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BIOL 112 > L4 Proteins 2 + Nucleic acids > Flashcards

L4 Proteins 2 + Nucleic acids Flashcards

1
Q

What does the tertiary structure do?

A

It finishes the folding of a polypeptide to its final form?

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2
Q

Can proteins be fully formed after the tertiary structure?

A

Yes, many proteins consist of only one polypeptide so they are fully formed after tertiary structure formation (vs getting to a quaternary form)

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3
Q

Does the formation of a tertiary structure require or release energy?

A

It releases energy, ie it occurs automatically

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4
Q

What types of interactions contribute to the tertiary structure formation? (4)

A
  • ionic bonds
  • hydrogen bonds
  • disulfide bonds
  • hydrophobic interactions
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5
Q

Where do the ionic bonds, h-bonds, disulfide bonds and hydrophobic interactions occur for the tertiary structure?

A

Between the amino acid side chains in the interior of the protein

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6
Q

What do the side chain interactions determine? (the ionic bonds, h-bonds, disulfide bonds and hydrophobic interaction in the side chains)

A

They determine the tertiary structure

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7
Q

Which interaction is the most important determinant of protein folding / tertiary structure?

A

Hydrophobic interactions because hydrophobic stretches of amino acids automatically rearrange towards the interior of a protein (away from water)

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8
Q

What are coiled coils?

A

Coiled coils are two alpha-helices wrapped around eachother

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9
Q

How are coiled coils formed? (4)

A
  • Hydrophobic amino acids at every 4th position generates a band of hydrophobicity running along the length of the alpha-helix and slowly rotating around it
  • Hydrophobic interactions then ensures that two such alpha helices come together just at that band, which results in the coiled coil
  • It is a tertiary structure if both alpha helices are from the same polypeptide
  • It is a quaternary structure if the alpha-helices are from two different polypeptides
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10
Q

Where can coiled coils occur ?

A

In proteins such as keratins giving strength to tendons, hair or feathers

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11
Q

How does curling and uncurling hair work?

A
  • It reduces or breaks the disulfide bonds in keratin which allows for the manipulation of the shape of hair
  • Then the disulfide bonds must be oxidised/reformed to keep hair in the new shape
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12
Q

What is a quaternary structure?

A

A quaternary structure indicates several polypeptides interaction to form a bigger protein complex

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13
Q

Examples of quaternary structures (2)

A
  • hemoglobin → 4 ind. polypeptides
  • keratin → 3 alpha helices
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14
Q

What is hemoglobin

A

Hemoglobin is a protein in red blood cells that carries oxygen to different organs and tissues and transports carbon dioxide from the organs back to the lungs.

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15
Q

What is the importance of the primary structure (the amino acid sequence) ?

A

The primary structure is sufficient for protein folding, or in other words, all of the information needed about protein folding is encoded in the primary structure.

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16
Q

What are 2 examples that prove that the primary structure (the amino acid sequence) has all of the info needed to fold?

A

1) A single amino acid mutation in the protein hemoglobin changes the conformation of the hemoglobin, resulting in the shape change of red blood cells, since red blood cells are made up of hemoglobin

2) A typical protein sufficiently diluted in watery solutions denatures (unfolds) at high temperatures, but will renature (refold), when temperature is lowered

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17
Q

SUMMARY what is the primary structure?

A

the sequence of amino acids in a polypeptide

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18
Q

SUMMARY what is the secondary structure?

A

the formation of alpha helices and beta pleated sheets in a polypeptide

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19
Q

SUMMARY what is the tertiary structure?

A

the overall three dimensional shape of a polypeptide (includes contributions from secondary structures)

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20
Q

SUMMARY what is the quaternary structure?

A

the shape produced by combinations of polypeptides (thus combinations of tertiary structures)

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21
Q

What is protein turnover?

A
  • Protein turnover refers to the replacement of older proteins as they are broken down within a cell
  • Breakdown & resynthesis
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22
Q

What is the range of the half life of protein turnover?

A

It ranges from minutes to weeks
The average is about 2 days

23
Q

Why is protein turnover important?

A

Because proteins get damaged often

24
Q

What are some examples of protein turnover? (3)

A
  • fever
  • pH change
  • egg becomes hard by boiling bc proteins denature and get all entangled when they try to renature
25
Q

What are chaperones?

A

Chaperones are specialized proteins that help keep other proteins (temporarily exposed hydrophobic regions) from interacting inappropriately with one another

26
Q

How do chaperones keep proteins from interacting inappropriately with other proteins?

A

They do so by sequestering some newly synthesized proteins to give them time to fold

27
Q

When do chaperones play their role? (2)

A

After synthesis or after stress-related unfolding

28
Q

What are nucleotides?

A

Nucleotides are made up of a 5-carbon sugar, a nitrogenous base and a phosphate group

29
Q

What are nucleotides building blocks of?

A

RNA and DNA

30
Q

What kind of sugar is in RNA?

A

Ribose

31
Q

What kind of sugar is in DNA

A

Deoxyribose
→ DNA lacks an oxygen at carbon 2

32
Q

Which nucleotides make up RNA (4)?

A
  • cytosine
  • uracil
  • guanine
  • adenine
33
Q

Which nucleotides make up DNA (4)?

A
  • cytosine
  • thymine
  • guanine
  • adenine
34
Q

What are cytosine, uracil, and thymine?

A

They are pyrimides

35
Q

What are guanine and adenine

A

They are purines (which is bigger than pyrimides)

36
Q

How do nucleotides polymerize?

A

Nucleotides polymerize via phosphodiester linkages, with 3’ hydroxyl group of the polymer forming a covalent bond with the 5’ phosphate group of the incoming molecule

37
Q

What does 5’ to 3’ entail

A

RNA and DNA molecules always start with a 5’ phosphate group and end with a 3’ hydroxyl

38
Q

What type of reaction is nucleotide polymerization? (condensation or hydrolysis)

A

Condensation

39
Q

What is DNA ?

A

DNA is a self-replicating material that is present in nearly all living organisms as the main constituent of chromosomes. It is the carrier of genetic information.

40
Q

What is DNA made up of?

A

DNA is made up of two antiparallel strands held together by hydrogen bonds between the bases

41
Q

How do the bases pair up? (guanine, adenine, cytosine, thymine)

A

Gunanine (G) pairs with cycstine (C)
Adenine (A) pairs with thymine (T)

42
Q

How many H bonds does a G-C (guanine-cytosine) have?

A

3 H-bonds

43
Q

How many H bonds does a A-T (adenine-thymine) have?

A

2 H-bonds

44
Q

Which base pairing is stronger? G-C or A-T?

A

G-C (bc it has 3 H bonds while A-T has 2)

45
Q

How are the sugars, phosphates and bases arranged on the double helix of DNA?

A

The double helix of DNA has a sugar-phosphate backbone on the outside and the bases on the inside arranged like rungs on a ladder

46
Q

What does DNA carry?

A

the genetic information

47
Q

What is RNA?

A

RNA is a nucleic acid present in all living cells. Its principal role is to act as a messenger carrying instructions from DNA for controlling the synthesis of proteins

48
Q

What came first in evolution RNA or DNA?

A

RNA

49
Q

How many strands does RNA have?

A

1

50
Q

How does RNA work like an enzyme catalyzing certain reactions?

A

Because it can form into complicated 3D structures similar to proteins

51
Q

Where does folding occur in RNA?

A

Folding occurs between nucleotide bases within the same macromolecule pair via H-bonds

52
Q

What is the stem-loop structure of RNA?

A

It is a structure that contributes to the regulation of mRNA function

53
Q

What are the differences between RNA and DNA? (3)

A
  • RNA is 1 strand ; DNA is 2 strands
  • DNA is more stable than RNA
  • RNA has uracyl and DNA has thymine

BIOL 112 (7 decks)

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