chapter 1: BIOLOGICAL MOLECULES: proteins!

Question 1

the four different groups of atoms bonded to an α-carbon

what is the structure of amino acids?

Answer 1

• an amino acid consists of a central alpha carbon (α-carbon) atom
  > known as an asymmetrical carbon

four diff groups of atoms bonded to α-carbon are:
- hydrogen atom
- amino/amine group (-NH2)
- carboxyl/ carboxylic acid group (-COOH)
- variable R group known as a side chain
> R group differs with each amino acid

• the R group/ side chain of each amino acid determines its chemical properties
• the simplest R group/ side chain is just a hydrogen atom
  > the amino acid with this R group is glycine

Question 2

how many common amino acids are there and what are the 4 main groups they are classified under?

Answer 2

• 20 naturally occuring amino acids are used to synthesise proteins

groups that amino acids are classified into:
* non-polar amino acids
* polar amino acids
* acdic amino acids (electrically charged)
* basic amino acids (electrically charged)

Question 3

what are the properties of the side chain (R group) in non-polar amino acids?

Answer 3

• have a non-polar side chain
• contains hydrocarbon chain or carbon ring
• and are therefore hydrophobic

Question 4

what are the properties of the side chain (R group) in polar amino acids?

Answer 4

• have a polar side chain
• usually contains functional groups with oxygen, nitrogen and sulfur in the R group
• hydrophilic

Question 5

what are the properties of the side chain (R group) in acidic amino acids?

electrically charged amino acids

Answer 5

• have a side chain with a carboxyl group which is acidic and negativly charged at cellular pH
• hydrophilic

Question 6

what are the properties of the side chain (R group) in basic amino acids?

electrically charged amino acids

Answer 6

• have a side chain with an amino group which is basic and posiitvely-charged at cellular pH
• hydrophilic

Question 7

properties of amino acids

are amino acids soluble?

Answer 7

• they are soluble/ able to dissolve in water and other aqeous solution where they form ions
• generally insoluble in organic solvents

Question 8

properties of amino acids

what is the zwitterion formation?

Answer 8

• in aqueous solution, amino acids exists as ions having both a positive and a negative charge
  > also known as dipolar ions
  > zwitterion

ions formed by:
- the loss of a hydrogen ion ( H+) from the carboxyl group (COOH), making it negatively charged (-COO^-)
- and the gain of a hydrogen ion (H+) by the amino group (-NH2), making it positively charged (-NH3^+)

Question 9

properties of amino acids

what are the buffering capabilities of amino acids?

Answer 9

• due to the presence of both the amino group and the carboxyl group
  > amino acids possess both acidic and basic properties
  > amphoteric
• aqueous solutions of amino acids can function as buffer solutions which can resist small changes in pH
  > when small amounts of acids or alkalis are added to it
• in an acidic solution
  > hydrogen ions conc is high and the pH is decreased
  > the COO- group of zwitter ion accepts the excess H+ ions to form COOH
  > overall molecule becomes positively charged
• in an alkkaline solution
  > (OH- conc is high and pH is increased)
  > the NH3+ group of zwitter ion donates H+ ions to form -NH2 and the overall molecule becomes negatively charged

-the ability of amino acids to function as buffers is essential in biological systems
> function to prevent any sudden changes in cellular pH that could adversely affect the activity of enzymes and the functions of other proteins

Question 10

describe the formation of peptide bonds

Answer 10

• a condensation reaction occurs between the carboxyl group of one amino acid and the amino group of another amino acid to form a covalent peptide bond
• (CONH)
  > via the removal of one water molecule
  > the resulting compound is called a dipeptide

-in cells, peptide bonds are synthesised by ribosomes during the process of translation
- peptidyl transferase, an enzyme, catalyses the formation of peptide bonds between amino acids in cells
-

Question 11

describe the breaking of peptide bonds

Answer 11

-the peptide bond between adjacent amino acids residues can be broken by hydrolysis to yield amino acid monomers
- the addition of a water molecule is required to break a peptide bond
> proteases catalyses the hydrolysis reaction

Question 12

what is the structure of a polypeptide chain?

Answer 12

• a polypeptide chain has two different ends- amino end and the carboxyl end
• at the start of the polypeptide chain is a free amino group
  >not included in the formation of the peptide bond
  >called the N terminus
• the opposite end has a free carboxyl group and is called the carboxyl end (C-terminus)
• the repeating sequence of atoms (-NCC-) is called the polypeptide backbone
  > extending from the backbone are the side chains/ R groups of amino acids
• each specific polypeptide has a unique linear sequence of amino acids
  > a great variety of polypeptide chains can be synthesised from just a limited set of monomers
• polypeptide chains fold proteins into specific shapes held in place with 4 different types of bonds and itnerations
  > different linear sequences determine the specific three-dimensional shape/ configuration/ conformation of proteins

Question 13

what are the bonds stabilising protein in its unique structure?

Answer 13

• after amino acids are joined by peptide bonds to form a polypeptide
  > the polypeptide is then folded to form a specific shape/ three dimensional conformation
  > polypeptides are folded in the lumen of the rough endoplasmic reticulum in a eukaryotic cell

four types of bonds and interaction maintain the shape of each protein:
- hydrogen
- ionic bond
- hydrophobic interations
- disulfide bonds

bonds and interactions can occur between amino acid residues in:
- different parts of the same polypeptide ( INTRAmolecular or INTRA-chain)
- between different polypeptides( INTERmolecular or INTER-chain)

Question 14

how do hydrogen bonds help stabilise protein in its unique structure?

Answer 14

hydrogen bonds may form between
- the C=O and N-H of amino acid residues on the polypeptide backbone in secondary structures of proteins
OR
- polar R groups of amino acid residues in the tertiary and quatenary structure of proteins

• an individual hydrogen bond is a weak bond
  > if it occurs frequently in the structure of a protein, collectively, multiple hydrogen bonds are strong and are able to maintain the conformation and stability of the protein
• hydrogen bonds are disrupted by a change in temperature and pH of the surrounding medium

Question 15

how do ionic bonds help stabilise protein in its unique structure?

Answer 15

• ionic bond is an electrostatic attraction/interaction formed between a negatively charged acidic R group and a positively chargen basic R group
  > in the tertiary and quaternary structure of proteins
• ionic bonds can be disrupted by a change in temperature and the pH of the surrounding medium
  > pH changes cuases the charges on the acidic and basic R groups to be altered potentially disrupting ionic bonds

Question 16

how do disulfide bonds/disulfide bridges help stabilise protein in its uniquee structure?

Answer 16

• a disulfide bond is formed between two cysteine amino acids residues with sulfhydryl groups (-SH) on their R groups in the tertiary and quaternary structure of proteins
• disulfide bonds are strong covalent bonds that can be broken only under high temperatures

Question 17

how do hydrophobic interactions help stabilise protein in its unique structure?

Answer 17

• hydrophobic interactions are formed between amino acids residues with R groups that are non-polar and are therefore hydrophobic
• these interactions form in the tertiary and quaternary structure of proteins
• they can form more stable interactions with each other than with water molecules
  > thus, they tend to group together to avoid interacting with water in an aqueous environment
• if a polypeptide chain contains a number of these groups and is in aqueous environment
  > the polypeptide chain will tend to fold such that the maximum number of hydrophobic R groups come into close contact with each other in the interior of protein and are shielded from water
  > and the hydrophilicc R groups would be exposed to the environment
  > found on the exteiror of the protein surface

Question 18

what is protein denaturation?

Answer 18

denaturation is the unfolding of the three-dimensionsla conformation of a protein due to:
- increase in temperature away from optimum temperature or
- change (increase or decrease) in pH away from the optimum pH

• when a protein molecule denatures, it loses its quaternary, tertiary and secondary structure but retains its primary structure
• since the function of a protein depends on its folded 3D shape, denaturation leads to the loss of its function

Question 19

how does the increase in temperature cause proteins to denature?

Answer 19

• increasing temperature increases thermal agitation/ vibrations of protein molecules
  > causes R group interactions such as hydrogen bonds, ionic bonds and hydrophobic interactions in the tertiary and quaternary structures to be disrupted/ break
• hydrogen bonds in the secondary structures may also be disrupted
  ( *the number of H bonds broken in the secondary structures increases with increasing temperatures > causes the extent of unfolding of secondary structures to increase with increasing temperatures) *
• the protein is denatured as it unfolds and loses its 3D structure
  *
• disulfide bonds are strong covalent bonds
  > usually broken only at very high temperatures by high heat energy but protein denaturation usually occures before it can happen
  > enzymes with very high optimum temperatures usually cconsist of many disulfide bonds in their tertiary and quaternary structures

Question 20

how does the changes in pH cause protein denaturation?

Answer 20

• pH changes ( can either be and increase or decrease in H+ concentration) can result in changes in the charges of the R groups such as:
  > alteration of charges on acidic and basic R grouos of amino acid residues
  > an unchanged polar R group becoming charged

> hence changes in pH results in the disruption of and ionic bonds and hydrogen bonds respectively
hydrophobic interations and disulfide bonds remain unaffected

Question 21

difference in structure & property between globular and fibrous protein

what is the difference in their shape?

Answer 21

globular protein: polypeptide chain is tightly folded to form a spherical shape
fibrous protein: polypeptide chains are cross-linked at intervals to form long, rope-like fibres or sheets

Question 22

difference in structure & property between globular and fibrous protein

what is the difference in the regularity of amino acid sequence?

Answer 22

globular protein: rarely exhibit regular, repetitive amino acid sequences

fibrous protein: regular and repetitive sequence of amino acids
eg in collagen,
- every third residue in collagen is glycine
- tripeptide sequence glycine-proline-hydroxyproline recurs frequently

Question 23

difference in structure & property between globular and fibrous protein

what is the difference in the main bonds and interactions in quaternary structure?

Answer 23

globular proteins: quaternary structure is established mainly by hydrophobic interactions, ionic bonds and hydrogen bonds between polypeptide chains (weak)

fibrous proteins: quaternary structure is stablished mainly by strong, extensive network of hydrogen bonds and covalent cross-links between polypeptide chains

Question 24

difference in structure & property between globular and fibrous protein

what is the difference in their level of protein structure of greatest importance?

Answer 24

globular proteins: tertiary structure most important
fibrous protein: secondary structure most important

Question 25

difference in structure & property between globular and fibrous protein

what is the difference in their solubility?

Answer 25

globular proteins: generally more soluble than fibrous proteins in aqueous medium
- hydrophilic R groups of amino acids residues on protein exterior
- hydrophobic R groups amino acids buried in interior

fibrous protein: generally insoluble in aqueous medium
- large number oh hydrophobic R groups of amino acid residues on protein exteiror

Question 26

difference in structure & property between globular and fibrous protein

what is the difference in their functions?

Answer 26

globular protein: metabolic functions
eg. haemoglobin, enzymes, hormones, antibodies

fibrous protein: structural support
eg. collagen, keratin

Question 27

globular protein

what is the function of haemoglobin?

Answer 27

• haemoglobin is a globular protein ( with a non-protein compopenent) found in the red blood cells and functions in transporting oxygen in the blood
• it also acts as a pH buffer to maintain pH at optimum level of blood

Question 28

globular protein

what is the structural organisation of haemoglobin like?

Answer 28

primary structure: 4 individual polypeptide chains
- 2 alpha chains (subunits)
- 2 beta chains (subunits)

secondary structure: parts of each chain are folded into alpha helices, stabilised by hydrogen bonds formed between atoms of the polypeptide backbone

tertiary structure: each chain is folded into a globular structure, stabilised by bonds like
> hydrogen bonds, disulfide bonds, ionic bonds and hydrophobic interactions formed between R groups of amino acid residues

quaternary structure:
- the 4 folded chains assemble together via R group interactions

• each subunit contains a haem group ( so in total there are 4 haem groups per haemoglobin molecule
• the haem group is a prosthetic group which is a non-protein component of haemoglobin required for its function
  > ocnsists of a porphyrin ring and an iron ion (Fe2+)
• O2 binds to the Fe2+ of the haem group

Question 29

relating haemoglobin’s structural features to its properties & functions

structure: globular shape

Answer 29

property: compact
function: allows many haemoglobing molecules to be packed in a red blood cell

Question 30

relating haemoglobin’s structural features to its properties & functions

structure: has a quaternary structure
consists of 4 subunits
(2 α- chains and two β chains)

Answer 30

function: haemoglobin molecule can carry 4 oxygen molecules
> increases capacity for transport of oxygen, making haemoglobin an efficient oxygen carrier

Question 31

relating haemoglobin’s structural features to its properties & functions

structure: each subunit has a haem prosthetic group that contains a porphyrin ring bound to an Fe2+ ion

Answer 31

property: Fe2+ of a haem group in each subunit can bind to one oxygen molecule
function: this enables haemoglobin to transport oxygen

property: Fe2+ can combine reversibly with oxygen
function: this allows release of oxygen at metabolically active tissues

Question 32

relating haemoglobin’s structural features to its properties & functions

the haem group is orientated such that its Fe2+ is complexed to an amino acid residue on one face, leaving the other face accessible to bind oxygen

Answer 32

function: this enables haemoglobing to transport oxygen

Question 33

relating haemoglobin’s structural features to its properties & functions

structure: each subunit has a deep hydrophobic cleft, lined with amino acid residues with non-polar, hydrophobic R groups

Answer 33

function: provides a binding site for haem group, which is hydrophobic

Question 34

relating haemoglobin’s structural features to its properties & functions

structure: each subunit is folded into a tertiary structure such that most of its amino acid residues with hydrophilic (acidic, basic and polar) R groups are on the exterior surface while amino acids residues with hydrophobic R groups are buried in the interior

Answer 34

property: soluble in aqueous medium
function: suitable for transport in aqueous cytosol of red blood cells

Question 35

relating haemoglobin’s structural features to its properties & functions

structure: 4 subunits are held together by non-covalent R group interactions
(hydrophobic itneractions, hydrogen and ionic bonds in the quaternary structure)

Answer 35

function: binding of oxygen to haem group of one subunit causes its tertiary structure to change
> this then causes the tertiary structure of other subunits change
> all subunits then gain an increased affinity for oxygen

this phenomenon is known as cooperative binding of oxygen, for faster loading and unloading of oxygen from haemoglobin molecules

Question 36

what is the function of collagen?

Answer 36

• collagen is a fibrous protein
• collagen is usually deposited outside the cells in the extracellular matric and has a structural support function
  > supports tissues and gives cells a structure
  > forms the major components in bone, connective tissues , tendons, ligaments and skin

Question 37

protein with quaternary structure

what is collagen?

Answer 37

• collagen is a fibrous protein that is insoluble and has high tensile strength

Question 38

describe the primary structure of collagen

Answer 38

• each polypeptide chain is about 1000-1400 amino acid residues long

each chain consists of a repetitive sequence of three amino acid residues
- G-X-Y
- which gives the polypeptide chain a regular helical structure
> where G is glycine
> X is often proline
> Y is proline or hydroxyproline
> this allows the three chains to coil together to form a triple helix

• every third amino acid in the polypeptide chain is a glycine
  > glycine has the smallest R group (H atom) which allos it to fit into the centre of the triple helix
  > this enables tight packing of the three polypeptide chains in the triple helix

Question 39

describe the quaternary structure of collagen

Answer 39

• a tropocollagen molecule consists of three polypeptide chains wound around one another to form a right-handed triple helix
• with tropocollagen, many inter-chain hydrogen bonds are formed between the polypeptide backbones of the three polypeptide chains, resulting in high tensile strength
  > hydrogen bonds are formed between the O atom of CO group of an amino acids residue and H atom of NH group of another amino acid residue on another chain

Question 40

describe the beyong quaternary structure of collagen

Answer 40

• the N terminus of one tropocollagen is covalently cross-linked to the C terminus of a neighbouring tropocollagen
• bundling of many covalently cross-linked tropocollagen molecules that are parallel to each other to form a collagen fibril
  > collagen fibrils then bundle to form collagen fibres, further increasing tensile strength
• parallel, staggered arrangement of tropocollagen molecules in bundles ensure that there is no weak spot along the length of the fibrils

Question 41

relating collagen’s structural features to its properties

what are the structural features that causes collagen to be insoluble in water (property) and provide structural support in connective tissues (function)?

Answer 41

1. large molecular size of the tropocollagen molecule- each polypeptide chain has about 1000 to 1400 amino acid residues
   > long fibrous structure
2. large number of hydrophobic R-groups of proline residues on the exteriour of the triple helix/ tropocollagen

Question 42

relating collagen’s structural features to its properties

what are the structural features that cause collagen to have ** high tensile strength** (property)** and provide structural suppose in connective tissues** (function)?

Answer 42

1. every third amino acid of each polypeptide chain is glycine, which has a small R group, a H atom
   > its small size allows it to fit inot the centre of the triple helix
   > allows tight packing of the three polypeptide chains
2. repetitive amino acid sequence (glycine, often proline and hydroxyproline) gives each polypeptide chain a regular helical shape
   > aids the formation of numerous inter-chain hydrogen bonds between the three polypeptide chains in tropocollagen
   > this extensive H bonding stabilises the fibrous structure of collagen
3. many tropocollagen molecules are covalently cross-linked with neighbouring tropocollagen molecules running parallel to them to form a collagen fibril
   > fibrils then bundle to form collagen fibre

Question 43

relating collagen’s structural features to its properties

what structural feature of collagen ensures that ther is no weak spot running through collagen fibril ( property) and enables collagen to** provide structural support in connective tissues** ( function)?

Answer 43

• parallel, staggered arrangement of tropocollagen molecules in bundles to form collagen fibril (longitudinal displacemnt of tropocollagen molecules

Question 44

what does the primary structure of polypeptides refer to?

Answer 44

• refers to the specific type, number and sequence of amino acid residues that make up a polypeptide chain
• each protein’s polypeptide chain is unique in its type, number and sequence of amino acids
  > which is dictated by the unique DNA base sequence of the gene
• the sequence of amino acids determines the overall shape, which also determines the function of the protein
• at the primary structure level, only peptide bonds are present, holding the amino acid residues together to form the polypeptide chain
• • ## the polypeptide is not folded yet at the primary structure level

Question 45

what does the secondary structure of proteins refer to?

Answer 45

• it refers to the regular structures formed by coiling and folding of polypeptide chain into alpha helix or beta -pleated sheet
• these coils and folds are maintained by hydrogen bonds
  > formed between the O atom of the C=O group and the H atom of the N-H group of the neighboring amino acid residues on the polypeptide backbone
• R-groups are not involved in the formation of these hydrogen bonds

Question 46

secondary structure of proteins

what is an alpha-helix?

Answer 46

• the α-helix is made when a part of a polypeptide chain is coiled into a helical form
• it is stabilised by the hydrogen bonds formed between the O atom of the C=O group of one amino acid and the H of the -NH group of another amino acid, that is 4 residues away in the polypeptide backbone
• bonds are formed within the same polypeptide chain, hence also known as ‘ intra-chain hydrogen bonds’
• there are 3.6 amino acid residues in every turn of the α- helix

Question 47

secondary structure of proteins

what is a Beta-pleated sheet?

Answer 47

• a β-pleated sheet is formed when segments of the same polypeptide chain is folded back and forth into a zigzag, sheet-like shape/ conformation
• hydrogen bonds are formed between O atom of the CO group of one amino acid residue and the H atom of the NH group of another amino acid residue of the same polypeptide backbone
• the H bonds are formed between more than one segment of the same polypeptide chain, lying side by side
• ## the polypeptide chain may either run in the same direction( parallel β- pleated sheets) or in opposite directions ( anti-parallel β-pleated sheets)

Question 48

what does the tertiary structure of a protein refer to?

Answer 48

• it refers to compact, globular, 3D conformation of a protein formed by further folding and bending of the polypeptide chain
• R group interactions maintain the tertiary structure of a folded protein > 4 types of interactions
• hydrophobic interactions, ionic bonds and hydrogen bonds are weak interctions but their cummulatice effects help to maintain the protein’s unique 3d shape
  ionic bonds: formed between R groups of negatively charged acidic and positively charged basic amino resides
  hydrophobic interactions: formed between the R groups of the non-polar amino acid residues
  hydrogen bonds: formed between the R groups of polar amino acid residues
• strong covalent bonds reinforce the protein’s 3D shape
  disulfide bonds: formed between R groups of cysteine residues

Question 49

what does the quaternary structure of proteins refer to?

Answer 49

• many proteins are made up of a single folded polypeptide chain and have only three levels of structure
• but some proteins are made of 2 or more folded polypeptide chains known as subunits which are already folded into their tertiary structures
  > subunits associate to form one functional complex protein molecule, giving the protein its quaternary structure
• the subunits are held together by R group interactions such as ionic bonds, hydrogen bonds, hydrophobic interactions and sometimes disulfide bond to form a
  > multi-subunit/ multimetric protein
  >