Amphibia

The Amphibia descended from the lobe-finned fishes and were the first vertebrates to colonize land approximately 370 MYA. Some recent discoveries of intermediate fossil forms from Greenland have firmly established the link between lobe-finned fish and amphibians. These early fossils show the evolution of limbs from the fins of these fish-like ancestors. Most species of Amphibia are extinct and the only living representatives include the frogs and toads, salamanders and snake-like caecilians.

Features

Amphibia have true lungs but also rely heavily on breathing through their skin. Reproduction involves external fertilization in most species and young must develop through a larval stage in water.

Ecology

All species are predators with many species feeding on insect prey. Amphibians have become well known for the dramatic population declines in recent years and as ecological indicators of catastrophic damage to ecosystems. Many factors have been linked to the global decline including, habitat destruction, pollution, competition with invasive species, climate change and fungal infections by chytrids.

Table 6-10. Representative of the Animalia – Lower Chordata

|Domain |Group |Representatives |Features |Ecology |

|  |Chordata |  |Notochord, nerve cord and gill |  |

| | | |slits | |

|  |  |Amphioxus preserved specimen|  |  |

|  |  |Amphioxus slide - |  |  |

| | |notochord, nerve cord and | | |

| | |gill slits | | |

|  |Fish |Preserved fish, shark |Scales, gills, bony skeleton in |Heterotrophic herbivores and |

| | | |most forms (except sharks) |carnivores, parasites, freshwater |

| | | | |and marine forms |

|  |Amphibia |Frog skeleton |Lungs, skin without scales, lay |Heterotrophic herbivores and |

| | | |unprotected eggs in water, |carnivores, always near freshwater|

| | | |alternation of generations |for reproduction |

| | | |(aquatic tadpole larva, | |

| | | |terrestrial adults), bony | |

| | | |skeleton, tetrapods (four limbs) | |

|  |  |Preserved frogs? |  |  |

Domain Eukarya- Reptilia

The first reptile descendants of the amphibian appeared about 320 MYA. The Reptilia is diverse group and contains the turtles, lizards and snakes, crocodiles and dinosaurs. Some authorities have also included birds in with reptiles because of their close evolutionary relationship with predatory dinosaurs.

Features

Except for the snakes, reptiles have 4 limbs, scales to protect the skin and prevent desication and they lay eggs. The amniotic egg of reptiles is considered to be among the most important events in vertebrate evolutionary history, freeing reptiles from a dependence on water for development and opening up exploitation to all terrestrial environments. The egg, protects the embryo from the external environments, is self-contained and has a yolk of nutrients for early embryonic development.

Ecology

This group is ecologically diverse, occupying almost all terrestrial, freshwater and marine ecosystems, except at the higher, extreme latitudes. There are herbivores and carnivores and the densest concentration is in the tropics and sub-tropics. The limited distribution is due to ectothermy or cold-bloodedness of these species.

Domain Eukarya - Aves

There are over 9000 species of birds and they first descended from carnivorous, theropod dinosaur ancestors about 150 MYA. Recent fossil discoveries of feathered dinosaurs in China have confirmed the evolutionary link between birds and carnivorous dinosaurs.

Features

The lack of teeth, hollow bones, possession of a 4-chambered heart and feathers are important characteristics of birds.

Ecology

Birds have colonized the entire planet from pole to pole and everywhere in between. There are herbivores, carnivores, carrion feeders and many species that feed on the nectar of flowering plants like our North American hummingbirds. The nectivorous birds of the tropics are critical to distributing and pollinating plants in the tropics. Some species are also known for the great migrations and migratory distances from wintering areas in the tropics to breeding areas at extreme higher latitudes. Pelagic species spend most of their lives at sea, coming back to land only to breed once every 12 – 18 months. Birds have been an important food source for humans since the Jungle fowl were first domesticated by the Chinese over 3000 years ago.

Domain Eukarya - Mammalia

The first mammals appeared about 225 MYA nearing the end of the reign of the Dinosaurs. These species were small, nocturnal insectivores known primarily from bones of the skull and mandible. The extinction of the Dinosaurs about 65 MYA lead to an explosive radiation of mammals. There are two or three groups of mammals depending on the authorities – Monotremes (not considered mammals by some biologists), Marsupials and Eutherians.

Features

The primary characteristics of mammals are the possession of hair and mammary glands. The Monotremes still lay leathery eggs. The Marsupials are named after the marsupium or pouch on the female where young complete their development. The young of Eutherian mammals complete their development inside the uterus of the female.

Ecology

Like birds, mammals have colonized the entire planet, including all major ecosystems – terrestrial, freshwater and marine. The great herds of ungulates that migrate across Africa are examples of herbivores. Bats are primarily, nocturnal insectivores but some species specialize on fruits and nectar. The big cats of Africa and Asia along with the wolves of North America and Europe are examples of predators. Whales, dolphins and seals have colonized marine habitats while otters have invaded many freshwater ecosystems in the northern and southern hemispheres.

Table 6-11. Representatives of the Animalia - Vertebrates

|Domain |Group |Representatives |Features |Ecology |

|  |Reptilia |Snake skeleton |Amniote egg, lungs, bony |Heterotrophic herbivores and |

| | | |skeleton, scales, tetrapods (four|carnivores, more common in tropics|

| | | |limbs) |and sub-tropics (cold-blooded), |

| | | | |primarily terrestrial with some |

| | | | |marine and freshwater forms |

|  |  |Other reptile skeletons |  |  |

|  |  |  |  |  |

|  |Mammalia |Cat skeleton |Lungs, tetrapods, bony skeleton, |Heterotrophic herbivores and |

| | | |hair, mammary glands, 4 chambers |carnivores, found all over the |

| | | |heart |world, terrestrial, aerial |

| | | | |(flying), marine and freshwater |

| | | | |forms |

|  |  |Study skin |  |  |

|  |  |Mount |  |  |

|  |  |  |  |  |

|  |Aves |Pigeon skeleton |Lungs, tetrapods, bony skeleton, |  |

| | | |feathers, 4 chambers heart | |

|  |  |Study skin |  |  |

|  |  |Mount - Great Horned Owl |  |  |

BIOLOGICAL CHEMICALS, NUTRITION AND HEALTH

Introduction

Do you eat all your greens? Are you overweight? Did you do some carbo-loading before your last marathon? Are you taking vitamin supplements? Do you have enough fiber in your diet? Do you suffer from excessive flatulence? How many times have you been asked or heard someone else ask these and other similar questions? The reason is that nutrition and diet have received a great deal of attention over the past 30 years. For instance, look at the weight control and dieting organizations that have recently appeared: Weight Watchers, Jenny Craig, Diet Workshop, Nutri/System, etc. There are always one or two cookbooks in the top ten best selling books. The general public has become extremely health conscious and one of the variables they can directly control is their diet. One of the reasons for this intense interest in diet is that research has revealed the impact of poor versus healthy diets on the quality of life of an individual, especially as he/she grows older. But how will you ever know if you are eating the right foods? What is a healthy diet?

A healthy diet is a balanced diet. The balance is between proteins, carbohydrates and fats. These are the most important organic chemicals in biology. They represent the major food groups and a proper balance of these chemicals is crucial for a healthy diet. Vitamins and minerals are some other important organic and inorganic molecules that must supplement the major food groups. Biochemists have devised some simple tests for detecting these chemicals. In Part I of this lab you will learn how to test for proteins, carbohydrates and fats in foods. You will address the following questions:

1. How do we test for different chemicals?

2. How do we test for carbohydrates, fats and proteins?

3. Why are the tests different?

Exercises

Part I Testing for the major food groups

carbohydrates - simple

carbohydrates - complex

fats

proteins

Materials

Part I

Carbohydrates

test tube racks, hot plate, 400 ml beaker, 3 test tubes,

onion juice, potato juice, Benedict's Reagent, distilled water

test tube racks, 3 test tubes, onion juice, potato juice,

Lugol's Iodine, distilled water

Fats and Lipids

Sudan III, extracts of flour, cream, coconut, margarine, filter paper,

pencils, dedicated Pasteur Pipet, water bath

Proteins

Biuret's Agent, egg white, chicken broth, distilled water, test tubes,

test tube rack, CuSO4, wax pencils

Common foods for testing

gelatin, Lite and Regular Pancake Syrup, Instant and Ground Coffee,

honey, olive oil, peanut oil, candy

[pic]

Part II

Digital Blood Pressure Monitor

Finger Pulse Oximeter

EXPERIMENTATION

Part I - Each bench works as a team

Carbohydrates. There are different tests for different types of carbohydrates. The Benedict's test is for simple sugars (mono and some disaccharides). In the first experiment you will use the Benedict's test to confirm the presence (+) or absence (-) of simple sugars in three solutions in the test tubes below. Mark the test tubes 1, 2, 3 with a wax pencil. Then mark the tubes at the 1 cm and 3 cm marks from the bottom with a metric ruler before adding the solutions below.

Tube 1) onion juice to the 1cm mark, followed by Benedict's Reagent to the 3 cm mark

Tube 2) potato juice to the 1 cm mark, followed by Benedict's Reagent to the 3 cm mark

Tube 3) water to the 1 cm mark, followed by Benedict's Reagent to the 3 cm mark

[pic]

Heat the tubes for three minutes in boiling water. Remove the tubes with tongs and place in test tube rack. Observe the presence or absence of color changes in the tubes. A red-orange color is a positive, indicating the presence of sugars. Fill in your results in the Table below. Which solution contained the most sugars?

Starting Ending

Tube Color Color

1 onion

2 potato

3 water

Lugol's Iodine is used for testing for starches, which are polysaccharides or complex carbohydrates. You will test the same materials from above for the presence of starches using Lugol's Iodine. Mark three tubes, 1, 2, 3, using wax pencils and metric rulers. Mark the tubes at the 1 cm mark. Prepare the tubes following the instructions below.

Tube 1) onion juice to the 1 cm mark, add 3+ drops of Lugol's Iodine

Tube 2) potato juice to the 1 cm mark, add 3+ drops of Lugol's Iodine

Tube 3) water to the 1 cm mark, add 3+ drops of Lugol's Iodine

Observe each tube for any color changes. A blue-black color is a positive, indicating the presence of starches. Record your results in the table below. Which solution contained the most starch?

Starting Ending

Tube Color Color

1 onion

2 potato

3 water

Fats and Lipids. The monomers are glycerol and three fatty acids. You will be testing for fat polymers. Extracts of four foods (flour, cream, coconut, margarine) have been prepared before lab with 95% ETOH. Mark a piece of filter paper with a pencil for each food type (F=flour, C=cream, Co=coconut, M=margarine) and water for a control (W). You will blot these on a piece of filter paper in the marked circles using the Pasteur Pipet.

[pic]

[pic]

Allow the chemicals to dry completely on the paper. After drying, soak the paper in Sudan III for 3 minutes. Remove the paper with forceps and rinse in a water bath for 1 minute. Note record any stains in the table below. Which substance had fats?

Starting Ending

Tube Color Color

Flour - F

Cream - C

Coconut - Co

Margarine - M

Water - W

Proteins. Amino acids are the monomers of proteins. You will be testing for protein polymers. The Biuret Reagent is used to test for the presence of proteins. Fill the test tubes according to the instructions below.

Tube 1) add 1 dropper of egg white solution and 1 dropper of Biuret's Reagent and mix

Tube 2) add 1 dropper of chicken broth and 1 dropper of Biuret's Reagent and mix

Tube 3) add 1 dropper of water and 1 dropper of Biuret's Reagent and mix

[pic]

A positive result for protein is a change from blue to violet. Record your results in the table below. Which solution contained the most protein?

Starting Ending

Tube Color Color

1 egg white

2 chicken

3 water

Unknowns. Each bench will receive an unknown. Conduct each of the tests above and note which chemicals are found in each unknown (+ or -).

[pic]

Sugar Starch Fats Proteins

Part II

Take the vital signs for the resting or basal rate of your lab partner. First use the Digital Blood Pressure Monitor. Follow the instructions beginning on page 10 of the manual. Record data for resting or basal Heart Rate. Record the Blood pressure readings from this cuff and enter the data for resting or basal Blood Pressure into Table 7-2. Use the Finger Pulse Oximeter to take the Heart Rate of your lab partner and their Oxygen Saturation measurement. Enter those data into Table 7-2.

Next, think of an alternative activity that could affect these measurements. Consider various types of exercise like walking down the hallway or walking up and down the stairs, walking outside around the building, etc. Enter the post experimental heart rate into Table 7-3 and compare it with the basal Heart Rate. Finally, wait 5 minutes after the experimental activity and measure the cool-down rate for Heart Rate. Enter this data into Table 7-4. A healthy drop in Heart Rate is considered to be 12 BPM/minute but it may vary depending on the level of vigorous activity you chose for your experiment.

Table 7-2. Resting Measurements

|Measurement |Lab Partner 1 |Lab Partner 2 |

|Resting HR |  |  |

|Resting Systolic |  |  |

|Resting Diastolic |  |  |

|Measurement (Oximeter) |  |  |

|Resting HR |  |  |

|Resting Oxygen Saturation |  |  |

Table 7-3. Alternate Activity Measurements

|Measurement |Lab Partner 1 |Lab Partner 2 |

|Alternative activity HR |  |  |

|Alternative activity Systolic |  |  |

|Alternative activity Diastolic |  |  |

|Measurement (Oximeter) |  |  |

|Alternative activity HR |  |  |

|Alternative activity Oxygen Saturation |  |  |

Table 7-4. Cool-down Measurements

|Measurement |Lab Partner 1 |Lab Partner 2 |

|Cool-down HR |  |  |

|Cool-down Systolic |  |  |

|Cool-down Diastolic |  |  |

|Measurement (Oximeter) |  |  |

|Cool-down HR |  |  |

|Cool-down Oxygen Saturation |  |  |

INTERPRETATION

Now that you have finished these experiments and observations, how did your work answer the questions addressed in the Introduction? What about your diet? Are you eating a well-balanced meal? Is everything that tastes good actually healthy for your?

What were the effects of behavior (e.g., exercising, other) on these measurements?

SEMINARS

SEMINAR

Public speaking will become a very important part of your graduate life. You may be asked to present company products to potential buyers, run a company meeting, make and or write speeches for political office, instruct employees on how to work sophisticated equipment or present a case in court. In the seminar labs in this course you will make a short presentation on a topic in Biology. After the formal presentations we will discuss and debate various topics or issues raised during the presentations. These presentations and discussions will introduce you to 1) some of the necessary exercises involved in putting together a good presentation, 2) how to listen critically and formulate opinions about materials being presented, 3) debate the issues in a professional manner. Putting together a presentation involves researching the topic (library, newspapers, scientific journals, internet), collecting ideas, putting together different ideas into a cohesive presentation and most importantly - staying within a time limit. Debate and discussion involves paying close attention to someone else's arguments and giving them the same attentiveness and respect that you expect while you are speaking.

The topics for the presentations will parallel general lecture topic areas: Medicine, Genetics, Anatomy and Physiology, Evolution, Animal Behavior, Ecology, Conservation Biology. Each student will put together their presentations in a series of stages outlined on the syllabus.

1) pick a general topic area (see above) and send it to your instructor

2) bring in a copy of research article and give it to your lab instructor

3) present you topic in lab

No two students can choose the same topic. The lecture professor will put a list of the presentations on a web page. Topics are accepted on a first come – first served basis. Topics must be OK’d by the lecture professor. Everyone should see each other's lists and topics before the seminar so they can speak or debate cogently about each of the topics presented. Attendance during these labs is mandatory and there will be a severe penalty for unexcused absences. See your lecture professor if there are any scheduling problems for the labs.

How to select a topic?

There must be some biological phenomenon that has sparked your interest. Find a topic you were always curious about but didn't have time to pursue. If you are having trouble finding a topic, your instructor will provide you access to a collection of articles by major topic areas that you can choose from. Your instructor will also provide you with a list of topics that students have presented in previous years. Please note that I cannot accept topics on psychoses or mental illness (e.g., schizophrenia, bulimia, depression, dementia, ADHD, etc.).

There are several key resources available to you in the library. Check the newspapers, especially the NY Times Tuesday or Sunday Science sections. In addition there are several important journals that summarize recent discoveries in Biology: Discover, Science, Scientific American, Science News, Nature, Bioscience, just to name a few. Your first problem will be trying to find a topic but your biggest problem will be trying to narrow it down to 15 minutes. The Internet is another excellent source for gathering information. Work on these presentations well in advance.

How to make a presentation?

Find some interesting and related articles. Read through your articles. Try to put together some unifying theme that you would find interesting and easy to present. If you can't understand what you are trying to present, then nobody else will either.

Make an outline of the important points you want to get across. Organize the outline so that it follows a logical progression. Fill in the outline with the important facts but be creative and make it relevant.

I strongly suggest powerpoint or some other presentation software but please make sure it works prior to the day of your presentation. It is OK to have 3x5 cards but do not read from a script. Do not read from the powerpoint slides.

How to stay within the time limit?

"New Yorker 1: How do I get to Carnegie Hall?

New Yorker 2: Practice, practice, practice."

Your biggest challenge will be trying to present a complex topic in 5 minutes. It is OK to go over the time limit but it is not to be under the time limit. Practice your presentation. My general rule is that it takes about a 30-60 seconds to cover the material on a single powerrpoint slide.

Am I done when I finish my presentation?

Just when you think it's over after your presentation, you find out it's not over until the fat lady sings. At the end of the presentations we will discuss some of the interesting issues raised by students in their presentations. Be prepared to take notes on each other's presentations and discuss issues you found interesting and or controversial. You will be required to have one question for each presentation. For example, if there are 4 presentations being given in lab then you should have 4 questions for lab (one question for addressing some aspect of one of the seminars being presented). Use the evaluation sheet handout in lab and write your question below the group that is presenting.

TRANSCRIPTION AND TRANSLATION

Introduction

The information to build proteins is encoded in the DNA. You will conduct a simulation of the two-step process of protein production involving 1) Transcription and 2) Translation where the information to build the protein is extracted from DNA and used for protein production inside the cell.

Exercises

Part I Transcription and Translation

You will simulate the two-step process of Transcription and Translation based on a gene sequence in a Microsoft Excel file sent to you by your instructor. Transcription occurs in the nucleus where messenger RNA (mRNA) is transcribed from DNA. This step involves creating mRNA from a sequence of nitrogenous bases from DNA that make up the gene used to produce a protein. A series of base pairings for mRNA are constructed using the rules in Table 9.1. Adenine from DNA will only pair up with Uracil on mRNA. Thymine from DNA pairs with Adenine from mRNA and Cytosine from DNA pairs up with Guanine on mRNA, etc. (see Table 9.1)

Table 9.1. Base pairings of DNA and mRNA

|DNA |mRNA |

|A (Adenine) |U (Uracil) |

|C (Cytosine) |G (Guanine) |

|G (Guanine) |C (Cytosine) |

|T (Thymine) |A (Adenine) |

The second step of Translation occurs at the Rough Endoplasmic Reticulum (rough ER). It is at the rough ER where the mRNA pairs up with a transfer RNA (tRNA) molecule that holds an amino acid used to build a protein. A triplet from the mRNA attaches to its complementary triplet on a tRNA molecule according to matching base pairings in Table 9.2.

Table 9.2. Base pairings of mRNA and tRNA

|mRNA |tRNA |

|U (Uracil) |A (Adenine) |

|G (Guanine) |C (Cytosine) |

|C (Cytosine) |G (Guanine) |

|A (Adenine) |U (Uracil) |

Each tRNA molecule contains an amino acid that will be attached to the protein in a sequence according the triplets of bases on the mRNA molecule. An example of how Transcription of DNA leads to production of mRNA, and then how Translation leads from mRNA to tRNA and its accompanying amino acid is illustrated in Table 9.3.

Table 9.3. From DNA to mRNA to tRNA to amino acids and a protein.

|Example Sequences |  |  |  |

|DNA |mRNA |tRNA |Amino Acid attached to tRNA |

|AAA |UUU |AAA |Phenylalanine |

|ACG |UGC |ACG |Cysteine |

|CGC |GCG |CGC |Alanine |

|CTT |GAA |CUU |Glutamic acid |

|GTG |CAC |GUG |Histidine |

The protein produced from Transcription and Translation in Table 9.3 would be made up of Phenylalanine – Cysteine-Alanine-Glutamic Acid-Histidine from the original sequence encoded in the DNA and eventually produced in the rough ER. The sequence of tRNA bases and their respective amino acids are listed in alphabetical order in the Appendix on Transcription and Translation and in your Microsoft Excel file.

In this exercise you will simulate building a protein in an Excel spreadsheet.

Step 1

Open your Excel file. Fill out the spreadsheet with the appropriate nitrogenous bases and find out the corresponding amino acid for each triple. See the example in Table 9.4 below.

Table 9.4. Worksheet.

|Example |DNA |mRnA |tRNA |Amino Acid |

| 1 |C |G |C |  |

| 2 |T |A |U |  |

| 3 |A |U |A |  |

|triplet |  |  |CUA |Leucine |

|  |  |  |  |  |

The gene or instructions to build the protein will be a random sequence of 30 nitrogenous bases from DNA selected from an XL spreadsheet. Fill in that table with the complementary base pairs for mRNA, tRNA, each triplet and the corresponding amino acid. There is a unique icon for each Amino Acid. Arrange these icons in their proper sequence in your Excel spreadsheet. See the example in Table 9.5.

Table 9.5 Example

|Example |DNA |mRnA |tRNA |Amino Acid |Amino Acid Icon |

| 1 |C |G |C |  |  |

| 2 |T |A |U |  |  |

| 3 |A |U |A |CUA - Leucine | |

| 4 |G |C |G |  | |

| 5 |G |C |G |  | |

| 6 |A |U |A |GGA - Proline | |

| 7 |C |G |C |  |  |

| 8 |G |C |G |  |  |

| 9 |T |A |U |CGU - Alanine |  |

| 10 |C |G |G |  |  |

| 11 |T |A |U |  |  |

| 12 |T |A |U | |  |

| | | | |GUU - Glutamine | |

| | | | | | |

| 13 |A |U |A |  |  |

| 14 |T |A |U |  |  |

| 15 |G |C |G | |  |

| | | | |AUG - Tyrosine | |

| | | | | | |

| 16 |G |C |G |  |  |

| 17 |G |C |G |  |  |

| 18 |C |G |C | |  |

| | | | |GGC - Proline | |

| | | | | | |

| 19 |T |A |U |  |  |

| 20 |C |G |C |  |  |

| 21 |A |U |A | |  |

| | | | |UCA - Serine | |

| | | | | | |

| 22 |A |U |A |  |  |

| 23 |A |U |A |  |  |

| 24 |A |U |A | |  |

| | | | |Phenylalanine | |

| | | | | | |

| 25 |G |C |C |  |  |

| 26 |C |G |C |  |  |

| 27 |T |A |U |CCU - Glycine |  |

| | | | | | |

| | | | | | |

| 28 |C |G |C |  |  |

| 29 |A |U |A |  |  |

| 30 |G |C |G |CAG - Valine | |

| | | | | |  |

| | | | | | |

SETTING UP YOUR BLOG AND LAB SAFETY

Introduction

This lab will be a basic introduction to LB 101 labs this semester. It will cover setting up a laboratory blog and lab safety. Please bring an electronic device with Internet access (e.g., laptop) to each lab this semester. You will need it for access to your lab manual and the post-lab quizzes through Canvas. You will need to download the lab manual (top of the syllabus page). I am a Mac person and the lab was produced on a Mac, so be aware that the figures may not print correctly on a Windows computer.

Exercises

Personal introductions. We will start by going around the room and asking everyone to identify themselves, tell us where you are from, state your major and name one memorable event that occurred during the past summer, especially something that may be related to your major or career aspirations.

Setting up the blog. During the first lab we will set up your bog for the laboratory portion of the course. Each blog entry is a simple list of the equipment and exercises for lab that week. Check the syllabus link on picking a blogger option, how to name your blog and Example blogs for weeks 1 and 2. You can set up a blog using one of the popular sites (Google – blogspot, WordPress, Tumbler, etc.).

Here is what it looks like using Google’s Blogger. Sign into your gmail account with your username and password.

[pic]

Go to the Latest Gmail.

[pic]

Go to the Setting Grid and select Blogger.

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Post a topic – Setting up your blog.

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You’ll need to show your lab instructor a blog entry each week this semester during lab so remember your link and password. The link below has instructions on how to set up a blog, name the blog and password hints. Send your instructor an e-mail with the public link to your blog.



1) Lab safety, potential lab hazards. A safe lab starts with a clean lab. Please make sure to clean up your lab space and put away all materials at the end of lab. The potential hazards in this lab are glassware, glass slides, and hazardous chemicals. You will be advised about how to handle glassware and proper disposal of chemicals before each lab. There is a special satellite chemical waste disposal area in each lab.

2) COVID 19 precautions. You will be cleaning your lab space and materials so the lab space will be safe for the next lab taught in this room. Wipe down your equipment (e.g., microscopes, slides, etc.) with the alcohol swabs provided in lab.

ACKNOWLEDGMENTS

The laboratory portion of the course is the outcome of many discussions I had with my colleagues from Saint Anselm College. I would like to thank the Biology 1 Committee, J. Feick, C. Hieber, B. Stahl and B. Vallari, who contributed ideas and constructive criticism. The labs also benefited from the valuable input of Bio. 1 veterans, P. McGrail, M. Roach and C. Ford. Joe Catanese was very helpful in developing the framework for the Brainstorming Section as a simulation of how Biologists actually conduct scientific research.

In this edition, we used the Appendixes from the Bio 1 manual written by Lynda Harding (California State University at Fresno). Drs. J. Piatt and D. Derksen kindly provided computer facilities at the U. S. Fish and Wildlife Service center in Anchorage AK. I am grateful for the use of Mr. T. Van Pelt's PowerBook in finishing up the manual while at sea in the Gulf of Alaska. Cathy Ford, Valerie Buttignol, Margaret Roach and Robyn Blaise, all helped with editing the most recent laboratories and any changes made in subsequent years. Finally, I would like to thank D. Lavoie who was very supportive throughout the revision of the Biology 1 labs and oversaw the final printing of this document while I was busy having fun, conducting fieldwork in Alaska.

APPENDIX - THE BALANCE

Ohaus Dial-O-Gram

The Ohaus Dial-O-Gram balances (Figure 1) used in this laboratory have a capacity of 310 g and are accurate to 0.01 g. To use these balances:

[pic]

Move all of the sliding weights to their zero notches. Zero the balance by turning the screw knob on the left end of the balance arm until the pointer on the right end of the arm is centered.

Place weighing paper or a weighing boat on the pan.

Weigh by turning the large knob on the front of the balance until the pointer is centered. Read the ones and tenths digits from the center of the dial, looking at where the line up with the zero line on the outer scale. Read the hundredths digit on the outer scale by finding the line on the outer scale that best lines up with any of the lines on the inner scale. Record the weight of the weighing boat.

Add the sample to be weighed to the weighing boat. Again turn the large knob to center the pointer.

If the pointer remains above the center line, turn the knob back to zero. Slide the front weight (10 g scale) to the right until the pointer moves down, then move it left one notch. Now center the pointer with the large knob.

If the pointer remains above the center line when the front weight is pushed clear to the right, return the front weight to its zero position. Slide the rear weight to the right until the pointer moves down, then move it left one notch. Slide the front weight to the right until the pointer moves down, then move it left one notch. Now center the pointer with the large knob.

If the pointer still remains above the center line, your sample weighs more than 310 g, and cannot be weighed on this balance.

Otherwise, read the weight by adding the readings on the front and rear beams to the weight indicated on the dial. Subtract the weight of the weighing boat.

[pic]

Triple-Beam Balance Model 700

This balance has a capacity of 610 g (2610 g with accessory weights) and is accurate to 0.1 g.

Move all of the sliding weights to their zero notches. Zero the balance by turning the screw knob on the left end of the balance arm (under the pan) until the pointer on the right end of the arm is centered.

Place weighing paper or a weighing boat on the pan.

Move the front weight (10 g scale) to the right until the pointer is centered on the zero line at its right end. Record the weight of the weighing boat.

Add the sample to the weighing boat. Move the front weight to the right until the pointer is centered.

If the pointer is above the line even when the front weight is clear to the right, move the front weight back to the left. Slide the back weight (100 g scale) to the right until the pointer drops, then move it back one notch. Now move the front weight to the right until the pointer is centered.

If the pointer is above the line even when the front and back weights are clear to the right, move the front and back weights to the left. Slide the center weight (500 g scale) to the right until the pointer drops. Then move it back one notch. Slide the back weight to the right until the pointer drops, then move it back one notch. Slide the front weight to the right until the pointer is centered.

Record the weight and subtract the weight of the weighing boat.

To weigh out a specified amount of sample:

To weigh a specified quantity of sample on either balance, zero the balance and determine the weight of the weighing boat. Set the balance to the total of the weight of the boat and the amount you wish to measure. Gradually add sample to the weighing boat until the pointer is centered.

Appendix - DNA Fingerprinting Simulation

This exercises is a simulation of DNA profiling using gel electrophoresis. DNA profiling involves isolating a strand of DNA and its nitrogenous bases, cutting it with restriction enzymes into fragments and comparing the fragments among individuals. In this exercise, you will create your own DNA molecule with 48 nitrogenous base pairs and compare your DNA with DNA from your classmates. The goal of this exercise is to illustrate the process of DNA fingerprinting.

Step 1 - Create your own DNA using MS Excel

We have set up a spreadsheet in MS Excel that will randomly assign you nitrogenous bases along a single strand of DNA. Click on cell E2 to select the number in that cell. Click and hold the small box in the lower right corner of cell E2. Pull down the column to E48. This will fill this column with a series of random numbers.

Next, click on cell F2. Click and hold the small box in the lower right corner of cell F2. Pull down the column to F48. This will fill this column with a series of nitrogenous bases (A, T, C, G). This column is your DNA strand with 48 nitrogenous bases.

Step 2 - Cut your DNA strand with a restriction enzyme

Use a restriction enzyme to cut your DNA at the sequence of G C C. Every time you see the sequence of GCC, cut the DNA strand into fragments at G and C.

Example

A Fragment 1 = 5 bases

T

G

T

G

cut here

C Fragment 2 = 8 bases

C

T

A

A

A

T

G

cut here

C Fragment 3 = 6 bases

C

T

T

A

A

Step 3 - Enter your fragments on to the electrophoresis gel

We have a hypothetical gel in an MS Excel. Enter your name in the first column to designate the lane in the gel for your DNA. The top row of the gel is numbered 1-48 corresponding to the number of nitrogenous bases in a given fragment of DNA. The DNA travels across the blackboard with the heavier fragments travelling the shortest distance from the right side of the spreadsheet. The smaller fragments travel faster towards the left side of the spreadsheet. Fill in the cells with an X that correspond to the size of each of your DNA fragments (see Example John Doe).

|Number of nitrogenous |1 |2 |

|bases/fragment | | |

|AAA |UUU |Lysine |

|AAC |UUG |Asparagine |

|AAG |UUC |Lysine |

|AAU |UUA |Asparagine |

|ACA |UGU |Threonine |

|ACC |UGG |Threonine |

|ACG |UGC |Threonine |

|ACU |UGA |Threonine |

|AGA |UCU |Arginine |

|AGC |UCG |Serine |

|AGG |UCC |Arginine |

|AGU |UCA |Serine |

|AUC |UAG |Isoleucine |

|AUG |UAC |Methionine |

|AUU |UAA |Isoleucine |

|CAA |GUU |Glutamine |

|CAC |GUG |Histidine |

|CAG |GUC |Glutamine |

|CAU |GUA |Histidine |

|CCA |GGU |Proline |

|CCC |GGG |Proline |

|CCG |GGC |Proline |

|CCU |GGA |Proline |

|CGA |GCU |Arginine |

|CGC |GCG |Arginine |

|CGG |GCC |Arginine |

|CGU |GCA |Arginine |

|CUA |GAU |Leucine |

|CUC |GAG |Leucine |

|CUG |GAC |Leucine |

|CUU |GAA |Leucine |

|GAA |CUU |Glutamic acid |

|GAC |CUG |Aspartic Acid |

|GAG |CUC |Glutamic acid |

|GAU |CUA |Aspartic Acid |

|GCA |CGU |Alanine |

|GCC |CGG |Alanine |

|GCG |CGC |Alanine |

|GCU |CGA |Alanine |

|GGA |CCU |Glycine |

|GGC |CCG |Glycine |

|GGG |CCC |Glycine |

|GGU |CCA |Glycine |

|GUA |CAU |Valine |

|GUC |CAG |Valine |

|GUG |CAC |Valine |

|GUU |CAA |Valine |

|UAA |AUU |Stop |

|UAC |AUG |Tyrosine |

|UAG |AUC |Stop |

|UAU |AUA |Tyrosine |

|UCA |AGU |Serine |

|UCC |AGG |Serine |

|UCG |AGC |Serine |

|UCU |ACA |Serine |

|UGA |ACU |Stop |

|UGC |ACG |Cysteine |

|UGG |ACC |Tryptophan |

|UGU |ACA |Cysteine |

|UUA |AAU |Leucine |

|UUC |AAG |Phenylalanine |

|UUG |AAC |Leucine |

|UUU |AAA |Phenylalanine |

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