Lecture 4: Proteins and Nucleic Acids Flashcards

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1
Q

What occurs during the tertiary folding structure?

A
  • Folding includes side chains
  • Can result in a fully functional protein
    -Formed by a bunch of low energy interactions
    -This is still a monomer
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2
Q

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

A
  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
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3
Q

How is the disulphide bond/bridge created during folding?

A

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

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4
Q

Hydrophobic interactions during tertiary folding

A

-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

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5
Q

What’s the major force of protein folding?

A

Hydrophobic interactions

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6
Q

What happens during the quaternary structure?

A

-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

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7
Q

Dimer vs Tetramer

A

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

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8
Q

Consequences of increased temperature on protein

A
  • Increased temperature can cause proteins to denature
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9
Q

Consequences of mutations

A

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

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10
Q

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

A
  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
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11
Q

What is protein turnover?

A

-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

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12
Q

What are chaperones?

A

-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

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13
Q

Basic Structure of Nucleotides

A
  1. Nitrogenous Base
  2. Backbone made up of sugar
  3. Phosphate group
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14
Q

What are the sugars found in DNA and RNA?

A

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

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15
Q

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

A

Carbons 3 prime and 5 prime

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16
Q

Are phosphates monomers or polymers?

A

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

17
Q

Name the two types of nitrogenous bases

A

-Pyrimidines
-Purines

18
Q

Pyrimidines vs Purines (and examples)

A

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

19
Q

What direction do RNA and DNA polymerize in?

A

5 prime to 3 prime direction

20
Q

Phosphodiester linkages

A

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)

21
Q

Why doesn’t purine pair with another purine?

A

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

22
Q

What bonds with guanine?

A

Cytosine bonds with guanine

23
Q

What bonds with adenine?

A

Adenine bonds with thymine

24
Q

How do nucleotides bond?

A

-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

25
Q

Does RNA form a double helix?

A

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

26
Q

What does RNA do?

A

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

27
Q

How do hydrophobic interactions influence the double alpha-helix?

A

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

28
Q

Why is the alpha helix structure beneficial?

A
  • Provides extra strength to tendons, hair and feathers
29
Q

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

A

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

30
Q

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

A

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)

31
Q

Why is protein turnover important?

A

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

32
Q

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

A

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

33
Q

How is DNA formed?

A

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

34
Q

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

A

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

35
Q

Which is more stable DNA or RNA?

A

DNA due to the helical structure

36
Q

Hydrogen bonding in RNA vs DNA

A

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

37
Q

What bases are found in RNA vs DNA?

A

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

38
Q

Does DNA have a tertiary/quarternary structure?

A

No, only primary and secondary

39
Q

What is the secondary structure of RNA?

A

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