Biochemistry

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Chapter 3

• Biochemistry

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Section 3-1 Carbon Compounds (Biochemistry)

• Organic compounds
• Must contain C and H, covalently bonded
  together.
• Usually O or N is also present.
• Methane (CH4) is the simplest of all organic
  compounds

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Properties of Carbon

1. Can form 4 bonds
2. Can bond with itself forming chains
3. Can form single (-), double( ), or triple bonds
   ( ).
4. May form straight chains, branched chains or rings

Glycine Amino acid
Glucose
Fatty acid
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Functional Groups

• Clusters of atoms that influence properties of
  the molecules they make up
• OH (hydroxyl group) found in organic alcohols
  

Hydroxyl group
Ethanol
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• 2. COOH (carboxyl group) - found in organic
  acids
• 3. -NH2 Amino
• found in Amino acids
• N
• H H

Amino group
Carboxyl group
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• Phosphate Group
• involved in energy transfer

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Fun with Functional Groups

• Hydroxyl Group (- OH)
• Amino Group (-NH2)
• Carboxyl Group (-COOH)
• Methyl Group (-CH3)

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Now lets put these together!!

• Monomers
• - simplest form of the molecule. Only one unit

Glucose
Amino Acid
Fatty Acid
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• 2. Polymers
• 2 or more monomers linked

Tripeptide
Sucrose
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• 3. Macromolecule
• A larger polymer- made up of thousands of
  monomers

Polypeptide (protein)
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The formula for Glucose is C6H12O6 and Fructose
is also C6H12O6, when they are combined together,
the new compound, Sucrose is C12H22O11. How
could that be?

• C6H12O6
• C6H12O6
• _____________________
• C12H24O12
• - C12H22O11
• ______________
• H2O

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• In order to link two monomers together, a water
  molecule needed to be removed.
• This is called Dehydration synthesis
  (Condensation). This is a building up reaction
  or Anabolic reaction.
• Between any two monomers linked together, a water
  molecule will be removed. So if you link 3
  glucose molecules together, 2 water molecules
  will be removed.
• Endergonic reaction

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Dehydration SynthesisCondensation
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• To reverse the reaction, if you put the water
  molecule back into the polymer, the water breaks
  the polymer into the monomers that made it up.
• This is Hydrolysis.
• Exergonic reaction. This is a breaking down
  reaction or Catabolic reaction.

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Energy Currency

• Life processes need a constant energy source
  (free energy needed at all times)
• is the compound
  that is available as the free energy.
• When it breaks down, energy is released from the
  last phosphate group bond (-PO4-).
• It then becomes ADP (Adenosine Diphosphate) (
  the energy is released).

ATP Adenosine Triphosphate
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Currency for the Cell
ATP The Perfect Energy
                                                                                   
AMP ADP ATP
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ATP releasing a phosphate group to yield ADP and
energy
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Section 3-2 Molecules of Life

• 65 of human body is made up of water. The rest
  is
• Carbohydrates
• Proteins
• Lipids
• Nucleic Acids

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Carbohydrates

• -ose ending
• Made up of C, H, O in a 121 ratio.
• HO ratio is always 21
• General formula is (CH2O)n
• Grouped as Monosaccharides, Disaccharides and
  Polysaccharides
• Provide the body with energy (free or stored)

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Monosaccharides

• Simple sugars C6H12O6
• Glucose, Galactose, and Fructose.
• Are Isomers
• (same chemical formula, different structure)
• Provide quick energy (fructose is fruit sugar
  Remember the oranges!!)

Glucose
Galactose
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Disacharides

• Double sugars. C12H22O11 .
• Two monosaccharides joined by dehydration
  synthesis/condensation
• Provide fast energy
• Glucose Glucose Maltose

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• Glucose Fructose Sucrose (table sugar)

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Glucose Galactose Lactose (milk sugar)
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Polysaccharides

• 3 or more monosaccharides joined together.
  (CH2O)n.
• Animal starch (Glycogen in liver)
• Starch (plant starch Amylose)
• Cellulose most abundant biomolecule on earth.
  Gives plant cell walls rigidity).
• Branched and unbranched chains.
• Stored energy. To be used within 4 8 hours

Amylose (starch)
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Cellulose
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Glycogen
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Carbohydrate lab

• Build a water model get initialed
• Each pair should build glucose Initialed
• With an adjoining pair, undergo
  Condensation/Dehydration Synthesis
• Get initialed
• Undergo Hydrolysis Get initialed
• Break apart model kits and put back in bag and on
  front lab table.
• Complete ALL questions in the lab

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Dehydration SynthesisCondensation
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C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
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The energy bank

• Retirement fund - Lipids
• Investments (savings) - Starches
• Checking accounts Double sugars
• ATMs Simple sugars
• Cash in your pocket ATP

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Proteins

• Made up of C, H, O and N ( sometimes S)
• Main component of blood, muscles, skin, cell
  membranes, enzymes and hormones
• Polymers of the monomer Amino Acid (21 different
  ones)
• Function for structure regulation
• ine ending

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Amino Acids

• Made up of
• an amino group (-NH2)
• a carboxyl group (-COOH)
• a variable radical group (R).

H
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• Very large molecules. Long chains, folds and
  chains
• Dipeptides form when 2 amino acids join together
  through dehydration synthesis
• Joined at a peptide bond (-C-N-) bond

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• Polypeptides form when gt3 amino acids are joined
• Highly twisted and bent due to H-bonding
• Require large amounts of energy (ATP) to break
  these down

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CH3
CH3
CH3
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Protein Lab

• Draw an basic amino acid and label the functional
  groups
• Circle the amino groups for each blue
• Circle the carboxyl groups for each red
• Radical group in yellow
• Construct the 3 amino acids and get signed
• Form a polypeptide using your three amino acids
• Get this polypeptide signed
• On the diagram, circle the peptide bond
• Complete all questions on the lab

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Lipids

• Contain C, H, and O but the H to O ratio is gt21
  (more C - Hs, the more Energy!)
• Fats, oils, waxes, and sterols (do not dissolve
  in water)
• Stores large quantities of energy for long term
  storage
• Component of bilipid layer of cell membranes
• Unbranched chains
• Monomers of Fatty Acids and Glycerol

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The Monomers of Lipids
Hydrocarbon chain
Hydroxyl groups
Carboxyl group
Fatty Acid
Glycerol
-COOH group of each Fatty acid is polar. It is
attracted to water Hydrophilic The hydrocarbon
chain of the fatty acid is Hydrophobic being
repelled by water.
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Each pair should make a Glycerol model
Three Hydroxyl groups with Hs Cs
Hydroxyl groups This is where dehydration
synthesis will occur
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Now make each of the following Fatty Acids
Butryic acid
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Classification of Lipids

• Triglycerides
• 3 Fatty acids and 1 glycerol molecule
• Saturated, unsaturated, polyunsaturated

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• Saturated fats contain the maximum of
  Hydrogens.
• No double bonds between carbons. Solid at room
  temp.
• Butter, animal fat, lard
• Unsaturated fats contain at least 1 C-C double
  bond.
• Reduces the number of Hs by 2. Olive oil,
  peanut oil, canola oil, margarine. Liquid at room
  temp.
• Polyunsaturated fats contain many C-C double
  bonds.
• Clear liquid at room temp.
• Vegetable oil, safflower oil. Aka no flavor
  oil!
• Plant seeds and fruit

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• 2. Phospholipids
• 2 Fatty acids and 1 glycerol
• Form bilipid layer of cell membranes
• Since lipids are hydrophobic, they make a good
  barrier between cell and outside of cell

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• 3. Waxes
• 1 Fatty acid chain and a long alcohol chain
• Waterproofing, protective cuticle on outside of
  plants, earwax
• 4. Sterols/Steroids
• - 4 fused carbon rings with functional
  group attached
• - Animal Hormones, testosterone, estrogen,
  cholesterol (needed for normal nerve cell
  functioning)

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Enzymes

• An organic catalyst (Proteins)
• Regulate the rate of a reaction
• What do they do?
• 2H2O2 -gt 2H2O O2 (Hydrogen peroxide breaking
  down into water and oxygen)
• One molecule of catalase can break down 40
  million molecules of H2O2/second
• CO2 H2O lt-gt HCO3- H (How carbon dioxide is
  carried in your blood as a bicarbonate ion)
• One molecule of carbonic anhydrase can process
  one million molecules of CO2/sec

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Complex Carbohydrate Intolerance is caused by a
deficiency of an intestinal enzyme called
alpha-galactosidase, which results in the
incomplete digestion of complex carbohydrates.
Flatulence, abdominal pain, bloating and
cramping.
Take Beano that contains the alpha galactosidase
enzyme
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• Since all organic compounds are covalently
  bond, to break one of these bonds, high energy,
  heat, pressure or enzymes are needed.
• All reactions need a kick to get started This
  kick is called Activation energy.
• Enzymes lower the amount of activation energy
  needed.

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How Enzymes work

• Enzymes enter into a reaction, bonding with the
  substrate at the Active site
• Forms an enzyme-substrate complex
• Specificity due to the shape of the active site
• Lock and Key Theory of enzyme specificity
• Enzymes are reusable
• End in ase.

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Enzymes are affected by

• Temperature
• As temp gt, enzyme activity gt up to an optimum.
  Then it decreases or stops. In humans, its 37C.
• The active sites are denatured (altered)
• pH
• Most enzymes work best at 6 to 8. Pepsin in
  stomach works best at 2
• Concentration
• As the of enzymes gt, the rate of activity gt.
  As the concentration of the substrate gt, rate of
  reaction decreases

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Nucleic Acids

• Control all cellular activities and genetic
  information
• DNA - Deoxyribonucleic acid
• RNA - Ribonucleic acid

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Polymers of nucleotides

• A phosphate group, nitrogen base a 5 Carbon
  sugar

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Basic differences

• DNA double stranded, with Deoxyribose sugar and
  found only in the nucleus
• RNA single stranded, with Ribose sugar and may
  be in nucleus, cytoplasm or ribosomes. 3
  different types

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Glucose
Fructose
Polysaccharide
Disaccharide
Fatty Acid
Dipeptide
Nucleotide
Lipid
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  Carbohydrates Proteins Lipids Nucleic Acids
Elements Present        
HO ratio        
Monomer        
Polymer        
ending        
Uses        
Examples        
Structure