proteins

Question 1

amino acids and their structure

Answer 1

building blocks of proteins
consists of a central carbon atom (a-carbon) bonded to a hydrogen atom, an amino group, a carboxyl group and a variable R group that is unique to each amino acid. the R groups of AA determines their physical and chemical properties

Question 2

two types of amino acids

Answer 2

essential : obtained from the diet as organisms lack the long and complex reaction pathways required for their synthesis, to ensure proper nitrogen balance and adequate growth
non-essential : synthesized from readily-available metabolites

Question 3

properties of AA

Answer 3

amphoteric as they contain a basic group (NH3 that can accept H+) and a acidic group (-COOH hat can donate H+). allows them to resist slight pH changes, serving as pH buffers
soluble in water and ionises to form zwitterions (ions with both +ve and -ve charges). amino group receives H+, becomes positively charged and carboxyl group dissociates to release H+ to become negatively charged

Question 4

pH buffers and importance in biological systems

Answer 4

minimises change in pH when a small amount of acid or alkali is added. essential as any sudden change in pH could affect performance of proteins like enzymes

Question 5

classification of R groups of amino acids

Answer 5

non-polar : contains many C-H bonds, forms hydrophobic interactions
polar : presence of O that forms hydrogen bonds with water
acidic : donate H+ and becomes negatively charged
basic : receive H+ and becomes positively charged
both acidic and basic (electrically charged side chains) can form ionic and hydrogen bonds)

Question 6

peptide bond

Answer 6

condensation reaction between amino group of one AA and carboxyl group of another AA, with the removal of one molecule of water.
reverse reaction is hydrolysis that breaks the peptide bond condensation
successive reactions adds more AA to the chain that forms a polypeptide chain with a free -NH2 group at one end (amino terminal end) and a free -COOH group at other end (carboxyl terminal end)

Question 7

primary structure

Answer 7

specific number and sequence of AA joined by peptide bonds in a polypeptide chain
determines the type and location of chemical reactions and hence the pattern of folding that confers the specific 3d conformation of an particular protein
the sequence of AA is determined by the sequence of DNA of a gene in the cell

Question 8

secondary structure

Answer 8

repeated coiling and folding of a polypeptide chain in a specific pattern
coils and folds are maintained by hydrogen bonds between oxygen of -C=O in a peptide bond and hydrogen of -N-H in a peptide bond
two common types are a-helix and b-pleated sheet
regions of polypeptide chains without a regular secondary structure have a random coil or loop conformation

Question 9

a-helix

Answer 9

made up of a single polypeptide chain coiled in a right-handed spiral structure
3.6 AA residues per turn
maintained by H bonds between every 4th peptide bond, formed between oxygen of -C=O of one AA and hydrogen of -N-H 4 AAs away in a single polypeptide chain
each successive turn is held to adjacent turns by 3 to 4 H bonds, conferring significant stability

Question 10

b-pleated sheet

Answer 10

consists of two or more b-pleated strands aligned side by side and held together by hydrogen bonds formed between oxygen of -C=O of an AA on one region and the hydrogen of -N-H group of an AA on the adjacent region
strands can run parallel (6.5 AA per fold, every two H bonds are pointed towards each other /) or anti-parallel (7 AA per fold, H bond are vertical and parallel to each other)

Question 11

tertiary structure

Answer 11

specific three dimensional conformation formed by further coiling and folding of a single polypeptide chain
allows AA that are far apart in primary structure and in different types of secondary structure can interact within completely folded protein
stabilised by hydrogen bonds, ionic bonds, hydrophobic interactions and disulfide bonds between R groups of AA

Question 12

hydrogen bonds

Answer 12

weak electrostatic attraction between a hydrogen atom that is bonded to a strongly electronegative atom (donor) and a lone pair of electrons on a strongly electronegative atom in a neighbouring molecule (acceptor)
oxygen and nitrogen (highly electronegative) vs carbon and hydrogen
formed between polar R groups of AA

Question 13

ionic bonds

Answer 13

electrostatic attractions formed between oppositely charged R groups

Question 14

hydrophobic interactions

Answer 14

force of aggregation of non-polar molecules in the presence of water
formed between non-polar R groups which interact and cluster at the core of the protein to avoid contact with water
causes polypeptide to fold and shield as many hydrophobic R groups from aqueous environment

Question 15

disulfide linkage

Answer 15

covalent bonds between sulfhydryl groups of two cysteine residues which are brought close together by the folding of polypeptides
disulfide linkages are strongest among another interactions in tertiary structure and contribute to the stability of a protein

Question 16

differences between alpha helix and beta pleated shape

Answer 16

shape of alpha helix is a spiral/coil while beta pleated sheet is a zigzag sheet
hydrogen bonds in alpha helix is between C=O of a peptide bond of one AA and N-H of peptide bond of AA 4 residues away, while in beta pleated sheet it is between C=O of peptide bond on one beta strand and N-H of peptide bond on an adjacent strand

Question 17

nature of disulfide linkages and how they help to stabilise tertiary structure of proteins

Answer 17

disulfide bonds are strong covalent bonds, formed when 2 cysteine residues that contain sulfhydyrl groups are oxidised. this helps to maintain the tertiary structure by increasing resistance to high temperatures and pH denaturation

Question 18

quaternary structure

Answer 18

association of two or more polypeptides chains to form a functional protein. each polypeptide forms a subunit, held together by hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions between R groups of AA to form a multimeric protein (not all proteins have quaternary)

Question 19

globular protein

Answer 19

folded into compact spherodial molecules with hydrophobic R groups in the interior of protein while polar R groups are on the exterior, making them soluble in aqueous medium

Question 20

haemoglobin

Answer 20

quaternary globular protein with 4 polypeptide subunits (2 alpha globin chains and 2 beta globin chains) responsible for transporting oxygen in blood

Question 21

structure of haemoglobin

Answer 21

quaternary globular proteins with 4 polypeptide subunits, 2 alpha globin chains and 2 beta globin chains. each globin chain coils into alpha helix and folds into a globular tertiary structure, hydrophobic R groups in interior while hydrophobic R groups are on the exterior in contact with aqueous medium

Question 22

structure of globin chain in haemolobin

Answer 22

each chain associated with a prosthetic group (haemoglobin group) which resides in a hydrophobic pocket in protein subunit, consisting of a porphyrin ring with an iron 2+ ion in the centre, allowing reversible binding with oxygen

Question 23

structure of subunits in haemoglobin

Answer 23

subunits are packed tightly in a tetrahedral on formation, hence one haemoglobin protein has 4 haem groups and can bind up to four oxygen molecules reversibly

Question 24

cooperative binding

Answer 24

binding of one oxygen molecule results in conformation changes of adjacent subunits, increasing their affinity to oxygen at high oxygen concentrations

Question 25

how does haemoglobin carry out its function at different oxygen partial pressures?

Answer 25

haemoglobin has sigmodial oxygen dissociation curve, showing that it undergoes cooperative binding with oxygen. hence it can effectively load oxygen in the lungs where partial pressures is higher and release it in tissues where partial pressure is lower

Question 26

explain the difference between shape of oxygen dissociation curve for haemoglobin and myoglobin

Answer 26

myoglobin is a single polypeptide chains that stores oxygen, and hence is unable to undergo cooperative binding with oxygen. haemoglobin has a sigmodial shaped ODC due to interactions between 4 subunits of haemoglobin where binding of 1 oxygen molecule increases the affinity of other subunits for oxygen.

Question 27

advantage of myoglobin having higher oxygen affinity that haemoglobin

Answer 27

high affinity allows myoglobin to store oxygen in muscle tissues, ensuring a readily available supply during periods of high oxygen demand like during exercise

Question 28

explain how structure of haemoglobin is related to its function

Answer 28

quaternary globular structure protein with four subunits packed tightly together in tetrahedral conformation - makes it compact so more haemoglobin can be packed in each RBC for more efficient transport of O2 hydrophobic R-groups in interior, hydrophillic R-groups on exterior - haemoglobin soluble in aqueous medium to transport O2 in blood associated with a haem group (porphyrin ring with Fe2+ ion - reversible binding to O2, for uptake of O2 from lungs and release at respiring tissues in body quaternary structure maintained by weak IMF like H bonds, ionic bonds and hydrophobic interactions - flexibility to change conformation upon binding to O2 for cooperative binding. in O2 rich env. binding of one O2 molecule results in a conformational change of adjacent subunits, increasing haemoglobin OA, increase uptake of O2

Question 29

fibrous protein

Answer 29

regular elongated repeating structures that give high tensile strength, often perform structural roles

Question 30

structure of collagen

Answer 30

structural fibrous protein found in connective tissues each collagen polypeptide chain contains abt 1000 AA, usually with repeating triplet sequence of Gly-X (often proline)-Y (often hydroxyproline) each chain coiled into left handed helix, would around one another by further coiling to form a basic triple helix structure (troopocollagen) almost every 3rd amino acid in each PP is a glycine which is the smallest AA that fits into the center of troopocollagen, which allows the strcture to be very compact which enhances the stability of the structure as it allows for more H bonds 3 PP chains of troopocollagen held by H bonds between peptide bond -NH of glycine and peptide -C=O in adjacent PP

Question 31

structure of troopocollagen

Answer 31

troopocollagen molecules lie parallel in staggered arrangement to form fibrils with strong covalent cross-links between adjacent troopocollagen molecules, occurring between lysine or hydroxylysine residues at C-terminus with similar residues at N-terminus many collagen fibrils and bundle to form collagen fibres via cross-links hydrogen bonding between PP chains within tropocollagen, covalent cross-links between tropocollagen, and bundling of collagen fibrils into fibres - give rise to high tensile strength to maintain structural integrity and withstand mechanical forces without undergoing excessive stretching or damage, facilitating its structural role in connective tissue. troopocollagen arranged in staggered arrangement in fibrils - minimises points of weaknesses along the length of the fibrils for high tensile strength, facilitating its structural role in connective tissue. non-polar R groups form hydrophobic interactionsand large size of collagen makes the protein insoluble in aqueous medium

Question 32

denaturation

Answer 32

loss of 3d shape by breaking of bonds, causing protein to lose its biological function secondary, tertiary and quaternary levels of the protein structure can be changed due to the disruption of the weaker interactions

Question 33

effect of high temp on proteins

Answer 33

causes atoms in proteins to gain kinetic energy and vibrate faster. further increase in temperature disrupts weak bonds such as hydrogen bonds, ionic bonds, hydrophobic interactions that maintains the specific 3D shape of the molecule. protein structure unfolds and non-polar side chains that used to be in the core of the protein are exposed to aq. env, causing them to aggregate randomly with other PP, resulting in irreversible chain to protein structure. extreme high temperature may eventually break disulfide bonds.

Question 34

effect of pH on protein structure

Answer 34

deviation from the optimum pH can neutralise charges on acidic and basic R groups, disrupting ionic bonds. at low pH, increase in the concentration of hydrogen ions in the solution can combine with -COO- to form -COOH. at high pH, increase in hydroxyl ions (OH-) can remove hydrogen ions from -NH3+ on R-groups of amino acids to form -NH2. changes to the charge distribution on the acidic and basic R-groups may disrupt hydrogen bonds formed between these acidic/basic R-groups and polar R-groups. when the polypeptide chain unfolds, the non-polar R-groups are exposed to the aqueous medium and would aggregate with each other, resulting in irreversible change to the protein structure.