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Presentation on theme: "CHAPTER 3 : PROTEINS."— Presentation transcript:



Individual protein molecules can be described by… “ up to four levels of structure” : primary structure : : secondary structure, tertiary structure and quatenary structure :  linear sequence of amino acid  The 3D structures residues in protein  Forces responsible for maintaning OR stabilizing these 3 levels are primarily “noncovalent” PROTEOMICS  the study of large sets of proteins PROTEINS (structurally) Globular (e.g. enzymes) Fibrous/ structural proteins (e.g. α-keratin)






9 1) PRIMARY STRUCTURE Defined as the linear arrangement/ specific sequence of amino acids in a polypeptide chain linked through covalent peptide bonds. -In order to function properly, peptides and proteins must have the correct sequence of amino acids - Sometimes called "covalent structure of proteins” = all of the covalent bonding within proteins defines the primary structure. -In contrast, the higher orders of proteins structure (i.e. secondary, tertiary and quaternary) involve mainly non-covalent interactions.

10 e.g. INSULIN - In the protein hormone insulin, 51 amino acids are found - Using 51 amino acids there are 1.55 x 1066 different possible sequences - Many other proteins contain many more amino acids then insulin, but only the correct precise sequence is produced by the body -The procedure used to synthesize the correct sequence of amino acids in proteins is guided by the genetics of DNA and RNA.


1. Long chains of amino acids will commonly fold or curl into a regular repeating structure 2. Repeating conformations of peptide chains which are stabilised by hydrogen bonds between H of amino groups and O of carbonyl group of the peptide backbone Protein conformation = local conformation of the backbone = 3D arrangement of various atoms of the molecule   This structure will add new properties to a protein like strength, flexibility and etc…

13 Carbonyl: carbonyl functional group which is a divalent group consisting of a carbon atom with a double-bond to oxygen Amide: a functional group containing a carbonyl group linked to a nitrogen atom.

14 common secondary structure right-handed screw a) α helices
left-handed screw a) Resembles a ribbon wrapped around a tube (similar to a circular staircase) b) Hydrogen bonds are found parallel to the helix axis c) Very stable but flexible (therefore it is often seen in parts of a protein that need to bend or move) parallel b) β structure (β strands and β sheets) anti-parallel a) Two or more ribbons of amino acids are involved b) Hydrogen bonds are formed between the two (or more) polypeptide strands c) These line up to form a pleated like structure (similar to folds in fabric) d) Tends to be rigid but less flexible than α helices. c) β turn A structure in which the polypeptide backbone folds back on itself Often responsible for;- -sharp bends and twists (in α helices) - hair-pins (in β sheets) c) Useful for connecting helices and sheets

15 THE α HELIX A spiral formed by coiling of the polypeptides chain around the fibre axis α helix present in more complex globular proteins All carbonyl group (in α helix) point toward C-terminus Average content of α helix in the proteins = 26% Bottom : N-terminus Top : C-terminus The α helices found in proteins are almost right-handed “right handed α helix”  the backbone turns in a clockwise direction (when viewed along the axis from its N-terminus) If you imagine that the right handed helix is spiral staircase, you will be turning to the right as you walk down the staircase -blue ribbon  indicates the shape of the polypeptide backbone - All the side chains (R groups)  project outward from the helix axis


H bond

18 β SHEETS Hydrogen bonding occurs between neighbouring polypeptide chains rather than within one as in α helix Fibrous and insoluble in aqueous solvents This class includes i) β STRANDS ii) β SHEETS β STRANDS Portions of the polypeptide chain that are most fully extended Proteins rarely contain isolated β strands because the structure by itself is not significantly more stable than other conformations When multiple β strands are arranged side-by-side -Are stabilised by H bonds between carbonyl oxygen and amide hydrogens on adjacent β strands -β sheets sometimes called as β pleated sheet -A typical β sheet contains  from 2 to as many as 15 individual β strands β SHEETS

19 β SHEETS a) parallel b) anti-parallel
The hydrogen bonded chains extended in the same directions Neighbouring hydrogen bonded polypeptide chains run in opposite directions -Running in the same N- to C- terminal direction -the H bonds  not perpendicular to the β strands -The H bonds are evenly spaced but slanted -Are less stable than anti-parallel sheets -running in opposite N- to C- terminal directions -the H bonds  essentially perpendicular to the β strands -the space between H-bonded pairs alternatively wide and narrow

20 TURNS and LOOPS In α helix or β strand BUT turns and loops
Consecutive residues have a similar conformation that is repeated throughout the structure In α helix or β strand BUT Regions that found in proteins which contain stretches of non-repeating 3D structure These regions can cause directional changes in the polypeptide backbone Connect α helices and β strands Allow the polypeptide chain to fold back on itself, producing 3-dimensional shape seen in native structure turns and loops

21 LOOPS TURNS Usually found on the surfaces of proteins
(often contains hydrophilic residues) -Loops containing only a few (up to five) residues will be referred as turns if they cause an abrupt change in the direction of a polypeptide chain -β turns (or reverse turns);- a) the most common types of tight turns b) usually connect different antiparallel β strands c) common types of β turns are;- “TYPE I” and “TYPE II” (both types produce an rapid/ abrupt change in the direction of the polypeptide chain) -All turns have internal hydrogen bonds that stabilize the structure


23 β TURNS “Note that the hydrogen bonds between
Occur more than twice as frequently as type II Always have Gly as the third residue “Note that the hydrogen bonds between the peptide groups of the 1st and 4th residues of the bends”

During and after protein synthesis, a protein folds into α helices and β sheets These areas of secondary structure bind together and fold on each other in specific ways Once the process of protein synthesis is completed, the protein takes its final shape. This stable form of the protein is known as the mature form, also known as the tertiary structure by DEFINITION…. 1) The shape of fully folded polypeptide chains 2) Results from the folding of its secondary structural elements (which may already posses some regions of α helix and β structure) into a closely packed 3D structure

25 2 types of tertiary structures:
…important feature of tertiary structure… Amino acid residues that are far apart in the primary structure are brought together, permitting interactions among their side chains 2 types of tertiary structures: Supersecondary structures (MOTIFS) Domains

26 Native protein = the naturally occurring form of protein
TERTIARY STRUCTURE Most native proteins occurs at this state. Native protein = the naturally occurring form of protein

so that distant regions of the chain are brought closer

28 TERTIARY STRUCTURE Disulfide bridge  though covalent, are also element of tertiary structure (they are not part of the primary structure since they form only after the protein folds)

Triose phosphate isomerase = catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde-3-phosphate (GAP), an essential process in the glycolytic pathway.

(a) SUPERSECONDARY STRUCTURES (a.k.a motifs) -Are recognizable combinations of α helices + β strands + loops (that appear in a number of different proteins) -Sometimes  motifs are associated with a particular function (although structurally similar motifs may have different functions in different proteins) …common motifs… One of the simplest motifs -Occurs in a number of calcium-binding proteins (since Glutamate and Aspartate residues in the loop of calcium-binding proteins form part of the calcium-binding site) -Also called as helix-turn-helix in certain DNA-binding proteins (since the residues that connect the helices form a reverse turn. The α helices residues in DNA-binding proteins bind DNA)

31 The individual α helices have opposite orientations
Consists of two amphipathic α helices that interact through their hydrophobic edges - e.g. ;- leucine zipper The individual α helices have opposite orientations -Parallel in the coiled-coil motif Consists of two parallel β strands linked to an intervening α helix by 2 loops - The helix connects the C-terminal end of one β strand to the N-terminal end of the next Often runs parallel to the two strands

32 - Consists of 2 adjacent antiparallel β strands connected by a β turn
Is an antiparallel β sheet composed of sequential β strands connected by loops or turns -May contain one or more hairpins but, more typically the strands are joined by larger loops - This is a β sheet motif linking four antiparallel β strands such that;- strands 3 and 4 (form the outer edges of the sheet) strand 1 and 2 (are in the middle of the sheet)

33 Is formed when β strands or sheets stack on the top of one another
Figure shows an example of a β sandwich where the β strands are connected by short loops and turns.. BUT β sandwich can also be formed by the interaction of 2 β sheets in different regions of the polypeptide chain

(b) DOMAINS Are compact units which are discrete and independently folded May consist of combinations of motifs Are usually connected by loops, BUT they are also bound to each other THROUGH weak interactions (formed by the amino acid side chains on the surface of each domain) Some domain structures occur in many different proteins while others are unique In general, proteins can be grouped into families according to… “ similarities in domain structure and amino acid sequence”

- Commonly used classification scheme groups are;- α category domains consist almost entirely of α helices and loops consist only β sheets and nonrepetitive structures that link β strands β category domains have supersecondary structures such as the βαβ motif and others (in which regions of α helix and β strand alternate in the polypeptide chain) α/β category domains consist of local clusters of α helices and β sheet (where each type of secondary structure arises from separate contiguous regions in the polypeptide chain) α+β category domains - Within each of the 4 main structural categories, protein domains can be further classified by the presence of characteristic folds;- Is a combination of secondary structures that form the core of a domain “ some domain have easily recognizable folds such as the β meander. However, other folds are more complex” folds


37 3.4 QUATERNARY STRUCTURE -Many protein exhibit an additional level of organization called as quaternary structure

38 QUATERNARY STRUCTURES (quaternary structure)
by DEFINITION… (1) Quaternary structure refers to the organization and arrangement of subunits … IN … a protein with multiple subunits multisubunit protein = an oligomer (proteins with only one polypeptide chain are monomers) (2) Quartenary structure is the stable association …OF... multiple polypeptide chains resulting in an active unit Not all proteins exhibit quartenary structure Usually, each polypeptide within a multisubunit protein folds more-or-less independently into a stable tertiary structure the folded subunits then associate with each other to form the final structure (quaternary structure)

39 common shorthand method for describing oligomeric proteins
SUBUNITS each subunit = a separate polypeptide chain the subunits within an oligomeric protein always have a defined stoichiometry the arrangement of the subunits give rise to a stable structure -the subunits of a multisubunit protein may be… identical different Dimers and tetramers predominate Each type often has a different function common shorthand method for describing oligomeric proteins Uses ;- Greek Letters  to identify types of subunits Subscript numerals  to indicate number of subunits Example ;- α2βγ protein  contains 2 subunits designated α  EACH 1 of subunits designated β and γ

40 proper alignment of the subunits
-Subunits are held together by many weak, noncovalent interactions hydrophobic interactions electrostatic forces -principle forces involved -contribute to the proper alignment of the subunits Hydrogen bonding ionic bonding Van der Walls interaction involved in the interactions between subunits in rare instances between cysteine residues in different polypeptide chains disulfide bonds - The subunits of an oligomeric protein can be often separated in the laboratory because…intersubunit forces are usually rather weak…

This protein has 2 identical subunits with α/β barrel folds -The identical subunits associate through weak interactions between the side chains found mainly in loop regions

This protein has identical all-β subunits that bind symmetrically -The identical subunits associate through weak interactions between the side chains found mainly in loop regions

43 Determination of the subunit composition of an oligomeric protein
SUBUNITS Determination of the subunit composition of an oligomeric protein -essential step in the physical description of a protein Molecular weight of native oligomer  estimated by gel-filtration chromatography Molecular weight of each chain  SDS-polyacrylamide gel electrophoresis

Disruption of the protein native conformation, commonly caused by HEATING (but only with small range of temperature) as a result Most of the denatured proteins ;- Retain considerable internal structure Some of the denatured proteins ;- May unfold completely to form a random coil -Small denatured proteins can spontaneously renature, or refold Can cause loss of biological activity since the protein will malfunction Amount of energy needed for the process is often small (perhaps equivalent to the energy needed for the disruption of 4 hydrogen bonds) Is a cooperative process  the destabilization (of just a few weak interactions) leads to almost complete loss (of native conformation)

45 How DENATURATION can occur ??
Modest increase in temperature will result in unfolding and loss of secondary and tertiary structure 1 Thermal Most proteins are stable at temperatures up to 50oC to 60oC Requires a reducing agent that disrupts disulfide bridge, which will finally allowing protein to unfold e.g. urea and guanidinium salts 2 Chaotropic Agents By allowing molecules to solvate nonpolar groups in the interior of proteins e.g. hydrophobic tails of detergents  sodium dodecyl sulfate The water molecules disrupt the hydrophobic interactions that normally stabilize the native conformations 3 Detergents Denature proteins by penetrating the protein interior and disrupting hydrophobic interactions

46 Thermal denaturation of horse apomyoglobin and ribonuclease A
PROTEIN DENATURATION Thermal denaturation of horse apomyoglobin and ribonuclease A (the midpoint of T range over which denaturation occurs = Tm)

47 Regain its native conformation
RENATURATION Occur at Tm ;- Most proteins have a characteristics “melting” T (Tm) that corresponds to the T at the midpoint of the transition between the native and denature forms  Tm depends on pH and the ionic strength of the solution Regain its native conformation Regain correct set of disulfide bonds For this case, renaturation of Ribonuclease A can occur if :- Urea is removed Small amount of 2-mercaptoethanol is added Regain full enzymatic activity

3.6 COLLAGEN 3.7 STRUCTURES MYOGLOBIN ND HEMOGLOBIN 3.8 ANTIBODIES AND BIND AND SPECIFIC ANTIGENS 2 groups (a group of 5) for each sub topic Reference : Text Book Only Presentation Date : Week 10

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