I feel as though these chapters just threw me protein structure. I come

with very limited knowledge of proteins and their structure, so these

chapters had a bit too much detail for all at once. I find it

fascinating that all of the amino acids used by organisms to make proteins

are in the L form. I hope we talk about this more in class, because I do

not quite understand the evolutionary mechanism behind that- I suppose the

authors of the text also do not. It's amazing that proteins are so

easily protocoled by DNA, and in vitro synthesis is such a demanding

process- sometimes not even getting the correct folding result. In the

cell, the protein may fold into the needed tertiary structure and partner

with other proteins to form the quaternary structure. These structures

allow such a high level of diversity in both form and function. The

section in Chapter 6 on the actual details of kinetics folding remains a

bit unclear to me.

Chapter 5 primarily discussed proteins: alpha amino acids form the

basic building blocks of these molecules. It was interesting to see how

the chemical structure of the amino acids and their different properties -

eg. hydrophilic, hydrophobic, polar, nonpolar, etc. - allow molecules to

interact in ways that are studied in biology and are important to

life.. I thought the authors' discussion of the use of L and D amino

acids was particularly odd, in that I must agree with their question as to

why one enantiomer is used exclusively in amino acids. I wonder if

someone will discover the reason behind this at some point, and whether

proteins of D-amino acids could be useful. Overall, I felt this chapter

was fairly clear, so I don't have any questions.

Chapter 6 continued the discussion of proteings, but moved on to

secondary and tertiary structure. Despite reading the section on the

different helices and the beta sheet, I was very confused by these

concepts, and especially wondered how they figured it out (since it's so

unclear to me). The discussion of different types of proteins, and some

examples at least put the structures into context. The synthesis

of these proteins is amazingly complex - molecules cross link and

fold in on themselves in precise ways. Because of this it is somewhat

logical to think of it in thermodynamic terms. The overall complexity of

such molecules, however, still impresses me, as does the fact that we know

as much as we do about them. This chapter covered a lot of material, so I

don't feel as though I have a thorough understanding of it yet, so

hopefully the lectures will clear up some of my questions and make things

fall into place.

I found this material to be quite interesting. Trying to visualize how the

side chains of each amino acid would affect the structure of the overall

polymer was challenging but intriguing. The overwhelming number of

possibilities for both primary and the three dimensional structures of

these molecules was amazing. It was fascinating to see how the structure

of hugely complex molecules really made logical sense based on a basic

knowledge of the side chains and how different parts of the polypeptides

could interact with each other. The formation of the peptide bonds also

provided a good analogy to the bonding between nucleic acids, in the

thermodynamic aspects, the seeming elimination of water, and in how it

seems like it could be carried out indefinitley because of the two free

unreacted ends, just like in DNA/RNA. What I thought was the most

interesing, however, were the evolutionary implications. The universality

of the genetic code indicates that all life arose in the same manner, but

what it truly intriguing is the conservation of protein sequences between

species. The homologous sections, as well as the number of differences,

both point towards a common evolutionary ancestor as well as a point of

divergence in order to allow the development of mutations. The fact that

these differences occur, but that the proteins maintain the same basic

functions in both species is really incredible and illustrates the

evolutionary process. Additionally, it is amazing how essentially all of

the eventually extremely complex and diverse structural and functional

aspects of proteins are contained within a simple four character, triplet

code.

Ch. 5

Chapter 5 introduces proteins by going systematically through amino

acids. The zwitterionic and nonionic forms of AA are first explained. The

chirality of amino acids is discussed along with the idea that there are

two enantiomeric forms. But, biologically only the L form is incorporated

into proteins. The amino acids are then introduced systematically:

1. aliphatic/alkane side chains

2. hydroxyl or sulfur containing side chains--more hyfrophilic than

aliphatics. Cysteine is important-->CYSTINE

3. aromatic amino acids--most hydrophobic, absorb light in UV region

4. basic amino acids--histine plays an ezymatic role, strongly polar

5. acidic amino acids and their amides--only AAs to carry a negative charge

at pH7, hydrophilic and tend to be on the surface

6. modified AAs--phospheoserine, 4-hydroxyproline, ( )-hydroxylysine, (

)-carboxyglutamic acid.

Then they discuss peptide bonds in great detail. The end of the chapter

begins to discuss the gene-->protein processes, including,

stop/initiation/regular codons which code for a particular amino

acid. Post-translational processing of proteins is discussed briefly at

the end.

This chapter I understood relatively well I think.

Ch. 6

This chapter begins to elaborate on the secondary and tertiary structures

of proteins, begining with helicies and sheets. Two catagories of proteins

are discussed--fibrous, and globular.

FIBROUS--keratins, fibroin, collagen, elastin

GLOBULAR--variations in folding are important for different functions. The

rules for tertiary folding are listed. The thermodynamics of foldig is

discussed--entropy, various electrostatic interactions, hydrophbicity,

etc. The dynamics of globular protein structure is discussed in relation

to kinetically regulated paths of formation. It is mentioned that proteins

have an ability to be denatured and then when returned to physiological

conditions, naturally return to their "natured" formations. However,

chaperonins are molecules that seem to help the proteins with proper

folding. Motion within globular structures is discussed. It seems normal

that there would be motion within the globular protein because the proteins

are multiple molecules bonded together, and molecules are in constant

motion with changes in energy as they interact with their environment.

The biggest idea I think of this chapter is that all levels of protein

structure are determined by the amino acid sequence which is determined by

gene sequence.

It is interesting to see that net charge on a polypeptide can

range from +2 to -2 as it does for Glu-Gly-Ala-Lys depending on the

pH. Is this nature in contrast to or similar to that observed for

DNA? Also, the charge becomes 0 at the isoelectric point. Does DNA have

an isoelectric point? Lastly, both DNA and proteins can be separated by

gel electrophoresis. Is this done for both depending on charge? For DNA,

the degree of supercoiling can also cause separation, right?