Lesson 3: Amino Acids and Protein Structure

Question 1

What is a protein?

Answer 1

• Proteins consist of one or more peptide chains (single, unbranched chains of amino acids)
• The chains are folded into specific 3-D shapes as defined by the sequence and length of amino acids. The different shapes give proteins their function.

Question 2

What are some functions of proteins?

Answer 2

1) Enzymes (ex: protein kinase)
2) Structural proteins (ex: collagen and elastin)
3) Transport proteins (ex: hemoglobin)
4) Motor proteins (ex: actin and myosin)
5) Storage proteins (ex: iron)
6) Signal proteins (ex: insulin)
7) Receptor proteins (ex: different proteins in your eyes)
8) Transcription regulators (ex: lac repressor)
9) Special-purpose proteins (ex: antibodies)

Question 3

Describe the structure of antibodies.

Answer 3

Composed of four peptide chains - two identical light chains and two identical heavy chains. These chains are held together by disulfide bonds.

Question 4

What is the function of an antibody?

Answer 4

An antibody is a Y shaped protein that has the ability to bind to an antigen at the end of each arm.

• Note: An antigen is a foreign molecule that shouldn’t be in the body.

Question 5

Describe how antibodies work in fighting infections.

Answer 5

1) Antibodies can bind to the virus and neutralize it.
- The top regions of the antibody can bind to the
surface of the virus, preventing the virus from binding
to our cells.
2) Phagocytes (a part of our immune system) have receptors on their membrane that can recognize the bottom of the antibody. The phagocyte can then take up the virus, which is attached to the antibody and destroy the virus.

Question 6

What characterizes strongly hydrophilic amino acids?

Answer 6

Strongly hydrophilic amino acids are CHARGED! (either positive or negative charges)

Question 7

What characterizes mildly hydrophilic amino acids?

Answer 7

Mildly hydrophilic amino acids are NOT CHARGED but have polar covalent bonds

-> polar covalent bonds have more than just carbons and hydrogens

Question 8

What are the characteristics of the special case amino acids?

Answer 8

The special case amino acids are GENERALLY HYDROPHOBIC

Question 9

Why is cysteine a special case amino acid?

Answer 9

Two cysteines can bind to each other and form a disulfide bond which helps to promote protein function

Question 10

Why is glycine a special case amino acid?

Answer 10

It has a single hydrogen as its R group so when the protein folds onto itself it will have a small side chain.

Question 11

Why is proline a special case amino acid?

Answer 11

The R group comes back and binds to itself forming a ring

Question 12

What characterizes hydrophobic amino acids?

Answer 12

Hydrophobic amino acids have NONPOLAR R groups.
These R groups are hydrocarbons (only including carbon and hydrogens)

Question 13

Why is there so much protein diversity?

Answer 13

There are so many possible combinations or possible sequences for a protein.

Question 14

What dictates the protein’s function?

Answer 14

A protein’s SHAPE

Question 15

How does the sequence of amino acids determine the protein’s shape?

Answer 15

The amino acid sequence drives the interactions with water and intramolecular bonding of the linear amino acid chain.

• Nonpolar (hydrophobic) amino acids are sequestered in the inside of a protein
• While polar (hydrophilic) amino acids are on the outside of the protein

Question 16

What is the primary level of protein structure?

Answer 16

The sequence of amino acids

Question 17

What bonds stabilizes the primary level?

Answer 17

Peptide bonds! -> Covalent

Question 18

What is the secondary level of protein structure?

Answer 18

The polypeptide chains form alpha helices or beta pleated sheets.

Question 19

What bonds stabilizes the secondary level?

Answer 19

Hydrogen bonds!

• NOTE: for the secondary level, hydrogen bonding (noncovalent interactions) only occurs between atoms in the peptide backbone. R GROUPS ARE NOT INVOLVED

Question 20

What are alpha helices?

Answer 20

• A ribbon-like structure

Every 4th amino acid, hydrogen bonding takes place between the amino group and carboxyl group in the peptide backbone. These interactions stabilizes the ribbon-like structure.

Remember: R groups are not involved in stabilizing the structure

Question 21

What are beta pleated sheets?

Answer 21

• Several segments of an individual polypeptide chain are held together by hydrogen-bonding in adjacent strands.
• The R groups in each strand project above and below the plane of the sheet. (They are not involved in stabilizing the structure also)

Note: parallel beta sheets go in the same direction and antiparallel beta sheets go in opposite directions

Question 22

What is the tertiary level of protein structure?

Answer 22

Alpha helices, beta pleated sheets, and unstructured regions are folded into specific 3-D shapes.

Question 23

What is the function of unstructured regions in the tertiary level of a protein?

Answer 23

Unstructured regions can provide binding sites for other molecules

Question 24

What bonds stabilize the tertiary structure?

Answer 24

1) Hydrogen bonding
2) Disulfide bonds/bridges -> COVALENT
3) Ionic interactions/salt bridges
4) Hydrophilic/Hydrophobic interactions (van der Waals)

Question 25

Describe disulfide bonds.

Answer 25

A disulfide bond is a COVALENT BOND between TWO cysteines. It contributes to the folding of the protein.

Question 26

Describe ionic interactions in the tertiary structure.

Answer 26

Ionic interactions/salt bridges can form between oppositely charged amino acid side chains

Question 27

Describe hydrophilic/hydrophobic interactions in the tertiary structure

Answer 27

Hydrophobic amino acids will be clustered inward to the center of the protein structure, while hydrophilic amino acids will be on the outside exposed to water.

Question 28

What are the different types of hydrogen bonding in the tertiary structure?

Answer 28

1) Hydrogen bonding between backbone to backbone
2) Hydrogen bonding between backbone to side chain
3) Hydrogen bonding between side chain to side chain

Question 29

How are membrane proteins special?

Answer 29

While normally, hydrophobic amino acids are sequestered while the hydrophilic amino acids are on the outside. For membrane proteins, the hydrophobic amino acids are on the outside forming contact with the hydrophobic fatty acid tails. While the hydrophilic amino acids are in the interior forming hydrogen bonds with one another.

Question 30

What is the quaternary level of protein structure?

Answer 30

Multiple 3-D protein structures are assembled to form larger protein molecules.

• Note: each individual protein is called a subunit.
• Note: not all proteins have a quaternary structure

Question 31

What bonds stabilize the quaternary structure?

Answer 31

1) Hydrogen bonding
2) Disulfide bonds/bridges -> COVALENT
3) Ionic interactions/salt bridges
4) Hydrophilic/Hydrophobic interactions (van der Waals)

• Note: The same forces that stabilize the tertiary structure stabilize the quaternary structure

Question 32

How is hemoglobin an example of a quaternary structure?

Answer 32

Hemoglobin is made up of two copies of alpha globin and two copies of beta globin.

Note: That each hemoglobin subunit carries a molecule of HEME, which is bound to an oxygen molecule. So each hemoglobin protein can carry four molecules of oxygen.

Question 33

What is the function of hemoglobin?

Answer 33

Because each subunit of hemoglobin carries heme, hemoglobin is an oxygen-carrying protein that carries oxygen in our body.

Question 34

Why are misfolded proteins dangerous?

Answer 34

Misfolded proteins do not carry out the appropriate function so therefore they are the primary cause of many human degenerative and neurodegenerative diseases, including:

1) Alzheimer’s Disease
2) Parkinson’s Disease
3) Huntington’s Disease
4) ALS

Question 35

What are chaperones?

Answer 35

Are protein helpers

Question 36

What is a chaperone’s function?

Answer 36

1) Chaperones can help stabilize the structure of a protein while it folds.

2) Chaperones can also recognize misfolded proteins by correcting it or getting rid of it.