Chapter 1-2 Protein Structure PDF

Chapter 1-2 Wednesday, August 28, 2024 2:20 PM Learning Outcomes ✔ Identify the 20 amino acids, and group them according to the chemical properties of their side chains Distinguish between primary, secondary, tertiary, and quaternary structures Describe the properties of the pr...

Chapter 1-2 Wednesday, August 28, 2024 2:20 PM Learning Outcomes ✔ Identify the 20 amino acids, and group them according to the chemical properties of their side chains Distinguish between primary, secondary, tertiary, and quaternary structures Describe the properties of the principal types of secondary structure, including the ɑ helix, the β sheet, and the reverse turn. Explain how the hydrophobic effect serves as the primary driving force for folding of polypeptide chains into globular proteins Section 2.1 Several Properties of Protein Structure are Key to their Functional Versatility Protein: - Are linear polymers composed of monomers called amino acids - (proteins are like long chains made up of small building blocks. These building blocks are called amino acids, they link together in a line, they form a protein. Imagine beads on a string, where each bead is an amino acid, and the entire string is the protein - Contain a wide range of functional groups whose reactive properties are essential to the function of the protein (e.g., enzyme function) - Can interact with one another and other macromolecules to form complex assemblies - Can be rigid or flexible Flexibility and Function: - Conformational flexibility - Binding induces conformational change - Structure dictates function Section 2.2 Proteins are Built from a Repertoire of 20 Amino Acids An ɑ-amino acid consists of the ɑ-carbon linked to: - An amino group - A carboxylic acid group - A hydrogen atom - A distinctive R group (or amino chain) Chiral amino acid - Have four different group bonded to the ɑ carbon - Exist as two mirror-image forms called the L isomer and the D isomer - Proteins only contain L isomers Ionization State as a function of pH - At neutral pH free amino acids exist as zwitterions, with a charged amino group (NH3 +) and carboxyl group COO- - When both groups are protonated it means that the amino group become NH3+ and the carboxyl group becomes COOH this means they're are acidic. While, if both groups are deprotonated the amino group becomes NH2 and the carboxyl group loses its proton and become COO-, this means they are less acidic or basic. The zwitterionic form is when the amino group is protonated while the carboxyl group is deprotonated, it keeps the overall net charge zero - pH is a measure of concentration The 20 amino acids - The 20 amino acid side chains: ○ Vary in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, an chemical reactivity ○ Can be placed into four groups § Hydrophobic § Polar § Positively charged § Negatively charged - Have three-letter abbreviations and one letter symbols Hydrophobic Amino Acids Polar Amino Acids - Side chain that make polar amino acids hydrophilic and more reactive than hydrophobic amino acids - Cysteine = contains a sulfhydryl (thiol, -SH) group - Pairs of -SH groups can form disulfide bond (later) - Histidine = often found in enzyme active sites (next) - Unequal sharing of covalent bond - Have nonpolar side chains of different shapes and sizes that: ○ Do not interact well with polar substances such as water ○ Pack together to form compact structures ○ Potential for hydrogen bonding - Tryptophan = bulkiest hydrophobic amino acid ○ Contain an indole group in its side chain ○ Potential for hydrogen bonding Histidine Can Bind or Release Proton - Histidine has a pKa value near 6, which is near physiological pH, allowing it to accept or donate protons readily in a pH range of 6-7 Positively Charged Amino Acids Negatively Charged Amino Acids - Negative refers to likely charge at physiological pH - Carboxylate functional group - Protonated (aspartic acid and glutamic acid) only at a highly acidic pH - Positive refers to likely charged at physiological pH (7.4 pka) - Highly hydrophilic (polar) - Arginine: contains a guanidinium group - Will interact with DNA because DNA is negative (-) Seven of the 20 Amino Acids have Ionizable side chains - Lower the number (pKa) represent the lower affinity - Everything on the right is deprotonated (negative) - Everything on the left is protonated (positive charge or neutral) Section 2.3 Primary Structure: Amino Acids are Linked by Peptide Bonds to Form Polypeptide Chain - Peptide bond (amide bond) formation involves: ○ Linkage of the ɑ-carboxyl group of one amino acid to the ɑ-amino group of another amino acid ○ Poly peptide Directionality - Residue = each amino acid unit in a polypeptide - Polypeptide chains have directionality ○ ɑ-amino group § (N-terminal) ○ ɑ-carboxyl group § (C-terminal) The polypeptide Backbone - The polypeptide consists of: ○ The main chain (or backbone) ○ Distinctive amino acid chains (R-groups) - The backbone has hydrogen-bonding potential ○ Carbonyl (C=O) group are hydrogen bond acceptors ○ NH groups are hydrogen-bond donor - Peptide bonds are planar Disulfide Bonds - Cross-links - Formed by the oxidation of pair of cysteine residue - Cysteines can form disulfide bond Two linked cysteines are called cystine Section 2.4 Secondary Structure: Polypeptide Chains Can Fold into regular structures - Secondary structure = three-dimensional structure formed by hydrogen bonds between main chain N-H and C=O groups of amino acids nearby in the linear sequence - Examples of secondary structure include ○ ɑ helices ○ β pleated sheets ○ Turns The Alpha Helix is a Coiled Structure Stabilized by Intrachain Hydrogen Bonds - ɑ helix = tightly coiled, rodlike structure, with R groups extending outward in a helical array - All of the backbone CO and NH groups form hydrogen bonds except those near the end of the ɑ helix ɑ-helices - An example of interactions between outward facing side chains of two a-helices - Lucine form hydrophobic interactions hold that two ɑ-helices together (excludes water) Beta Sheets Are Stabilized by Hydrogen Bonding Between Polypeptide Strands An Antiparallel β sheet - β strand: common form of secondary structure - The NH group and the CO group of each amino acid are respectively - β pleated sheet: formed by adjacent β strands hydrogen bonded to the CO group and the NH group of a partner on - Hydrogen Bonds link 2 or more β strands to form β sheet the adjacent chain - Adjacent strands in a β sheet may run in ○ the same direction (parallel) ○ the opposite direction (antiparallel) ○ a combination of directions (mixed) A Representation of a Twisted β Sheet A Protein Rich in β Sheets Polypeptide Chains can Change Direction by Making Reverse Turns and Loops - polypeptide chains can reverse directions with reverse turns (or β turns, hairpins turns) or loops. 3D form and function example - β-sheets in the core hold the protein together - flexible loops at the top and bottom can interact with other proteins, substrates, etc Section 2.5 Tertiary Structure: Proteins Can Fold into globular or Fibrous Structures - tertiary structure: the overall fold of polypeptide chain - myoglobin = a highly compact globular ɑ helical protein with a heme prosthetic group ○ interior is almost exclusively hydrophobic amino acids except for 2 critical histidine residues (later) Globular protein are characterized by: - a highly structure compact structure - a lack of symmetry - solubility in water The Distribution of Amino Acids Is Related to the Protein's Folding and Function (1/2) The Distribution of Amino Acids Is related to the Protein's Folding and Function (2/2) - The protein surface has many charged amino acids - membrane-embedded protein have: - The interior is tightly packed with mostly nonpolar residues ○ many hydrophobic amino acids in contact with the hydrophobic membrane ○ many polar and charged amino acids surrounding a water-filled channel - - Section 2.6 Quaternary Structure: Polypeptide Chains can Assemble into Multi subunit An example of a Homodimer structures - many proteins are composed of multiple polypeptide chains called subunits - quaternary structure = the spatial arrangement of subunits and the nature of their interactions ○ can be as simple as two identical polypeptide chains (homodimer) ○ can be as complex as dozens of different polypeptide chains An Example of an ɑ2β2 Heterotetramer - Hemoglobin carries oxygen The presence of proline helps define Fibrous Proteins Provide Structural Support for Cells and Tissues Structure of the Protein Collagen overall helical structure of our collagen - fibrous proteins = form long, extended structures that feature repeated sequences - consists of three intertwined helical polypeptide strands that form a ○ examples: ɑ-keratin, collagen super helical cable - Collagen = main fibrous component of skin, bone, tendon, cartilage, and teeth ○ stabilized by hydrogen bonds between strands ○ glycine (Gly) appears at every third residue. ○ interior is crowded and only glycine can fit ○ The sequence glycine-proline-hydroxyproline recurs frequently ○ hydroxyproline: proline post-translationally modified (later) Section 2.6 The Amino Acid Sequence of a Protein Determines its Three-dimensional Structure Reduction and denaturation of ribonuclease - ribonuclease: single polypeptide chain consisting of 124 amino acid residues cross-linked by four disulfide bonds sulfhydryl - BME reduces disulfide bonds (cysteine) - Urea disrupts ○ hydrogen bonds and electrostatic interactions - See how the primary structure is not disrupted, it broke all secondary, tertiary, and quaternary structure but primary structure is not disrupted not breaking peptide bonds - Re-oxidation Disulfide pairing Protein Folding is a highly cooperative Process - protein folding and unfolding is an "all or none" process ○ results from a cooperative transition Abnormal Protein Folding and Diseases - Protein mis-folding and aggregation are associated with neurological disorders Prion Diseases ○ Alzheimer, Parkinson, Hungington - Creutzfeldt-Jacob disease and kuru - Mad cow disease and scrapie - Amyloidosis normally soluble proteins converted into insoluble fibrils rich in beta sheets - Transmission agent is protein! ○ Fibrils are prone to aggregate - Normal prion protein (PrP) is converted to an altered conformation, which then aggregates ○ Abnormally folded aggregates serve as a nucleus to recruit more protein to (abnormal beta-sheet conformation, next slide) abnormally fold (prior example coming up) - PrPSC catalyzes conversion of Prp into PrPSC (next slides) - Neuronal cell death follows - These are protein misfolding Beta sheets conversion PrpSC Some Common and Important Covalent Modification of Amino Acid Side Chains The Biological Significance of Post translational Modifications - Post-translational modification: alterations in the structure of a protein after its synthesis in - Protein phosphorylation regulates enzyme activity (to be converted in Enzymes: regulatory the cell strategies) - Lack of appropriate protein modifications can result in pathological conditions - Lack of vitamin C prevents hydroxylation of collagen ○ Results in abnormal collagen fibers that are unstable to main normal tissue strength -