Biochem Lecture 2

Question 1

What are the two chemical groups common to all amino acids?

Answer 1

Carboxyl group (COO-)
Amino group (NH3+)

Question 2

What is a peptide?

Answer 2

Amino acids bonded together through a peptide bond.

Question 3

What is a residue?

Answer 3

When an amino acid is part of a peptide or protein, it is called a residue.

Question 4

Is a peptide bond charged or polar?

Answer 4

It is an uncharged polar bond. The O has a partial neg charge and the N has a partial pos.

Question 5

How do residues participate in hydrogen bonding?

Answer 5

The partial charges on the O and N molecules of the amino and carboxyl groups now bonded together make them able to undergo hydrogen bonding. The O is attracted to the H on the N.

Question 6

In which direction are polypeptides read?

Answer 6

By convention, they are read from Amino terminus to carboxy terminus.

Question 7

What is the primary structure of proteins?

Answer 7

It is the linear sequence of amino acids which is determined by the genetic code.

Question 8

What are the secondary structures of proteins?

Answer 8

alpha helices, beta pleated sheets,

loops

Question 9

What stabilizes the secondary structures of proteins?

Answer 9

Hydrogen bonding between the C=O and the N-H. Allows all amino acid sequences to form these secondary structures.

Question 10

Where are the R-groups in an alpha helix?

Answer 10

There is no room inside the helix, so the R-groups are directed towards the outside.

Question 11

What is a coiled coil?

Answer 11

Two alpha helices combine and wrap around each other. This can be because of polar and nonpolar residues grouping.

Question 12

What is an alpha chain?

Answer 12

Three polypeptide chains coil together in a spiraled triple helix.

Question 13

How are beta sheets stabilized?

Answer 13

Hydrogen bonding between the C=O and the N-H across strands in the sheet.

Question 14

Where are the R-groups in a pleated sheet?

Answer 14

They are above and below the plain.

Question 15

What is a loop, and what can it do?

Answer 15

Part of the sequence not part of a regular folding. Serves as a connecting region.

Question 16

How are loops stabilized?

Answer 16

Loops can be different shapes and sizes for any given protein, but they are not random and are stabilized by covalent and non-covalent interactions.

Question 17

What are short loops called that have five or less residues?

Answer 17

Turns.

Question 18

What are supersecondary structures?

Answer 18

AKA Motifs. These are patterns in secondary structures such as orientation of strands in beta sheets and interaction between alpha helices and sheets. Examples are greek key, beta meander, and beta barrel.

Question 19

What makes tertiary protein structures?

Answer 19

Folding and packing together of secondary structures.

Question 20

What is the hydrophobic effect?

Answer 20

Proteins in solution generally fold so that their hydrophobic residues are inside and their polar, hydrophilic residues are outside. This is one of the major driving force in the folding of proteins.

Question 21

What interactions stabilize tertiary structures?

Answer 21

Disulfide bridges,
hydrophobic interactions,
hydrogen bonds,
ionic bonds

Question 22

What are the two global classifications of tertiary structure?

Answer 22

Globular: spherical
Fibrous: rod-like

Question 23

What is a domain?

Answer 23

Stable structural elements within a protein that have individual functions. A separate structural and functional entity.

Question 24

What is the difference between identical sequences and conserved sequences?

Answer 24

In the primary structure of two proteins, identical residues are exactly the same and conserved have several residues interchanged with ones having the same chemical properties.

Question 25

What are protein families?

Answer 25

Proteins with similar domains and therefore similar functions.

Question 26

What is a quaternary structure?

Answer 26

Association of more than one polypeptide chain relative to each other into multi-subunit proteins. The chains are called subunits.

Question 27

What stabilizes quaternary structure?

Answer 27

Covalent and non-covalent interactions.

Question 28

What is the fully active form of proteins?

Answer 28

In the tertiary or quaternary level of structure.

Question 29

What are conformational changes?

Answer 29

Proteins change shape in response to different stimuli in order to carry out their function.

Question 30

What are chaperones?

Answer 30

Proteins that aid in folding but are not themselves included in the end result.

Question 31

What are the three methods to determine the 3d structure of a protein?

Answer 31

X-ray chrystallography: for any protein size, but requires a protein chrystal
Nuclear Magnetic Resonance: Only for small proteins <200 residues
Cryo-electron microscopy: only very large proteins

Question 32

What cause sickle cell anemia?

Answer 32

One amino acid is changed out from a polar one to a non polar one. This causes the protein to form a rod instead of a sphere-like shape.