Peptides

Question 1

Where does a peptide bond form?

Answer 1

Between two amino acids

Middle of a dipeptide

Question 2

How does a peptide bond form?

Answer 2

Condensation reaction between two amino acids which results in the loss of h2o

Question 3

What are some characteristics of the peptide bond?

Answer 3

Rigid
Planar
Partial double bond character
Nearly always trans

Question 4

Which type are pure single bonds?

Answer 4

Between α-carbon and carbonyl carbon

Between α-carbon and peptide nitrogen

Question 5

What do the single peptide bonds allow for?

Answer 5

Free rotation

Question 6

What type of chains do small peptides form?

Answer 6

Flexible

Question 7

What type of structure does α-helix have?

Answer 7

Rod-like structure

Side chain extend our from the rod

Question 8

What stabilises the alpha helix structure?

Answer 8

Hydrogen bonds between every main C=O and the N-H group four residues ahead in the sequence

Question 9

What is the pitch of the alpha helix?

Answer 9

1.5Å

Question 10

What is the diameter of an alpha helix?

Answer 10

5.4Å

Question 11

What types of turns can alpha helixes have? Which is in proteins?

Answer 11

Right or left

Right in proteins

Question 12

What is a β sheet made from?

Answer 12

Almost fully extended peptide chains called β-strands

Question 13

How is the β sheet stabilised?

Answer 13

Hydrogen bonds between strands

Question 14

Which directions can strands run in?

Answer 14

Same direction (parallel) 
Opposite direction (antiparallel)

Question 15

What is the most common amount of strands per sheet?

Answer 15

2-5

Question 16

What are most proteins made of?

Answer 16

Mixture of alpha helixes and beta sheets

Question 17

What is a β-turn?

Answer 17

Regular structure allowing a reverse of direction

Question 18

What is a β-turn made up of?

Answer 18

four residues

Question 19

What do β-turns often connect?

Answer 19

The strands of antiparallel β-sheets

Question 20

In β-turns, what does the C=O of residue n H-bond to?

Answer 20

the N-H of residue n+3

Question 21

What do peptide bonds form?

Answer 21

The backbone of the protein

Question 22

Where are disulfide bonds formed?

Answer 22

Between two cysteine residues

Question 23

What do disulfide bonds form?

Answer 23

Crosslinks within the peptide backbone or peptide chains

Question 24

How do you sequence large proteins?

Answer 24

They need to be broken down into smaller peptide fragments before the sequence is read

Question 25

What is an example of chemical cleavage?

Answer 25

Cyanide bromide

Cleaves the carboxyl side of methoinine resides

Question 26

What is an example of an enzymic cleavage?

Answer 26

Cleaves the carboxy side of lysine and arginine residues

Question 27

What does the Edman degradation determine?

Answer 27

The primary sequence peptides up to 50 amino acids

Question 28

How does Edman sequencing work?

Answer 28

The N terminal amino acid residue reacts with phenyl isothiocyanate, treatment with two different amino acids produces a phenyl thiohydantoin

Question 29

What does analysis of the thiohydantoin show?

Answer 29

Do it by hplc

Shows the amino acids at this position

Question 30

How do you reconstruct a protein sequence?

Answer 30

The cyanogen bromide peptides and trypsin peptides are overlapped to complete the primary structure of the protein

Question 31

What is a primary structure?

Answer 31

Amino acid sequence

Question 32

What is a secondary structure?

Answer 32

α-helixes, β-sheets, β-turns

Question 33

What is a tertiary structure?

Answer 33

overall 3D structure of molecule