name: …………………… ( ) class: date:€¦ · question 1: proteins fulfil a wide range of...
TRANSCRIPT
1
Chem!stry
Name: …………………… ( ) Class: ……………… Date: …… / …… / ……
Biochemistry: Macroconcept – Systems
Natural Monomers and Polymers: Amino Acids, Peptides and Proteins
Question 1: Proteins fulfil a wide range of biologically important functions within the human body.
State at least three different roles that proteins fulfil within the human body:
(Answer on page 8).
Figure 1 shows a short chain protein or peptide composed of eight different amino acids linked together. A total
of twenty different amino acids function as the monomers from which the polymeric proteins and peptides are
produced.
N C
C
C
H
H
O
N
H
C
C
C
O
N
H
C
C
C
O
N
H
C
C
C
O
N
H
C
C
C
O
N
H
C
C
C
O
N
H
C
H
C
C
O
N
H
C
C
C
O H
OH
H HC
H
H HS
H
H HH
H
H HO
H
H
H HC
C
CC
C
C
H
H HC
H HC
O
H
O
H H
H H
H
H HC
C N
CN
HH
H
H
H H
C
C N
CC
CC
C
C
H
H
HH
H
H
H
H HS
C
H
H
H
Figure 1. A short chain protein or peptide.
Question 2: Proteins are naturally occurring polyamides. Give the name and structural formula
(showing at least three repeating units) of a synthetic polyamide:
Structure:
Name: …………………………………………………………………
(Answer on page 8).
2
Figure 2 shows the general structure of an amino acid, the building block for peptide and protein synthesis.
N C
H
R
C
H
H O H
O
Figure 2. The basic structure of an amino acid. Amino acids contain an amine group (–NH2) and a carboxylic acid group (–COOH). The 20 naturally occurring amino acids differ from each other by virtue
of the R group. For example:
alanine R = –CH3 serine R = –CH2OH
N C
H
H
C
H
H O H
O
N C
C
H
C
H
H O
OHH
SH
H
Figure 3. The structural formula of the amino acid glycine.
Figure 4. The structural formula of the amino acid cysteine.
Question 3: Which one of the two amino acids, either glycine shown in Figure 3 or cysteine shown in Figure 4, exhibits optical isomerism? To support your answer, draw the structural
formulae of the two optical isomers for the amino acid that you have chosen:
(Answer on page 9).
Question 4: When adjusted to the correct pH, known as the isoelectric point, an amino acid will form a Zwitterion in which the amine group is protonated and the carboxylic acid group has
ionized. The isoelectric point for the amino acid alanine = 6.00. Draw the structural formulae of the amino acid alanine at pH = 4.00, pH = 6.00 and pH = 8.00. For each pH value, state which
electrode (anode or cathode) the amino acid alanine will be attracted towards:
pH = 4.00
Anode: Cathode:
pH = 6.00
Anode: Cathode:
pH = 8.00
Anode: Cathode:
(Answer on page 9).
3
The carboxylic acid group (COOH) of one amino acid can react with the amine group (NH2) of a second
amino acid to form a peptide bond and water. This process is known as a condensation reaction and is
catalysed by enzymes within the human body. Note: while biologists refer to the CONH group as a peptide
bond, chemists refer to this functional group as an Nsubstituted amide.
amino acid (A) + amino acid (B) peptide + water
for example:
serine + leucine peptide + water
If fewer than 50 amino acids join together in a single chain, the resulting product is described as a peptide. If 50
or more amino acids join together in a single chain, then the resulting product is described as a protein. Note:
the numerical value of 50 has been arbitrarily assigned. It is used as a guideline and is therefore not absolute.
Question 5: Give the structural formula of the peptide that is formed when the two amino acids
serine and phenylalanine undergo a condensation reaction together:
+
serine
N C
C
H
C
H
H O
OHH
CC
CC
C
CH
H
H
H
H
H
phenylalanine
N C
C
H
C
H
H O
O HH H
OH
(Answer on page 9).
+ H2ON C
H
C
C
O H
OH
HH
OH
H
N C
H
C
C
O H
OH
HH
C C
HC
H H
H
H H
H
H
N C
H
C
C
H
H
O
N
H
C
H
C
C
O H
O
H H H
C C
HO C
HH
H H
H
H HH
4
Question 6: Give the structural formula of the peptide that is formed when the three amino acids
serine, cysteine and leucine undergo a condensation reaction together:
leucine
+N C
C
H
C
H
H O
OHH
OH
H
serine
N C
C
H
C
H
H O
OHH
SH
H
cysteine
+H
H
N C
H
C
C
O H
O
H HC
C
H H
CH
H H
H H
(Answer on page 9).
Question 7: Give the structural formula of the peptide that is formed when the four amino acids
leucine, methionine, serine and histidine undergo a condensation reaction together:
leucine
methionine
serine
histidine
N C
H
C
C
O H
OH
HH H
CC
H H
CH H
H HH
N C
H
C
C
O H
OH
HH H
CH H
SC
H
H
H
N C
H
C
C
O H
OH
HH H
C
C N
CN H
HH
N C
H
C
C
O H
OH
HH H
OH
+ + +
(Answer on page 10).
5
Question 8: Give the structural formulae and names of the amino acids that are formed when the peptide shown below is hydrolysed, i.e. split apart through the addition of water. Note: peptides
can be hydrolysed by refluxing with either dilute aqueous acids or alkalis.
N C
C
C
H
H
O
N
H
C
C
C
O H
OH H
H H H HH S
H
(Answer on page 10).
Question 9: Give the structural formulae and names of the amino acids that are formed when the peptide shown below is hydrolysed, i.e. split apart through the addition of water. Note: peptides
can be hydrolysed by refluxing with either dilute aqueous acids or alkalis.
N C
C
C
H
H
O
N
H
C
C
C
O
N
H
C
C
C
O H
OH H H
H H H H H HO H C
H C
CC
C
CH H
HH
H
(Answer on page 10).
6
Question 10: Give the structural formulae and names of the amino acids that are formed when
the peptide shown below is hydrolysed, i.e. split apart through the addition of water. Note: peptides can be hydrolysed by refluxing with either dilute aqueous acids or alkalis.
N C
H
C
C
O
N
HH
H
C
H
C
C
O
N
H
C
H
C
C
O
N
H
C
H
C
C
O H
O
H HC
H HS
C
H
H
H
H HC
C N
CN
H HH
H HC
C
CC
C
C
H
H H
H
H
H
HH
(Answer on page 10).
Figure 5. The figure on the right-hand-side shows the simplified three-dimensional structure of the peptide
hormone insulin. Insulin takes its name from the Latin word “insula” meaning “island” as it is produced by
cells within the Islets of Langerhans in the pancreas.
One of insulin’s most significant roles within the human body is the regulation of carbohydrate
metabolism. Individuals suffering from Type I diabetes mellitus do not produce sufficient insulin and have to
inject samples of the peptide hormone into their bodies.
The exact sequence of amino acids comprising the
insulin molecule, the so-called primary structure, was determined by British molecular biologist Frederick Sanger. It was the first protein for which the primary
structure was completely determined. For this he was awarded the Nobel Prize for Chemistry in 1958. In
1967, after decades of work, Dorothy Hodgkin determined the spatial conformation of the molecule
by means of X-ray diffraction studies. Dorothy Hodgkin was awarded the Nobel Prize for Chemistry in 1964 “For her determinations by X-ray techniques
of the structures of important biochemical substances.”
Picture and literature reference:
http://www.3dchem.com/molecules.asp?ID=196 http://nobelprize.org/nobel_prizes/chemistry/laureates/1964/press.html
7
The primary structure of a protein is determined by the sequence of amino acids from which it is composed.
The secondary and tertiary structures of a protein are determined by intra-molecular bonding, i.e. the different
ways in which the functional groups within the protein chain interact with each other.
Question 11: Study the peptide chain shown below and propose possible ways in which the various functional groups may interact with each other, resulting in the formation of intra-molecular
bonds that will contribute to the final three-dimensional structure of the molecule. Electronegativity values (Pauling sale): H = 2.1 C = 2.5 N = 3.0 O = 3.5 S = 2.5
NH
CH C
CO
H
OH
H
C
C C
C
CC
H H
H
HH
N
CH C
CO
NH
CH C
CO
NH
CH C
CO
H
H
C
H
C
H
H
H
H
S
C
H
H
H
C
O H
O
NH
CH H
CO
H
H
C
H
H
C
H
H
N
H
H
O
CH H
NCH
CN
HO H
CC N
C
O H
NC C
C
H O
CN C
N
H
H H
H
H OH
H
H OH
H
H
CO
N
C
H H
HC
C OH
H
C
CC
C
C C
H
H
H H
H
N H
C HC
C O
N H
C HC
C O
N H
C HC
C
H
H
O
O
N
H
H
H
H
S
C
H
H
C O
CH H
N H
H
H
C
O
H O
H
CH H
phenylalanine
glutamicacid
glutamicacid serine
cysteine cysteine
lysine
phenylalanine
(Answer on page 11).
8
Question 12: A protein chain may be described as a system. a) Briefly describe the different ways in which a protein chain can be considered as a system.
b) Which different systems within the body do proteins form part of? c) Provide examples of other molecules that can be considered as systems, or can be considered
to be part of a system. For each example, rationalise your choice.
(Answer on page 12).
Answers
Question 1:
● Transport proteins – haemoglobin transports oxygen throughout the body.
● Chemical messengers – the peptide hormone insulin regulates the level of glucose in the blood.
● Immune system – various immunoglobulins form part of the body’s defence against infection.
● Biological catalysts – various enzymes increase the rate of chemical reactions within the body.
● Structural proteins – elastin and collagen are important components of connective tissue.
● Contractile proteins – The relative movement of actin and myosin fibres results in muscle contraction.
● Protection from the environment – keratin (hair) covers the bodies of mammals and helps to protect the body
from temperature fluctuations, radiation and physical harm.
Question 2:
H
C C
H
C
H
H
N
O
HO
H
C
O
C
H
H
C
H
H
N
H
C
O
C
H
H
C
H
H
N
H
H
nylon 3,3
CC
C
C C
CN
H
C
O
C
CC
C
C C
N
H
C
O
C
CC
C
C C
N C
O
OH
H
H
HH
HH
HH
HH
H
HH
H
kevlar
9
Question 3:
N
CC
HC
OH
O
HH
H
H
S
H
N
CC
HCO
HO
HH
H
H
S
H
optical isomers of cysteine
Question 4:
N C
H
C
C
O
OH
H HH H
H
H
pH = 4.00
attractedtowards the
cathode
N C
H
C
C
O
OH
HH H
H
pH = 8.00
attractedtowards the
anode
N C
H
C
C
O
OH
HH H
H
H
pH = 6.00
attractedtowards both
the anode andthe cathode
Question 5:
N C
C
C
H
H
O
N
H
C
C
C
O H
OH H
H H H HO C
C
CC
C
CH H
H H
H
H
Question 6:
N C
H
C
C
H
H
O
N
H
C
H
C
O
N
H
C
H
C C
C
O H
O
H
H
H H H H HO S C
H C CH
H
H H
H
H H
10
Question 7:
CH H
C
C N
CN H
HH
CH H
CH H
SC
H
H
H
N C
H
C
C
O
N
HH
H
C
H
C
O
N
H
C
H
C
C
O
N
H
C
H
C
O H
O
H HC
C CH
H
H H
H
H H
H
H
HO
Question 8:
N C
H
C
C
O H
OH
HH H
H
N C
H
C
C
O H
OH
HH
H
HS
+
alanine cysteine
Question 9:
N C
H
C
C
O H
OH
HH
H
HO
N C
H
C
C
O H
OH
HH H
H
N C
H
C
C
O H
OH
HH H
CC
CC
C
CH H
H
H
H
+ +
serinealanine
phenylalanine
Question 10:
phenylalanine
alanine
methioninehistidine
N C
H
C
C
O H
OH
HH H
H
N C
H
C
C
O H
OH
HH H
CH H
SC
H
H
H
N C
H
C
C
O H
OH
HH H
C
C N
CN H
HH
N C
H
C
C
O H
OH
HH H
CC
CC
C
C
H
H H
H
H
+ + +
11
Question 11:
C S S C
H
HH
H
C C
N
C
C
N
H
O
O
N
H H
disulphidebridge
C
H
H
C
N
C
C
H
H
C
O
O H
H
O
O
H
CH C
C
N
H
O
H
H
H
hydrogenbonding
N HC
H
H
H
H
C
H
H
C
H
H
C
H
H
C
N
C
H
H
O O
C
O
C
H
H
C
H
H
C
H
H
C
C
N
H
O
H
ionic
bond
CC C
CC C
C
H H
H H
H
H
H
C
N
C
H
O
H
CCC
CCC
C
HH
HH
H
H
H
C
C
N
H
O
H
hydrophobicpocket
12
Question 12:
a) The answer should include references to the generalisations that can be made about a system:
● Systems have elements that interact with each other to perform a function.
● Systems are composed of subsystems.
● Systems may be influenced by other systems.
● Systems interact.
● Systems follow rules.
b) Examples include:
● Transport systems.
● Central nervous systems and hormonal messengers.
● Immune system.
● Catalysts in biochemical pathways.
● Connective tissue.
● Muscle.
c) Both DNA and RNA could be considered as systems. Both molecules are composed of subsystems
(adenine, cytosine, guanine, thymine and uracil). Both molecules interact with other systems, for example,
enzymes. Both molecules follow “biochemical rules” during replication and protein biosynthesis.
Glucose could be considered to be part of a system as it is converted into carbon dioxide and water during the
various stages of cellular respiration. The glucose, and its metabolites, interact with a variety of different
enzymes while moving through a precise sequence of biochemical reactions.
Worksheet by Dr. Chris Slatter