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Chapter 3: Protein Structure and Function -- Part 1
There are macromolecules that play a central role in life.
Chapter 3 begins with a discussion of key properties of proteins and continues with a description of the chemical properties of the building blocks.
You need to learn the names, symbols, and properties of the 20 common amino acids at this point as they will recur throughout the text.
The behavior of weak acids and bases can be reviewed in the appendix to Chapter 3 or in an introductory chemistry text.
The chapter begins with the discussion of the amino acids and then moves on to the linear sequence of the acids.
Next, it describes the folding of the linear polymers into the structures of the proteins.
The higher orders of structure are dictated by the primary structure.
You should know that the majority of functional proteins exist in water and that their structures are stable by the forces and interactions you learned about in Chapter 1.
The chapter ends with a discussion of the theory of how proteins fold.
You should be able to complete the objectives once you have mastered this chapter.
The key properties of the proteins are listed.
Understand how it can be used.
Rationalize the preferences of the different amino acids.
Give evidence that the folding of theprotein appears to be a cooperative transition, and explain why that means it is an "all or none" process.
The structure of cysteine should be drawn.
Match the side chain types in the right column with the side chain types in the left column.
The states of Gly and Pro are different in different places.
Match the levels of structures in the left column with the levels in the right column.
Most proteins lose their biological activity when exposed to acidic pH.
After the synthesis of a polypeptide chain, several amino acids can be modified.
Match the type of modifying group in the left column with the appropriate residues in the right column.
You can see the structure of cysteine.
All the ionizable groups are protonsated.
Histidine is a poor buffer because no one group of ionized people is capable of donating or accepting protons without changing the pH.
The dipeptides can be formed by the 20 L amino acids.
There are possible f and y angles for the main polypeptide chain.
Glycine is less constrained because it lacks an R group.
Proline is more constrained than most of the others because of the R group.
A, b, c, d, and so on.
The polar peptide bonds of the main chain are involved in internal hydrogen bonding in both a-helical and b sheet structures.
The secondary structures are not as polar as the linear sequence.
Most polar and charged residues are located on the surface of the molecule.
The statement is incorrect due to the fact that most of the nonpolar residues are buried in the interior of the proteins.
The statement is incorrect because not all water-soluble proteins have b sheet secondary structures.
Myoglobin lacks b sheet structures and is mostly a-helical.
A low pH 2 will cause the ionizable side chains to be ionized and will cause a large net positive charge to the protein.
The repulsion of adjacent positive charges and the disruption of salt bridges can cause the unfolding of theProtein and loss of biological activity.
The attachment of a fatty acid chain to aProtein can increase its hydrophobicity.
The bond is very stable despite being energetically favored.
In most or ganisms, only one of the two types of biomolecules can be stereoisomers.
The quantities that can be isolated are too small for the direct determination of a primary amino acid sequence.
Recent advances in gene cloning and amplification allow for easy analysis of the genes for a particular molecule.
Two research groups in New York and Los Angeles are analyzing the same type of human cell in the same way.
The f and y values of each amino acid in a run of several are approximately :140U and ;147.
A survey of the location of reverse turns shows that most are located at the surface of the molecule.
Wool and hair are elastic, and both contain long polypeptide chains which are twisted about each other to form cablelike assemblies.
Silk is rigid and resists stretching; it is composed of antiparallel b pleats, which are often stacked and interlocked.
Explain the characteristics of the secondary structures of the proteins.
The cleft where the alanine is located is found in a particular enzyme.
There is no effect on activity if the alanine is changed to a glutamate and the activity is lost.
Provide an explanation for the observations.
The red blood cell has a glycoprotein called Glycophorin A.
There is a portion of the polypeptide that is folded into a helix.
There are long acyl chains in the interior of the bilayer.
Some scientists believe that directions for folding are given to the ribonuclease during its synthesis.
The native three-di mensional structure of aProtein was an automatic consequence of its primary structure.
The earlier view of folding was complicated by the discovery that ribosomes are the location of synthesis.
Both views can be reconciled with the discovery of chaperone proteins.
Suppose you are studying the structure of a monomeric protein that has an unusu ally high proportion of aromatic amino acid residues throughout the chain.
There is a proliferation of computer programs for predicting folding based on sequence.
It is too easy to reverse engineer a routine that will produce the correct answer if the sequence and structure are available.
The solution of HCl has a pH of 2.1.
The charged form of the imidazole ring of histidine is believed to be involved in a reac tion.
Only the N-terminal a-amino group and the C-terminal a-carboxyl group will be ionized.
The internal groups are not ionizable.
Water must be removed.
The acti vation energy barrier makes bonds stable.
The D or the L isomeric form of a substrate is what the metabolism is catalyzed by.
If an animal is to be able to digest a plant's proteins and make its own from them, both the animal and the plant have to make their own.
Knowledge about any one of the three types of sequence yields information about the other two.
It is expected that the coding sequence for a particular protein will be the same among members of the same species.
The published primary amino acid sequence is likely to be the same.
A b sheet is what the structure is most likely to be.
The "low" numbers imply that it is an antiparallel sheet.
The parallel b sheet would have higher numbers.
The CO and NH groups of residues 2 and 3 are not able to form hydrogen bonds.
The groups can't form hydrogen bonds in the hydrophobic environment.
They are more likely to have hydrogen bonds with water.
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