Biochemistry Notes PDF

16 Ibrahim Aldarbi Asma’a Abu-Qtaish Nabil Bashir Protein structure BIOCHEMISTRY-DENTAL, IST SEMESTER, 2023 Four Levels of Protein structure Three basic levels: primary, secondary, and tertiary; some proteins have quaternary structure, some don’t. Primary structure of a protein is the sequence...

16 Ibrahim Aldarbi Asma’a Abu-Qtaish Nabil Bashir Protein structure BIOCHEMISTRY-DENTAL, IST SEMESTER, 2023 Four Levels of Protein structure Three basic levels: primary, secondary, and tertiary; some proteins have quaternary structure, some don’t. Primary structure of a protein is the sequence of amino acid residues that constitute the polypeptide chain and the sequence positions of disulfide bonds. Disulfide bond: formed by connecting two sulfur atoms, each from a cysteine. As said before, the primary structure is determined by the amino acids, but what determines the amino acids? The genes, for any polypeptide chain or protein, there’s a gene responsible for synthesizing it, so any defect in the gene, will cause a defect in the primary structure. Gene: sequence of deoxynucleotides, consisting a part of DNA’s strand (so it’s a piece of DNA), it has 5’ end and 3’ end. The primary structure is very important, because it will determine the secondary and tertiary structures of the protein, mentioning that the tertiary structure is the functional form of a protein. In conclusion, if you don’t have a correct primary structure, you won’t have a correct functioning protein. Defected primary structure = defected protein. Four Levels of Protein structure Secondary structure description of its peptide backbone conformations, i.e., which of its peptide bonds are in α-helix, β-sheet, β-turn, or unordered conformations. The secondary structure of a typical peptide chain in globular proteins VARIES continuously throughout the length of the chain. the secondary structure of chains in fibrous proteins are usually constant throughout the length of chains. α-helix, β-sheet, and β-turn are the basic elements of the secondary structure. The pattern of how the individual stretches of α-helix and β-sheet are arranged relative to one another in three-dimensional space is called SUPERSECONDARY STRUCTURE. Tertiary structure refers to the three-dimensional structure(conformation) of a polypeptide chain, that is, the three-dimensional arrangement of all atoms in each amino acids residues. VERY COMPACT, irregular-spheres. STRUCTURAL DOMAINS & FUNCTIONAL DOMAINS. It’s the folding of the secondary structure elements in three-dimensional structure of a protein. It’s the functional form of a protein. Four Levels of Protein structure Some proteins are made of multiple polypeptides connected with each other. These are known as multimeric proteins. Quaternary structure describes the number and relative positions of the subunits in a multimeric protein. Not all proteins found in this structure. It’s the aggregation of more than one polypeptide chain (subunit). One subunit: monomer (so it doesn’t have a quaternary structure). Two subunits: dimer. Three subunits: trimer. Four subunit: tetramer. Diagram helps you to understand the previous terminology Primary structure: amino acid sequence, these amino acids are connected by peptide bonds (bonds in circle). Secondary structure: this is one of the shapes of this structure, the alpha helix, looks like coiled, we will talk about each structure in details soon. Tertiary structure: many secondary structure elements folded on each other, forming this compact structure, remember that this is the functional form of a protein. Quaternary structure: more than one subunit (polypeptide chain) are composing this structure, in fact this is a hemoglobin molecule, which contains four subunits (tetramer). Important: if any protein have a quaternary structure, then its tertiary structure isn’t functional, its functional form is the quaternary structure. A condensation reaction: PEPTIDE BOND FORMATION Proteins are linear polymers formed by covalently linking the α-carboxyl group (because it’s connected to α-carbon) of one amino acid to the α-amino group (because it’s connected to α-carbon) of another amino acid with a peptide bond (also called an amide bond). The formation of a dipeptide from two amino acids is accompanied by the loss of a water molecule in a condensation reaction that is energetically unfavorable. α α Definitions Each amino acid unit in a polypeptide is called a residue. The short chain of amino acids is known as an oligopeptides - fewer than 20-30 amino acid residues Longer peptides are referred to as polypeptides- contain as many as 1000 residues. Directionality of reading A polypeptide chain has polarity because its ends are different, with an α-amino group at one end and an α-carboxyl group at the other. The amino end is the beginning of a polypeptide chain, it’s called N-terminus because it contains free α-amino group. C-terminus, which contains free carboxyl group, it’s the end of the polypeptide chain. Only the first and last amino acids have free groups, all other amino acids both their amino group and carboxyl group are busy in the formation of peptide bond. Amino acids sequence is read from N-terminus to C-terminus Directionality of reading At physiological pH, the charge of this oligopeptide chain is -1, why? N-terminus: +1. C-terminus: -1. Amino acid number 4: -1. Directionality of reading At pH=2, the charge of this oligopeptide chain is +1, why? N-terminus: +1. C-terminus: neutral, it will be protonated. Amino acid number 4: neutral, it will be protonated. Directionality of reading At pH=11, the charge of this oligopeptide chain is -2, why? N-terminus: neutral, it will be deprotonated. C-terminus: -1. Amino acid number 4: -1. Note: Dr.Nabil didn't mention Tyr & Cys in this example, so we just care about Asp charge, although they may get deprotonated at this ph. Backbone and side chains A polypeptide chain consists of a regularly repeating part, called the main chain or backbone, and a variable part, comprising the distinctive side chains. PEPTIDE BOND PLANES Peptide bonds have double bond character, why? electrons are delocalized over the O-C-N (in other words, the resonance of the electrons). One consequence is six atoms end up confined to a peptide plane as shown. Side chains freely rotate, while the peptide bond is rigid, as mentioned earlier, it doesn’t rotate. Adjacent peptide planes along a peptide chain can rotate with respect to each other at the α– carbon atom, this rotation is limited, only certain angles are possible between adjacent planes because of the steric hindrance, group bumping into each other prevent all other angles (complete rotation). The groups of each peptide bond plane must move together, they cannot move independently. Only certain angles are allowed between adjacent peptide bond planes due to steric hindrance. It has a zig-zag structure and is planar. It has a double bond character rigid. 6 4 5 2 3 1 Importance of the Primary Structure Primary structure of a protein is the sequence of amino acid residues that constitute the polypeptide chain and the sequence positions of disulfide bonds • Example: Leu—Gly—Thr—Val—Arg—Asp—His The primary structure of a protein determines the other levels of structure. As said earlier, any defect in the primary structure (mutations, at the level of gene) will lead to defect in the function of the protein. A single amino acid substitution can give rise to a malfunctioning protein, as is the case with sickle-cell anemia. Sickle cell hemoglobin (HbS) • The function of hemoglobin is to bind oxygen at heme group, and • • • • • • • • transport it from lungs to tissues, and transport CO2 and H+ from tissues to lungs. Hemoglobin: aggregation of 4 subunits, so it’s tetramer, 2 α-chains (2x 141aa)+2 β-chains(2x146)=574aa On each β-chain at position 6: val instead of glu 2/574 . It is caused by a change of amino acids in the 6th position of β globin Glu: Negatively charged A.A (Glu to Val).-type change Val: Non-polar A.A (Not charge), pI: 6.87→7.09 that’s why the pI get less negative. The mutation results in: arrays of aggregates of deoxy hemoglobin molecules → insoluble FIBERS intracellularly → cell fragile (anemia) deformation of the red blood cell → clogging in blood vessels and tissues → ischemia → anoxia → cell necrosis → extreme pain. Trait: rarely symptomatic Trait selective advantage against consequences of malaria Patients have variable frequency and severity of crisis, ones with homozygous (the change is on both β-chains) are in very serious and dangerous case which requires blood transfusion to avoid the previously mentioned problems appears. SECONDARY STRUCTURE • It’s the three-dimensional structure of the backbone. • While talking about the secondary structure, we are talking about a region in the polypeptide chain, not the whole chain as in the primary structure. • The two bonds within each amino acid residue freely rotate. • • • the bond between the α-carbon and the amino nitrogen • the bond between the α-carbon and the carboxyl carbon A hydrogen-bonded, local arrangement of the backbone of a polypeptide chain. Polypeptide chains can fold into regular structures (depending on what amino acids are found in that region of the chain) such as: • Alpha helix • Beta-pleated sheet • Turns • Loops • Look at the planes, how peptide bond is rotated in a limited way, notice that peptide bonds and R groups are in trans position to avoid hindrance during the rotation. The α helix • Remember that the secondary structure folding is based on the amino • • • • • • • acids, in some regions, there are specific amino acids that make the folding of this region looks like that, other amino acids don’t have the ability to make this α helix. The peptide chain could be twisted or coiled clockwise (right handed) or counterclockwise(left handed) Peptides with L-amino acids form right handed The helix has an average of 3.6 amino acids per turn. The pitch of the helix (the linear distance between corresponding points on successive turns) is 3.6 X 0.15=0.54 nm It is very stable because of the linear hydrogen bonding, between the hydrogen attached to the amino group of a first amino acid and the oxygen attached to the carbonyl group of a fifth amino acid. The trans side chains of the amino acids project outward from the helix, thereby avoiding steric hindrance with the polypeptide backbone and with each other. This is the helix from above: Hydrogen bond Amino acids NOT found in α-helix • Glycine: too small-strong broker • Proline- strong broker • No rotation around N-Cα bond • No hydrogen bonding of α-amino group • Close proximity of a pair of charged amino acids with similar charges • Amino acids with branches at the β-carbon atom because they are too large (valine, threonine, and isoleucine)