Biological Molecules PDF

Biological Molecules - Hydrogen bonds help hold together the two strands of DNA, keeping its structure stable. Atom : basic unit of matter, consisting of a dense central nucl...

Biological Molecules - Hydrogen bonds help hold together the two strands of DNA, keeping its structure stable. Atom : basic unit of matter, consisting of a dense central nucleus - Hydrogen bonds also give water its unique properties, surrounded by a cloud of negatively charged electrons. like its ability to stick together and stay liquid over a wide range of temperatures. Molecules : stable combinations of atoms held together by covalent bonds. Hydrophilic - Water-loving Compounds : molecules with more than one type of atom. - Participate in hydrogen bonding - Enhance solubility in and interacts with water Covalent bonds : between atoms with shared pairs of electrons. - Happens between polar molecules - E.g. amino acids, sugars Non-polar covalent bonds : occur when bonding electrons are Hydrophobic shared equally between two atoms, resulting in no charges on the - Water-fearing (water phobic) atoms. - Non polar molecules, essentially insoluble in water - Forms into aggregates, minimizing exposure to polar Polar covalent bond : occurs when bonding electrons are shared surroundings unequally between two atoms, resulting in partial charges on the - E.g. fats steroids atoms. E.g. HCl (hydrochloric acid) Van der Waals interactions are weak attractions between Ionic bond : involves the complete transfer of one or more valence molecules that are close to each other, especially when they're not electrons, resulting in full charges on the resulting ions. E.g. NaCl attracted to water (hydrophobic molecules). (table salt) - These interactions happen due to temporary changes in the charge distribution within molecules. Polar molecules : have an asymmetric distribution of electrical - When molecules are very close, slight shifts in their charge and tend to be more reactive. E.g. H2O charges create weak, temporary attractions, even - Contains : O, N, S though they aren't charged overall. - These weak bonds are important when molecules, Non-polar molecules : lack polarized bonds, without like antibodies and viral antigens, need to fit closely electronegative atoms. together to interact. - Inert - Van der Waals forces only - Fats, waxes, CO2 work over short distances and - Contains : C, H help pull two molecules or surfaces together if their ・Proteins & phospholipids have both polar and nonpolar regions. shapes fit well. Ions : atoms or molecules that have gained or lost one or more Water : life supporting properties result from its structure. electrons, giving them an electric charge. - It is asymmetric - Cations : lost electrons (Na+) - Both covalent O-H bonds are highly polarized - Anions : extra electrons (Cl-) (more stable because - All 3 atoms readily form H-bonds they fill their outer electron shell) - Requires a lot of heat to evaporate - Excellent solvent for many substances Free radicals : molecule or atom that has an unpaired electron, - Determines the interactions between many biological making it highly reactive and unstable. solutes - Formed during normal metabolism Acids : release protons. Bases : accept protons. - Highly reactive and damage macromolecules such as DNA, lipids, proteins and carbohydrates Amphoteric molecules : can act as either acids or bases (e.g. - May play a role in ageing water). - Can donate or accept electrons readily - Ex. superoxided (O2-) and hydroxyl radical (OH-) ・Biological processes are sensitive to pH. ・Free radicals = a cause of disease - Changes in pH affect the ion state and function of - Aberrant free radicals (unmanaged free radicals) proteins Hydrogen bonds : weak attractions between molecules. Buffers : in living systems resist changes in pH. E.g. bicarbonate ions and carbonic acid buffer the blood. ・Hydrogen atoms with a slight positive charge are attracted to another atom (like oxygen or nitrogen) that has a slight negative Bohr Effect : helps hemoglobin release more oxygen in active charge. (opposites attract) tissues, like muscles during exercise. When muscles are working hard, they produce more carbon dioxide, which lowers the pH ・When hydrogen forms a bond with certain atoms (like oxygen or (makes the blood more acidic) in that area. This acidic nitrogen), it gets a partial positive charge.This positively charged environment makes it easier for hemoglobin to let go of oxygen, hydrogen is then attracted to the negatively charged part of another giving the muscles the oxygen they need. atom. Carbon : central to organic compounds ・Ketosis is a metabolic state characterized by elevated levels of - Size and electronic structure allow carbon to generate ketone bodies in the blood or urine. Physiologic ketosis is a many molecules normal response to low glucose availability, such as - Binds up to 4 other atoms low-carbohydrate diets or fasting, that provides an additional - Carbon-containing backbones, may be linear, energy source for the brain in the form of ketones. branched or cyclic - Very stable Glycosidic bonds : -C-O-C links between sugars. Hydrocarbons : contain only carbon and hydrogen Disaccharides : 2 sugars, used as a source of readily available - Simplest group of organic molecules energy. These are the 3 most common : - Do not occur often in living cells Glycosidic bonds : -C-O-C links between sugars. Common Functional groups (R) in living organisms - Replace hydrogens on carbon skeleton Disaccharides : 2 sugars, used as a source of readily available - Groups of atoms giving organic molecules different energy. These are the 3 most common : characteristic and properties 1Macromolecules : large structural and functional molecules in cells Carbohydrates : simple sugars and sugar polymers; energy source Oligosaccharides : chains of a few sugars (2-10) found bound to Lipids : nonpolar molecules consisting of fatty acids: energy cell surface proteins & lipids, used for cell recognition. store, structural and hormonal function Nucleic acids : polymers of nucleotides that store and transmit These are examples of “simple” sugars/carbs genetic information Proteins : polymers of amino acids, abundant functions Polysaccharides : polymer of many sugar units 2Building blocks of macromolecules : Sugars - Glycogen→animal product of branched glucose Fatty acids polymers; animal storehouse of surplus chemical Nucleotides energy Amino acids - Starch→ plant product of both branched and 3Metabolic intermediates : unbranched glucose polymers, plant surplus of stored Products formed along metabolic pathways leading to end energy products - Glycosaminoglycans (GAGs): structural unbranched Might have no function polysaccharides; composed of two different sugars; 4Molecules of miscellaneous function : often found in extracellular space to maintain Vitamins structure (lubricant or shock absorber); also is an Hormones important component of Heparin ATP cAMP Metabolic waste products Carbohydrates Function : chemical energy storage molecules, durable building materials. These are examples of “complex” sugars/carbs. Structure : ・Heparin (6,000- 40,000 Da) a medication and naturally Chemical formula : (CH2O)n occurring glycosaminoglycan. As a medication it is used as an - Ketose - carbonyl (C=O) on an internal carbon anticoagulant (blood thinner). Specifically, it is also used in the - Aldose - carbonyl on a terminal carbon treatment of heart attacks and unstable angina - Hexoses - glucose, mannose, galactose (all aldoses), and fructose (ketose) Fiber - Pentoses - ribose, xylose (both aldoses) - Primarily indigestible polysaccharides (e.g. cellulose) - Ruminant animals (e.g. cows) (ferment cellulose ・Sugars can be linear or form ring structures. prior to full digestion) Complex carbs=good : chemical structure and fiber makes it harder for our bodies to digest it and energy is released over a longer time. Steroids : build around 4 ringed hydrocarbon skeleton, nonpolar. - High in fiber - Low glycemic index - Helps you feel full with free calories - Naturally stimulates metabolism Phospholipds : resemble a fat but only 2 fatty acid chain + Simple carbs=bad : smaller molecules of sugar that we can phosphate group bound to glycerol bound to small polar group digest quickly. If not used immediately it is converted into fat. - Primarily function in cell membranes - Low in fiber and nutrients - High glycemic index - Empty calories converted to fat - High blood glucose level=feel tired Nucleic acids Nucleic Acid : polymers of nucleotidea that store and transmit genetic information. 2 types of nucleic acids : - Deoxyribonucleic acid (DNA) : storage if genetic information - Ribonucleic acid (RNA) : transmission of genetic information into proteins ・Another major class of lipids is steroids, which have structures totally different from the other classes of lipids Nucleotides : (deoxy)ribose sugar + phosphate group + nitrogenous base Lipids - Distinguished by their base Lipids : diverse group of molecules. (fats, steroids, phospholipids). Fats : glycerol linked by these ester bonds to 3 fatty acids creating a non-polar molecule (due to the ester linked bond between the polar bydroxyls of glycerol and the polar carboxylates of the fatty acids). - Long term storgae of engery Fatty acids : long unbranched hydrocarbon chains with a single carboxyl group. - Saturated : no double bonds - Unsaturated : contains double bonds - (monosaturated or polunstaurated) ・In DNA/RNA nucleotides are connected by 3’-5’ phosphodiester - Cis- and trans- describe whether the hydrogen atoms bonds between the phosphate of one nucleotide and 3’ carbon of are on the same or opposite side of the double bond the next ribose sugar. ・Alternate functions of nucleotides : - Adenosine triphosphate (ATP)→ cellular energy - Guansoine triphosphate (GTP)→ activates G proteins within a cell Amphipathic : having both hydrophilic and hydrophobic parts.  Proteins Proteins : MAcromolecules that perform virtually all of a cell’s activities (molecule tools and machines) Major functions : - Enzymes - Transporters - Hormones, growth factors ・Conatin R groups that act as strong organic acids, bases - Regulators of cell function (e.g. gene transportation) - Structural and/or movement machinery ・Almost always fully charged at pH 7 - antibodies , toxins etc. ・Can form ionic bonds (E.g. histones with arginine (+charge) bind ・Each protein has a unique and defined structure to enable its to negatively charged phosphate groups of DNA) function and allow it to selectivity interact with molecules ・Building blocks of proteins + amino acids All amino acids have : - An α carbon - An animo acid - A carboxyl group ・R groups weakly acidic or basic - A variable R group ・Not fully charged at pH 7 ・Amino acids of a polypeptide chain are joined by peptide bonds ・Can form H bonds with other molecules (e.g. H2O) since they ・Average polypetides chain contain 300 amino acids (resideues) have atoms with a partial negative or positive charge. ・Many proteins contain other components which are added to the polypeptide following synthesis - Carbohydrates → glycoproteins - metal -conatining groups → metalloproteins - Organic groups → flavoproteins ・R groups hydrophobic, generally lacking O and N. ・Cannot interact with water or form electrostatic bonds, use hydrophobic and van der waals interactions. ・Vary primarily in size and shape → allows them to pack tightly into the protein core. ・20 different amino acid ・Amino acid side chains (R groups) → diverse structure and function 1. Polar charged 2. Polar uncharged 3. Nonpolar 4. Unique properties ・Cysteine contains a reactive sulfhydryl group (-SH) or thiol group Disulfide bridge : covalent bond between 2 sulfhydryl groups (-SS-). - Can form between distant cysteine residues within and across different proteins - Help stabilze intricate shapes or proteins ・Also, modifiable by free radicals to form oxized forms of Cysteine (Sulfernic Acid, cystine and many others).  protein, triggered by binding. 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 - Subunits may or may not be identical Homodimer : 2 identical subunits Heterodimer : 2 different subunits ・Quaternary structure of multi-protein complexes (or multimer): different proteins each with specific function, physically associate (e.g. pyruvate dehydrogenase→ 60 polypeptide chains that make up to 3 different enzymes.) Structure of proteins : ・These interactions are often highly dynamic Primary structure : sequence of amino acids in the polymer (critical to the protein function) ・The folded state of a protein allows it to exert it’s function Secondary structure : conformation of adjacent amino acids Denaturing : the unfolding or disorganization of a protein, into… usually associated with a loss of function - α-helix - Deterages - β-sheet - Reducing agents - hinges - Organic solvents - turn - Radiation - loops - Heat - finger-like All interfere with various interactions that stabilze a protein extensions tertiary structure - stabilized by hydrogen bonds ・Most proteins are capable of self-assembly spontaneously. Tertiary structure : conformation of the entire polymer ・Mutations in the amino acid sequence can negatively impact - Stabilizes by non-covlent bonds between R groups protein folding and function. - Determined using : X-rays crystallography, NMR - Predicted (still in development) : AlphaFold Caterirgized as : Fibrous Proteins : - Elongated shape - Outside cell - E.g. keratin, elastin Globular protein : - Compact shape Protein misfolding : deadly - Often within a cell consequences. - E.g. myoglobin 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 ・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 Domains within a protein : 2 or more distinct regions in a polypeptide, each with specific function. Conformational changes : dynamic movement of regions of a Molecular Chaperones : “helper proteins” to prevent nonselective interactions during protein folding to achieve proper 3D conformation. - Heat shock protein 70 (Hsp 70) family binds emerging proteins and prevents inappropriate interactions. - Chaperonins (TriC) allow large new proteins to assemble without interference from other macromolecules; processes up to 15% of the cells’ 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.