COLLEGE OF SAINT MARY FALL 2008 FOUNDATIONS OF CHEMISTRY

INSTRUCTOR: DR. PETER ILICH

PROJECT: AMINO ACIDS, PROTEINS & ENZYMES

MY NAME, YEAR OF STUDY, MAJOR (optional)

DATE ________ (draft) ________ (final paper)

Typing conventions::

TIMES NEW ROMAN -- the template text

TIMES NEW ROMAN italics -- my comments

Abstract:

Amino acids, peptides, proteins and enzymes are one of the four major groups of molecules in our body. In this report I will briefly describe the chemical properties of amino acids and explain how they combine into larger units -- peptides & proteins. This is followed by an overview of the structure and function of proteins, their interaction and combination with other major biomolecules -- lipids, carbohydrates and nucleic acids -- and concluded with the most important roles of amino acids acids and proteins in the chemistry and biology of our bodies in health and disease.

Amino Acids [Ch. 20]:

Amino acids are organic chemical compounds with two functional groups: (1) carboxylic group, -COOH and (2) amino group , -NH₂. Both groups are positioned on the same carbon atom -- called alpha-carbon. Given at right is α-amino ethanoic acid or alanine, at right:

The amino group can be position on different carbon atoms but the amino acids found in our body are α-amino acids. The methyl group in alanine is called a RESIDUE; the residue could be a hydrogen atom or another group; there are 21 different residues found in natural amino acids and therefore 21 different amino acids in our bodies.

COMMENT: Now you may list all, or several other amino acids and also mention their trivial names, as well as three- letter and one-letter codes (these codes very important in biochemistry and medicinal chemistry!)

COMMENT: You MUST say few words about the STEREOCHEMISTRY of natural amino acids, for example:

In 3-D space the four groups, H-atom, CH₃-, NH₂- and COOH- groups in alanine are arranged as four corners of a tetrahedron, at left.

The four DIFFERENT groups on a tetrahedral carbon atom can be arranged in space so that they remind of LEFT or of RIGHT hand; we say that such molecule has handedness (chirality). All natural amino acids are left-handed; we use the thick- and dash-line formulas to show this, right:

(S)-Alanine, Ala, A

COMMENT: Now you have to mention that amino acids have acidic group, COOH, and basic group, NH2, so they have properties of both acids and bases. You should mention the approximate pKa range of amino acid groups (roughly between 2 and 11). Definitely mention that amino acid exist as double ions "zwitterions", show a structure of, for example, alanine zwitterion.

COMMENT: Now is a good place to say something about the Metabolism of Amino Acids [Ch. 25]. Metabolism of aminoacids (AA) is of course essential for the functioning of our bodies but we will describe it very briefly:

You should emphasize that AA are one of the sources of nitrogen in living organisms; mention the urea cycle but do not spend too much time or space on it.
Mentioned and perhaps give a formula of one or two major reactions of amino acids, from the textbook.
Definitely mention the division of AA into non-essential (those we can synthesize in our bodies) and essential -- those AA that we cannot synthesize in our bodies and need to consume in our diet (e.g. tryptophan, Trp, W).

Keep this whole part short (1/2 - 3/4 page).

PEPTIDES & PROTEINS:

Most of the amino acids in our bodies are not free, single molecules, but parts of larger molecules - peptides and proteins.

Two amino acids, Gly and Ala (left) can combine to give a dipeptide and a water molecule; such chemical reaction is called condensation, at right:

A dipeptide can condense with another amino acid to form tripeptide, then tetraapeptide, and so on. In the end a polypeptide is formed: a long, string-like macromolecule that can contain thousands or hundreds of thousands of amino acids. Note that a peptide consist of a long string of Ca, C=O and NH groups; when bound together, the carbonyl and amino groups are called an amide, or amido group. In peptides the NH and C=O groups are on opposite sides and therefore a peptide bond is also known as trans-amido bond. This is very important for the structure and function of peptides and their composite compounds -- proteins. Given below is a generic pentapeptide:

Notice that during the condensation reaction the carboxylic, COOH, and the α-amino groups, α-NH₂, of single amino acids are condensed into amides and are not anymore active as acids and bases. Only one, terminal COOH and one, terminal NH₂ group remain, in a small as well as in a peptide that contains a million amino acids. The "R" groups are the residues, H in Gly, CH₃- in alanine, phenol in Phe, ... etc. The string of amino acids is called a SEQUENCE or PRIMARY STRUCTURE of peptide or protein. The sequence is an importnat determinant of the molecular structure and biological properties of peptides.

COMMENT: You may want to mention that in some peptides and proteins in living organisms the sequence is preserved through evolution. In other cases the sequence is variable. Sometimes a change in a single amino acid and a certain peptide in our body can have devastating physiological consequences (e.g. sickle cell anemia, HIV-AIDS); these instances are known as single-point mutations.

COMMENT: Now you may talk about the 3-D structures and shapes of peptides and proteins; there is much of this material available on, for example, Google Image, but do not get carried away and put too much material. It is essential that you mention two major types of so-called secondary peptide structures: a-helix [Textbook, Fig. 20.6] and b-sheet [Fig. 20.7]and show their 3-D formulas. All known peptides are made of helices and sheets or combinations thereof. Some peptides do not have much of structure and are called random coils.

COMMENT: You may want to add, on your own, about the physiological and medical implications of peptides structures. The process of peptide folding (PEPTIDE FOLDING!) into proper helix or sheet structure is essential; if a protein gets miss-folded it causes severe pathologies in our bodies, for example BSE (Bovine Spongiform Encephalopathy, or "mad cow" disease) and Alzheimer's disease. There is a lot of this type material on the Internet.

COMMENT: Now you may follow the rest of the Chapter 20 and mention the major issue: globular proteins, -S-S- bonds and hair-styling, ... etc. but do not elaborate too much. If you wish, at this point you may add your own little "pet project", i.e. describe a particular peptide or protein that has important physiological function; you may Google out an amazing amount of this type material.

Both small and large peptides are found in our bodies; small peptides, like the tetrapeptide luteinizing hormone releasing hormone, LHRH, can regulate very important functions in our bodies. In other living organisms, certain smaller peptides can have lethal effects on humans; for example, the toxic substance in many poisonous mushrooms are cyclic peptides [e.g. you may check for Amanitin on Google Image].

ENZYMES [Ch. 22]:

COMMENT: This is a large and complex area but it is so important that you will have to mention at least something about it.

All chemical reactions in our bodies are CATALYZED. A CATALYST is an agent which helps a chemical reaction but itself does not undergo a chemical change. For example, if hydrogen and oxygen gas are in contact with finely dispersed platinum [check the Periodic Table of Elements to see where is platinum, Pt] they will make water, H₂O. Platinum powder in this reaction does not change; it is a catalyst. The biological catalysts are made of peptides and other non-peptide groups and together they make proteins. All of major catalysts in our bodies are proteins.

COMMENT: Now you may follow parts of the Ch. 22 (but not all of it; e.g. you may choose to skip writing too much about "High energy compounds", Ch. 22.9). It is important to mention that enzymes are specific, i.e. an enzyme reacts with certain compounds but not with all compounds. Another important thing is that some enzymes in living organisms are very efficient, more efficient than anything we human are able to put together. Now you may choose to add a little project on your own, e.g. HIV protease, or you may go to Google Image and just type "Enzyme". If you need help and guidance with this email me or stop by; I'll be more than glad to help you.

SUMMARY:

COMMENT: Once done, it is good to summarize the topic. In your summary, mention the amino acids, the peptides, the primary, secondary, etc,... structure, the importance of sequence preservation (genetic modifications), and protein folding, and the function and importance of enzymes.

COMMENT: All of these these are actually very interesting -- and useful knowledge -- and it is easy to get carried away and make a large report with a lot of pictures and formulas. Try not to exceed ten (10) pages total.