Proteins PDF

Proteins - the most diverse macromolecules and occur in an enormous diversity of sizes and shapes 1 Functions of proteins Catalysis, e.g. alcohol dehydrogenase Transport, e.g. hemoglobin Motor, e.g. actin and myosin in skeletal muscle cells...

Proteins - the most diverse macromolecules and occur in an enormous diversity of sizes and shapes 1 Functions of proteins Catalysis, e.g. alcohol dehydrogenase Transport, e.g. hemoglobin Motor, e.g. actin and myosin in skeletal muscle cells __________, e.g. tendons, hair __________, e.g. antibodies __________, e.g. hormones, transcription factors Actin filaments (red) and microtubules (green) are two different kinds of proteins that provide structure to cells. 2 https://www.nature.com/scitable/topicpage/protein-function-14123348/ Protein abnormalities and diseases Sickle cell anemia: abnormality of hemoglobin Metabolic diseases: dysfunction of protein enzymes Neurodegenerative diseases: misfolded proteins 3 https://www.researchgate.net/figure/Protein-aggregation-in-late-onset-neurodegenerative-diseases_fig5_321979225  How can proteins present their specific functions? Polypeptides are folded into a specific conformation depending on the amino acid sequence. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/translation https://www.nobelprize.org/prizes/chemistry/2024/summary/ Topic outline - Proteins Protein Composition and Structure Knowledge & Building blocks: the 20 amino acids comprehension: Peptide bonds: formation of polypeptides Define, List, Label, Arrange, Summarize, Four levels of protein structures: primary, Describe, Discuss secondary, tertiary and quaternary From Structure to Function Hemoglobin as an example Application & Analysis: Illustrate, Interpret, Compare, Analyze 6 Amino acids Learning Objectives: Identify the 20 common amino acids and describe their physical and chemical properties Understand the biological importance of some amino acids and small peptides 7 Amino acids Key readings: Campbell, Farrell & McDougal, Biochemistry Chapter 3, Amino acids and peptides. Lehninger Principles of Biochemistry, 7th Edition Chapter 3, Section 3.1 Amino acids. Biochemistry, Berg, Tymoczko & Stryer 7th Edition Chapter 2, Section 2.1 Proteins are built from a repertoire of 20 amino acids. Supplementary readings: Lehninger Principles of Biochemistry, 7th Edition Chapter 1, Section 1.2 Chemical Foundations 8 Common structural features of all a-amino acids carboxylate group The a-carbon atom is attached by amino group side chain (R group) The R group determines the identity of the particular amino acid. R group 9 3D-shape (Stereochemistry) of amino acids The Ca of all amino acids (except glycine) is a chiral center with four different groups bonded to it, giving rise to two stereoisomers. Almost all naturally occurring amino acids found in proteins are L- isomers. Exception: D-amino acids are found in proteins that make up bacterial cell wall. 10 How to distinguish L- and D-amino acids? “CORN” rule : -COOH, the -R group and -NH2 CORN is produced with a clockwise eye movement L-form http://swift.cmbi.ru.nl/teach/alg/infopages/proteins.shtml 11  Importance of stereochemistry Thalidomide tragedy Sedative effect Tetratogenic Thalidomide: - was developed in 1950s to aid morning sickness. - A few years after it was launched, ~10,000 infants worldwide were born with malformed limbs. Under biological conditions, the (R)- and (S)-enantiomers interconvert, so separating the isomers before use is ineffective. http://www.sciencemuseum.org.uk/broughttolife/themes/controversies/thalidomide 12 https://www.acs.org/content/acs/en/molecule-of-the-week/archive/t/thalidomide.html Classification of the 20 amino acids Classification of the 20 amino acids is on the basis of the chemical characteristics of their R groups. A. Hydrophobic amino acids with nonpolar R groups B. Polar amino acids with neutral R groups C. Charged amino acids with R groups that have a positive or negative charge at physiological pH 13 Polar vs. non-polar covalent bond Polar covalent bond is a result of unequal share of e le c tron s between two bonded atoms of different e le c tron e gativity Non-polar Elements Electro-negativity C C C 2.5 C S S 2.5 N 3.0 d- d+ Polar O 3.5 O H 14 http://en.wikipedia.org/wiki/Chemical_polarity A. Hydrophobic amino acids with nonpolar R groups Glycine – the simplest amino acid Alanine, Valine, Leucine, Isoleucine have aliphatic hydrocarbon chain Proline – has a cyclic 5-membered aliphatic ring 15 A. Hydrophobic amino acids with nonpolar R groups Methionine – the electronegativity of sulfur is similar to that of carbon Phenylalanine and Tryptophan contains aromatic side chains 16 B. Polar amino acids with neutral R groups Serine, Threonine and Tyrosine have hydroxyl (-OH) groups attached to a hydrophobic side chain Asparagine and Glutamine have carboxylamide Both –OH and carboxylamide are good at forming hydrogen bonds 17 Phosphorylation on Serine/Threonine/Tyrosine as a key regulatory protein post-translational modification Signal transduction often involves covalent modification of protein by phosphorylation and dephosphorylation. ATP is the most common donor of phosphoryl groups. The terminal (g) phosphoryl group of ATP is transferred to a specific amino acid, Serine/Threonine/Tyrosine of the acceptor protein. 18 B. Polar amino acids with neutral R groups Cysteine contains a sulfhydryl (-SH) group -SH group of cysteine can ionize at high pH Oxidation of two –SH yields a disulfide bridge, which can stabilize protein structure 19 Proper folding of insulin requires disulfide bonds https://www.mun.ca/biology/scarr/Insulin_posttranslational_modification.html Chain A Insulin contains 1 intra-chain and 2 inter-chain disulfide bonds Chain B 20 Aromatic amino acids absorb ultraviolet Absorbance µ [protein] Absorbance at 280 nm can be used to measure the concentration of proteins as most proteins contain aromatic amino acid residues. C. Charged amino acids Negatively charged amino acids carboxylate groups of aspartate and glutamate have pKa of 3.7 and 4, respectively. They are ionized (negatively charged) at physiological pH. 22 C. Charged amino acids Positively charged amino acids pKa of the amino group of lysine ~ 10.5 pKa of the guanidino group of arginine ~ 12.5 pKa of the imidazole ring of histidine ~ 6.0 The side chains of lysine and arginine are amphipathic 23 Acetylation of histone lysine residues plays a key regulatory role in transcription HAT: histone acetylases HDAC: histone deacetylases https://www.nature.com/articles/s12276-020-0382-4 Modified from https://humgenomics.biomedcentral.com/articles/10.1186/s40246-018-0163-5/figures/1 DNA in chromatin is tightly associated with histone proteins, which package DNA into nucleosomes. Acetylation of histone lysine residues opens up the chromatin structure, allows binding of RNA polymerase for transcription process. Deacetylation of the histone lysines leads to the closed chromatin conformation which is unable to bind RNA polymerase.  Rare amino acid: Selenocysteine - the 21st amino acid Selenocysteine is attached to a unique tRNA that recognizes stop codon UGA. Selenocysteine has been found in 25 human selenoproteins