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10.3: Gel Electrophoresis - Biology

10.3: Gel Electrophoresis - Biology


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Obtain simulated DNA samples and perform a gel electrophoresis generating a DNA fingerprint. Use this information to determine the guilt or innocence of the suspect.

Step 1: Setting up the agarose gel

  1. Obtain a gel former, comb, and masking tape. The instructor will demonstrate how to build the gel. Place the gel set-up in a safe location. Once the gel has been poured, do not move until solidified.
  2. Gently pour the agarose into the gel former until the level of the agarose is about 3⁄4 the length of the teeth of the comb. The tape will prevent the molten gel from spilling out of the apparatus. The agarose is kept in a 60oC water bath to keep it molten. Agarose solidifies at room temperature so return the flask to the bath immediately after use.

Step 2: Preparation of samples and gel electrophoresis

  1. Obtain two simulated DNA samples A and B. The samples are not DNA but dyes that migrate in a manner similar to restriction fragments.
  2. Remove the tape from the gel former. Carefully remove the comb. Your instructor will demonstrate how to load the samples on the gel. Record which sample you load into which lane of the gel.
  3. Seal the top of the wells with a drop of molten agarose as demonstrated.
  4. Place the gel in the gel box. Samples are closest to the negative (black) electrode. Add 1X electrophoresis buffer to just cover the gel. Place the cover on the apparatus and connect the red and black leads (red is positive, black is negative).
  5. Notify your instructor at this point and s/he will turn on the voltage for you. The gel is run at ~90 volts for 20 minutes. Once the voltage is applied, observe that samples migrate towards the positive electrode (red). Do not leave the gel until you are sure that the samples are migrating in the correct direction.
    * Complete Section10.5, Concept Review while the gel is running
  6. Turn off the power supply. Unplug the leads. Visualize the bands of dye which represent the DNA fragments.

CLEAN UP:

Rinse gel equipment with water. Put gloves, paper towels in the regular trash. Dispose of electrophoresis buffer as instructed (you may recycle it, check with instructor). Wash hands.


Unfolding the Mystery of Life, Biology Lab Manual for Non-Science Majors

a. be late for class. You will miss important instructions.

b. eat or drink in the laboratory

c. ingest any reagents or chemicals used in the laboratory

d. pour chemicals down the sink unless instructed otherwise

2. Dispose of laboratory materials as instructed. Take note of the location of:

c. Sharps container for disposal of glass slides and small sharp objects

3. Take note of the location of the:

b. Eye wash and emergency shower

c. Emergency power shut off button

d. Location of security phone

4. Report all spills, unsafe conditions, or accidents to the instructor.

5. Wash your hands before leaving the laboratory

6. Keep work area neat and organized. Clean up when done with the laboratory exercise.

7. Push in your chair before you leave.

UNFOLDING THE MYSTERY OF LIFE:

BIOLOGY LABORATORY MANUAL

FOR NON-SCIENCE MAJORS

Mercer County Community College – West Windsor NJ

Ellen Genovesi, Laura Blinderman & Patrick Natale

Biology Department

Published 2019

Cover design by Alexis Halka, MCCC student

Preface

This laboratory manual is intended for use in a biology laboratory course taken by non-science majors, pre-biology, and pre-allied health majors.

Safety Precautions

a. be late for class. You will miss important instructions.

b. eat or drink in the laboratory

c. ingest any reagents or chemicals used in the laboratory

d. pour chemicals down the sink unless instructed otherwise

2. Dispose of laboratory materials as instructed. Take note of the location of:

c. Sharps container for disposal of glass slides and small sharp objects

3. Take note of the location of the:

b. Eye wash and emergency shower

c. Emergency power shut off button

d. Location of security phone

4. Report all spills, unsafe conditions, or accidents to the instructor.

5. Wash your hands before leaving the laboratory

6. Keep work area neat and organized. Clean up when done with the laboratory exercise.

7. Push in your chair before you leave.

“I understand all of the safety procedures and information presented and I have been given an opportunity to ask questions concerning this safety information.”

Name __________________________________ Date ____________

Contents

Page Safety Precautions ……….……….……… ii

Exercise 1: The Metric System of Measurement ……….………..………..…1

1.2 Metric System Prefixes and the Metric Ladder 1.3 Measuring Distance

1.4 Measuring Mass 1.5 Measuring Volume 1.6 Measuring Temperature

Exercise 2: Microscopy ……….……. ………..…8

2.1 Parts of the Microscope

2.2 Care of the Compound Light Microscope 2.3 Focusing the Microscope

2.4 Total Magnification 2.5 Diameter of Field

2.6 Observation of Microorganisms

Exercise 3: The Scientific Method ………..………..…..17

3.3 Solubility of Gas in Water Experiment 3.4 Graphing Data

Exercise 4: Cell Membrane Biology ……….…….……….…..27

4.1 Introduction 4.2 Diffusion 4.3 Osmosis

Exercise 5: Biomolecules ……….………. ……….34

5.1 Introduction 5.2 Carbohydrates 5.3 Lipids

6.1 Introduction 6.2 Catalase

Exercise 7: Photosynthesis………. ………50

Exercise 8: Human Genetics & Cytogenetics…..……….……….………56

8.1 Human Genetics - Terms and Concepts 8.2 Human Traits Determined by Single Genes 8.3 Sex Linkage

8.4 Cytogenetics –Introduction

8.5 Cytogenetics – Terms and Concepts 8.6 Reading Karyotypes

Exercise 9: Using Genetic Crosses to Analyze a Stickleback Trait…….…….………..65

9.2 Stating the Hypothesis: Which Phenotype Is Dominant?

9.3 Obtaining the Data: Do the Results from the Experiment Support Your Hypothesis?

Exercise 10: Protein Gel Electrophoresis ………. …….…..…. 70 10.1 Blood detection using the Kastle-Meyer test

10.2 DNA Fingerprinting 10.3 Gel Electrophoresis 10.4 Results

Exercise 11: Isolation of DNA From Plants ……….……….…. ….……76 11.1 Introduction

11.2 Procedure 11.3 Questions

Exercise 12: Animal Tissues………..………. ………..83

12.1 Introduction to Tissue Types 12.2 Organ Specimen

12.4 Evolution of Mammalian Red Blood Cells 12.5 Blood Typing

Exercise 13: Microbiology, Food Microbiology and Disease Transmission . ..…….…. 92

13.2 Classifying Individual Bacterial Cells by Shape

13.3 Testing environments for the Presence of Bacteria/Fungi 13.4 Food Microbiology

13.5 Activity – Yogurt Production 13.6 Disease transmission

THE METRIC SYSTEM OF MEASUREMENT

To apply the metric system to the measurement of weight, distance, volume, and temperature

Universal Standards

The metric system was designed in France in the 18th century. Before then, it was common for units of length, area, and weight to vary from one country to another and even within the same country. Length could be measured in feet, miles, spans, cubits, hands, furlongs, palms, rods or chains. The metric system brought order to the confusing systems of weights and measures then being used in Europe. In 1875, most industrialized countries signed the Treaty of the Meter which formed the International Bureau of Weights and Measures. We now call this system the International System of Units. Although the US uses this system for scientific measurement, most people still use the more complicated system that involves inches, feet, miles, cups, pints, quarts, ounces, and pounds. The United States, Burma, and Liberia are the only countries that do not routinely use the metric system

The meter is the standard unit of linear measure. One meter (39.4 inches) is roughly equivalent to one yard (3 feet). 1 kilometer (km) is 0.6 miles. A finger is measured in cm (2.54 cm in 1 inch). A micrometer (micron) is not visible by unaided human eye. Most cells are in the micron range. To see an object much smaller, an electron microscope must be used.

The gram is the basic unit for measuring mass. There are 0.454 kilograms in a pound.

The basic unit of temperature is degrees Celsius. Body temperature is 37 oC.

Volume is a three dimensional space occupied by a gas, liquid, or solid.

Liquid volume is measured in liters. One liter = 1.06 quarts.

1.2 Metric system prefixes and the metric ladder

prefix fraction decimal scientific notation nano (n) = 1 billionth 1/1,000,000,000 0.000000001 10-9

micro () = 1 millionth 1/1,000,000 0.000001 10-6

milli (m) = 1 thousandth 1/1,000 0.001 10–3 centi(c) = 1 hundredth 1/100 0.01 10–2 kilo (k) = 1 thousand 1000 1000 103

kilometer meter centimeter milimeter micromete nanometer 1000 100 10 1000 1000

 The metric system is based on units of 10. Count zeros. Consult the metric ladder as to how many spaces to move the decimal point.

 Move the decimal left when converting from a smaller to larger value (DIVIDE)

 Move the decimal right when converting from a larger to smaller value (MULTIPLY)

a. One meter is how many kilometers? The question involves going from a smaller value (meter) to a larger value (kilometer). Move the decimal to the left (divide)

1.0 meter  .001 kilometers = 1 X 10 -3 kilometers

b. How many millimeters are in 5 meters? The question involves going from a larger value (meters) to a smaller value (millimeters). Move 3 decimal places to the right (multiply).

5.0 meters  5000 millimeters = 5 X 103 millimeters

c. How many liters are in 80 nanoliters? The question involves converting a small value (nanoliters) to a larger value (liters). Move the decimal to the left 9 places

1.3 Measuring Distance

Most objects encountered in biology range from under a millimeter to meters in length or diameter.

1. Obtain a human bone. Handle with care. Consult the articulated skeleton to find out the location of the bone.

What part of the body is the bone from? __________________________

The scientific name of the bone is the __________________________

2. Measure the length of the bone in centimeters (cm).

The length of the bone = _______ cm = ______ millimeters (mm) = ______ m

3. Use the meter stick to measure the length of your arm or leg, thumb.

The body part, the __________=_______centimeters (cm) =______ millimeters (mm)

1.4 Measuring Mass

An electronic scale is used to measure the mass of an object. The instructor will demonstrate its use.

1. Obtain a small object such as dice. The mass of the object is _______ grams (g) = _________milligrams (mg)

2. Tare the weigh boat. Empty the salt into the weigh boat. The mass of the salt is ________ g = ________ mg

1 pound = 0.454 kilograms 1 inch = 2.54 centimeters 1 kg = 2.2 pounds 1 meter = 39.4 inches

1 quart = 0.946 liters 1 liter = 1.057 quarts

A person weighs 90,000 grams (g). What is the mass in kilogram (kg)? ______ What is the mass in pounds? __________

What is your height in inches ________ = _______ centimeters = ______ meters

Could a normal person be 3 meters tall? ___ What is this height in feet/inches? ___

A bottle of water is 500 ml. Approximately how many cups of water does a person consuming this bottle drink? _____________ cups

1.5 Measuring volume

The volume of an object is the amount of space it takes up.

Volume in cubic centimeters (cc or cm3)

1. Measure the volume of a small item, such as dice, using a small metric ruler.

The volume of the item is ________ cc (cubic centimeters or cm3)

2. A solid volume of 1 cubic centimeter (cc) equals a liquid volume of 1 milliliter (ml). A person receives an injection of insulin (an important drug for diabetics).

3. Fill a 50 ml graduated cylinder with 20 ml H20. Bend down so meniscus is at

eye level. A meniscus is the curvature of the surface of the water. Measure at the lowest point of the meniscus.

3. Use the displacement method to determine the volume of the item that you measured in step 1. Examine the meniscus to insure accuracy.

The volume of the item is _______ ml = _______ cc (cubic centimeters)

Question: What is displacement?

1.6 Measuring temperature

Celsius (C) = 5 (

Fahrenheit (F) = (

C X 1.8) + 32

1. Obtain a thermometer and record the temperature of the following environments:

 Room temperature _______ o C  Ice water temperature _______ o C  Skin temperature _______ o C

 Water boils at 212 o F or _______ o C.

 Body temperature is 37 o C or _______ o F  Water freezes at 32 o F or _______ oC

1. How many decimal positions are moved to convert a meter to a kilometer? ___

2. What metric measure would you use for your height? ________

3. How many millimeters are in 9 centimeters? ________

4. How many meters are in 90 millimeters ________

5. How many grams are in 1 kilogram? ________

6. How many kilograms are in one microgram? ________

7. 1800 milliliters = ________liters

8. 1,200,000,000 nanograms (ng) = ________grams

9. 1,200,000,000 ng ________milligrams ________g ________kg

10.What is one metric measurement used for volume? ________

11.Body temperature is ________degrees Celsius

12.A block measures 3 X 4 X 2 cm.

What is its volume in cubic centimeters(cc)?______ in milliliters (ml)? ______

*Replace all items used in the laboratory and push in your chair when done *Have your work checked by the instructor.

 To gain experience in the care and use of the compound light microscope  To prepare wet mounts of animal and plant tissues

 To observe living protozoa and vinegar eels

Light microscopes use light rays as an energy source. The compound light microscope is used to view objects in the micrometer (micron) range. These microscopes can magnify an object up to 1000 times.

2.1 Parts of the microscope

Become familiar with the location and function of the following parts.

1. Arm and Base

2. Ocular lens – magnifies by 10X

3. Revolving nosepiece – contains 3 objective lenses

scanning objective lens magnifies by 4X

low power objective lens magnifies by 10X

high power objective lens magnifies by 40X

4. Stage and stage clips – hold the slide for viewing

5. Stage adjustment knobs – located below the stage to control forward/reverse and side to side movement of the stage

6. Coarse adjustment knob – for focusing ONLY when using scanning objective

7. Fine adjustment knob –brings object into clearest focus

The Compound Light Microscope

2.2 Care of the Compound Light Microscope

1. Only lens paper should be used to clean the lenses

2. Always carry the microscope by grasping the arm with one hand and supporting the base with the other

3. Do not force anything on the microscope 4. When finished working with the microscope:

2.3 Focusing the Microscope - letter e slide

1. Rotate the nosepiece so that the scanning objective is over the light source.

2. Obtain a letter e slide from the instructor. Use the stage clip to secure the slide onto the mechanical stage. Use the stage adjustment knobs to bring the letter e

under the scan objective and over the light source.

3. Use the coarse adjustment knob to bring the letter e into focus. Once the letter e is in focus, the image can be made sharper by using the fine adjustment knob.

Draw the “e” as you observe it with the microscope and describe the principle of

DRAWING DESCRIPTION OF INVERSION

4. Move the slide so that the pointer is on the letter e. Rotate the low power objective lens into place and use the fine adjustment knob to bring the slide into focus.

5. Focus using the high power objective lens and the fine adjustment knob. Do not use the coarse adjustment knob with the high power objective lens. Record observations on high power.

2.4 Total Magnification

Total magnification is calculated by multiplying the objective lens power X the ocular lens power. Complete the following table

Objective lens Magnification Total magnification

2.5 Diameter of Field: determining the size of a single cell

A. Measuring the diameter of field

The field is the circle of light that you observe when you look into the microscope. The diameter of this field changes as you increase magnification. There is an inverse relationship between magnification and diameter of field.

1. Place a thin, clear, metric ruler on the stage. Hold it in place with the stage clip.

2. Use the scan objective to focus and observe the millimeter marks on the ruler.

The space from one hatch mark to the next is a millimeter. Numbers indicate centimeters.

a. Diameter of field using scan objective lens ______ mm. Include half spaces.

b. Diameter of field using low power objective lens = 1.8 mm _______ m

c. Diameter of field using high power objective lens = 0.5 mm ________ m

Question: Why is the diameter of the field of view considered to have an inverse relationship with magnification?

B. Human epithelial cell

Question: What domain and kingdom do humans belong to?

Domain __________________________ Kingdom ___________________

1. Obtain a flat toothpick and obtain a sample of your cheek epithelial cells from the inside lining of the oral cavity.

2. Smear the cells on a clean glass slide and dispose of toothpick in biohazard trash.

3. Obtain a small bottle of methylene blue dye. Make sure that the dropper does not actually touch the slide (do not contaminate the dropper bottle with your cheek cells). Let a small drop of methylene blue dye fall onto the slide.

4. Place a clear cover slip on top of the specimen.

5. Bring the epithelial cells into focus using the scan objective and the coarse adjustment knob. Zoom in on a few cells by using the low powerobjective lens.

7. Switch the objective lens to high power. Sketch one cell

8. Label the cell membrane, nucleus, and cytoplasm of the cell

9. What is the genetic material found in the nucleus of this eukaryotic cell? _________

Question: What domain and kingdom do onion cells belong to?

Domain __________________________ Kingdom ___________________

1. Remove the thin, transparent epidermis (skin) from an onion leaf. Alternately, you may view a prepared slide of onion root tip. Do not discard commercially prepared slides.

2. Place on a clean slide and add a drop of methylene blue. Do not contaminate the dropper (do not touch the onion skin with the dropper). Cover with a clear slip.

3. Observe with the scanning objective lens using the coarse adjustment knob first, then the fine adjustment knob.

4. Observe using the low power objective lens. Make sure you see the rectangular shaped onion cells. Confirm with the instructor, if necessary. Sketch the onion cells. Be sure to indicate the total magnification used in your drawing,

2.6 Observation of microorganisms (Kingdom: Protista)

Members of the kingdom Protista are single celled eukaryotic organisms. They have a nucleus and a complex internal cellular structure. The microorganisms you will view today are commonly found in pond water. The kingdom Protista is divided in phyla based in part on the different organelles that enable motility. Flagella are long whip like tails. Cilia, much shorter though more numerous than flagella, beat like little oars. A pseudopod is a cytoplasmic extension that acts as a “false foot”. In addition to many Protists you may also see bacteria and multicellular animals called rotifers.

Question: What domain do members of the kingdom, Protista, belong to?

Domain ________________________ Kingdom: Protista

1. Prepare a wet mount of microorganisms by adding 1 drop of the culture to a clean slide. Cover with cover slip. Do NOT add methylene blue to these living organisms.

2. Observe under scan, then low power. Do you see any structures inside the organism? Try to observe using high power. Confirm the observation with your instructor.

3. Use the following website, the student identification key or a pond guidebook to identify 2 different organisms found in your pond water sample.

4. Sketch the observed microorganisms 

Name of organism _____________ Name of organism _____________

Vinegar Eels, Tubatris aceti, are small animals found in the nematode phylum. Question: What domain and kingdom do Vinegar Eels belong to?

Domain __________________________ Kingdom ___________________

Click the scan objective lens into place, wrap the cord securely, and return the microscope to the cabinet

Dispose of slides in the sharps container. The letter e slide is not discarded

Clean the lab bench area replacing items as directed by the instructor Do not leave any items in the sink or on the lab bench

THE SCIENTIFIC METHOD: SOLUBILITY OF GAS IN WATER

 To engage in the scientific method

 To test a hypothesis concerning the effect of temperature on the solubility of carbon dioxide in water

 To gain practice in the analysis and graphing of data

 To formulate conclusions about changing levels of atmospheric CO2 over time

3.1 Introduction

Science is a dynamic, methodical, approach to acquiring knowledge about the natural world. One element of the scientific method is a hypothesis, which provides a possible explanation for a particular observation. The hypothesis reflects the state of knowledge before the experiment has been performed. A hypothesis does not need to be correct, but it must be testable. A hypothesis has the potential to be falsified if data suggests another explanation for the observations. Some hypotheses are confirmed by numerous experiments conducted by many scientists and these, such as gravity, and a round earth, become theories.

A theory is a coherent set of hypotheses which have been confirmed through repeated experimental tests. Theories are not easily discarded because a great deal of evidence supports them. For example, if you fall off a building you do not have a possibility of floating because "gravity is just a theory". One theory discarded in the face of new evidence was the centered view of the planetary orbits. The earth-centered view held that the sun and planets orbit the earth. This was falsified by the Copernican system which places the sun at the center of planetary orbits.

The scientific method attempts to eliminate two general types of experimental error.

Random error occurs due to the imperfection of instruments that measure data. Another source of error in experimentation is bias. A preference, or bias, for a certain outcome. may lead us to unconsciously ignore data that does not fit our hypothesis.

The steps of the scientific method

3.2 Experimental design

The experiment is designed so that only one variable is tested at a time. The aspect that varies between groups is called the experimental (independent) variable. There can only be one experimental variable per experiment.

The group that receives the experimental treatment is the experimental group. For example, if the effect of aspirin on heart disease is being investigated, the experimental group is the group of individuals taking aspirin. There may be more than one experimental group within an experiment. For example, one group may take a pill containing no aspirin, another group consumes one aspirin a day, while a third group may take 2 aspirins a day.

The control group (control treatment) provides the baseline to which the experimental group will be compared. The control group is often a group that receives water or a placebo, or a group that receives the standard treatment. For example, in the aspirin study, the control group would receive a pill that looks the same as aspirin, but contains no active ingredient (a placebo).

Controlled variables are quantities that a scientist wants to remain constant between the experimental and control groups. The controlled variables insure that only one experimental variable is tested per experiment. There are usually a number of controlled variables in a single experiment. If you are examining the effect of aspirin on heart disease, controlled variables might include that all participants are adults, are the same sex, have no other health complications, similar levels of blood cholesterol, and non-smokers. Controlling these variables insures that only the experimental variable is investigated and the reliability of the data obtained is increased.

The dependent variable changes in response to experimental variable. Simply put, the dependent variable is what is measured to assess the experimental outcome.

4. Collect and analyze data 1. Observation

Results must be counted or measured in some way so that discrete information can be obtained. In the aspirin example, the number of people who develop heart disease is counted as well as the age at which signs of heart disease are apparent.

The experiment should be conducted a number of times to insure that the results are real. In addition, within an experiment there should be an appropriate number of

replications. An experiment designed to investigate the effects of fertilizer on plants would use many plants in each group.

3.3 Solubility of gas in water

Scientists hypothesize that approximately 250 million years ago, during the Permian period, the world's oceans became depleted of oxygen. A chain of events then led to the Permian mass extinction, a time during which most living species became extinct.

A. View the NOVA video and complete the worksheet http://www.youtube.com/watch?v=y6ig6zKiNTc

1. How many years ago did the Permian mass extinction occur?

2. What % of species became extinct in the Permian mass extinction?

3. Mammal like reptiles and exotic ocean animals were present during the Permian period. What types of life were NOT on Earth 250 million years ago?

4. How many major extinctions have occurred on Earth?

5. What type of gas did the volcanoes in the Siberian Traps release?

6. Water can hold a type of gas critical to living organisms (fish and other aquatic animals require it to survive). What is this gas?

7. What type of gas do deadly bacteria in the lower layers of some lakes produce?

8. What does this gas smell like?

9. Develop a flowchart of the events that led to the Permian extinction a. Anaerobic bacteria thrive in the oceans and produce hydrogen sulfide b. Atmospheric carbon dioxide levels increase

d. Dissolved oxygen levels in the oceans drop

e. Hydrogen sulfide accumulates in the oceans and atmosphere f. Most aquatic life that depends on oxygen dies

g. 95 percent of Earth's life is killed by hydrogen sulfide h. Oceans warm

Concept question: Explain (briefly) how volcanic eruptions can change the atmospheric and ocean environments

B. Experiment

Atmospheric gases, such as oxygen and carbon dioxide, are soluble in water. How much of a particular gas dissolves in water depends on the temperature of the water and on the pressure of that gas above the water.

The gas in carbonated water (seltzer) is carbon dioxide. The high pressure inside the bottle causes more carbon dioxide to dissolve in the water than would dissolve at typical ground-level atmospheric pressures.

Carbonated water at room temperature Carbonated water at 4 oC

3 glass beakers 40 oC water bath

State the hypothesis prior to beginning the experiment. The hypothesis indicates at which temperatures you believe CO2 gas will be more or less soluble in water.

Read through the entire procedure before beginning the experiment

1. Obtain 3 - 250 ml beakers. Place one beaker on a bed of ice.

2. Pour 100 ml of ice-cold carbonated water into the beaker on ice.

3. Pour 100 ml room temperature carbonated water into the other 2 beakers.

4. Immediately place a beaker in the 40oC water bath. Bring the beaker on ice and

the beaker at room temperature with you so that you can observe them simultaneously.

5. Record observations in the data table.

6. After 5 minutes, determine the temperature of each water environment by placing the thermometer in the carbonated water.

Temperature of carbonated water oC

Questions Refer to sections 3.1 and 3.2

1. The aspect that varies between groups in the experiment is called the

experimental (independent) variable. Identify the experimental variable in the experiment.

2. Controlled variables are extraneous factors that are kept constant to minimize their effect on the outcome of the experiment. Identify 3 controlled variables

3. The control group provides the baseline to which the experimental groups will be compared. Identify the control treatment in the experiment.

4. The dependent variable changes with respect to the experimental (independent) variable. The dependent variable is what is measured in the experiment. Identify the dependent variable.

Graphing Data

1. Examine the graph below:

a. As temperature increases, the solubility of oxygen in water ___________.

2. Fish require oxygen to live. As water passes through gills, dissolved oxygen (DO) is transferred to blood. Dissolved oxygen in water is affected by:

Photosynthesis: During light hours, aquatic plants produce oxygen. Mixing: Waves and waterfalls aerate water and increase oxygen concentration.

Decomposition: As organic material decays, bacteria consume oxygen. Salinity: As water becomes more salty, its ability to hold oxygen decreases.

a. At which temperature is dissolved oxygen highest?___ oC

b. A trout requires more DO when the water temperature is 24 oC (75

degrees F) as compared to when the water temperature is 4 oC . (to support

an increase in metabolic activities). How do the DO levels compare at these two temperatures?

3. High levels of CO2 have been implicated in global warming and as a causative

factor in mass extinctions.

a. Construct a line graph of the 1970–2018 data by decade from 1970 and ending with to 2010.

b. State a conclusion as to the change in CO2 levels over time.

Carbon dioxide measurements from the Mauna Loa observatory in Hawaii

(values rounded to nearest tenth)

1970 316.9 1980 338.8 1990 354.4 2000 369.6 2010 389.9

1971 326.3 1981 340.1 1991 355.6 2001 371.1 2011 391.7

1972 327.5 1982 341.5 1992 356.5 2002 373.3 2012 393.9

1973 329.7 1983 343.1 1993 357.1 2003 375.8 2013 396.5

1974 330.2 1984 344.7 1994 358.3 2004 377.5 2014 398.7

1975 331.1 1985 346.12 1995 360.8 2005 379.8 2015 400.8

1976 332.0 1986 347.4 1996 362.6 2006 381.9 2016 404.2

1977 333.8 1987 349.19 1997 363.7 2007 383.8 2017 406.6

1978 335.4 1988 351.6 1998 366.7 2008 385.6 2018 408.5

1979 336.8 1989 353.1 1999 368.4 2009 387.4 2019

NAME: ______________________ SECTION: ________________________

X axis label: _________________________________________________

CELL MEMBRANE BIOLOGY

 To understand the relationship between homeostasis, diffusion, and osmosis

 To investigate passive mechanisms of transport across the plasma (cell) membrane

 To examine hypertonic, hypotonic, and isotonic solutions with respect to cellular homeostasis

4.1 Introduction

Homeostasis is defined as the maintenance of a stable internal environment. In order to maintain homeostasis, cells continually transport substances in and out across the cell (plasma) membrane.

The cell membrane is the cellular structure that regulates the transport of materials into and out of the cell. The lipid bilayer architecture of the cell membrane allows certain molecules to pass through while keeping others out. The cell membrane is

selectively permeable.

Enter cell: Ions Nucleotides

Leave cell: Ions Urea Water

Carbon dioxide Secreted proteins

4.2 Diffusion

throughout the system. Diffusion is considered a form of passive transport because no energy is required in the process. Diffusion can occur in a gas, a liquid, or a solid medium. Diffusion also occurs across the selectively permeable membranes of cells.

All molecules possess kinetic energy which provides the force for movement. Molecules are in constant motion and as they move, they collide with each other. The more molecules in an environment, the higher the concentration of molecules, the higher the frequency of molecular collisions and the faster the speed of diffusion.

How might these factors influence the rate of diffusion?

 Medium molecules diffuse in (gas, liquid, solid)

 Molecular weight of the molecule

Molecular Weight and Diffusion Rate

Molecular weight is an indication of the mass and size of a molecule. The purpose of this experiment is to determine the relationship between molecular weight and the rate of diffusion through a semisolid gel. You will investigate two dyes, methylene blue and potassium permanganate.

Molecule Molecular weight Color

Methylene blue 300 grams/mole blue Potassium permanganate 150 grams/mole purple

Petri dish of agar semi-solid gel Methylene blue solution

Potassium permanganate solution Small straws

Figure 4.1 Placing a drop of dye into a small well on an agar plate

1. Obtain a Petri dish of agar

2. Take the plastic straw and gently stick down into the agar. Lift up withdrawing a small plastic plug of agar. Repeat.

3. Place a single drop of each dye into the agar well. (Figure 4.1).

4. After 20 minutes, place a small, clear metric ruler underneath the Petri dish to measure the distance (diameter) that the dye has moved. Enter the data in Table

Molecular weight (grams/mole)

Diameter after 20 minutes

Diameter after 40 minutes

Potassium permanganate

Describe the relationship between molecular weight and speed of diffusion

B. Diffusion across a selectively permeable membrane

Cells acquire the molecules and ions they need from their surrounding extracellular fluid. In living cells, the ability of a molecule to cross the cell membrane is influenced by its size, charge, lipid solubility, and other characteristics. Small molecules such as water, oxygen, amino acids, and ions easy cross the membrane by passive transport processes that do not require energy (diffusion and osmosis). Other molecules do not easily fit through the lipid bilayer and the cell must expend energy to bring them across.

You will investigate two molecules, starch and iodine, for their ability to cross a selectively permeable membrane. A colorimetric test is employed to assess the movement of these molecules. Dialysis tubing is a transparent material with

microscopic pores that allow only small molecules to pass. It provides a model of the cell membrane and has many uses in industry and medicine.

Materials Beaker Dialysis tubing Starch solution Iodine (IKI) Procedure

1. Obtain a piece of dialysis tubing that has been pre-cut by the instructor. Thoroughly wet the tubing and open the ends. Tie a knot in one end.

2cm) starch solution to the dialysis bag. Tie a knot at the top of the tubing. Rinse the bag briefly with tap water to remove any traces of starch.

3. Fill the beaker approximately ½ full with tap water.

4. Add iodine (IKI) to the beaker of water until a deep yellow color is obtained.

5. Submerge the dialysis bag in the water and incubate at room temperature until a color change is observed (

1. Did starch diffuse across the selectively permeable membrane? How do you

2. Did iodine diffuse across the selectively permeable membrane? How do you

3. Which is the smaller molecule, iodine, or starch?

4. Is diffusion a passive, or an active transport process (choose one)?

4.3 Osmosis

Osmosis is a special case of diffusion in which water molecules pass through a selectively permeable membrane, but larger molecules do not. Osmosis proceeds from a region of high water concentration, across a semi-permeable membrane, to a region of lower water concentration until equilibrium is reached.

A solute is a solid substance, such as salt or sugar that is dissolved in a solvent. Water is usually the solvent in living systems.

A typical animal cell contains a salt concentration of 0.9%. A solution of equal solute concentration is referred to as isotonic. A cell placed in an isotonic environment will experience movement of water inside and outside the cell, but there will be no change in the biology of the cell.

A hypertonic solution contains a high solute concentration with respect to cells. For example, a solution containing 10% salt is hypertonic. When a cell is placed in a hypertonic environment, there is a net movement of water to the outside of the cell (from the higher water environment inside the cell). The cell shrinks in response.

A solution of low solute concentration is referred to as hypotonic. A solution containing 0.5% salt is hypotonic with respect to the cell. When a cell is placed in a hypotonic environment, there is a net movement of water into the cell. The cell swells in response.

Activity: Osmosis in eggplant and potato cells

Thin slice of eggplant Two slices of potato pre-cut NaCl (table salt)

1 piece of weigh paper or plastic

1. Obtain a thin slice of eggplant. Sprinkle the eggplant with salt. Place on a piece of plastic or weigh paper. Incubate at room temperature for approximately 10 minutes.

2. Obtain two pieces of peeled potato, approximately 2 cm X 0.25cm. Label two test tubes with a wax marker at the 5 cm point

Tube 1: Add distilled water to the 5 cm mark Tube 2: Add 10% sodium chloride to the 5 cm mark

Add a potato piece to each tube and incubate at room temperature for

15 minutes Pour off the solution and feel each potato piece. Rinse test-tubes thoroughly with water to remove traces of salt and potato starch

1. Describe how the eggplant slice looks.

2. In terms of osmosis, why does it appear this way?

3. Were eggplant cells exposed to a hypertonic or a hypotonic environment (choose 1) 4. What is the experimental variable in the potato experiment?

5. Identify 2 controlled variables in the potato experiment

6. Which potato piece is stiff? Explain why with respect to osmosis.

7. What happens to human red blood cells when placed in saline, an isotonic solution?

Laboratory Exercise 4

NOTES

 To investigate carbohydrates, lipids, and proteins

 To perform colorimetric tests to identify specific biomolecules

 To analyze data and identify features of the scientific method

 To identify the components of an unknown sample

5.1 Introduction

Humans are omnivores in that they consume a variety of food types from several different ecosystem levels. The biomolecules we consume - carbohydrates, lipids, and proteins - provide us with energy and building blocks for our bodies to function. Vitamins and minerals are important dietary components required in small amounts.

Water is not a nutrient or a source of calories but is critical to life.

5.2 Carbohydrates

Carbohydrates include sugars and starches and are composed of monosaccharide building blocks. Glucose is a simple sugar, a monosaccharide. Fructose is a monosaccharide found in honey, tree fruits, berries, and many vegetables. It is the sweetest naturally occurring sugar.

Two simple sugars joined together form a disaccharide. An example of a

disaccharide is sucrose (table sugar) which is formed by glucose + fructose. Lactose, also known as milk sugar, is a disaccharide composed of a galactose and a glucose molecule. The enzyme, lactase is required to break down lactose into its two monosaccharide sugars. Lactase is normally secreted by intestinal cells. In many people, the production of lactase diminishes with age and they become lactose intolerant.

Glucose + Fructose C6H12O6 C6H12O6

Starches are polysaccharides which contain many linked sugar molecules.

Benedicts Test for Sugar

Reducing sugars (most 6 carbon sugars) react with a copper containing reagent called Benedict's. Benedict's reagent is blue, but when heated in the presence of a reducing sugar, changes color. Green, yellow (+sugar), orange (++ sugar), or red (+++ sugar).

Benedict's reagent Wax pencil

Test-tubes and rack 70o C water bath

Hypothesize about which substance(s) will produce a color change in the Benedict's test.

2. Draw a line 1 cm from the bottom of each test tube and another line 2 cm from the bottom of each tube.

3. Fill in Table 1 to specify which tube will receive which test substance.

4. Add the appropriate test solution to the level of the 1 cm line.

5. Add Benedict's reagent to the 2 cm line of each tube. Mix gently. Record initial color in Table 5.1. This is the color after Benedict’s reagent has been added but before heat.

6. Boil, or heat tubes in the hot water bath for 5 minutes. Record data in Table 5.1

Table 5.1 Benedict's test for sugar

Tube Contents Color before heating

Name of sugar (section 5.2) 1 Distilled water

1. The aspect that varies between test-tubes in the experiment is the experimental

(independent) variable. Identify the experimental variable in the experiment.

2. The negative control group provides the baseline to which the experimental group is compared. The control group is often a "no treatment" condition. Identify the negative control in the experiment. (Choose from column marked Contents in Table 5.1)

3. The positive controltreatment provides a known effect or response in the

experiment. Identify the positive control in the experiment. (Choose from column marked Contents in Table 5.1)

4. Controlled variables are extraneous factors that are kept constant to minimize their effect on the outcome of the experiment. The volume of Benedict's reagent added to each tube is a controlled variable. Identify 3 additional controlled variables.

5. The dependent variable changes in response to the experimental variable and is used to assess the experimental outcome. Identify the dependent variable.

6. Do your results support your hypothesis? Explain.

Iodine test for starch

Lugol's reagent (IKI) is an amber color which, in the presence of starch, turns dark blue.

Materials Wax pencil

Test-tubes and rack Potassium iodide (IKI)

2. Draw a line 1 cm from the bottom of each test tube (use a wax marker).

3. Add the appropriate test solution to the level of the 1 cm line. If using potato or onion piece, or paper, a test tube is not required.

4. Add 3 drops of IKI (iodine). If using potato or onion piece, or paper, the IKI can be dropped directly onto the substance.

5. Record data in Table 5.2

Table 5.2Iodine test for starch

Check if starch present  1 Distilled water

* do not require a test tube

5.3 Lipids

Lipids include oils, fats, and waxes. Lipids provide stored energy, are essential components of cell membranes and are the building blocks of certain hormones. Dietary lipids are insoluble in water and cannot be utilized by the body unless broken down into smaller molecules. The body digests lipids by breaking them down into tiny components by emulsification with bile salts and by enzymes called lipases. The emulsification of lipids occurs in the small intestine.

Emulsification of lipids

test tubes and rack vegetable oil water

1. Draw a line at the 1 cm mark and the 2 cm mark on 2 test tubes. 2. Add vegetable oil to the 1 cm mark in both test tubes.

3. Add an additional cm of water to each test tube. 4. Add 10 drops of detergent to one of the tubes

5. Cover the tubes with parafilm and shake vigorously about 30 times (instructor will demonstrate).

1. Describe the results (do not include the presence of foam) with respect to lipid emulsification.

2. Identify the experimental variable in the lipid experiment.

3. Which tube represents the control group in the lipid experiment?

4. List 3 controlled variables in this experiment

5.4 Proteins

Proteins are complex molecules often with a 3 dimensional structure. These

biomolecules are composed of amino acids building blocks joined by peptide bonds. Proteins form structural components of cells, insulin, hemoglobin, muscle, enzymes, eye, hair color, and thousands of other essential body components. Proteins can be identified using the Biuret test. In the presence of peptide bonds, Biuret reagent turns from blue to purple.

Test tubes Test tube racks Wax pencil Biuret reagent

Hypothesize about which substance(s) will produce a color change with the Biuret test

2. Draw a line 1 cm from the bottom of each test tube and another line 2 cm from the bottom of each tube.

3. Fill in Table 3 to specify which tube will receive which test solution.

4. Add the appropriate test solution to the level of the 1 cm line.

5. Add Biuret reagent to the 2 cm line of each tube. Mix gently.

6. Record data in Table 5.4.

Table 5.4 Biuret test for protein

Tube Contents Final Color Check if protein present 1 Distilled water

What is the composition of your unknown sample? _______________

5.5 Summary

1. What are the three main classes of biomolecules tested in this lab? ____________

2. Biruet reagent tests for the presence of _______ and if positive turns a ____color.

3. Benedict’s reagent tests for the presence of ____ and if positive turns a ____color.

4. Iodine tests for the presences of _________ and if positive turns a _______ color.

5. One carbohydrate category is starch. What is the other?____________________

6. Which test requires high heat after the addition of colorimetric reagent? ________

7. What type of biomolecule is egg white? __________________

8. List 3 substances that contain carbohydrates tested in the laboratory ___________

9. What are the building blocks of proteins? __________________

10.Saturated fats and oils are in the biomolecules category of __________________

11.What color change, if any, would glucose produce in the iodine test? __________

12.What test solution was the negative control in all experiments in today's lab? ____

13.Identify two biomolecules contained in milk_____________/________________

14.What is paper made from and why would paper test positive in the iodine test?

 To examine the function and properties of enzymes in living cells

 To distinguish between substrate, enzyme, and product in a reaction

 To collect and analyze data on tissue-specific catalase activity

 To collect and analyze data on the effect of temperature on catalase action

6.1 Introduction

All living organisms depend on enzymes to catalyze (speed up) chemical reactions. Without enzymes, reactions would not occur fast enough to support life. There are many types of enzymes, active in all types of cells. Each reaction uses a specific enzyme.

Allenzymes are proteins. The amino acid sequence determines the three dimensional shape of the enzyme. This shape is critical because it allows the enzyme to interact with its substrate molecule, the molecule that the enzyme works on. Enzyme action changes the substrate into a product(s). The enzyme itself remains unchanged in the reaction, it can be reused. Each enzyme works best at a specific temperature and pH. Most enzymes in the human body exhibit maximal activity at 37o C and a pH around

7. Extremes in temperature and pH can change the shape of the enzyme rendering it inactive.

Substrate + Enzyme

Product(s) + Enzyme

1. All enzymes are proteins.

2. Enzymes speed up, or catalyze, chemical reactions, often by many thousand-fold.

3. Enzymes are required in small amounts.

4. Many enzymes require assistants, called cofactors. Cofactors may be metal ions such as iron and zinc, or vitamins.

5. Enzymes can be reused. They are unchanged by the reaction.

6. Enzymes are specific. The substrate is the substance that the enzyme works on. Each substrate is digested by a specific enzyme.

7. Enzymes are affected by pH (acidity) and temperature. The rate of the reaction is dependent on these two variables.

6.2 Catalase

Cells produce hydrogen peroxide (H2O2) as a toxic by-product of normal cellular

reactions. The enzyme catalase quickly breaks down hydrogen peroxide into water and oxygen. In other words, catalase protects cells from the toxic effects of hydrogen peroxide. All aerobic cells produce catalase. One molecule of catalase enzyme may work on 40 million molecules of hydrogen peroxide per second!


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Chapter 1 Introduction.

1.1 Special Chemical Requirements of Biomolecules.

1.2 Factors Affecting Analyte Structure and Stability.

1.2.3 Effects of Solvent Polarity.

1.3 Buffering Systems Used in Biochemistry.

1.3.1 How Does a Buffer Work?

1.3.3 Additional Components Often Used in Buffers.

1.4 Quantitation, Units and Data Handling.

1.4.1 Units Used in the Text.

1.4.2 Quantification of Protein and Biological Activity.

1.5 The Worldwide Web as a Resource in Physical Biochemistry.

1.5.2 Web-Based Resources for Physical Biochemistry.

1.6 Objectives of this Volume.

Chapter 2 Chromatography.

2.1 Principles of Chromatography.

2.1.1 The Partition Coefficient.

2.1.2 Phase Systems Used in Biochemistry.

2.1.3 Liquid Chromatography.

2.2 Performance Parameters Used in Chromatography.

2.2.3 Physical Basis of Peak Broadening.

2.2.4 Plate Height Equation.

2.2.7 Significance of Performance Criteria in Chromatography.

2.3 Chromatography Equipment.

2.3.1 Outline of Standard System Used.

2.3.2 Components of Chromatography System.

2.3.3 Stationary Phases Used.

2.4 Modes of Chromatography.

2.4.4 Hydrophobic Interaction.

2.4.6 Immobilized Metal Affinity Chromatography.

2.5 Open Column Chromatography.

2.5.2 Industrial Scale Chromatography of Proteins.

2.6 High Performance Liquid Chromatography (HPLC).

2.6.2 Stationary Phases in HPLC.

2.6.3 Liquid Phases in HPLC.

2.7 Fast Protein Liquid Chromatography.

2.8 Perfusion Chromatography.

2.8.1 Theory of Perfusion Chromatography.

2.8.2 Practice of Perfusion Chromatography.

2.9 Membrane-Based Chromatography Systems.

2.9.2 Applications of Membrane-Based Separations.

2.10 Chromatography of a Sample Protein.

2.10.1 Designing a Purification Protocol.

2.10.2 Ion Exchange Chromatography of a Sample Protein: Glutathione Transferases.

2.10.3 HPLC of Peptides From Glutathione Transferases.

Chapter 3 Spectroscopic Techniques.

3.1.1 A Brief History of the Theories of Light.

3.1.2 Wave-Particle Duality Theory of Light.

3.2 The Electromagnetic Spectrum.

3.2.1 The Electromagnetic Spectrum.

3.2.2 Transitions in Spectroscopy.

3.3 Ultraviolet/Visible Absorption Spectroscopy.

3.3.2 Equipment Used in Absorption Spectroscopy.

3.3.3 Applications of Absorption Spectroscopy.

3.4 Fluorescence Spectroscopy.

3.4.1 Physical Basis of Fluorescence and Related Phenomena.

3.4.2 Measurement of Fluorescence and Chemiluminescence.

3.4.3 External Quenching of Fluorescence.

3.4.4 Uses of Fluorescence in Binding Studies.

3.4.5 Protein Folding Studies.

3.4.6 Resonance Energy Transfer.

3.4.7 Applications of Fluorescence in Cell Biology.

3.5 Spectroscopic Techniques Using Plane-Polarized Light.

3.5.2 Chirality in Biomolecules.

3.5.3 Circular Dichroism (CD).

3.6.1 Physical Basis of Infrared Spectroscopy.

3.6.2 Equipment Used in Infrared Spectroscopy.

3.6.3 Uses of Infrared Spectroscopy in Structure Determination.

3.6.4 Fourier Transform Infrared Spectroscopy.

3.6.5 Raman Infrared Spectroscopy.

3.7 Nuclear Magnetic Resonance (NMR) Spectroscopy.

3.7.1 Physical Basis of NMR Spectroscopy.

3.7.2 Effect of Atomic Identity on NMR.

3.7.5 Measurement of NMR Spectra.

3.8 Electron Spin Resonance (ESR) Spectroscopy.

3.8.1 Physical Basis of ESR Spectroscopy.

3.8.2 Measurement of ESR Spectra.

3.8.3 Uses of ESR Spectroscopy in Biochemistry.

3.9.1 Origin of Laser Beams.

3.9.2 Some Uses of Laser Beams.

3.10 Surface Plasmon Resonance.

3.10.1 Equipment Used in SPR.

3.10.2 Use of SPR in Measurement of Adsorption Kinetics.

Chapter 4 Mass Spectrometry.

4.1 Principles of Mass Spectrometry.

4.1.2 Overview of MS Experiment.

4.1.4 Equipment Used in MS Analysis.

4.2 Mass Spectrometry of Proteins/Peptides.

4.2.2 MS Modes Used in the Study of Proteins/Peptides.

4.2.3 Fragmentation of Proteins/Peptides in MS Systems.

4.3 Interfacing MS With other Methods.

4.4 Uses of Mass Spectrometry in Biochemistry.

4.4.1 MS and Microheterogeneity in Proteins.

4.4.2 Confirmation and Analysis of Peptide Synthesis.

4.4.4 Post-Translational Modification Analysis of Proteins.

4.4.5 Determination of Protein Disulfide Patterns.

4.4.6 Protein Sequencing by MS.

4.4.8 Analysis of DNA Components.

Chapter 5 Electrophoresis.

5.1 Principles of Electrophoresis.

5.1.2 Historical Development of Electrophoresis.

5.2 Nondenaturing Electrophoresis.

5.2.1 Polyacrylamide Nondenaturing Electrophoresis.

5.2.2 Protein Mass Determination by Nondenaturing Electrophoresis.

5.3 Denaturing Electrophoresis.

5.3.1 SDS Polyacrylamide Gel Electrophoresis.

5.3.2 SDS Polyacrylamide Gel Electrophoresis in Reducing Conditions.

5.3.3 Chemical Crosslinking of Proteins – Quaternary Structure.

5.4 Electrophoresis in DNA Sequencing.

5.4.1 Sanger Dideoxynucleotide Sequencing of DNA.

5.4.4 Single Strand Conformation Polymorphism Analysis of DNA.

5.5 Isoelectric Focusing (IEF).

5.5.3 Titration Curve Analysis.

5.6.1 Dot Blotting and Immunodiffusion Tests with Antibodies.

5.6.2 Zone Electrophoresis/Immunodiffusion Immunoelectrophoresis.

5.6.3 Rocket Immunoelectrophoresis.

5.6.4 Counter Immunoelectrophoresis.

5.6.5 Crossed Immunoelectrophoresis (CIE).

5.7 Agarose Gel Electrophoresis of Nucleic Acids.

5.7.1 Formation of an Agarose Gel.

5.7.2 Equipment for Agarose Gel Electrophoresis.

5.7.3 Agarose Gel Electrophoresis of DNA and RNA.

5.7.4 Detection of DNA and RNA in Gels.

5.8 Pulsed Field Gel Electrophoresis.

5.8.1 Physical Basis of Pulsed Field Gel Electrophoresis.

5.8.2 Equipment Used for Pulsed Field Gel Electrophoresis.

5.8.3 Applications of Pulsed Field Gel Electrophoresis.

5.9 Capillary Electrophoresis.

5.9.1 Physical Basis of Capillary Electrophoresis.

5.9.2 Equipment Used in Capillary Electrophoresis.

5.9.3 Variety of Formats in Capillary Electrophoresis.

5.10 Electroblotting Procedures.

5.10.1 Equipment Used in Electroblotting.

5.10.3 Southern Blotting of DNA.

5.10.4 Northern Blotting of RNA.

5.10.5 Blotting as a Preparative Procedure for Polypeptides.

5.11.1 Transformation of Cells.

5.11.2 Physical Basis of Electroporation.

Chapter 6 Three-Dimensional Structure Determination of Macromolecules.

6.1 The Protein-Folding Problem.

6.1.1 Proteins are only Marginally Stable.

6.1.2 Protein Folding as a Two-State Process.

6.1.3 Protein-Folding Pathways.

6.2 Structure Determination by NMR.

6.2.1 Relaxation in One-Dimensional NMR.

6.2.2 The Nuclear Overhauser Effect (NOE).

6.2.3 Correlation Spectroscopy (COSY).

6.2.4 Nuclear Overhauser Effect Spectroscopy (NOESY).

6.2.5 Sequential Assignment and Structure Elucidation.

6.2.7 Other Applications of Multi-Dimensional NMR.

6.2.8 Limitations and Advantages of Multi-Dimensional NMR.

6.3 Crystallization of Biomacromolecules.

6.3.3 Physical Basis of Crystallization.

6.3.4 Crystallization Methods.

6.3.5 Mounting Crystals for Diffraction.

6.4 X-Ray Diffraction by Crystals.

6.4.2 Diffraction of X-Rays by Crystals.

6.5 Calculation of Electron Density Maps.

6.5.1 Calculation of Structure Factors.

6.5.2 Information Available from the Overall Diffraction Pattern.

6.5.4 Isomorphous Replacement.

6.5.5 Molecular Replacement.

6.5.7 Calculation of Electron Density Map.

6.5.8 Refinement of Structure.

6.6 Other Diffraction Methods.

6.7 Comparison of X-Ray Crystallography with Multi-Dimensional NMR.

6.7.1 Crystallography and NMR are Complementary Techniques.

6.7.2 Different Attributes of Crystallography- and NMR-derived Structures.

6.8.2 Finding a Protein Structure in the Database.

Chapter 7 Hydrodynamic Methods.

7.1.1 Definition of Viscosity.

7.1.2 Measurement of Viscosity.

7.1.3 Specific and Intrinsic Viscosity.

7.1.4 Dependence of Viscosity on Characteristics of Solute.

7.2.1 Physical Basis of Centrifugation.

7.2.2 The Svedberg Equation.

7.2.3 Equipment Used in Centrifugation.

7.2.4 Subcellular Fractionation.

7.2.5 Density Gradient Centrifugation.

7.2.6 Analytical Ultracentrifugation.

7.2.7 Sedimentation Velocity Analysis.

7.2.8 Sedimentation Equilibrium Analysis.

7.3 Methods for Varying Buffer Conditions.

7.4.1 Flow Cytometer Design.

7.4.3 Detection Strategies in Flow Cytometry.

7.4.4 Parameters Measurable by Flow Cytometry.

References and Further Reading.

Chapter 8 Biocalorimetry.

8.1 The Main Thermodynamic Parameters.

8.1.1 Activation Energy of Reactions.

8.2 Isothermal Titration Calorimetry.

8.2.1 Design of an Isothermal Titration Calorimetry Experiment.

8.2.2 ITC in Binding Experiments.

8.2.3 Changes in Heat Capacity Determined by Isothermal Titration Calorimetry.

8.3 Differential Scanning Calorimetry.

8.3.1 Outline Design of a Differential Scanning Calorimetry Experiment.

8.3.2 Applications of Differential Scanning Calorimetry.

8.4 Determination of Thermodynamic Parameters by Non-Calorimetric Means.

8.4.1 Equilibrium Constants.

Chapter 9 Bioinformatics.

9.1 Overview of Bioinformatics.

9.2.1 Nucleotide Sequence Databases.

9.2.2 Protein Sequence Databases.

9.2.4 Expressed Sequence Tag Databases.

9.2.5 Single Nucleotide Polymorphism (SNP) Database.

9.3 Tools for Analysis of Primary Structures.

9.3.5 Predicting Secondary Structure.

9.3.6 Identifying Protein Families.

9.4 Tertiary Structure Databases.

9.4.3 Specialist Structural Databases.

9.5 Programs for Analysis and Visualization of Tertiary Structure Databases.

9.6.1 Modelling Proteins from Known Homologous Structures.

9.6.3 Applications of Homology Modelling to Drug Discovery.

Chapter 10 Proteomics.

10.1 Electrophoresis in Proteomics.

10.1.1 Two-Dimensional SDS PAGE.

10.1.2 Basis of 2-D SDS PAGE.

10.1.3 Equipment Used in 2-D SDS PAGE.

10.1.4 Analysis of Cell Proteins.

10.1.5 Free Flow Electrophoresis.

10.1.6 Blue Native Gel Electrophoresis.

10.1.7 Other Electrophoresis Methods Used in Proteomics.

10.2 Mass Spectrometry in Proteomics.

10.2.1 Tagging Methodologies Used in MS Proteomics.

10.2.2 Isotope-Coded Affinity Tagging (ICAT) for Cysteine-Containing Proteins.


Global Gel Electrophoresis Systems Market Size 2021: Analysis By Emerging Trends, Industry Share, Top Impacting Factors, Key Manufactures, Applications and Forecasts Up To 2027

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Apr 12, 2021 (The Expresswire) -- Global “Gel Electrophoresis Systems Market" Research Report 2021-2027:

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Table of Contents with Major Points:

Detailed TOC of Global Gel Electrophoresis Systems Market Research Report 2021-2027, by Manufacturers, Regions, Types and Applications

1 Gel Electrophoresis Systems Market Overview
1.1 Product Overview and Scope of Gel Electrophoresis Systems
1.2 Gel Electrophoresis Systems Segment by Type
1.3 Gel Electrophoresis Systems Segment by Application
1.4 Global Gel Electrophoresis Systems Market Size Estimates and Forecasts
1.5 Gel Electrophoresis Systems Industry
1.6 Gel Electrophoresis Systems Market Trends

2 Global Gel Electrophoresis Systems Market Competition by Manufacturers
2.1 Global Gel Electrophoresis Systems Sales Market Share by Manufacturers (2015-2021)
2.2 Global Gel Electrophoresis Systems Revenue Share by Manufacturers (2015-2021)
2.3 Global Gel Electrophoresis Systems Average Price by Manufacturers (2015-2021)
2.4 Manufacturers Gel Electrophoresis Systems Manufacturing Sites, Area Served, Product Type
2.5 Gel Electrophoresis Systems Market Competitive Situation and Trends
2.6 Manufacturers Mergers and Acquisitions, Expansion Plans
2.7 Primary Interviews with Key Gel Electrophoresis Systems Players (Opinion Leaders)

3 Gel Electrophoresis Systems Retrospective Market Scenario by Region
3.1 Global Gel Electrophoresis Systems Retrospective Market Scenario in Sales by Region: 2015-2021
3.2 Global Gel Electrophoresis Systems Retrospective Market Scenario in Revenue by Region: 2015-2021
3.3 North America Gel Electrophoresis Systems Market Facts and Figures by Country
3.4 Europe Gel Electrophoresis Systems Market Facts and Figures by Country
3.5 Asia Pacific Gel Electrophoresis Systems Market Facts and Figures by Region
3.6 Latin America Gel Electrophoresis Systems Market Facts and Figures by Country
3.7 Middle East and Africa Gel Electrophoresis Systems Market Facts and Figures by Country

4 Global Gel Electrophoresis Systems Historic Market Analysis by Type
4.1 Global Gel Electrophoresis Systems Sales Market Share by Type (2015-2021)
4.2 Global Gel Electrophoresis Systems Revenue Market Share by Type (2015-2021)
4.3 Global Gel Electrophoresis Systems Price Market Share by Type (2015-2021)
4.4 Global Gel Electrophoresis Systems Market Share by Price Tier (2015-2021): Low-End, Mid-Range and High-End

5 Global Gel Electrophoresis Systems Historic Market Analysis by Application
5.1 Global Gel Electrophoresis Systems Sales Market Share by Application (2015-2021)
5.2 Global Gel Electrophoresis Systems Revenue Market Share by Application (2015-2021)
5.3 Global Gel Electrophoresis Systems Price by Application (2015-2021)

6 Company Profiles and Key Figures in Gel Electrophoresis Systems Business
7 Gel Electrophoresis Systems Manufacturing Cost Analysis
8 Marketing Channel, Distributors and Customers
9 Market Dynamics
9.1 Market Trends
9.2 Opportunities and Drivers
9.3 Challenges
9.4 Porter's Five Forces Analysis

10 Global Market Forecast
10.1 Global Gel Electrophoresis Systems Market Estimates and Projections by Type
10.2 Gel Electrophoresis Systems Market Estimates and Projections by Application
10.3 Gel Electrophoresis Systems Market Estimates and Projections by Region
10.4 North America Gel Electrophoresis Systems Estimates and Projections (2021-2027)
10.5 Europe Gel Electrophoresis Systems Estimates and Projections (2021-2027)
10.6 Asia Pacific Gel Electrophoresis Systems Estimates and Projections (2021-2027)
10.7 Latin America Gel Electrophoresis Systems Estimates and Projections (2021-2027)
10.8 Middle East and Africa Gel Electrophoresis Systems Estimates and Projections (2021-2027)

11 Research Finding and Conclusion
12 Methodology and Data Source

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An immobilized fork as a termination of replication intermediate in Bacillus subtilis ☆

The structure of a DNA intermediate associated with termination of chromosome replication in Bacillus subtilis and derived from a unique BamHI 24.8 × 10 3 base-pair (bp) region of the chromosome has been investigated. The intermediate has properties expected for a forked structure. Gel electrophoresis followed by Southern transfer and hybridization to cloned DNA has shown it to comprise single strands of 15.4 × 10 3 bp and 24.8 × 10 3 bp, in approximately equimolar amounts. After purification away from the bulk of chromosomal DNA, electron microscopy of the intermediate established that 15% of the DNA was present as branched molecules and a significant proportion (11 of 31) of these contained two arms of matching length. The average dimensions (best estimates) of this unique class of Y-shaped molecule were 9.5(± 0.3) × 10 3 , 15.1(± 0.4) × 10 3 and 24.6(±0.6) × 10 3 bp for the stem, arms and end-to-end length, respectively. These values are consistent with the single strand composition of the intermediate as found. Furthermore, hybridization of the single strands to DNA from known locations within the BamHI 24.8 × 10 3 bp region has established the orientation of the forked intermediate relative to the genetic map. The intermediate presumably reflects the immobilization of the clockwise replication fork within the 24.8 × 10 3 bp region, at a location approximately 15.4 × 10 3 bp from the right end.


CPSC536A - Notes for Class 3

In nature, Restriction Enzymes play an important role in chopping up DNA during "import" of outside DNA. Engineers chop up DNA for further analysis.

3.2 Electrophoresis

3.3 Gel-Transfer Hybridization

Techniques similar to this technique (southern blotting) are northern blotting (for RNA) and western blotting (for proteins).

20 bases in length known to be part of the sequence) is added. DNA polymerase starts to build the second strand starting at the primer. When this is done, the double strand is denatured again, and the cycle restarts (see slides #16,#17). The reaction uses up nucleotides and primers, while the enzymes involved (in particular, DNA polymerase) survive the process.

Sequencing

The process of building partial replicas and reading the lengths can be automated. The altered nucleotides are distinctly marked, and the 4 types of partial replicas are build in one process. The replicas "race" in one gel-lane and the sequence is determined by laser-reading the (noisy) marks (coded as colors) of the nucleotides along the lane. (see slides #19, #20)

Cloning

Small DNA rings (plasmids) are opened using Restriction. A new piece of DNA is annealed to the two sticky ends. The result is a new, altered plasmid as well as unwanted n- (original), 2n-, 3n, . -sized rings. The construct can be amplified or translated into proteins in the bacterium E. Coli there are also techniques for testing whether the insertion was successful. Slides #22, #23: The plasmid contains a residence gene (Amp R ), so that the presence of the plasmid in E. Coli can be determined by checking for this resistance. If LacZ' is inoperative, the insertion was successful.


A Butterfly and Biotechnology

Southern blotting is used for finding specific DNA sequence from a DNA sample by using the combination of techniques like gel electrophoresis, capillary electrophoresis and hybridization. The DNA from the gel (after gel electrophoresis)is transferred to a nitrocellulose membrane and hybridization analysis is done for finding out the sequence of our interest using a probe)

Let us discuss here the steps involved in doing Southern blotting. The steps are
1) Preparation of Sample
2) Restriction of the Sample
3) Gel Electrophoresis
4) Pre-treatment of the gel
5) Blotting
6) Hybridization

1) Preparation of Sample: (plant/animal/bacterial)

For tissue or blood samples the DNA could be obtained by treating with SDS (Sodium dodecyl Sulphate)
If we are going to have the DNA from a bacterial sample, there are separate protocols for extracting genomic DNA and pDNA. For extracting DNA from plants, CTAB (cetyltrimethyl ammonium bromide)
is used. This CTAB binds with the DNA and helps in better extraction using phenol. This CTAB is used specifically for plants, because they contain more carbohydrates than animal and bacterial cells.

2) Restriction of the Sample:

Specific restriction enzymes could be used fro restricting the sample of DNA. Only one restriction enzyme can be used or more than one enzyme could also be used. For restricting the sample of DNA containing 1 micro gram per microlitrethe following amount of buffer, enzyme could be used. (Choose the buffer corresponding to the enzyme you use) This volume could also be scaled up.




3) Gel Electrophoresis:
Agarose gel electrophoresis is the next step. The restricted sample is run in the agarose gel (% of the gel depends on the sample)

4) Pre-treatment of the gel:
The gel is pre-treated with 0.25 mol/litre HCl for 30 min and also treated with an alkali.
The reasons for pre-treatment:


Global Gel Electrophoresis Systems Market Size 2021 By Industry Share, Key Findings, Company Profiles, Growth Strategy, Developing Technologies, Demand, Investment Opportunities and Forecast by Regions till 2027

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May 25, 2021 (The Expresswire) -- “Gel Electrophoresis Systems Market” report provides a detailed evaluation of the market by highlighting information on different aspects which include drivers, restraints, opportunities, threats, and global markets including progress trends, competitive landscape analysis, and key regions expansion status. This report is comprehensive numerical analyses of theGel Electrophoresis Systems industry and provides data for making strategies to increase the market growth and success. Keyword Market finds essential elements of the this market in light of present industry, this market requests, business methodologies used by Keyword Market players and the future prospects from different edges in detail.

The research report studies theGel Electrophoresis Systems market using different methodologies and analyses to provide accurate and in-depth information about the market. For a clearer understanding, it is divided into several parts to cover different aspects of the market. This report is aimed at guiding people towards an apprehensive, better, and clearer knowledge of the market.

The Major Players in the Gel Electrophoresis Systems Market include:

Gel electrophoresis is a method for separation and analysis of macromolecules (DNA, RNA and proteins) and their fragments, based on their size and charge.

Market Analysis and Insights: Global Gel Electrophoresis Systems Market

The global Gel Electrophoresis Systems market size is projected to reach USD million by 2027, from USD million in 2020, at a CAGR of % during 2021-2027.

With industry-standard accuracy in analysis and high data integrity, the report makes a brilliant attempt to unveil key opportunities available in the global Gel Electrophoresis Systems market to help players in achieving a strong market position. Buyers of the report can access verified and reliable market forecasts, including those for the overall size of the global Gel Electrophoresis Systems market in terms of revenue.

On the whole, the report proves to be an effective tool that players can use to gain a competitive edge over their competitors and ensure lasting success in the global Gel Electrophoresis Systems market. All of the findings, data, and information provided in the report are validated and revalidated with the help of trustworthy sources. The analysts who have authored the report took a unique and industry-best research and analysis approach for an in-depth study of the global Gel Electrophoresis Systems market.

Global Gel Electrophoresis Systems Scope and Market Size

Gel Electrophoresis Systems market is segmented by company, region (country), by Type, and by Application. Players, stakeholders, and other participants in the global Gel Electrophoresis Systems market will be able to gain the upper hand as they use the report as a powerful resource. The segmental analysis focuses on revenue and forecast by Type and by Application in terms of revenue and forecast for the period 2016-2027.

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The report identifies various key manufacturers in the market. It helps the reader understand the strategies and collaborations that players are focusing on combat competition in the market. The comprehensive report provides a significant microscopic look at the market. The reader can identify the footprints of the manufacturers by knowing about the global revenue of manufacturers, the global price of manufacturers, and production by manufacturers during the forecast period of 2016 to 2019.

On the basis of product type, this report displays the production, revenue, price, market share and growth rate of each type, primarily split into:

● Horizontal Gel Electrophoresis Systems

● Vertical Gel Electrophoresis Systems

On the basis of the end users/applications, this report focuses on the status and outlook for major applications/end users, consumption (sales), market share and growth rate for each application, including:

● Research Organizations and Institutions

The Gel Electrophoresis Systems Market competitive landscape provides details and data information by players. The report offers comprehensive analysis and accurate statistics on revenue by the player for the period 2016-2021. It also offers detailed analysis supported by reliable statistics on revenue (global and regional level) by players for the period 2016-2021. Details included are company description, major business, company total revenue and the sales, revenue generated in Gel Electrophoresis Systems business, the date to enter into the Gel Electrophoresis Systems market, Gel Electrophoresis Systems product introduction, recent developments, etc.

Some of the key questions answered in this report:

● What is the global (North America, Europe, Asia-Pacific, South America, Middle East and Africa) sales value, production value, consumption value, import and export of Gel Electrophoresis Systems?

● Who are the global key manufacturers of the Gel Electrophoresis Systems Industry? How is their operating situation (capacity, production, sales, price, cost, gross, and revenue)?

● What are the Gel Electrophoresis Systems market opportunities and threats faced by the vendors in the global Gel Electrophoresis Systems Industry?

● Which application/end-user or product type may seek incremental growth prospects? What is the market share of each type and application?

● What focused approach and constraints are holding the Gel Electrophoresis Systems market?

● What are the different sales, marketing, and distribution channels in the global industry?

● What are the upstream raw materials and manufacturing equipment of Gel Electrophoresis Systems along with the manufacturing process of Gel Electrophoresis Systems?

● What are the key market trends impacting the growth of the Gel Electrophoresis Systems market?

● Economic impact on the Gel Electrophoresis Systems industry and development trend of the Gel Electrophoresis Systems industry.

● What are the market opportunities, market risk, and market overview of the Gel Electrophoresis Systems market?

● What are the key drivers, restraints, opportunities, and challenges of the Gel Electrophoresis Systems market, and how they are expected to impact the market?

● What is the Gel Electrophoresis Systems market size at the regional and country-level?

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With tables and figures helping analyse worldwide Global Gel Electrophoresis Systems market trends, this research provides key statistics on the state of the industry and is a valuable source of guidance and direction for companies and individuals interested in the market.

Some Points from TOC:

1 Gel Electrophoresis Systems Market Overview
1.1 Gel Electrophoresis Systems Product Overview
1.2 Gel Electrophoresis Systems Market Segment by Type
1.2.1 Type 1
1.2.2 Type 2
1.2.3 Type 3
1.2.4 Others
1.3 Global Gel Electrophoresis Systems Market Size by Type (2016-2027)
1.3.1 Global Gel Electrophoresis Systems Market Size Overview by Type (2016-2027)
1.3.2 Global Gel Electrophoresis Systems Historic Market Size Review by Type (2016-2020)
1.3.3 Global Gel Electrophoresis Systems Market Size Forecast by Type (2021-2027)
1.4 Key Regions Market Size Segment by Type (2016-2020)
1.4.1 North America Gel Electrophoresis Systems Sales Breakdown by Type (2016-2027)
1.4.2 Europe Gel Electrophoresis Systems Sales Breakdown by Type (2016-2027)
1.4.3 Asia-Pacific Gel Electrophoresis Systems Sales Breakdown by Type (2016-2027)
1.4.4 Latin America Gel Electrophoresis Systems Sales Breakdown by Type (2016-2027)
1.4.5 Middle East and Africa Gel Electrophoresis Systems Sales Breakdown by Type (2016-2027)

2 Global Gel Electrophoresis Systems Market Competition by Company
2.1 Global Top Players by Gel Electrophoresis Systems Sales (2016-2020)
2.2 Global Top Players by Gel Electrophoresis Systems Revenue (2016-2020)
2.3 Global Top Players Gel Electrophoresis Systems Average Selling Price (ASP) (2016-2020)
2.4 Global Top Manufacturers Gel Electrophoresis Systems Manufacturing Base Distribution, Sales Area, Product Type
2.5 Gel Electrophoresis Systems Market Competitive Situation and Trends
2.5.1 Gel Electrophoresis Systems Market Concentration Rate (2016-2020)
2.5.2 Global 5 and 10 Largest Manufacturers by Gel Electrophoresis Systems Sales and Revenue in 2019
2.6 Global Top Manufacturers by Company Type (Tier 1, Tier 2 and Tier 3) (based on the Revenue in Gel Electrophoresis Systems as of 2019)
2.7 Date of Key Manufacturers Enter into Gel Electrophoresis Systems Market
2.8 Key Manufacturers Gel Electrophoresis Systems Product Offered
2.9 Mergers and Acquisitions, Expansion

3 Global Gel Electrophoresis Systems Status and Outlook by Region (2016-2027)
3.1 Global Gel Electrophoresis Systems Market Size and CAGR by Region: 2016 VS 2020 VS 2027
3.2 Global Gel Electrophoresis Systems Market Size Market Share by Region (2016-2020)
3.3 Global Gel Electrophoresis Systems Market Size Market Share by Region (2021-2027)
3.4 North America Gel Electrophoresis Systems Market Size YoY Growth (2016-2027)
3.5 Asia-Pacific Gel Electrophoresis Systems Market Size YoY Growth (2016-2027)
3.6 Europe Gel Electrophoresis Systems Market Size YoY Growth (2016-2027)
3.7 Latin America Gel Electrophoresis Systems Market Size YoY Growth (2016-2027)
3.8 Middle East and Africa Gel Electrophoresis Systems Market Size YoY Growth (2016-2027)

4 Global Gel Electrophoresis Systems by Application
4.1 Gel Electrophoresis Systems Segment by Application
4.1.1 Application 1
4.1.2 Application 2
4.1.3 Application 3
4.1.4 Others
4.2 Global Gel Electrophoresis Systems Sales by Application: 2016 VS 2020 VS 2027
4.3 Global Gel Electrophoresis Systems Historic Sales by Application (2016-2020)
4.4 Global Gel Electrophoresis Systems Forecasted Sales by Application (2021-2027)
4.5 Key Regions Gel Electrophoresis Systems Market Size by Application

10 Company Profiles and Key Figures in Gel Electrophoresis Systems Business
10.1 Company Profile 1
10.1.1 Company Profile 1 Corporation Information
10.1.2 Company Profile 1 Description, Business Overview and Total Revenue
10.1.3 Company Profile 1 Gel Electrophoresis Systems Sales, Revenue and Gross Margin (2016-2020)
10.1.4 Company Profile 1 Gel Electrophoresis Systems Products Offered
10.1.5 Company Profile 1 Recent Development

10.2 Company Profile 2
10.2.1 Company Profile 2 Corporation Information
10.2.2 Company Profile 2 Description, Business Overview and Total Revenue
10.2.3 Company Profile 2 Gel Electrophoresis Systems Sales, Revenue and Gross Margin (2016-2020)
10.2.4 Company Profile 1 Gel Electrophoresis Systems Products Offered
10.2.5 Company Profile 2 Recent Development

10.3 Company Profile 3
10.3.1 Company Profile 3 Corporation Information
10.3.2 Company Profile 3 Description, Business Overview and Total Revenue
10.3.3 Company Profile 3 Gel Electrophoresis Systems Sales, Revenue and Gross Margin (2016-2020)
10.3.4 Company Profile 3 Gel Electrophoresis Systems Products Offered
10.3.5 Company Profile 3 Recent Development
…………………………….

11 Gel Electrophoresis Systems Upstream, Opportunities, Challenges, Risks and Influences Factors Analysis
11.1 Gel Electrophoresis Systems Key Raw Materials
11.1.1 Key Raw Materials
11.1.2 Key Raw Materials Price
11.1.3 Raw Materials Key Suppliers
11.2 Manufacturing Cost Structure
11.2.1 Raw Materials
11.2.2 Labor Cost
11.2.3 Manufacturing Expenses
11.3 Gel Electrophoresis Systems Industrial Chain Analysis
11.4 Market Opportunities, Challenges, Risks and Influences Factors Analysis
11.4.1 Industry Trends
11.4.2 Market Drivers
11.4.3 Market Challenges
11.4.4 Porter’s Five Forces Analysis

12 Market Strategy Analysis, Distributors
12.1 Sales Channel
12.2 Distributors
12.3 Downstream Customers

13 Research Findings and Conclusion
Continue…

Detailed TOC of Global Gel Electrophoresis Systems Market @ https://www.marketgrowthreports.com/TOC/17717911

Market is changing rapidly with the ongoing expansion of the industry. Advancement in the technology has provided today’s businesses with multifaceted advantages resulting in daily economic shifts. Thus, it is very important for a company to comprehend the patterns of the market movements in order to strategize better. An efficient strategy offers the companies with a head start in planning and an edge over the competitors. Market Growth Reports is the credible source for gaining the market reports that will provide you with the lead your business needs.

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Watch the video: ΠΑΝΕΛΛΗΝΙΕΣ ΕΞΕΤΑΣΕΙΣ - ΜΕ ΠΑΓΙΔΕΣ Η ΒΙΟΛΟΓΙΑ ΒΑΤΑ ΤΑ ΘΕΜΑΤΑ ΣΤΗΝ ΠΛΗΡΟΦΟΡΙΚΗ (June 2022).


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