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The Molecules of Cells Chapter 3 Overview • Introduction to Organic Compounds • Categories of Reactions • Molecules of Life – – – – Carbohydrates Lipids Proteins Nucleotides What Are Organic Compounds? Unique to living systems Contain C & at least one H atom Each has a functional group: – Specific atoms/groups of atoms covalently bonded to C – Have specific physical & chemical properties Why Carbon? Versatile bonding Can covalently bond with up to 4 atoms Forms stable bonds Helps form backbone for other elements to bond with How Do Cells Build Organic Compounds? Monomer: Individual subunit of larger molecules needed to maintain cell structure & function e.g. amino acids Polymer: Combination of 3 to millions of subunits e.g. proteins Hydrocarbons H covalently bonded to C e.g. gasoline, other fossil fuels All 2 million+ are non-polar Some of Earth’s most important energy sources (electric & heat energy) Functional Groups Specific atoms or groups of atoms covalently bonded to carbon atoms in organic compounds More reactive than hydrocarbon groups Can affect how structurally similar molecules work e.g. estrogens & testosterone (different positions of functional groups determines sexual traits) Types of Functional Groups Hydroxyl – Alcohols, sugars, amino acids – Water-soluble —OH Methyl – Fatty acid chains – Insoluble in water H C H H Types of Functional Groups continued Carbonyl – – – – Sugars, amino acids, nucleotides Water-soluble Aldehyde if at end of carbon backbone Ketone if within carbon backbone C H O —CHO (aldehyde) C O CO (ketone) Types of Functional Groups continued Carboxyl – – – – Amino acids, fatty acids Water-soluble Highly polar Acts as acid by giving up H+ C OH O —COOH (non-ionized) C O- O —COO(ionized) Types of Functional Groups continued Amino – Amino acids, some nucleotide bases – Water-soluble – Acts as weak base by accepting H+ N H H —NH2 (non-ionized) H N H+ H —NH3+ (ionized) Types of Functional Groups continued Phosphate – Nucleotides (e.g. ATP), DNA, RNA, some proteins, phospholipids – Water-soluble – Acidic O- O P O O- — P Types of Functional Groups continued Sulfhydryl – Cysteine (an amino acid) – Helps stabilize protein structure via disulfide bridges —SH —S—S— (disulfide bridge) Categories of Reactions (1) Functional Group Transfer a.k.a. exchange reaction AB + CD → AD + BC 1 molecule gives up group to another Making & breaking of bonds e.g. ATP gives phosphate group to glucose in cellular respiration (2) Electron Transfer a.k.a. redox reaction One molecule loses e-s Another gains them e.g. cellular respiration, where glucose is oxidized (loses e-s) to CO2 & O is reduced (gains e-s) to H 2O (3) Rearrangement Internal bonds reform to turn one organic compound into another = structural isomer of original (same molecular formula, different order of bonding) (4) Condensation a.k.a. synthesis reaction A + B → AB 2 molecules covalently bond to form a larger molecule (1 water molecule produced for each joining) Making of bonds (= anabolic) e.g. Na & Cl forming NaCl, amino acids forming a protein (5) Cleavage a.k.a. decomposition reaction AB → A + B Molecule is split into 2 smaller ones Breaking of bonds (= catabolic) e.g. glycogen being broken down into glucose, carbs being broken down into simpler sugars e.g. hydrolysis Cleavage reaction Molecule split by enzyme action OH & H from H2O attached to exposed sites e.g. hydrolysis of sucrose into glucose & fructose Factors Influencing Reaction Rates For reactions to occur, atoms & molecules must collide with enough force to overcome repulsion between e-s Temperature – ↑ temp, ↑ rxn rate – ↑ kinetic energy, ↑ collisions Concentration of reactants – ↑ concentration, ↑ frequency of collisions Particle size – Smaller move faster so collide more frequently Catalyst – Substance that speeds up chemical rxns – Does not become chemically changed or part of product Molecules of Life • Carbohydrates • Lipids • Proteins • Nucleotides (1) Carbohydrates Sugars & starches Make up 1-20% of cell mass Contain C, H, O Important source of energy Also serve some structural purpose e.g. ribose & deoxyribose in RNA & DNA Classified by size & solubility (a) Monosaccharides “1 sugar” Building blocks of other carbs Most water-soluble sugars 2 or more –OH groups bonded to C backbone 1 aldehyde or ketone (carbonyl) group —CHO CO Most have a 5-C or 6-C ring Monosaccharide Structure glucose fructose ribose galactose deoxyribose (b) Disaccharides Double sugar Consist of 2 monosaccharides Must be broken down to be absorbed (c) Oligosaccharides “Few” or short-chain sugars Includes disaccharides Often found as side-chains on lipids & proteins (d) Polysaccharides “Many sugars” Chains of glucose Least water-soluble of carbs More complex = less soluble Good energy storage product Must be broken down to be absorbed Polysaccharide Structure: Starch Spiral structure OH groups stick out from coils Storage carbohydrate of plants Polysaccharide Structure: Glycogen Filamentous (branched) chains Storage carbohydrate of animal tissues Equivalent to starch in plants Stored in muscle & liver cells Polysaccharide Structure: Cellulose Every other sugar is “upside-down” Sheets form by H-bonding between chains Structural carbohydrate of plants Makes up cell walls Polysaccharide Structure: Chitin Modified polysaccharide Nitrogen groups attached to glucoses Strengthens cuticle of arthropods & cell walls of fungi =structural carbohydrate of animals & fungi Simple Carbohydrates a.k.a. simple sugars Monosaccharides & disaccharides Taste sweet Few essential nutrients & high in calories e.g. candy, milk products, fruit Complex Carbohydrates a.k.a. starches & fibres Oligosaccharides & polysaccharides Taste pleasant but not sweet e.g. whole grains, legumes, starchy vegetables (potatoes, etc.) Fibre = cellulose ↑ fibre in diet = ↓ risk of cancer, diabetes, hypertension, etc. Processing plant foods decreases the amount of fibre & vitamins In excess, carbs can lead to: • Increased blood sugar • Excess sugar being stored as fat • Increased risk of heart disease, etc. Diet rich in whole grains, fruits, & vegetables may reduce risk of heart disease & some cancers (2) Lipids Fats & oils Contain C, H, O Less O than carbs Some also have P Non-polar Insoluble in water (a) Fatty Acids Carboxyl group attached to backbone of up to 36 atoms Each C is covalently bonded to 1-3 H atoms (i) Saturated fatty acids C backbones completely filled with attached H atoms Single covalent bonds only Animal fats: Usually solid at room temperature Associated with heart disease, clogged arteries, etc. = bad fats e.g. palmitic acid, stearic acid (ii) Unsaturated fatty acids Not all Cs have H attached ≥1 double covalent bond Causes kinks in tails Plant fats: Usually liquid at room temperature Mono- vs. polyunsaturated fats Mono-unsaturated e.g. oleic acid – Only 1 double bond – Thought to lower cholesterol Polyunsaturated e.g. linoleic acid – More than 1 double bond Partial hydrogenation of vegetable oils Artificial saturation Turns liquid oils into solids (e.g. margarine) Oil is heated; H2 gas & nickel catalyst added Breaks C double bonds & attaches H Partial hydrogenation & trans-fatty acids Partial hydrogenation = bad! Fat is now saturated Trans-fats created by heat (e.g. deep frying) & hydrogenation Double bonds fold in unnatural direction Enzymes that process fat are unable to process transfatty acids in a normal way Domino effect: Because trying to process trans-fatty acids, don’t process essential fatty acids properly Essential fatty acids Body can manufacture some (palmitic acid, oleic acid, etc.) Others must be ingested via foods (omega-3 & omega-6 fatty acids) (b) Neutral Fats 3 fatty acid tails attached to glycerol backbone = triglycerides Large & found throughout entire body “Body fat” used for insulation, protection, energy production Yield > double the energy of complex carbs e.g. butter, lard, veg. oils (c) Phospholipids Glycerol backbone with phosphorus group & 2 fatty acid tails – Tails are non-polar – Head is polar Make up double-layered cell membranes Help regulate what crosses boundary of cell (d) Waxes Long-chained fatty acids bonded to long-chain alcohols or carbon rings Repel water Protect Lubricate Add pliability to hair, skin, etc. (e) Sterols Backbone of 4 C-rings Differ in functional groups In all eukaryotic cell membranes Steroids are essential for human life (homeostasis, vitamin D, sex & metabolic hormones) Cholesterol Found only in animal foods Made in liver Can’t dissolve in blood Is carried to & from cells by lipoproteins (LDL & HDL) Note: cholesterol itself is not bad LDL (low-density lipoprotein) Carries cholesterol through blood to body cells Can form fatty deposits (plaques) in artery walls – Eventually blocks blood flow – Leads to heart attack, stroke, etc. HDL (high-density lipoprotein) Carries cholesterol through blood to liver (will eventually be processed & excreted) High levels appear to protect against heart attack (may remove excess cholesterol from plaques, which slows build-up) (3) Proteins Make up 10-30% of cell mass Contain C, H, O, N & sometimes S & P Form basic structural material & aid in cell function Long chains of amino acids (from 50 to 10,000+) joined by peptide bonds Sequence of amino acid chain dictates which protein is made (a) Amino Acids Amino group (NH3+), carboxyl group (COO-), H atom, & R group Can act as bases or acids R 20 amino acids – Identical except for R group – Chemically unique Types of R-groups: Acidic In neutral solutions, R-group can lose proton to become negatively-charged If interaction with basic R-group, forms salt bridge: helps stabilize a protein Types of R-groups: Basic In neutral solutions, R-group can gain proton to become positively-charged If interaction with acidic R-group, forms salt bridge: helps stabilize a protein Types of R-group: Aromatic R-group is an aromatic (benzene) ring Generally hydrophobic & non-reactive Types of R-group: Sulfur R-group contains S Helps stabilize globular protein structure Types of R-group: Uncharged Hydrophilic R-groups can form H-bonds Types of R-group: Inactive Hydrophobic R-groups do not form H-bonds Rarely reactive Usually buried deep within a protein Types of R-groups: Special R-group & amino group are directly connected Usually located at the turn of a polypeptide chain in 3D protein structure Essential & non-essential amino acids Non-essential: – Can be synthesized from other substances in the body Essential: – Can not be synthesized in the body – Must come from food – If not adequate intake, can’t make proteins • Unable to sustain body structurally & functionally = illness & eventually death 9 essential amino acids Histidine Isoleucine Leucine Lysine Methionine (cysteine partially meets needs because has S) Phenylalanine (tyrosine partially meets needs) Threonine Tryptophan Valine Most animal sources: “Complete protein”: all of essential aas Vegetables: Missing or low in certain aas If combine different vegetables, can get all essential aas Lysine & tryptophan hard to get from plants so vegetarians need to ensure adequate intake From Amino Acids to Proteins Amino acids form proteins by dehydration reactions Peptide bonds form between amino acids 2 amino acids bonded together = dipeptide Many amino acids linked = polypeptide Types of Proteins Structural = hair, tendons, ligaments Contractile = muscles Defensive = antibodies Signal Transport = e.g. hemoglobin Storage Plus many more! (b) Levels of Protein Structure 1° structure Linear polypeptide chain (unique sequence of amino acids) Determined by inherited genetic info 2 ° structure Proteins tend to twist or bend H-bonds form between NH & CO groups α-helix (coiled) or β-pleated sheet Tertiary structure Proteins continue to fold upon themselves Quaternary structure Two or more polypeptide chains bonding & folding together (c) Other Types of Protein Structure Glycoprotein: Oligosaccharide + polypeptide Lipoprotein: Lipid + protein Both types important in cellular processes The Importance of Structure Protein structure determines biological function 3D structure allows recognition & binding with specific molecular targets” (d) Fibrous Proteins Mostly 2° structure; some have quaternary structure Insoluble in water Structural functions: chief building materials of body e.g. collagen, elastin, keratin Globular Proteins Tertiary or quaternary structure Water-soluble Chemically active Used in all biological processes e.g. antibodies, enzymes, proteinbased hormones (e) Enzymes Biological catalysts that keep metabolic & biochemical reactions happening Decrease the amount of activation energy required for chemical rxn to proceed May be pure protein or may have cofactor (e.g. vitamin, metal ion) Chemically specific – Named for type of reaction they catalyze – Usually end in “ase” Some must be activated before use Others are inactivated directly after use All have an active site: Allows binding of substrate so that rxns can proceed Why Is Protein Structure Important? Structure dictates function Proteins can only function if configured in specific way Denaturation of Proteins Breaking of H-bonds that results in shape change Caused by temperature, pH, foreign substances, etc. Can’t perform physiological functions Active site is destroyed when bonds are broken e.g. high fevers • Denature proteins in body • Proteins can no longer function • Can result in serious damage/death Denaturation is usually irreversible e.g. albumin in cooked egg can’t regain original shape one way Note: not all changes are bad—can sometimes result in variation in traits (4) Nucleotides Contain C, H, O, N, P: N base, sugar, & phosphate 5 N bases: adenine, thymine, guanine, cytosine, uracil Important in energy production, metabolism, cell signalling Nitrogen-Containing Bases Purines (double-ringed) Adenine Guanine Pyrimidines (single-ringed) Thymine Cytosine Uracil (a) DNA Genetic material contained in cell nucleus (replicates itself before cell division so info in cells is identical) Contains deoxyribose sugar Each species has unique base sequences somewhere in their DNA molecules The History of DNA Pre-1920s scientists knew that: – Genes are responsible for variation in traits among individuals of a species – Genes are located within chromosomes – Chromosomes are made of DNA & proteins BUT most researchers thought genes were made of proteins that held heritable traits – Diverse traits from diverse molecules? Frederick Griffith (1928): – Tried to develop vaccine against Streptococcus pneumoniae – Did not succeed BUT managed to transfer genetic material from one bacterial strain to another Oswald Avery (1940s): – DNA-digesting enzymes (NOT protein-digesting) prevented bacterial cells from becoming pathogenic Thus, genes are made of DNA Still … How does DNA store genetic info? The answer lies in the structure of DNA DNA Structure Polymer of nucleotides: – Phosphate – Deoxyribose sugar – Nitrogen-containing base (A, C, G, T) All nucleotides are identical except for base What does DNA actually look like? Clues in Chargaff’s ratios: In any species #A = #T #G = #C Differs between species e.g. humans 30% A/T & 20% G/C E.coli 26% A/T & 24% G/C Also clues in X-ray shadows: X-ray diffraction of DNA crystals No direct picture of DNA structure but could tell: (a) long & thin (b) helical (c) repeating subunits Watson & Crick Model DNA resembles ladder Bases on each strand pair to make rungs G pairs with C A pairs with T Explains Chargaff’s ratios Also … Ladder is twisted = double helix Explains x-ray shadows Watson & Crick Model DNA is a double helix of nucleotides Sugar-phosphate backbone Nucleotides held together at N bases by H bonds How does DNA store genetic info? Sequence of bases in DNA codes for genetic info Different sequences = different information (b) RNA Carries out protein synthesis Similar to DNA except: – Single strand of nucleotides – Ribose instead of deoxyribose – Uracil replaces thymine (c) ATP Stores & releases chemical energy for all life processes Adenosine, ribose, 3 phosphate groups Enzymes transfer terminal PO4- group from ATP to other compounds so can use energy released from bonds breaking Brief Overview of How ATP Works ADENOSINE P P P Energy via glucose P ADENOSINE P P + So essentially: ATP ADP + P + energy energy