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BIO206 > Amino Acids > Flashcards

Amino Acids Flashcards

1
Q

What determines how a protein ‘folds’ into its structure?

A

The amino acid sequence

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2
Q

How do proteins contribute to their function?

A

3D structure and their chemical reactivity

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3
Q

How many different amino acids are used to build proteins?

A

20 different amino acids

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4
Q

What is the composition of amino acid?

A

Central carbon, amino group, carboxyl group, hydrogen, and side chain (R group)

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5
Q

What is consistent and what is variable between amino acids?

A

The side chain or R group is variable between amino acids. Everything else is consistent.

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6
Q

What does the amino acid R group vary in?

A

Size and shape, hydrophobicity, hydrogen bond forming ability, charge and chemical reactivity

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7
Q

What are the four categories of amino acids?

A

Acid, base, non-charged polar and non-polar

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8
Q

What strongly influences the protein folding of amino acids?

A

Their hydrophobicity

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9
Q

For cytoplasmic protein, where do hydrophilic and hydrophobic amino acids prefer to be?

A

Hydrophilic amino acids prefer being on the surface (besides water), and hydrophobic amino acids prefer clustering in the center of the protein (away from water)

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10
Q

Are amino acids with nonpolar side chains hydrophobic or hydrophilic?

A

Hydrophobic

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11
Q

Are amino acids with polar side-chains hydrophobic or hydrophilic?

A

Hydrophilic

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12
Q

How many amino acids with non-polar side chains are there?

A

10 in total

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13
Q

How many amino acids with polar, uncharged side chains are there?

A

5 in total

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14
Q

What is true about the amino acids with polar, charged side chains?

A

Their R groups contain acidic/basic groups

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15
Q

How many amino acids with polar, charged side chains are there?

A

5 in total, 2 acidic amino acids and 3 basic amino acids

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16
Q

What is common between optical isomers?

A

They have identical chemical composition, but they are arranged in 2 different 3D conformations

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17
Q

What does it mean when enzymes are stereospecific?

A

They can distinguish between D and L forms

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18
Q

What are the two optical isomers called?

A

L- and D- forms

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19
Q

How are amino acids linked to one another?

A

Via peptide bonds

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20
Q

What happens while the peptide bond forms?

A

Two amino acids gets condensed into one molecule

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21
Q

What is the pattern of the peptide backbone?

A

Repeating pattern of the atoms N-C-C

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22
Q

Where are the R groups linked to?

A

Central carbon

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23
Q

Why are amino acids technically no longer ‘amino acids’ once they are polymerized?

A

Because the chemical composition of their amino and carboxyl end has changed.

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24
Q

What are amino acid residues?

A

The ‘remainders’ of amino acids within a peptide

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25
Q

What is a peptide?

A

Any chain of amino acids linked to one another

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26
Q

How are proteins different from peptide?

A

Proteins are usually longer peptide which has folded into a unique 3D shape which has a defined function

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27
Q

How long would a typical protein be?

A

100-1000 amino acids long

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28
Q

What is N-terminus and C-terminus?

A

N-terminus is amino terminus and C-terminus is carboxyl terminus

29
Q

What strongly influences protein folding?

A

The polarity of the R group

30
Q

What is the basic strategy to stably fold proteins in an aqueous environment?

A
  1. Cluster hydrophobic amino acids together; put them away from water.
  2. Expose hydrophilic (polar) amino acids on the surface, allow them to interact with water
31
Q

Where can disulfide bonds form?

A

Disulfide bonds can form between two cysteine side chains in proteins

32
Q

What amino acid restricts the flexibility of peptide backbone?

A

Proline

33
Q

What can cystines do?

A

Cystines can form covalent, disulfide bonds to hold polypeptides together

34
Q

What is conformation?

A

It is the final folded structure of a protein

35
Q

What amino acids are on the surface and inside of a conformation?

A

Polar amino acids are on the surface, and non-polar amino acids are inside.

36
Q

How can conformation change?

A

With an interaction with other molecules

37
Q

Is proper folding guarantee?

A

No, because sometimes protein misfold, sometimes they require help from chaperone proteins to fold properly

38
Q

What are the 4 levels of complexity of protein structure?

A

Primary, secondary, tertiary, and quaternary structure

39
Q

What is primary structure?

A

Linear amino acid sequence of the protein

40
Q

What is secondary structure?

A

Small segments of peptide backbone form simple 3D structures

41
Q

What is tertiary structure?

A

The entire peptide backbone folds into the full 3D structure of the protein

42
Q

What is quaternary structure?

A

More than one folded protein combine into a larger structure

43
Q

What causes the protein to form fiver-like precipitates?

A

A single amino acid substitution in the beta-hemoglobin

44
Q

What is E6V mutation?

A

Glutamic acid to valine mutation at the 6th position

45
Q

What are the major secondary structures?

A

Alpha-helix and beta-sheet

46
Q

How are secondary structures created and stabilized?

A

By intramolecular hydrogen bonds

47
Q

What is alpha-helix?

A

A right hand helix

48
Q

Where do the R groups in an alpha-helix point to?

A

Outward

49
Q

What holds the alpha-helix together?

A

Hydrogen bonds between the NCC peptide backbone

50
Q

Where does the hydrogen bond form?

A

Between every backbone C=O group and N-H group of the amino acid reside located 4 residues downstream of peptide

51
Q

C=O groups of aa1 forms hydrogen bonds with?

A

N-H group of aa5

52
Q

What does the amphipathic alpha-helix look like?

A

One side of the helix will be hydrophobic and the other side hydrophilic

53
Q

What is beta-sheet?

A

Adjacent chains held together by hydrogen bonds between backbone residues

54
Q

Differentiate between different configurations of beta-sheet.

A

Antiparallel - backbone run in opposite direction. Parallel- backbone run in same direction.Mixed- combination of parallel and antiparallel.

55
Q

When viewed from the edge, how does beta-sheet appear?

A

Rippled or “pleated”

56
Q

How do the side chains in B-sheet look like?

A

Side chains alternate pointing up and down

57
Q

In beta-sheet, how many amino acids are there per strand? How many strands per sheet?

A

5-10 amino acids per strands, and 2-15 strands per sheet (avg. ~ 6)

58
Q

How can you determine the direction of each sheet in B-sheet?

A

By the relative positions of N, central C, and C’

59
Q

What forms hydrogen bonds in B-sheet?

A

N-H and C=O of neighbouring amino acids

60
Q

Where does hydrogen bonding occur in B-sheet?

A

Hydrogen bonding occurs once every two amino acid pairs

61
Q

What sequence determines the secondary structure?

A

Primary structure

62
Q

What is tertiary structure?

A

3D arrangement of the polypeptide; folding of all the secondary structures together

63
Q

What is single domain?

A

Single structure of proteins that are folded.

64
Q

Why do some proteins have multiple domains?

A

Because different regions of a single polypeptide can fold independently.

65
Q

What is the function of regulatory domains?

A

Allows for protein / protein interactions

66
Q

What is quaternary structure?

A

Multiple protein associates together to form a larger, more complex structure

67
Q

What are the different X-mer of quaternary structure and how many polypeptide chains are there in each?

A

Monomer - 1
Dimer - 2
Trimer - 3
Tetramer - 4
Pentamer - 5
Hexamer- 6
Octamer - 8

68
Q

What is it called when subunits in quaternary structure are different? identical?

A

Different subunits - heteromer
Identical subunits - homo

69
Q

In quaternary structures, what could AA be called? Let AA be two identical subunits or protein

A

Homodimer of two protein A.

(homo because identical, dimer because two polypeptide chains)

BIO206 (5 decks)

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