1st Semester 60 - BIOLOGY JUNCTION

DNA Model

Structure of DNA Lab

Introduction:

Deoxyribonucleic acid (DNA) is one of the two types of nucleic acids found in organisms and viruses. The structure of DNA determines which proteins particular cells will make. The general structure of DNA was determined in 1953 by James Watson and Francis Crick. The model of DNA that they constructed was made of two chains now referred to as the double helix. Each chain consists of linked deoxyribose sugars and phosphates units. The chains are complementary to each other. One of four nitrogen-containing bases connects the chains together like the rungs of a ladder. The bases are cytosine, guanine, thymine, and adenine. The DNA molecule looks like a spiral staircase. The structure of DNA is illustrated by a right handed double helix, with about 10 nucleotide pairs per helical turn.

DNA is a polymer. The monomer units of DNA are nucleotides. Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to the sugar, and a phosphate group. (See Table 1.) There are four different types of nucleotides found in DNA, differing only in the nitrogenous base. Adenine and guanine are purines. Purines are the larger of the two types of bases found in DNA. They have two rings of carbons & nitrogens. Cytosine and thymine are pyrimidines and have a single carbon-nitrogen ring. (See Table 2.) The sequence of these bases encodes hereditary instructions for making proteins—which are long chains of amino acids. These proteins help build an organism, act as enzymes, and do much of the work inside cells.

Table 1

DNA Nucleotide
(Sugar + Phosphate + Base)

Table 2

Pyrimidine (single ring of C & N)	Purine (double ring of C & N)

Materials:

Colored paper (any 5 different colors to run templates), scissors, transparent tape, coat hanger, hole punch, string or fishing line

Procedure:

Use the section of DNA you have been assigned (Human hemoglobin or Chicken Hemoglobin), and figure out the sequence of bases present on the complementary strand of this molecule Table 1.

Human Hemoglobin		Chicken Hemoglobin
Left Strand	Complementary Strand	Left Strand	Complementary Strand
TAA		GTT
TGT		TGT
CGA		CCG
CCG		CCG
CTG		CGA
GTC		GTC
CAA		TAT
GTC		CGA
CTT		TTG
TGA		AGG

Count the number of bases (A, T, C, and G) you will need for both strands of the DNA model your group has been assigned, and cut out these bases. (60 total)
Cut out a sugar and a phosphate for each of your DNA bases. (120 of each)
Construct a nucleotide for each base that you have cut (sugar + phosphate + base) by taping these together. (20 total nucleotides)
Using your assigned DNA sequence from Table 1, line up the nucleotides in the right order forming he left strand of your DNA molecule. (30 nucleotides)
Add the other complementary nucleotides to form the right strand by taping the bases together (A bonds with T; C bonds with G).
Once the strand is complete, secure it by adding more transparent tape or ask your teacher to laminate your model.
Punch two holes at the top of your model, and attach the DNA model to a coat hanger with string.
Carefully twist your model into a double helix (5 base pairs in a 1/2 turn and 10 in a complete turn).
Attach thin fishing line to the sides of the nucleotides to hold the turns in place.
Hang your model from the ceiling using the top of your coat hanger.

TEMPLATES:

Adenine

Thymine

Cytosine

Guanine

Phosphate

Sugar

Questions & Observations:

1. What 2 molecules make up the sides of the DNA molecule?

2. What nitrogen bases form the rungs of the DNA double helix?

3. What is meant by the complementary strand of DNA?

4. What sugar makes up DNA nucleotides?

5. How are nucleotides named?

6. DNA is the instructions for building what molecule in our cells?

7. What would happen if one or more bases on the DNA strand were changed?

Ecology

Ecology

All Materials © Cmassengale

Ecology is the study of interactions between organisms (biotic part) and their nonliving environment (abiotic factors)

Biotic factors includes plants, animals, fungi, & microorganisms. They may be producers, consumers, or decomposers.

Abiotic factors include climate, soil, temperature, water, air, sunlight, humidity, pH, and atmospheric gases.

Habitat is the place a plant or animal lives, while its niche is its total way of life.

Life is organized into levels:

Organism (any single living thing)

Population (members of the same species living in one place)

Community (all the populations living in an area)

Ecosystem (community living in a similar habitat such as a forest)

Biomes (ecosystems covering wide areas & with similar climates & organisms)

Biosphere ( all the living & nonliving things on earth)

Producers:

	Make their own food through photosynthesis or chemosynthesis
	Includes plants, algal protists, & some bacteria

Consumers:

	Can’t make their own food
	May be herbivores (feed only on plants), carnivores (feed only on animals), or omnivores (feed on plants & animals)

Decomposers:

	Break down dead plants & animals (detritus)
	Recycle nutrients
	Called detritivores
	Include fungi & bacteria

Sunlight is the ultimate energy for all life on earth, but only producers can get their energy directly from the sun.

Energyflowinecosystemimage

Trophic levels are feeding levels of producers & consumers in an ecosystem:

	1st Trophic Level is producers that use sunlight directly
	2nd Trophic Level includes herbivores that feed directly on plants
	Higher Trophic Levels are carnivores feeding on each other

energypyramid

Food chains & food webs:

	Chains show who eats whom in an ecosystem.
	Webs are made up of several food chains.
	Always begin with producers absorbing sunlight.
	Producers store energy in the chemical bonds of the food they make.
	Stored energy is passed to consumers when they eat producers or other consumers.
	Some energy is lost at each trophic level as heat when consumers “burn” food during cellular respiration.
	Both energy & nutrients must move through an ecosystem.

Three main elements that must move through an ecosystem:

	Water
	Carbon
	Nitrogen

Water or Hydrologic Cycle:

	Cells are 70 – 90% water
	Water is needed for metabolic processes
	Water is most important for terrestrial organisms because of desiccation (drying out)

Steps in the water Cycle:

Evaporation Transpiration
(water loss from lakes, rivers, oceans…) (water loss from plant leaves)

¯ ¯

Condensation
(water vapor forms clouds)

Precipitation
(water returns to earth as sleet, rain, snow…)

Surface Runoff
(returns water to bodies of water or to groundwater)

Carbon Cycle:

	Consists of photosynthesis, cellular respiration, & decomposition
	Begins with producers taking carbon dioxide from the air during photosynthesis
	Carbon dioxide used in cellular respiration
	Decomposing plants and animals return Carbon to the soil

Carbon Cycle Steps:

Plant leaves take carbon dioxide from air

Plants store carbon in carbohydrates or starches
(photosynthesis)

Plants & animals release carbon dioxide back into the air
(cellular respiration)

Decomposers return carbon to environment
(decomposition)

Nitrogen:

	Needed by all organisms
	Used to make proteins & nucleic acids (DNA & RNA)
	Air made up of 80% nitrogen
	Only Cyanobacteria & Rhizobium bacteria can use nitrogen directly from the air (nitrogen fixation)
	Bacteria found in the soil & on the roots of legumes (beans, peas …)

Steps in the Nitrogen Cycle:

Cyanobacteria & Rhizobium take nitrogen from air
(nitrogen fixation)

Convert nitrogen gas into ammonia

Nitrifying bacteria in soil change ammonia into nitrates

Plants can absorb & use nitrates to make proteins

Consumers eat plants & get proteins containing nitrogen

Decomposers break down dead organisms & return nitrogen to air
(called ammonification)

Anaerobic bacteria in soil release nitrogen from nitrates into air
(called denitrification)

Three main types of ecosystems:

	Terrestrial (land)
	Freshwater (rivers, ponds, lakes …)
	Marine (oceans & seas)

Terrestrial ecosystems are divided into 7 biomes with similar climates & organisms

Seven Terrestrial Biomes:

	Tropical Rain Forest (jungle)
	Savanna (tropical grasslands)
	Deserts
	Grasslands
	Deciduous Forest
	Taiga (coniferous forest)
	Tundra

Tundra:

	Cold & dark most of the year
	Includes the arctic
	Permafrost is the top layer of soil that thaws & in which plants grow
	No trees, but sedges & grass, mosses, & lichens
	Many migratory animals
	Lemmings & ptarmigans are year round residents
	Approximately 20 cm annual rainfall

Tundra

Taiga:

Coniferous forest
Extends across northern Eurasia & North America
Contains conifers or evergreens (spruce, cedar, fir, pine …)
Needle like leaves withstand weight of snow
Bear, deer, moose, wolves, mountain lions …
Sequoia or redwood (largest conifer) grows here
Bristle cone pine oldest living conifer found here

Coniferous Forest

Temperate Deciduous Forest:

South of taiga in North America, eastern Asia, & Europe
High annual rainfall (75-150 cm)
Moderate temperatures
Well-defined seasons of about equal length
Trees loose leaves in winter (deciduous)
Show stratification (plant layers):
1. Canopy – broad leaf deciduous trees forming uppermost layer
2. Under story – shrubs
3. Forest Floor – herbaceous plants
Songbirds, deer, rabbits, foxes, squirrels, frogs 7 toads, lizards …

Temperate Deciduous Forest

Tropical Rain forest:

Near equator
Warm climate (20 -25 degrees C)
Plentiful rainfall (190 cm/year)
Contains the greatest diversity of plants & animals
Insects, monkeys & apes, snakes, tropical birds, leopards…
Animals & plants brightly colored
Poor soil for agriculture

Rainforest

Grasslands:

Mostly grasses with a few trees due to less rainfall
Moderate climates
Good for agricultural crops
Grazing & burrowing animals dominate
Also called prairies

Grassland

Savanna:

Tropical grasslands
Warm climate & rainy season
Antelope, zebra, lions, wildebeests, hyenas, elephants…
Suffer from floods & drought

(26KB)

Deserts:

Low annual rainfall
Subject to strong winds
Days usually hot & nights cold
Sahara desert is without vegetation
Succulents such as cacti & other water storing plants
Most animals nocturnal
Lizards, snakes, roadrunners, insects, tarantula, hawks, rodents, coyotes…

Desert

Aquatic Biomes:

May be freshwater or saltwater
Wetlands near oceans have brackish water (mixture of fresh & salt waters)
Part of the part water or hydrologic cycle
Often polluted by man’s activities

Lakes & Rivers:

Freshwater
Oligotrophic lakes are nutrient poor (catfish, carp…)
Eutrophic lake are nutrient rich (trout, bass…)
Deep lakes have layers or strata where different plants & animals live
Phototropic organisms in upper layers for light
Estuary at mouth of river contains brackish water

Ocean Zones:

Intertidal zone
1. Along shoreline
2. Wave action
3. Lots of light so many producers
4. Starfish, sand dollars…
Neritic Zone
1. Ocean water above continental shelf
2. Coral reef found here
3. Surrounds continents & receives light in upper layers
Oceanic Zone
1. Beyond continental shelf
2. Deepest area (up to 7 miles)
3. Bottom doesn’t receive light so animals adapted to darkness (many produce their own light, feed on other animals…)
4. Deepest area called abyss
5. Upper area gets light & called the photic zone (lots of seaweed here)
6. Floaters called plankton (microscopic organisms)
7. Swimmers such as fish called nekton
8. Bottom dwellers called benthos

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Energy in food

The Heat is On – The Energy Stored in Food

Introduction:

Plants utilize sunlight during photosynthesis to convert carbon dioxide and water into glucose (sugar) and oxygen. This glucose has energy stored in its chemical bonds that can be used by other organisms. This stored energy is released whenever these chemical bonds are broken in metabolic processes such as cellular respiration.

Cellular respiration is the process by which the chemical energy of “food” molecules is released and partially captured in the form of ATP. Cellular respiration is the general term which describes all metabolic reactions involved in the formation of usable energy from the breakdown of nutrients. In living organisms, the “universal” source of energy is adenosine triphosphate (ATP). Carbohydrates, fats, and proteins can all be used as fuels in cellular respiration, but glucose is most commonly used as an example to examine the reactions and pathways involved.

Marathon runners eat a large plate of pasta the night before a competition because pasta is a good source of energy, or fuel for the body. All foods contain energy, but the amount of potential energy stored will vary greatly depending on the type of food. Moreover, not all of the stored energy is available to do work. When we eat food, our bodies convert the stored energy, known as Calories, to chemical energy, thereby allowing us to do work. A calorie is the amount of heat (energy) required to raise the temperature of 1 gram (g) of water 1 degree Celsius (°C). The density of water is 1 gram per milliliter (1g/ml) therefore 1 g of water is equal to 1 ml of water. When we talk about caloric values of food, we refer to them as Calories (notice the capital “C”), which are actually kilocalories. There are 1000 calories in a kilocalorie. So in reality, a food item that is listed as having 38 Calories has 38,000 calories. Calories are a way to measure the energy you get from the food you eat.

Just as pasta can provide a runner energy to run a marathon, a tiny peanut contains stored energy that can be used to heat a container of water. For this lab exercise, you will indirectly measure the amount of Calories in couple of food items using a calorimeter. A calorimeter (calor = Latin for heat) is a device that measures the heat generated by a chemical reaction, change of state, or formation of a solution. There are several types of calorimeters but the main emphasis of all calorimeters is to insulate the reaction to prevent heat loss. We will be using a homemade calorimeter modeled after a constant-volume calorimeter. A particular food item will be ignited, the homemade calorimeter will trap the heat of the burning food, and the water above will absorb the heat, thereby causing the temperature (T) of the water to increase. By measuring the change in temperature (∆T) of a known volume of water, you will be able to calculate the amount of energy in the food tested

Objective:

In this experiment, you will measure the amount of energy available for use from three types of nuts, a plant product. This process of measuring the energy stored in food is known as calorimetry.

Materials:
large paper clip, oC thermometer, soft drink can, soft drink can with openings cut into the side, mixed nuts, matches, water, electronic balance, pencil & paper, 100 ml graduated cylinder, calculator

Procedure:

Carefully, cut out two openings along the side of a soft drink can. This will serve as your support for the second drink can that will contain water & sit on top.

Bend a large size paper clip so that a nut can be attached on one end and the other end will sit flat inside the cut-out soft drink can.

Use the graduated cylinder to accurately measure 100g (100ml) of water. Pour this water into the uncut soft drink can.
Place the thermometer in the uncut can and measure the water temperature after 3 minutes. Record this temperature on data table 1.

Mass the nut (g) that you will burn and record this mass on data table 1.
Attach the nut to the bent end of your paper clip and carefully set the clip & nut into the cut-out soft drink can on bottom. Make sure the cans are sitting on a flat, nonflammable surface!

Carefully light the nut from the bottom using a match and record the change in water temperature as the nut burns (thermometer in the can during burning). Immediately after the nut finishes burning, record the final (highest) water temperature on data table 1.
Measure the mass (g) of the remaining nut & record this in the data table 1. (Mass the burned nut and paper clip together and then subtract the mass of the nut to get the mass of the nut alone.)
Complete the data table1 by calculating the change in mass of the nut.
Repeat this experiment with the other two types of nuts .
When all three nuts have been burned, complete the analysis on data table 2.

Results:

Table 1 – Results of Burning
	PECAN	WALNUT	ALMOND
oC H2O temperature Before burning oC
oC H2O temperature After burning oC
Difference in oC H2O temperature oC
Mass of Paper Clip g
Mass of Nut Before Burning
Mass of Paper Clip and Nut After Burning g
Mass of Nut ALONE After Burning (Subtract paper clip mass from mass of nut & paper clip after burning) g (Subtract paper clip mass from mass of nut & paper clip after burning) g

Table 2 – Data Analysis from Nut Calorimetry
	PECAN	WALNUT	ALMOND
Mass Difference of Nut Before & After Burning (Subtract mass of nut after burning from Mass of nut before burning) g
Temperature Difference of H2O Before & After Burning (Subtract original water temp. from final water temp.) oC
Calories Required to Change the Temperature of 100 g of H2O (Multiply temperature change by 100)Cal
Average Calories per gram in the Nut (Divide the total calories by the mass difference of the nut before & after burning)Cal/g
Average kilocalories or food calories per gram (Divide the calories per gram by 1000)kcal/g

Questions & Conclusion:

Where did the energy stored in the nut originally come from?
During what process was this energy stored in the nut, & where specifically was it stored?
What simple sugar made by plants is a common source for stored energy?
Which group of macromolecules would a nut contain — carbohydrates, lipids, or protein?
What is the name for stored energy?
Give some examples of how organisms would use this stored energy.
In this experiment, discuss what happened to the energy stored in the nut.
Why was the final mass of the nut less than the original mass of the nut? (Remember that matter can’t be destroyed in a chemical reaction.)

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DNA Patterns

DNA Patterns

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Diffusion and Osmosis

Diffusion and Osmosis

Introduction:
In this exercise you will measure diffusion of small molecules through dialysis tubing, an example of a semi permeable membrane. The movement of a solute through a semi permeable membrane is called dialysis. The size of the minute pores in the dialysis tubing determines which substance can pass through the membrane. A solution of glucose and starch will be placed inside a bag of dialysis tubing. Distilled water will be placed in a beaker, outside the dialysis bag. After 30 minutes have passed, the solution inside the dialysis tubing and the solution in the beaker will be tested for glucose and starch. The presence of reducing sugars like glucose, fructose, and sucrose will be tested with Benedict’s Solution. The presence of starch will be tested with Lugol’s solution (iodine-potassium-iodide).

Procedure:

Obtain a 30 -cm piece of 2.5-cm dialysis tubing that has been soaking in water. Tie off one end of the tubing to form a bag. To open the other end of the bag, rub the end between your fingers until the edges separate.
Place 15 mL of the 15% glucose/ 1% starch solution in the bag. Tie off the other end of the bag, leaving sufficient space for the expansion of the bag’s contents. Record the color of the solution in Table 1.1.
Test the 15% glucose / 1% starch solution in the bag for the presence of glucose. Your teacher may have you do a Benedict’s test. Record the results in Table1.1.
Fill a 250 mL beaker or cup 2/3 full with distilled water. Add approximately 4 mL of Lugol’s solution to the distilled water and record the color in Table 1.1. Test the solution for glucose and record the results in Table 1.1.
Immerse the bag in the beaker of solution.
Allow your set up to stand for approximately 30 minutes or you see a distinct color change in the bag or the beaker. Record the final color of the solution in the bag, and of the solution in the beaker, in Table 1.1.
Test the liquid in the beaker and in the bag for the presence of glucose. Record the results in Table 1.1.

Table 1.1

	Initial Contents	Initial Solution Color	Final Solution Color	Initial Presence of Glucose	Final Presence of Glucose
Bag	15% Glucose & 1% starch
Beaker	H2O + IKI

Analysis of Results:
1. Which substance(s) are entering the bag and which are leaving the bag? What experimental evidence supports your answer?

_______________________________________________________________________

2. Explain the results you obtained. Include the concentration differences and membrane pore size in your discussion.

________________________________________________________________________

3. Quantitative data uses numbers to measure observed changes. How could this experiment be modified so that quantitative data could be collected to show that water diffused into the dialysis bag?

________________________________________________________________________

4. Based on your observations, rank the following by relative size, beginning with the smallest : glucose molecules, water molecules, IKI molecules, membrane pores, starch molecules.

_______________________________________________________________________

5. What results would you expect if the experiment started with glucose and IKI solution inside the bag and only starch and water outside? Why?

________________________________________________________________________

Osmosis:
In this experiment you will use dialysis tubing to investigate the relationship between solute concentration and the movement of water through a semi permeable membrane by the process of osmosis. When two solutions have the same concentration of solutes, they are said to be isotonic to each other. If the two solutions are separated by a semi permeable membrane, water will move between the two solutions, but there will be no net change in the amount of water in either solution. If two solutions differ in the concentration of solutes that each has, the one with more solute hypertonic to the one with the less solute. The solution that has less solute is hypotonic to the one with more solute. These words can only be used to compare solutions.

Procedure:
1. Obtain six 30-cm strips of presoaked dialysis tubing.

2. Tie a knot in one end of each piece of dialysis tubing to form six bags. Pour approximately 25 mL of each of the following solutions into separate bags:

Distilled water
0.2 M sucrose
0.4 M sucrose
0.6 M sucrose
0.8 M sucrose
1.0 m sucrose

Remove most of the air from the bags by drawing the dialysis bag between two fingers. Tie off the other end of the bag. Leave sufficient space for the expansion of the contents in the bag.

3. Rinse each bag gently with distilled water to remove any sucrose spilled during filling.

4. Carefully blot the outside of each bag and record in Table 1.2 the initial mass of each bag.

5. Fill six 250 mL beakers 2/3 full with distilled water.

6. Immerse each bag in one of the beakers of distilled water and label the beaker to indicate the molarity of the solution in the dialysis bag. Be sure to completely submerge each bag.

7. Let them stand for 30 minutes.

8. At the end of 30 minutes remove the bags from the water. Carefully blot and determine the mass of each bag.

9. Record your group’s results in Table 1.2. Obtain data from the other lab groups in your class to complete Table 1.3: Class Data.

Table 1.2 Dialysis Bag Results: Individual Data

Contents in Dialysis Bag	Initial Mass	Final Mass	Mass Difference	% Change in Mass
a). Distilled Water
b). 0.2 M
c). 0.4 M
d). 0.6 M
e). 0.8 M
f). 1.0 M

To Calculate:

% change in mass

Final Mass-Initial Mass

100

———————–

Initial Mass

Table 1.3 Dialysis Bag Results: Class Data

percent change in Mass of Dialysis Bags

Bag Contents	Group 1	Group 2	Group 3	Group 4	Group 5	Group 6	Total	Class Average
Distilled Water
0.2 M
0.4 M
0.6 m
0.8 M
1.0 M

10. Graph the results for both your individual data and class average on the following graph. For this graph you will need to determine the following:

a). the independent variable. __________________________________

b). the dependent variable. ___________________________________

Graph Title ______________________________________________

Analysis of Results:
1. Explain the relationship between the change in mass and the molarity of sucrose within the dialysis bag.

________________________________________________________________________

2. Predict what would happen to the mass of each bag in this experiment if all the bags were placed in a 0.4 M sucrose solution instead of distilled water. Explain your response.

________________________________________________________________________

3. Why did you calculate the per cent change in mass rather than using the change in mass?

________________________________________________________________________

4. A dialysis bag is filled with distilled water and then placed in a sucrose solution. The bag’s initial mass is 20 g. and its final mass is 18 g. Calculate the percent change of mass, showing your calculations in the space below.

5. The sucrose solution in the beaker would have been ___________________ to the distilled water in the bag.

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