BIOCHEMISTRY

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Aim What chemicals are found in organisms?

• Do Now
• What is an element? An isotope?
• Describe the process of homeostasis.
• What did Robert Browne contribute to
• science?
• 4. How do we distinguish organic compounds from
• inorganic compounds

• HW 1 Due Friday
• Read Chapter 2 pages
• Pages
• Answer questions 6, 7, 10, 14, 15, 16, 21, 29

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I. CHEMICAL BONDS
A. Definition of chemical bond

1. Chemical bonds hold the atoms in a molecule
   together.
2. There are 2 types of chemical bonds ionic and
   covalent.

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B. IONIC BONDS

1. Occur when 1 or more electrons are TRANSFERRED
   from one atom to another.
2. When an atom loses an electron it is a POSITIVE
   charge.
3. When an atom gains an electron it is a NEGATIVE
   charge
4. These newly charged atoms are now called IONS
5. Example NaCl (SALT)

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I. Types of Bonds found in living things
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B. COVALENT BONDS

1. Occur when electrons are SHARED by atoms.
2. These new structures that result from covalent
   bonds are called MOLECULES
3. In general, the more chemical bonds a molecule
   has the more energy it contains

SHARING IS CARING!
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C. MIXTURES

1. Water is not always pure. It is often found as
   part of a mixture.
2. A mixture is a material composed of TWO OR MORE
   ELEMENTS OR COMPOUNDS THAT ARE PHYSICALLY MIXED
3. Ex salt pepper mixed, sugar and sand can be
   easily separated

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D. SOLUTION

• Two parts
• SOLUTE SUBSTANCE THAT IS BEING DISSOLVED (SUGAR
  / SALT)
• SOLVENT - the substance in which the solute
  dissolves
• Materials that do not dissolve are known as
  SUSPENSIONS.
• Blood is the most common example of a suspension.
  
• Cells other particles remain in suspension.

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E. FORMULA

1. The chemical symbols and numbers that compose a
   compound ("recipe")
2. Structural Formula Line drawings of the
   compound that shows the elements in proportion
   and how they are bonded
3. Molecular Formula the ACTUAL formula for a
   compound

C2H6O
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F. ACIDS BASES

• Acids always (almost) begin with "H" because of
  the excess of H ions (hydrogen)
• Ex lemon juice (6), stomach acid (1.5), acid
  rain (4.5), normal rain (6)
• Facts about Acids
• Acids turn litmus paper red (pink) and usually
  taste SOUR.
• You eat acids daily (coffee, vinegar, soda,
  spicy foods, etc)

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• 2) Bases always (almost) end with -OH because of
  the excess of hydroxide ions (Oxygen Hydrogen)
• EX oven cleaner, bleach, ammonia, sea water,
  blood, pure water
• Facts about Bases
• Bases turn litmus BLUE.
• Bases usually feel SLIPPERY to touch and taste
  BITTER.

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G. Neutralization Reactions

1. When an acid reacts with a base to produce a salt
   and water.

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H. pH SCALE

• measures degree of substance alkalinity or
  acidity
• Ranges from 0 to 14
• 0 5 strong acid
• 6-7 neutral
• 8-14 strong base

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1. The goal of the body is to maintain HOMEOSTASIS
   (neutrality) to do this when pH is concerned,
   we add weak acids bases to prevent sharp
   changes in pH.
2. These are called BUFFERS

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II. Biochemistry

• Some scientists say that the human body is a
  walking periodic table, since it contains a
  variety of chemicals found in our environment.

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ORGANIC COMPOUNDS
LIPIDS
PROTEINS
NUCLEIC ACIDS
CARBOHYDRATES
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A. CARBOHYDRATES

• Living things use carbohydrates as a key source
  of ENERGY!
• Plants use carbohydrates for structure
  (CELLULOSE)
• include sugars and complex carbohydrates
  (starches)
• contain the elements carbon, hydrogen, and oxygen
  (the hydrogen is in a 21 ratio to oxygen)

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1. Monosaccharides (simple sugars)

• all have the formula C6 H12 O6
• all have a single ring structure
• (glucose is an example)
• Sugars end in -ose

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2. Disaccharides (double sugars)

1. all have the formula C12 H22 O11
2. sucrose (table sugar) is an example

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3. Polysaccharides

1. Formed of three or more simple sugar units
2. Glycogen - animal starch stored in liver
   muscles
3. Cellulose - indigestible in humans - forms cell
   walls
4. Starches - used as energy storage

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4. Dehydration Synthesis

• Combining simple molecules to form a more complex
  one with the removal of water
• ex. monosaccharide monosaccharide ----gt
  disaccharide water
• (C6H12O6 C6H12O6 ----gt C12H22O11 H2O
• Polysaccharides are formed from repeated
  dehydration syntheses of water
• They are the stored extra sugars known as starch

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5. Hydrolysis

• Addition of WATER to a compound to SPLIT it into
  smaller subunits
• (also called chemical digestion)
• ex. disaccharide H2O ---gt monosaccharide
  monosaccharide
• C12 H22 O11 H2 O ---gt C6 H12 O6 C6 H12 O6

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B. Lipids (Fats)

1. Fats, oils, waxes, steroids
2. Chiefly function in energy storage, protection,
   and insulation
3. Contain carbon, hydrogen, and oxygen but the HO
   is not in a 21 ratio
4. Tend to be large molecules -- an example of a
   neutral lipid is below

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• 5. Neutral lipids are formed from the union of
• one glycerol molecule and 3 fatty acids
• 6. 3 fatty acids glycerol ----gt neutral fat
  (lipid)
• 7. Fats -- found chiefly in animals
• 8. Oils and waxes -- found chiefly in plants
• Oils are liquid at room temperature, waxes are
• solids
• 10. Lipids along with proteins are key components
  
• of cell membranes
• 11. Steroids are special lipids used to build
  many reproductive hormones and cholesterol

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C. PROTEINS

1. contain the elements carbon, hydrogen, oxygen,
   and nitrogen
2. composed of MANY amino acid subunits
3. It is the arrangement of the amino acid that
   forms the primary structure of proteins.
4. The basic amino acid form has a carboxyl group on
   one end, a methyl group that only has one
   hydrogen in the middle, and a amino group on the
   other end.
5. Attached to the methyl group is an R group.

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AN R GROUP IS ANY GROUP OF ATOMS THIS CHANGES
THE PROPERTIES OF THE PROTEIN!
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6. FUNCTIONAL GROUPS

1. There are certain groups of atoms that are
   frequently attached to the organic molecules we
   will be studying, and these are called functional
   groups.
2. These are things like hydroxyl groups which form
   alcohols, carbonyl groups which form aldehydes or
   ketones, carboxyl groups which form carboxylic
   acids, and amino groups which form amines.

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7. Major Protein Functions

1. Growth and repair
2. Energy
3. Buffer -- helps keep body pH constant

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8. Dipeptide

1. formed from two amino acid subunits
2. Formed by the process of Dehydration Synthesis
3. amino acid amino acid ----- dipeptide water

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9. Hydrolysis of a dipeptide

1. Breaking down of a dipeptide into amino acids
2. dipeptide H2O ---gt aminoacid amino acid

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10. Polypeptide (protein)

1. composed of three or more amino acids linked by
   synthesis reactions
2. Examples of proteins include insulin, hemoglobin,
   and enzymes.
3. There are an extremely large number of
   different proteins.
4. The bases for variability include differences in
   the number, kinds and sequences of amino acids in
   the proteins

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Summary
Compound Building Blocks
Carbohydrates Monosaccharides (glucose)
Lipids 1 Glycerol 3 Fatty acids
Proteins Amino acids
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Saccharide tells you its a carbohydrate
Peptide tells you its a protein
Compound 1 (mono) 2 (di) 3 or more (poly)
Carbohydrates Mono- sacccharides Di- saccharides Poly- saccharides
Proteins Amino acids Di- peptide Poly- peptide
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NUCLEIC ACIDS

• in all cells
• composed of NUCLEOTIDES
• store transmit heredity/genetic information
• Nucleotides consist of 3 parts
• 1. 5-Carbon Sugar
• 2. Phosphate Group
• 3. Nitrogenous Base

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DNA (deoxyribonucleic acid)

• contains the genetic code of instructions that
  direct a cell's behavior through the synthesis of
  proteins
• found in the chromosomes of the nucleus (and a
  few other organelles)

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RNA (ribonucleic acid)

• directs cellular protein synthesis
• found in ribosomes nucleoli

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CHEMICAL REACTIONS

• a process that changes one set of chemicals into
  another set of chemicals
• REACTANTS elements or compounds that enter into
  a chemical reaction
• PRODUCTS elements or compounds that are
  produced in a chemical reaction
• Chemical reactions always involve the breaking of
  bonds in reactants and the formation of new bonds
  in products.

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• In a reaction, energy is either TAKEN IN
  (ENDOTHERMIC) or GIVEN OFF (EXOTHERMIC)
• Can you think of an everyday example of each type
  of reaction?

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Enzymes and Enzyme Action

• catalyst inorganic or organic substance which
  speeds up the rate of a chemical reaction without
  entering the reaction itself
• enzymes organic catalysts made of protein
• most enzyme names end in -ase
• enzymes lower the energy needed to start a
  chemical reaction. (activation energy)
• begin to be destroyed above 45øC. (above this
  temperature all proteins begin to be destroyed)
• End in -ase

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• It is thought that, in order for an enzyme to
  affect the rate of a reaction, the following
  events must take place.
• The enzyme must form a temporary association with
  the substance or substances whose reaction rate
  it affects. These substances are known as
  substrates.
• The association between enzyme and substrate is
  thought to form a close physical association
  between the molecules and is called the
  enzyme-substrate complex.
• While the enzyme-substrate complex is formed,
  enzyme action takes place.
• Upon completion of the reaction, the enzyme and
  product(s) separate. The enzyme molecule is now
  available to form additional complexes.

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How do enzymes work?

• substrate molecules upon which an enzyme acts
• the enzyme is shaped so that it can only lock up
  with a specific substrate molecule
• enzyme
• substrate -------------gt product

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"Lock and Key Theory"

• each enzyme is specific for one and ONLY one
  substrate (one lock - one key)
• this theory has many weaknesses, but it explains
  some basic things about enzyme function

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Factors Influencing Rate of Enzyme Action

• 1. pH - the optimum (best) in most living things
  is close to 7 (neutral)
• high or low pH levels usually slow enzyme
  activity
• A few enzymes (such as gastric protease) work
  best at a pH of about 2.0

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• 2. Temperature - strongly influences enzyme
  activity
• optimum temperature for maximum enzyme function
  is usually about 35-40 C.
• reactions proceed slowly below optimal
  temperatures
• above 45 C most enzymes are denatured (change in
  their shape so the enzyme active site no longer
  fits with the substrate and the enzyme can't
  function)

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• 3. Concentrations of Enzyme and Substrate
• When there is a fixed amount of enzyme and an
  excess of substrate molecules -- the rate of
  reaction will increase to a point and then level
  off.