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Biology 2300 - Cell Biology > Chapter 3 - The Macromolecules of the Cell - Proteins > Flashcards

Chapter 3 - The Macromolecules of the Cell - Proteins Flashcards

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1
Q

What are macromolecules?

A

Large molecules composed of thousands of covalently connected atoms.

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2
Q

What are the four biological macromolecules?

A
  • proteins (amino acids)
  • nucleic acids (nucleotides)
  • polysaccharides (sugars)
  • lipids (fatty acids)
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3
Q

How are polymers of macromolecules made?

A

Synthesized by condensation reactions in which monomers of the macromolecules are linked together by the removal of a water molecule.

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4
Q

What are proteins?

A

Macromolecules that consists of one or more polypeptides folded into a conformation specified by the linear sequence of amino acids.

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5
Q

What are the two ways proteins can be classifed?

A

By structure and by function

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6
Q

What are the classes proteins can be classified based on function and how many?

A

9 classes of proteins
- enzymes
- structural
- motility
- regulatory
- transport
- signaling
- receptor
- defense
- storage

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7
Q

What is the function of enzymes?

A

Serve as catalysts that greatly increase the rate of chemical reactions

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8
Q

What is the function of structural proteins?

A

Provide physical support and shape to cells and organelles, giving them their characteristic appearances

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9
Q

What is the function of motility proteins?

A

Play a key role in the contraction and movement of cells and intracellular materials.

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10
Q

What is the function of regulatory proteins?

A

Responsible for the control and coordination of cellular functions and that cellular activities are regulated to meet cellular needs.

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11
Q

What is the function of transport proteins?

A

Involved in the movement of other substances into, within, and out of the cell.

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12
Q

What is the function of signaling proteins?

A

Mediate communication between cells in an organism.

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13
Q

What is the function of receptor proteins?

A

Enable cells to respond to chemical stimuli from their environment.

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14
Q

What is the function of defensive proteins?

A

Prove protection against disease.

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15
Q

What is the function of storage proteins?

A

Serve as reservoirs of amino acids.

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16
Q

What are the classes proteins can be classified based on structure and how many?

A

2 ways to classify proteins based on structure:
- globular proteins
- fibrous proteins

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17
Q

What are globular proteins?

A

Involved in cellular structure or are enzymatic.

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18
Q

What are fibrous proteins?

A

Purely structural in nature within the cell.

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19
Q

What are the monomers that make up proteins?

A

Amino acids

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20
Q

What are amino acids?

A

Monomeric nit of proteins consisting of a carboxylic acid with an amino group and one of a variety of R groups attached to the alpha carbon

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21
Q

How many amino acids are used for protein synthesis

A

20 amino acids are used.

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22
Q

What are the stereoisomers that an amino acid can exist in? Is there an exception to this?

A

Amino acids can exist in two conformations: L-conformation and D-conformation. L-conformation is the most commonly seen isomer that amino acids exist in nature. The reason for the two conformations is because there are 4 different groups for each amino acid around the alpha carbon. The exception to this is glycine which is the only amino acid that does not have 4 different functional groups around the alpha carbon.

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23
Q

How many classes of R groups are there and what are the names of each classification?

A

3 R groups:
- non-polar (hydrophobic)
- polar, charged (hydrophilic)
- polar, uncharged (hydrophilic)

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24
Q

How are amino acids linked to form a polypeptide chain?

A

Amino acids are linked together in a chain-like fashion through the use of a condensation (dehydration) reaction in which a water molecule is removed.

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25
Q

What is the name of the bond that links amino acids together? How is it formed?

A

The name of the bond that links amino acids together is known as a peptide bond, which is a covalent bond between the amino group of one amino acid and the carboxyl group of a second amino acid. C-N bond

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26
Q

What is a protein?

A

It is a polypeptide chain (or complex of several peptides) that has a unique, stable, 3D structure and is biologically active

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27
Q

Define monomeric proteins.

A

A protein that consists of a single polypeptide chain that has folded and coiled spontaneously as the chain is formed.

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28
Q

Define multimeric proteins

A

A protein that consists of two or more polypeptide chains that are often referred to as polypeptide subunits.

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29
Q

What kind of bonds are used when polypeptides are folded into its conformation?

A
  • disulfide bonds
  • hydrogen bonds
  • ionic bonds
  • van der Waals interactions
  • hydrophobic interactions
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30
Q

How can the interactions by these bonds be disrupted? What is this process called?

A

Can be disrupted through heat, high salt or chemical treatment. This is referred to as denaturation of the polypeptide.

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31
Q

What are disulfide bonds?

A

A special covalent bond that helps stabilize protein conformation. Forms between the sulfur atoms of two cysteine amino acid residues.

32
Q

How are disulfide bonds formed?

A

Formed through an oxidation reduction reaction that removes the two hydrogen atoms from the sulfhydryl groups of the two cysteines forming the disulfide bond.

33
Q

What are intramolecular disulfide bonds?

A

Interaction between two cysteine molecules along the same polypeptide chain that are brought together through the folding process.

34
Q

What are intermolecular disulfide bonds?

A

Interaction between two cysteine molecules on two polypeptides that are then covalently linked to one another.

35
Q

What are hydrogen bonds?

A

Weak attractive interaction between an electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom.

36
Q

How does hydrogen bonding affect amino acids?

A

R groups of amino acids can participate in hydrogen bonding and this can allow this bond type to form between residues that are distant along the sequence but brought close together through the folding process of the polypeptide.

37
Q

What are hydrogen bond donors?

A

Have hydrogen atoms linked covalently to more electronegative atoms.

38
Q

What are hydrogen bond acceptors?

A

Have an electronegative atom that attracts the donor hydrogen.

39
Q

What are ionic bonds?

A

It is an attractive force between a positively charged chemical group and a negatively charged chemical group.

40
Q

What is another name for ionic bonds?

A

Electrostatic interactions.

41
Q

How is the polypeptide chain folding dictated?

A

Since some of the R groups are positively charged and some are negatively charged the folding is dictated by the attraction of oppositely charged R groups and repulsion of R groups with the same charge.

42
Q

How does pH affect ionic bonds?

A

If the pH value becomes very high or low that the R groups lose its charge, the ionic bond will be disrupted and this accounts for denaturation.

43
Q

What are van der Waals interaction?

A

Weak attractive interaction between two atoms caused by transient asymmetries in the distribution of charge in each atom.

44
Q

What are hydrophobic interactions?

A

Tendency of hydrophobic groups to be excluded from interactions with water molecules

45
Q

What is the role of hydrophobic interactions in amino acid and protein conformation?

A

Plays a role in maintaining conformation of proteins and excludes the molecules interaction with water

46
Q

Where are amino acids with hydrophilic R groups located?

A

Where they can interact maximally with the surrounding water molecules.

47
Q

Where are amino acids with hydrophobic R groups (non-polar) located?

A

Usually located inside the polypeptide away from the surrounding water molecules because they are excluded by water and usually interact with each other.

48
Q

What molecules are used to aid for the proper folding of certain proteins?

A

Molecule chaperones

49
Q

What are molecule chaperones?

A

Protein that facilitates the folding of other proteins but is not a component of the final folded structure.

50
Q

What are the four levels of organization of protein structures?

A
  • primary
  • secondary
  • tertiary
  • quaternary
51
Q

What is a primary structure?

A

Amino acid sequence in a polypeptide chain.

52
Q

What is described through the discussion of the primary structure?

A

The order in which the amino acids appear from one end of the molecule to the other.

53
Q

How are amino acid sequences written?

A

N-terminus to C-terminus of the polypeptide.

54
Q

What is the direction in which the polypeptide is synthesized?

A

N-terminus to C-terminus.

55
Q

What was the first protein to have its complete amino acid sequence determined?

A

Hormone insulin, 1953, Fredrick Sanger

56
Q

How many polypeptides make up insulin?

A

2 polypeptides, A subunit and B subunit (21 and 30 amino acids respectively)

57
Q

What is the role of disulfide bonds in tertiary stucture?

A

It stabilizes the tertiary structure of many proteins.

58
Q

How is the primary structure of a protein important genetically?

A

The amino acid sequence of the polypeptide is determined by the order of nucleotides in the corresponding mRNA which reflects the DNA sequences in the gene that encodes the protein.

59
Q

How is the primary structure important structurally?

A

The order and identity of amino acids directs the formation of higher order structures (secondary and tertiary)

60
Q

How is the primary structure significant?

A

It determines the organization of the higher levels of structures of the protein’s organization.

61
Q

What is a secondary structure?

A

Level of protein structure involving hydrogen bonding between atoms in the peptide bonds along the polypeptide backbone creating two main patters called the alpha helix and beta sheet conformations

62
Q

What is the alpha helix structure?

A

A spiral consisting of a backbone of amino acids linked by peptide bonds with the specific R groups of the individual amino acid residues sticking out from it

63
Q

How many amino acids are present per turn on an alpha helical structure?

A

3.6 amino acids

64
Q

How does the alpha helix allow for hydrogen bonding?

A

The distance between the peptide bonds is close enough for the formation of a hydrogen bond between the NH group adjacent to one peptide bond and the CO group adjacent to the other

65
Q

How do the hydrogen bonds in the alpha helix contribute to the structure?

A

The bonds are all nearly parallel to the main axis of the helix and therefore tend to stabilize the spiral structure by holding the turns on the helix together

66
Q

What is the beta sheet structure?

A

An extended sheetlike secondary structure of proteins in which adjacent polypeptides are linked by hydrogen bonds between amino and carbonyl groups.

67
Q

Where are the R groups located in a beta pleat structure?

A

Amino acid groups stick out on alternating sides of the amino acids.

68
Q

What are the two ways protein regions that form beta pleats?

A

Parallel and antiparallel beta sheets.

69
Q

What are parallel beta sheets?

A

When two interacting protein regions run in the same N-terminus to C-terminus direction.

70
Q

What are antiparallel beta sheets?

A

When two interacting protein regions run in opposite N-terminus to C-terminus directions

71
Q

What is a beta propeller?

A

Several antiparallel beta sheets associates symmetrically around a central axis

72
Q

What are examples of amino acids that are found in alpha helices?

A

leucine, methionine, glutamate

73
Q

What are examples of amino acids that are found in beta sheets?

A

phenylalanine, isoleucine, and valine

74
Q

What is unique about proline?

A

It is considered to be an helix breaker because the R group is covalently attached to the amino nitrogen and therefore does not have any hydrogen atoms available for hydrogen bonding.

75
Q

What conformational change does proline bring to the helix?

A

If present in a helix, it introduces a bend

76
Q

What is a tertiary structure?

A

level of protein structure involving interactions between amino acid side chains of a polypeptide, regardless of where along the primary sequence they happen to be located

77
Q

What is native conformation?

A

3D folding of a polypeptide chain into a shape that represents the most stable state for that particular sequence of amino acids.

Biology 2300 - Cell Biology (6 decks)

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