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Animation

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Biochemistry

Biochemistry = the chemistry of life

Elements - These are single substances which cannot be broken down any more. there are 110 different elements that are known to man.

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Biochemistry

The four most common elements in living things are:

1) Carbon

2) Hydrogen

3) Oxygen

4) Nitrogen

Black = Carbon; Yellow = Hydrogen; Red = Oxygen

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Biochemistry

Each element contains atoms. Each atom has a structure which is called the atomic structure. The atomic structureincludes:

1) Protons - Positively charged particles

2) Neutrons - Neutral (uncharged) particles

3) Electrons - Negativelycharged particles

Electrons

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Each element has a specific number of electrons which are distinctly arranged in the shell

First shell - 2 electronsSecond shell - 8 electrons

A stable atom will have8 electrons in the outer shell (or, if there's only one shell, a stable atom would have 2 electrons)

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Is this a stable atom? Why or why not?

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Biochemistry

Compounds - These are two or more elements combined.These elements are bonded together. There are two typesof bonds which may be used to link elements together.

Molecular modelof water. It is a compound becausethere are three elements bondedtogether.

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Ionic Bonding - The atoms transfer the electrons. The atoms acquire a charge and then become ions.

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Covalent Bonding - The elements share atoms toform a molecule.

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Formula - A formula shows the ratio of elements, or the structure of the compounds. There are two types of formulas:

1) Empirical Formula - This shows the symbols of theelements, followed by a numerical subscript whichidentifies the ratio of the atoms.

Ex: H2O means there are two hydrogen atoms and one oxygen atom (if nothing iswritten after the letter, it is understood thatthere is only one there).

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Biochemistry

H2O2 = two hydrogen and two oxygen

How many of each is in a molecule of sugar? C6H12O6

6 Carbon12 Hydrogen6 Oxygen

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Structural Formula - This formula shows how the atomsare arranged (its structure!!). For example, sugarC6H12O6 looks like this.

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Biochemistry

Glucose and fructose have the same molecular formulaC6 H12O6, but they have different structural formulas

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Inorganic Compounds - These do not contain both carbon and hydrogen. They may contain one or the other,but they don't contain both. Examples of inorganic compounds:

Water - H2OSalts - NaCl

Acids - HCl

Bases - NaOH

*** Water is essential for life functions of cells.It is a solvent for other substances to dissolve in.Most chemical reactions occur only in water solutions

CO2

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Biochemistry

Organic compounds - These are formed in nature byactivities of living organisms. ***They always containboth carbon and hydrogen.

Carbon is special because it can form 4 covalent bonds while most others can only form 2 bonds. Therefore, it can form long chains and rings.

Count the number of bonds to carbon

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Biochemistry

There are 4 major kinds of organic compounds found in living things:

1) Carbohydrates 2) Proteins

3) Lipids (Fats) 4) Nucleic Acids

Carbohydrates - These are compounds that are made up of C, H & O.

The elements are usually in a ratio of2(H) : 1(O)

Ex: C6H12O6

12:6 = 2:1

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Biochemistry

There are 3 types of carbohydrates: A) Monosaccharides Mono = 1B) Disaccharides Di = 2C) Polysaccharides Poly = 3 or more

A) Monosaccharides These are simple sugars. Theyusually end in the letters "ose" - glucose, fructose, galactose etc. These have the molecular formula ofC6H12O6

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B) Disaccharides - These are carbohydrates made up of2 simple sugars put together.

Ex: Maltose, Sucrose, Lactose

Sucroseis two glucosemoleculesput together

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Biochemistry

If you put two glucose moleculestogether (C6H12O6), how many C'sH's and O's should you have

Actually, the formula isC12H22O11

Why?

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Biochemistry

2 hydrogen and 1 oxygen are missing - in order to putthese two molecules together, a water molecule mustbe taken out. This process is called dehydration synthesis

(dehydration = lose water)(synthesis = put together)

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Biochemistry

Animation of dehydration synthesis and hydrolysis

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+

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=

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Biochemistry

Hydrolysis - This is the opposite process of dehydrationsynthesis. It is when you add water to a compound andthe compounds separate (break down) Hydro = waterLysis = break up

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Biochemistry

Polysaccharaides: These are carbohydrates madeup of many sugar units synthesized into long chains calledpolymers. The units may be the same, or they maybe different. Examples: starches, cellulose etc.

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Biochemistry

Proteins - Proteins contain C, H, O, and N. They mayalso contain sulfur. They are used to make cellstructures such as the membrane as well as other things

*** All enzymes are proteins!!

*** Many hormones are proteins

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Biochemistry

The units which make up proteins are called aminoacids. You will learn this also as "the building blocks of proteins" An amino acid has two distinctparts: 1) an amino group 2) a carboxyl group

H N

H

- C

O

OHAmino Group

Carboxyl Group COOH

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Every amino acid has both of these groups (amino groupand carboxyl group). However, each amino acid is different by what is between the two groups. The different group in the middle vary, and are representedby the letter "R"

Biochemistry

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A protein consists of many of these amino acid unitslinked together. They are linked together (synthesized)by the process of???????? __________________

Dehydration Synthesis

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Dehydration Synthesis of a protein

Dipeptide (AKA: Protein)

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Polypeptide (AKA: Protein)

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A protein with many amino acids linked together AKA: Polypeptide

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A protein has 1 or more chains of amino acids. They maybe folded, twisted or coiled.

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Lipids - These are fats and oils (ask me about a fat lip)Lipids are made of C, H< O, but are in a different ratiothan carbohydrates.

The H:O ratio is greater than 2:1 lipids are used for:

1) Stored Energy2) Cell Structures (cell membranes)

3) Cushioning Organs

C12H24O

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24:212:1H:O Ratio Carbohydrate Lipid

2:1 >2:1

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A lipid consists of 3 fatty acids and 1 glycerol

1glycerol

3 fattyacids

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A lipid is made by the process of dehydration synthesisof 3 fatty acids and 1 glycerol molecule.

Fluid-MosaicModelof Cell Membrane

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Biochemistry

Enzymes - ALL enzymes are proteins!!!

Enzymes control chemical reactions. They help the reactions to occur, but they are not changed or used up in the reaction!!!

Therefore, they can be used over and over again (although,eventually, they do break down (disintegrate) over time).

***Enzymes are classified as catalysts.

Catalysts are substances that increase the rate of areaction, but are not changed.

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Biochemistry

Structure of Enzymes:

1) They are proteins - so they are made up of? ____

2) They may have a non-protein coat called a co-enzymeThe coenzyme helps the enzyme function properly and without it, some enzymes may not be able to function atall. Vitamins act as coenzymes.

3) Enzymes have an active site. This is where enzymeaction occurs. The enzymes are usually bigger thanthe molecules that they act upon.

Amino acids!!

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Biochemistry

4) Enzyme-substrate complex - The enzyme forms a temporary association with the substances whose reaction it controls.

ActiveSite

The substance actedupon is called the substrate

The point where contactis made is called the active site

After the reaction is over, theenzyme separates from the substrateand may be used elsewhere.

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Which is the enzyme and which is the substrate? How do youknow? What kind of reaction is this?

The enzyme does not get changed inthis reaction - therefore it is the greenone. Another clue is that it is bigger than the substrate.

This is a hydrolysis reaction because the substrate is being broken down

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Biochemistry"Lock and Key" Model - A lock has a specific shape. Only one specific key willopen that lock. This model is used to describe howenzymes work - their shape has to fit the substrate, otherwise, the enzyme will not work on the substrate.

Notice how theyfit together, like a lockand a key

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Hydrolysis with enzymeaction

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Dehydrationsynthesis ofproduct withuse of anenzyme

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Dehydration synthesis of a product with enzyme

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6) Replacement of Enzymes Enzymes are only around for a limited time because theydo decompose at some point. Therefore, organismsmust synthesize enzymes continuously. The DNA of thecell has the "blueprint" for making enzymes.

7) Name of enzymes:Enzymes end in the letters "ASE" (KNOW THIS!!!)They are usually named after the substrate that it acts upon

Ex: Maltase works on maltoseLipase works on lipids

This is not always true - salivary amylase works oncarbohydrates

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Biochemistry

Chemical Nature of Enzymes

1) Rate of enzyme action

The rate varies with conditions in the cellular environment:

There are 3 factors that affect the rate of enzyme actions

a) pH level (acidic or basic) b) Temperature

c) How much (concentration) of enzyme OR substrate is available.

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Biochemistry

a) pH. pH is measured on a scale of 0-14. The lowend is acidic. The high end is basic. 7 is neutral (middle)

0-1 2 3 4 5 6 (7) 8 9 10 11 12 13 14stronglyacidic

moder-atelyacidic

slightlyacidic

neutral slightlybasic

moderatelybasic

stronglybasic

How to remember if a pH is acidic or basic: go from left to rightwhen you read - low numbers on left, high numbers on rightAlphabet: "A" is left of "B" - low numbers are acidic, high numbers are basic

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Biology

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Biochemistry

Each enzyme acts most effectively within a certain pH range

Ex: Pepsin (found in your stomach) works best in acidic conditions. Your stomach is very acidic. Would pepsinwork in your mouth?

B) TemperatureThe rate of the reaction is generally slow at low temperatures.As the temperature increases, so does the rate of the reaction,but only up to a point!! If the temperature gets too high,then the shape of the enzyme changes and no longer functions.

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Biochemistry

When an enzyme's shape is changed due to high temperatures, it is said to be denatured. They can'tfit into the substrate any more.

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Biochemistry

**** Human enzymes become denatured at temperaturesnear 400 C which is a few degrees above body temperatureHuman body temperature is 370 C

C) Relative amount (aka: concentration) of enzyme or substrate

The rate of the enzyme activity will increase as the amount of substrate increases, but only up to a point.The rate levels off as more substrate is added (becauseyou only have so much enzyme available to work on thesubstrate)

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Cellular Respiration

Cellular respiration is the process where chemical bond energy in food is converted to a form of useable energy.

** Chemical energy is always called ATP (which stands forAdenosine Triphosphate). Tri = 3 (3 phosphates)

ATP is released by the process of hydrolysis

The reaction is controlled by the enzyme "ATP-ase"

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H2O + ATP ATP-ase ADP + Energy

This formula may be reversed (that is why there aretwo arrows in different directions)

The arrow pointing to the right is ?Hydrolysis

The arrow pointing to the left is?Dehydration synthesis

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Biochemistry

There are 2 types of cellular respiration:

1) Aerobic Respiration - Free oxygen is used

2) Anaerobic Respiration - Free oxygen is not used

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Aerobic Respiration

C6H12O

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6 H2O

+ 6 CO2

+ 36 ATP

Glucose is broken down into CO2 and H2OBond energy is released gradually. Why?

Energy released too quickly would be too muchfor the cell to handle.

Usually 36 molecules of ATP is released for every moleculeof glucose used. 36 ATP is very important - remember it!!

Enzymes+ 6O2

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Aerobic Respiration

This equation is balanced because all of the numbers on theleft of the arrow equal the numbers on the right of the arrow

C6H12O6 + 6 O2 --------> 6 H2O + 6 CO2

C's on left = ____?H's on left = ____?O's on left = ____?

C's on right = _____?H's on right = _____?O's on right = _____?

61218

61218

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Aerobic Respiration

There are 2 phases of aerobic respiration:

1) The first phase is anaerobic (no oxygen is present)It occurs in the cytoplasm just outside of the mitochondria. When glucose is broken down, it's called glycolysis

Glucose -----------> Pyruvic acid + 2 ATP

is broken

down into

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Aerobic Respiration

2) The second phase is aerobic (oxygen present)

• Pyruvic acid enters the mitochondria• Pyruvic acid is oxidized (loses H atoms)• 34 Molecules of ATP are produced• CO2 and H2O are produced as waste products• There is a net gain of 36 molecules of ATP (2 from phase 1 and 34 from phase 2).

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Aerobic Respiration

Glucose + 2 ATP -------> 2 Pyruvic acid + 2 ATP (Phase 1) (Cytoplasm)

2 Pyruvic acid + O2 ---------> CO2 + H2O + 34 ATP (Phase 2) (Mitochondria)

Net output : 36 molecules of ATP per molecule of glucose

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Anaerobic Respiration

Anaerobic Respiration (AKA: Fermentation) is donewithout free oxygen present.

Organisms that carry out anaerobic respiration:

Yeast Bacteria Your muscle cells (sometimes)

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Anaerobic Respiration

The end products of anaerobic respiration vary depending on the type of organism that is carryingout the anaerobic respiration!!!!

Yeast:

Glucose ----------> 2 Alcohol + 2 CO2 + 2 ATP

Bacteria & Muscle Cells

Glucose --------> 2 Lactic Acid + 2 ATP

CO2 is what makes the dough rise!!!

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Aerobic Vs. Anaerobic

Aerobic Anaerobic

36 ATP Produced 2 ATP Produced

Oxygen on left of arrow

No Oxygen anywhere!

Carbon Dioxide, Water & 36 ATP are products

Carbon Dioxide, Lactic Acid OR Alcohol are the products. NO WATER is produced

Plants & Animals Yeast, Bacteriaor Muscle Cells

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Biochemistry