B.2

(B.2.2)
• Zwitterion (dipolar)
– amino acids contain both acidic and basic groups in the same molecule
• therefore, are amphoteric in nature (capable of behaving as acids or bases)
– amines can accept a proton
– carboxylic acids can donate a proton

• Buffers
– buffer solution
• the pH of the solution is "resistant" to small additions of either a strong acid or strong base
• used as a means of keeping pH at a nearly constant value
– the amphoteric nature of amino acids makes it possible for them to act as buffers in aqueous solutions
• when a strong acid, H + , is added to an amino acid, the zwitterion accepts the proton, thus minimizing the effect of the acid added
• if a strong base OH is added, the zwitterion donates H + to neutralize the base to form water

• Isoelectric point
– the isoelectric point is the pH value at which the negative and positive charges are equal
• this is unique for each a.a. at a certain pH
– used to separate proteins in electrophoresis

(B.2.3)
• amino acids will link together to form proteins
• enzymes are necessary!
• the link is between carboxyl group on one a.a. and the amino group on the other
• water is formed and remaining N and C link together with a peptide bond
• peptide bonds YouTube (1:14)

(B.2.4)
• determined by the number, kind, and order of a.a. in the polypeptide.
• held together by simple peptide bonds.

Two types of spontaneously, regular, repeating structures as the polypeptide is made
1. alpha helix – a coil or zigzag shape that results from the hydrogen bonds along the strand

2. beta pleated sheets – back and forth folding of polypeptides because of hydrogen bonds between adjacent polypeptides or in the same strand

• highly specific looping and folding of the polypeptide because of the following interactions
between their R-groups:
– covalent bonding-- disulfide bridges formed when two cysteine molecules combine due to sulfur in their R groups
– hydrogen bonding-- between polar groups on the side chain
– ionic attractions-- formed between polar side groups
– van der Waal’s attractions-- between non-polar side groups
• this tertiary level is the final level of organization for proteins containing only a single polypeptide chain

Quaternary Structure
• linkage of two or more polypeptides to form a single protein in precise ratios and with a precise 3-D configuration.
• some proteins have a prosthetic group (a non-peptide)
– these proteins are called conjugated proteins
• ex. hemoglobin
• John Kyrk folding
• Protein folding

Quaternary Structure example

(B.2.6)
• Structure
– fibrous proteins provide structure and strength ( muscle, cartilage, skin, bones, hair)
• Transport
– hemoglobin in the red blood cells is vital in carrying oxygen
• Hormones
– have a regulatory effect on specific cells/organs in the body
• Immunoproteins
– play a key role in the fight against infection (antibodies)
• Energy Storage
– play an important role in the human body as energy storage
• Enzymes
– catalyze biochemical reactions (1000’s) within the body

(B.2.5)
• there are various analytical techniques that can be used to identify proteins and amino acids
• main two are:
1. paper chromatography
2. electrophoresis

• break peptide bonds in the protein and obtain constituent a.a.
–
(use 6 M HCl, 110
°
C)
• place sample spot on paper and set paper in solvent
• amino acids separate based on polarity
• calculate R f value and compare to amino acids with know values
R f
 distance distance moved moved by spot by solvent

• this technique separates charged molecules based on their ability to migrate when an
electric field is applied to the system sample is placed in a gel and electricity applied
• different a.a. will move at different rates towards a (+) or (-) electrode
• will stop at different distances
– this is its isoelectric point where a particular a.a. will not move as its charges are balanced
– distances can then be compared with known values for identification