Chapter 2: Molecules of the Cell 2020 PDF

Molecules of the Cell Chapter 2  Introduction Chemicals are the raw materials that make up – our bodies, – the bodies of other organisms, and – the physical environment.  Basic Chemistry Matter is anything that takes up space and has weight. (know the pha...

Molecules of the Cell Chapter 2  Introduction Chemicals are the raw materials that make up – our bodies, – the bodies of other organisms, and – the physical environment.  Basic Chemistry Matter is anything that takes up space and has weight. (know the phases)  Basic Chemistry Matter is anything that takes up space and has mass. All matter, living or nonliving, is made up of Elements. Energy is the ability to do work. Matter and Energy can be exchanged, but cannot be destroyed  Basic Chemistry Elements are substances that cannot be broken down to simpler substances with different properties. 92 elements Periodic table of the elements  Elements that make up 95% of living organisms (by weight) – C Carbon  Elements that make up 95% of living organisms (by weight) – C Carbon – H Hydrogen  Elements that make up 95% of living organisms (by weight) – C Carbon – H Hydrogen – N Nitrogen  Elements that make up 95% of living organisms (by weight) –C Carbon –H Hydrogen –N Nitrogen –O Oxygen  Elements that make up 95% of living organisms (by weight) –C Carbon –H Hydrogen –N Nitrogen –O Oxygen –P Phosphorus  Elements that make up 95% of living organisms (by weight) –C Carbon –H Hydrogen –N Nitrogen –O Oxygen –P Phosphorus –S Sulfur  Elements in the human body 96% of Weight in the 4 % makes up the rest human body 5. Ca (calcium) 1. C arbon, 6. P (phosphorus) 2. O xygen 7. K (potassium) 8. S (sulfur) 3. H ydrogen 9. Na (sodium) 4. N itrogen 10. C (chloride) 11. Fe (iron)  Trace elements occur in small amounts and are essential to life – You need 0.15mg of iodine/day, deficiency causes goiter – Most table salt has added iodine – Fluoride common ingredient in Earth’s crust Helps maintain healthy teeth – Iron Commonly added to foods Fluoride deficiency  Atoms (exam) Atom: The smallest part of an element that displays the properties of the element. Atoms are made up of subatomic particles.  Subatomic particles Neutrons: Uncharged Protons: Positively charged Electrons: Negatively charged – As a whole, neutral, as charges balance each other © 2017 Pearson Education, Inc.  Subatomic Particles: Calculations Atomic Number Protons = Atomic Number Atomic Mass Neutrons = Atomic Mass – Atomic Number Electrons = # of Protons  Atomic Symbol Atomic Number Atomic Mass  Atomic chemistry Elements = Atoms Nucleus Protons Neutrons Orbit Electrons  Electrons Negative Charge Found in shells or orbits  Electron Shell Holds a specific number of electrons – Shell nearest the nucleus can hold up to two – More distant shells can hold up to eight (some more) 1st Shell = 2 2nd Shell = 8 3rd Shell = 8  Isotopes 12 13 14 C C C 6 6 6 * *radioactive Atoms of the same element with a differing numbers of neutrons Structure of Atoms (AKA elements) Some Terminology for you to know: – Isotope – Atomic Number – Atomic Mass – Ion  Radioactive Isotopes – Research and medicine PET scans: diagnose heart disorders and some cancers Treat Cancer – Uncontrolled exposure to radioactive isotopes can damage DNA 1986 Chernobyl nuclear accident released large amounts of radioactive isotopes Naturally occurring radon gas may cause lung cancer https://youtu.be/hLkv_j3BxFg Low Levels of Radiation 29  Radiation As radioactive isotopes decay, energy is released in the form of subatomic particles (radiation).  Chemical Bonds Ionic: electrons given away or received from one atom to another ie. Na+ and Cl- Covalent: electrons shared between atoms Polar Non-polar Hydrogen: weak attraction between H atoms and O, N, and Fl. Causes surface tension in water.  Elements and Compounds Compounds form when two or more different elements bond together (example: H2O) https://www.boundless.  Compounds & Molecules – Two or more atoms – From the same or different elements – Held together by interactions among their outermost electron shells – Comprise matter Molecules http://www.theoildrum.com/node/8884  Ionic Bonding Ions are charged particles that form when electrons are transferred from one atom to another. Sodium Chlorine Sodium chloride (Na) (Cl) (NaCl)  Covalent Bonding Sharing electrons allowing each atom to have a completed outer shell. Non-polar Covalent Bonds: Equal sharing of electron Polar Covalent Bonds: Unequal sharing of electrons – If electrons spend more time around one atom than the other The electrons in water spend more time around Oxygen than H Molecules develop regions of partial positive and negative charges – H partial (+), O partial (-) Periodic table of the elements  Covalent Bonds (a) Non-Polar: (b) Polar  slightly negative The nucleus with a Figure 2-6 (-) larger positive charge exerts a stronger pull on electrons. Electrons spend more time near the nucleus with the larger charge. The nucleus with a smaller positive charge exerts a weaker pull on electrons. ( +) slightly positive ( +) http://www.youtube.com/watch?v= QqjcCvzWwww Hydrogen Bonding 42  Chemistry of Water Life came from water – 1st cell(s) evolved from water – Organism 70-90% water – Water is Polar – Water molecules are held together via _______ bonding?  Properties of Water 1. Water has a high heat capacity. 2. Water temperature falls slower than other liquids. 3. Water has a High Heat of Vaporization 4. Water is a commonly used solvent. 5. Water molecules are Cohesive & Adhesive 6. Water has high surface tension  Properties of Water Water is a commonly used solvent. Solutes: solutions contain solutes (molecules). – Ex. Salt-water NaCl dissolved in H2O Hydrophillic: molecules that are attracted to water – Loves Water – Polar molecules Hydrophobic: molecules that are NOT attracted to water. – “fears” water – Non-polar, non-ionized – Oils Identify the Solute and Solvent  Properties of Water Water has high surface tension Hydrogen bonding causes water to have a high surface tension.  Properties of Water Liquid water is more dense than ice Molecules are closer together in liquid Is this expected?  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ice lattice liquid water Figure 2.11  Acids, Bases, and pH Water-based solutions can be acidic, basic, or neutral – Small fraction of water molecules break apart into hydroxide and hydrogen ions H2O → OH– + H+ Acids: Chemical compound donates hydrogen ions (H+) – pH range 0-6 Bases: Chemical compounds that removes hydrogen ions (H+) – pH range 8-14 pH 7 Neutral – Solutions inside living cells  pH (potential of hydrogen) scale describes amount of H+ in solution 52  Buffer – Molecule that helps maintain nearly constant pH of a solution Accepts or releases H+ in response to small changes in H+ concentration – In excess H+, a buffer combines with H+ – In excess OH– , a buffer releases H+ – Blood pH = 7.35 – 7.45 © 2017 Pearson Education, Inc.  Biological Molecules Essential for Life 1. Carbohydrates 2. Protein 3. Lipids 4. Nucleic Acids  Organic compounds Carbon – almost all molecules made by our cells are composed of Carbon. Organic compounds contain carbon. – Organic Chemistry – the study of organic compounds Carbon atoms bond to form larger molecules.  Hydrocarbons Life’s molecular diversity is based on the properties of carbon! Functional Groups Polar, found in sugars, nucleic acids, (deoxy/ribose), some Amino acids Sugars, our class will not study this one; however, it does Make certain regions of a molecule hydrophilic This is a very important functional group. It is found in the head groups of fatty acids, the carboxyl amino group In amino acids. This functional groups in amino acids directly participates in the formation of the peptide bonds and it gives fatty acids it’s hydrophilic head group This is also a very important functional group. It is how amino acids acquired their name. This functional groups in amino acids directly participates in the formation of the peptide bonds. It is also important for the nitrogen bases A, T, G, C Although in the cell it is ionized so add another H group to the nitrogen (at least form amino acids) Mainly important for the phosphodiester linkages found in DNA and RNA. Also, proteins can change phophylation patters changing their function Changes gene expression in cells known as an epigenetic effect. Can cause gene mutation and silencing. We will Discuss this later.  Biological molecules The molecules of ALL LIVING things fall into 4 main classes 4 types of macromolecules in cells: 1. Carbohydrates: sugars, starches 2. Lipids: fats, oils, hormones 3. Proteins: enzymes 4. Nucleic Acids: DNA, RNA  Macromolecules Cells make macromolecules: (Macro?) Large Cellular Molecules Made by grouping together smaller molecules called monomers Monomers grouped together (hundreds or thousands of them) make polymers  Making a MacroMolecule Polymers are formed via dehydration synthesis  Breaking Down Macromolecules Polymers broken apart to make monomers by hydrolysis  Carbohydrates Range from small à large macromolecules. – Small sugar molecules: table sugar – Long starch molecules in pasta and potatoes – Strong molecules such as cellulose in plants  Carbohydrates Types of carbohydrates: – - Monosaccharides. What does the pre-fix mono- mean? – - Disaccharides What does the pre-fix Di- mean? – - Polysaccharides What does the pre-fix Poly- mean?  Monosaccharides Simple sugars composes of a single sugar monomer One molecule (mono?) Glucose is broken down to form energy  Connection: Carbon skeleton with life’s molecules Simple sugars are the monomers of carbs.  Disaccharides Cells construct disaccharides via dehydration reaction What does dehydration mean?  Disaccharides Cells construct disaccharides via dehydration reaction Maltose: used to make beer, malt, whiskey, malted candy. What does dehydration mean? – Loss of water  Disaccharides Lactose is a disaccharide for via reaction? Glucose + Galactose  Disaccharides Sucrose is the most common disaccharide.  Polysaccharides Macromolecules Hundreds of thousands of monosaccharides linked together Poly? Which reactions?  Polysaccharides Macromolecules Hundreds of thousands of monosaccharides linked together Which reactions? Dehydration Synthesis  3 common polysaccharides – Starch – Glycogen – Cellulose Polysaccharides in plants and animals.  Starch – Starch: used by plant cells for energy storage ie. Potatoes and grains (wheat, corn, rice) are major sources of starch Humans and most animals have enzymes that can hydrolyze plant starch à glucose.  Glycogen – Glucose is stored in animal (humans) cells as glycogen. – Glycogen is stored in the liver and muscle cells. – When you body needs sugar glycogen is hydrolyzed to glucose and release.  Cellulose § Most abundant organic compound on Earth § Plant cells § Major component in wood § Animals cannot breakdown cellulose § Lack the enzyme § Fiber § House Termites: posses the enzyme that breakdown cellulose. Macro- Molecule Monomer Subunit Polymer Polysaccharides: Starch, Carbohydrates Monosaccharide (i.e. Glucose) Glycogen, Cellulose, Chitin Proteins Amino Acids polypeptide Glycerol + fatty Acid Fats Lipids Polar Head + Fatty Acid Tail Phospholipid 4-fused rings Steriods Nucleic Acids Nucleotide DNA, RNA  Lipids Diverse but they share 1 trait – Hydrophobic Not huge macromolecules Not polymers!  3 important types of lipids Fats Phospholipids Steroids  Fats Energy storage molecule Stored in adipose cells (fat cells) http://study.com/academy/lesson/energy-yielding-nutrients-carbohydrates-fat- protein.html  Structure of Fats RXN?  Fats also perform essential functions – Cushioning: many pressure-sensitive areas of body have fat as padding – Insulation: provide protection against heat loss around body core and insulates nerve cells during transfer of electrical impulses  Fatty Acids 1. Unsaturated Fatty Acids 2. Saturated Fatty Acids  Fatty Acids Unsaturated Fatty Acid: Double bond in hydro carbon chain Healthier Essential for the body Stack less easily Saturated Fatty Acid: No Double bond in hydro carbon chain Solid at room temperature Why are unsaturated fatty acids healthier?  Unsaturated vs saturated Saturated Fatty Acids – Solid at room temperature – ie. Butter, lard Unsaturated Fatty Acids – Liquid at room temperature – ie. Oils  TYPES OF FATS Saturated Fats Unsaturated Fats Margarine Cell membrane INGREDIENTS: SOYBEAN OIL, FULLY HYDROGENATED COTTONSEED OIL, PARTIALLY HYDROGENATED COTTONSEED OIL AND SOYBEAN OILS, MONO AND DIGLYCERIDES, TBHO AND CITRIC ACID ANTIOXIDANTS Plant oils Trans fats Omega-3 fats Figure 3.12  Phospholipds Lipid Structurally similar to fats  Phospholipds Main component of the cell membrane  Steroids Different from fats in structure and function but still lipids (hydrophobic) Carbon skeleton bent to form four fused rings Cholesterol is the base steroid from which other steroids are produced – Example: sex hormones Macro- Molecule Monomer Subunit Polymer Polysaccharides: Starch, Carbohydrates Monosaccharide (i.e. Glucose) Glycogen, Cellulose, Chitin Proteins Amino Acids polypeptide Glycerol + fatty Acid Fats Lipids Polar Head + Fatty Acid Tail Phospholipid 4-fused rings Steriods Nucleic Acids Nucleotide DNA, RNA  Proteins To form protein, amino acids are linked by dehydration synthesis to form peptide bonds. 20 different Amino Acids The chain of amino acids is also known as a polypeptide.  Proteins Are Polymers Formed by dehydration synthesis Bond between two amino acids: peptide bond  Amino Acid Structure Central carbon atom bonded to H Carboxyl Group Amino Group R-group R-group is different for of the 20 amino acids  Proteins Proteins perform most of the body’s functions: – Defenses: antibodies – Cell Signaling: covey messages – Catalyze chemical reactions (enzymes) 4 levels of proteins Structure Macro- Molecule Monomer Subunit Polymer Polysaccharides: Starch, Carbohydrates Monosaccharide (i.e. Glucose) Glycogen, Cellulose, Chitin Proteins Amino Acids polypeptide Glycerol + fatty Acid Fats Lipids Polar Head + Fatty Acid Tail Phospholipid 4-fused rings Steriods Nucleic Acids Nucleotide DNA, RNA  Nucleic acids Our blueprint which makes us who we are & how to function Store information used to make proteins 2 Types of Nucleic Acids: 1. DNA: deoxyribonucleic acid 2. RNA: ribonucleic acid Nucleotides: are monomers of nucleic acids  Nucleotide structure DNA: is a 5 carbon sugar (deoxyribose) bonds to a phosphate group and a nitrogenous base. Nitrogenous Bases  Each Strand of DNA is a polymer of nucleotides Sugar Phosphate Backbone Nitrogenous Base  DNA is a Double-stranded helix 2 strands of DNA for a double helix Hydrogen bonds hold the 2 strands together at nitrogenous bases  RNA Ribonucleic acid 5 carbon sugar (ribose) Single stranded RNA does not have Thymine (T). T is replaced with Uracil (U). DNA compared to RNA Macro- Molecule Monomer Subunit Polymer Polysaccharides: Starch, Carbohydrates Monosaccharide (i.e. Glucose) Glycogen, Cellulose, Chitin Proteins Amino Acids polypeptide Glycerol + fatty Acid Fats Lipids Polar Head + Fatty Acid Tail Phospholipid 4-fused rings Steriods Nucleic Acids Nucleotide DNA, RNA