proteins

Question 1

what does an amino acid contain

Answer 1

consists of alpha carbon atom covalently bonded to
- hydrogen atom, amino group (NH2), carboxyl group (COOH) and variable R group (determines its chemical and physical properties = different for each amino acid)

Question 2

what are neutral amino acids

Answer 2

1. have non polar R groups taht are hydrophobic
2. have polar R groups that hydrophillic = sum of positive and negative charges are equal

Question 3

what are electrically charged amino acids

Answer 3

1. negatively charged R groups = acidic AA = R group has carboxyl group that dissociates to form COO-
2. positively charged R groups = basic AA = R group has amino group that accepts H+ to form NH3+

Question 4

properties of amino acids

Answer 4

1. exist as zwitter ions = has both negative and positive charges after beinf ionised in water (becomes neutral dipolar ion)
2. act as buffer (maintain pH of SOLUTION)
   - when acid is added: COO- of zwitter ion accepts H+ = becomes COOH = no change in pH of solution, but AA becomes positively charged
   - when base is added: NH3+ of zwitterion loses H+, H+ neutralises added OH- = NH3+ becomes NH2 = pH of solution maintained but AA becomes negatively charged

Question 5

how are polypeptides formed

Answer 5

• formed when amino acids are joined via condensation reaction
• OH is lost from carboxyl group, H atom is lost from amino group = forms peptide bond with the lost of one water molecule = peptide bond covaltently bonds the 2 amino acids together

Question 6

primary structure

Answer 6

number and sequence of amino acids in a single polypeptide chain
maintained by peptide bonds
determines pattern of folding of polypeptide chain = determines conformation

Question 6

features of polypeptides

Answer 6

1. after condensation reaction, amino acids making up the polypeptide are called residues
2. regularly repreating part excluding side chain = polypeptide backbone, variable R groups stick out
3. polypetide chain is directional: start of chain is always NH2 (N terminus), end of chain is always COOH (C terminus)
   4.polypeptides fold into a specific conformation = form complmemntary clefts = determines proteins’s function

Question 7

secondary structure

Answer 7

regular coiling/pleating of a singple polypeptide chain
maintained by intramolecular hydrogen bonding bteween CO and NH groups of polypeptide backbone
R groups not involved

Question 8

examples of secondary structure

Answer 8

alpha helix: single polypeptide chain wound into helical structure, turns of helix libked tigether by hydrogen bonds btwn CO and NH groups of one and next turn respectively, formed btwn groups at every 4th peptide bond, 3.6 AA residues in every turn of helix

beta pleated sheet: two or more regions of single polypeptide chain by hydrgeon bondinf btween CO group of one segment and NH group of another segment, chains may run parallel or anti parallel to form folded flat sheet

Question 8

tertiary structure

Answer 8

formed by further extensive folding and bending of single polypeptide chain = gives rise to specific 3D conformation of protein = form compact globular protein
involves R groups
maintained by 4 type of intramolecular interactions

Question 9

what are hydrogen bonds

Answer 9

formed between R groups of polar amino acids
identifying: look out for OH-/C=O/H atom
not a type of covalent bond!!

Question 10

what are ionic bonds

Answer 10

formed between amino aicds containing oppositely charged R groups
look out for: COO-/NH3+ at end of polypeptide chain

Question 11

what are hydrophobic interactions

Answer 11

formed between amino aicds with hydrophobic R groups = the R groups aggregate together
look out for: CH/CH3 groups

Question 12

what are disulfide bonds

Answer 12

formed between 2 cystenine amino acids by oxidation of sulfydryl (-SH) groups, SH groups lose their H atoms, a type of covalent bond
look out for sulfur atoms/-SH

Question 13

quartenary structure

Answer 13

association of 2/more polypeptide chains into 1 functional protein molecule (into fibrous or globular protein)
each polypeptide is subunit
maintained by the 4 interactions formed between the R groups of amino acid residues of different subunits
R groups involved

Question 14

molecular strucuture of haemoglobin

Answer 14

1. quaternary structure with 4 polypeptide subunits, namely 2
   α-globin* subunits and 2
   β-globin* subunits;
2. secondary structure: Each polypeptide is made up of α-helices
3. tertiary structure: Each subunit is folded into a globular* tertiary structure = most of its amino acids with
   hydrophilic R groups are on external surface, while most of its hydrophobic amino acids
   with R groups* are buried in interior, away from aqueous
   surrounding;
4. Each subunit is associated with a haem* prosthetic group consisting of a porphyrin ring*
   and an iron ion / (Fe2+ );
5. 4 subunits held together by weak intermolecular interactions formed between R groups
   (hydrogen bonds, ionic bonds and hydrophobic interactions), = allows movement that
   influences affinity for oxygen allowing for cooperative binding* of oxygen;

Question 15

how does structure of haemoglobin relate to its functions

Answer 15

polypeptide subunits:;

1. soluble in water = can be transported and carry oxygen from
   lungs to tissues vice versa: arrangement of its 2 α-globin* subunits and 2 β-globin* subunits are most of its hydrophilic amino acid side chains are on external
   surface while its hydrophobic amino acid side chains are buried in interior;
2. each subunit is made of globin polypeptide and a prosthetic (non-protein) component called
   haem group*;
3. 1 Hb molecule can carry up to
   4 oxygen molecules, at a time forming oxyhaemoglobin: each haem group consists of a porphyrin ring* and an iron ion (Fe2+ ) = Fe2+ of haem group binds temporarily to oxygen molecule (4 subunits = 4 Fe2+ from 4 haem groups)
4. cooperative binding* of oxygen: 4 subunits held together by weak intermolecular interactions formed between = allows movement that influences affinity for oxygen
5. binding of one oxygen molecule to one haemoglobin subunit induces a
   conformational* change in remaining 3 subunits = their affinity for oxygen increases

Question 16

molecular structure of collagen

Answer 16

Collagen is a fibrous protein
1. made up of a chain of amino acids * joined by peptide bonds.
2. sequence is usually a repeating unit of glycine-X-Y where X is usually proline and Y is usually hydroxyproline
6. loose helical polypeptide chains coil, held together by hydrogen bonds, =
triple helix of tropocollagen
7. small glycine* residues allow formation of a very tight/compact triple helical structure
8. bulky, inflexible proline and hydroxyproline confer rigidity on the molecule.
9. covalent cross-links* form between lysine* residues at the C and N ends of adjacent/parallel tropocollagen molecules = form a collagen fibril
10. bundles of collagen fibril form a collagen fibre.
11. staggered arrangement of tropocollagen molecules give rise to a banded appearance;

Question 17

how does strucutre of collagen relate to its function (8 points)

Answer 17

1. fibrous structural protein
2. high tensile strength; has 3 polypeptide* chains wound together to form a tropocollagen* molecule, numerous hydrogen bonds* form between amino acids of adjacent polypeptide chains
3. molecule insoluble in water: extensive H bonds already formed between
   residues in different polypeptides, limiting interaction with water molecules;
4. small glycine* residues able tofit in axis/center of triple helix = allow formation of a very tight/compact triple helical structure;
5. bulky, inflexible proline and hydroxyproline confer rigidity on the molecule.
6. covalent cross-links* form between lysine* residues at the C and N ends of adjacent/parallel tropocollagen molecules = form fibrils = increase tensile strength
7. bundles of fibrils unite to form long collage fibres = increase tensile strength
8. high tensile strength: staggered arrangements/longitudinal displacement minimises points of weaknesses along the length of the fibrils;

Question 18

fibrous vs globular protein
(shape, solubility in water, amino acid sequence, length of polypeptide, function)

Answer 18

Shape
- fibrous: long polypeptides form long straight fibres
- globular; polypeptide chain folded into spherical shape
Solubility:
- fibrous: insoluble = extensive hydrogen bonds form between residues of different polypeptides
- globular: soluble = polar R groups can form hydrogen bonds with water
AA sequence:
- fibrous: less variety of AA = has repetitive regular sequence
- gloubular: more variety of AA = non repetitive AA sequence
Length of polypeptides
- fibrous: may vary yet protein is still functional
- globular: akways identical or else protein may not be functional
function
- fibrous: structural
- globular: protein with metabolic role

Question 19

properties of proteins

Question 20

testing for proteins (biuret test)

Answer 20

1.place 2cm3 of test solution of test tube
2. add equal volume of 5% KOH solution and shake mixture
3. add 2 drops of 1% copper sulphate solution, shaking well with each drop

observations
proteins present: blue solution turns violet
proteins absent: blue solution remains blue

Question 21

why does collagen not have a tertiary structure

Answer 21

it is a fibrous structural protein = does not have a globular shape which is an outcome of extensive folding in forming tertiary structure