Lecture 2: The polypeptide chain and the amino acid sequence of proteins

Question 1

How is the primary structure formed?

Answer 1

• dehydration reaction between 2 amino acids ( removal of H2O)
• this reaction occurs on the ribosome of the cell
• peptide bonds formed ONE AT A TIME starting at the N-terminal

Question 2

true or false, does the polypeptide chain have direction?

And indicate the direction from start to end

Answer 2

true

N-terminal to C- terminal

Question 3

What does it mean by RESIDUE

• all units of a polypeptide chain are therefore amino acid residues

Answer 3

an individual amino acid

• after dehydration, what remains of each amino acid is called an amino acid residue
• therefore these are structures that LACK A HYDROGEN ATOM of the amino group (-NH-CHR-CO-)
• or the hydroxy moeity of the carboxyl group (NH2-CHR-CO-)
• or both

Question 4

What are proteins?

Answer 4

• are polypeptides defines by amino acid sequence
• these sequences are specified by the DNA
• the amino acid sequence of a protein is also called the PRIMARY STRUCTURE

Question 5

true or false, the primary structure dictates how a polypeptide will fold?

Answer 5

true

Question 6

Why does primary structure dictate higher levels of polypeptide structure?

Answer 6

• due to the chemical nature of the backbone and side chain (R- groups) positioned along the chain
• each protein contains a defined sequence of amino acids containing all the information necessary for a protein to fold into its biologically active 3-D structure

Question 7

true or false does the human myoglobin a.a sequence the same as a whales’?

Answer 7

true
(Val, Leu, Ser, Glu,Gly, Asp..)
- same # of amino acids
- very similar sequence
- same oxygen binding

Question 8

What are the consequences of a mutation in the DNA?

Answer 8

• the amino acid sequence will be changed, thus the structure of the protein is altered, and possibly the function as well

Question 9

Give an example of mutation in humans, and its consequences

Answer 9

SICKLE CELL ANEMIA
alteration of amino acid sequence for the gene which codes for the biconcave structure of hemoglobin, can alter it to become sickle shaped, thus causing sickle cell anemia
CYSTIC FIBROSIS
-mutation, resulting in defective channel protein CFTR, this impairment can prevent Na+ ions from exiting the cell into the lumen, thus eg. sweat tends to be very salty

Question 10

How does sickle cell anemia occur? what base changes occur, and what amino acids are coded for instead? Why is this change harmful?

Answer 10

1. ) single substitution resulting in a different amino acid in protein causes sickle cell disease (Glu - Val)
2. ) inherited substitution of one amino acid
3. ) substitution occurs on the 6th position on the polypeptide
4. ) thus abnormal hemoglobin tends to crystallize, deforming some of the cells into a sickle shape
5. ) a person who has sickle cell anemia will have a life punctuated by “sickle cell crises”.
6. ) “sickle cell crises” occurs when the angular cells clog tiny blood vessels

Question 11

In sickle cell anemia, which position on the polypeptide is substituted from Glu - Val?

Answer 11

6th position

Question 12

What is the normal shape of hemoglobin?

Answer 12

biconcave

Question 13

How many amino acids does hemoglobin have?

Answer 13

146 amino acids

Question 14

what can be concluded from the similarity of the human and whale amino acid sequence for myoglobin?

Answer 14

amino acid sequences can indicate evolutionary relatedness eg. myoglobin

Question 15

How does length of the polypeptide chain vary?

Answer 15

• often 200-400 residues

- sometimes > 1000 (collagen -skin)

Question 16

How do polypeptides fold up?

Answer 16

• peptide bond delocalised double bond

- no rotation- the peptide unit is RIGID AND PLANAR and ALMOST ALWAYS TRANS

Question 17

true or false is the peptide bond almost always trans?

Answer 17

true

Question 18

What geometrical shape of the peptide unit?

Answer 18

planar

Question 19

Where can’t the polypeptide rotate?

Answer 19

the peptide bond

Question 20

Define torsion?

Answer 20

the action of twisting or the state of being twisted

Question 21

Which bonds can be rotated in an amino acid? (torsion)

Answer 21

between :
N-Calpha
Calpha -C (carboxyl)
- this is because these bonds are SINGLE BONDS

Question 22

Why do sickle cells crystallize?

remember from Glu- Val; in the 6th position

Answer 22

• their structure results in an exposed hydrophobic region
• this is because Valine is hydrophobic
• therefore valine will tend to aggregate with other neighboring cells’ exposed valine; as it tries to get “away” from the surrounding water.
• thus molecules crystallize into a fibre
• capacity to carry oxygen is reduced
• sickle cells are also sticky, thus they tend to block blood vessels

Question 23

Why is the peptide bond important?

Answer 23

• for stability and structure of proteins

Question 24

does the peptide bond exist as a resonance structure?

Answer 24

yes

- being a mixture of N-C and N=C bond

Question 25

what does the resonance structure tell us about the peptide bond?

Answer 25

• that it has a partial double bond character
• there is no rotation about the peptide bond
• almost always trans ( Ca atoms from each amino acid are on opposite planes of the peptide bond)

Question 26

What is the significance of the singly bonded terminal carbon and nitrogen atoms?

Answer 26

potentially gives rise to many different arrangements of the polypeptide

Question 27

true or false, is it the localization of the pi electron orbitals over O-C-N which accounts for the partial double bond character of the C-N bond

Answer 27

true

Question 28

What causes a given polypeptide to fold up to just one stable, biologically active structure?

Answer 28

• the planar peptide bonds limits the folding pattern of proteins as ROTATION CAN ONLY OCCUR AROUND N-Calpha and Calpha-C=O bonds

Question 29

What does the secondary structures regular, repetitive backbone depend on?

Answer 29

• the formation of HYDROGEN BONDS

- between N-H and C=O groups of the polypeptide

Question 30

What does a hydrogen bond involve?

Answer 30

• involves an interaction betweeen:
• an H atom ATTACHED to an electronegative donor (eg. atom D)
• and an electronegative acceptor atom (eg. atom A)
  D-H——–A