Proteins

Question 1

What are proteins?

Answer 1

-Proteins are macromolecules of high molecular mass , composed of amino acids
-Vital because they account for more than 50 percentage of total dry cell mass
- Each type of protein has a unique 3D conformation, Proteins are extensively in structure,consistent in diverse functions

Question 2

Biuret test

Answer 2

Method :
- Add 2cm^3 of sodium hydroxide in 2cm3 of sample solution ,add 1% copper sulphate to the mixture drop by drop,shake the mixture after every drop
Observation : Purple colour present
Conclusion: Proteins are present
Basis for the test :

Question 3

Some rolled of enzymes - extra reading

Answer 3

-catalyse chemical reaction
- hormones which serve as signalling molecules between tissues
-antibodies which serve to bind to antigens
- Transport proteins
-Signal transduction (bind to signal molecules outside cell)
- structural proteins like collagen
- Transcription factors DNA,gene expression
-DNA packaging
-Storage of substances
- cell-cell recognition or cell-cell adhesion

Question 4

What are Amino acids

Answer 4

• All proteins are made from the same set of 20 amino acids
• All amino acids contain the elements CHON.
• 2 amino acids contain sulfur

Question 5

Structure of amino acids

Answer 5

1. Each amino acid consists of a central alpha central atom covalently bonded to basic amino group(-NH2),an acidic carboxyl (-COOH),a hydrogen atom and R group ( side-chain)

(Acidic amino acids)- neg charged R groups due to presence of -COOH in R groups
(Basic)- positively charged amino acids ,-NH2 , in their R groups
(Neutral)- amino acids with uncharged R groups

2. Different types of bonds exist within the polypeptide chain
   non-polar and non-polar ——- hydrophobic interactions
   Polar and polar ——————— hydrogen bonds
   Polar and (basic/acidic)———— hydrogen bonds
   Acidic and basic ———————- ionic bonds
   Both R grp containing sulfhydryl group - disulfide bonds

Question 6

Properties of amino acids

Answer 6

• colourless,crystalline solid
  -high melting point, but if temp too high then it will decompose
• generally soluble in water but insoluble in organic solvents (dissolve in water to form charged ions)
  -Amino acids is amphoteric as they contain both acidic and basic group. When it dissolves in aq medium, the acidic carboxyl group donates a H+ and become negatively charged. OR They basic amino group accepts a H+ and become positively charged
• amino acid that has both positive and negative charges called zwitterion. each amino acid as isoelectric point where zwitterion concentration at maximum

Question 7

Importance of amphoteric nature of amino acids

Answer 7

• act as buffers in solutions
  -resist pH change when small amounts of acid or alkali added to it , thus maintain a relatively stable pH
• Amino acids act as a buffer by donating H+ as pH increases and accepting H+ as pH decreases .

BUT this property is retained in forming polypeptide or peptides - coz some things essential to biological systems where any sudden pH could add early affect the activity of proteins or enzymes is needed.

Question 8

Dipeptide

Answer 8

• 2 amino acids combine to form dipeptide via condensation
  -condensation involves the removal of one water molecule
• peptide bond is the covalent bond between amino group of one amino acids and carboxyl group another amino acids during condensation
  -Peptidyl transferase catalyses the formation of the peptide bond
• dipeptide possesses a free amino group at one end and a free carboxyl group at the other end so that further condensation between dipeptide and amino acids can happen

Question 9

Hydrolysis

Answer 9

• Dipeptides are broken down into 2 amino acid molecules when the peptide bond between the amino acids are hydrolysed
• involves the addition of a water molecule

Question 10

Polypeptide

Answer 10

• amino acids polymerase forms a polypeptide chain
• For the polypeptide chain, amino acids are always added at the carboxyl end of existing amino acid chain.
• This it has a N-terminal ( amino end ) and C-terminal ( carboxyl end )

Question 11

Structure of proteins

Answer 11

• a protein is a functional unit ( one more more polypeptides precisely folded and coiled into a molecule of specific 3D comformation )
  -Each protein possesses a characteristic 3D conformation and its function is dependent on the unique conformation
• primary,secondary,tertiary,quaternary structure

Question 12

Primary structure

Answer 12

• primary structure of protein molecules refers to its number,type and sequence of amino acids held together by peptide bonds in the linear polypeptide chain
• The primary structure of a protein contains information for the protein’s folding into a specific shape
• The amino acid sequence determined further level of organisation within protein( coz diff bonds between R groups can lead to different properties and functions of proteins)
  -A CHANGE IN HUST ONE AMINO ACID CAN ALTER PROPERTIES of polypeptide and in TURN

Question 13

Secondary structure

Answer 13

• a polypeptide coils and folds into a geometrically regular repeating structures, mainly alpha and B pleated sheets
  -Have stabilised hydrogen bonds between carboxyl and amino groups in the main chain of the polypeptide

Alpha helix :
- elastic and flexible ( extended spiral shape )
- one complete turn after every 3.6 amino acids
- conformation stabilised by formation of intramolecular hydrogen bonds between carboxyl and amino group of every fourth peptide bond
- h bonds weak but tgt strong

Example : keratin - fibroid protein consisting of alpha helices

B pleated sheet :
- flexible but not elastic
-2 or more regions of one polypeptide lie parallel to each other , held by intramolecular hydrogen bonds between carboxyl and amino groups in polypeptide backbone [ starands can be parallel(same) and anti-parallel(opposite direction))
- segments of polypeptide chain are folded in patterns due to hydrogen bonding between amino acids at regular intervals of polypeptide chain
* Found in proteins that require strength ( e,g silk fibroin used by silkworms to spin their cocoon threads)

Question 14

Tertiary structure

Answer 14

• further bent,coiled,folded to form precise 3D conformation
• specific 3D conformation maintained by weak ( hydrophobic interactions,ionic bonds,intramolecular hydrogen bonds) and strong ( disulfide bonds) between -SH of 2 cysteine amino acids

Importance : diversity of globular proteins due to diff in their tertiary structure & 3D conformation responsible for biological activity of protein

E.g of protein with tertiary structure ( enzymes )
- amino acid residues wich constitues enzyme’s active site are often not close to each other in primary sequence, as tertiary folding will bring the close tgt in 3D space
- enzyme specificity cuz of specific conformation of active site allowing only substrates that are of complementary shape to bind to it.

Question 15

Quaternary structure

Answer 15

• many highly complex proteins consists of aggregation of 2 or more polypeptide chains
  subunit: each polypeptide chain
• subunits held together by intermolecular hydrogen bonds,ionic bonds,disulfide bonds and hydrophobic interactions between R groups of amino acids
  -the spatial arrangement of 2 or more polypeptide chains give rise to quaternary structure

E.g
1. Antibodies
4 polypeptide chain that make up antibody brought tgt so that antigen-bonding site has a specific conformation that enables the antibody to recognise specific antigen

Question 16

Types of bonds in proteins

Answer 16

Intramolecular hydrogen bonds :
- between -NH grp and C=O group of amino acid at regular intervals of the polypeptide chain ( secondary structure). Gives rise to alpha helixes and B-pleated sheets
- between R grps polar and polar/acidic/basic amino acids of a polypeptide chain ( tertiary structure )

Intermolecular Hydrogen bonds :
- formed between R groups of polar and acidic/basic/polar amino acids of 2 or more polypeptide chains ( quaternary structure )

Ionic bond :
- Only at suitable pH, formed between R groups of positively charged and negatively charged amino acids
- formed between R groups of same polypeptide chain ( tertiary structure ) or between R groups of 2 or more polypeptide chains ( quaternary structure )
- bonds unstable and broken when pH changes

Disulfide bond :
- a strong covalent bond formed between sulfhydryl groups of 2 molecules of cysteine
-2 molecules of cysteine in different regions of same polypeptide chain (tertiary structure ) or in different polypeptide chains ( quaternary structure )
- Disulfide bond is the strongest of all chemical bonds between R groups.This bond can be broken by reducing agents and pH

Hydrophobic interactions :
- some amino acids have R groups that are non-polar
- in a cytoplasm, proteins assume globular tertiary shape
-As a polypeptide fold into a functional 3D conformation,amino acids with polar/charged (hydrophilic) R grps project out of the protein and interact with the aq medium
- while amino acids with non polar R grps shielded inside protein and do not interact with aq medium

• non-polar R grps are buried in clusters inside the core of the protein.Once close together,hydrophobic interactions help them hold together.
  *the polar/charged R groups face outwards to form hydrogen bonds with the surrounding water,making protein soluble

Question 17

Effects of temperature and pH (general )

Answer 17

• Denaturation: Loss of 3D conformation of a protein molecule
• happens when bonds that maintain the 3D conformation is broken, causing molecule to unfold and change shape,loses biological function
• some reversible some irreversible
• primary structure unaffected

Question 18

Temperature affected

Answer 18

• Increasing temperature leads ,increase KE supplied to protein
• high heat disrupts (H bonds,hydro inter)that maintain secondary and tertiary structure of protein
  -loss of specific 3D conformation of protein,denatured protein

Question 19

pH affected

Answer 19

• change in pH,alters ionic charge of COO^-(acidic) and NH3^+(basic) R grps of amino acids in protein
  ( addition H+ in acid) can combine with COO- gro and form COOH
  (Removal of H+) can cause NH3+ grps of amino acids to donate H- and form NH2

Question 20

Haemoglobin

Answer 20

• a globular protein in rbc that transport oxygen
  Structural features :
• consists of 4 polypeptide chains : 2 alpha ,2 Beta
• polypeptide chain coils to form, alpha helices ( 2*), then further bent and folded into globular protein subunit maintained by hydrogen ,ionic bonds,hydrophobic interactions between R grps of amino acids
  -4 protein subunits packed tgt ,held tgt by H bonds,ionic bonds,hydrohpobic interactions in a nearly spherical haemoglobin
• results in compact haemoglobin,allows packing of more haemoglobin into RBC,more o2 molecules carried and transported
• since Hb is contact with aq medium, hydrophilic R grps on surface face outwards and interact with aq medium ,maintaining solubility of hb in aq medium
  -allows mobility arnd body via bloodstream and hb can bind and transport O2 molecules dissolved in blood
• hydrophobic R grps face inwards into centre of hb and shielded from aq medium, hydrophobic interactions between hydrophobic R grps inside the hb are imp for holding the molecule in its precise 3D conformation
• each protein subunit has prosthetic haem grp with an FE2+ which binds a molecule of O2 reversibility and allows oxygen to be readily released to respiring tissues
• a complete hb molecule, with 4 haem grps,can carry and transport 4 O2 molecules at a time, enabling more nsport of O2 arnd the body
• Due to allosteric nature, hb undergo changed in conformation , binding of O2 to one haem grp facilitates binding of oxygen to other haem grps on the same hb molecule, thus facilitating easier binding and release of subsequent oxygen molecules

Question 21

Collagen

Answer 21

Description:
- most abundant fibrous protein( found in skin,tendons,cartilage,bones,teeth,walls of blood vessels of vertebrates )
- imp structural protein in connective tissue and basement membrane

Structural :
- basic structural unit is tropocollagen which consists abt 3 polypeptide chain (each 1000 amino acid residue held tgt by peptide bonds )
- each polypeptide amino sequence follows pattern Glycine-X-Y ( X - anything/proline , Y- hydroproxyline/hydroxylysine)
-polypeptide chain coils into shape of loose helix ( high proportion of proline and hydro proline prevents formation of intramolecular bonds req for a-helices )
- three helical polypeptide chai wind tightly arnd each other ,bound to one another by intermolecular H bonds,forming tropocollagen /triple helix
(Almost every third amino acid in polypeptide chain is glycine)
(Glycine’s small size allows three helical polypeptide chains lie close tgt and form tight coil )

• tropocollagen interacts with other tropocollagen running parallel to it
• end of parallel tropocollagen molecules are staggered,Covent cross-links form between carboxyl end of one tropocollagen and amino end of another tropocollagen, cross-linking forms collagen fibril
• cross-links are out of step with each other,giving greater tensile strength
• collagen fibrils assemble to form collagen fibres
• fibres —> flexible but Inelastic structure of support thus high tensile strength and withstand large pulling forces

Question 22

G-protein linked receptor (signalling protein )

Answer 22

Description:
-are transmembrane proteins involved in cell signalling ( cell signalling is detection of specific signalling molecules on extra cellular surface of cell, and the responses the signal triggers within cell )
- G-protein receptors work with G protein ,which are present on the cytoplasmic side of the cell surface membrane

Structural features :
- each G comprises a single polypeptide chain coiled into 7 transmembrane a-helices
- polypeptide chain further bent,folded,Coiled into a tertiary structure ,held tgt by h bond,ionic bond,disulfide bond and hydrophobic interactions between R grps of amino acids)
- G are embedded in and spam the plasma membrane,held by weak hydrophobic interactions so signals detected outside the cell can be transduced to the inside of cell
( non-polar R groups of amino acids residues on the receptor for hydrophobic interactions with non- polar fatty acid tails of the membrane phospholipid molecules)
- 2 binding sites: extracellular specific binding site & intercellular G-protein binding site
- extracellular parts of G protein linked receptors may be glycosylated as they serve as the binding site for ligands
( extracellular regions are recognised and bounds by hydrophilic ,polar ligands which are unable to pass freely across the membrane )