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Jan 15, 2016
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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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Biochemistry
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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Biochemistry
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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Biochemistry
Ionic Bonding - The atoms transfer the electrons. The atoms acquire a charge and then become ions.
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Biochemistry
Covalent Bonding - The elements share atoms toform a molecule.
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Biochemistry
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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Biochemistry
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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Biochemistry
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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Biochemistry
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
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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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Biochemistry
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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Biochemistry
Polypeptide (AKA: Protein)
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Biochemistry
A protein with many amino acids linked together AKA: Polypeptide
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Biochemistry
A protein has 1 or more chains of amino acids. They maybe folded, twisted or coiled.
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Biochemistry
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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Biochemistry
A lipid consists of 3 fatty acids and 1 glycerol
1glycerol
3 fattyacids
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Biochemistry
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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Biochemistry
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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Biochemistry
Hydrolysis with enzymeaction
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Biochemistry
Dehydrationsynthesis ofproduct withuse of anenzyme
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Biochemistry
Dehydration synthesis of a product with enzyme
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Biochemistry
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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Biochemistry
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Biochemistry
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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Biochemistry
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