Lecture 4: Proteins and Nucleic Acids

Question 1

What occurs during the tertiary folding structure?

Answer 1

• Folding includes side chains
• Can result in a fully functional protein
  -Formed by a bunch of low energy interactions
  -This is still a monomer

Question 2

List the interactions that occur during the tertiary step of protein folding(5)

Answer 2

1. Hydrogen bonds between side chain and carbonyl group
2. Hydrogen bonds between two side chains
3. Hydrophobic interactions + van der waals interactions between uncharged side chains
4. Disulfide bonds between cysteines(amino acid)
5. Ionic bond between the amino and carboxyl group

Question 3

How is the disulphide bond/bridge created during folding?

Answer 3

Cysteines have a sulfide group, during the folding to get the tertiary structure the cysteines come close together even if they have many amino acids between them and they then form a disulfide bond
-The disulfide bond is the only covalent bond that forms outside of the peptide bond and the only covalent bond between two amino acids

Question 4

Hydrophobic interactions during tertiary folding

Answer 4

-Stretches of hydrophobic amino acids will rearrange away from water(minimizes disruption of hydrogen network)
-All the hydrophilic amino acids will rearrange to interact with water, they will be on the outside

Question 5

What’s the major force of protein folding?

Answer 5

Hydrophobic interactions

Question 6

What happens during the quaternary structure?

Answer 6

-Some proteins are not yet functional after the tertiary folding, so they must undergo another step of folding to become a quaternary structure
-In the quaternary stage proteins have to form either a dimer or tetramer

Question 7

Dimer vs Tetramer

Answer 7

Dimer: Combination of two polypeptides
Tetramer: Combination of four polypeptides

Question 8

Consequences of increased temperature on protein

Answer 8

• Increased temperature can cause proteins to denature

Question 9

Consequences of mutations

Answer 9

Mutate a single amino acid in a polypeptide chain can partially or sometimes completely destroy protein function or it can do nothing at all

Question 10

How would you prove that proteins carry everything needed for folding in their primary sequence?

Answer 10

1. Heat up the ribonuclease(protein) to 80 degrees.
2. At 80 the protein will denature.
3. Bring the protein back down to 20 degrees, if it refolds at 20 degrees this proves that the primary sequence contains everything needed for folding

Question 11

What is protein turnover?

Answer 11

-Half-life
-Breakdown of protein into amino acids and then resynthesis of proteins
-Break down of old useless proteins to then make more new ones
-Occurs constantly in cells

Question 12

What are chaperones?

Answer 12

-Specialized proteins that help keep other proteins from interacting inappropriately with another.
-They keep proteins separated from each other until they mature and individually fold and then they are released

Question 13

Basic Structure of Nucleotides

Answer 13

1. Nitrogenous Base
2. Backbone made up of sugar
3. Phosphate group

Question 14

What are the sugars found in DNA and RNA?

Answer 14

DNA: Deoxyribose (H)
RNA: Ribose (OH)

Question 15

What carbons are used in the elongation of DNA and RNA?

Answer 15

Carbons 3 prime and 5 prime

Question 16

Are phosphates monomers or polymers?

Answer 16

-They can occur as monomers(monophosphate)
-They can also occur as polymers(diphosphate, triphosphate)
-Contain “energy rich” bonds

Question 17

Name the two types of nitrogenous bases

Answer 17

-Pyrimidines
-Purines

Question 18

Pyrimidines vs Purines (and examples)

Answer 18

Pyrimidines: made up of a single aromatic rings (Cytosine, Uracil(RNA), Thymine(DNA))
Purines: made up of a double aromatic ring (Guanine, Adenine)

Question 19

What direction do RNA and DNA polymerize in?

Answer 19

5 prime to 3 prime direction

Question 20

Phosphodiester linkages

Answer 20

Occur to create DNA/RNA chain
-Rleases water
-Bond between OH of phosphate(attached to 5’ carbon)and OH of pentose sugar(attached to 3’ carbon)

Question 21

Why doesn’t purine pair with another purine?

Answer 21

Purine-Pyrimidine is the only pair that can fit within the DNA double helix

Question 22

What bonds with guanine?

Answer 22

Cytosine bonds with guanine

Question 23

What bonds with adenine?

Answer 23

Adenine bonds with thymine

Question 24

How do nucleotides bond?

Answer 24

-Nitrogenous bases are found on the inside of the double helix since they contain all of the genetic material.
-Phosphates are found on the outside of the double helix
-Hydrogen bonding between nucleotides

Question 25

Does RNA form a double helix?

Answer 25

Occasionally, RNA forms a double helix(it is short lived)

Question 26

What does RNA do?

Answer 26

Stores genetic information and executes it(cutting other RNA molecules)

Question 27

How do hydrophobic interactions influence the double alpha-helix?

Answer 27

At every fourth position of each alpha helix there is a hydrophobic amino acid. When two alpha helixes come together to create the double helix they make sure that all of the hydrophobic amino acids are aligned which gives rise to the double helix shape

Question 28

Why is the alpha helix structure beneficial?

Answer 28

- Provides extra strength to tendons, hair and feathers

Question 29

How to tell if an alpha-helix is in the tertiary or quaternary structure?

Answer 29

Tertiary Structure: Both alpha-helixes come from the same polypeptide chain Quaternary Structure: Each alpha-helix comes from a different polypeptide chains making a polymer

Question 30

What stages of protein folding require energy and which stages release energy?

Answer 30

Primary Structure: Requires energy(peptide bond formation) Secondary Structure: Releases energy(occurs spontaneously) Tertiary Structure: Releases energy(occurs spontaneously) Quaternary Structure: Releases energy(occurs spontaneously)

Question 31

Why is protein turnover important?

Answer 31

-Proteins often get damaged due to changes in pH or temperature changes thus it is important to constantly be replacing them

Question 32

What does a long DNA/RNA molecule begin and end with?

Answer 32

Begins with a 5' phosphate group and ends with a 3' hydroxyl

Question 33

How is DNA formed?

Answer 33

Two antiparallel strands held together by hydrogen bonds between the bases(A-T, C-G)

Question 34

Which is more stable A-T or G-C?

Answer 34

G-C is more stable than A-T, since G-C forms three hydrogen bonds

Question 35

Which is more stable DNA or RNA?

Answer 35

DNA due to the helical structure

Question 36

Hydrogen bonding in RNA vs DNA

Answer 36

RNA: hydrogen bonding occurs within the same macromolecule DNA: hydrogen bonding occurs within different macromolecules

Question 37

What bases are found in RNA vs DNA?

Answer 37

RNA: A, U, G, C DNA: A, T, G, C

Question 38

Does DNA have a tertiary/quarternary structure?

Answer 38

No, only primary and secondary

Question 39

What is the secondary structure of RNA?

Answer 39

Single strand of RNA folds back on itself to form a double helix "stem" and single stranded "loop"