Amino Acids and Proteins B.2

• there are about 20 amino acids that occur naturally

• they are the basic “building blocks” of life/proteins

Draw the general formula of 2-amino acids (2- because both functional groups are attached to the second carbon)

NH2CHRCOOH

http://www.rationalresponders.com/third_revolution

Properties of 2-amino acids (B.2.2)

• Zwitterion (dipolar) – amino acids contain both acidic and basic groups

in the same molecule • therefore, are amphoteric (capable of behaving as

acids or bases) in nature – 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 in a strong acid, H+ is added to an amino acid (the

zwitterion accepts the proton) thus minimizing the effect of the acid added • if in a strong base, the zwitterion donates H+ to neutralize

the base (OH-) to form water

• Isoelectric point– Kahn academy video (5:25)– 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 a process called electrophoresis

Condensation Reactions in order to form polypeptides (B.2.3)

• amino acids will link together to form polypeptides (proteins)

• enzymes are necessary!• the link/bond 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)

Primary Structure

• determined by the number, kind, and order of a.a. in the polypeptide.

• held together by simple peptide bonds.

Proteins have a complex structure which can be explained by defining four levels of structure (B.2.4)

What is a protein video 3:38

Secondary Structure Two types of spontaneously, regular, repeating

structures as the polypeptide is made1. 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

Tertiary Structure • 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 amino acids 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 protein folding• Protein folding

Quaternary Structure example

Analysis of Proteins (B.2.5)

• there are various analytical techniques that can be used to identify proteins and amino acids

• main two are: 1. paper chromatography2. electrophoresis

Paper Chromatography• 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 Rf value and compare to amino acids

with know values

solventbymoveddistancespotbymoveddistanceR f

http://www.google.com/url?sa=i&rct=j&q=paper+chromatography+protein+separation&source=images&cd=&cad=rja&docid=yFWDLs1qAz-ELM&tbnid=I7q_011sOib6IM:&ved=0CAUQjRw&url=http://www.membrane-solutions.com/chromatography_paper_supplies.htm&ei=0sKJUZ-QLaediQL8t4GICw&bvm=bv.46226182,d.cGE&psig=AFQjCNE5sji9CvpXaUd-qVrCWyAkKINzHw&ust=1368069183869553

Electrophoresis• 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

Protein Functions (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