DNA

an inevitable result of the order of nucleotides on DNA.

1. Isolation and purification of the protein followed by direct analysis of amino acid sequence

2. determination of the nucleotide sequence of the gene that codes for the protein

What are some of the significant biochemical conclusions that can be made by studying and comparing dequence information for different proteins?

1. We are now discovering "families of proteins"  that are related by common sequence features and therefore similar biological function. 

2. Information about the evolutionary development of a protein is available from sequence data. 

3. Amino acid sequence can be serched for changes that may lead to dysfunction of a protein.

4. Knowledge of the amino acid sequence of a protein may lead to conclusions about its three-dimensional structure (native confirmation). 

The influence of side chains is noted especially in the natural tendency for globular proteins in an aqueous environment to fold by packing_________________________________________.

This arrangement buries __________amino acid residues away from H₂O and allows _____ and _____ amino acid residues (groups___ & ____) on the surface to interact with H₂O.

1. nonpolar amino acid residues into a hydrophobic core with a hydrophilic surface of polar amino acid residues. 

2. nonpolar

3. polar

4. charged

5. II & III

What is a primary structure?

What is the native conformation of a protein?

The amino acid sequence that is determined by the sequence of nucleotides in the gene for each protein.

The unique three-dimensional structure defined by secondary, tertiary, and quaternary levels.  

The folding of a protein from a random coild into a highly organized structure results in a large decrease in what?

Conformational entropy

From this observation, at first we would predict that the more ordered native conformation is thermodynamically less stable than the random coil; however, other forces are at work that more than offset the loss in entropy and lead to protein structures that are stabilized. 

atoms of amino acid residues

atoms of amino acid residues with water

1. hydrogen bonding

2. hydrophobic

3. ionic

trans

C---N (peptide bond)

αC--N

αC--C

1. What is an α-helix?

2. The fundamental interactions that hold the polypeptide unit in that arrangement are hydrogen bonds between the ______ group of one amino acid residue and the ________ group of the amino acid four residues ahead in the chain. 

A rodlike structure formed by a tightly coiled polypeptide backbone. 

N---H, C==O

There are ____ amino acid residues for each turn in the coil. All of the  NH and C==O groups in the main chain of the α-helix region are _______bonded, leading to a large number of favorable interaction and a highly stabilized strucutral unit. 

No _______bonding between ________ is present. 

3.6

hydrogen

hydrogen R side chains

Explain why α-helices are not predominant in all proteins if it is a highly stabilized structure?

What is an amino acid that severely disrupts α-helix structure?

Secondary structure is dependent on primary structure, and the presence of some amino acids favor the formation of these strucutres, whereas other amino acids destabilize this structure. The main constraining factor in α-helix structure is the exten of interactions between adjacent R side chains. The presence of several adjacent, larger side chains will destabilize the helix and make the structure less favorable. Similarly, several adjacent like-charged side chains repel each other a destabilize hydrogen bonding in the main chain. 

Proline

amide nitrogen

hydrogen bonding

turn

1. Parallel-polypeptide chains run in the same direction (N-C, or C-N)

2. Anti-parallel- polypeptide chains alternate in direction. This is more common in proteins. 

1. They reverse the direction of the main polypeptide chain. 

2. They connect regions of more regular secondary structure (α-helix and β-sheets)

Why are bends considered to be nonregular secondary structure elements?

What is the name of an extended bend?

They are not periodic. 

A loop.

Individual elements of secondary structures are often combined into stable, geometrical arrangements called what?

What holds together supersecondary structures?

Supersecondary structure, or structural motifs.

Favorable noncovalent interactions between side chains. 

What are globular proteins?

What are fibrous proteins?

What is the name of the structure similar to that of a rope that is found in fibrous proteins as a secondary structure?

Water-soluble proteins that play dynamic biological roles in cells.

Proteins that usually perform a structural role (like collagen), and therefore have their own characteristic secondary structure. 

Triple helix, or superhelix. This structure has very high tensile strength with little ability to stretch, which is why it's used in bones and tendons. 

The tertiary structure of a protien describes what?

When do tertiary structures result"?

The positions of all atoms in a protein including the side chains. 

They result when there is the combination of several motifs of secondary structure into a compact arrangement, causing close spatial encounter of amino acids that may be far apart in the polypeptide chain. 

What is the central dogma of protein folding?

What is the definition of native confirmation?

The primary structure determines the secondary and tertiary structures. 

The preordained three-dimensional structure that is the functional form of the protein. The combination of all structure types. 

In the early evens, the formation of local secondary structure begins in a phase known due to its speed as the burst phase. It is often followede by a hydrophobic collapse, bringing nonpolar R side chains of amino acids together, which agregate or coalesce, expelling water from the area and effectively making the molecule more compact. 

The intermediate protein folding stages, the secondary structure is stabilized and domains are created by the combination of motifs. Hydrogen bonding, electrostatic interactions, and disulfide bonds are imprtant binding forces. 

The final steps involve packing domains into a copact core. 

What do molecular chaperones do?

How do molecular chaperones work?

They are proteins that assist in the folding of other proteins by protecting and stabilizing transitory intermediates of folding proteins and guide them through the folding process. 

They bind to unfolded or partially folded polypeptide chains and prevent the formation of interactions that do not lead to the biologically active structure. They also cover exposed non-polar regions on unfolded protein chains to avoid improper or unfruitful hydrophobic interactions. 

Are molecular chaperones substrate specific?

What were molecular chaperones originally called, and why were they called this??

No; they have little substrate specificity and may accept many differen types of unfolded proteins into their protective, interior environments. 

Heat shock proteins because they play a role in preventing the aggregation of heat-denatured polypeptides

What is denaturation?

What structures does denaturation disrupt?

Denaturants disrupt only __________ interactions, not the ________linkages of the ________ structure.

The comlete loss of organized structure in a protein.

Secondary and Tertiary

noncovalent

covalent

primary

What does it mean if a protein in monomeric?

What does it mean if a protein is oligomeric?

Quarternary structures that are the result of associations between identical or nearly identical subunits are called ________. If the subunits are very different, they are described as being _________.

It is composed of only one continuous polypeptide chain

It is composed of two or more polypeptide chains called subunits

Homotypic

Heterotypic

The biological function of hemoglobin is to...

whereas the function of myoglobin is to...

transport oxygen over large distances via the blood of aerobic organisms

act as a reserve supply of oxygen within a local region