BGM1002/L02 Protein Structure

Question 1

What are proteins?

Answer 1

Complex polymers made of amino acid monomers joined by peptide bonds

Question 2

How many levels of complexity do proteins exhibit?

Answer 2

4

Question 3

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

Answer 3

L-isomers

Question 4

How many covalent bonds can carbon form?

Answer 4

4

Question 5

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

Answer 5

sp3 hybridisation

Question 6

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

Answer 6

2 stereoisomers

Question 7

What do chiral enantiomers affect? And how?

Answer 7

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

Question 8

How is a chiral enantiomer indicated?

Answer 8

L-/D- or S/R

Question 9

What does L-/D- mean?

Answer 9

Configuration relative to D-glyceradehyde

Question 10

What does S/R mean?

Answer 10

Absolute configuration

Question 11

How is absolute configuration determined?

Answer 11

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

Question 12

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

Answer 12

Bacterial cell walls
Non-ribosomal peptides

Question 13

What handedness do alpha-helices have?

Answer 13

Right-handedness

Question 14

How are interactions between proteins and other molecules specific?

Answer 14

They display a preference for specific chiral forms

Question 15

What 3 uses does Thalidomide have?

Answer 15

Anti-cancer
Leprosy treatment
Graft-versus host disease treatment

Question 16

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

Answer 16

Development arrest of limbs in foetuses

Question 17

Which enantiomer of Thalidomide causes complications?

Answer 17

S-enantiomer

Question 18

Which enantiomer of Thalidomide is therapeutic?

Answer 18

R-enantiomer

Question 19

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

Answer 19

Body converts R- to S-Thalidomide

Question 20

What charge do acidic amino acids have?

Answer 20

Negative

Question 21

What charge do basic amino acids have?

Answer 21

Positive

Question 22

What is minimised when a protein folds?

Answer 22

Hydrophobic residue on its surface

Question 23

What amino acid do most proteins start with?

Answer 23

Methionine

Question 24

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

Answer 24

Hydrogen bonding

Question 25

What 4 enzymes is Selenocysteine an essential component of?

Answer 25

Glutathione peroxidase Thioredoxin reductase De-ionase Formate dehydrogenase

Question 26

How is Selenocysteine encoded?

Answer 26

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

Question 27

How is Hydroxyproline produced?

Answer 27

Post-translational modification of proline (hydrogenation)

Question 28

What vitamin is required for synthesis of Hydroxyproline?

Answer 28

Vitamin C

Question 29

What is the purpose of Hydroxyproline in collagen?

Answer 29

Attachment point for glycans

Question 30

What 2 things does vitamin C deficiency cause?

Answer 30

Scurvy Breakdown of cell walls

Question 31

What is each amino acid in sequence called?

Answer 31

Residue

Question 32

What is vital for a protein's function?

Answer 32

Charge of protein at given pH

Question 33

Why are peptide bonds rigid and planar?

Answer 33

Partial double bond character

Question 34

What does the polypeptide bond link?

Answer 34

2 alpha carbon atoms from neighbouring amino acids

Question 35

What 3 ways can a phosphate backbone spin?

Answer 35

𝚽-phi 𝚿-psi 𝛚-omega

Question 36

What is a phi rotation?

Answer 36

C'-N'C𝛂-C

Question 37

What is a psi rotation?

Answer 37

N-C𝛂-C'-N

Question 38

What is an omega rotation?

Answer 38

C𝛂-C'-N-C𝛂

Question 39

What 2 rotations do proteins fold into structure around?

Answer 39

Phi and Psi

Question 40

Are most peptides Cis or Trans?

Answer 40

Trans

Question 41

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

Answer 41

Atomic number Distance from nucleus of valence electrons

Question 42

What is the electronegativity series for peptides?

Answer 42

O>N>C=H

Question 43

Which group in amino acids is slightly negative?

Answer 43

Carbonyl group

Question 44

Which group in amino acids is slightly positive?

Answer 44

Amide group

Question 45

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

Answer 45

H-bond is 0.1x strength of covalent bond

Question 46

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

Answer 46

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

Question 47

What does an alpha helix consist of?

Answer 47

A-helix B-strand

Question 48

What degree of repeat does an alpha helix have?

Answer 48

100 degrees - 3.6 residues per turn

Question 49

How long is a pitch in DNA?

Answer 49

5.4Å

Question 50

Which way do side chains point in DNA?

Answer 50

Outwards

Question 51

How many residues point the same way in DNA?

Answer 51

3-4

Question 52

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

Answer 52

Proline

Question 53

What is the average number of residues in DNA?

Answer 53

11

Question 54

How many residues form a repeat in beta-strands?

Answer 54

2

Question 55

How long are residue repeats in beta-strands?

Answer 55

7Å

Question 56

Name the 3 preferred amino acids for beta-strands.

Answer 56

Ile, Tyr, Val

Question 57

What is the average length of a beta-strand?

Answer 57

6 amino acids

Question 58

Why are parallel strands weaker than antiparallel strands?

Answer 58

Geometric imperfections

Question 59

Why are most sheets right-handed?

Answer 59

To accommodate L-amino acid side chains

Question 60

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

Answer 60

50%

Question 61

What 3 structures does DNA consist of?

Answer 61

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

Question 62

What determines the secondary structure of proteins?

Answer 62

Hydrogen bonds between peptide bond carbonyls and amides