AMINO ACIDS AND PROTEINS

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AMINO ACIDS AND PROTEINS

• QCA

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WHAT THE NEED TO KNOW

• State the general formula for an amino acid as
  RCH(NH2)COOH.
• State that an amino acid exists as a zwitterion
  at a pH value called the isoelectric point.
• State that different R groups in amino acids may
  results in different isoelectric points.
• Describe the acid-base properties of amino acids
  at different pH values.
• Explain the formation of peptide (amide) linkage
  between amino acids by condensation and
  subsequent condensation polymerisation to from
  polypeptides and proteins.
• Describe the acid and alkaline hydrolysis of
  proteins and peptides to form amino acids or
  carboxylates.

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WHAT THIS MEANS

• Learning about amino acids and proteins is
  important/relevant proteins more important that
  genes!
• What an amino acid looks like
• How different amino acids have different
  properties
• How to make proteins from amino acids and how to
  break proteins to give amino acids

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SERIES OF FOUR LESSONS

• LESSON ONE
• Introduction into Biochemistry, why proteins are
  great and relevant to learn about.
• Outcomes To know the general formula of amino
  acids. To know different amino acids have
  different functional groups
• LESSON TWO
• Recap on structure of amino acid they must
  know this! Then go on to properties of amino
  acids
• Outcome To know how different functional groups
  affect the properties of amino acids. To know
  how amino acids act as zwitterions. To know the
  meaning of an isoelectric point

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SERIES OF FOUR LESSONS

• LESSON THREE
• Practical. Look at properties of amino acids by
  chromoatography
• Outcome know about different properties of amino
  acids (and how this relates to R groups)
• LESSON FOUR
• Go through making and breaking of proteins by
  addition or removal of water.
• Outcome Be able to draw join two amino acids by
  condensation reaction and how they can be
  separated by acid alkaline hydroysis. Know about
  condensation polymerisation to make proteins.

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LESSON ONE - STARTER

• Write down five things in your books about amino
  acids
• Talk to the person next to you about amino acids
  for one minute Ill call on you to find out
  some ideas (write all on board, discuss)
• Answer the following questions
• Where do amino acids come from?
• If we add amino acids together, what do we get?
• What is special about amino acids?
• (Ask for examples of answers, correct any
  misconceptions)

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MAIN ACTIVITIES

• Link topic to the GCSE Biology topic food
  digestion, protein breaks down to give peptides
  and amino acids, amino acids get absorbed
• Relevance of topic talk about important
  proteins and enzymes
• Insulin and glucagon diabetes case study?
• http//www.yteach.co.uk/page.php/resources/view_al
  l?idprotein_nucleic_acid_structure_primary_second
  ary_tertiary_quaternary_three_dimensional_double_h
  elix_DNA_t
• Keratin hair
• http//www.yteach.co.uk/page.php/resources/view_al
  l?idprotein_nucleic_acid_structure_primary_second
  ary_tertiary_quaternary_three_dimensional_double_h
  elix_DNA_t_page_15fromsearch
• Albumin cooking eggs
• http//www.yteach.co.uk/page.php/resources/view_al
  l?idprotein_nucleic_acid_structure_primary_second
  ary_tertiary_quaternary_three_dimensional_double_h
  elix_DNA_t_page_16fromsearch
• http//www.yteach.co.uk/page.php/resources/view_al
  l?idprotein_nucleic_acid_structure_primary_second
  ary_tertiary_quaternary_three_dimensional_double_h
  elix_DNA_t_page_17fromsearch
• 3. Discuss R groups
• Card sort activity to introduce R groups
• R group interaction discuss how interactions
  cause different secondary, and therefore
  tertiary, protein structures, and changing amino
  acids will change functional group interactions,
  so entire protein could be effected diseases?
• Some r groups are basic, some acidic leads on
  to next lesson

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LESSON TWO - STARTER

• Recap on last lesson write down five things you
  learnt last lesson
• Recap on last lesson involuntary volunteer
  pick on pupils to give information from last
  lesson write it up on board and they should
  copy into their books

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MAIN ACTVITIES

• Draw out the structure of glycine on the board
• Ask the students to draw the structure in acidic
  conditions remind them that acids have low pH
  values, which means excess hydrogen ions
  (protons) (NH3, COOH)
• Ask the students to draw the structure in
  alkaline conditions high pH (low hydrogen
  levels) (NH2, COO-)
• Draw the correct structures on the board
• Explain that functional groups follow the same
  rules
• COOH becomes COO- in alkaline conditions
• NH2 becomes NH3 in acidic conditions
• This exaggerates what happens to the general
  formula
• And thus affects the isoelectric point
• The specific point at which amino acid are not
  ions (these are given to students they do not
  need to remember them all)

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PLENARY

• Define the isoelectric point
• Sort the amino acids (from the card sort
  resource) into groups
• Acidic R groups, alkaline R groups, neutral amino
  acids
• Hydrophilic/hydrophobic (if appropriate)
• Match the structures to their names

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Amino Acid Chemistry Q. 1
H
O
H
C
C
N
OH
H
H
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Q. 2
H
O
H
C
N
C
OH
H
H
Amine Group
Carboxylic Acid Group
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Q. 3

• The -COOH Group is able to donate a protein and
  therefore acts as an acid

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Q. 3

• The -COOH Group is able to donate a protein and
  therefore acts as an acid
• The -NH2 Group is able to accept a proton
  (because of the lone pair)

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Structure of R Groups

• Variety of R groups, for example
• -CH3 (Alanine)
• -CH2OH (Serine)
• -CH2CO2H (Aspartic Acid)
• -(CH2)3-CH2NH2 (Lysine)
• Different properties polar, non-polar, acidic,
  basic

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Structure of R Groups

• Variety of R groups, for example
• -CH3 (Alanine) NON-POLAR
• -CH2OH (Serine) POLAR
• -CH2CO2H (Aspartic Acid) ACIDIC
• -(CH2)3-CH2NH2 (Lysine) BASIC

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Amino acids - R group attractions

• Types of attraction interactions among side
  functional groups in proteins

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LESSON 3
All word documents will be on wiki.
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LESSON THREE
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Ninhydrin Chromatography

• Put spots of 0.01M of amino acid solution 1.5cm
  from the bottom of the chromatography paper. To
  do this first practice with water and filter
  paper, using a capillary tube!
• Make sure you note down which spots are which
  amino acid solution, and allow the spots to dry
• Prepare a solvent mixture of
• 12 cm3 of butan-1-ol
• 3 cm3 of ethanoic acid
• 6 cm3 of distilled water
• In a 1 dm3 beaker and cover the the top with
  cling film to produce a saturated environment
• Carefully, roll the chromatography paper into a
  cylinder and insert it, so it is standing up,
  into the beaker
• Leave for 20 minutes (the solvent should have
  reached the top of the chromatography paper)
• Remove the chromatography paper from the beaker
  and mark (with a pencil) the solvent level
• In a fume cupboard, spray the paper lightly with
  the ninhydrin solution (Ninhydrin is a mixture of
  1M Copper Sulfate, 2M Nitric Acid and 8M Ammonia
  - so use gloves!). Purple dots will form at the
  positions occupied by different amino acids. Dry
  in an oven for 10 minutes
• Work out the Rf value of each amino acid using
  the following expression
• Rf Value distance moved by amino acid
• Distance moved by solvent
• 10. Work out which amino acids the solutions you
  used contain, from the list of Rf values

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Worksheet

• Draw an amino acid
• Highlight the parts of the amino acid that gives
  it its specific acid/base properties
• Explain why these parts give the amino acids
  their properties
• Consider the following amino acids. Work out what
  the R groups are and their chemistry (ie whether
  they are polar/non-polar/acidic/basic)
• Alanine
• Serine
• Aspartic Acid
• Lysine

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LESON FOUR

• Possible starter ask students to jot down
  notes on what they know about polymerisation from
  GCSE and AS. (Should have met addition
  polymerisation when looking at hydrocarbons.)
  Discuss and lead towards condensation
  polymerisation.
• Condensation water comes out of air
• Polymerisation form a long chain polymer from
  monomer units by breaking bond of monomer
  (remember double bond of ethane) and making new
  bonds with next monomer and so on.
• Move from what (condensation) polymerisation is
  to how it can be applied to amino acids (monomer)
  and Proteins (polymer)
• Activity - Get them to draw two amino acids next
  to each other (should know the structure of an
  amino acid by now) And let them attempt to work
  out how the bond is made.
• To do Go through the peptide link on the board.
  Make sure that the OH and H that are removed
  during the polymerisation reaction are coloured
  differently so the students are clear on what is
  happening. See attached.
• Other ideas
• Could use model kits here with two amino acids
  (two glycines) to demonstrate the bonds being
  broken and water coming out. Then pass the model
  round so the students can make the peptide link.

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Condensation reaction

• Joining of two amino acids dipeptide
• Lots of condensation reactions polymerisation
  polymer made polypeptide/protein
• Animation of the reaction that could show on
  projector http//www.biotopics.co.uk/as/aminocon.
  html

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Condensation reaction
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Possible notes to give them/ talk them through

• The peptide link
• The amino acids in a protein chain are linked by
  elimination of a molecule of water between the
  NH2 of one amino acid and the COOH of the next.
  Such a link is called a peptide link.
• This type of link is not easily formed under lab
  conditions but is readily formed in living
  systems where enzymes catalyse the reaction.
• Long chains of amino acids polypeptides can
  be formed in this way.

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LESSON FOUR

• Activity discussion on how proteins are broken
  down. Ask questions, get them to discuss what
  they already know
• Include
• That the process must be reversible.
• Could bring in digestion and pepsin and that need
  to break proteins down to amino acids (smallest
  building blocks) so that we can re use them.
  Also on a molecular level proteins are broken
  down and turned over in cells all the time.
• The opposite of condensation, taking away water
  is what? Bring in acid/alkali hyrolysis.
• See if they can work out the reaction that
  happens during hydrolysis.
• http//www.biotopics.co.uk/as/condensation_and_hyd
  rolysis.html
• http//www.biotopics.co.uk/as/dipeptidehydrolysis.
  html - animation of hydrolysis
• To do make notes on how a dipeptide (two amino
  acids joined together by condensation reaction)
  can be hydrolyses back to the two starting amino
  acids. See attached.
• Plenary questions on the two reactions. See
  worksheet attached.

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GOOD WEBSITES

• http//www.chemguide.co.uk/organicprops/aminoacidm
  enu.htmltop
• http//www.chem4kids.com/files/bio_aminoacid.html