Download presentation
Presentation is loading. Please wait.
1
Amino acids and proteins
2
ILO 1-Explain the chemical structure ,classification, and properties of amino acids and how peptides are formed. 2-Describe the order of protein organization. 3-Relate the structures of amino acids and proteins to their properties. 4-Describe the physical and chemical changes due to protein denaturation 5-state different classifications of proteins giving examples. 6-Explain protein folding and pathophysiological consequences of protein misfolding.
3
Outlines Amino acid structure Amino acid properties Protein structure
Forces that stabilize protein structure Levels of protein organization Protein Classification Protein folding Protein misfolding Denaturation
4
From: Protein Data Bank PDB ID: 1B0E
Protein Structure Protein Structure From: Protein Data Bank PDB ID: 1B0E Kalus, W., Zweckstetter, M., Renner, C., Sanchez, Y., Georgescu, J., Grol, M., Demuth, D., Schumacher, R., Dony, C., Lang, K., Holak, T. A.: structure of the IGF-binding domain of the insulin-like growth factor-binding protein-5 (IGFBP-5): implications for IGF and IGF-I receptor interactions. EMBO J 17 pp (1998)
5
Orders of protein structure
Primary structure (Amino acid number, type & sequence) Secondary structure (α-helix, β-sheets & β turns) Tertiary structure(assembly of secondary structures( Quaternary structure
6
Levels of Proteins Structure
Taken from Lehninger, Principles of Biochemistry, 3rd Edition
7
Primary structure (Amino acid number, type & sequence)
8
Primary structure It is the type, number and sequence of amino acids in the polypeptide chain It is determined by DNA sequence of its gene. It includes the location of any disulfide bonds. It determine 2ry ,3ry and quaternary structure of protein. Any change in the type, number and sequence of amino acids lead to serious disease.
9
T C A G DNA A G U C RNA Transcription C1-21
10
Translation T A C A T C G A T C G DNA A G U C mRNA U A C A U C tRNA 1
Ribosome messenger A G U C mRNA U A 1 C A U 2 Ile C tRNA transfer Met RNA 的序列是轉譯成蛋白質的訊息 (mRNA),每三個小單位成為一個密碼 (例如上面的第一個密碼 AUG)。另外,需要一種專門用來運輸胺基酸的 tRNA,每種胺基酸都有其特定的 tRNA,這群 tRNA 的一端接著其特定胺基酸 (如 Met),另一邊則是反密碼 (如 UAG),會與 mRNA 上面的密碼互補接合;如此就可按照 mRNA 上面的密碼,利用 tRNA 把對應的胺基酸一個一個接上去。當兩個胺基酸被帶到一起時,核糖體上面的 rRNA 就會把這兩個胺基酸連接在一起 (向右箭頭)。 Translation
11
T A C A T C G A T C G DNA A U G U A G C U A G C A U C U G A tRNA
mRNA A U 2 C U 3 Asp G A tRNA Met Ile 胺基酸 一個一個接上去,tRNA 任務完成後就獨自離開,漸漸形成蛋白質的長鏈。
12
T A C A T C G A T C G DNA A U G U A G C U A G C
mRNA Met Ile Asp 蛋白質 的長鏈形成,最後脫離製造蛋白質的核糖體。 Protein
13
Primary structure
14
Secondary structure (α-helix, β-sheets & β turns)
15
Folding of the polypeptide chain into regular or irregular structure.
Secondary structure The formation of the hydrogen bonds (C=O•••N-H) between peptide bond units of the polypeptide backbone. Folding of the polypeptide chain into regular or irregular structure.
16
Secondary structure - helix Loops - pleated sheets Turn or bends
Regular conformation (regular repeating units) - helix - pleated sheets Turn or bends Collagen helix Irregular conformation Loops Coils
17
Irregular conformations
They are as important biologically as the regular repeating units They form the antigen binding sites of antibodies.
18
Irregular loops or coils
important biological conformations, eg. Antigen binding sites of antibodies. Irregular loops or coils Biologically unimportant conformations of denatured proteins. Random coils
19
Regular conformations 1- α-helix
It is the most common confirmation. It is a spiral structure. polypeptide backbone is twisted about each α-carbon to form rod like structure, with R groups of the amino acids residues protrude outward from the helical backbone.
20
1- α-helix A complete turn of the helix contains an average of 3.6 aminoacyl residues The twisting of α-helix is right handed(clockwise)
21
Alpha helix is a virtual solid cylinder
Alpha helix is a virtual solid cylinder. There is almost no space along the axis, which makes it a very stable structure.
22
Each peptide bond form a Hydrogen bond to
AA 4th amino acids AA AA AA AA R peptide bond of 4th amino acid above in primary structure Peptide bond of 4th amino acid below in primary structure AA AA AA AA 4th amino acids
23
Certain amino acids destabilize a helix
2 adjacent R groups with the same charge ; e.g Lys, Arg 2 adjacent bulky side chains such as isoleucine , Leucine Pro and Gly (helix breakers)
24
N is apart of rigid ring Impossible rotation of N-Cα bond No substituent hydrogen is attached to N to form hydrogen bond. N atom of proline is a part of a rigid ring that creates a bend in -helix
26
Strengthening of αlpha helix
Strengthening of - Helix by 2 oppositely charged R groups
27
Examples of alpha helix
Keratins - entirely α-helical Protein of epidermal layer of skin ,nail ,hair ,hooves , horns, wool) Its rigidity is determined by the disulfide bonds between the polypeptide chains. Myoglobin- 80% helical.
28
Beta pleated sheet Beta denotes that it was the second regular structure described. It is formed of short stretches of (5-10) amino acids arranged alongside one another to form extended sheet. It has pleated outer surface and visualized as broad arrows. β-sheets is stabilized by H-bonding between amide hydrogen and carbonyl oxygen.
29
Beta pleated sheet Beta- sheets are pleated because the α- carbons are alternatively slightly above and below the plane of the main chain of polypeptide.
30
Α-helix Contain residues adjacent in primary structure Β-sheet Contain stretches of amino acids from different structural regions.
32
Beta pleated sheet stabilized by hydrogen bonds
Interchain hydrogen bonds between separate polypeptide chains Intrachain hydrogen bonds between segments of same polypeptide
33
β-sheets are said to be pleated
The R groups of adjacent residues protrude in opposite directions from zigzag structure, above and below the planes of polypeptide chain .
34
- pleated sheet The term ‘ form’ came from the fact that it was first recognised in -keratin.
35
Secondary structure
36
Types of beta pleated sheet
Parallel Adjacent chains having the same NH to CO orientation Antiparallel Antiparallel: Adjacent chains having opposite NH to CO orientation
37
C N Parallel C N C N Antiparallel N C
39
Examples of - pleated sheets
Β-keratin as silk fibroin & spider proteins consists of layers of antiparallel β- sheets rich in glycine and alanine. These small amino acids have small side chains which allow close packing of each layered sheet.
40
Compare alpha helix and beta pleated sheet
Beta pleated sheat Alpha helix Zigzag (fully extended) coiled Shape Not fixed 3.6 amino acids/turn No of amino acids Hydrogen bond Inter-chain Intra-chain Intra-chain hydrogen bond Stabilized by Two or more polypeptide chains or segments of the same polypeptide as it folds back on itself One polypeptide chain Parallel Anti parallel Rt handed alpha helix Lt handed alpha helix Types No Yes Disruption by proline Silk fibroin Alpha keratin Myoglobin ,hemoglobin Examples
41
strand, shown as a flat arrow pointing toward the carboxyl end
Figure 5.20c Secondary structure helix Hydrogen bond pleated sheet strand, shown as a flat arrow pointing toward the carboxyl end Figure 5.20 Exploring: Levels of Protein Structure Hydrogen bond
42
β-bends (reverse turns, β- turns):
Found where a polypeptide chain reverses direction(usually at the connection of 2 adjacent segments of antiparallel β-pleated sheet Usually composed of 4 amino acid residues ,the first amino acid being hydrogen-bonded to the fourth
44
Stabilized by hydrogen and ionic bonds between the first & fourth A
Stabilized by hydrogen and ionic bonds between the first & fourth A.A within the turn.
45
β-bends (reverse turns, β- turns):
Β-turn occurs mainly at protein surfaces Contain glycine and proline. Glycine causes a kink in the polypeptide chain because it is small and flexible. Imino group of proline assume the cis configuration that is amneable to a tight turn.
46
Supersecondary structure(structural motifs)
Specific ordering of secondary structures which appear in more than one protein. Longer ordering makes a Domain. Β-Barrel Leucine zipper Β -α- Β Greek key
47
Tertiary structure of proteins:
Three-dimensional structure of a protein. Refers to the final arrangement of domains in the Polypeptides. It arranges secondary structural elements in a specific way that suits the function of the protein. It brings A.A. far apart in the primary structure near to each other to suit the function of a protein.
48
Forces stabilizing the tertiary structure of proteins:
Disulfide bonds Stabilize the native conformation of the protein. Hydrophobic interactions In the interior of the protein to hide the hydrophobic residues. Hydrogen bonds Formed between polar residues and water and between other polar groups within the protein. Ionic interactions. To stabilize the protein structure.
49
Domain Locally folded compact region of the protein which has distinct tertiary structure and usually has a specific function.
50
The final conformation of the polypeptide
Represent the state of lowest energy and greatest stability The final conformation is dedicated by the primary structure
51
Final overall shape of the protein is classified according to axial ratio(length/breadth)
Fibrous proteins Globular proteins
52
Fibrous proteins Globular proteins Axial ratio >10 <10 Shape Rod like (cylindrical) spheroid Solubility in water Low(high content of hydrophobic amino acids) High (polar and charged groups on the surface) Secondary structure Usually contain one type of secondary structure α-keratin: has only α-helices β-ketain: has only β-sheats Collagen: has only collagen helix Contain one or more types: Myoglobin and hemoglobin have only α-helices. Pancreatic ribonuclease has a little α-helix and a lot of antiparallel β-sheats. Functions and examples Structural rather than dynamic functions: Collagen :mechanical support α-keratin: protective function of hairs and nails. Different functional roles: Catalysis :enzymes Contraction: actin Transport: hemoglobin Defense: immunoglobulin Receptors: Storage :ferritin
53
Quaternary structure:
A protein that contain 2 or more polypeptide chains held together by noncovalent forces.
54
Quaternary structure:
The protein subunits (or monomers) are held together by non-covalent interactions “e.g. hydrogen bond, ionic bonds .
55
Quaternary structure:
One Subunit (one poly peptide chain)-monomeric Two subunits- dimeric Three subunits- trimeric Proteins with multiple polypetide subunits are polymeric proteins.
56
Quaternary structure Subunits function independently
Lactate dehydrogenase (4 polypeptide chains) Subunits work cooperatively Hemoglobin(two α-chain and two non α-chains held together by electrostatic bonds.
57
Function of subunits in the quaternary structure
Function independantly e.g;Hemoglobin Function cooperatively
58
Hemoglobin structure α β β α heme
59
Cooperatively of Hemoglobin
Binding of oxygen to one subunit of HB tetramer increase the affinity of the other subunits for oxygen
62
Summary The levels of organization of proteins Primary structure Secondary structure Tertiary structure Quaternary structure 2. The peptides and peptide bond formation 3-Characters of peptide bond
63
The optically inactive amino acid is
Glycine (B) Serine (C) Threonine (D) Valine
64
Tertiary structure of a protein describes
(A) The order of amino acids (B) Location of disulphide bonds (C) Loop regions of proteins (D) The ways of protein folding
65
This structure best describes
A- an amino acid B-a tripeptide C-a tetrapeptide D-a fatty acid E-a trisacharide
Similar presentations
© 2025 SlidePlayer.com Inc.
All rights reserved.