Proteins, Chemical Reactions, and pH

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Unit 2B Biochemistry Part 2

• Proteins, Chemical Reactions, and pH

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Proteins

• Of all the organic compounds, proteins are the
  largest, most complex, and most diverse.
• While 70 of the body is water, most of the other
  30 is protein!

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Proteins

• Made of elements C, H, O, N
• Made of amino acids (the monomer)
• Peptide bonds link amino acids together to make
  polypeptides
• One or more polypeptides fold into a Protein

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Proteins are Diverse

• 20 amino acids are used to make proteins
• Different combos of amino acids lead to different
  functioning proteins
• DNA tells the proteins how to assemble.

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Amino Acids

• Amino acids are compounds with an amino group
  (-NH2) on one end and a carboxyl (-COOH) group on
  the other end.

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• Each amino acid consists of one of each of the
  following, connected to each other by covalent
  bonds.
• 1) carboxyl group (-COOH)
• 2) amino group (-NH2)
• 3) one central carbon atom (-C-)
• Between the amino and carboxyl groups
• 4) one lone hydrogen atom (-H)
• Comes off the central carbon
• 5) 'R' (variable) group - one of 20 different
  side chains

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• Circle each amino group, box each carboxyl group
  and label each R group (-R).

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• Because of their uniform structure, any amino
  acid can bond to any other amino acid using a
  covalent bond called a peptide bond.
• What process will link together two individual
  amino acids?

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• On the two amino acids below, circle the atoms
  that must be removed in order to create a peptide
  bond.
• Hint These atoms create a __________
• molecule, which is a product of the reaction.

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Polypeptides

• Segments of amino acids are called polypeptides
• When they are first assembled, polypeptides are
  linear (straight) chains.
• They are not yet functioning proteins!

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• R groups on the amino acids interact with each
  other causing the polypeptide to fold into a
  specific 3-dimentional shape or structure.

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• Once it is completely and correctly folded, it is
  considered a protein.
• (other small changes or modifications may also
  occur before the protein is completely
  functional)
• The structure of each protein in unique
  Structure leads to function!

Protein Folding
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• How many amino acids are shown in the polypeptide
  below? (Hint count the R groups)
• How many peptide bonds are shown in the
  polypeptide below? (Hint peptide bonds are
  between which two atoms?)
• How many water molecules were released as this
  polypeptide was formed? (Hint one for each
  bond made!)

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Chemical Reactions

• Everything that happens in an organism is based
  on a chemical reaction!
• Change one set of chemicals into another
• Chemical bonds change
• Reactants- elements/compounds that enter the
  reaction
• Products- are produced by the reaction

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When bonds are made or broken

• - Energy is absorbed (taken in) or released
  (given off)
• Reactions releasing energy can (but not always)
  occur on their own, or spontaneously.
• Reactions absorbing energy will not occur without
  a source of energy

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Example

• Paper is made of cellulose which burns in the
  presence of oxygen, and releases energy in the
  form of heat and light. But this packet is not
  spontaneously bursting into flames right now. Why
  not? What is missing?

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Where does your body get energy for chemical
reactions?
Plants?
Make food by photosynthesis and turn it into
energy by cellular respiration.
Animals?
Eat food and turn it into energy by cellular
respiration.
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Activation Energy

• Is the amount of energy that a reaction needs to
  get started
• Every reaction requires a certain amount of
  activation energy to get started, regardless of
  whether it is an energy-absorbing or
  energy-releasing reaction.

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Energy absorbing reactions (Endergonic)

• Products have more energy than the reactants
• Products are larger, less stable, and more
  complex than reactants
• It takes more energy to break bonds in the
  reactants than is released by making new bonds in
  the products

• Examples dehydration synthesis photosynthesis

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Dehydration Synthesis
(Energy Absorbing)
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Energy releasing reactions (Exergonic)
Reactants have more energy than the
products Reactants are larger, less stable, and
more complex than products More energy is
released when new bonds are formed in the
products than was needed to break the old bonds
in the reactants
Examples hydrolysis cellular respiration
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Dehydration Synthesis
(Energy Absorbing)
Hydrolysis
(Energy releasing)
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Enzymes

• Some chemical reactions would be too slow or have
  too high of an activation energy without a little
  help.
• Catalyst- a substance that speeds up a chemical
  reaction
• works by lowering the activation energy
• Cells make special proteins called enzymes to act
  as catalysts for chemical reactions.
• There is one type of enzyme for each type of
  chemical reaction (its shape makes it specific
  for its job)

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Would the hill be higher or lower with an enzyme
present?
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HOW DO ENZYMES WORK?

• 1. They provide a site for the reactants to be
  brought together to react.
• 2. They help to break the bonds of the reactants.
• This reduces the energy needed for the reaction.
• Enzyme Catalyzed Reaction- a reaction sped up
  by an enzyme

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• Substrates- what the reactants are called in an
  enzyme catalyzed reaction.
• Substrates bind to a place on the enzyme called
  the active site which has a specific shape.

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2 Models help explain how enzymes work

• 1. "Lock and Key Model" The substrates fit the
  active site of an enzyme like a key fits into a
  lock. A very specific interaction!
• This provides the site for the reactants to come
  together.

Substrate Enzyme
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• 2. Induced-fit Model The enzyme binds the
  substrate(s) and slightly changes its shape to
  hug the substrate(s) tightly (like a
  handshake).
• This places strain on existing bonds, allowing
  bonds to break and the chemical reaction to go
  forward.

Example of an enzyme-catalyzed reaction
____________ is formed by combining
___________________ and water in the presence of
the enzyme _______________________.
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WHY arent enzymes considered a reactant or a
product?

• After the product is released from the enzyme,
  the enzyme is recycled and used again.
• Enzymes are reusable!

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Common Hydrolytic Enzymes(The suffix "ase"
commonly indicates that a protein is an enzyme)

• 1. protease- any enzyme that speeds hydrolysis or
  breakdown of proteins
• 2. sucrase (a disaccharidease) - an enzyme which
  speeds the breakdown of ___________________
• 3. lipase - any enzyme which speeds the breakdown
  of _________________________
• 4. nuclease - any enzyme which speeds the
  breakdown of _______________________
• 5. amylase - an enzyme which speeds the breakdown
  of amylose (starch!)

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FACTORS AFFECTING ENZYME ACTIVITY

• Temperature, pH, and regulatory molecules affect
  enzyme activity
• An increase in temperature will increase the rate
  of a reaction to a certain point
• After that point, the enzyme will no longer work

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• Denaturation - when a protein unfolds and loses
  its overall shape (and thus function) due to
  increased temp or changes in pH.
• Denatured enzymes lose the shape of their active
  site and will no longer function.

Think! Why are temperature and pH important
factors in maintaining homeostasis?
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pH

• Water is one of the most important inorganic
  substances in living organisms.
• Sometime water molecules will break apart
  (dissociate) to form ions.
• Ion- a positively or negatively charged atom (set
  of atoms) due to loss or gain of electrons

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• About 1 water molecule in 550 million splits in
  this way.
• Because the number of positive H ions is equal
  to the number of negative OH- ions, water is
  neutral.
• pH scale- measures the concentration of H ions
  in solution H

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pH Scale

• Measured 0-14
• Each step represents a factor of 10
• 7 is neutral (like water- has equal amounts of H
  and OH-)
• Lower from 7 becomes more acidic (has more H)
• Higher from 7 becomes more basic/alkaline (has
  less H)

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• Order these substances in order of increasing
  acidity human blood, acid rain, bleach,
  seawater, stomach acid.

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• Acid, Base, or Neutral? Strong or Weak?
• pH 7_______ pH 13.5_____
• pH 8_______ pH 2________
• Which one is more acidic
• pH of 2 -or- pH of 4
• How many times more?___________
• Which one is more basic? Tomato juice -or-
  Soap
• How many times more?________

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Definitions of acids and bases

• ACID- compound that forms H ions in solution
• Acids have more H than OH-
• BASE- compounds that forms OH- ions in solution
• Bases have more OH- than H

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• Study the reaction below. Is this substance an
  ACID or BASE?
• 
  (circle)
• Dissociation In Water
• HCl H
  Cl-
• Hydrogen Chloride Hydrogen ion
  Chloride ion
• Study the reaction below. Is this substance an
  ACID or BASE?
• 
  (Circle)
• Dissociation
  In Water
• NaOH Na OH-
  Sodium Hydroxide Sodium ion
  hydroxide ion

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ACIDS BASES
Solutions have a pH_______7 Solutions have a pH ______ 7
Taste sour Taste bitter
Can corrode metals Can denature proteins (feel "slippery")
In solution H _____ OH- In solution H _____ OH-
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acid
neutral
Base
Draw a solution with more H than OH- Range of pH ______________ H ______ OH- in this type of solution. Draw solution with equal numbers of H and OH- Range of pH ______________ H ______ OH- in this type of solution. Draw solution with more OH- than H Range of pH ______________ H ______ OH- in this type of solution.
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Sample acids and bases
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BUFFERS

• Controlling pH is important for maintaining
  homeostasis in cells. The pH of most cells in
  the human body must be kept between 6.5 and 7.5.
  
• Buffers- Weak acids or bases that react with
  strong acids or bases to prevent sharp, sudden
  changes of pH.
• Example Sudden pH changes in blood are
  prevented by buffers such as bicarbonate and
  phosphate ions.