Chemistry Powerpoint Worksheet

Chemistry PowerPoint Notes  

1. What makes up everything in the universe?  

2. Name 2 properties of all matter.  


3. Define mass.  


4. How does weight differ from mass?  


5.What are elements?  


6. Name the 4 elements that make up most of a living thing.  


7. What is used to represent an element?  

8. Name the smallest part of an element.  

9. What are the 2 main regions of an atom?  

10. Where is the nucleus of an atom found and what does it contain?  

11. What is the charge on a proton?              A neutron?  

12. All atoms of the same element have the ________ number of protons.  

13. The number of protons in an atom determines the _________________________.  

14. What is the charge on an electron?  

15. If you know the number of protons in an atom, how can you determine the number of electrons?  


16. Do all the atoms of the same element have the same number of neutrons?  

17. Atoms of the same element with different numbers of neutrons are called ___________.  

18. The mass of an atom is centered in the ___________.  

19. The number of protons PLUS neutrons in an atom determines its ___________________.  

20. What atomic particle has a negative charge?  

21. Why isn’t the mass of an electron used to determine the atomic mass of an element?  


22. Where are electrons found?

23. Which electrons in an atom have the most energy?  

24. How many energy levels are there & name them?  

25. How many electrons will each energy level hold?  


26. Elements are arranged on a __________________ by their atomic _____________.  

27. What are Periods & what do they tell you about elements?  


28.What are Families & what do they tell you about elements?  


29. Two or more elements combined together make a _____________.  

30. Chemical ______________ represent compounds.  

31. _____________ are the smallest part of a compound.  

32. ______________ in chemical formulas tell the number of atoms of each element.  

33. _____________ in a formula tell the number of molecules.  

34. Compounds have ____________ properties than its elements.  

35.  The outermost _______________ in elements determine if they will combine.  

36. Elements with ___________ outer energy levels are stable & won’t react.  

37. Why do elements tend to react with other elements?  


38. Chemical _____________ represent chemical reactions.  

39. ______________ appear on the right of the equation, while ___________ are on the left.  

40. Chemical bonds store ____________.  

41. How do covalent bonds form?


42. How do ions form?


43. Positive ions _________ electrons, while negative ions ___________ electrons.  

44.  Define energy.  


43. Give some examples of different forms of energy.  

44. Atoms are in constant ________________, which determines the atom’s ____________.  

45.  List the 3 main states of matter.  

46. _______________ energy must be added or removed to change the state of matter.  

47. In reactions the amount of product must ____________ the amount of reactants.  

48. Most of an organism’s energy comes from _____________ in foods.  

49. _______________ reactions release energy.  

50. Give an example of an exergonic reaction in cells.  

51. _________________ reactions store energy.  

52.  Give an example of an endergonic reaction in cells.  

53. Most reactions in cells are _________________.  

54.  _________________ energy is the energy needed to start a reaction.  

55. Catalysts _____________ the amount of activation energy needed.  

56. Catalysts in organisms are called ______________ and are usually ______________.  

57. Enzymes act on ____________ which join at the _______________ site.  

58. Can enzymes be reused?  

59. Redox reactions stands for _________________________ reactions.  

60. The oxidized substance _____________ electrons & becomes _____________ charged.  

61. The reduced substance _____________ electrons & becomes _____________ charged.  

62. Define solution.


63. The _____________ is dissolved in the ____________ in a solution.  

64. _______________ is the universal solvent.  

65. A solution becomes _____________ when no more solute will dissolve.  

66. ______________ solutions have water as the solvent & are important to ______________.  

67. What is the dissociation of water?


68. Write the equation for this.


69.  OH is the ______________ ion, while H+ is the ______________ ion.  

70. Acids produce _____________ ions, while bases have an excess of ________ ions.  

71. The _______ scale measures the concentration of H+ ions and goes from ____________.  

72. From 0 to 7 are ___________, a pH of 7 is __________, & above 7 to 14 are _________.  

73. _____________ are used in the body to control pH and keep it near a pH of ______ or neutral.  


Catalase Bi Sample Lab 2



Enzyme Rate of Reaction for Catalase


Life would not be possible without chemical reactions. Chemical reactions are responsible for speeding up the process. A chemical reaction is the process of breaking chemical bonds, forming new bonds or both. The four things that can speed up a chemical reaction is heat, increasing the concentration of reactants, decreasing the concentration of products, and enzymes. Enzyme is a catalase, most the time a protein. Enzymes can control the rate of a reaction, and they also lower activation energy. Enzymes are important in regulating chemical pathways, synthesizing materials needed by cells, releasing energy, and transferring information. Enzymes are involved in digestion, respiration, vision, movement, and thought. There are several things that can affect the function of enzymes like temperature, the pH, and the amount of reactant or product. Simple cells may have as many as 2000 different enzymes, each one catalyzing a different reaction. In this particular lab, your hands act as the enzyme “Catalase”. This enzyme, which is found in your cells, splits hydrogen peroxide, a byproduct made by your cells during cellular respiration,  into water and oxygen.


If  time is increased, then more hydrogen peroxide molecules will be split into water and oxygen


The materials used in this lab were pencils, scissors, envelope, 100 paper hydrogen peroxide molecules, and a watch with a second hand so that a person would be able to keep time for the person tearing the strips.


Take a paper template and cut out 100 hydrogen peroxide molecules. Place the cut out pieces into an envelope. Then have a person act as a catalase and take one piece of the paper molecules out of the envelope at a time and rip it in two and  place the pieces back into the envelope. Have a person hold the envelope person, while another student keeps track of the “tearing” time intervals (10, 20, 30 ,60, and 60 seconds). Count how many molecules are  ripped at the end of each time interval and record this number in your data table. When all time intervals and counts are completed, use the formula below to figure the reaction rate for catalase. Record this rate in  your data table.
M2 – M1 = reaction rate
T2 – T1




Time in seconds


Ripped Hydrogen Peroxide Molecules


Rate of reaction



3 .3


10 .35


24 .47


63 .65


124 1.02


1. What is an enzyme? What are its functions in living things?
Enzymes are proteins in living systems. Enzymes can control the rate of a reaction, and they lower activation energy.


2. Name several things things that can affect the function of an enzyme?
Temperature, the amount of reactant or product and the pH.

3. Write the chemical equation for the breakdown of hydrogen peroxide by the enzyme catalase.
hydrogen peroxide + catalase yields water + oxygen

4. An enzyme’s efficiency increases with greater substrate concentration, but only up to a point. Why?
all of the active sites of the enzymes become filled with hydrogen peroxide molecules


5. If you were allowed to continue this lab and rip hydrogen peroxide molecules for 240 and 300 seconds. What would happen to the rate of reaction and why would this happen?
It would increase.


6. What can you say about the length of time and the rate of the reaction?
The less time, the more the reaction rate is lowered, and the more time, the more the reaction rate is higher.


7. What would happen to the rate of reaction if you remove the water  and oxygen molecules as soon as they are produced?
It would be faster.


Error Analysis:
All pieces must be returned to the envelope each time interval to correctly simulate what occurs within a cell.


Discussion and Conclusion:
As the time intervals increased, the reaction rate of catalase increased also. In a living cell, more hydrogen peroxide would be broken down by catalase over a longer period of time.



Catalase Lab Sample 1



Enzyme Rate of Reaction for Catalase


Enzymes are an important part of life that regulate chemical reactions with in the body. Enzymes speed up chemical reactions in four different ways, one way is heat, another is increasing the rate of reactants, the third way is decreasing the amount of products and the fourth way is enzymes, which speed up reaction without themselves being used up. Enzymes are also involved in digestion, respiration, reproduction, vision, movement, thought, and also in the productions of other enzymes. Simple cells may have as many as 2000 enzymes with each one catalyzing a different reaction. An enzyme can speed up a reaction making it 10, 000,000,000 times faster. An enzyme is a catalyst. A catalyst is a chemical that reduces the amount of activation interim needed for a reaction. Without enzymes a reaction would take much longer than if it had and enzyme. Enzymes also the control the rate and direction of the reaction.
Without catalysts chemical reactions would take much longer that the average human life expectancy. So that would mean that in 76 years only a couple chemical reactions would take place. Since our bodies have enzymes though hundreds of chemical reactions a day. If our bodies didn’t have catalysts our bodily cells couldn’t function. Some bacteria, however, possess a defense mechanism which can minimize the harm done by the two compounds. These resistant bacteria use two enzymes to catalyze the conversion of hydrogen peroxide  back into diatomic oxygen and water. One of these enzymes is catalase and its presence can be detected by a simple test. The catalase test involves adding hydrogen peroxide to a cultures sample or an agar slant.


The reaction rate of catalase splitting hydrogen peroxide into water and oxygen will increase over time.

The materials used consisted of 100 paper H2O2 molecules, a data table, paper, pencil, calculator, scissors, watch with a second hand, and an enzyme rate of reaction catalase worksheet.

Cut out 100 hydrogen peroxide paper molecules. Double check to make sure there are only 100 paper molecules and place them in an envelope. Then one person will keep track of the time while another person acts as a catalase and tears the paper hydrogen peroxide molecules in half. The torn paper molecules should be returned to the envelope each time. Another person times the person acting as the catalase.  The time intervals in which the paper molecules are to be ripped are 10 seconds, 20 seconds, 30 seconds, and two different 60second periods of time. The results should be  recorded in a data table. The reaction rate for catalase is figured using the formula:
M2 – M1 = Reaction Rate
T2  –  T1





Time in Seconds Ripped H2O2 Molecules Rate of Reaction
0-10 5 .5
10-30 13 .4
30-60 31 .6
60-120 61 .5
120-180 91 .5


1. What is an enzyme? What are its functions in living things?
chemicals that reduce the amount of activation energy needed for reactions to occur; they are proteins in cells that control metabolic reactions


2. Name several things that can affect the functioning of an enzyme.
temperature, pH, and the amount of reactant or product


3. Write the chemical equation for the breakdown of hydrogen peroxide by the enzyme catalase.
H2O2   +   Catalase –>  H2O  + O2


4. An enzyme’s efficiency increases with greater substrate concentration, but only up to a point. Why?
once all active sites are filled, the enzyme’s reaction rate won’t continue increasing


5. If you were allowed to continue this lab and rip hydrogen peroxide molecules for 240 and 300 seconds, what would happen to the reaction rate and why would this happen?
there would be more molecules ripped because of the increased amount of time


6. What can you say about the length of time and the reaction rate?
The more time available, the faster the reaction will occur.


7. What would happen to the reaction rate if you removed the water and oxygen molecules as soon as they were produced?
The rate of reaction would go even faster


Error Analysis:
The counting of the time  may have been off a couple of seconds.


Discussion and Conclusion:
The data shows that the more time there is, the more hydrogen peroxide molecules will be ripped. The catalase in the lab ripped about 6 molecules every 5 seconds. The same thing occurs in a cell as more hydrogen peroxide is produced, catalase speeds up breaking down this waste into water and oxygen.




Catalase Peroxide Lab



Enzyme Rate of Catalase




Enzymes are molecular substances found in cells.  Enzymes act as catalysts and most are proteins.  Enzymes bind temporarily to one or more of the reactants of the reaction they catalyze. In doing so, they lower the amount of activation energy needed and thus speed up the reaction.
 Not only do enzymes economize energy usage, but also provide a variety of other functions. Cells uses an enzyme (catalase) to rid itself of a poisonous substance (hydrogen peroxide). The rate at which this occurs depends on the amount of catalase that is available. In this lab we are going to measure the time it takes for a disc of filter paper, soaked with different concentrations of enzyme, to make its way to the top of a plastic vial filled with peroxide.  Rate of enzyme activity = distance (depth of hydrogen peroxide in mm)/time (in sec).

Catalase catalyzes the decomposition of hydrogen peroxide into water and oxygen.  One molecule of catalase can break 40 million molecules of hydrogen peroxide each second.

2H2O2 —–> 2H2O + O2


Students will prepare various dilute solutions from a 100% enzyme solution.
Students will determine how enzyme concentration affects reaction rate.



6 medicine cups for dilutions, *catalase stock solution, clear plastic vial, forceps, 18 filter paper disks, Hydrogen Peroxide (H2O2), paper towel, apron, safety glasses, watch with second hand, marker, metric ruler, calculator

* The enzyme has been prepared for you as follows: 50g of peeled potato was mixed with 50 ml cold distilled water and crushed ice and homogenized in a blender for 30 seconds. This extract was filtered through cheesecloth and cold distilled water was added to a total volume of 100 ml. Extract concentration is arbitrarily set at 100 units/ml. ENZYME SHOULD BE KEPT ON ICE AT ALL TIMES!!


  1. Make a series of dilutions of the enzyme catalase using the following table.


Final Quantity Needed Concentration of Final Solution mL of Catalase mL of Water
10 ml 100% c10 0
10 ml 80% 8 2
10 ml 60% 6 4
10 ml 40% 4 6
10 ml 20% 2 8
10 ml 0% 0 10



  1. Use a marking pencil and mark the enzyme solutions as follows: 100%, 80%, 60%, 40%, 20%, and 0%.
  2.  Fill a clear vial with 20 mL of hydrogen peroxide.
  3. Using your forceps, pick up one filter paper disk and submerge it in the 100% enzyme solution for 5 seconds. Continue to hold the disk with the forceps.
  4. Using your forceps, pick up one filter paper disk and submerge it in the 100% enzyme solution for 5 seconds. Continue to hold the disk with the forceps.
  5. Remove the disk from the solution and blot it dry, for five seconds, using your paper towel.
  6. Drop the disk in the hydrogen peroxide and measure the time it takes for the disk to rise up from the bottom. Begin timing as soon as the disk touches the surface of the hydrogen peroxide.
  7. Use the metric ruler to measure the distance the disk sinks into the hydrogen peroxide. multiply by two to determine the entire distance the disk traveled. Enter the time and distance the disk traveled in the column for Trial 1 in the data table below.



% Catalase

Time in seconds

Distance in millimeters

Reaction Rate mm/s
Trial 1 Trial 2 Trial 3 Avg. Trial 1 Trial 2 Trial 3 Avg.


  1. Repeat the above steps for the remainder of the solutions. Remember to use clean filter paper each time you use a different solution. Enter the times and distances for trial 2 and 3 in their appropriate columns.

Analysis & Conclusion:

1. Which concentration of catalase had the fastest reaction time?

2. Which concentration of catalase had the slowest reaction time?

3. What is catalase & why is it important to cells in your body?



4. How did you know that catalase was present in the above compounds?


5. What 2 substances form when catalase breaks down hydrogen peroxide?


6. What type of organic compound is catalase?

7. Produce a line graph of the above data. Use the enzyme concentration as the independent variable and the reaction rate as the dependent variable.

Graph Title:__________________________________________________


8.  Based on the graph and overall slope of the line, what can you conclude about the effect of enzyme concentration on reaction rate?




Bioenergetics Powerpoint Worksheet

ppt Questions


1. What is bioenergetics?


2. All organisms require ____________ to perform their functions.

3. Name the 2 main kinds of energy.

4. What is kinetic energy?


5. Give 2 examples of kinetic energy.


6. What is potential energy?


7. Potential energy is stored in ____________ __________.

Two Types of Energy Reactions

8. What is an endergonic reaction?


9. Give an example of an endergonic reaction.


10. What serves as the energy for photosynthesis?

11. During photosynthesis, the light energy is stored in the chemical bonds of what sugar?

12. What are the two raw materials (reactants) for photosynthesis?

13. What is an exergonic reaction?


14. Give an example of an exergonic reaction.

15. Where does the energy for cellular respiration come from?


16. Energy released during cellular respiration that can be used by cells is called _________.

Metabolic Reactions of Cells

17. Define metabolism of cells.


18. From what compound do animals get their energy (ATP) to do cellular work?

19. Name the 2 types of metabolism.


20. Explain anabolic pathways and give an example.



21. Explain catabolic pathways and give an example.



22. The energy that drives catabolic pathways in organisms comes from breaking _____________ ___________ and producing the energy molecule ___________.

Cellular Energy – ATP

23. Name the 3 components that make up ATP.




24. How many phosphate groups are in ATP?

25. The last two phosphate groups on ATP are bonded with ___________ ___________ bonds.

26. Which phosphate bond contains the MOST energy?

27. Give the formula for a phosphate group.

28. Name the process that breaks the bonds of ATP to release energy.

29. How often does phosphorylation occur in cells?


30. What enzyme weakens the last phosphate bond so it can be broken?

31. Organisms use ___________ to break down energy-rich __________ to release the potential  energy stored in its bonds.

32. Energy released from the chemical bonds of glucose are trapped & stored in ________ until a cell needs energy.

33. What does ATP stand for?

34. How much ATP do cells use?


35. What coupled reactions make ATP and then release its energy.


36. Is hydrolysis exergonic or endergonic?

37. Is energy stored or released during hydrolysis?

38. Is dehydration exergonic or endergonic?

39. Is energy stored or released in dehydration?

40. When ATP is broken down to release energy, what two things form?


41. During hydrolysis of ATP, a molecule of ___________ is added to split the ________ phosphate bond.

42. What happens to the energy released from the hydrolysis of ATP?


43. During dehydration of ATP, a molecule of ___________ is removed to join a free phosphate and __________ making more ATP again.

44. Where is the energy stored in the dehydration process to form ATP?



45. How many high-energy phosphate bonds does ATP have?

46. Is photosynthesis anabolic or catabolic?

47. Is photosynthesis exergonic or endergonic?

48. The breakdown of ATP is due to hydrolysis or dehydration?

49. Water is added or removed in the breakdown of ATP?

50. Which of the following are coupled reactions in organisms:

     a. hydrolysis – dehydration?

     b. Anabolism – Catabolism?

     c. Endergonic – Exergonic?


AP Lecture Guide 02 & 03 – Chemical Context of Life & Water

AP Biology: CHAPTERS 2 & 3


1. What are the most common elements in the human?



2. Helium has an atomic number of 2 and atomic mass of 4. Explain.



3. Define isotope and give some examples.




4. How are isotopes used in biology?




5. What happens when electrons change levels?




6. What is the significance of valence numbers?




7. Why do atoms form covalent vs. ionic bonds?




8. How do non-polar covalent bonds differ from polar covalent bonds?




9. What is a hydrogen bond? How does it form and how is it different from a covalent bond?




10. Sketch a few molecules of water, indicate their polarity, and where H bonds form.





11. Why is H bonding so important to water’s properties?




12. List the “special” properties of water and give an example of why the property may be

important to living things.

a. ________________________________________________________________________




b. ________________________________________________________________________




c. ________________________________________________________________________




d. ________________________________________________________________________






Amino Acids

Listed below are the common names and structural formulas of the twenty amino acids found in proteins. They are arranged alphabetically.

Structure of alanine. [str5ala.jpg]
Structure of arginine. [str5arg.jpg]
Structure of asparagine. [str5asn.jpg]
Structure of aspartic acid. [str5asp.jpg]
aspartic acid
Structure of cysteine. [str5cys.jpg]
Structure of glutamic acid. [str5glu.jpg]
glutamic acid
Structure of glutamine. [str5gln.jpg]
Structure of glycine. [str5gly.jpg]
Structure of histidine. [str5his.jpg]
Structure of isoleucine. [str5ile.jpg]
Structure of leucine. [str5leu.jpg]
Structure of lysine. [str5lys.jpg]
Structure of methionine. [str5met.jpg]
Structure of phenylalanine. [str5phe.jpg]
Structure of proline. [str5pro.jpg]
Structure of serine. [str5ser.jpg]
Structure of threonine. [str5thr.jpg]
Structure of tryptophan. [str5trp.jpg]
Structure of tyrosine. [str5tyr.jpg]
Structure of valine. [str5val.jpg]

Amylase on Starch Lab


Enzyme Amylase Action on Starch


In this experiment you will observe the action of the enzyme amylase on starch. Amylase changes starch into a simpler form: the sugar maltose, which is soluble in water. Amylase is present in our saliva, and begins to act on the starch in our food while still in the mouth.
Exposure to heat or extreme pH (acid or base) will denature proteins. Enzymes, including amylase, are proteins. If denatured, an enzyme can no longer act as a catalyst for the reaction.
Benedict’s solution is a test reagent that reacts positively with simple reducing sugars like maltose, but will not react with starch. A positive test is observed as the formation of a brownish-red cuprous oxide precipitate. A weaker positive test will be yellow to orange.


Distilled water
Benedict’s qualitative solution
3 graduated cylinders (10mL)
250-ml beaker
Stirring rod
3 test tubes (16 x 125mm)
Test tube rack
Wax pencil
Water Bath


Add 1g of cornstarch to a beaker containing 100ml of cold distilled water. While stirring frequently, heat the mixture just until it begins to boil. Allow to cool.


1. Fill the 250-mL beaker about 3/4 full of water and place on the hot plate for a boiling water bath. Keep the water JUST AT BOILING.

2. Mark 3 test tubes A, B and C. “Spit” between 1 and 2 mL of saliva into each test tube.

3. Into tube A, add 2 mL of vinegar. Into tubes B and C, add 2 mL of distilled water. Thump the tubes to mix.

4. Place tube B into the boiling water bath for 5 minutes. After the five minutes, remove from the bath, and place back into the test tube rack.

5. Add 5 mL of the starch solution to each tube and thump to mix. Allow the tubes to sit for 10 minutes, occasionally thumping the tubes to mix.

6. Add 5 mL of Benedict’s solution to each tube and thump to mix. Place the tubes in the hot water bath. The reaction takes several minutes to begin.


Tube A: Starch + saliva treated with vinegar (acid)

    • Was the test positive or negative? _______________________

What does this indicate?__________________________________________________



Tube B: Starch + saliva and water, treated in a boiling water bath

    • Was the test positive or negative? _______________________

What does this indicate?__________________________________________________



Tube C: Starch + saliva

    • Was the test positive or negative? _______________________

What does this indicate?__________________________________________________




1. What is the function of an enzyme?


2. Where does a substrate attach to an enzyme?

3. If an enzyme is present in a reaction, less ________________ _________________ will be needed to get the reaction started.

4. What is a common suffix found at the end of most biological enzymes?

5. Most enzymes are macromolecules called ________________.

6. Define denaturation of proteins.



7. Name 3 things that can denature or unfold an enzyme.


8. In this lab, what weak acid denatured the protein?

9. What was the purpose of placing one test tube in a hot water bath?


10. What happens to enzymes in your body whenever you run fever?




Amylase Writeup

What to Include in Your Lab Write–Up
Lab: Enzyme Amylase Action on Starch


  • What is an enzyme
  • Describe an enzyme’s structure
  • Explain how an enzyme works (substrate, active site)
  • What’s amylase
  • Where is amylase found
  • What denatures amylase (proteins)
  • Describe the Benedict’s test

Exposure to heat or extreme pH will …

The materials used include…

Type the procedure in paragraph form.


Complete this table

Test Tube Contents of Tube Color of Tube After Heating + or – Benedict’s test Enzyme Denatured

Yes or no

A Starch + Saliva + Vinegar
B (Starch + Saliva) Heated
C Starch + Saliva


  • Restate the hypothesis
  • Explain the results of the Benedict’s test on Tube C (color change, contents of tube, NOT heated)
  • Explain the results of the Benedict’s test on Tube A ( color change, contents on tube, what was added before heating)
  • Explain the results of the Benedict’s test on Tube B ( color change, contents on tube, heating tube)
  • Tell what denaturing proteins is & how did the Benedict’s test show this.


Analyzing Biomolecules


Information for the Public
Nobel Prize Winners in Chemistry
9 October 2002

Revolutionary Analytical Methods for Biomolecules

The Nobel Prize in Chemistry for 2002 is being shared between scientists in two important fields: mass spectrometry (MS) and nuclear magnetic resonance (NMR). The Laureates, John B. Fenn and Koichi Tanaka (for MS) and Kurt Wüthrich (for NMR), have contributed in different ways to the further development of these methods to embrace biological macromolecules. This has meant a revolutionary breakthrough, making chemical biology into the “big science” of our time. Chemists can now rapidly and reliably identify what proteins a sample contains. They can also produce three-dimensional images of protein molecules in solution. Hence scientists can both “see” the proteins and understand how they function in the cells.

Why study biological macromolecules?
All living organisms – bacteria, plants and animals – contain the same types of large molecules, macromolecules, which are responsible for what we call life. Events in the cells are controlled by nucleic acids (such as DNA) that may be termed the cells’ “directors”, while the various proteins are the cells’ leading actors. Each protein has a biological function that may vary with its environment. The protein hemoglobin, for example, transports oxygen to all the cells in the body.

Protein research itself is not new, but proteomics, i.e. studies of how different proteins and other substances act together in the cell, is a relatively new field of research that has grown enormously in the past few years. As the gene sequences of more and more organisms have been mapped and the research frontier has advanced, new questions have cropped up: how can it be that man’s 30,000-or-so genes code for hundreds of thousands of different proteins? What happens if a gene is damaged or is missing? How do diseases such as Alzheimer’s or mad cow disease originate? Can the new chemistry be used to diagnose and treat more quickly the diseases that are threatening mankind?

To be able to tackle questions such as these chemists are in constant pursuit of more knowledge of proteins and how they function together with each other and with other molecules in the cells. This is because small variations in a protein’s structure determine its function. The next step is to study the dynamics: what do protein molecules look like at the very moment when they are interacting with one another? What happens at the decisive moments? To understand, we need to see.

Fig 1. This protein consists of a long chain of amino acids that is pleated, folded and wound together like a ball of wool. It is this three-dimensional image of the protein one needs to achieve to be able to understand the function of that protein. This protein molecule, which was one of the first to have its structure determined with NMR, has a diameter of approximately one millionth of a centimeter
(10-8 m).

Mass spectrometry – a method of identifying molecules
Mass spectrometry now allows us to identify a substance in a sample, rapidly, on the basis of its mass. This technique has long been used by chemists on small and medium-sized molecules. The method is so sensitive that it is possible to trace very small quantities of each type of molecule. Doping and drug tests, foodstuff control and environmental analysis are examples of areas where mass spectrometry is now in routine use.

The foundations of mass spectrometry were already in place at the end of the nineteenth century. The first analyses of small molecules were reported in 1912 by Joseph J. Thompson. Several of the Nobel Prizes of the twentieth century depended directly on mass-spectrometric analysis. Examples are Harold Urey’s discovery of deuterium (Nobel Prize in Chemistry 1934) and the discovery of the fullerenes, “carbon footballs” that gave Robert Curl, Sir Harold Kroto and Richard Smalley the Nobel Chemistry Prize in 1996.

The goal of using mass spectrometry for macromolecules as well long attracted the scientists. During the 1970s a number of successes were achieved in transferring macromolecules to ions in the gas phase, termed desorption technology. These have formed the basis for the revolution in this field during the past twenty years.

Macromolecules may be large in comparison with other molecules but we are nevertheless dealing here with incredibly small structures. Hemoglobin molecules, for example, have a mass of a tenth of a thousand-millionth of a thousand-millionth of a gram (10-19 g). How to weigh something that is so small? The trick is to cause the individual protein molecules to let go of each other and spread out as a cloud of freely hovering, electrically charged protein ions. A common method of subsequently measuring the mass of these ions – and hence identifying the proteins – is to accelerate them in a vacuum chamber where their time of flight (TOF) is measured. They “reach their targets” in an order determined partly by their charge and partly by their mass. The fastest ones are those that are lightest and have the highest charge.

Today there are two principles for causing proteins to transform into the gas phase without losing their structure and form, and it is the discoverers behind these methods that are being rewarded jointly with half the Nobel Prize in Chemistry. In one of these methods, of which John B. Fenn is the originator, the sample is sprayed using a strong electrical field to produce small, charged, freely hovering ions. The other method, instead, uses an intense laser pulse. If this is done under suitable conditions (as to the energy, structure and chemical environment of the sample) the test molecules take up some of the energy of the laser pulse and become released as free ions. The first person to show that this phenomenon, soft laser desorption, could be used for large molecules such as proteins was Koichi Tanaka.

Fenn’s contribution – hovering through spraying
During 1988 John B. Fenn published two articles that were to mean a breakthrough for mass spectrometry with “electrospray” for macromolecules. In the first, studies of polyethylene glycol molecules of unknown mass showed that the method could handle large molecule masses with high charges. The second publication reported the use of the method on medium-sized whole proteins as well. The release of ions is achieved by spraying the sample using an electrical field so that charged droplets are formed. As the water gradually evaporates from these droplets, freely hovering “stark naked” protein molecules remain. The method came to be called electrospray ionization, ESI.

As the molecules take on strong positive charges, the mass/charge ratio becomes small enough to allow the substances to be analyzed in ordinary mass spectrometers. Another advantage is that the same molecule causes a series of peaks, since each can take up a varying number of charges. While this complicates the pattern, at first confusing the researchers, it also gives information that makes identification easier.

 Fig 2. The principles for mass spectrometry of biomolecules.

Tanaka’s contribution – hovering through blasting
At the same time exciting things were happening in another part of the world. At the Japanese Shimadzu instrument company in Kyoto, a young Japanese engineer, Koichi Tanaka, reported an entirely different technique for the first critical stage. At a symposium in 1987 and a year later in print, Tanaka showed that the protein molecules could be ionized using soft laser desorption (SLD). A laser pulse strikes the sample which, unlike in the spray method, is in a solid or viscous phase. When the sample takes up the energy from the laser pulse it is “blasted” into small bits. The molecules let go of one another, released as intact hovering molecule ions with low charge which are then accelerated by an electrical field and detected as described above by recording their time of flight. Tanaka was the first to demonstrate the applicability of laser technology to biological macromolecules. The principle is fundamental for many of today’s powerful laser desorption methods, particularly the one abbreviated MALDI (Matrix-Assisted Laser Desorption Ionization) but also SELDI (Surface Enhanced Laser Desorption Ionization) and DIOS (Direct Ionization on Silicon).

Applications of mass spectrometry
Both electrospray ionization (ESI) and soft laser desorption (SLD) have many areas of application. The sophisticated biochemical analyses now possible were but dreams a few years ago. Interactions between proteins are very important to study in order to understand the signal systems of life. Such non-covalent biomolecule complexes can be examined with ESI. The method is superior to other methods in the rapidity, sensitivity and identification of the actual interaction. Mass spectrometric analytical methods are relatively cheap, enabling them to spread quickly to laboratories all around the world. Today soft laser desorption (in the form of MALDI) and electrospray are standard methods for structure analyses of peptides, proteins and carbohydrates which make it possible to quickly analyze the protein content of intact cells and living tissue. The following examples of current fields of research gives a picture of the application versatility generated by this year’s Nobel Prize. Applications include:

Pharmaceuticals development
The early phase of pharmaceuticals development has undergone a paradigm shift. Combined with fluid separation, ESI-MS has made it possible to analyze several hundreds of compounds per day.

Scientists have recently discovered new ways of studying the spreading of malaria. Early diagnosis is possible thanks to the soft laser desorption method. The oxygen-bearing part of human hemoglobin is used here to absorb the energy of the laser pulse.

Ovarian, breast and prostate cancer
New methods for early diagnosis of different forms of cancer have been reported at a rapid rate during the past year. By having a surface that cancer cells adhere to – and then analyzing this with soft laser desorption – chemists can discover cancer faster than doctors can.

Foodstuff control
ESI technology has also made progress for small molecules. During the past few months we have learned that preparation of the food we eat can give rise to a number of substances hazardous to health, e.g. acrylamide which can cause cancer. With mass spectrometry, food is analyzed rapidly at various stages of production. By modifying the temperature and the ingredients, the harmful substances can be avoided or minimized.

NMR for biological macromolecules
Where mass spectrometry gives answers to questions about e.g. a protein, such as “what?” and “how much?”. NMR in one sense answers the question “what does it look like?” Even the largest proteins are too small to be studied at sufficient resolution with any type of microscope. To be able to form a picture of what a protein really looks like, then, other methods must be used. NMR (Nuclear Magnetic Resonance) is one such method. By interpreting the peaks in an NMR spectrum one can draw a three-dimensional picture of the molecule being studied. One finesse is that the sample can be in a solution, in the case of proteins their natural environment in the cell.

Before the advent of NMR, X-ray crystallography was the only method available for determining the three-dimensional structure of the substance. In 1957 the first true three-dimensional structure of a protein, myoglobin, was presented. This was rewarded with a Nobel Prize in Chemistry to Max Perutz in 1962. X-ray crystallography is based on the diffraction of X rays in protein crystals, and has since contributed to a further series of Nobel Prizes. As a complement to X-ray crystallography, chemists long sought a method that would also function in a solution, i.e. an environment that better resembles the one the biomolecules surround themselves with naturally.

The physicists Felix Bloch and Edward Purcell discovered as early as in 1945 that some atom nuclei, through what is called their nuclear spin, absorb radio waves of a certain frequency when placed in a powerful magnetic field. This was rewarded with the Nobel Prize in Physics in 1952. A few years earlier it was discovered that the frequency for nuclear resonance depended not only on the strength of the magnetic field and the type of atom but also on the chemical environment of the atom. In addition, the nuclear spins of different nuclei could affect each other, generating fine structures, i.e. a further number of peaks in the NMR spectrum.

Fig 3. The sample to be examined is placed in a very strong magnetic field. The figure shows a super-conducting magnet cooled by liquid nitrogen and helium. Pulses of radio waves are sent into the sample which emits a radio wave “answer”. This response is analyzed electronically and the result is an NMR spectrum.

The applicability of the NMR method was initially limited by its low sensitivity: it required incredibly concentrated solutions. But in 1966 the Swiss chemist Richard Ernst (Nobel Prize in Chemistry 1991) showed that this sensitivity could be increased dramatically if, instead of slowly varying the frequency, the sample was exposed to short and intense radio frequency pulses. He also contributed, during the 1970s, to the development of a way of determining what nuclei were adjacent to one another in a molecule, e.g. two atoms bound to each other. By interpreting the signals in an NMR spectrum it was thus possible to gain an idea of the appearance of the molecule, its structure. The method was successful for relatively small molecules but, for larger ones, it was hard to differentiate between the resonances of the different atom nuclei. An NMR spectrum of this kind could look like a grass lawn in section – thousands of peaks where it was impossible to decide which peak belonged to which atom. The scientist who finally solved this problem was the Swiss chemist Kurt Wüthrich.

Kurt Wüthrich – showed that NMR was possible for proteins
At the beginning of the 1980s, Kurt Wüthrich developed an idea about how NMR could be extended to cover biological molecules such as proteins. He invented a systematic method of pairing each NMR signal with the right hydrogen nucleus (proton) in the macromolecule (see fig. 4). The method is called sequential assignment and is today a cornerstone of all NMR structural investigations. He also showed how it was subsequently possible to determine pair wise distances between a large number of hydrogen nuclei and use this information with a mathematical method based on distance-geometry to calculate a three-dimensional structure for the molecule.

Fig 4. If one knows all the measurements of a house one can draw a three-dimensional picture of the house. In the same way, by measuring a vast number of short distances in a protein it is possible to create a three-dimensional picture of its structure, as shown schematically in the figure.

The first complete determination of a protein structure with Wüthrich’s method came in 1985. At present 15-20% of all the thousands of known protein structures have been determined with NMR. The structures of the others have been determined chiefly with X-ray crystallography; a few with other methods such as electron diffraction or neutron diffraction.

Areas of application for NMR with macromolecules
In many respects, the NMR method complements X-ray crystallography for structural determination. If the same protein is investigated with both methods, in the one case in solution and in the other crystallized, the same result is generally obtained, with the exception of certain superficial areas that are affected by the environment in both cases – in the crystals by the tightly packed protein molecules, in solution by the surrounding molecules of the solvent. While the strength of X-ray crystallography lies in being able to determine accurately really large three-dimensional structures, the NMR method has other unique advantages. The fact that the investigation takes place in a solution means that physiological conditions can be approximated. A particular strength of NMR is its ability to demonstrate unstructured and very mobile parts of a molecule. It is possible to elucidate the mobility, the dynamics, and how it varies along a protein chain. Isotope labeling can also be used to facilitate the identification of the atoms.

One example of NMR-determined protein structures comes from studies of the prion proteins involved in the development of a number of dangerous diseases such as mad cow disease (Nobel Prize in Medicine to Stanley Prusiner in 1997). Here Wüthrich and coworkers have shown with NMR methodology that the healthy form of prion proteins has two parts: approximately half of the protein chain assumes a well-ordered, fairly rigid three-dimensional structure in a water solution (121-231 in the picture below), while the other half is without structure and very mobile (23-120).

NMR can also be used in studies of structure and dynamics of other biological macromolecules such as DNA and RNA.

Fig 5. Structure of prion protein, determined with NMR. Half of the protein chain (23-120) is disordered and quite flexible in water solution.

NMR is also used in the pharmaceuticals industry to determine the structure, and hence the properties, of proteins and other macromolecules that can be interesting target molecules for new pharmaceuticals. Pharmaceutical molecules are designed to fit into the structure of the protein – like a key in a lock. The perhaps most important industrial use of NMR is in the search for small potential pharmaceutical molecules that can interact with a given biological macromolecule. If the small molecule binds to the large one, the NMR spectrum of the large molecule is normally changed. This may be used to “screen” a large number of pharmaceuticals candidates at an early stage of the development of a new drug.

The Laureates
John B. Fenn
Virginia Commonwealth
Dept. of Chemistry
1001 W. Main St.
P.O. Box 842006
Richmond, VA 23284-2006
US citizen. Born 1917 (85 years) in New York City, USA. PhD in chemistry 1940 and Professor at Yale University 1967–1987. Professor Emeritus 1987 at Yale University, Connecticut, USA. Since 1994 Professor at Virginia Commonwealth University, Richmond, Virginia, USA.

John B. Fenn


Koichi Tanaka
Shimadzu Corp.
1. Nishinkokyo Kuwabaracho
Kyoto 604-8511
Japanese citizen. Born 1959 (43 years) in Toyama City, Japan.
B. Eng 1983 at Tohoku University, Japan. R&D engineer at Life Science Business Unit, Analytical & Measuring Instruments Division, Shimadzu Corp., Kyoto, Japan.Koichi Tanaka
Kurt Wüthrich
Swiss Federal Institute of Technology Zürich
ETH Hönggerberg, HPK
CH-8093 Zürich
The Scripps Research Institute
10550 North Torrey Pines Rd,
La Jolla, CA 92037
Swiss citizen. Born 1938 (64 years) in Aarberg, Switzerland. PhD in inorganic chemistry 1964 at The University of Basel. Since 1980 Professor of Molecular Biophysics at ETH, Zürich, Schweiz. Visiting Professor of Structural Biology at The Scripps Research Institute, La Jolla, California, USA

Kurt Wüthrich