Lecture 2: Proteins Flashcards
proteins
polymers of amino acids, with each amino acid residue joined to its neighbor by a peptide bond.
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
- 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 - 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 - 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 - 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
classification of proteins
- based on functions
- chemical nature and solubility
proteins can be denatured by
- heat
- pH change
- organic solvents
- chaotropic agens: urea and guanidium hydrochloride
a protein’s function depends on its nature
what are the chemical bonds involved in Protein structure?
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
Differentiate between Fibrous and Globular Proteins?
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
describe the alpha helix secondary structural element?
- 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
Describe the Beta pleated sheet secondary structural element ?
- 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.
*
- The antiparallel pleated sheet, in which neighbouring hydrogen bonded polypeptide chains run in opposite directions.
- The parallel pleated sheet, in which the hydrogen bonded chains extend in the same direction.
denaturization
loss of structural integrity of a protein with accompanying loss of activity
due to heat, ph, organic solvents and chaotropic agents
Primary (1°) Structure
linear sequence of amino acids in a popypeptide chain
linked by peptide bonds
Secondary (2°)
local folding of the polypetide in some regions
the alpha helix and beta pleated sheet structures
maintained by Hydrogen Bonding
Tertiary (3°)
- overall spatial arrangement of atoms in proteins
- 3D structure of a protein
maintained by all 4 types of bonds
Quaternary (4°)
- formed by assmbly of individual polypeptides into a functional cluster
- interactions between proteins
chemical bonds in protein structures
- ionic
- disulphide bridges
- Hydrogen bonding
- hydrophobic interactions
ionic bonding
- 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
disulphide bond(bridge)
- results from the oxidation of neighbouring -SH groups on amino acid molecule(cysteine)
- strong and not easily broken
hydrogen bonding
- 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
Hydrophobic interactions
- 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
alpha helix folding
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.
beta pleated sheet
- 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
antiparallel pleated sheets
neighbouring H bonded polypetide chain extend in opposite directions
Fibrous proteins
- 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
globular proteins
- 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
Anfinsen’s experiment
- 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
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%.
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
