Biological molecules ‘Chromatin Innucleus #7/ Mitochondrion© Most biological molecules are made from covalent combinations of six important elements, whose chemical symbols are CHNOPS. the letters stand for the chemical abbreviations of carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. © The four most important elements, which account for more than 99% of the atoms found in living things, are: Carbon Hydrogen Oxygen Nitrogen © Biological molecules, or biomolecules, are built by joining atoms through covalent bonds. © e@@O Carbon Mitrogen Phosphorus: Hysrogen Oxyatn sulfurWhy is carbon so special? ® Carbon has 4 valence electrons. © Carbon can form up to four bonds with other atoms. ® This allows carbon (C) to form lots of different types of structures and molecules, all with different functions. ® Carbon can form long chains or ring structures, which can be thought as the ‘basic skeletons’ of organic molecules to which groups of other atoms attach.Some definitions to keep in mind... © Organic molecule: contains at least C (carbon) and H (hydrogen) © Macromolecule (‘giant molecule”): large biological molecule, such as a protein or nucleic acid ® Monomer: a relatively simple molecule which is used as a basic building block for thr synthesis of a polymer. Many monomers join together make a polymer. ® Polymer: a giant molecule made from many similar repeating subunits joined together in a chain.Monomers and polymers a eed Fatty acids and Ee eed glicerol = Y v Polysaccharides Lipids acids (1 Monomer (F) Ponmer MonosaccharidesThe Biomoecules of Life Carbohydrates ProteinsCarbohydrates ® Molecular formula: shows the atoms an its amount ® Structural formula: shows the arrangements of the atoms using a diagram. © Ring structure: When the chain ‘closes’CHO ns —— OH HO—C —H H—cC —OH H—C —OH CH20H ‘OH | H—C—OH 1o—cC—Il i—c—oll CH,OH o-D-Glucase: (Fischer projection) CELON oO ! ou (| Ho ' OH OU ceoD-Glucowe (Haworth projection) Ho—C—It H—C—OH oO Ho—cC—Il H—c—oll i—c CH;OH f-D-Glucose (Fischer projection) CHOW Oo oll I He OU B-D-Glucose (faworth projection)Formation of the glycosidic * bond: Condensation Monosaccharides have to major functions: *Commonly used as a source of energy ‘Are important as building blocks for larger molecules *Monosaccharides and disaccharides are sugars. = HO ‘Condensation D-Glucose Glyoosidic bond Monosacchanide Monosaccharide Disaccharide (Mattose)Polysaccharides. © Polysaccharides are polymers of monosaccharides. They are unsweet, and complex carbohydrates. They are insoluble in water and are not in crystalline form. Examples:starch, glycogen,cellulose. © Starch and glycogen ® Cellulose © Structure and functionPolysaccharides. ® Polysaccharides are polymers of monosaccharides. They are unsweet, and complex carbohydrates. They are insoluble in water and are not in crystalline form. Examples:starch, glycogen,cellulose. ® Starch and glycogen ® Cellulose ® Structure and functionStorage of glucose ® Glucose is the main form of energy for cells, which is why it is important for livinf organisms to store it. © If glucose was accummulated in cells: |. It would affect osmotic properties 2. It would interfere with the cell chemistry ® How to solve the problem? Glucose is converted toa storage polysaccharide form: Starch in plants Glycogen in animals ® Glucose can become quickly available again for the organism, by a quick enzyme-controlled reactionStorage of glucose ® Glucose is the main form of energy for cells, which is why it is important for livinf organisms to store it. © If glucose was accummulated in cells: |. It would affect osmotic properties 2. It would interfere with the cell chemistry ® How to solve the problem? Glucose is converted toa storage polysaccharide form: Starch in plants Glycogen in animals ® Glucose can become quickly available again for the organism, by a quick enzyme-controlled reactionStarch and glycogen © Starch: ® Mixture of two substances: amylose and amylopectin ® Amylose: 1,4 linked molecules of glucose --- Unbranched ® Amylopectin: 1,4 linked glucose, but with branvhes (1,6 linkages) ° Glycogen: ® Only one type of molecule, similar to amilopectin, but more branched enon “once 1. gycouce bona orm chain oy j “oye | “O Giyconisic bond " ee r yey a Te my? gycosicic bonds i +0 toe form branches VE ‘e | Te oF fe me ise Hoh fo oo oH ao oy my 4 On HoH Oe Ones “ a an, , oon ee enn t rs os SiacCellulose © Most abundant molecule on the planet (due its presence in plant cell walls and slow rate of breakdown) © Mechanically strong molecule — form cell walls ® Differs from starch and glycogen, because cellulose is formed by B-glucose. ® This arrangement allows formation og hydrogen bonds — OH CH,OH OH CH,OH (c) Cellulose: 1-4 linkage of B glucose monomersLipids ® The lipids are a heterogeneous group of naturally occuring compounds (organic), that are related more by their physycal than by their chemical properties. ® They have in common the property of being relatively insoluble in water and soluble in nonpolar solvents such as ether and chloroform. ® 'True lipids’ are esters formed by fatty acids combinig with an alcohol.Classification of lipids Simple Compound Derived lipids lipids lipids. Esters of fatty Esters of fatty acids. Composed acids : and alcohol contain of hydrocarbon, ather groups also rings and a long hydro- Waxes carbon side Esters of long chain chain cids and glycerol)/ fatty acids and long chan ‘CaaS sail SS aFatty acids ‘Fatty acids are important component of lipids in plants, animals, and microorganisms. “A fatty acid consists of a straight chain of carbon atoms, with hydrogen atoms along the length of the chain and at one end of the chain, and a carboxyl group (~COOH) at the other end. It is that carboxy! group that makes it an acid (carboxylic acid). “Fatty acids are included in the group of derived lipids “If the carbon-to-carbon bonds are all single, the acid is saturated; if any of the bonds is double or triple, the acid is unsaturated and is more reactive.Fatty acid structure ‘arboxy! “0, oO e — Acid fiead fo Hydroearban tailSaturated and unsaturated fatty acids ane : (a) Carboxyl-o. 0 {b) “8 group \ Nf £ Hydrocarbon chain© Fatty acids are not found ina free state in nature; commonly they exist combined with glycerol forming triglycerides. ® Alcohols are a series of organic molecules wich contain a hydroxil group (-OH) attached to a carbon atom. ® Glycerol is an alcohol with three carbons and three hydroxyl groups. © The reaction between an acid and an alcohol, called condensation, produces a chemical known as ester. The chemical link established between an alcehol and an acid is called ester bond. In every condensation reaction water is formed. © Tryglicerides are esters formed by one molecule of glycerol combined with three fatty acids.Condensation reaction Glycerol whe ES re Fatty acid Ester tinkage> acho= motecuse Cracgieerot (Hare tat (naturated): Fi te) Ol (untaturatecy: Famy acids toos wen ange bonds” Du canta onthe bode ‘berenen all carbon pare botwean one or more pairs ‘ol carbon atoms.meee a ii type of Wale Phosphol se : onpolar portio Phosphoryla aicondl Hydrophite head Hydrophobic tailsRoles of lipids ® Triglycerides ® Energy source © Energy reserves (storage form of energy — adipose tissue) ® Body insulation and protection around organs ® Sensory qualities (adds flavor and texture to food) © Contribute to satiety ® Phospholipids © Form structure of membranes, matrix of cell wall, mielin sheath, among others. © Carriers of ions across membranes ® Perform many vital functions within the bodyPhospholipids are constituents of membranes © Phospholipids are composed of a hydrophilic head, which is attracted to water, and two hydrophobic tails, which repel water. Because these cells contain molecules that simultaneously attract and resist water, they are considered amphipathic (both water- soluble and non-water-soluble). fa} Phospholipid molecule (b) Phospholipid bilayer hydrophobic molecules: hydrophilic molecules pass through freely do not pass throvah treatyCopyright © The LicGraw- Ht Companies, ine Permission required br production or aspiny. polar head nonpetar tall Phospholipid polar: polar:Different lipids: how do they look? Phospholipid O Triacylglycerol a idyicholineProteins ® Amino acids © Peptide bond © Primary, secondary, third and cuaternary structureProteins © Extremely important group of biological molecules. WHY? © Huge variety, but common basic monomers: amino acids Amino Acid Structure Hydragen Amino Carboxyl "7 Ere eg +H —N — be x | SS o- H R R-group (variant)Amino acid table a ee ! t wtf matte? fee dn mpthic® wgled a8 on a pe meme or ° gion Qr a *. i z ag emy on t creme nn ‘Alanine Wil Valo i) Lucie Lu] clucin Bie) eth (hath Tryptophan Tip} Pemyttanine Pe} Prone Prop wt . yt “ 3. . “te whe mga whee wee < m pa ou Qt ' 2 a st Qi SS ° me, o om Bering (Serf Threonine (Th} Cysteine (Cys) Tyrosine (Tyr) Asparagine (Aan) > . uf. uf! a Foote wh wh le 5 e it t f fof. r te in : = & & EF oe ee ce eo ~ oe pr - a Acidic Basic Aspanic Acid (Auph Gnstamec Acts (Ou) Apne (hy Argenme (Ara) i Hest (inPeptide bond © Twe amino acids can join together by a peptide bond ® In this reaction one molecule of water is formed ® Dipeptide: molecule formed by two amino acids ® Polypeptide: molecule formed by many amino acids linked Polypetides are another example of polymers and macromolecules Amino acid 1 Amino acid 2 etd Peptide bond© Protein molecule may have just one polypeptide chain, or two or more chains interacting with each other @ & Oru Amino Acids Oligopeptide Os 000909. Dipeptides ProteinStructure of proteins © Primary structure: is the sequence of amino acids ina polypeptide or protein. ® Secondary structure: is the structure of a protein molecule resulting from the regular coiling or folding of the chain of amino acids. E.g. B-pleated sheet c-helix. ® Tertiary structure: is the compact structure of a proteinmolecule resulting from the three-dimensional coiling of the already-folded chain of amino acids. IMPORTANT: different kind of bonds (SEE BOOKLET) ® Quaternary structure: is the three-dimensional arrangement of two or more polypeptides, or of a polypeptide and a non-protein component such as haem, in a protein molecule.We can find both kinds of secondary structures by ie asta oe fe i 5 4 e 4 aHellx BPieated sheatSTRUCTURE OF PROTEINS ‘SECONDARY STRUCTURE The corkscraw-fike twists cor pleated folds formed hy hydrogen bonds between amino acidsin the polypeptidechain PRIMARY STRUCTURE The sequence of amino acidsin a polypeptide chain, similarto the sequence of letters thi spell out a specific word Figurez39 What i Ug]A Golde To Bolagy, Second Edition ©.FOIPWH Freeman ant Porat (QUATERNARY STRUCTURE ‘Two or more polypeptide chains bonded together TERTIARY STRUCTURE The complex three-dimensionel shape formed by multiple twists and bends inthe polypeptide chain, based ‘on the sidechains’ interactions with exch ‘other and with theaqueous solvent.Globular and fibrous proteins © Globular proteins: folded and ‘curled’. Usually soluble in water (because hydrophilic groups remain on the outside). Many globular proteins have roles in metabolic reactions, For example: enzymes and myoglobin ® Fibrous proteins: Do not curl-up, but form long strands. Usually not soluble in water, and have structural roles. For example: collagen and keartin. Myngrobin, » globular proteinee Nucleic acids are molecules that store information for cellular growth and reproduction © There are two types of nucleic acids: - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) © These are polymers consisting of long chains of monomers called nucleotides ® A nucleotide consists of a nitrogenous base, pentose sugar and a phosphate group.DNA and RNA are nucleic acids, long, thread-like polymers made up ofa linear array of monomers called nucleotides All nucleotides contain three components: 1. A nitrogen heterocyclic base 2. A pentose sugar 3. A phosphate residue Purine or pyrimidine base o Phosphate Oy ‘| Pentosemical Structure of DNA- Ribonucleotides have a 2’-OH Deoxyribonucleotides have a 2’-H Purine or pyrimidine base Phosphate et 0 | PentoseI nee ~o o aytieiie Purines 0 oO q i CH ag 8 HN “oT es my doey ! & oe ~~ Flo eet _ 20. -CH “Ex Lo N Thyme GRNAD Pyrimidineshe_nucleus contains the cél’DNA4genome) NA ‘is synthesized in the nucleus and exported ath oplasm INUCIeuS 2a ——S Bu al | ris DaOn ae SRNA {MRNA} transtation —— ProleneMitotic chramosome ‘Chromatin (-600 om Chromatin fiber diameter) Nucleosomes (0mm in dinmoter) Histones DNAReplication DNA Transcription RNA Translation Protein —cec cen 8048 cec co> OFC FOO CoO et a a en Template strand : Polypeptide Amino terminus 7 Carboxyl || terminusi Base Nucleosides Nucleotides RNA Adenine (A) Adenosine (A) Adenosine 5'-monophosphate (AMP) Guanine (G) Guanosine (G) ‘Guanosine 5'-monophesphate (GMP) ‘Cytosine (C) Cytidine (C) ‘Cytidine 5'-monophosphate (CMP) Uracil (U) Uridine (U) Uridine 5'-monophosphate (UMP) DNA Adenine (A) Deoxyadenosine (A) Deoxyadenosine 5'-monophosphate (dAMP) Guanine (G) Deoxyguanosine (G) Deoxyguanosine 5'-monophosphate (GMP) ‘Cytosine (C) Deoxycytidine (C) Deoxycytidine 5'-monophosphate (CMP) Thymine (T) Deoxythymidine (T) Deoxythymidine 5'-monophosphate (dTMP)x-ray diffraction patterns produced by DNA fibers Rosalind Franklin and Maurice WilkinsPe Types of RNA Percentage Type Abbreviation of Total RNA Function in the Cell Ribosomal RNA TRNA 75 Major component of the ribosomes Messenger RNA mRNA 5-10 Carries information for protein syn- thesis from the DNA in the nucleus to the ribosomes Transfer RNA tRNA 10-15. Brings amino acids to the ribosomes for protein synthesis© Ribosomes are the sites of protein synthesis - they consist of ribosomal DNA (65%) and proteins (35%) - they have two subunits, a large one and a small one © Messenger RNA carries the genetic code to the ribosomes - they are strands of RNA that are complementary to the DNA of the gene for the protein to be synthesized cD: Cmall enhunit Farne cuhenit BihnenmaRNA and brings specific amino acids to the ribosome for protein synthesis ® Each amino acid is recognized by one or more specific tRNA © tRNA hasa tertiary structure that is L-shaped - one end attaches to the amino acid and the other binds to the mRNA by a 3-base complimentary sequenceof codon First letter of codon (5'end) _—— Second letter —__—_— c A GImportant conclusion NUCLEIC ACIDS NUCLEOTIDES NUCLEOSIDES PHOSPHORIC ACID NITROGENOUS BASES SUGAR purines and pyrimidines ribose and deoxyribose A&G CT&UOo? | “o-F=0 Hc 7 am 5'End =H, ke Xo Thymine (T) | Phosphodiester So—p=o0 linkage | NH, ~ SN 1 ‘ Adenine (A) a