Lecture 2: Proteins

Question 1

proteins

Answer 1

polymers of amino acids, with each amino acid residue joined to its neighbor by a peptide bond.

Question 2

A protein’s shape depends on four levels of structure, state and describe them and types of bonding within them.

A protein’s shape depends on four levels of structure

Answer 2

1. Primary (1°) Structure-
   -refers to the number and sequence of amino acids, that constitute a polypeptide chain.
   -main mode of linkage is the peptide bond linking the alpha carboxyl group on 1 aa residue to the alpha amino group of another
2. Secondary (2°) Structure
   -refers to the local folding (Spatial conformation) of the polypeptide chain in some regions
   -has 2 types, the alpha helix foldin and Beta helix
   -both structures are stabilized by H bonds
3. Tertiary (3°) Structure
   -refers to the overal spatial arrangement of atoms in a protein
   -stabilized by the 4 types of bonds already discussed, largely Hydrophobic interactions and Disulphide bridges e.g
   -consists of 2 classes of proteins, FIBROUS and GLOBULAR
4. Quaternary (4°) Structure
   -interactions between proteins
   -is the assembly of individual polypetides into a larger functional cluster
   -is stabilized by H bonding, ionic and hydrophobic interactions

The tertiary structure of proteins is determined by the primary structur

Question 3

classification of proteins

Answer 3

• based on functions
• chemical nature and solubility

Question 4

proteins can be denatured by

Answer 4

• heat
• pH change
• organic solvents
• chaotropic agens: urea and guanidium hydrochloride

a protein’s function depends on its nature

Question 5

what are the chemical bonds involved in Protein structure?

Answer 5

ionic bonds
* acidic and basic R groups exist in ionized state at certain pHs
* due to the opp charges, they are attracted towards each other to form weak ionic bonds
* can be broken by pH change

Diulfide bond/ Bridge
* cysteine contains a sulphydryl group –SH as part of the R (functional) group
* if 2 molecules of cysteine line up alongside each other, neighbouring sulphydryl groups can be oxidised and form a disulphide bond.
* are strong and not easily broken

Hydrogen bonding
* H atoms part of an OH or NH group are slightly positve
* because the electrons that are shared in OH and NH are attracted more towards the O or N atoms
* the H+ may then be attracted towards a neighbouring electronegative (δ-) oxygen or nitrogen atom

Hydrophobic interactions
* nonpolar R groups on peptide chains are hydrophobic
* in an aq environment the chain will tend to fold so that the maximum number of hydrophobic groups come into close contact and exlude interaction with water.
* hydrophobic groups tend to point inwards towards the centre of the roughly spherical molecule while the hydrophilic groups face outwards into the aqueous environment making the protein soluble.

This is how many globular protein such as haemoglobin fold up

Question 6

Differentiate between Fibrous and Globular Proteins?

Answer 6

Fibrous
consist of parallel polypeptide chains cross-linked at intervals to form long fibres or sheets (fillaments)

Globular
are tightly folded to form a spherical shape and are soluble in water.

collagen in tendons and bones, silk in spider webs and keratin hair.

solubility of globular proteins is due to the hydrophobic interactions of the nonpolar R groups

Question 7

describe the alpha helix secondary structural element?

Answer 7

• refers to the local folding of the pp chain in some regions
• stabilized by H bonding between an O atom on a carboxyl group of one aa residue and a H atom on an amino group of another aa which is 4 aa further along the chain.
• is present in both fibrous and globuklar proteins

Question 8

Describe the Beta pleated sheet secondary structural element ?

Answer 8

• the sheets are arranged in a parallel fashion, either running in the same direction or in opposite directions (parallel and antiparallel
• stabilized by H bonds occuring between neighbouring polypeptide chains rather than within one as in helices.
  *

1. The antiparallel pleated sheet, in which neighbouring hydrogen bonded polypeptide chains run in opposite directions.
2. The parallel pleated sheet, in which the hydrogen bonded chains extend in the same direction.

Question 9

denaturization

Answer 9

loss of structural integrity of a protein with accompanying loss of activity

due to heat, ph, organic solvents and chaotropic agents

Question 10

Primary (1°) Structure

Answer 10

linear sequence of amino acids in a popypeptide chain

linked by peptide bonds

Question 11

Secondary (2°)

Answer 11

local folding of the polypetide in some regions

the alpha helix and beta pleated sheet structures

maintained by Hydrogen Bonding

Question 12

Tertiary (3°)

Answer 12

• overall spatial arrangement of atoms in proteins
• 3D structure of a protein

maintained by all 4 types of bonds

Question 13

Quaternary (4°)

Answer 13

• formed by assmbly of individual polypeptides into a functional cluster
• interactions between proteins

Question 14

chemical bonds in protein structures

Answer 14

1. ionic
2. disulphide bridges
3. Hydrogen bonding
4. hydrophobic interactions

Question 15

ionic bonding

Answer 15

• strong electrostatic force of attraction between a pair pof opposite charges
• carboxyl and amino group exists in ionized state at certain ph allowing for ionic bonds
• easily broken by change in pH

Question 16

disulphide bond(bridge)

Answer 16

• results from the oxidation of neighbouring -SH groups on amino acid molecule(cysteine)
• strong and not easily broken

Question 17

hydrogen bonding

Answer 17

• H is part of NH or OH hence becomes slightly positive
• electrons shared are attracted towards the more electronegative O N atoms
• the H is thus attracted to a neighbouring partially negative N or O atom
• several H bonds contribute to stability

interacton of C=O and NH groups in alpha helix

Question 18

Hydrophobic interactions

Answer 18

• nonpolar R groups are hydrophobic
• hence the chain will fold so that the max number of hydrophobic groups come to close contact exluding water molecules
• hydrophobic molecules tend to point inwards whilst hydrophilic groups face outwards into aq enviroment making the protein soluble

Question 19

alpha helix folding

Answer 19

H bonds form between oxygen atom on carbonyl group in an amino acid and another amino acid that is four amino acids farther along the chain

• helix is right handed
• torsion angles φ = -57° and ϕ= + 47°
• n= -3.6 residues per turn
• pitch= 5.4 Å.

Question 20

beta pleated sheet

Answer 20

• polypeptide chain sheets are arranged in parallel or antiparallel manner(i.e running in different directions)
• H bonding occurs between neighbouring polypeptide chains rather than within one as in helices

Question 21

antiparallel pleated sheets

Answer 21

neighbouring H bonded polypetide chain extend in opposite directions

Question 22

Fibrous proteins

Answer 22

• consist of parallel polypeptide chains cross-linked at intervals to form long fibres or sheets.(filaments)
• insoluble and physically tough

* collagen- tendons and bones
* silk- spider webs
* keratin- hair

Question 23

globular proteins

Answer 23

• tightly folded into a spherical shape
• fold in such a way hydrophobic groups point inside with hydrophillic groups pointing out
• very soluble in water

enzymes, antibodies, hormones, hemoglobin

Question 24

Anfinsen’s experiment

Answer 24

• urea- disrupts H bonding
• β-mercaptoethanol- disrupts disulphide bridges
• used enzyme ribonuclease

used the 2 chemicals to denature enzymes

explanation:
removal of urea first
* allows H bonds to form hence protein folds into the proper 3 D structure
* correct disulphide bridges can form between adjacent cysteines in the proper folded manner

removal of β-mercaptoethanol first
* in presence of urea protein is unfolded
* hence it adopts a random conformation
* leading to formation of disulphide bridges between cysteines in a misfolded manner (loss of structural integrity
* hence polypeptide chain locks ito a misfolded structure wuth no no activity

Question 25

Anfinsen’s Experiment

Experiment #1:
Add both urea and β-mercaptoethanol to a solution of enzyme. Activity is lost.
Remove urea by dialysis; then remove β-mercaptoethanol by dialysis. Activity is recovered 100%.

Experiment #2:
Add both urea and β-mercaptoethanol to a solution of enzyme. Activity is lost.
Remove β-mercaptoethanol by dialysis; then remove urea by dialysis. Only ~1% of activity is recovered. N = 82 = 64, 1/64 ~ 1%.

Answer 25

Urea disrupts the hydrogen bonding whilst betamercaptoethanol reduces disulfide bonds

Exp 1
* removal of urea allows formation of H bonds allowing the protein to fold into proper 3D structure
* removal of the latter ensures correct disulfide bridges cysteine residues that are adjacent in the correct flded manner
-hence no loss in structural integrity= no loss in activity

Exp 2
* in the presence of urea the protein unfolds
* hence the protein has a random confromation without proper allignment of cysteines
* leading to formation of disufide brides between cysteines in a misfolded manner
* hence protein is locked in a misfolded manner leading to loss of structural integrity

Protein Mis-folding Is the Basis of Numerous Human Diseases