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BIO1332 - Biochemistry > Amino Acids and Proteins > Flashcards

Amino Acids and Proteins Flashcards

1
Q

What are the four major types of molecules?

A
  • Proteins
  • Nucleic Acids
  • Lipids
  • Carbohydrates
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2
Q

What do proteins contribute to the cells?

A
  • Enzymes
  • Structural proteins
  • Proteins interact with RNA and DNA
  • Transport Systems (Lipid bound proteins)
  • Glycosylated Proteins
  • Cell recognition
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3
Q

What is mean by glycosylated proteins?

A

Interact with sugars

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4
Q

What is lactoferrin?

A

Iron binding protein

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5
Q

What happens to lactoferrin when binding with iron?

A

The shape of the protein changes substantial

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6
Q

Why is it good that lactoferrin changes shape when bound with iron?

A

Other molecules can distinguish between iron-free and the iron bound forms

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7
Q

Are proteins linear or nonlinear polymers?

A

Linear polymer

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8
Q

What is monomer called that makes up protein?

A

Amino Acids

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9
Q

What groups do amino acids have?

A
  • Amino group
  • Carboxyl group
  • Side chain
  • Hydrogen
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10
Q

What is the carbon called which the amino group and carboxyl group is bonded to?

A

a-carbon

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11
Q

Do amino acids have the same general structure?

A

Yes

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12
Q

What distinguishes amino acids from one another?

A

Variation in the side chains

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13
Q

What is bonded to the a-carbon in an amino acid?

A
  • Side chain group
  • Carboxyl group
  • Amino group
  • Hydrogen atom
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14
Q

How do you name amino acids?

A

End in -ine

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15
Q

What can we do for convenience when naming an amino acid?

A

Abbreviate to a three letter code

Some can be shortened to one letter

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16
Q

What are the four main groups of amino acids?

A
  • Hydrophobic amino acids with nonpolar R groups.
  • Polar amino acids with neutral R groups but the
    charge is not evenly distributed.
  • Positively charged amino acids with R groups that
    have a positive charge at physiological pH.
  • Negatively charged amino acids with R groups that
    have a negative charge at physiological pH.
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17
Q

What can Glycine be abbreviated to?

A
  • Gly

- G

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18
Q

What is the side chain of glycine?

A

H atom

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19
Q

What is chirality?

A

A molecule or ion which can not be superposed by its mirror image by any rotation or translation combination

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20
Q

Does glycine have chirality?

A

No

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21
Q

Does all amino acids except for glycine have chirality?

A

Yes

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22
Q

Is glycine flexible?

A

Yes

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23
Q

Why is proline an unusual amino acid?

A

As the side chain bonds to the amine

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24
Q

What does the structure of proline do to the protein?

A

Causes tight restraint

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25
Q

Does prolines peptide bond cause trans or cis or trans and cis conformations?

A

Trans and cis

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26
Q

Where do you normally find proline?

A

In proteins that need to be rigid

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27
Q

What protein needs proline?

A

Collagen

28
Q

Where can histidine be found?

A

At the active sites of enzymes

29
Q

What is the pka of histidine?

A

6.7 - Near neutral

30
Q

Is histidine the only amino acid with a pKa near neutral?

A

Yes

31
Q

Why is histidine important?

A

As the near neutral pH can allow the side chain to alter its charge at physiological pH

32
Q

How can the charge of histidine be modulated?

A

By the amino acids surrounding it in the 3D structure of the protein

33
Q

Why is histidine found at the active site of enzymes?

A

The imidazole ring can bind and release protons during enzymatic reactions

34
Q

What is the side chain called on the amino acid cysteine?

A

Free thiol (SH) group

35
Q

When a cysteine and cysteine react together what bond is formed?

A

Covalent bond

36
Q

What is another name for the bond formed between two cysteine?

A

disulphide bond

37
Q

What is the importance of disulphide bonds in proteins?

A

Correctly folds the protein

38
Q

What pKa does the cysteine side chain have?

A

8.4

39
Q

Where can you find cysteine?

A

At the active site of an enzyme

40
Q

What do two cysteine produce?

A

A cystine

41
Q

Is the reaction oxidation or reduction when forming cystine?

A

Oxidation

42
Q

What do we need to worry about when talking about cysteine and cystine?

A

The spelling

43
Q

Is this correct?

cystine + cystine —> cysteine

A

No, cysteine + cysteine —> cystine

44
Q

What are zwitterions?

A

A molecule which has two functional groups. One functional group is has a positive charge. One functional group has a negative charge

45
Q

What are amino acids in a neutral solution?

A

zwitterions

46
Q

What overall charge net does a zwitterion have?

A

Zero

47
Q

What is another word for zwitterions?

A

Dipolar ions

48
Q

What is meant by protonated?

A

addition of a proton

49
Q

What does deprotonated mean?

A

removal of a proton

50
Q

In dipolar form is the amino group in an amino acid deprotonated or protonated?

A

Protonated

51
Q

In dipolar form is the carboxyl group in an amino acid deprotonated or protonated?

A

Deprotonated

52
Q

Is the carboxyl or amino group the first to be protonated when the pH is raised to 2?

A

Carboxyl group

53
Q

When the pH gets to 9 what happens to the amino group?

A

Is deprotonated

54
Q

What pH does the dipolar form persist to?

A

9

55
Q

Are the side chains in amino acids charged or not charged?

A

Can be both

56
Q

Do amino acids with aromatic side chains absorb strongly?

A

Yes

57
Q

What do two amino acids form?

A

Peptide

58
Q

What bond is formed between two amino acids?

A

Peptide bond

59
Q

Finish the sentence:

Amino acids join together to make a peptide by the loss of a….

A

molecule of water

60
Q

Are peptide chains in proteins in the trans or cis conformation?

A

Trans

61
Q

Why are peptide chains in proteins in a trans conformation?

A

To prevent steric clashes

62
Q

What amino acid at an exception from being a trans conformation?

A

Proline

63
Q

What transformation does proline have?

A

Cis

64
Q

Are the side chain of an amino acid in a TRANS conformation on the same or different side of the chain?

A

Different

65
Q

Are the side chain of an amino acid in a CIS conformation on the same or different side of the chain?

A

Same

66
Q

What is the amino acid sequences direction?

A

From amino terminal residue (N-terminal) to carboxyl terminal residue (C-terminal)

67
Q

What are bond lengths measure in?

A

Angstroms

BIO1332 - Biochemistry (19 decks)

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