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BGM1002-Biochemistry > BGM1002/L02 Protein Structure > Flashcards

BGM1002/L02 Protein Structure Flashcards

1
Q

What are proteins?

A

Complex polymers made of amino acid monomers joined by peptide bonds

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2
Q

How many levels of complexity do proteins exhibit?

A

4

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3
Q

What type of isomer are amino acids (in proteins)?

A

L-isomers

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4
Q

How many covalent bonds can carbon form?

A

4

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5
Q

What formation do electron shells form with 4 bonds in carbon?

A

sp3 hybridisation

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6
Q

How many possible configurations does carbon have with 4 different substituent groups?

A

2 stereoisomers

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7
Q

What do chiral enantiomers affect? And how?

A

Polarised light
Rotation of plane of light clockwise (+) or anticlockwise (-)

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8
Q

How is a chiral enantiomer indicated?

A

L-/D- or S/R

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9
Q

What does L-/D- mean?

A

Configuration relative to D-glyceradehyde

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10
Q

What does S/R mean?

A

Absolute configuration

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11
Q

How is absolute configuration determined?

A

Based on priority of substituent groups around chiral centre according to Cahn-Ingold-Prelog sequence

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12
Q

Give 2 examples of where D-amino acids are found in nature.

A

Bacterial cell walls
Non-ribosomal peptides

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13
Q

What handedness do alpha-helices have?

A

Right-handedness

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14
Q

How are interactions between proteins and other molecules specific?

A

They display a preference for specific chiral forms

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15
Q

What 3 uses does Thalidomide have?

A

Anti-cancer
Leprosy treatment
Graft-versus host disease treatment

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16
Q

What effect did Thalidomide have when given as anti-nausea to pregnant women?

A

Development arrest of limbs in foetuses

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17
Q

Which enantiomer of Thalidomide causes complications?

A

S-enantiomer

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18
Q

Which enantiomer of Thalidomide is therapeutic?

A

R-enantiomer

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19
Q

Why is there no safe way to administer R-Thalidomide?

A

Body converts R- to S-Thalidomide

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20
Q

What charge do acidic amino acids have?

A

Negative

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21
Q

What charge do basic amino acids have?

A

Positive

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22
Q

What is minimised when a protein folds?

A

Hydrophobic residue on its surface

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23
Q

What amino acid do most proteins start with?

A

Methionine

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24
Q

What type of bonding can uncharged side chains be involved with?

A

Hydrogen bonding

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25
Q

What 4 enzymes is Selenocysteine an essential component of?

A

Glutathione peroxidase
Thioredoxin reductase
De-ionase
Formate dehydrogenase

26
Q

How is Selenocysteine encoded?

A

With a modified stop codon which forms an mRNA structure allowing U to be accepted

27
Q

How is Hydroxyproline produced?

A

Post-translational modification of proline (hydrogenation)

28
Q

What vitamin is required for synthesis of Hydroxyproline?

A

Vitamin C

29
Q

What is the purpose of Hydroxyproline in collagen?

A

Attachment point for glycans

30
Q

What 2 things does vitamin C deficiency cause?

A

Scurvy
Breakdown of cell walls

31
Q

What is each amino acid in sequence called?

A

Residue

32
Q

What is vital for a protein’s function?

A

Charge of protein at given pH

33
Q

Why are peptide bonds rigid and planar?

A

Partial double bond character

34
Q

What does the polypeptide bond link?

A

2 alpha carbon atoms from neighbouring amino acids

35
Q

What 3 ways can a phosphate backbone spin?

A

𝚽-phi
𝚿-psi
π›š-omega

36
Q

What is a phi rotation?

A

C’-N’C𝛂-C

37
Q

What is a psi rotation?

A

N-C𝛂-C’-N

38
Q

What is an omega rotation?

A

C𝛂-C’-N-C𝛂

39
Q

What 2 rotations do proteins fold into structure around?

A

Phi and Psi

40
Q

Are most peptides Cis or Trans?

A

Trans

41
Q

Why does attraction of different elements for electrons vary? (2)

A

Atomic number
Distance from nucleus of valence electrons

42
Q

What is the electronegativity series for peptides?

A

O>N>C=H

43
Q

Which group in amino acids is slightly negative?

A

Carbonyl group

44
Q

Which group in amino acids is slightly positive?

A

Amide group

45
Q

How does the strength of a Hydrogen bond compare to a covalent bond?

A

H-bond is 0.1x strength of covalent bond

46
Q

Why is hydrogen bonding vital for protein structure? (2)

A

Backbone hydrogen bonding in secondary structure
Higher level structures have larger H-bonding contributions

47
Q

What does an alpha helix consist of?

A

A-helix
B-strand

48
Q

What degree of repeat does an alpha helix have?

A

100 degrees - 3.6 residues per turn

49
Q

How long is a pitch in DNA?

A

5.4Γ…

50
Q

Which way do side chains point in DNA?

A

Outwards

51
Q

How many residues point the same way in DNA?

A

3-4

52
Q

Which amino acid is a Cis isomer and cannot be in alpha-helices?

A

Proline

53
Q

What is the average number of residues in DNA?

A

11

54
Q

How many residues form a repeat in beta-strands?

A

2

55
Q

How long are residue repeats in beta-strands?

A

7Γ…

56
Q

Name the 3 preferred amino acids for beta-strands.

A

Ile, Tyr, Val

57
Q

What is the average length of a beta-strand?

A

6 amino acids

58
Q

Why are parallel strands weaker than antiparallel strands?

A

Geometric imperfections

59
Q

Why are most sheets right-handed?

A

To accommodate L-amino acid side chains

60
Q

How much of DNA structure do alpha-helices and beta-strands comprise?

A

50%

61
Q

What 3 structures does DNA consist of?

A

Alpha-helices, beta-strands, loops & turns etc.

62
Q

What determines the secondary structure of proteins?

A

Hydrogen bonds between peptide bond carbonyls and amides

BGM1002-Biochemistry (29 decks)

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