Biochemistry

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Biochemistry

• The Chemistry of Life

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Basic Chemistry

• Atom
• Simplest unit of matter
• Made up of three different subatomic particles

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Subatomic Particles

• Protons
• Have a positive charge ()
• Have mass
• Located in nucleus
• Neutrons
• Are neutral, have no charge (0)
• Have mass
• Located in nucleus
• Electrons
• Have a negative charge (-)
• Almost no mass
• Located in energy levels outside of nucleus

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• Atomic Number
• Tells you the number of protons an atom has, and
  also the of electrons
• Atoms are neutral
• Protons () Electrons (-)

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• Atomic Mass
• Add together the number of protons and neutrons
  in nucleus of atom
• Electrons hardly contribute any mass

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• Isotopes
• Atoms of one type of element with different
  atomic masses
• Same of protons
• Different neutrons
• Changes the mass only, the properties are the
  same

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• Radioactive Isotopes
• The nucleus of some isotopes is unstable
• The atom with emit radiation
• Radiation can be measured with tools
• ex. Geiger counter
• These isotopes can be used as useful tools in
  science
• Ex
• Carbon-14 dating
• Radiation treatment for cancer

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• Elements
• Substance made of only one type of atom
• Each element has a unique atomic
• Elements most commonly found in living things
• Carbon (C)
• Hydrogen (H)
• Oxygen (O)
• Nitrogen (N)

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• Compounds
• Two or more elements chemically combined
• Atoms held together by bonds.
• Once bonds form, compounds will have new, and
  different properties

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• Organic Compounds
• Contains carbon and hydrogen (and often O, N)
• Ex Glucose (C6H12O6), carbohydrate, lipids,
  proteins
• Inorganic Compounds
• Doesnt contain carbon and hydrogen together
• Ex H2O, CO2, NH3, NaCl

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• Why do atoms form compounds?
• Bonds that form between atoms give atoms a stable
  outer electron level.
• Called a stable octet of valence electrons (8)

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Types of Chemical Bonds

• Ionic Bonds
• One or more electrons are transferred from one
  atom to another.
• Neutral atoms become positive negative ions
• Forms salts
• (Ex NaCl)
• Ionic bond attraction between () and (-) ions

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• Covalent Bonds
• Electrons are shared between atoms
• Each bond represents a shared pair of electrons
• Can form single, double or even triple bonds

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• Covalent bonds form molecules
• Subscripts in the formula tell of each atom
• Ex H2O, NH3, CO2, CH4

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Ionic Bonds Transfer electrons
Covalent Bonds Share Electrons
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Properties of Water

• Water is necessary for life
• Contains covalent bonds

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Water Molecules H2O (look like Mickey Mouse)
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• Water is a Polar molecule (like a magnet)
• The bonds are polar
• Oxygen attracts the electrons more than Hydrogen

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• Hydrogen Bonding
• bonding between the () H of one molecule and the
  (-) end of another molecule.
• Makes water good at sticking to itself and other
  substances
• Makes water good dissolver

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• Cohesion water sticks to itself
• Ex
• Water forms beads on smooth surface
• Surface Tension allows insect to skate

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• Adhesion water sticks to other substances
• Ex Capillary action water molecules rise up
  small tubes

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• Heat Capacity
• Water has a relatively high heat capacity
• Ex
• Lakes and oceans can absorb a lot of heat from
  sun without a drastic temperature change

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• Water as a Solvent
• Dissolves most ionic and covalent substances
• Universal Solvent many things can dissolve in
  it.

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• Solute substance being dissolved
• Solvent substance in which solute dissolves
• Solution evenly disbursed mixture
• Suspensions material in the water but just
  suspended not dissolved (ex blood cells in
  blood)

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pH of Solutions

• pH Scale way to measure concentration of H ions
  in solution
• Ranges from 0 to 14
• Pure water is neutral pH 7

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• Litmus Paper
• Used to test pH of a solution
• Red acidic
• Blue basic

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• Acids Form H ions
• pH is lt7
• Ex HCl (stomach acid), lemon juice

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• Bases Produces OH- (hydroxide ions)
• Also called alkaline
• pH gt7
• Ex Lye (NaOH) used as drain cleaner

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• Buffers
• Maintain pH at a certain level
• Usually between 6.5 7.5 (close to neutral)
• Helps to maintain homeostasis in organism

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Major Types of Chemical Reactions

• Dehydration Synthesis (Condensation)
• Chemically combine two smaller molecules
• Water is removed
• Dehydrate remove water
• Synthesis to make

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• Hydrolysis
• Break apart large molecule into smaller pieces
• Water is added
• Hydro water Lysis to break

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• Polymerization
• Create a large molecule (polymer)
• Join up smaller monomer units
• Often a dehydration synthesis reaction
• Ex
• Join amino acids (monomer) to make protein
  (polymer)
• Join glucose (monosaccharide) to make starch
  (polysaccharide)

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Organic Compounds
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Carbohydrates

• Sugars and starches
• FUNCTION
• Used as an energy source
• Energy released during cellular respiration
• Made of carbon, hydrogen and oxygen
• Ex
• C6H12O6, C12H22O11
• Ratio of H of O is always 21

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• Basic Structure
• Ring made of 5 carbons and 1 oxygen
• Rings can join up by dehydration synthesis

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3 Types of Carbohydrates

• Monosaccharide's 1 sugar ring
• Disaccharides 2 sugar rings
• Polysaccharides many sugar rings

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• Monosaccharide's (Simple sugars)
• All have formula C6H12O6
• Single ring structure
• End in -ose
• Ex glucose, fructose, galactose

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• Disaccharides double sugars
• All have formula C12H22O11
• End in -ose
• Ex sucrose, lactose, maltose

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• Polysaccharides 3 or more sugar units
• Ex
• Starch (energy storage in plants)
• Glycogen (how animals store sugar in liver)
• Cellulose (plant cell walls)
• Chitin (insect exoskeletons)

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• Simple sugars form into complex sugars by
  dehydration synthesis (condensation).
• Combining molecules by removing water
• Monosac. Monosac. ? Disac. Water
• C6H12O6 C6H12O6 ? C12H22O11 H2O

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and H2O
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• Complex sugars are broken down into simple sugars
  by hydrolysis.
• Breaking down molecules by adding water
• Also called chemical digestion
• Disac. Water ? Monosac. Monosac.
• C12H22O11 H2O ? C6H12O6 C6H12O6

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Dehydration Synthesis and Hydrolysis are
OPPOSITE Reactions
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Chemical reactions are often enzyme mediated.
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Lipids

• Fats, oils and waxes
• FUNCTION
• Long term energy storage
• Insulation
• Protective coating around cells
• Cell membranes
• Made of carbon, hydrogen, and oxygen
• Ratio of H to O is not 21
• Ex C15H26O6 (fewer oxygens)

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• Animals store energy mostly as fats
• Plants store energy mostly as oils

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Lipids

• Made up of
• 1 glycerol molecule
• 3 long fatty acid chains
• Looks like a giant letter E
• Also called a triglyceride

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GLYCEROL
Note 3 OH groups
FATTY ACID CHAIN
Note CARBOXYL GROUP COOH group at end of
molecule
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Basic Lipid Structure
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• Lipids are
• formed by dehydration synthesis
• broken down by hydrolysis

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Saturated vs. Unsaturated Fats

• Saturated
• all single bonds between carbon atoms
• Unsaturated
• One or more double bonds between carbon atoms
• Makes fatty acid more bent

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Proteins

• Protein Structure
• Made of carbon, hydrogen, oxygen and NITROGEN
• Large complex polymer molecules that can have a
  large range of sizes, shapes and properties

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Proteins

• FUNCTIONS
• Enzymes speed up chemical reactions
• Hormones chemical messengers
• Antibodies defend against disease
• Hemoglobin binds oxygen to red blood cells
• Cell growth and repair
• Cell Membrane Channels

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• Amino Acid basic building block of proteins

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Parts of an Amino Acid

• Carboxylic Acid Group
• Amino Group
• R-Group (varies depending on amino acid)

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Examples of Different Amino Acids

• There are 20 different amino acids
• All have different R groups

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• Peptide Bond bond between amino acids
• Dipeptide two amino acids joined.
• Polypeptide many amino acids joined
• Proteins are polypeptides

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Forming a Peptide Bond
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and H2O
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H2O
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• Amino acids join up to form proteins at ribosome
• The function of the protein comes from its
  specific sequence of amino acids and the shape
  the protein forms
• The code for the specific sequence of amino
  acids comes from DNA

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Nucleic Acids

• Large complex macromolecule
• Stores information in code
• Composed of carbon, hydrogen, oxygen, nitrogen
  and phosphorus

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• Structure of Nucleic Acids
• Made of chains of nucleotides
• Nucleotide (made of 3 components)
• Phosphate Group
• Sugar
• Nitrogenous Base

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Two Types of Nucleic Acids

• DNA (Deoxyribonucleic Acid)
• Contain genetic information
• Found in nucleus
• Divides when cell divides
• RNA (Ribonucleic Acid)
• Copies code from DNA
• Takes code to ribosomes for protein synthesis
• Found in nucleus and cytoplasm

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Differences Between DNA RNA

• DNA
• Double strand of nucleotides
• Sugar is deoxyribose
• Nitrogenous Bases
• Adenine, Thymine, Cytosine, Guanine
• RNA
• Single strand of nucleotides
• Sugar is ribose
• Nitrogenous bases
• Adenine, Uracil, Cytosine, Guanine

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