Lecture 2 - Proteins

Question 1

What makes up a protein?

Answer 1

Amino acids

Question 2

How are amino acids linked?

Answer 2

Peptide bonds

Question 3

What is each amino acid composed of?

Answer 3

amino group, alpha-carbon atom, carboxyl group, and side-chain group

Question 4

Why is it useful for side chains of amino acids to be able to rotate?

Answer 4

Gives the polypeptide freedom to have the side chain in any orientation

Question 5

What is the primary structure of a protein?

Answer 5

Amino acid sequence from 5’ to 3’

Question 6

What is the secondary structure of a protein?

Answer 6

Local 3D structure composed of alpha helixes and beta sheets (both of which involve H-bonds between non-sidechain groups on amino acids)

Question 7

What configurations can beta sheets have?

Answer 7

Parallel and antiparallel

Question 8

What interactions are involved in the secondary structures of proteins?

Answer 8

Hydrogen bonds, and electrostatic and van der Waals attractions

Question 9

How is a protein folded in an aqueous environment?

Answer 9

The hydrophobic core region is in the center with nonpolar side chains and the polar side chain sits on the outside of the molecule to form hydrogen bonds with water

Question 10

What is the tertiary structure of a protein?

Answer 10

Globular 3D structure of the protein determined by interactions between often distant amino acids

Question 11

What is the quaternary structure of a protein?

Answer 11

3D structure of a protein complex (protein complex with the orientation of the proteins within it)

Question 12

What are protein families?

Answer 12

Protein families consist of related proteins as they have the same domains and order of domains - critical domains and 3D structure will be very similar amongst family members

Question 13

What are some common domains?

Answer 13

Immunoglobulin module, fibronectin type 3 module, and kringle module

Question 14

What is some information about domains?

Answer 14

• Functional units of a protein
• Each domain confers on a protein a specific function
• A given domain may occur multiple times on a given protein and will be found on many different ones
• A protein may have one or many domains
• Novel proteins are often a result of the addition or subtraction of domains
• Often named after the first protein that was found to have that domain

Question 15

What determines a protein’s chemistry?

Answer 15

The surface conformation

Question 16

What are many changes in proteins driven by?

Answer 16

Phosphorylation

Question 17

What are kinases and protein phosphatases?

Answer 17

Kinases are enzymes that can transfer a phosphate onto another protein or something else and protein phosphatases can reverse the kinase addition

Question 18

What do ubiquitous cell regulators do?

Answer 18

Bind and hydrolyze GTP - GTPases/GTP binding proteins

Question 19

How does signaling by phosphorylated proteins work?

Answer 19

When GDP falls off and GTPase is bound to GTP, it can gain the ability to interact with other proteins, is active in its cellular function, and has enzymatic activity - In GTP bound state, RAS protein can activate kinase

Question 20

How does signaling by GTP binding protein work?

Answer 20

Guanine nucleotide exchange factor (GEF) promotes the exchange of GDP for GTP making it active, and GAP inactivates it by promoting enzymatic activity by stimulating its GTP enzymatic activity and hydrolyzing it into the GDP-bound state