AMINO ACIDS AND PROTEINS QCA

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.

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

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

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.

LESSON ONE - STARTER 1.Write down five things in your books about amino acids 2.Talk to the person next to you about amino acids for one minute – I’ll call on you to find out some ideas (write all on board, discuss) 3.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)

MAIN ACTIVITIES 1.Link topic to the GCSE Biology topic – food digestion, protein breaks down to give peptides and amino acids, amino acids get absorbed 2.Relevance of topic – talk about important proteins and enzymes Insulin and glucagon – diabetes – case study? ree_dimensional_double_helix_DNA_thttp:// ree_dimensional_double_helix_DNA_t Keratin – hair ree_dimensional_double_helix_DNA_t_page_15&from=searchhttp:// ree_dimensional_double_helix_DNA_t_page_15&from=search Albumin – cooking eggs ree_dimensional_double_helix_DNA_t_page_16&from=searchhttp:// ree_dimensional_double_helix_DNA_t_page_16&from=search ree_dimensional_double_helix_DNA_t_page_17&from=searchhttp:// ree_dimensional_double_helix_DNA_t_page_17&from=search 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

LESSON TWO - STARTER 1.Recap on last lesson – write down five things you learnt last lesson 2.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

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) (N + H 3, COOH) Ask the students to draw the structure in alkaline conditions – high pH (low hydrogen levels) (NH 2, COO - ) Draw the correct structures on the board Explain that functional groups follow the same rules –COOH becomes COO - in alkaline conditions –NH 2 becomes N + H 3 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)

PLENARY 1.Define the isoelectric point 2.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

Amino Acid Chemistry Q. 1 C H H C N O OH H H

Q. 2 C H H C N O OH H H Amine Group Carboxylic Acid Group

Q. 3 The -COOH Group is able to donate a protein and therefore acts as an acid

Q. 3 The -COOH Group is able to donate a protein and therefore acts as an acid The -NH 2 Group is able to accept a proton (because of the lone pair)

Structure of ‘R’ Groups Variety of ‘R’ groups, for example: -CH 3 (Alanine) -CH 2 OH (Serine) -CH 2 CO 2 H (Aspartic Acid) -(CH 2 ) 3 -CH 2 NH 2 (Lysine) Different properties: polar, non- polar, acidic, basic

Structure of ‘R’ Groups Variety of ‘R’ groups, for example: -CH 3 (Alanine) NON-POLAR -CH 2 OH (Serine) POLAR -CH 2 CO 2 H (Aspartic Acid) ACIDIC -(CH 2 ) 3 -CH 2 NH 2 (Lysine) BASIC

Amino acids - R group attractions Types of attraction interactions among side functional groups in proteins

LESSON 3 All word documents will be on wiki.

LESSON THREE

Ninhydrin Chromatography 1.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! 2.Make sure you note down which spots are which amino acid solution, and allow the spots to dry 3.Prepare a solvent mixture of: 1.12 cm3 of butan-1-ol 2.3 cm3 of ethanoic acid 3.6 cm3 of distilled water 4.In a 1 dm3 beaker and cover the the top with cling film to produce a saturated environment 5.Carefully, roll the chromatography paper into a cylinder and insert it, so it is standing up, into the beaker 6.Leave for 20 minutes (the solvent should have reached the top of the chromatography paper) 7.Remove the chromatography paper from the beaker and mark (with a pencil) the solvent level 8.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 9.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

Worksheet Draw an amino acid Highlight the parts of the amino acid that gives it it’s 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

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.

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:

Condensation reaction

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.

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 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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