Cell Biology, Chapter 4

Front 1

What is the distinction between a protein and a polypeptide?

Back 1

A polypeptide is a linear polymer of amino acids linked by peptide bonds. A protein is a functional unit consisting of one or more polypeptides.

Front 2

What is the chemical basis of the differences among amino acids? How do these differences account for the function of proteins?

Back 2

The different properties of amino acids (e.g. hydrophobic/hydrophilic, charged/uncharged) are determined by their particular side chains. These difference cause the polypeptide to fold into a particular 3D shape that performs a given function.

Front 3

What are the four levels of protein structure. Give basic definitions of each of these.

Back 3

1. Primary Structure- the linear sequence of amino acids making up the polypeptide chain.
2. Secondary Structure- conformation of portions of the protein
3. Tertiary Structure- conformation of the entire protein
4. Quaternary Structure- association of multiple polypeptide subunits into functional proteins.

Front 4

What determines the AA sequence of the primary structure? What does this suggest about the effect of mutations on proteins?
What bonds are operative in the primary structure?

Back 4

The DNA sequence of the gene determines the AA sequence. Mutations will effect his sequence, and thereby affect protein structure.

Covalent peptide bonds are operative in the primary structure.

Front 5

What are individual amino in a polypeptide chain called?

Back 5

The individual amino acids in a polypeptide chain are called residues.

Front 6

What are the two basic types of amino acids?

Back 6

Polar amino acids, which are hydrophilic; and, non-polar amino acids,which are hydrophobic.

Front 7

What is the secondary structure? What kind of bonds are involved in the secondary structure? What parts of the molecule participate in these bonds? Name the 2 common secondary structures. Why are they observed so frequently?

Back 7

The secondary structure describes the conformation of portions of the polypeptide. Secondary structures (alpha helix & beta pleated sheet) form as a result of hydrogen bonding between elements in the peptide backbone (NH~O=C). The side chains are not involved in this hydrogen bonding. Since these structures are somewhat independent of AA type, they are observed in many proteins.

Front 8

What level of protein structure has the alpha helix? In what pattern, and along what axis does the hydrogen bonding occur? Where does this place the R-groups?

Back 8

The alpha helix is part of the secondary structure. Hydrogen bonding occurs between every 4th amino acid in the chain. The hydrogen bonding is parallel to the cylindrical axis of the helix. The R-groups are on the outside of the helix.

Front 9

What are the physical properties of the alpha helix. Give an example that illustrates this.

Back 9

The alpha helix is stretchable in the direction of its cylindrical axis, because that movement only involves the breaking of hydrogen bonds, not covalent bonds. The wool protein has a lot of alpha helices, so it is a stretchy fabric.

Front 10

How are some alpha helices able to cross the lipid bilayer? Why is this biologically significant?

Back 10

Alpha helices with hydrophobic side chains can integrate into the lipid bilayer. This allows for the existence of transmembrane proteins, since it allows for domains on both sides of the plasma membrane.

Front 11

What is a coiled coil? What level of polypeptides structure is this? What is the chemical basis of this phenomenon?

Back 11

A coiled coil is multiple alpha-helices intertwining to form a single thread. The is on the level of secondary structure. Coiled coils results when two alpha helices each have a stripe of hydrophobic amino acid chains (on every 4th amino acid); these hydrophobic regions associate with each other, forming the coiled coil.

Front 12

What is a beta-pleated sheet? What level of protein structure? How are the H-bonds oriented with respect to the sheet? What are physical properties of beta sheets; give an example.

Back 12

Beta-pleated sheet is a secondary structure that resembles an accordion surface. The H-bonds are perpendicular to the orientation of the sheet, unlike the parallel alpha-helical h-bonds. Beta-sheets are unstretchable; like silk threads.

Front 13

Can you see an alpha helix in only one strand of the amino acid? What about beta-sheets? If not, what must the orientation of the multiple chains be wrt the others?

Back 13

Since the alpha-helix has parallel H-bonds, it does not need a nearby chain to assemble. However, beta-sheet h-bond perpendicularly, they need an adjacent chain that runs antiparallel (opposite direction) to the first chain.

Front 14

What is true of the regions of a polypeptide that are not parts of the secondary structure?

Back 14

These hinges and loop are often the most flexible parts of the protein. Not surprisingly, these regions are the sites of the protein's biological activity.

Front 15

What is the tertiary structure of a protein? What bonds are operative at the tertiary level?

Back 15

The tertiary structure refers to the intramolecular (i.e. not involving other polypeptides) conformation of the entire polypeptide. Non-covalent interactions between the R-groups are operative at the tertiary level.

Front 16

What are the 2 basic protein shapes that emerge from tertiary structures? Describe the typical functions of each of these.

Back 16

The two protein shapes that emerge from tertiary structure are fibrous proteins (long strands or sheets that resist pulling) and globular proteins (ball-like, with complex shapes)

Front 17

Name 4 kinds of forces that exist in tertiary structures. What do all these forces have in common? What force is the exception to this rule?

Back 17

All these forces are non-covalent interactions (except disulfide bridges, which are covalent) occurring among the R-groups of a single polypeptide.

1. Van der Waals force- between non-polar side chains.
2. Hydrogen bonds- when they occur btw R-groups, they're tertiary; when among backbone components, they're secondary.
3. Ionic bonds (between charged R-groups)
4. Disulfide bridges- -SH groups between cysteine molecules stabilizes structure (tertiary if within one polypeptide; quaternary if between two polypeptides).

Front 18

What do studies showing that denatured proteins will spontaneously renature in vitro prove?

Back 18

The information necessary for proper folding is inherent in the primary structure. Also, for any given protein there is only one stable conformation.

Front 19

How do proteins typically organize its components in an aqueous environment?

Back 19

They will have a hydrophobic region at the core, shielded from water, and a hydrophilic surface with hydrophiilic amino acids.

Front 20

What is quaternary structure? What bonds are operative at the level of quaternary structure? What kinds of bonds are these?

Back 20

Quaternary structure refers to the linking of multiple polypeptides by intermolecular R-group interactions. These interactions are mostly non-covalent, except for disulfide bridges.

Front 21

What is a disulfide bridge? What levels of protein structure have it? Why is it noteworthy.

Back 21

A disulfide bridge is a covalent bond between the -SH's of 2 cysteine AAs. The disulfide bridge is seen at the tertiary and quaternary level. Disulfide bridges are noteworthy because they are the only covalent bonds observed outside the primary structure.

Front 22

What are molecular chaperones?

Back 22

Molecular chaperones are proteins that bind to the polypeptide to encourage it to fold correctly.

Front 23

What is the difference between a protein and a polypeptide?

Back 23

All proteins are also polypeptides. Not all polypeptides are also proteins.

A polypeptide is a chain of amino acids, while a protein is a functional unit consisting of one or more polypeptide.

Front 24

What are protein domains? How did protein domains evolve?

Back 24

Protein domains are regions of a protein that fold independently and function independently from the other domains. Certain exons got added to existing genes, imbuing the new protein with the functional properties of the added domain. For instance, a calcium-sensitive domain added to a protein will make the new protein calcium sensitive.

Front 25

How, in general, does the cell control the activity of proteins? How, more specifically, does the cell accomplish this? Define allosteric interactions.

Back 25

Cells control the activity of their proteins by altering their shapes between active and inactive conformations. Most proteins can be controlled through allosteric interactions, which involve shape changes as a result of binding to a non-active site.

Front 26

What are two common and important types of allosteric control? Describe the general processes.

Back 26

Protein phosphorylation (by kinases) involves the addition to a phosphate group to the protein, changing its shape and thus its function.

GTP/GDP are also allosteric regulators of protein activity.