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Amino Acids:

Amino Acids:

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Amino Acids:. Peptide Bond. * Elimination of water upon formation. * Peptide bond is flat. Non-polar. Aromatic. Residues (R’s):. + Charged. Polar, uncharged. - Charged. Groups of Amino acids:. Amino Acid Types:. * Water-loving ( polar ): - Charged: Has an NH3+, or COO- - PowerPoint PPT Presentation

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Page 2: Amino Acids:

Peptide Bond

Page 3: Amino Acids:

* Elimination of water upon formation. * Peptide bond is flat.

Page 4: Amino Acids:

Non-polarAromatic

+ Charged

- ChargedGroups of Amino acids:

Residues(R’s):

Polar, uncharged

Page 5: Amino Acids:

* Water-loving (polar):- Charged: Has an NH3+, or COO-- not charged: Typically, contain an oxygen.* Water-’hating’ (non-polar):-Typically, R’s do not contain any oxygen, or Aromatic.

* Small – Flexible (Glycine)

Amino Acid Types:

Page 6: Amino Acids:

CCOON

H HH H

Amino acid:

Page 7: Amino Acids:

Let’s build a peptide (short protein):

A. Receive a page of an amino acid. Draw in the atoms of the “R” group.

B. Color the R group by category:Charged positively – BlueCharged negatively – RedPolar uncharged – BlackNon-polar, Aromatic – Yellow

Step One: Prepare amino acid

Page 8: Amino Acids:

Step Two: Connecting by peptide bond3. Find the –OH group for the COOH and the –H from the NH2 side. Circle them. 4. With your neighbor: One cuts out the OH, and the other the –H.5. Bring the C=O and N-H together with a bond. Use Clip to connect.

Page 9: Amino Acids:

We just made a class – size peptide. It has two edges: COOH and a NH2.

The 3-dimentional structure will be determined by the categories of the amino acids (coloring)..

Page 10: Amino Acids:

1. How many 3-digit numbers are possible using 2,3,4? Explain.

2. Like-wise, how many 3-long proteins can be made at random from just 3 amino acids: Alanine, Histidine, Serine?

3. Repeat but using all possible 20 known amino acids.

Page 11: Amino Acids:

Diversity of Structures creates diversity of

functions... In fact, proteins range between 20 to 1000 amino acids (average ~ 100 amino acids).

Which means ______ random combinations!

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Diversity of Amino Acid Sequences generated diversity at least as large of 3D structures.

Lamin

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..but how does the amino acid sequences (primary structure) determine the 3D structure?

The side chains interact:

Page 16: Amino Acids:

Hydrogen Bond

•Occurs between a hydrogen ‘donor’ and ‘acceptor’:

Donor = Has a partially charged H.Acceptor = Has a partially negatively charged.

Page 17: Amino Acids:

Electrostatic Interactions:

•Opposite charge – attraction•Same charge = repultion

Page 18: Amino Acids:

Disulfide BondsAn actual covalent bond.

Is relatively strong, but not very common.

Page 19: Amino Acids:

Van der Waals Interactions* Between atoms that are close enough:Attraction between electrons of one atom to the nucleus of another.

* The weakest of all, but numerous. * Associated with hydrophobic exclusion.

Page 20: Amino Acids:

Hydrophobic Exclusion:Rejection by the surrounding water forces R groups to come together, minimizing the contact with water.

A MAJOR force in protein folding into domains.

Hydrophobic folding

Page 22: Amino Acids:
Page 23: Amino Acids:

Splitting Water1 out of every 550 million water molecules can spontaneously break into and OH- (‘Hydroxyl’):

H2O H+ (‘proton’) + OH- (‘Hydroxide’)

H+: No electrons, only 1 proton)OH_: One Extra e-.

Page 24: Amino Acids:

Acids: Chemicals that dissociate in water to H+ ions.Bases: Chemicals that dissociate in water and absorb H+ and therefore reduce the acidity H+ Concentration is measured in molarity: Mole = 6.02x1023. 1 Molar = one mole per liter.

Pure water contain 10-7 moles/liter.

Page 25: Amino Acids:

pH: Power of Hydrogen

* pH is the (– logarithm) of H+ concentration. bases are low in H+ (high in OH-).* Accordingly pure water is:-log (10-7) = 7

14* Therefore, a change in one unit of pH in fact means a ‘jump’ of ten fold the concentration.

Page 26: Amino Acids:

pH: Power of HydrogenpH ranges from 1 to 14:

71 14High H+ Low H+

Acids BasesNeutral2 3 4 5 6 9 10 11 12 138

pH of solutions is typically examined with indicator diesAdd examples of the household materials to the scale

Page 27: Amino Acids:

The pH Scale Measures the Concentration of H+ ions.

Acidic Basic(Colors of an indicator)

Low pH High pH

Page 28: Amino Acids:

Demo: Adding acid to a protein solution from Egg white.

a. Describe: What happened? b. What other conditions would give the same effect?

So, acids can be harmful to proteins

Page 29: Amino Acids:

Hydrogen Bonds are interrupted by acids and sometimes by bases.

Many of the forces that hold a protein fold together are hydrogen bonds:

O-H····O

H+

Page 30: Amino Acids:

To maintain the pH of a body solution we use substances that can stabilize the pH. They are called buffers. The most important buffer in our body (pH 7.4) is carbonate:

H2O + CO2 H2CO3 HCO3-+ H+

So, is this an acid or a base?

Page 31: Amino Acids:
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Exercise:

Use Toobers and Tacks to demonstrate how the primary sequence of a protein can determine the 3-dimentional structure of a protein.