HSS2305 Molecular Mechanisms of Disease Lectures 2 & 3 - Biological Molecules PDF

HSS2305: Molecular Mechanisms of Disease Lectures 2 and 3 – Biological Molecules Prof. Keir Menzies Welcome back to lectures 2 and 3 Biological Molecules Chemistry of Life Understanding cellular function requires knowledge...

HSS2305: Molecular Mechanisms of Disease Lectures 2 and 3 – Biological Molecules Prof. Keir Menzies Welcome back to lectures 2 and 3 Biological Molecules Chemistry of Life Understanding cellular function requires knowledge of structure Structure and function in cells is closely related to the structure of molecules and atoms The study of chemistry is essential for understanding cell biology Chemistry of Life Atomic bonds Atom: basic unit of matter that consists of a dense central nucleus surrounded by a cloud of negatively Covalent Bonds: between atoms charged electrons with shared pairs of electrons Molecules: stable combinations of atoms held together by covalent bonds. Compounds: are molecules with more than one type of atom  Chemistry of Life atomic bonds Example Acids: Example Salts: HCl NaCl (Hydrochloric Acid) Table Salt  Chemistry of Life Polarity Polar molecules: have asymmetric distributions of electrical charge. Tend to be more reactive. H 2O Contain: O, N, S Nonpolar molecules: lack polarized bonds, without electronegative atoms. Inert. Fats, waxes, CO2 Contain: C, H Many biological molecules (i.e. proteins, phospholipids) have both polar and nonpolar regions  Chemistry of Life Ionization Ions: i.e. some atoms are so strongly electronegative that they capture electrons from other atoms during a chemical reaction Cations à lost electrons (Na+) Anions à extra electrons (Cl-) i.e. anions are stable because they fill their outer electron shell Free radicals: unstable atoms or molecules with unpaired electrons. Highly reactive. formed during normal metabolism highly reactive and damage macromolecules such as DNA, lipids, proteins and carbohydrates may play a role in aging Ex. Superoxide (O2-) and hydroxyl radical (OH·) Can donate or accept electrons readily Chemistry of Life Free radicals – A cause of Disease One of the greatest enemies to our health is free radicals Chemistry of Life Free radicals – A cause of Disease One of the greatest enemies to our health includes aberrant free radicals (unmanaged free radicals) http://youtu.be/KCF6prDSrHE  Chemistry of Life Hydrogen Bonds covalently bound hydrogen has a partial positive charge and attracts electrons of a second atom H-bonds occur in biological molecules, such as between the strands of DNA H-bonds determine the structure and properties of water Chemistry of Life Hydrophilic and Hydrophobic interactions Hydrophilic water-loving participate in hydrogen bonding enhance solubility in & interactions with water occur between polar molecules i.e. amino acids, sugars Hydrophobic water-fearing nonpolar molecules, essentially insoluble in water form into aggregates, minimizing exposure to polar surroundings i.e. fat, steroids Van der Waals interaction weak bonds between hydrophobic molecules based on electrostatic interactions transient charge asymmetries result in momentary charge separations à dipoles i.e. antibodies and viral antigens van der Waals forces operate over very short ranges and serve to pull together two surfaces that are complementary in shape  Chemistry of Life water The life-supporting properties of water result from its structure it is asymmetric both covalent O–H bonds are highly polarized all three atoms readily form H- bonds it requires a lot heat to evaporate it is an excellent solvent for many substances it determines the interactions between many biological solutes  Chemistry of Life Acids, Bases, Buffers Acids release protons Bases accept protons Amphoteric molecules can act as either acids or bases For example, water: hydronium water hydroxide H3O+ ↔ H+ + H2 O ↔ OH– + H+ Acid Amphoteric Base Biological processes are sensitive to pH Changes in pH affect the ion state and function of proteins Buffers in living systems resist changes in pH i.e. bicarbonate ions and carbonic acid buffer the blood HCO3– + H+ ↔ H2CO3 Chemistry of Life Acids, Bases, Buffers The Bohr Effect allows for enhanced unloading of oxygen from hemoglobin in metabolically active peripheral tissues such as exercising skeletal muscle. Increased skeletal muscle activity results in localized increases in the partial pressure of carbon dioxide which in turn reduces the local blood pH.  Biological Molecules Carbon – central to organic compounds size & electronic structure allow carbon to generate many molecules binds to up to 4 other atoms carbon-containing backbones, may be linear, branched or cyclic very stable Hydrocarbons: contain only carbon and hydrogen Simplest group of organic molecules Do not occur often in living cells  Biological Molecules Common Functional groups (R) in living organisms replace hydrogens on carbon skeleton groups of atoms giving organic molecules different characteristics and properties.  Biological Molecules Classification 1. Macromolecules Carbohydrates Lipids Nucleic acids Proteins 2. Building blocks of macromolecules Sugars Fatty acids Nucleotides Amino acids 3. Metabolic intermediates Products formed along metabolic pathway leading to end products Might have no function 4. Molecules of miscellaneous function Vitamins, hormones, ATP, cAMP, metabolic waste products  Biological Molecules Macromolecules Large structural and functional molecules in cells 1. Carbohydrates - simple sugars and sugar polymers; energy source 2. Lipids – nonpolar molecules consisting of fatty acids; energy store, structural and hormonal function 3. Nucleic acids - polymers of nucleotides that store and transmit genetic information 4. Proteins - polymers of amino acids, abundant functions Biological Molecules carbohydrates Biological Molecules carbohydrates Function: chemical energy storage molecules durable building materials Structure: chemical formula à (CH2O)n Ketosis is a metabolic state characterized by elevated levels Ketose - carbonyl (C=O) on an internal carbon of ketone bodies in the blood or Aldose - carbonyl on a terminal carbon urine. Physiologic ketosis is a Hexoses. Glucose, mannose, galactose (all aldoses), and fructose (ketose) normal response to Pentoses. Ribose, xylose (both aldoses) low glucose availability, such as low-carbohydrate diets or fasting, that provides an additional energy source for the brain in the form of ketones. sugars can be linear or form ring structures Ketone bodies: acetone, acetoacetic acid, and beta-hydroxybutyric acid  Biological Molecules carbohydrates Glycosidic bonds: –C—O—C– links between sugars Disaccharides: 2 sugars, used as a source of readily available energy. These are the three most common: Oligosaccharides: chains of a few sugars (2-10) found bound to cells surface proteins and lipids, used for cell recognition. These are examples of “simple” sugars/carbs Biological Molecules carbohydrates Polysaccharides: polymer of many sugar units Glycogen à animal product of branched glucose polymers; animal storehouse of surplus chemical energy Starch à plant product of both branched and un-branched glucose polymers, plant surplus of stored energy Glycosaminoglycans (GAGs): structural unbranched polysaccharides; composed of two different sugars; often found in extracellular space to maintain structure (lubricant or shock absorber); also is an important component of Heparin Heparin (6,000- 40,000 Da) a medication and naturally occurring glycosaminoglycan. As a medication it is used as an anticoagulant (blood thinner). Specifically, it is also used in the treatment of heart attacks and unstable These are examples of “complex” sugars/carbs angina. Biological Molecules carbohydrates Fiber Primarily indigestible polysaccharides Ex. Cellulose Ruminant animals (ex. Cows) Ferment cellulose prior to full digestion https://www.youtube.com/watch?v=jzv_OeVGhlI Biological Molecules Good vs. Bad carbs What is the difference between a good carb and a bad carb? What are some examples of each? Biological Molecules Good vs. Bad carbs Biological Molecules Good vs. Bad carbs Biological Molecules Lipids Another major class of lipids is steroids, which have structures totally different from the other classes of lipids  Biological Molecules Lipids Lipids = diverse group of molecules fats, steroids, phospholipids hydrophilic hydrophobic Fats: glycerol linked by three ester bonds to three fatty acids creating a non-polar molecule (due to the ester linked bond between the polar hydroxyls of glycerol and the polar carboxylates of the fatty acids) Amphipathic: having both hydrophilic and hydrophobic parts Long term storage of energy Fatty Acids: long un-branched hydrocarbon chains with a single carboxyl group Saturated – no double bonds Unsaturated – contains double bonds (Monounsaturated or Polyunsaturated) Cis- and trans- describe whether the hydrogen atoms are on the same or opposite side of the double bond Comparison of fats  Biological Molecules Lipids Steroids: built around 4 ringed hydrocarbon skeleton, nonpolar Cholesterol belongs to the steroid family of lipid (fat) compounds Phospholipids: resembles a fat but only 2 fatty acid chain + phosphate group bound to glycerol bound to small polar group Primarily function in cell membranes Biological Molecules Nucleic acids  Biological Molecules Nucleic acids Nucleic Acid = Polymers of nucleotides that store and transmit genetic information Two types of nucleic acids: Ribonucleotide (would need to be just “H” if it was a Deoxyribonucleic acid (DNA) à storage of deoxyribonucleotide) genetic information Nitrogenous Bases: Ribonucleic acid (RNA) à transmission of genetic information into proteins Nucleotide: (deoxy)ribose sugar + phosphate group + nitrogenous base Nucleotides distinguished by their nitrogenous bases (DNA) (RNA)  Biological Molecules Nucleic acids RNA In DNA/RNA nucleotides are connected by 3’-5’ phosphodiester bonds between the phosphate of one nucleotide and the 3’ carbon of the next ribose sugar Alternate functions of nucleotides: Adenosine triphosphate (ATP) à cellular energy Guanosine triphosphate (GTP) àactivates G 3’ proteins within a cell 5’ Biological Molecules Proteins Biological Molecules Proteins Macromolecules that perform virtually all of a cell’s activities molecular tools and machines Major functions: Enzymes Transporters Hormones, growth factors Regulators of cell function (i.e. gene transcription) Structural and/or movement machinery Antibodies, toxins etc. Each protein has a unique and defined structure to enable it’s function and allow it to selectively interact with molecules https://www.youtube.com/watch?v=iaHHgEoa2c8  Biological Molecules Proteins Building blocks of proteins = amino acids All amino acids have: an α carbon an amino group a carboxyl group a variable R group Amino acids of a polypeptide chain are joined by peptide bonds Average polypeptide chain contains ~ 300 amino acids (residues) Many proteins contain other components which are added to the polypeptide following synthesis carbohydrates à glycoproteins metal-containing groups à metalloproteins organic groups à flavoproteins Biological Molecules Proteins 20 different amino acid Amino acid side chains (R group) à diverse structure and function 1. Polar charged 2. Polar uncharged 3. Nonpolar 4. Unique properties  Biological Molecules Proteins contain R groups that act as strong organic acids, bases almost always fully charged at pH 7 can form ionic bonds i.e. histones with arginine (+ charge) bind to negatively charged phosphate groups of DNA  Biological Molecules Proteins R groups weakly acidic or basic not fully charged at pH 7 can form H bonds with other molecules (i.e. H2O) since they have atoms with a partial negative or positive charge  Biological Molecules Proteins R groups hydrophobic, generally lack O & N cannot interact with water or form electrostatic bonds, use hydrophobic & van der Waals interactions vary primarily in size & shape àallows them to pack tightly into protein core Biological Molecules Proteins  Biological Molecules Proteins Cysteine contains a reactive sulfhydryl group (-SH) or thiol group Disulfide bridge = covalent bond between two sulfhydryl groups (-SS-) Can form between distant cysteine residues within and across different proteins Help stabilize intricate shapes of proteins Also, modifiable by free radicals to form oxidized forms of Cysteine (Sulfenic Acid, cystine and many others)  Biological Molecules Proteins Structure of Proteins: Primary structure = sequence of amino acids in the polymer critical to the protein function Secondary structure = conformation of adjacent amino acids into: α-helix β-sheet Hinges Turn Loops Finger-like extensions *Stabilized by hydrogen bonds Biological Molecules Proteins α-Helix ß-Sheet  Biological Molecules Proteins Structure of Proteins: Tertiary structure = conformation of the entire polymer stabilized by non-covalent bonds between R groups determined using: X-Ray crystallography NMR Predicted (still in development) AlphaFold Categorized as: Fibrous protein elongated shape outside cell i.e. keratin, elastin Globular protein compact shape often within a cell i.e. myoglobin https://www.youtube.com/watch?v=gg7WjuFs8F4  Biological Molecules Proteins Structure of Proteins: Domains within a Conformational changes = protein = two or more distinct regions in a dynamic movement of regions polypeptide, each of a protein, triggered by with specific function binding  Biological Molecules Proteins Structure of Proteins: Quaternary structure = for proteins composed of subunits, it refers to the manner in which subunits interact Individual subunits may be linked by covalent disulfide bonds or noncovalent bonds Hemoglobin - a and b globin * Even though it consists of Subunits may or may not be 4 subunits it is considered a identical single protein with a single homodimer – 2 identical subunits function Heterodimer – 2 different subunits  Biological Molecules Proteins Quaternary structure of multi-protein complexes (or multimer): different proteins, each with specific function, physically associate i.e. pyruvate dehydrogenase à 60 polypeptide chains that make up 3 different enzymes These interactions are often highly dynamic  Biological Molecules Proteins The folded state of a protein Amino acid interactions allows it to exert it’s function Denaturing: the unfolding or disorganization of a protein, usually associated with a loss of function detergents reducing agents organic solvents radiation Hydrophobic collapse heat à all interfere with various interactions that stabilize a proteins tertiary structure most proteins capable of self-assembly spontaneously mutations in amino acid sequence can negatively impact protein folding and function  Biological Molecules Proteins Protein Misfolding – Deadly consequences Creutzfeld-Jakob Disease (CJD) – ”Mad Cow Disease”: Rare, progressive, fatal disorder Lesions in the brain causing loss of motor coordination and dementia results from misfolded protein in the brain  Biological Molecules Proteins Protein Misfolding – Deadly consequences Healthy brains contain a normal protein, prion protein (PrPc). CJD brains have insoluable prion protein (PrPSc), which is identical or similar to PrPc but is misfolded. “Mad cow disease”, kuru, and scrapie are also caused by PrPSc. Biological Molecules Proteins – Molecular Chaperones = “helper proteins” to prevent non- selective interactions during protein folding to achieve proper 3D conformation Heat shock protein 70 (Hsp 70) family bind emerging proteins and prevent inappropriate interactions Chaperonins (TriC) allow large new proteins to assemble without interference from other macromolecules; processes up to 15% of the cells’ proteins  Biological Molecules Proteins Proteome = entire inventory of proteins produced by a specific cell, tissue, organ or organism Proteomics = the field of protein biochemistry; similar to “genomics” for the study of global gene expression Gel electrophoresis Mass spectrometry Protein microarray Questions?