Chemical Principles and Biomolecules (Chapter 2) Lecture Materials for Amy Warenda Czura, Ph.D. Suffolk County Community College Eastern Campus

Transcription

1 Chemical Principles and Biomolecules (Chapter 2) Lecture Materials for Amy Warenda Czura, Ph.D. Suffolk County Community College Eastern Campus Primary Source for figures and content: Tortora, G.J. Microbiology An Introduction 8th, 9th, 10th ed. San Francisco: Pearson Benjamin Cummings, 2004, 2007, Amy Warenda Czura, Ph.D. 1 SCCC BIO244 Chapter 2 Lecture Slides

2 Chemistry = the study of atoms and molecules -All matter is composed of atoms -Atoms bond together to form molecules Atom = smallest unit of matter (Matter = anything with mass &takes up space) -consists of 3 types of subatomic particles: 1. protons (p): + charge, in nucleus 2. neutrons (n): neutral, in nucleus 3. electrons (e`): - charge, around nucleus Amy Warenda Czura, Ph.D. 2 SCCC BIO244 Chapter 2 Lecture Slides

3 Atomic number = number of p in the nucleus Atomic Mass = total number of p + n Chemical element = all atoms with same # of protons that behave the same way. -92 naturally occurring elements -only 26 commonly found in living things Most abundant in life: Symbol Atomic # Mass Hydrogen H 1 1 Carbon C 6 12 Nitrogen N 7 14 Oxygen O 8 16 Isotope = atoms with same # of protons but different numbers of neutrons. e.g. oxygen 3 isotopes in nature. 16 O (8p, 8n) (99.76% of all) 17 O (8p, 9n) 18 O (8p, 10n) Amy Warenda Czura, Ph.D. 3 SCCC BIO244 Chapter 2 Lecture Slides

4 Electron Configurations -electrons organized into 18e 8e shells around the nucleus -shells = regions 2e 8e corresponding to different energy levels -innermost shell can hold up to 2 e` -2 nd and 3 rd : 8 e` each -4 th, 5 th, 6 th : 18 e` each -shells are filled from inside to outside Atoms have the same number of electrons as they do protons (neutral charge) Valence shell = outer most electron shell (atoms want this shell to be full) Valence = combining capacity/bonding capacity; the number of extra or missing electrons in the outer most shell Amy Warenda Czura, Ph.D. 4 SCCC BIO244 Chapter 2 Lecture Slides

5 e.g. Mg atomic #12 electron shells: 2, 8, 2 2 extra electrons O atomic #8 electron shells: 2, 6 needs 2 electrons -atoms with outer shells more than half full want to take electrons to make a full valence shell -atoms with outer shells more than half empty want to give away electrons to drop to lower full shell -atoms with full valence shells are inert -a gain/loss of electrons results in the atom no longer being neutral: Ion = atom with unequal numbers of protons and electrons -cation = positive charge, more p than e` -anion = negative charge, more e` than p Amy Warenda Czura, Ph.D. 5 SCCC BIO244 Chapter 2 Lecture Slides

6 Molecules any two or more atoms held together by attractive forces called chemical bonds Compound a molecule that contains at least two different kinds of atoms chemically bonded e.g. O 2 = molecule H 2O = molecule and compound Types of Chemical Bonds 1. Ionic Bonds -electrons are gained or lost, and equal but oppositely charged ions attract each other e.g. Na atomic #11: e` 2:8:1 Cl atomic # 17: e` 2:8:7 -Na donates 1 e` to Cl -both now have full valence but unequal charge (Na + & Cl - ) Amy Warenda Czura, Ph.D. 6 SCCC BIO244 Chapter 2 Lecture Slides

7 -resulting ions attracted forming an ionic bond -create the new molecule NaCl 2. Covalent Bonds -atoms share one or more pairs of electrons -these bonds are stronger and more common in living organisms than ionic bonds -shared e` orbit nuclei of both atoms simultaneously Amy Warenda Czura, Ph.D. 7 SCCC BIO244 Chapter 2 Lecture Slides

8 single covalent bond = one pair e` shared e.g. H 2 or CH 4 double covalent bond = 2 pair e` shared e.g. O 2 triple covalent bond = 3 pair e` shared e.g. N 2 Nonpolar covalent bond = equal sharing of e` Polar covalent bond = one atom shares e` more of the time, causes one side of molecule to be + and other to be - (common with H bonded to O or N) Amy Warenda Czura, Ph.D. 8 SCCC BIO244 Chapter 2 Lecture Slides

9 3. Hydrogen Bonds -result from polar covalent bonds -when H is bound to a large atom like O or N the large atoms takes the electrons more time setting up a slightly positive charge on the hydrogen side of the molecule and negative on oxygen or nitrogen side. -the + H gets attracted to the - O or N in another molecule creating a weak bond between molecules -H-bonds too weak to form molecules -act as bridges between existing molecules or within large molecules Amy Warenda Czura, Ph.D. 9 SCCC BIO244 Chapter 2 Lecture Slides

10 Chemical Reactions: -making or breaking bonds input material = reactant (or substrate) resulting material = product -takes energy to make a bond, release energy when breaking a bond Endergonic reaction absorbs more energy than it releases (feels cold) Exergonic reaction releases more energy than it absorbs (feels hot) 3 types of reactions common to living cells: 1. Synthesis reactions = form new bonds A + B AB (anabolic reaction) 2. Decomposition reactions = break bonds AB A + B (catabolic reaction) 3. Exchange reactions = original bonds are broken and new bonds are formed AB + CD AD + BC Amy Warenda Czura, Ph.D. 10 SCCC BIO244 Chapter 2 Lecture Slides

11 Activation energy = amount of energy needed to disrupt the stable electron configuration of any molecule or atom so it reacts Reaction rate = frequency of interactions containing sufficient energy to bring about a reaction (can be increased by heat, pressure, or concentration of reactants) Catalyst = substance that can speed a chemical reaction without being permanently altered or consumed Enzyme = biological catalyst -acts on a specific substance = substrate -binds substrate at the active site on enzyme -catalyzes only one reaction e.g. sucrase: sucrose glucose + fructose -an enzyme lowers the activation energy of the reaction by orienting the substrate in a way to increase the probability of a reaction Amy Warenda Czura, Ph.D. 11 SCCC BIO244 Chapter 2 Lecture Slides

12 *enzymes function to speed up reactions at temperatures compatible with life Important Biological Molecules 1. Inorganic molecules: -lack C and H chains -often formed by ionic bonds, but not always e.g. H 2 O, O 2, CO 2, salts, acids, bases 2. Organic molecules -based on C and H chains -structurally complex -typically formed by covalent bonds e.g. sugars, amino acids, vitamins, etc. Important Inorganic Molecules A. Water -most common, most important to life -polar molecule Amy Warenda Czura, Ph.D. 12 SCCC BIO244 Chapter 2 Lecture Slides

13 -Water important because of its properties: 1. H-bonding resists rapid temp change -each H 2 O can bond with 4 others -high boiling point -low freezing point -liquid at temps compatible with life 2. Good solvent -polar and ionic substances dissociate easily in water to form solutions Amy Warenda Czura, Ph.D. 13 SCCC BIO244 Chapter 2 Lecture Slides

14 3. Chemical reactivity -polarity allows it to serve as reactant in many reactions: Hydrolysis: decomposition using water AB + H 2 O AOH + BH Condensation/ Dehydration synthesis: synthesis using water AOH + BH AB + H 2 O B. Acids, Bases, Salts Acid = substance that dissociates into H + and anions (proton donor) Base = substance that dissociates into OH - and cations (proton acceptor) Salt = substance that dissociates into cations and anions that are not H + or OH - Amy Warenda Czura, Ph.D. 14 SCCC BIO244 Chapter 2 Lecture Slides

15 Maintaining a normal range of H + and OH - ions is necessary for most biological processes ph = logarithmic expression of amount of H + in solutions -stands for potential of hydrogen -Log scale = 10 fold change -ph calculated as log 10 [H + ] in moles/liter (scale 0-14) Acidic solution = more H + than OH - ph below 7 Basic/Alkaline solution = more OH - than H + ph above 7 Pure H 2 O has equal H + and OH - neutral solution ph of 7 Amy Warenda Czura, Ph.D. 15 SCCC BIO244 Chapter 2 Lecture Slides

16 -buffers are used in living things to absorb H + ions released during metabolism to keep the ph from changing -most organisms grow best around neutral ph Organic Molecules -carbon based molecules -produced by living things -C, atomic # 6, can participate in up to 4 covalent bonds -allows formation of large molecules with other atoms: H, O, N, S, P, etc. Classes of Organic Molecules 1. Carbohydrates -sugars & starches -composed of C:H:O in 1:2:1 ratio -necessary for DNA, cell walls, amino acids, nutrient reserves Amy Warenda Czura, Ph.D. 16 SCCC BIO244 Chapter 2 Lecture Slides

17 3 groups based on complexity of structure: monosaccharide = simple sugar disaccharide = 2 bonded simple sugars polysaccharide = 3 or more bonded sugars (chemical reactions in biological systems usually involve water: hydrolysis or dehydration synthesis) 2. Lipids -fats and waxes -composed of C, H, O but usually O < C -function in energy storage, cell membranes, cell walls Amy Warenda Czura, Ph.D. 17 SCCC BIO244 Chapter 2 Lecture Slides

18 Common examples of lipids: A. Glycerides = glycerol + fatty acids (C + H hydrocarbon chain) triglyceride = fat Amy Warenda Czura, Ph.D. 18 SCCC BIO244 Chapter 2 Lecture Slides

19 B. Phospholipids = glyceride + phosphate group attached to the glycerol Bipolar molecule: Hydrophilic head group (phosphate+ glycerol) Hydrophobic tail group (hydrocarbon chains) -make up bilayer cell membranes Amy Warenda Czura, Ph.D. 19 SCCC BIO244 Chapter 2 Lecture Slides

20 C. Steroids / Sterols: carbon rings -eukaryotes and mycoplasmas in cell membranes 3. Proteins -most abundant organic molecules in cells -composed of C, H, O, N, sometimes S -essential to cell structure and function: -enzymes (all chemical reactions) -toxins -transport and movement -structure -regulation Amy Warenda Czura, Ph.D. 20 SCCC BIO244 Chapter 2 Lecture Slides

21 -constructed from amino acids: Amino acid structure: -central carbon -carboxyl group (COOH) -amino group (NH 2 ) -H -R group = unique side chain 20 different amino acids: vary on nature of R group Amy Warenda Czura, Ph.D. 21 SCCC BIO244 Chapter 2 Lecture Slides

22 Amy Warenda Czura, Ph.D. 22 SCCC BIO244 Chapter 2 Lecture Slides

23 -proteins formed from long strings of peptide bonded amino acids: -amino group of one bound to carboxyl group of next via dehydration synthesis (resulting bond = peptide bond) -chain of peptide bonded amino acids = polypeptide protein -proteins only work if folded correctly Levels of protein organization: 1. Primary structure = unique sequence of amino acids dictated by the DNA, linear order of amino acids Amy Warenda Czura, Ph.D. 23 SCCC BIO244 Chapter 2 Lecture Slides

24 2. Secondary structure = local twisting and folding of polypeptide due to H-bonds, creates α-helices and β-pleated sheets 3. Tertiary structure = global folding due to chemical interactions between R-groups (H-bonds, ionic bonds, disulfide links, hydrophobic interactions, etc.) If a protein consists of a single polypeptide it will be complete at this stage. If it requires multiple polypeptides ---> Amy Warenda Czura, Ph.D. 24 SCCC BIO244 Chapter 2 Lecture Slides

25 4. Quaternary structure = aggregation of 2 or more polypeptide chains Denaturation = loss of protein shape due to unfavorable temp, ph, salinity, etc. Loss of native conformation, protein no longer functional Amy Warenda Czura, Ph.D. 25 SCCC BIO244 Chapter 2 Lecture Slides

26 Conjugated proteins = combinations of amino acids with other components (organic or inorganic) e.g. glycoprotein: protein with a carbohydrate attached 4. Nucleic Acids -2 types : deoxyribonucleic acid (DNA) ribonucleic acid (RNA) -composed of nucleotides, each has 3 parts: -nitrogen containing base -pentose sugar (ribose or deoxyribose) -phosphate group -nucleotides are linked together: sugar of one to phosphate of next creating a linear backbone with the bases hanging off the side Amy Warenda Czura, Ph.D. 26 SCCC BIO244 Chapter 2 Lecture Slides

27 Nitrogenous bases: Purines: Adenine (A) Guanine (G) Pyrimidines: Cytosine (C) Thymine (T) Uracil (U) DNA -double helix: 2 strands intertwined -backbone = alternating dexoyribose sugar and phosphate -held together by H-bonds between bases: A to T (two H-bonds) G to C (three H-bonds) (no U) Amy Warenda Czura, Ph.D. 27 SCCC BIO244 Chapter 2 Lecture Slides

28 -DNA contains genes -genes = specific order of bases on a strand of DNA that encodes RNA which usually encodes a protein Amy Warenda Czura, Ph.D. 28 SCCC BIO244 Chapter 2 Lecture Slides

29 RNA -single stranded linear molecule -backbone = ribose & phosphate -bases = A, U, G, C (no T) -3 types: 1. mrna = template for a protein 2. rrna = forms ribosomes: factory for protein synthesis 3. trna = carrier to bring amino acids to the ribosome High Energy Molecules -ATP = adenosine triphosphate: adenine + ribose + 3 phosphate groups Amy Warenda Czura, Ph.D. 29 SCCC BIO244 Chapter 2 Lecture Slides

30 -hydrolysis of 3rd phosphate bond releases energy for use by cell ATP ADP + P + free energy -when cell has extra energy, phosphate is bonded to ADP to store energy as ATP Amy Warenda Czura, Ph.D. 30 SCCC BIO244 Chapter 2 Lecture Slides