Unit 2: BiochemistryA. Matter, Water & pHB. Macromolecules and MetabolismC. Enzymes

atommoleculeadhesioncohesionfreezing pointspecific heatpH

organic moleculemonomerbiological macromoleculescarbohydratelipidsnucleic acidprotein

catalystenzymetemperature

BIO.A.2.1 Describe how the unique properties of water support life on Earth. BIO.A.2.1.1 Describe the unique properties of water and how these properties

support life on Earth (e.g., freezing point, high specific heat, cohesion).

BIO.A.2.2 Describe and interpret relationships between structure and function at various levels of biochemical organization (i.e., atoms, molecules, and macromolecules).

BIO.A.2.2.1 Explain how carbon is uniquely suited to form biological macromolecules.

BIO.A.2.2.2 Describe how biological macromolecules form from monomers. BIO.A.2.2.3 Compare the structure and function of carbohydrates, lipids, proteins,

and nucleic acids in organisms.

BIO.A.2.3 Explain how enzymes regulate biochemical reactions within a cell. BIO.A.2.3.1 Describe the role of an enzyme as a catalyst in regulating a specific

biochemical reaction. BIO.A.2.3.2 Explain how factors such as pH, temperature, and concentration levels

can affect enzyme function.

Unit 2: Biochemistry MATTER / WATER

a) elementb) atomc) iond) moleculee) bondf) energyg) hydrogen bonds h) polarity: polar vs. nonpolar i) cohesion vs. adhesion j) surface tension k) capillary action

THE CONCEPT OF PHa) pHb) acid vs. basec) indicatord) pH scalee) acidic and basic substancesf) pH of blood, cells, stomachg) neutralization reactionh) bufferi) alkalosis vs. acidosisj) 3 causes of acidosis

ENZYMES – ORGANIC CATALYSTSa) catalystb) enzymec) reactant vs. productd) how an enzyme works e) substratef) active siteg) enzyme-substrate complexh) shapei) enzyme specificity j) effect of temperature k) effect of pH l) effect of concentrationm) optimumn) amylaseo) pepsinp) trypsinq) digestion: functions of enzymesr) denaturation

MACROMOLECULESa) monomer units & polymer units

Biochemistry - Unit 2 Structure of MatterChapter 4.1 & 4.2

Define the term matter. Distinguish among elements, atoms, ions and molecules. List the main elements that compose organisms. Create a model of the structure of an atom with labels. Contrast covalent and ionic bonds. Analyze the structure of carbon and its importance to living organisms.

The Characteristics of Water Chapter 4.4 Construct the structure of a water molecule. Differentiate between polar and nonpolar molecules. Summarize hydrogen bonds. Draw conclusions how the structure of water is related to its various properties. Compare and contrast adhesion and cohesion as related to surface tension and capillary action.The Concept of pH Chapter 4.4 Use pH indicators to determine the pH of various substances. Differentiate between acids and bases and their position on the pH scale. Draw conclusions regarding the role of buffers in maintaining pH homeostasis.Building Blocks of Life: Macromolecules Chapters 5.1, 5.2, 5.3, 5.4 Identify the 4 macromolecules of life & their monomer units. Construct macromolecules. Compare and contrast properties of the macromolecules. Analyze the importance of carbon to the structure of biological macromolecules.

Enzymes: Organic Catalysts Chapter 5.5 Explain the cause & effect relationship between enzymes and activation energy. Summarize the reaction of peroxidase/hydrogen peroxide & its importance in the body. Relate how an enzyme’s shape is important to its function. Compare & contrast the effect of pH, temperature and concentration on enzyme activity. Summarize how an enzyme interacts with its substrate. Illustrate the importance of enzymes. Investigate and summarize the concept of enzyme specificity. Interpret how denaturation affects enzyme activity.

ATOMS = BUILDING BLOCKS Atoms are the basis of chemistry. They are the basis for everything in the Universe. You should start by remembering that matter is composed of atoms. Atoms and the study of atoms are a world unto themselves. We're going to cover basics like atomic structure and bonding between atoms. As you learn more, you can move to the biochemistry tutorials and see how atoms form compounds that help the biological world survive.

SMALLER THAN ATOMS? Are there pieces of matter that are smaller than atoms? Sure there are. You'll soon be learning that atoms are composed of pieces like neutrons, electrons, and protons. But guess what? There are even smaller pieces moving around in those atoms. Scientists have many names for those pieces, but you may have heard of nucleons and quarks. Nuclear chemists and physicists work together with particle accelerators to discover the presence of these tiny, tiny, tiny pieces of matter.

Even though those super tiny atomic particles exist, there are three basic parts of an atom. The parts are the electrons, protons, and neutrons. What are electrons, protons, and neutrons? A picture works best. You have a basic atom. There are three pieces to an atom. There are electrons, protons, and neutrons. That's all you have to remember. Three things! As you know, there are over 100 elements in the periodic table. The thing that makes each of those elements different is the number of electrons, protons, and neutrons. The protons and neutrons are always in the center of the atom. Scientists call the center of the atom the nucleus. The electrons are always found whizzing around the center in areas called orbitals.

You can also see that each piece has either a "+", "-", or a "0." That symbol refers to the charge of the particle. You know when you get a shock from a socket, static electricity, or lightning? Those are all different types of electric charges. There are even charges in tiny particles of matter like atoms. The electron always has a "-" or negative charge. The proton always has a "+" or positive charge. If the charge of an entire atom is "0", that means there are equal numbers of positive and negative pieces, equal numbers of electrons and protons. The third particle is the neutron. It has a neutral charge (a charge of zero).

Biochemistry 3

Structure of MatterAll substances on earth are made of different combinations of the 109 known elements. Oxygen (O), gold (Au) and Iron (Fe) are examples of elements. Notice that each element is identified by an abbreviation (H = hydrogen, Na = sodium, K = potassium)

1. Element_______________________________________________________________________________________________________________________________________

Approximately 25 elements occur in living things. Four of these elements make up 96% of the living matter in your body.

2. Main elements of life:____________________________________________________

Reread the following passage after completing the next page as a refresher of vocab words.In the human body, oxygen & hydrogen exist mainly in the form of water. Carbon’s importance to life starts with its

versatile bonding behavior. Each carbon atom can share pairs of electrons with as many as 4 other atoms. This provides

a stable covalent bond since the electrons are shared equally. The carbons can either form a line that we call a

‘backbone’ or a ring structure. Other atoms such as hydrogen, oxygen, and other elements can bond to the carbons and

form many of the various compounds found in our body! The covalent bonds allows 3-D shapes of organic compounds to

form. Organic compounds are any compound that has one or more carbon molecules in addition to other elements. Some

examples are carbohydrates, proteins, fats, nucleic acids, hormones, & vitamins.

4 College Prep Unit 2:

The word atom comes from the Greek word atomos meaning “indivisible.”

3. Atom= ________________________________________________________________________

Please write the charge below:

Protons: _____

Neutrons: _____

Electrons: _____

Sometimes atoms can lose their electrons or gain extra electrons. This changes the electrical charge of the atom…it is now called an ion.

4. Ion = ________________________________________________________________________

The atoms of most elements interact with one another forming molecules. Molecules can be made up of atoms of the same element (O2) or of different elements (CO2). When atoms form molecules, they either share or donate electrons creating a bond. Bonds contain ENERGY and holds two or more atoms together.

5. Bond = ________________________________________________________________________

6. Covalent bond= __________________________________________________________________

7. Ionic bond= __________________________________________________________________

8. Molecule = __________________________________________________________________

__________________________________________________________________

* Important biological molecules: ____________________________________

A subscript shows the number of atoms present in the molecule. If there is a single capital letter or a capital and lowercase without a subscript, it means that there is only one atom of that element in the molecule. The number of molecules is represented with a number infront of the formula.

Name Use Formula # Atoms # MoleculesSodium chloride Table salt NaClCalcium carbonate Limestone CaCO3

Methane Gas CH4

Hydrochloric acid Fertilizers & dyes 4HClCaffeine Sitmulant C8H10N4O2

Carbon dioxide Soft drinks, atmosphere 3CO2

Biochemistry 5

Structure of Matter ReinforcementComplete the following WITHOUT using your notes…

There are 109 known ____________________________ which are the smallest parts of matter. The four elements that make up 96% of the human body are _____________________________________. The smallest part of an element is an ____________________. A ______________________ holds two or more atoms together forming a _____________________________. Bonds contain ______________________. The subatomic particle that is responsible for bond formation is the ______________________________. If an atom gains an electron, it will have a ___________________________ charge. If an atom loses an electron, it will have a ___________________________ charge. Charged atoms are called _________________.

6 College Prep Unit 2:

Anticipation Guide:Try to place the following words where they belong in the paragraph. HYDROGEN MOLECULES UNEVENLY WEAK

POLAR molecules are __________________________ charged and form

________________________ bonds with other polar molecules. The bond formed between two

polar molecules is called a hydrogen bond. Hydrogen bonds are ________________________

bonds because the attraction does not involve sharing or donating electrons. These bonds exist

between two __________________ rather than between two atoms. Hydrogen bonds play a role in

making the shapes of things such as enzymes, protein and DNA. This is a twisted ladder strand of

DNA – held in that shape by hydrogen bonds. These bonds are broken fairly easily, which is what

allows DNA molecules to replicate, and water to flow.

WATER IS A POLAR MOLECULE!Water forms when 2 hydrogen atoms form covalent bonds with 1 oxygen atom. When this happens, it forms a molecule that looks like Mickey Mouse, with the hydrogens as the ears and the oxygen as the head. Since the negative electons in the hydrogen are being pulled towards the oxygen, the parts away from the oxygen become slightly positve. The oxygen, however, keeps it’s electrons away from the hydrogen, making that part slightly negative. Therefore, the water molecule has two “poles”, a negative and a positive. This causes a water molecule to act like a small magnet, attracting other polar substances such as wood, paper products, and glass.

NONPOLAR molecules are ___________________ charged and do NOT form bonds with

polar molecules.

Biochemistry 7

The Unique Properties of WaterChapter 4.4

1. What percentage of your cells consist of water? ________________________

2. What two qualities of water allow it to do “special things?”

_____________________________________________________________________

TEMPERATURE MODERATION

3. When a substance is heated, how are its molecules affected?

_____________________________________________________________________

4. When water is heated, some of the heat energy is used to

__________________________________________________________________. As are

result, the water undergoes ________________ temperature change than other substances.

5. How does this property affect land areas near oceans and lakes?

_____________________________________________________________________

6. When you sweat, water moderates temperature through ________________________.

7. Heat from the ______________ is used to break ________________ bonds of water,

releasing water molecules into the air. Since the heat is being taken away from the skin, the

result is cooling.

8 College Prep Unit 2:

LOW DENSITY OF ICE

8. In most substances, solids are ____________________ dense than liquids.

9. In water, the solid form (ice) is __________________________ dense than liquid water

because in ice the hydrogen bonds keep the molecules

_________________________________. This causes ice to _____________________.

10. How is this property of water important to living things?

_____________________________________________________________________

WATER’S ABILITY TO DISSOLVE OTHER SUBSTANCES

11. Water is a good solvent because it can

_____________________________________________________________________

12. Water is the main solvent inside all ___________________, in ____________________ and

in ____________________________.

This property of water allows chemical reactions to take place in living things!

Biochemistry 9

The Behavior of Water1. ______________________________________ = The tendency of water molecules to form

hydrogen bonds with other water molecules.

2. ______________________________________ = The tendency of water molecules to form

hydrogen bonds with other polar molecules.

3. Water also exhibits __________________________________________ which results from

both cohesion and adhesion working together creating hydrogen bonds on the surface of any

body of water.

4. Cohesion and adhesion also work together to direct water up

the stem of plants against gravity. This phenomenon is called

_______________________________________.

10 College Prep Unit 2:

+

+

Water is a very important molecule to living things. Answer each set of questions based on your observations.

Water in a beaker and graduated cylinder 1. Observe the water in the beaker and the graduated cylinder. Draw the shape of the water at the top of the beaker

and in the graduated cylinder.

Explain your observations using the terms cohesion, adhesion, polar and hydrogen bonds

Drop Shape on Glass and Wax Paper 1. Observe the water on the wax paper and glass slide. Move each and notice how the water moves. Which

substance, wax or glass, is polar? Which is non-polar? How can you tell?

Capillary Action 1. Observe the chromatography paper with ink on it. Is paper polar or nonpolar? Explain. Is the ink polar or

nonpolar? Explain.

2. Observe the chromatography paper with the crayon on it. Is the crayon polar or nonpolar? Explain.

Water and Oil 1. Observe the beaker of water and oil that has already been set up for you. Which is less dense?

2. Explain the mechanism that causes water molecules and oil molecules to separate from one another including the following terms: polar, nonpolar, hydrogen bond

Density of Ice1. What property of water is being shown in this beaker? Why is this important to living things?

Biochemistry 11

Anticipation Guide: pHPart ADirections: Read each statement and decide whether it is true or false. Write out the word TRUE or

FALSE on the line in front of the statement.

1. __________ pH is a measure of how much acid or base is in a liquid.

2. __________ The pH scale measures from 0-14.

3. __________ Distilled (pure) water has a pH of 1.

4. __________ Bases are between 0 and 7 on the pH scale.

5. __________ Acids contain a high amount of H+ ions.

6. __________ Bases contain a high amount of H+ ions.

7. __________ A buffer controls the pH of a liquid by accepting and donating OH- ions.

8. __________ The pH of your stomach acid is between 2-3.

9. __________ An indicator is a special chemical that changes color with different pH values.

10. __________ Litmus paper will change color when the pH goes past 7.

11. __________ Every step on the pH scale increases or decreases the ions by +10.

Part BNow, read page 12 of your packet and pages 85-86 in your text and correct the eleven statements

above. Then correct the answers on page 13 by rewriting the statements. IF they are false, change them, if they are true, rewrite them the same way.

12 College Prep Unit 2:

ACIDS AND BASES ARE EVERYWHERE

Every liquid you see will probably be either an acid or a base. The only exception would be distilled water. Distilled water is just water. That's it. Most water you drink has ions in it. Those ions in solution make something acidic or basic. In your body there are small compounds called amino acids. Those are acids. In fruits there is something called citric acid. That's an acid, too. But what about baking soda? When you put that in water, it makes a base. Vinegar? Acid.

pH is how much acid or base is in a liquid. Scientists use something called the pH scale to measure how acidic or basic a liquid is. The scale goes from 0 to 14. Distilled water is 7 (right in the middle). Acids are liquids that contain H+ ions. They are found between 0 and 7 on the pH scale. Bases liquids that contain OH- ions. They are found from 7 to 14 on the pH scale. Each step on the scale increases or decreases the ion concentration by ten times. Most of the liquids you find every day have a pH near 7. They are either a little below or a little above that mark. When you start looking at the pH of chemicals, the numbers go to the extremes. If you ever go into a chemistry lab, you could find solutions with a pH of 1 and others with a pH of 14. Those chemicals are very dangerous. There are pH values higher than 14 and lower than 0, but let's just start with 0-14.

There are many important acids and bases in biology. Your stomach has hydrochloric acid (HCl) in it to help break down your food. Hydrocloric acid can be any pH, depending on how it is made. The HCl in your stomach has a pH of 2-3. That is why it burns so much when you vomit. It is also where “acid reflux” gets its name; the acid in your stomach backs up into your esophagus. You also have many buffers in your body; they are chemicals that control the pH level to maintain homeostasis.

pH Indicators are very special chemicals; they will change color if you change the pH (by adding acid or base). Indicators change color at different pH values. Litmus changes at pH 7 but Phenolphthalein changes from pink to colorless at pH 9.

Indicator pH Color in Acid Color in BaseLitmus 7.0 Red BluePhenolphthalein 9.7 Colorless Red // PinkMethyl Orange 3.7 Red YellowBromophenol Blue 4.0 Yellow Blue

Biochemistry 13

Acid alkaline balance in the human body Name: _____________________ http://www.essortment.com/all/acidalkalineba_rkci.htm retrieved 19February2009

Approximately 50 to 60 percent of a human’s body weight is from water. The percentage varies based on several factors. For instance, fat holds very little water while muscle is about 75 to 77 percent water. The obese couch potato may contain 50 percent or less in water weight. On the other hand, a fit muscular person may have 60 to 65 percent of water in body weight. The water in the body can be compared to swimming pool water. Swimming pools are strictly monitored to keep the water at a certain pH balance. The water should not be too acidic nor too alkalitic. The fluid in the human body must stay within normal ranges also. Th normal pH balance in the human body is 7.35 to 7.45, (which is basically neutral). If the pH gets low (acidosis) or high (alkalosis) there will be specific problems that could be life threatening. The water in the human body is further broken down into specific categories. Intracellular fluid (ICF) is water actually contained inside cells. Extracellular fluid (ECF) is water outside the cells. Combined, ICF and ECF equal 60 percent on average of the total body weight. Extracellular fluid is further broken down into interstitial fluid, plasma, bone, connective tissue, and transcellular fluid. Interstitial fluid, primarily located in the lymphatic system, equals about 12 percent of body weight. Plasma, basically the liquid portion of the blood, equals about 4.5 percent of body weight. Connective tissue accounts for about 4.5 percent, with the smallest amount of 1.5 percent being composed of transcellular fluid. The body has several different ways to ensure that the pH balance stays in the normal range of 7.35 to 7.45. These are referred to as buffer systems. Through normal day to day activity in the body, acids are formed as waste products that need to be neutralized or eliminated. Some of the acids are released with CO2 from exhaling; others are excreted via the kidneys. These systems work together in the healthy human body to keep the pH level within normal ranges. If for some reason the buffering systems fail or are hindered, the pH balance will be upset. Either too much or too little of the acids will be neutralized. The causes of this can be as simple as the flu or as complications from trauma, disease or serious illness. Once the body senses the pH is out of kilter, it will attempt to compensate to correct the problem. The conditions for when this happens are known as acidosis or alkalosis. These are further broken down into either metabolic or respiratory in nature. This includes metabolic acidosis, respiratory acidosis, metabolic alkalosis, and respiratory alkalosis.

One of the chief buffers in the blood is bicarbonate, which helps neutralize acids. This is like taking an antacid for heartburn. Metabolic acidosis is caused by the loss of bicarbonates or an increased production of acids. Some causes for bicarbonate loss can be severe diarrhea, drug intoxication or abuse, or severe illness. Some causes for increased acid production include serious illness or injuries, and decreased blood flow. An example of this is when you leg "falls asleep". Blood flow is decreased allowing acid to build up. Upon standing, blood flow is restored. The tingly pin and needle sensation is caused from the excess acid in the tissues. The acid is then neutralized resulting in the pin and needle sensation subsiding.

Respiratory acidosis is usually caused by insufficient respirations or air exchange. This can be caused by head or chest trauma and respiratory diseases such as emphysema. In cases of emphysema, the lungs cannot perform normally due to an increase of dead air space. Acidosis develops slowly over a period of time. These are usually treated with bronchodilators and small amounts of oxygen to increase air exchange in the lungs. With a severe decrease in breathing caused by trauma or respiratory arrest, the amount of acid quickly increases. Adequate measures need to be taken to treat the cause. Metabolic alkalosis occurs when too much acid is excreted from the body. This can be caused by eliminating too much fluid by frequent urination, by excessive vomiting, or various diseases. If the body becomes too alkalitic, the nervous system and the heart can be affected. The heart may speed up and become irritable while breathing slows in order to compensate. By slowing respirations, less acid is "blown off" from the lungs. This is in contrast to hyperventilation often seen in metabolic acidosis. Metabolic alkalosis is treated based on findings from laboratory tests.

Respiratory alkalosis is caused when the body is stressed. Some of the causes include shock, sepsis, trauma and asthma. Too much acid is "blown off" from increased respirations or hyperventilation. In cases of hyperventilation of psychogenic origin, the increase in alkalosis causes the tingly sensation around the mouth and in the fingertips. Because of hyperventilation, blood is slowed to the brain so the respiratory center tells the body to increase respirations. In psychogenic hyperventilation, the symptoms of tingling and feeling of smothering continue to worsen. Treatment of respiratory alkalosis is basically to treat the cause. This can include the simple paper bag method for psychogenic hyperventilation, to using sedation to slow respiration. By slowing the breathing, the blood flow is returned to the brain. This allows the respiratory center to regulate itself and get the levels back to normal. Interesting, in psychogenic hyperventilation, if the person continues to hyperventilate, they often pass out. Respirations slow and return to normal, in turn the body gets back to normal.

Please answer the following questions below and underline the answers in the above reading.

1. How can water in our body be compared to swimming pools?

14 College Prep Unit 2:

2. What is acidosis?

3. What is alkalosis?

4. How does the body ensure that our pH stays between 7.35 & 7.45?

5. What are 2 ways the body releases the acids that build up from day to day activities?

6. What is the primary buffer in the blood system?

7. What are 3 causes for acidosis to occur in our bodies?

8. Explain what occurs when our legs ‘fall asleep,’ using the word acidosis, acid, and blood flow.

9. What are 3 causes for alkalosis to occur in our bodies?

10. How can our bodies be affected by alkalosis?

Biochemistry 15

The Concept of pH: RECAPAcid = _______________________________________________________________________________________

Base = _______________________________________________________________________________________

Indicator =________________________________________________________________________________

Sketch a pH scale

pH scale_______________________________________________________________________________________

pH in the Body

Blood: ________________ Cells: ___________________ Stomach: ______________

Buffer =_______________________________________________________________________________________

Alkalosis = _________________________________________________________________________________

Acidosis = _______________________________________________________________________________

Acidosis can be caused by …1) Breakdown of sugar produces ___________________________ as a waste product which reacts with water to

form _____________________________________________. Older people with poor circulation cannot get rid

of this substance fast enough and therefore experience acidosis.

2) When working out, if oxygen can’t get to cell fast enough, the cells start breaking down sugar without using

oxygen. This can occur in _______________________ tissue and results in

_______________________________ being produced.

3) Breakdown of fats releases acidic __________________________________. When fats are broken down

quickly, these molecules cannot decompose fast enough and therefore build up in the body.

16 College Prep Unit 2:

Section 5.1: Carbon Compounds1. Distinguish between organic and inorganic molecules. Give some examples.

2. How many electrons does carbon have? How does this affect its bonding ability?

3. What shapes can carbon molecules make?

4. Why are functional groups important in organic compounds? Name four common functional groups and their structural formulas. What does Hydrophilic mean and how does it pertain to functional groups?

5. How are monomers, polymers and macromolecules related to one another?

6. What are the four major categories of macromolecules (large molecules)?

7. Explain a dehydration (condensation) reaction and hydrolysis reaction.

Section 5.2: Carbon1. What are carbohydrates (include element ratios) and list 3 different types.

2. What are the 3 most common monosaccharides? Where are they found? What are they used for?

Biochemistry 17

3. Define disaccharide and give an example. What type of reaction (from question 7) is responsible for making them?

4. Define polysaccharide and give 3 specific examples along with their functions. Describe them in terms of monomers and polymers.

5. Are carbohydrates hydrophilic or hydrophobic? Explain

Section 5.3: Lipids1. What is a lipid? How are they different than carbohydrates? What are they used for?

2. Describe a fat. Distinguish between hydrophobic, hydrophilic, saturated and unsaturated as they pertain to fatty acids.

3. How are steroids different than other lipids? Give some examples.

Section 5.4: Proteins1. What makes up a protein? Is it a monomer or a polymer? Describe some of their functions in the body.

2. What are amino acids? How are they similar? How are they different? (Draw this)

18 College Prep Unit 2:

3. Define polypeptide and how they are created.

4. How does the theme of Form and Function relate to proteins? Give examples.

Biochemistry 19

Carbon-Based Macromolecules

Polymer Carbohydrates Proteins Lipids Nucleic Acids

Elements

Monomer

Polymer

Functions

20 College Prep Unit 2:

Enzymes – Organic Catalysts

Chemical reactions make life possible. Hundreds of chemical reactions are involved in a process as simple as digesting a chocolate bar. If these chemical reactions proceeded too slowly, not only would the chocolate bar remain in the stomach for a long time, but the ordinary activities of life would come to a halt as well. Since this is not the case, some substances in the body must be responsible for speeding up the process.

A substance that speeds up the rate of a chemical reaction is called a catalyst. Catalysts are NOT changed by the reactions they promote, and therefore they are not used up during the reaction – they can be used again and again. Catalysts work by lowering the amount of energy, called activation energy, needed to start a chemical reaction. They do this by either bringing substances together so less energy is needed to join them or weakening the bonds between atoms or molecules so less energy is needed to break them apart. Chemists often seek catalysts that will speed up reactions important to industry. Living organisms have done the industrial chemist one better - they contain their own special catalysts, which are known as enzymes. Nonliving substances that speed up chemical reactions are called inorganic catalysts. Catalysts of, relating to or derived from living organisms are called organic catalysts.1. Define catalyst:

___________________________________________________________________________________________________________________________________

2. How do catalysts work?

______________________________________________________________________________________________________________________________

3. What is the difference between inorganic and organic substances?__________________________________________________________________________________________________________________________________________________

Most enzymes are proteins that speed up the rate of a chemical reaction. Simple cells may have as many as 2000 different enzymes, each one catalyzing a different reaction. A single enzyme molecule can catalyze thousands of substrate reactions each second. Thus, only small amounts of any enzyme need to be present in a cell at any given time. An enzyme may accelerate a reaction by 10,000,000,000 times!!!! Thus a reaction that might take as long as 1500 years without an enzyme can be completed in just 5 seconds!

4. What is an enzyme?_________________________________________________________________________________________________________________________________

Biochemistry 21

Enzymes speed up a reaction by binding to the reactants, which are the substances that enter into a chemical reaction. The reactants affected by an enzyme are known as substrates. Substrates bind to enzymes at a region known as the active site. When an enzyme is interacting with its substrate, they form a temporary union called the enzyme-substrate complex. Enzymes not only break substrates apart, they also can join two substrates together! The substance(s) that result from a chemical reaction are called the products.

5. CIRCLE the word reactant and underline its definition. 6. CIRCLE the word substrate and underline its definition.7. LABEL the substrate (reactant) in the graphic below.8. LABEL the enzyme-substrate complex below.9. CIRCLE the word product and underline its definition. LABEL the products.10.LABEL the enzyme.

Enzymes are very specific. A particular enzyme can catalyze only one particular chemical reaction involving specific substrates. Scientists theorize that this has something to do with the shape of an enzyme’s active site. In fact, the fit between an enzyme’s active site and its substrate is often compared to that of a lock and a key. This phenomenon is called enzyme specificity.

11.How is shape important to an enzyme’s function?______________________________________________________________________________________________________________________________________________

12.Describe enzyme specificity in your own words:______________________________________________________________________________________________________________________________________________

It will help you to remember that the names of enzymes usually end with the suffix -ase. The rest of the name is often derived from the name of the substrate. For example, enzymes that break down proteins are called proteases. Enzymes that break down lipids are called lipases.

13.Circle the substances that is NOT an enzyme from the list below.

protease, peroxidase, ethanol, catalase, amylase

22 College Prep Unit 2:

Macromolecules POGIL

Carbon bonds: All organic compounds contain carbon. The outer shell of the carbon atom contains four electrons. In organic compounds, each carbon atom fills its outer shell by sharing four pairs of electrons with other atoms. That is, each carbon atom forms four covalent bonds. Some of these bonds may form between one carbon atom and another. A framework of carbon-to-carbon bonds forms the basic structure in most organic compounds. A carbon atom may be joined to another atom by a single bond, a double bond, or a triple bond.

Question: The following structural formulas show three different compounds of carbon and hydrogen.Below each structural formula, write the chemical formula for that compound. Label the doubleand triple bonds in these structures.

_______________________________ _______________________________ _______________________________

Carbohydrates: Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen. The proportion of hydrogen atoms to oxygen atoms in carbohydrates is the same as in water—two hydrogens to one oxygen. There are three basic types of carbohydrates: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides: Monosaccharides, or simple sugars, are the least complicated carbohydrates. In biology the three most common simple sugars are glucose, galactose, and fructose. These three sugars all have the same chemical formula (C6H1206), but their atoms are arranged differently (see below).

Questions:1. In what way do glucose and galactose differ from each other? Circle the parts of both compounds that show this

difference.

2. The chemical formula for all monosaccharides is _________________________________.

Biochemistry 23

Dehydration Synthesis and Hydrolysis: Carbohydrates, proteins, and lipids are all synthesized and broken down by the same types of reactions. In dehydration synthesis, a hydrogen ion (H+) from one molecule joins with a hydroxyl group (OH-) from another molecule to form water (H2O), leaving the two molecules bonded to the same oxygen atom. For example, when two molecules of glucose are joined by dehydration synthesis, they form maltose and water (see below).

In hydrolysis, complex organic molecules are broken down by the addition of the components of water - H+ and OH-. Both dehydration synthesis and hydrolysis require certain conditions of pH and temperature and the presence of particular enzymes.

1. In the space below, write the formula for the hydrolysis of maltose. (The reaction is the reverse of the dehydration synthesis of maltose.)

2. What are the products of the hydrolysis of maltose?

3. In what life process does hydrolysis occur?

Disaccharides: When two monosaccharides combine, they form a disaccharide. A disaccharide can consist either of two molecules of the same simple sugar combined or two different simple sugars combined. Some common disaccharides are maltose (or malt sugar), sucrose (or table sugar), and lactose (milk sugar). Maltose is made up of 2 glucose subunits. Sucrose is made up of glucose and fructose. Lactose is made up of glucose and galactose.

Questions:1. Name the monosaccharides that make up the following disaccharides:

a. maltose:b. sucrose:c. lactose:

2. What is the chemical formula for maltose, sucrose, and lactose? (Hint: Disaccharides = (2 x monosaccharide) – H2O)

3. Why is the chemical formula for disaccharides not two times that of the monosaccharides?

4. What are the common names for sucrose and lactose?

24 College Prep Unit 2:

Polysaccharides and Polymers: The most complex carbohydrates are the polysaccharides, which are made up of long chains of monosaccharides (or glucose-like units). Starch, cellulose, and glycogen are polysaccharides. Large molecules made up of chains of repeating units are called polymers. Polysaccharides, such as the ones mentioned above are polymers.

Questions:1. What substance is the repeating unit that makes up starch, cellulose, and glycogen?

2. Starch, cellulose, and glycogen are all made up of the same repeating unit. In what way do these three substances differ from one another?

3. Name another type of compound (beside polysaccharides) that fits the definition of a polymer,

Lipids: Lipids are a group of organic compounds that include fats, oils, waxes, and related substances. Lipids are composed of carbon, hydrogen, and oxygen, but there is no definite ratio of hydrogen to oxygen atoms in lipids as there is in carbohydrates. Simple lipids, which are the most common type, are made up of three fatty acid (CnH2nCOOH) molecules and one glycerol (C3H8O3) molecule.

Questions:1. Label each of the components in the equation below.

_________________________ _____________________________ ___________________________________ ____________

2. What type of reaction is shown in the equation?

3. What type of compound is glycerol?

4. Write the chemical formula for fatty acids.

5. What is the difference between a saturated and an unsaturated fatty acid?

Proteins: Proteins are the most abundant type of organic compound in cells. They are made up of many amino acid molecules bonded together. Proteins, which may be very large and complex, play a wide variety of roles in the cell. Some are structural, others are hormones, neurohumors, enzymes, or pigments.

Amino acids are made up of carbon, hydrogen, oxygen, and nitrogen; some also contain sulfur. Amino acids are bonded

Biochemistry 25

together to form proteins by dehydration synthesis. The type of bond formed between amino acids is called a peptide bond. It involves a carboxyl group from one molecule and an amino group from the other.

Questions:1. Name three foods that are high in protein.2. Below is the general formula for an amino acid. Circle the amino group and the carboxyl group.

3. Using the general formula for amino acids, in the space below show the formation of a peptide bond.

4. What does the R represent in the general formula for amino acids?

Enzymes: Enzymes are proteins that act as catalysts in living cells. A catalyst increases the rate of a chemical reaction, allowing it to proceed rapidly when it would otherwise occur only very slowly. Enzymes are highly specific in their catalytic activity. The specificity of enzyme action is the result of a"lock-and-key" arrangement in which the enzyme and the substance it reacts with (the substrate) join together at the active site to form an enzyme-substrate complex. When the reaction is completed, the enzyme and the newly formed reaction products separate, leaving the enzyme unchanged. Enzymes are highly efficient catalysts, and only small quantities are needed to catalyze the reaction of relatively large amounts of materials. Each enzyme has an optimum range of temperature and pH at which it operates most efficiently.

Questions:1. Is an enzyme "used up" by the reaction it catalyzes? Explain.

2. In what way does an enzyme affect the reaction it catalyzes? How does the enzyme produce this effect?

3. What is meant by enzyme specificity?

4. What is the active site of an enzyme?

5. The substance with which an enzyme reacts is its ______________________________.

6. Could life as we know it exist without enzymes? Explain.

26 College Prep Unit 2:

Questions 7-10 are based on the graphs above.7. According to graph A, at what temperature is enzyme activity the greatest?

8. According to graph B, what is the optimum pH for pepsin? As pH increases above that point, what happens to enzyme activity?

9. According to graph C, how does increasing enzyme concentration affect the rate of enzymeaction when the substrate concentration remains constant?

10. According to graph D, how does increasing substrate concentration affect the rate of enzymeaction when enzyme concentration remains constant?

Nucleic Acids: There are two types of nucleic acids found in living organisms—DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Both are giant molecules of high molecular weight, consisting of a series of nucleotide units bonded together. Each nucleotide consists of a five-carbon sugar bonded to a nitrogen base and a phosphate group. DNA contains the hereditary information and is stored in the nucleus, while RNA functions in protein synthesis.

Questions:1. What are the three basic components of the nucleotides that make up nucleic acids?

2. Where is DNA found in the cell?

3. Describe the basic functions of DNA.

4. Describe the basic functions of RNA.

Biochemistry 27

Extension Questions:1. Metabolism is the collective term used to describe all the chemical reactions taking place inside living organisms.

Why is water so important for metabolic reactions?

2. We store excess food in our body either in the form of carbohydrates (in muscles and the liver) or as fat (adipose tissue). When our body needs additional energy it uses the carbohydrate source first as a source of “quick” energy, then the fat. Why do you think carbohydrates are used as a source of quick energy rather than fat? Use complete sentences and scientific terminology in your response.

3. Look at the two types of fatty acids below, saturated and unsaturated. What is the difference between the two?

4. Saturated fats are solid fats, like the animal fats lard and butter, whereas unsaturated fats are more fluid and form oils, such as vegetable oil. Trans fats are plant oils that are artificially solidified to make them suitable for baking purposes. In recent years trans fats have been associated with negative health issues and are not as widely used. Explain in simple molecular terms what would have to be done to a plant oil to transform it to a trans fat.

28 College Prep Unit 2:

Biochemistry 29

Investigating The Action of PeroxidaseName: _________________________ ______ / 50 points

Observation: Enzymes speed up chemical reactions.

Questions: a) What is the basic action of the enzyme peroxidase in living organisms?b) Do enzymes change during a normal chemical reaction or are they reusable?c) Does a particular enzyme react with all substances?

Research: Refer to the Enzyme NOTES during this lab!In this lab, you will study an enzyme that is found in the cells of many living tissues (including chicken liver!). The name of the enzyme is peroxidase; it speeds up a reaction that breaks down hydrogen peroxide, a toxic chemical into water and oxygen. This reaction is important to cells because hydrogen peroxide (H2O2) is toxic but is produced as a byproduct of many normal cellular reactions. If cells did not break down the hydrogen peroxide, they would be poisoned and die.

a) What is the overall function of an enzyme? (1 pt)

_________________________________________________________________________

_________________________________________________________________________

Hypotheses:Propose a hypothesis for each of the questions asked in the beginning of the lab. Each hypothesis should include reference to both the independent and dependent variables. It should state what will happen. Be certain to use "if" and "then". (2 pts each = 6 pts)

a. _________________________________________________________________________

_________________________________________________________________________

b. _________________________________________________________________________

_________________________________________________________________________

c. _________________________________________________________________________

_________________________________________________________________________

Materials:3% hydrogen peroxidefresh livertest tubestest-tube holder

Methods:

30 College Prep Unit 2:

PART A – THE BASIC ACTION OF PEROXIDASE1. Pour about 1 cm of hydrogen peroxide into a clean test tube.2. Using forceps and scissors, cut off a SMALL (pea-sized) piece of liver and add it to the test

tube.3. Record ALL observations in results section a. Observe for at least 5 minutes. Describe

what is happening in your test tube.4. When the reaction is COMPLETELY finished, move onto part B. 5. While you are waiting, do part C.

PART B – ARE ENZYMES REUSABLE?6. Pour off the liquid into another test tube marked B. Leave the liver in test tube A.7. Add another SMALL (pea-sized) piece of liver to tube B. Record results section B.8. Add about 1 cm of hydrogen peroxide to the liver remaining in test tube A. Describe what

you observe in results section B.9. Clean both test tubes well.

PART C – CAN PEROXIDASE REACT WITH OTHER SUBSTANCES?10.Carbon dioxide is also produced as a result of cellular reactions. Obtain a test tube and fill it

with 1 cm of water.11.Blow through a straw into the water for 30 seconds to accumulate carbon dioxide. 12.Add a small piece of liver to see if the liver will react to the carbon dioxide and record your

results in results section C.13.Then, in a clean test tube, combine alcohol and liver. Does peroxidase react with alcohol?

Record your results.14.Before leaving the lab, clean up all your materials, clean test tubes, wipe area and wash

hands thoroughly!!! Failure to complete this part will result in lost points!!

Results:A

B TUBE A TUBE B

C

Biochemistry 31

INDIVIDUAL Analysis Questions: (33 pts) For this lab we will be answering analysis questions INSTEAD of writing a discussion. Answer using COMPLETE sentences when applicable. EXPLAIN your results

CONCISELY! Please do not use personal pronouns (I, you, we, our group) in your answers. Complete these by yourself!!!!

1. (1 pt) What was the OVERALL GENERAL purpose of this lab – parts A, B and C?

______________________________________________________________________

2. (2 pts) What is an enzyme and generally how does it work?

______________________________________________________________________

______________________________________________________________________

3. (1 pt) What was the ENZYME used in this lab? _________________________________

4. (1 pt) What was the SOURCE of the enzyme? _________________________________

5. (1 pt) What was the SUBSTRATE? _________________________________

6. (2 pts) What does this particular enzyme do specifically? Why does this benefit us? (See

background section). _________________________________________________

_________________________________________________________________________

_________________________________________________________________________

7. (1 pt) What was the purpose for part A? ______________________________________

_________________________________________________________________________

8. (2 pts) Analyze your hypothesis for part A. Was it correct or not and explain.

_________________________________________________________________________

_________________________________________________________________________

9. (1 pt) What gas is released in part A? ______________________________________

10. (1 pt) What was the liquid left after the reaction in part A? ______________________

11. (1 pt) What was the purpose for part B? ______________________________________

_________________________________________________________________________

_________________________________________________________________________

12. (2 pts) Analyze your hypothesis for part B. Was it correct? Why or why not?

_________________________________________________________________________

_________________________________________________________________________

_________________________________________________________________________

_________________________________________________________________________

32 College Prep Unit 2:

(4 pts) Are enzymes reusable OR do they change during a chemical reaction? Incorporate

your observations as you answer the question.

_________________________________________________________________________

_________________________________________________________________________

_________________________________________________________________________

13. (2 pts) Explain why there was no reaction in the tube with the new liver and the old

hydrogen peroxide. _____________________________________________________

________________________________________________________________________

________________________________________________________________________

14. (1 pt) What was the purpose for part C? _____________________________________

_____________________________________________________________________

_____________________________________________________________________

15. (2 pts) Analyze your hypothesis for part C. Was it correct or incorrect and why.

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

16. (4 pts) Based on your observations in part C, does peroxidase react with other

substances or just hydrogen peroxide? Explain in detail using information from your

notes. Incorporate results.

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

17. (2 pts) Name and define the term that is used to describe the phenomenon you just

explained in #16. Hint: It's in your Enzyme notes! _____________________

________________________________________________________________________

________________________________________________________________________

Biochemistry 33

ENZYME LAB EXTENSIONObjective: Investigate how environmental changes affect the enzyme functions.

Procedure:1. Choose one slip per group from the front desk. That slip will give one factor that you

must change for the enzyme.2. Design an experiment to test how the environmental change (IV) you selected will affect

the action of the enzyme.3. Write a separate report including your hypothesis, procedure, and a one paragraph

conclusion describing the lab using the following terms:Form and function, shape, denaturation, pH or heat, enzyme activity.

Use the space below and on the back to create a rough draft of your experiment and report.Independent Variable: _____________________________________________Dependant Variable: _____________________________________________Hypothesis: _________________________________________________________

_________________________________________________________What materials will you need?

Use the back of this paper to write your rough procedure.

Biochemistry Review- CP Bio

34 College Prep Unit 2:

Directions: These concepts are important for your test. Use a separate sheet of paper to complete this review.

I. Matter

a. What is the Atomic number of N? b. Give the number of protons, neutrons, and electrons.c. Give the number of electrons in outer shell.d. Differentiate Ionic vs. Covalent bonding using a Venn diagram.

II. Water

a. Define polarity. Draw a water molecule and show its polarity.b. Compare and contrast cohesion vs adhesion.c. Compare and contrast capillary action and transpirationd. List 3 unique properties of water and describe how they allow for life.

III. pHa. Differentiate between acids and bases.

a. What type of ions are in each?b. pH scale- What does it go from and how much is each step?c. Define buffers.

IV. Macromolecules- name the building blocks (monomers) as well as any special propertiesa. Carbohydratesb. Lipidsc. Proteinsd. Nucleic acidse. Vocab: glucose, amino acids, saturated, nonsaturated, fatty acid chains, glycerol,

nucleotides.

V. Enzymesa. What is the difference between “catalyst” and “enzyme”?b. Describe enzyme specificity.c. What are enzymes made of?d. Why does form and function matter in enzymes?

i. What happens to enzymes if they are heated or if the pH is changed?

Biochemistry 35

7 N Nitrogen

14.012

Unit II Biochemistry1. Label all seven parts of following diagram of water. Show the relative charges.

a. Why are these molecules considered polar?

b. What is unique about the dotted line?

c. List and describe 4 reasons this molecule is important to life.

a.

b.

c.

d.

Macromolecules:1. What element do all macromolecules share that make them “organic”? Why is this element so

important?

36 College Prep Unit 2:

2. Identify each of the following macromolecules and describe important characteristics of each.

Enzymes

1. The above diagram shows an enzyme at work. What is an enzyme?

2. What would happen if the pH or temperature of the environment above were to change? Be specific using key words.

Biochemistry 37