proteins

Question 1

how many naturally occurring amino acids are there

Answer 1

20

Question 2

are globular proteins soluble or insoluble in water

Answer 2

soluble

Question 3

what elements does amino acids contain

Answer 3

carbon, hydrogen, oxygen and sometimes sulfur (methionine and cysteine)

Question 4

what are the elements present in amino acids but not carbohydrates

Answer 4

nitrogen and sulfur

Question 5

3 examples of fibrous proteins

Answer 5

keratin, elastin and collagen

Question 6

are fibrous proteins soluble or insoluble in water

Answer 6

insoluble

Question 7

what is a prosthetic group

Answer 7

a non protein component in globular proteins

Question 8

give an example of a prosthetic group

Answer 8

haem group - contains an iron ion

Question 9

where is a disulphide bridge formed

Answer 9

between 2 cysteine amino acids

Question 10

test for presence of proteins and observation (3,1)

Answer 10

biuret’s test:
1. add 2cm3 of sodium hydroxide into a test tube containing 2cm3 of sample solution
2. add 1% copper (II) sulfate to the mixture drop by drop
3. shake the mixture after each drop
observation: purple colouration is observed if proteins are present

Question 11

structure of amino acids (5)

Answer 11

• basic amino group
• acidic carboxyl group
• a hydrogen atom
• R group
• alpha carbon

Question 12

4 types of bond formed between R groups
and where are they formed

Answer 12

non polar and non polar - hydrophobic interactions
polar and polar - hydrogen bonds
polar and acidic/basic - hydrogen bonds
acidic and basic - ionic bonds
cysteine and cysteine (-SH group) - disulfide bonds

Question 13

what is amphoteric molecules

Answer 13

it contain both an acidic and a basic group

Question 14

importance of amphoteric nature of amino acids (2)

Answer 14

• it can act as buffers in solutions,
• which can resist pH change

Question 15

formation of peptide bond (4)

Answer 15

• formed btw the N of -NH group of one amino acid and the O of -CO group of another amino acid
• removal of one water molecule
• catalysed by peptidyl transferase
• to form a chain of amino acids, the next incoming amino acid is always added to the carboxyl end of the dipeptide or existing chain of amino acids

Question 16

what are the 2 terminals of a polypeptide chain

Answer 16

n-terminal (amino end) and c-terminal (carboxyl end)

Question 17

describe the primary structure of a protein

Answer 17

it refers to its precise number, type and sequence of amino acids held together by peptide bonds

Question 18

describe the secondary structure of a protein

Answer 18

• the polypeptide chain coils and folds into geometrically regular repeating structures, mainly α-helices and β-pleated sheets
• it is held together by hydrogen bonds between the CO and -NH groups in the main chain of the polypeptide

Question 19

describe the tertiary structure of a protein

Answer 19

• the polypeptide chain is further bent, coiled and folded extensively to form a specific 3D conformation
• it is held together by INTRAMOLECULAR hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interaction between the R groups of amino acids

Question 20

importance of tertiary structure (2)

Answer 20

• leads to diversity of globular proteins due to differences in their tertiary structure
• the specific 3D conformation of a protein is responsible for the biological activity of the protein

Question 21

describe the quaternary structure of a protein

Answer 21

• it is the aggregation of two or more polypeptide chains
• each subunit is held together by intermolecular hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions between the R groups of amino acids

Question 22

what bonds are found in the primary structure

Answer 22

peptide bonds

Question 23

what bonds are found in the secondary structure

Answer 23

intramolecular hydrogen bonds between the CO and -NH groups in the main chain of the polypeptide

Question 24

what bonds are found in the tertiary structure

Answer 24

• hydrophobic interactions between non-polar R groups
• intramolecular hydrogen bonds between R groups of polar and polar/acidic/basic amino acids
• ionic bonds between R groups of positively charged and negatively charged amino acids
• disulfide bond between the -SH groups of 2 molecules of cysteine

Question 25

what can disulfide bond be broken down by and not be broken down by

Answer 25

only be broken down by reducing agents
cannot be broken down by heat or pH

Question 26

what is denaturation (3)

Answer 26

• it is the loss of the specific 3D conformation of a protein molecule, causing the molecule to unfold and change shape, and hence lose its biological function or activity
• it can be reversible or irreversible
• the primary structure of the protein is unaffected

Question 27

how does high temperature leads to denaturation (4)

Answer 27

• increasing temperature leads to an increase in the kinetic energy supplied to the protein,
• so molecular motion of protein increases
• the high heat disrupts the hydrogen bonds and hydrophobic interactions that maintain the secondary and tertiary structures
• this results in a loss of specific 3D conformation, leading to denaturation

Question 28

how does change in ph leads to denaturation (3)

Answer 28

• change in ph alters the ionic charge of the COO- (acidic) and NH3+ (basic) R groups of the amino acids
• the ionic bonds and hydrogen bonds that maintain the tertiary structures of the protein are disrupted,
• resulting in the loss of the specific 3D conformation of the protein, leading to denaturation

Question 29

structures and functions of haemoglobin (6)

Answer 29

1aS: Haemoglobin consists of 2 α chains and 2 β chains and each
polypeptide chain is coiled to form
α-helices (secondary structure)
which is further bent and folded into a globular protein subunit
1bS: The four protein subunits are
packed closely together, held together by hydrogen bonds, ionic
bonds and hydrophobic interactions, resulting in a compact molecule
1F: allows for packing of more haemoglobin (Hb) into the red blood cell, thus more oxygen molecules (O2) can be carried and transported
2S: The hydrophilic R groups of amino acids on the surface of the Hb molecule face outwards and interact with the aqueous medium
2F: maintaining the solubility of Hb in aqueous medium and allowing for mobility around the body via the bloodstream as Hb can bind and transport O2 dissolved in the blood
3S: The four protein subunits of Hb are packed such that the hydrophobic R groups of amino acids face inwards into the centre of the Hb molecule and are shielded from the aqueous
medium
3F: allows for Hb to be held in its precise
compact 3D conformation, thus more Hb can be packed into the red blood cell and more O2 is carried and transported
4S: Each protein subunit contains a prosthetic haem group with an Fe2+
4F: allows for the reversible binding of oxygen molecules (to Fe2+ of haem group), enabling Hb to carry and readily release O2 to respiring tissues
5S: A complete Hb molecule has (four protein subunits with) four haem groups
5F: Each Hb molecule can carry and transport four oxygen molecules at a time, enabling more efficient transport of O2 around the body
6S: The haemoglobin molecule is
allosteric in nature and can undergo changes in conformation
6F: such cooperative binding facilitates easier binding and release of subsequent oxygen molecules

Question 30

structures and functions of collagen (6)

Answer 30

1S: A fibrous protein made up of repetitive sequence of amino acids (Glycine-X-Y,
where X is frequently a proline and Y is hydroxyproline or hydroxylysine) held
together by peptide bonds;
2S: Each polypeptide chain coils into the shape of a loose helix;
3S: 3 helical polypeptide chains wind tightly around each other, and are bound to one another by intermolecular hydrogen bonds, forming a tropocollagen
4S. Almost every third amino acid of the tropocollagen polypeptide chain is glycine which has a small R group (H atom)
4F: This allows the 3 polypeptide chains of a tropocollagen molecule to be wound tightly together and form HBs in the triple helix structure, increasing tensile strength of the tropocollagen molecule and allowing tropocollagen to provide structural support in connective tissues.
5S. The ends of the parallel tropocollagens are staggered and covalent cross-links form between the carboxyl end of one tropocollagen and the amino end of another tropocollagen;
6S. The covalent cross-linking of tropocollagen molecules form collagen fibril and the collagen fibrils are further assembled to form collagen fibres

Question 31

structures and functions of GPLR (3)

Answer 31

1. The GPLR iis a single polypeptide chain coiled into 7 transmembrane α helices. Non-polar fatty acid tails of the membrane phospholipid molecules and non-polar R groups of AA residues on receptor form hydrophobic interactions, allowing GPLR to be embedded in and span the CSM
2. The GPLR has an extracellular region, which serves as the specific binding site for the ligand/signal molecule which is unable to pass freely across the membrance
3. The GPLR has an intracellular region, which serves as the specific binding site for the G protein.

Question 32

nature/structure of α helix (4)

Answer 32

1. it is elastic and flexible, taking the form of an extended spiral spring
2. it makes one complete turn for every 3.6 amino acids
3. the conformation is stabilised by the formation of intramolecular HB btw the O of C=O group and the H of the -NH group of every fourth peptide bond
4. the HB are easily disrupted by heat/pH

Question 33

nature/structure of β pleated sheets (4)

Answer 33

1. it is flexible but not elastic
2. 2 or more regions of one polypeptide chain lie parallel to each other and are held together by intramolecular HB formed btw the O of C=O group and the H of the -NH group in the main chain of polypeptide
3. segments of the polypeptide chain are folded in patterns as a result of HB btw the AA at regular intervals of the polypeptide chain
4. the HB are easily disrupted by heat/pH

Question 34

explain the significancce of the R groups of different AA to protein structure (4)

Answer 34

1. Different amino acids have different R groups to allow the formation of different bonds within the polypeptide chain
2. AA with acidic R groups can form ionic bonds with AA with
   basic R groups
3. AA with sulfhydryl groups (–SH) R groups can form disulfide bonds
4. AA with non-polar R groups can form hydrophobic interactions ;
5. AA with polar R groups can form hydrogen bonds with AA
   with polar/acidic/basic R-groups
6. Formation of these bonds can allow protein to assume and maintain its specific 3D conformation which is responsible for its specific function